Journal articles on the topic 'Multi-breed beef cattle'
To see the other types of publications on this topic, follow the link: Multi-breed beef cattle.
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 journal articles for your research on the topic 'Multi-breed beef cattle.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.
1
Cromie, A., R. Evans, F. Kearney, D. Berry, M. C. McClure, and J. McCarthy. "0410 Multi-breed genomic evaluations for 1 million beef cattle in Ireland." Journal of Animal Science 94, suppl_5 (October 1, 2016): 199. http://dx.doi.org/10.2527/jam2016-0410.
Full text
2
Bertrand, Joseph Keith. "Using actual and ultrasound carcass information in beef genetic evaluation programs." Revista Brasileira de Zootecnia 38, spe (July 2009): 58–63. http://dx.doi.org/10.1590/s1516-35982009001300007.
Full textAbstract:
Increased movement toward alliances and grid pricing in the U.S. has led to an increase interest in genetic values for carcass traits. The literature suggests that carcass genetic values are an effective tool to enhance selection for carcass traits, and that it is possible to select sires within a breed that can increase marbling score without adversely affecting external fat thickness or percent retail product relative to the breed mean. Ultrasound has been investigated as a cheaper means of collecting carcass information. The literature indicates that carcass traits measured via ultrasound on yearling seedstock will respond to selection. Although the literature is variable on the subject, there are reported genetic correlation (r g) estimates between live animal ultrasound and actual carcass attributes that are greater than .70 for all ultrasonically measured carcass traits. When r g between seedstock ultrasound and slaughter cattle carcass measures are > 0.70, similar or greater genetic progress in finished cattle carcass merit could be achieved by using ultrasound information entirely compared to using typical carcass progeny information; however, the maximum accuracy of prediction using ultrasound information in lieu of finished cattle carcass information would be r g. Therefore both actual and live animal, ultrasonically measured carcass traits should be included in genetic evaluation programs, which will allow for an increase in the accuracy of prediction of carcass genetic values on young seedstock animals due to the inclusion of ultrasound information, and will also allow for the possible production of high accuracy sires based on finished cattle progeny carcass information. Multi-breed models are being developed to allow for the prediction of genetic values for carcass traits in populations composed of animals of varying breed composition.
3
SHARMA, A. K., L. WILLMS, R. T. HARDIN, and R. T. BERG. "SELECTION RESPONSE IN A PUREBRED HEREFORD AND A MULTI-BREED SYNTHETIC POPULATION OF BEEF CATTLE." Canadian Journal of Animal Science 65, no. 1 (March 1, 1985): 1–9. http://dx.doi.org/10.4141/cjas85-001.
Full textAbstract:
Phenotypic, environmental and genetic trends were estimated for birth weight, preweaning average daily gain (ADG) and weaning weight in males and females combined; postweaning ADG and yearling weight in males; and 18-mo weight in females in a purebred Hereford and a multi-breed Synthetic population of beef cattle, for the period 1966–1978, from The University of Alberta Ranch at Kinsella. Mean selection differential, heritability, expected genetic response and actual genetic response were estimated for each trait. Methods employed to estimate trends were: (1) deviation from a control population, and (2) best linear unbiased prediction estimates of sire breeding values. Heritabilities, selection differentials and expected gains were higher for traits in the Synthetics than in the Herefords except for the 18-mo weight in females. Realized gains in most of the traits were also higher in Synthetics than in Herefords. Genetic trends obtained by the two methods were variable and deviated from the expected gains. Positive genetic trends for growth traits indicated effectiveness of the selection program in both populations. Key words: Beef cattle, selection response, growth traits
4
Smith, Jason K., Juan Piñeiro, and Justin Benavidez. "103 The Economics and Role of Beef X Dairy Calves in the Beef Supply Chain." Journal of Animal Science 99, Supplement_3 (October 8, 2021): 51. http://dx.doi.org/10.1093/jas/skab235.091.
Full textAbstract:
Abstract Utilizing beef genetics in dairy herds to produce terminal beef x dairy (BXD) crosses is a growing trend in the U.S. dairy industry. It has been estimated that more than two million U.S. BXD calves were born in 2020, which is a practice that is expected to continue to grow throughout the foreseeable future. While not a new concept, the widespread adoption, scale, and strategies currently being used to produce BXD calves have recently received considerable industry attention. Although the increased duration of feeding exposes BXD feeders to increased price and production risks when compared to straightbred beef cattle, these risks are met with several potential benefits. A prime example of such benefits includes a consistent supply of uniform, traceable feeder cattle that are easily age and source verified, that also serve as ideal candidates for enrollment in or development of other value-added marketing programs. Current demand, as indicated by newborn calf prices, suggests that the industry perceives BXD calves to be superior when compared to their straightbred dairy breed contemporaries, and at times, suggests that they may be overvalued. Sustaining such demand will require BXD calves to meet or exceed the performance and profitability expectations of the various production sectors of the beef industry. Results of a multi-year analysis of the economics of BXD calves as compared to cattle of straightbred beef or dairy breed composition will be presented. Furthermore, specific factors expected to influence value throughout the production supply chain will be outlined and discussed. Calfhood management practices that promote calf health, paired with genetic selection strategies focused on complementary traits that minimize cost of gain and increase cutability, such as feed efficiency, carcass yield, and muscularity, will play key roles in sustaining the value of BXD calves to all aspects of the beef supply chain.
5
Nawaz, Muhammad Yasir, Priscila Arrigucci Bernardes, Rodrigo Pelicioni Savegnago, Dajeong Lim, Seung Hwan Lee, and Cedric Gondro. "Evaluation of Whole-Genome Sequence Imputation Strategies in Korean Hanwoo Cattle." Animals 12, no. 17 (September 1, 2022): 2265. http://dx.doi.org/10.3390/ani12172265.
Full textAbstract:
This study evaluated the accuracy of sequence imputation in Hanwoo beef cattle using different reference panels: a large multi-breed reference with no Hanwoo (n = 6269), a much smaller Hanwoo purebred reference (n = 88), and both datasets combined (n = 6357). The target animals were 136 cattle both sequenced and genotyped with the Illumina BovineSNP50 v2 (50K). The average imputation accuracy measured by the Pearson correlation (R) was 0.695 with the multi-breed reference, 0.876 with the purebred Hanwoo, and 0.887 with the combined data; the average concordance rates (CR) were 88.16%, 94.49%, and 94.84%, respectively. The accuracy gains from adding a large multi-breed reference of 6269 samples to only 88 Hanwoo was marginal; however, the concordance rate for the heterozygotes decreased from 85% to 82%, and the concordance rate for fixed SNPs in Hanwoo also decreased from 99.98% to 98.73%. Although the multi-breed panel was large, it was not sufficiently representative of the breed for accurate imputation without the Hanwoo animals. Additionally, we evaluated the value of high-density 700K genotypes (n = 991) as an intermediary step in the imputation process. The imputation accuracy differences were negligible between a single-step imputation strategy from 50K directly to sequence and a two-step imputation approach (50K-700K-sequence). We also observed that imputed sequence data can be used as a reference panel for imputation (mean R = 0.9650, mean CR = 98.35%). Finally, we identified 31 poorly imputed genomic regions in the Hanwoo genome and demonstrated that imputation accuracies were particularly lower at the chromosomal ends.
6
Veselá, Z., J. Přibyl, P. Šafus, L. Vostrý, K. Šeba, and L. Štolc. "Breeding value for type traits in beef cattle in theCzech Republic." Czech Journal of Animal Science 50, No. 9 (December 11, 2011): 385–93. http://dx.doi.org/10.17221/4223-cjas.
Full textAbstract:
The type was evaluated in 5 424 young animals of twelve beef breeds. Ten type traits were evaluated: height at sacrum (HS), body length (BL), live weight (LW), front chest width (CW), chest depth (CD), pelvis (P), shoulder muscling (SM), back muscling (BM), rump muscling (RM) and production type (PT). The traits represent two groups: (1) traits scoring body measurements and body capacity (HS, BL, LW, CW, CD, P) and (2) traits scoring muscling (SM, BM, RM, PT). These fixed effects were included in the model: breed, sex, HYS, mother’s age, linear regression on age at evaluation and average gain from birth to evaluation. Fixed effects in the model explained 40% to 60% of variability. The highest values of heritability coefficient were estimated for HS (h<sup>2</sup> = 0.51) and LW (h<sup>2</sup> = 0.50). BL had the lowest values of heritability coefficient (h<sup>2</sup> = 0.25). The values h<sup>2</sup> = 0.25–0.32 were calculated for the traits scoring body capacity (CW, CD, P). The range of values for muscling traits was h<sup>2</sup> = 0.26–0.35. The coefficient of heritability for PT was h<sup>2</sup> = 0.34. All traits scoring muscling and PT showed high genetic correlations (r<sub>g</sub> > 0.95). The traits scoring body capacity (P, CW, CD) were highly genetically correlated with muscling r<sub>g</sub> > 0.83. Breeding values were determined by a multi-trait animal model. Standard deviations of breeding values were higher in HS (s<sub>BV</sub> = 0.71) and LW (s<sub>BV</sub> = 0.84), which was connected with a different method of evaluation of these traits. They were in the range of 0.19 (BL) to 0.30 (RM) in the other traits.
7
Pires, Bruno Carlos, Patrícia Tholon, Marcos Eli Buzanskas, Ana Paula Sbardella, Jaqueline Oliveira Rosa, Luiz Otávio Campos da Silva, Roberto Augusto de Almeida Torres, Danísio Prado Munari, and Maurício Mello de Alencar. "Genetic analyses on bodyweight, reproductive, and carcass traits in composite beef cattle." Animal Production Science 57, no. 3 (2017): 415. http://dx.doi.org/10.1071/an15458.
Full textAbstract:
In beef cattle, growth, reproductive, and carcass traits have been studied for improving productivity and quality of meat products. The aim of this study was to estimate genetic parameters for birth (BW), weaning (WW) and yearling (YW) weights, scrotal circumferences at weaning (SCW) and yearling (SCY), age at first calving (AFC), ribeye area (REA) and back fat thickness (BFT) in order to provide support for the evaluation program of the composite Canchim breed. Data on 12 967 (BW), 7481 (WW), 5131 (YW), 1447 (SCW), 1224 (SCY), 1400 (AFC), and 2082 (REA and BFT) animals were analysed using the Average Information Restricted Maximum Likelihood method under an animal model (single and multi-trait analyses). A substantial proportion of the variation in the bodyweights, scrotal circumferences and carcass traits was associated with the additive genetic term indicating that these traits may respond to the selection process. For AFC, a low heritability estimate was observed. Genetic correlations among bodyweights varied from 0.41 to 0.93. The genetic correlation among scrotal circumferences was 0.91. Important genetic correlations among YW, SCW, and SCY with AFC were observed (–0.48, –0.61, and –0.71, respectively), indicating that indirect responses to selection for these traits would be expected in the age of which the heifers calve. Furthermore, BFT presented an interesting result with calving performance due to the genetic correlation (–0.69) with AFC. Post-weaning weights showed moderate genetic correlations with REA. Many of the traits considered in the genetic evaluation of this breed are genetically correlated in a favourable manner. Genetic improvement through selection is expected for production, reproduction, and carcass traits in Canchim beef cattle.
8
Hernandez, Aakilah, Andrea N. Nunez Andrade, Eduardo E. Rodriguez, Kaitlyn Sarlo Davila, Raluca Mateescu, and Gabriel A. Zayas. "PSXV-3 Genome-Wide Association Study for Sweat Gland Area in Multi-Breed Brahman-Angus Population." Journal of Animal Science 100, Supplement_3 (September 21, 2022): 214. http://dx.doi.org/10.1093/jas/skac247.389.
Full textAbstract:
Abstract Thermal stress in subtropical regions is a major limiting factor in beef cattle productions with around $370 million being lost annually due to reduced performance. About 45% of beef cattle in the United States are in the southern and southeastern states where tropical and subtropical climates are most prevalent. Cattle utilize sweating to dispense most of their excess heat allowing them to return to their thermoneutral zone. The objective of this study was to conduct a genome-wide association study on sweat gland area in the Multi-breed Angus-Brahman herd of the University of Florida. Skin samples were collected along the shoulder from 337 cows of varying Brahman and Angus percentages. Cows were genotyped with the Bovine GGP F250k array. The biopsies were processed into histology slides and then ImageJ software was used to measure sweat gland area. A general linear model was used to test the significance of breed composition and age group on sweat gland area. Breed composition and age group had a significant effect on sweat gland area (P < 0.0001 and P < 0.0001, respectively), with sweat gland area increasing with Brahman percentage. Quality control was conducted using BLUPF90 software including a call rate of 0.90 and a minor allele frequency of 0.01 which left 125,035 SNPs available for the single-step genome wide association analysis. BLUPF90 software was used to fit a single locus mixed model to test the effect of each marker. There were a significant SNPs located in the MINDY1 and PRUNE1 gene, which are involved in cell proliferation and induction of cell motility. These results show that with selection on these SNPs, can improve the ability of cattle to adapt to thermal stress.
9
Farah, M. M., A. A. Swan, M. R. S. Fortes, R. Fonseca, S. S. Moore, and M. J. Kelly. "Accuracy of genomic selection for age at puberty in a multi-breed population of tropically adapted beef cattle." Animal Genetics 47, no. 1 (October 22, 2015): 3–11. http://dx.doi.org/10.1111/age.12362.
Full text
10
Steyn, Yvette, Daniela Lourenco, and Ignacy Misztal. "335 Genomic predictions with a multi-breed genomic relationship matrix." Journal of Animal Science 97, Supplement_3 (December 2019): 49–50. http://dx.doi.org/10.1093/jas/skz258.099.
Full textAbstract:
Abstract Multi-breed evaluations have the advantage of increasing the size of the reference population for genomic evaluations and are quite simple; however, combining breeds usually have a negative impact on prediction accuracy. The aim of this study was to evaluate the use of a multi-breed genomic relationship matrix (G), where SNP for each breed are non-shared. The multi-breed G is set assuming known genotypes for one breed and missing genotypes for the remaining breeds. This setup may avoid spurious IBS relationships between breeds and considers breed-specific allele frequencies. This scenario was contrasted to multi-breed evaluations where all SNP are shared, i.e., the same SNP, and to single-breed evaluations. Different SNP densities, namely 9k and 45k, and different effective population sizes (Ne) were tested. Five breeds mimicking recent beef cattle populations that diverged from the same historical population were simulated using different selection criteria. It was assumed that QTL effects were the same over all breeds. For the recent population, generations 1 to 9 had approximately half of the animals genotyped, whereas all 1200 animals were genotyped in generation 10. Genotyped animals in generation 10 were set as validation; therefore, each breed had a validation set. Analysis were performed using single-step GBLUP (ssGBLUP). Prediction accuracy was calculated as correlation between true (T) and genomic estimated (GE) BV. Accuracies of GEBV were lower for the larger Ne and low SNP density. All three scenarios using 45K resulted in similar accuracies, suggesting that the marker density is high enough to account for relationships and linkage disequilibrium with QTL. A shared multi-breed evaluation using 9K resulted in a decrease of accuracy of 0.08 for a smaller Ne and 0.11 for a larger Ne. This loss was mostly avoided when markers were treated as non-shared within the same genomic relationship matrix.
11
Johnston, D. J., B. Tier, and H. U. Graser. "Beef cattle breeding in Australia with genomics: opportunities and needs." Animal Production Science 52, no. 3 (2012): 100. http://dx.doi.org/10.1071/an11116.
Full textAbstract:
Opportunities exist in beef cattle breeding to significantly increase the rates of genetic gain by increasing the accuracy of selection at earlier ages. Currently, selection of young beef bulls incorporates several economically important traits but estimated breeding values for these traits have a large range in accuracies. While there is potential to increase accuracy through increased levels of performance recording, several traits cannot be recorded on the young bull. Increasing the accuracy of these traits is where genomic selection can offer substantial improvements in current rates of genetic gain for beef. The immediate challenge for beef is to increase the genetic variation explained by the genomic predictions for those traits of high economic value that have low accuracies at the time of selection. Currently, the accuracies of genomic predictions are low in beef, compared with those in dairy cattle. This is likely to be due to the relatively low number of animals with genotypes and phenotypes that have been used in developing genomic prediction equations. Improving the accuracy of genomic predictions will require the collection of genotypes and phenotypes on many more animals, with even greater numbers needed for lowly heritable traits, such as female reproduction and other fitness traits. Further challenges exist in beef to have genomic predictions for the large number of important breeds and also for multi-breed populations. Results suggest that single-nucleotide polymorphism (SNP) chips that are denser than 50 000 SNPs in the current use will be required to achieve this goal. For genomic selection to contribute to genetic progress, the information needs to be correctly combined with traditional pedigree and performance data. Several methods have emerged for combining the two sources of data into current genetic evaluation systems; however, challenges exist for the beef industry to implement these effectively. Changes will also be needed to the structure of the breeding sector to allow optimal use of genomic information for the benefit of the industry. Genomic information will need to be cost effective and a major driver of this will be increasing the accuracy of the predictions, which requires the collection of much more phenotypic data than are currently available.
12
Wang, Yachun, Flávio S. Schenkel, Stephen P. Miller, and James W. Wilton. "Comparison of models and impact of missing records on genetic evaluation of calving ease in a simulated beef cattle population." Canadian Journal of Animal Science 85, no. 2 (June 1, 2005): 145–55. http://dx.doi.org/10.4141/a04-035.
Full textAbstract:
This study compared the application of a bivariate linear-linear (LL) and a linear-threshold (LT) sire-maternal grandsire model for genetic evaluation of calving ease (CE), using birth weight (BW) as a correlated trait, and assessed the impact of missing records on genetic evaluation of CE in a simulated multi-breed beef population that mimicked phenotypic and genetic parameters of beef cattle in Ontario. Models included fixed age-of-dam by sex-of-calf, management group, breed and heterosis effects, and random direct and maternal genetic, maternal permanent environment and residual effects. The LL model was applied to BW and CE Snell scores, and LT model was applied to BW and CE raw scores. CE evaluations were similar between the LL and LT models with no obvious advantage for either model. The two models performed similarly with respect to accuracy and rank correlation of predicted genetic effects and recovered true values of genetic parameters and fixed effects, except for CE maternal heterosis from LL model. The effect of missing records was assessed using the LT model. All dispersion and location parameters were generally well recovered, even when the total proportion of missing records of both traits was up to 41%. Levels of missing CE and BW records that exist in Ontario do not seem to adversely affect genetic evaluation of CE. Key words: Accuracy, Gibbs sampling, heterosis, Snell score
13
Veselá, Z., L. Vostrý, and P. Šafus. "Linear and linear-threshold model for genetic parameters for SEUROP carcass traits in Czech beef cattle." Czech Journal of Animal Science 56, No. 9 (September 19, 2011): 414–26. http://dx.doi.org/10.17221/1292-cjas.
Full textAbstract:
The objective of this study was to estimate genetic parameters for the results of classifying of carcass traits by the SEUROP method in beef cattle in the Czech Republic using linear and linear-threshold models. Genetic parameters were calculated and evaluated in a set of 4276 animals of eleven beef breeds and crosses with dairy and dual-purpose breeds (Aberdeen Angus – 1376, Hereford – 994, Simmental – 651, Charolais – 524, Piemontese – 185, Galloway – 162, Blonde d’Aquitaine – 147, Limousine – 106, Highland – 53, Gasconne – 44, Belgian Blue – 34) in 2005–2008. Aberdeen Angus, Hereford, Charolais and beef Simmental were the most numerous breeds. Fixed effect of a classifier, fixed regression on age at slaughter by means of Legendre polynomial of the second degree separately for the each breed and sex and fixed regression on heterosis coefficient were included in a model equation. Genetic parameters were estimated by a multi-trait animal model using a linear model and a linear-threshold model in which carcass weight (CW) was considered as the linear trait and carcass conformation (CC) and carcass fatness (CF) grading as threshold traits. The heritability coefficient for CW differed only moderately according to the method of the genetic parameter estimation (0.295 in linear model and 0.306 in linear-threshold model). The heritability coefficient for CC was 0.187 in linear model and 0.237 in linear-threshold model. The heritability coefficient for CF grading was 0.089 in linear model and 0.146 in linear-threshold model. Genetic correlation between CW and CC was high (0.823 in linear model and 0.959 in linear-threshold model), the correlation between CW and CF was intermediate (0.332 and 0.328, respectively) and it was low between CF and CC (0.071 and 0.053). If CW was included in the model equation as fixed regression using Legendre polynomial, lower heritability coefficients for CC (0.077 and 0.078) and CF (0.086 and 0.123) were calculated and the correlation between CC and CF was negative (–0.430 and –0.429).
14
Rowan, Troy, Jesse L. Hoff, Tamar Crum, Jerry F. Taylor, Robert Schnabel, and Jared E. Decker. "36 A large multi-breed reference panel and maximizes genotype imputation accuracy in cattle." Journal of Animal Science 97, Supplement_2 (July 2019): 18. http://dx.doi.org/10.1093/jas/skz122.033.
Full textAbstract:
Abstract The use of array-based SNP genotyping in the beef and dairy industries has produced an astounding amount of medium-to-low density genomic data in the last decade. While low-density assays work exceptionally well in the context of genomic prediction, they are less useful in mapping and causal variant discovery. This project focuses on maximizing imputation accuracies to the marker set of two high-density research assays, the Illumina Bovine HD, and the GGP-F250 which contains a large proportion of rare and potentially functional variants (~850,000 total SNPs). This 850K SNP set is well-suited for both imputation to sequence-level genotypes and direct downstream analysis. For testing, 310 animals from multiple breeds, all with observed HD and F250 genotypes, were downsampled to various commercial chip densities ranging from 8K–130K markers. We use both well-established and novel measures of imputation accuracy to categorize precisely where, why, and how imputation errors are made. These metrics provide insights into downstream interpretation and identify situations where caution should be exercised when analyzing imputed variants. We find that a large multi-breed composite imputation reference comprised of 36,131 samples with either HD and F250 genotypes significantly increases imputation accuracy compared to a standard within-breed reference panel, particularly at low minor allele frequencies. Breed composition information for each animal in our testing panel allowed us to identify how a breed’s representation in the reference panel affects the imputation accuracy of both purebred and admixed animals. Starting chip density also impacts imputation accuracy, but gains appear to plateau at around 50,000 markers. The addition of the F250’s rare variation to the reference panel increased the imputation accuracy of rare variants from the HD assay by an average of 4.32%. We expect this low MAF content from the F250 to have a similar positive impact on rare variant imputation at the sequence level. Early work using 850K imputed data in genomic predictions has shown substantial increases in both chip heritability and prediction accuracies. Using a large multi-breed reference and the best practices identified through this work will maximize imputation accuracies in virtually all cattle populations, particularly ones that are highly admixed with little or no available pedigree information.
15
PUNDIR, R. K., P. K. SINGH, P. S. DANGI, and H. ZELIANG. "Characterisation and evaluation of Tho-Tho cattle of Nagaland." Indian Journal of Animal Sciences 88, no. 4 (April 17, 2018): 434–37. http://dx.doi.org/10.56093/ijans.v88i4.78810.
Full textAbstract:
Surveys were conducted in 24 villages of 4 districts of Nagaland, i.e. Kohima, Phek, Zuhneboto and Dimapur to characterise Tho-Tho cattle of Nagaland. A total of 242 cattle of different age and sex including 186 Tho-Tho and 56 desi/non-descript were recorded for physical and ten different morphometric traits. To know management and performance of Tho-Tho cattle, 76 farmers were interviewed form these districts. It was observed that Tho-Tho cattle was mainly reared for beef as people preferred beef over pork. Cattle population of the state showed sharp decline of 51% during the years 2007–2012 and needs immediate attention. Based on different physical and morphometric traits, it may be concluded Tho-Tho cattle are distinct as compared to indigenous cattle of Tripura, Mizoram, Manipur and Siri of Sikkim. Tho-Tho cattle were larger in size as compared of desi/non descript cattle of the state. Management and performance was more or less similar in the whole north-east region i.e extensive system of management. Multi-variate canonical discriminate analysis using different morphometric traits of indigenous cattle of Manipur, Meghalaya, Mizoram, Nagaland, Sikkim (Siri) and Tripura showed that Siri (Sikkim) and Tho-Tho (Nagaland) were significantly different than other indigenous cattle of the region and it was supported by physical traits also. Therefore, it is recommended that Tho-Tho cattle population may be registered as distinct cattle breed from Nagaland.
16
Upperman, Lindsay R., Larry A. Kuehn, and Matthew L. Spangler. "37 Genetic parameter estimates for days on feed, age at slaughter, and carcass traits in a multi-breed beef cattle population." Journal of Animal Science 98, Supplement_4 (November 3, 2020): 21–22. http://dx.doi.org/10.1093/jas/skaa278.040.
Full textAbstract:
Abstract The objective of this study was to estimate genetic parameters for days on feed (DOF), age at slaughter (AAS), and their relationships with carcass traits, including: marbling score (MARB), adjusted fat thickness (AFT), hot carcass weight (HCW), ribeye area (REA), and final live weight (FW). Data were from steers and heifers (n = 7,747) from the Germplasm Evaluation Program at the U.S. Meat Animal Research Center. All traits were analyzed with univariate and bivariate animal models using ASReml. Fixed effects fitted for all models included contemporary group (concatenation of birth year and season, sex, and experimental treatment group), breed fractions, and direct heterosis. Different endpoints were also investigated by fitting fixed linear covariates of AFT, HCW, REA, MARB, FW, and age (except AAS and DOF). For a given bivariate analyses, both traits were adjusted to the same endpoint. Univariate heritability estimates for AFT, AAS, DOF, FW, HCW, MARB, and REA ranged from 0.45–0.52, 0.52–0.59, 0.33–0.39, 0.34–0.55, 0.34–0.55, 0.54–0.55, and 0.50–0.56, respectively. Covariates of MARB and AFT led to the highest and lowest, respectively, heritability estimates for AAS and DOF. Depending on the endpoint, genetic correlations between AAS and AFT, FW, HCW, MARB, and REA ranged from 0.16 to 0.32, -0.08 to 0.33, 0.19 to 0.36, 0.14 to 0.20, and -0.06 to 0.13 (Table 1). Genetic correlations between DOF and AFT, MARB, and REA were negligible. Genetic correlations between DOF, FW, and HCW ranged from -0.10 to 0.29 and -0.37 to -0.17. Standard errors were less than 0.07 for all estimates. Phenotypic variability in DOF was low, and increased variability in AAS was due to differences in date of birth and thus weaning age. Results indicate DOF and AAS are moderately to highly heritable and generally lowly correlated with routine carcass traits. The USDA is an equal opportunity employer.
17
Hay, El Hamidi, and Andy Roberts. "Genotype × prenatal and post-weaning nutritional environment interaction in a composite beef cattle breed using reaction norms and a multi-trait model." Journal of Animal Science 96, no. 2 (January 29, 2018): 444–53. http://dx.doi.org/10.1093/jas/skx057.
Full text
18
Srivastava, Swati, Bryan Irvine Lopez, Sara de las Heras-Saldana, Jong-Eun Park, Dong-Hyun Shin, Han-Ha Chai, Woncheol Park, Seung-Hwan Lee, and Dajeong Lim. "Estimation of Genetic Parameters by Single-Trait and Multi-Trait Models for Carcass Traits in Hanwoo Cattle." Animals 9, no. 12 (December 2, 2019): 1061. http://dx.doi.org/10.3390/ani9121061.
Full textAbstract:
Hanwoo breed is preferred in South Korea because of the high standards in marbling and the palatability of its meat. Numerous studies have been conducted and are ongoing to increase the meat production and quality in this beef population. The aim of this study was to estimate and compare genetic parameters for carcass traits using BLUPF90 software. Four models were constructed, single trait pedigree model (STPM), single-trait genomic model (STGM), multi-trait pedigree model (MTPM), and multi-trait genomic model (MTGM), using the pedigree, phenotype, and genomic information of 7991 Hanwoo cattle. Four carcass traits were evaluated: Back fat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). Heritability estimates of 0.40 and 0.41 for BFT, 0.33 and 0.34 for CWT, 0.36 and 0.37 for EMA, and 0.35 and 0.38 for MS were obtained for the single-trait pedigree model and the multi-trait pedigree model, respectively, in Hanwoo. Further, the genomic model showed more improved results compared to the pedigree model, with heritability of 0.39 (CWT), 0.39 (EMA), and 0.46 (MS), except for 0.39 (BFT), which may be due to random events. Utilization of genomic information in the form of single nucleotide polymorphisms (SNPs) has allowed more capturing of the variance from the traits improving the variance components.
19
Graham, J. F., J. Byron, A. J. Clark, G. Kearney, and B. Orchard. "Effect of postweaning growth and bulls selected for extremes in retail beef yield and intramuscular fat on progeny liveweight and carcass traits." Animal Production Science 49, no. 6 (2009): 493. http://dx.doi.org/10.1071/ea08181.
Full textAbstract:
The present study is a component of a multi-site experiment, using Bos taurus cattle generated at four locations across southern Australia, designed to examine postweaning growth pathways for progeny whose sires were extreme in retail beef yield and intramuscular fat. Treatment and interaction effects on beef production and meat quality were examined within and across sites. The present paper describes the effect of postweaning growth and sire carcass type on liveweight and carcass traits at the Hamilton site. Angus sires selected on estimated breeding values for extremes in retail beef yield (RBY%), intramuscular fat (IMF%) (estimated breeding values for IMF% are derived by using live-animal ultrasound scanning) or both and sire breed types considered to be more extreme in those traits (Limousin, and Belgian Blue for yield, and Wagyu for intramuscular fat) were joined to crossbred and straight-bred cows. After weaning, the resultant 645 steer and heifer progeny were grown on a fast and slow growth path to ~550 kg and slaughtered, averaging 0.68 kg/day and 22.2 months, and 0.49 kg/day and 27.8 months for growth rate and age at slaughter, respectively. Growth path, sire carcass type and sex affected carcass traits; however, there were no sire carcass type by growth treatment interactions. The fast growth-path cattle were fatter, had more intramuscular fat (measured chemically), a higher Meat Standards of Australia (MSA) USA and AUS marble score, and a higher predicted MSA eating-quality score. Progeny of Wagyu sires were lighter at weaning and slaughter and had a lower hot standard carcass weight than the other sire carcass types. The Belgian Blue and Limousin progeny had a higher dressing percentage, a higher RBY% and a lower P8 and rib-fat depth and lower IMF% than the other sire breed types. Progeny of the high RBY% Angus had a lower rib-fat depth, a lower IMF% and higher RBY% than those selected for high IMF%. There was no difference in IMF% between the Wagyu or the high IMF% Angus. Progeny from the Belgian Blue, Limousin and Wagyu had a larger eye muscle area than the other sire breeds. The results indicate that simultaneous selection for supposedly antagonistic traits of IMF% and RBY% would result in carcass having high values of both measurements. Females were lighter than steers at slaughter, had a lower hot standard carcass weight, were fatter at the P8 and rib, and had a higher marble score and IMF%, a lower yield and a lower MSA-predicted eating-quality score than did steers. There was no interaction between postweaning growth and sire carcass type. These results indicate that with the use of appropriate sire carcass types and BREEDPLAN, and post-weaning nutrition, beef producers can confidently change carcass parameters to suit market specifications.
20
Voitenko, S. L., M. G. Porkhun, O. V. Sydorenko, and T. Y. Ilnytska. "GENETIC RESOURCES OF AGRICULTURAL ANIMALS OF UKRAINE AT THE BEGINNING OF THE THIRD MILLENNIUM." Animal Breeding and Genetics 58 (November 29, 2019): 110–19. http://dx.doi.org/10.31073/abg.58.15.
Full textAbstract:
Modern animal husbandry in Ukraine is an integral part of the market economy and is based on the use of advanced production technologies and not a large number of highly productive domestic or foreign breeds of farm animals. It has been established that the progress of the livestock industry is not possible without determining the changes that occur with breeds and livestock of breeding animals in the subjects of breeding business. It is well known that only breeding animals are able to display high genetic potential for productivity and to pass it on to offspring. Understanding of the state of the breeds is necessary to forecast product volumes that are consistent with country safety, and to determine the populations that need to be preserved or restored in the context of the global problem of wildlife biodiversity conservation.
The purpose of the work was to identify the species and breeds of farm animals that have formed the livestock sector of Ukraine at the beginning of the third millennium, and to identify changes that have occurred with the genetic resources of farm animals and to identify the breeds most vulnerable to the number of females under control.
Analysis of the state of dairy and combined dairy and meat breeds in the breeding herds of Ukraine made it possible to conclude that as of January 1, 2019, compared to the beginning of 2002, the number of cows in Ayrshire, Angler, Lebedyn, Simmental, Ukrainian Red-and-White Dairy, Ukrainian Black-and-White Dairy, Polish Red and Red Steppe decreased breeds. The increase in the number of cows occurs among the Ukrainian Whiteheaded, Holstein and Swiss breeds. Breeding herds for breeding cattle of Carpathian Brown, Ukrainian Brown Dairy breeds and Pintsgow are not functioning. The endangered include Angler, Ukrainian Whiteheaded, Ukrainian Brown Dairy and Polish Red breeds.
A comparative analysis of the number of cows of beef breeds in the subjects of breeding business of Ukraine in the dynamics of 2002–2019 indicates the preservation of all breeds, except for pentiges. In 2019, compared to 2002, cows increased in herds of Aberdeen-Angus breed, Hereford, Limousine, Southern Beef, Polissian Beef, Light Aquitan, Ukrainian Gray and Charolais. A significant decrease in the number of cows in Volinian Beef breed, the Znamensk type of Polissian Beef, Simmental Beef and Ukarainian Beef. The few in Ukraine at this stage include Hereford, Light Aquitan and Ukrainian Beef.
The state of pig breeding in the breeding farms on 01.01.2019 indicates the disappearance of breeding herds in which pigs of English selection Large White breed, Large Black and Myrgorod breeds were breed. At present, only Large White breeds and Landrace pigs can be competitive in numbers, and the rest should be considered non-numerical.
Sheep breeding, which is represented in Ukraine by the largest number of breeds and breed types, did not have any breeding herds in 2019, where in previous years bred Askanian Fine-Fleece breed, Askanian type of Black-Headed sheep with crossbred fleece, Olibs, North-Caucasian, Polwars, caucasian the Kharkiv type of the Ukrainian Meat-Fleece breed, the Tsigai breed and its two types, as well as the multi-breed type of the Karakul breed. Simultaneously with the disappearance of the above breeds new breeds or types appeared, among them: Bukovyna type of Askanian Meat-Fleece breed with crossbred fleece, Merinolandshaft, Dniprovian Meat (Dnipropetrovsk type), Romanivska. The smallest number of breeding queens of falcon and dark-headed Latvian breeds was established.
The changes that took place in the field of horse breeding of Ukraine during 2002–2019 relate to the creation and elimination of breeding herds in which horses were bred by Budyonnivska, Russian Heavy Draft and French Trotter breeds. No information is available in the State Register of Breeding Herds about the Gutsul and Torian breeds, as well as the Shetland Pony, may be regarded as the disappearance of these breeding herds. In 2019, compared to 2002, the number of mares of Newolexandrian Heavy Draft, Orlov Trotter, Russian Trotter, Trakenian, Ukrainian Saddle and Thoroughbred Saddle horse breeds declined significantly. The gene pool of horses has expanded only due to the Hanover breed.
Analysis of the status of other species and breeds of farm animals is not optimistic and indicates a decrease in the number of females and, consequently, a decrease in the gene pool of these breeds.Without the introduction of effective state conservation and support programs, as well as policy changes in the agricultural sector, Ukraine will continue to reduce livestock of agricultural animals, especially domestic autochthonous or local breeds, continuing the sad tradition of the world in reducing breed biodiversity.
21
Corbet, N. J., R. K. Shepherd, H. M. Burrow, K. C. Prayaga, J. van der Westhuizen, and D. J. Bosman. "Evaluation of Bonsmara and Belmont Red cattle breeds in South Africa. 2. Genetic parameters for growth and fertility." Australian Journal of Experimental Agriculture 46, no. 2 (2006): 213. http://dx.doi.org/10.1071/ea05224.
Full textAbstract:
Genetic parameters were estimated for growth and fertility indicator traits in a South African beef cattle population. Measurements on 5601 pedigreed progeny of 96 Bonsmara sires, 18 Belmont Red sires and 20 Bonsmara × Belmont Red cross sires were recorded over 19 years in 4 diverse climatic regions of South Africa. Growth traits were measured on growing stock from birth to 18 months at pasture. Cow weights were measured at calving and weaning. Age at first calving, and repeated measurements of calving day and calving interval were recorded on 1993 breeding females as indicators of reproductive performance. The traits were analysed using univariate and bivariate animal models with maternal effects fitted. Direct heritability of growth traits (0.11–0.42) and female fertility traits (0.02–0.13) suggested that genetic progress could be made by selection for some traits. Genetic correlations between growth and fertility traits were variable (–0.47–0.85) and indicated that multi-trait selection would be the best method of dealing with multidirectional forces on productivity traits. Genetic correlations between direct and maternal effects on liveweight traits were mostly negative indicating that genetic improvement of traits with strong maternal influence, such as weaning weight, would be complicated and supported the use of post-weaning weights with less maternal influence as selection criteria to improve the direct additive component of growth. The genetic parameter estimates provide useful reference values for estimation of breeding values in a proposed combined-breed genetic evaluation program.
22
Mills, Tess D., Kathy A. Larson, Mika Asai-Coakwell, Diego Moya Fernandez, John R. Campbell, and Bart Lardner. "85 DNA parentage in multi-sire breeding groups and sire repeatability on replacement heifer performance." Journal of Animal Science 97, Supplement_3 (December 2019): 73–74. http://dx.doi.org/10.1093/jas/skz258.153.
Full textAbstract:
Abstract The objective of this study was to apply DNA parentage testing in multi-sire breeding groups to assess repeatability of a sire’s impact on replacement females and terminal animals. Parentage testing was performed on DNA from 37 bulls and 1578 calves from a commercial ranch using natural breeding in four multi-sire breeding pastures over a four-year period (2015–2018). Parentage data was analyzed using Chi-square procedures. In 2016 and 2018, all bulls in the four breeding groups sired significantly different (P < 0.01) numbers of calves than expected. In 2015 and 2017, bulls in 2 of 4 and 3 of 4 breeding groups, respectively, sired significantly different (P < 0.01) numbers of calves than expected. For the 2015 and 2016 calf crops, three of 24 bulls used sired 30% of the calves and 33% of the selected replacement heifers. In 2017 and 2018, the calves born to the daughters of these three most prolific sires, averaged 4.5kg lower weaning weights than the average wean weights of the remaining calves. In 2018, all calves were tested for breed composition and vigour score using the EnvigourHX test from Neogen (Neogen Canada Inc., Edmonton Alberta, Canada). The average herd vigour score was 70%; the average vigour score for 2018 calves born to daughters of the top three prolific sires was 56%. Coupling production measures (weaning weights, birth dates, calving intervals) with sire parentage and vigour score data provides beef cattle producers with additional information to guide breeding choices to improve production in their operations.
23
Saad, Hamad M., Carolina L. Gonzalez-Berrios, Scott E. Speidel, R. Mark Enns, Ryan J. Boldt, Thomas R. R. Hansen, and Milt G. Thomas. "PSIII-4 Late-Breaking: Genetic Marker Association Study of Heifer Pregnancy in Red Angus Cattle." Journal of Animal Science 100, Supplement_4 (October 22, 2022): 35. http://dx.doi.org/10.1093/jas/skac313.050.
Full textAbstract:
Abstract Heifer pregnancy (HPG) is lowly heritable, yet economically relevant in beef cattle production systems. Hence, identifying single nucleotide polymorphisms (SNP) associated with phenotype could increase the amount of information used in the genetic evaluation of the trait. Using RNA-sequence data from lactating Holstein cows, a set of SNP (n = 69) were discovered among embryo mortality conceptuses (Conceptus-SNP) associated with maternal recognition of pregnancy on day 16 after artificial insemination (AI). To further study these SNP, our objective was to conduct analyses to identify markers associated with HPG in Red Angus. Phenotypic records and genotypes were provided by the Red Angus Association of America (RAAA). For phenotypes, a total of 59,387 cattle records, from the June 2022 RAAA genetic evaluation, were used in the analysis. For genotype data, a 47,860 SNP panel (excluding SNP on the X-chromosome) were formed by combining the historical RAAA genotype data (96,162 animals with genotypes) and genotypes from whole genome sequence of 30 prominent Red Angus AI sires. Markers were mapped to the ARS-UCD1.2 bovine reference genome and then imputed to 47,860 SNP panel using findhap software. A subset of SNP (n = 2,169 SNP; Conceptus-SNP and the multi-breed selected reduced panel [MSRP]) were extracted from the imputed genotypes file. Using PLINK software, genotype quality control procedure was performed so that animals with call rate < 0.9 were removed. A marker was removed if: it had minor allele frequency < 0.01, not in Hardy–Weinberg equilibrium (P < 0.00001), or in high linkage disequilibrium (r2 > 0.95). The final genotype file contained 96,667 animals with 2,137 SNP. A Bayes Cπ single-step super hybrid model (π = 0.99), using the BOLT software package, was used to estimate marker’s posterior probability of inclusion (PPI), the marker significance criterion in predicting HPG. A marker’s PPI was calculated as the average probability from four different Gibbs sampling chains of 75,000 iterations that included 5,000 iterations as burn-in. Markers rs42576394 (18:60583784) and rs42942055 (14:34249373) had PPI of 25.5 and 7.1%, respectively; suggesting association with HPG. None of the Conceptus-SNP had a detectable association with HPG; however, these Conceptus-SNP may be much more informative for genotype to phenotype association analyses for the trait of stayability. Such a trait would be measured with lactating mature beef cows and potentially more similar to the lactating Holstein cows from which the markers were discovered.
24
Chinarov, A. V. "Reserves of Meat Production: Breed Zoning of Beef Cattle Breeding in Russia." Economy of agricultural and processing enterprises, no. 12 (2020): 23–26. http://dx.doi.org/10.31442/0235-2494-2020-0-12-23-26.
Full textAbstract:
Based on the analysis of breeding work materials at the Russian meat cattle breeding, the importance and effectiveness of scientific breeds’ zoning was shown. Meat cattle which is bred at the Russian breeding farms is not worse than foreign one in terms of growth intensity, live weight, milk content and meat qualities. Multi-breeding is an objective necessity for the Russian Federation with its diverse natural and economic conditions. In 57 regions of the country, a comprehensive assessment of breeding and productive qualities of meat cattle is carried out. Strengthening the breeding base and matching the placement of cattle breeds to the natural and economic conditions of the regions is one of the most important conditions for the successful development of meat cattle breeding.
25
Hayes, Ben J., Nicholas J. Corbet, Jack M. Allen, Alan R. Laing, Geoffry Fordyce, Russel Lyons, Michael R. McGowan, and Brian M. Burns. "Towards multi-breed genomic evaluations for female fertility of tropical beef cattle1." Journal of Animal Science 97, no. 1 (October 29, 2018): 55–62. http://dx.doi.org/10.1093/jas/sky417.
Full text
26
Xu, Wang, Zhu, Liu, Li, Bordbar, Chen, et al. "Theoretical Evaluation of Multi-Breed Genomic Prediction in Chinese Indigenous Cattle." Animals 9, no. 10 (October 11, 2019): 789. http://dx.doi.org/10.3390/ani9100789.
Full textAbstract:
Genomic selection (GS) has been widely considered as a valuable strategy for enhancing the rate of genetic gain in farm animals. However, the construction of a large reference population is a big challenge for small populations like indigenous cattle. In order to evaluate the potential application of GS for Chinese indigenous cattle, we assessed the influence of combining multiple populations on the reliability of genomic predictions for 10 indigenous breeds of Chinese cattle using simulated data. Also, we examined the effect of different genetic architecture on prediction accuracy. In this study, we simulated a set of genotype data by a resampling approach which can reflect the realistic linkage disequilibrium pattern for multiple populations. We found within-breed evaluations yielded the highest accuracies ranged from 0.64 to 0.68 for four different simulated genetic architectures. For scenarios using multiple breeds as reference, the predictive accuracies were higher when the reference was comprised of breeds with a close relationship, while the accuracies were low when prediction were carried out among breeds. In addition, the accuracy increased in all scenarios with the heritability increased. Our results suggested that using meta-population as reference can increase accuracy of genomic predictions for small populations. Moreover, multi-breed genomic selection was feasible for Chinese indigenous populations with genetic relationships.
27
Crawford, A. D., and C. S. Mayne. "The effect of stocking rate on the performance of two breeds of dairy cattle at pasture." Proceedings of the British Society of Animal Science 2002 (2002): 43. http://dx.doi.org/10.1017/s1752756200006992.
Full textAbstract:
In Northern Ireland, grazed grass is the main diet offered to dairy cattle throughout the summer months. Whilst the Holstein-Friesian (HF) dairy cow is extremely efficient at converting grass into milk, there is evidence that the incidence of infertility in this breed is increasing (Mayne et al. 2001). This may reflect the fact that the breeding goals for the HF breed have been based primarily on selection for milk production with little emphasis for other traits such as fertility or health. In contrast, Norwegian dairy cattle (NC) have been selected using a multi trait index, with less emphasis on milk production and inclusion of other fertility and health traits. The overall objective of the present study was to evaluate the effect of varying stocking rate at pasture on performance of these two contrasting breeds.
28
Agnew, R. E., M. G. Porter, T. Yan, C. S. Mayne, and T. W. J. Keady. "An investigation of the efficiency of nutrient utilization for milk production by Holstein and Norwegian breeds of dairy cattle." Proceedings of the British Society of Animal Science 2002 (2002): 41. http://dx.doi.org/10.1017/s1752756200006979.
Full textAbstract:
Holstein-Friesian cattle are the predominant breed of dairy cattle in Northern Ireland. Breeding programmes for the Holstein Friesian have focused on improved milk production with little emphasis on functional traits such as fertility or disease resistance. In contrast Norwegian dairy cattle have been bred via a multi-trait selection procedure and there is evidence that problems associated with disease and fertility have tended to decrease in recent years. It is important, however, to investigate possible differences in efficiency of food use and partitioning of nutrients between the two breeds which may offset the potential advantages of improvements in secondary characteristics. Consequently, the objectives of this experiment were firstly to investigate the effects of breed type on the efficiency of utilization and partitioning of nutrients for milk production and secondly to investigate if there are differences in the energy requirement for maintenance and the efficiency of utilization of ME for lactation (kl) between the two breeds.
29
Pitchford, W. S., H. M. Mirzaei, M. P. B. Deland, R. A. Afolayan, D. L. Rutley, and A. P. Verbyla. "Variance components for birth and carcass traits of crossbred cattle." Australian Journal of Experimental Agriculture 46, no. 2 (2006): 225. http://dx.doi.org/10.1071/ea05248.
Full textAbstract:
During a 4-year period (1994–97) of the Australian ‘Southern Crossbreeding Project’, mature Hereford cows (n = 637) were mated to 97 sires from 7 breeds (Jersey, Wagyu, Angus, Hereford, South Devon, Limousin and Belgian Blue), resulting in 1334 calves. Heifers were slaughtered at around 16 months and steers at 23 months. The objective of the study was to quantify between- and within-breed genetic variation for numerous production and quality traits in a southern-Australian production system. Calf survival, birth weight and carcass production traits (carcass weight, fat depth, loin eye area, intramuscular fat) were obtained from these cattle. The carcass traits were loge-transformed because of a scale effect on the variance. Data were analysed using multi-variate animal models containing fixed effects of sex with random effects of management group, sire breed and animal. In addition, birth month and age of dam were included as fixed effects for birth weight. Covariances between survival and other traits could not be estimated from the multi-variate model so they were estimated from a series of bi-variate models. On average, management group and sire breed accounted for similar proportions of variance. Heritability ranged from 0.14 (survival), 0.17 (intramuscular fat), 0.28 (loin eye area), 0.29 (P8 fat depth), 0.31 (birth weight) to 0.50 (carcass weight). In general, environmental (management and residual) correlations between meat (carcass weight and loin eye area) and fat traits (fat depth and intramuscular fat) were positive, but the genetic correlations (both between and within breed) were negative. Management and genetic (co)variation has been quantified and can facilitate production of calves with carcasses suitable for specific market requirements.
30
Boichard, D., F. Guillaume, A. Baur, P. Croiseau, M. N. Rossignol, M. Y. Boscher, T. Druet, et al. "Genomic selection in French dairy cattle." Animal Production Science 52, no. 3 (2012): 115. http://dx.doi.org/10.1071/an11119.
Full textAbstract:
Genomic selection is implemented in French Holstein, Montbéliarde, and Normande breeds (70%, 16% and 12% of French dairy cows). A characteristic of the model for genomic evaluation is the use of haplotypes instead of single-nucleotide polymorphisms (SNPs), so as to maximise linkage disequilibrium between markers and quantitative trait loci (QTLs). For each trait, a QTL-BLUP model (i.e. a best linear unbiased prediction model including QTL random effects) includes 300–700 trait-dependent chromosomal regions selected either by linkage disequilibrium and linkage analysis or by elastic net. This model requires an important effort to phase genotypes, detect QTLs, select SNPs, but was found to be the most efficient one among all tested ones. QTLs are defined within breed and many of them were found to be breed specific. Reference populations include 1800 and 1400 bulls in Montbéliarde and Normande breeds. In Holstein, the very large reference population of 18 300 bulls originates from the EuroGenomics consortium. Since 2008, ~65 000 animals have been genotyped for selection by Labogena with the 50k chip. Bulls genomic estimated breeding values (GEBVs) were made official in June 2009. In 2010, the market share of the young bulls reached 30% and is expected to increase rapidly. Advertising actions have been undertaken to recommend a time-restricted use of young bulls with a limited number of doses. In January 2011, genomic selection was opened to all farmers for females. Current developments focus on the extension of the method to a multi-breed context, to use all reference populations simultaneously in genomic evaluation.
31
Paliy, A. P., T. L. Osipenko, and A. P. Palii. "Influence of cattle breed combinations on milk production: results of the Analysis of Variance." Ukrainian Journal of Ecology 11, no. 1 (January 20, 2021): 25–31. http://dx.doi.org/10.15421/2020_304.
Full textAbstract:
One of the main factors in increasing the efficiency of milk production is the breed. No breed in the world would be ideal for a variety of conditions and technological processes. Besides, like any biological system, the breed is in continuous change. The breed of cattle largely determines both the level of milk production and the quality of milk. Therefore, to improve the quality of milk, it is necessary to establish the degree of influence of zootechnical and technological factors on the condition of milk components. Among genetic factors, the breed of animals and the breed combination have a significant influence. During the research, a one-way analysis of variance of the breed's influence and breed combinations on productive indicators has been analyzed. The factor "breed" and "breed combination" were used as the analyzed factor, and the protein content in milk and the yield of milk protein was used as the dependent factor. Based on one-way and multi-way ANOVA, the degree of influence of the factors under study was assessed. It has been established that the breed has a significant, both direct and combined with other factors, influence on the protein content in milk and the yield of milk protein. The level of the breed's direct influence on the protein content is 1.0%, on the milk protein yield - 1.7%. The factors "father" and "calving number" have the most substantial combined effect. Their influence levels are 1.8%, 1.4%, respectively, with a high level of reliability (P=0.999). The same factors most influence the milk protein yield as the protein content (the levels of influence are 1.9%, 1.3%, respectively) with a high level of reliability (P=0.999). As a result of analyzing the data on changes in protein content and milk protein yield in cows of different breed combinations, it can be concluded that this factor can describe 4.5% of the variability in protein content and 11.4% of milk protein yield (P=0.999). The degree of joint influence of breed combinations with other studied factors was up to 6.6%.
32
Burke, Joan M., and James E. Miller. "Multi-species Grazing for Control of Gastrointestinal Nematodes – a Review." Journal of Animal Science 99, Supplement_2 (May 1, 2021): 36–37. http://dx.doi.org/10.1093/jas/skab096.066.
Full textAbstract:
Abstract Multi-species grazing, alternate grazing of cattle with sheep or goats, offers benefits to gastrointestinal nematode (GIN) control as GIN species differ between hosts. In the Southeastern United States, common GIN species of cattle include Cooperia spp., Ostertagia ostertagi, Haemonchus spp., whereas species of sheep and goats are Haemonchus contortus, Teladorsagia circumcincta, Trichostrongylus spp., Cooperia curticei, and Oesophagostomum spp. Anthelmintic resistance is widely prevalent in small ruminants, and is an increasing problem in cattle, but remains less prevalent. Thus, it is recommended to farmers to use a multi-faceted approach of GIN control, including multi-species grazing. Because management differs between cattle and small ruminants in regard to copper tolerance in minerals, predator control and fencing, alternate grazing of species has most commonly been used. Other considerations include age or susceptibility to GIN, as young calves may be vulnerable to GIN, but mature cows often have negligible GIN infection. Similarly, weanling lambs and kids are susceptible, and depending on breed, adults range from highly resistant to susceptible. Research indicates that GIN burden of more resistant animals is less influenced by multi-species grazing, and highly susceptible animals will likely need additional measures of control. The more resistant species used in the multi-species grazing may lend more control to the more susceptible. Some research showed reductions in O. ostertagi, but not C. oncophora in cattle during extended grazing of cattle and sheep, and reductions of H. contortus and T. colubriformis in sheep. However, other research reported similar worm burdens. Weight gains were improved in lambs grazed alternately with cattle in some studies, and most studies showed little benefit to cattle. Little has been published on alternate grazing with cattle and goats. The complex interactions, larger plot sizes needed, and time required to complete experiments limits published studies of this important management scheme.
33
Soini, Katriina, Eija Pouta, Terhi Latvala, and Taina Lilja. "Agrobiodiversity Products in Alternative Food System: Case of Finnish Native Cattle Breeds." Sustainability 11, no. 12 (June 20, 2019): 3408. http://dx.doi.org/10.3390/su11123408.
Full textAbstract:
Agrobiodiversity products i.e., products from native breeds and plant species can make a valuable contribution to a local food market while also maintaining and preserving ecological and cultural values. There have been attempts to create markets for these products, but they continue to be marginal across the world. Previous research revealed how various stakeholders perceive the native breeds and their products. This study applied a transdisciplinary, multi-actor co-production of knowledge approach that is often used in the food system research. The approach aims at improving the understanding of the ecological, regional and social embeddedness of a Finnish native breed, the Finncattle, and at co-creating feasible supply chains for Finncattle products. The study confirmed that the market does not work and the embeddedness may also constitute some challenges for the development of feasible product chains. The study suggested some practical solutions to overcome these challenges. Furthermore, the results revealed some weaknesses of the co-production of knowledge approach used and discussed possible reasons that can be further explored in future research.
34
Lowman, B. G., C. E. Hinks, E. A. Hunter, and N. A. Scott. "Effect of breed type, sex, method of rearing and winter nutrition on lifetime performance and carcass composition in a 20-month beef system: grazing performance." Animal Science 63, no. 2 (October 1996): 215–22. http://dx.doi.org/10.1017/s1357729800014764.
Full textAbstract:
AbstractIn a lifetime study of spring born cattle managed in a 20-month beef system, four feeding treatments were imposed during the 5-month winter period and two grass heights (low 6 to 8 cm, high 8 to 10 cm) during the subsequent grazing period. Three slaughter weights were imposed over the grazing period, early, mid and late, at an average of 67,110 and 154 days post turn-out. A multi-factorial design was used with three animal factors — maturity (early maturing Hereford crosses v. late maturing Charolais crosses), sex (heifer v. steer) and method of rearing (suckled calves v. bucket-reared calves). There were significant differences in growth rate for both sex and maturity (P < 0·001) and a highly significant negative effect of winter food level on summer growth rate (P < 0·001), the growth rate of food treatment 4 being proportionately 0·61 of that treatment 1.Sward height significantly influenced summer growth rate (P < 0·001) but showed no interaction with winter food level in any of the three grazing periods. Growth rates increased over the summer but differences between winter food treatments decreased with daily gains for food treatment 4 being proportionately 0·44, 0·81 and 0·84 of food treatment 1 as the grazing season progressed.Eliminating winter feeding treatment as a factor and including condition score at turn-out as a co-variate improved the variation explained and reduced differences in growth rate for the main effects with only the main effect of grass height remaining significant. This suggests that the condition of animals at turn-out in conjunction with the subsequent grazing sward height provides a simple practical guide to subsequent animal performance.
35
Senczuk, Gabriele, Vincenzo Landi, Salvatore Mastrangelo, Christian Persichilli, Fabio Pilla, and Elena Ciani. "Seven Shades of Grey: A Follow-Up Study on the Molecular Basis of Coat Colour in Indicine Grey Cattle Using Genome-Wide SNP Data." Genes 13, no. 9 (September 7, 2022): 1601. http://dx.doi.org/10.3390/genes13091601.
Full textAbstract:
Shades of grey and brown are a dominant component in mammal coat colours, representing a fundamental trait involved in a great number of processes including cryptism, sexual selection and signalling. The genetic mechanisms of the grey colouration in mammals are very complex and controlled by hundreds of genes whose effects and interactions are still largely unclear. In this study, we adopted a robust multi-cohort Fst outlier approach based on pairwise contrasts between seven grey indicine cattle breeds and both taurine and indicine non-grey cattle breeds in order to find genomic regions potentially related to the grey colouration. On the basis of three main drawn settings, built in order to control both the effect of the sample size and the genetic structure, we have identified some signals common to those obtained in a previous work employing only taurine cattle. In particular, using the top 1% Fst approach, we detected a candidate region (22.6–23.8 megabases) on chromosome 14 in which genes related to pigmentation have been already documented. In addition, when we constructed a phylogenetic tree using the significant markers identified in this study and including also the genotyping data at these loci of both the grey taurine and the extinct wild auroch, we found a topological repartition consistent with breed colour pattern rather than with the known bovine evolutionary history. Thus, on the basis of this evidence, together with the geographical distribution of the current taurine grey cattle, an ancestral indicine origin for the grey phenotype would seem to be a conceivable interpretation. In this context, a higher thermo-tolerance and less UV-induced damage of the grey phenotype might have favoured the retention of advantageous genes into the taurine genome during the post-Neolithic human-mediated cattle expansions.
36
Keady, T. W. J., A. D. Crawford, and C. S. Mayne. "A comparison of the Holstein Friesian and Norwegian cattle breeds for milk production at two levels of nutrient intake." Proceedings of the British Society of Animal Science 2001 (2001): 38. http://dx.doi.org/10.1017/s1752756200004208.
Full textAbstract:
Breeding programmes for Holstein Friesian (HF) animals have been based on improved milk production with little emphasis on functional traits such as fertility. This has resulted in a rapid increase in milk production potential of the national dairy herd but unfortunately this has been at the expense of issues such as longevity, especially due to poor reproductive performance. In contrast Norwegian (NC) dairy cattle have been bred via a multi-trait selection procedure for 25 years and there is evidence that fertility has improved during that period. These differences in selection procedures for the two breeds may have major effects on overall herd output and profitability within the grass-based systems of milk production employed in Northern Ireland. The present study is part of an overall study comparing the effects of HF and NC genotypes on food intake, animal performance, nutrient utilisation, behaviour, health, fertility and longevity. The objective of the present paper is to present the effects of breed on food intake and utilisation, and animal performance when offered two levels of nutrient inputs based on grass silage-based diets.
37
Kuca, Thibaud, Brandy M. Marron, Joana G. P. Jacinto, Julia M. Paris, Christian Gerspach, Jonathan E. Beever, and Cord Drögemüller. "A Nonsense Variant in Hephaestin Like 1 (HEPHL1) Is Responsible for Congenital Hypotrichosis in Belted Galloway Cattle." Genes 12, no. 5 (April 26, 2021): 643. http://dx.doi.org/10.3390/genes12050643.
Full textAbstract:
Genodermatosis such as hair disorders mostly follow a monogenic mode of inheritance. Congenital hypotrichosis (HY) belong to this group of disorders and is characterized by abnormally reduced hair since birth. The purpose of this study was to characterize the clinical phenotype of a breed-specific non-syndromic form of HY in Belted Galloway cattle and to identify the causative genetic variant for this recessive disorder. An affected calf born in Switzerland presented with multiple small to large areas of alopecia on the limbs and on the dorsal part of the head, neck, and back. A genome-wide association study using Swiss and US Belted Galloway cattle encompassing 12 cases and 61 controls revealed an association signal on chromosome 29. Homozygosity mapping in a subset of cases refined the HY locus to a 1.5 Mb critical interval and subsequent Sanger sequencing of protein-coding exons of positional candidate genes revealed a stop gain variant in the HEPHL1 gene that encodes a multi-copper ferroxidase protein so-called hephaestin like 1 (c.1684A>T; p.Lys562*). A perfect concordance between the homozygous presence of this most likely pathogenic loss-of-function variant and the HY phenotype was found. Genotyping of more than 700 purebred Swiss and US Belted Galloway cattle showed the global spread of the mutation. This study provides a molecular test that will permit the avoidance of risk matings by systematic genotyping of relevant breeding animals. This rare recessive HEPHL1-related form of hypotrichosis provides a novel large animal model for similar human conditions. The results have been incorporated in the Online Mendelian Inheritance in Animals (OMIA) database (OMIA 002230-9913).
38
Martin, Miriam S., Michael D. Kleinhenz, Brad J. White, Abbie Viscardi, Lily N. Edwards-Callaway, Terry E. Engle, Blaine Johnson, et al. "393 Young Scholar Award Talk: Investigation of Pain and Analgesic Strategies in Cattle Undergoing Painful Husbandry Procedures and Disease Conditions." Journal of Animal Science 100, Supplement_3 (September 21, 2022): 196–97. http://dx.doi.org/10.1093/jas/skac247.361.
Full textAbstract:
Abstract Cattle are stoic by nature and have long been subject to evolutionary pressure to mask pain to avoid becoming prey. Quantifying pain via biomarkers allows researchers to capture changes that are not easily detected by the human eye. Negative public perception of routine husbandry practices such as dehorning and castration is growing, increasing the need for the development of practices to relieve pain and suffering in cattle. The objective was to quantify pain associated with induced bacterial pneumonia, scoop and hot-iron dehorning, surgical castration, and hot-iron branding, and to investigate analgesic effectiveness. Calves were experimentally inoculated with Mannheimia haemolytica, scoop or cautery dehorned, surgically castrated, or hot-iron branded. Outcome variables were collected at baseline and following husbandry procedures and included serum cortisol; infrared thermography (IRT); mechanical nociceptive threshold (MNT); substance P; kinematic gait analysis; a visual analog scale; chute defense and behavior scoring; clinical illness score; computerized lung score; average activity and rumination; prostaglandin E2 metabolite; plasma serum amyloid A and rectal temperature. Responses were analyzed using repeated measures with calf nested in treatment designated as a random effect, and treatment, time, and their interaction designated as fixed effects. A combination of reduced activity levels, decreased force on calves’ right front limb, and increased visual analog scale pain scores all support that bacterial pneumonia in cattle is painful (P ≤ 0.01). Differences in right front force were observed in calves challenged with M. haemolytica and treated with flunixin transdermal (96.5 kg) and those given a placebo (85.5 kg), indicating that flunixin transdermal may attenuate specific pain biomarkers in cattle with respiratory disease (P < 0.01). Administration of a bupivacaine liposome suspension block at the time of dehorning and castration was as effective at controlling pain as a multi-modal approach of lidocaine and meloxicam (as evidenced by treatment differences in MNT, cortisol and gait analysis (P ≤ 0.04)). Oral meloxicam administration at branding reduced IRT differences from the branding and control site and reduced lying bouts (P < 0.01). Breed and sex effects were observed across a wide range of biomarkers and should be investigated in future pain studies. The need for long-acting analgesic options for cattle that demonstrate pain alleviation across multiple biomarkers is apparent and would be beneficial to alleviating pain from routine husbandry procedures like dehorning, castration, and branding, as well as painful disease conditions such as bovine respiratory disease.
39
VanEtten, T., F. Ireland, D. Vandever, D. Kesler, and M. Wheeler. "193 EVALUATION OF A NOVEL ELECTRONIC ESTRUS DETECTION DEVICE IN RECIPIENTS SYNCHRONIZED FOR EMBRYO TRANSFER." Reproduction, Fertility and Development 18, no. 2 (2006): 204. http://dx.doi.org/10.1071/rdv18n2ab193.
Full textAbstract:
The ability to detect estrus in cattle is an important aspect for both successful artificial insemination (AI) and successful embryo transfer (ET). The use of estrus detection devices has allowed producers to more precisely determine when to breed their cattle. There have been many types of devices including chin-ball marking harnesses, dye patches, and even electronic devices that monitor the animal's activity. With the growing popularity in timed AI and ET, these devices have again become of great interest. The latest tool for estrus detection is the multi-use TattleTale" Heat Detector (Microdyne Co., LLC., St. Joseph, MO, USA). The TattleTale" is an electronic device that is placed in a patch and affixed to the tail head. It is activated by a 3-s mount with subsequent mounts recorded per h through 12 h. Twelve hours after activation the device flashes indicating that the animal is ready for breeding. Such devices may allow breeders to determine exactly when estrus began as well as identify the peak estrus period, resulting in more accurate determination of optimal time for AI or ET. The objective of this study was to compare the accuracy of estrus detection devices when analyzing detection records and pregnancy rates. Cows from the Dixon Springs Agricultural Center (Simpson, IL, USA) were randomly separated into two groups based on estrus detection devices, one group receiving Kamar� patches (Kamor, Inc., Steamboat Springs, CO, USA) and the other receiving TattleTales. Both groups were synchronized using the OvSynch protocol (Syntex, Buenos Aires, Argentina). Cows were checked twice each day for four consecutive days, with a fifth day occurring a week later when the embryos were transferred. Estrus results were analyzed using a PROC UNIVARITE and GLM analyses with differences between treatment means determined by the LSD method of SAS (SAS Institute, Inc., Cary, NC, USA). The TattleTale detected a higher percentage (P < 0.05) of the cows in estrus (92 vs. 70%) than the Kamar� patch. Further, the TattleTale detected more asynchronous recipients (in estrus >48 h before expected) and synchronous recipients (in estrus <24 h than expected), although not significant with this sample size. In the present study, the TattleTale was more accurate in detecting estrus (i.e. fewer pregnancies were observed without estrus detected). Using the TattleTale information, a breeder would be able detect more animals in estrus and determine the most accurate time to breed or transfer embryos. Practically, the use of estrus detection devices in combination with timed AI and ET could allow for the exclusion of animals not in estrus in the optimal time windows for AI or ET, thus saving valuable semen and embryos that would be otherwise wasted on asynchronous females. The advantages of this device to producers include improved pregnancy rates based on timed breeding, lower herd management costs due to reduced quantities of wasted semen or embryos and fewer cows being resynchronized. This device also records any mounting activity missed by visual observation alone. This work was supported by USDA RRF W-1171.
40
Rolf, Megan M., Dorian J. Garrick, Tara Fountain, Holly R. Ramey, Robert L. Weaber, Jared E. Decker, E. John Pollak, Robert D. Schnabel, and Jeremy F. Taylor. "Comparison of Bayesian models to estimate direct genomic values in multi-breed commercial beef cattle." Genetics Selection Evolution 47, no. 1 (April 1, 2015). http://dx.doi.org/10.1186/s12711-015-0106-8.
Full text
41
Cardoso, Fernando Flores, Oswald Matika, Appolinaire Djikeng, Ntanganedzeni Mapholi, Heather M. Burrow, Marcos Jun Iti Yokoo, Gabriel Soares Campos, et al. "Multiple Country and Breed Genomic Prediction of Tick Resistance in Beef Cattle." Frontiers in Immunology 12 (June 23, 2021). http://dx.doi.org/10.3389/fimmu.2021.620847.
Full textAbstract:
Ticks cause substantial production losses for beef and dairy cattle. Cattle resistance to ticks is one of the most important factors affecting tick control, but largely neglected due to the challenge of phenotyping. In this study, we evaluate the pooling of tick resistance phenotyped reference populations from multi-country beef cattle breeds to assess the possibility of improving host resistance through multi-trait genomic selection. Data consisted of tick counts or scores assessing the number of female ticks at least 4.5 mm length and derived from seven populations, with breed, country, number of records and genotyped/phenotyped animals being respectively: Angus (AN), Brazil, 2,263, 921/1,156, Hereford (HH), Brazil, 6,615, 1,910/2,802, Brangus (BN), Brazil, 2,441, 851/851, Braford (BO), Brazil, 9,523, 3,062/4,095, Tropical Composite (TC), Australia, 229, 229/229, Brahman (BR), Australia, 675, 675/675, and Nguni (NG), South Africa, 490, 490/490. All populations were genotyped using medium density Illumina SNP BeadChips and imputed to a common high-density panel of 332,468 markers. The mean linkage disequilibrium (LD) between adjacent SNPs varied from 0.24 to 0.37 across populations and so was sufficient to allow genomic breeding values (GEBV) prediction. Correlations of LD phase between breeds were higher between composites and their founder breeds (0.81 to 0.95) and lower between NG and the other breeds (0.27 and 0.35). There was wide range of estimated heritability (0.05 and 0.42) and genetic correlation (-0.01 and 0.87) for tick resistance across the studied populations, with the largest genetic correlation observed between BN and BO. Predictive ability was improved under the old-young validation for three of the seven populations using a multi-trait approach compared to a single trait within-population prediction, while whole and partial data GEBV correlations increased in all cases, with relative improvements ranging from 3% for BO to 64% for TC. Moreover, the multi-trait analysis was useful to correct typical over-dispersion of the GEBV. Results from this study indicate that a joint genomic evaluation of AN, HH, BN, BO and BR can be readily implemented to improve tick resistance of these populations using selection on GEBV. For NG and TC additional phenotyping will be required to obtain accurate GEBV.
42
Akanno, Everestus C., Liuhong Chen, Mohammed K. Abo-Ismail, John J. Crowley, Zhiquan Wang, Changxi Li, John A. Basarab, Michael D. MacNeil, and Graham S. Plastow. "Genome-wide association scan for heterotic quantitative trait loci in multi-breed and crossbred beef cattle." Genetics Selection Evolution 50, no. 1 (October 5, 2018). http://dx.doi.org/10.1186/s12711-018-0405-y.
Full text
43
Mulim, Henrique Alberto, Luiz F. Brito, Luís Fernando Batista Pinto, José Luis Moletta, Lilian Regina Da Silva, and Victor Breno Pedrosa. "Genetic and Genomic Characterization of a New Beef Cattle Composite Breed (Purunã) Developed for Production in Pasture-Based Systems." Frontiers in Genetics 13 (July 18, 2022). http://dx.doi.org/10.3389/fgene.2022.858970.
Full textAbstract:
Purunã is a composite beef cattle breed, developed in Southern Brazil by crossing the Angus, Charolais, Canchim, and Caracu breeds. The goal of this study was to perform the first genetic characterization of the Purunã breed, based on both pedigree and genomic information. For this, 100 randomly selected animals were genotyped, and 11,205 animals born from 1997 to 2019 had pedigree information. The genetic analyses performed were principal component analysis, admixture, phylogenic tree, pedigree and genomic inbreeding, linkage disequilibrium (LD), effective population size (Ne), consistency of the gametic phase, runs of homozygosity (ROH), heterozygosity-enriched regions (HERs), and functional analyses of the ROH and HER regions identified. Our findings indicate that Purunã is more genetically related to the Charolais, Canchim, and Angus breeds than Caracu or Nellore. The levels of inbreeding were shown to be small based on all the metrics evaluated and ranged from −0.009 to 0.029. A low (−0.12–0.31) correlation of the pedigree-based inbreeding compared to all the genomic inbreeding coefficients evaluated was observed. The LD average was 0.031 (±0.0517), and the consistency of the gametic phase was shown to be low for all the breed pairs, ranging from 0.42 to 0.27 to the distance of 20 Mb. The Ne values based on pedigree and genomic information were 158 and 115, respectively. A total of 1,839 ROHs were found, and the majority of them are of small length (<4 Mb). An important homozygous region was identified on BTA5 with pathways related to behavioral traits (sensory perception, detection of stimulus, and others), as well as candidate genes related to heat tolerance (MY O 1A), feed conversion rate (RDH5), and reproduction (AMDHD1). A total of 1,799 HERs were identified in the Purunã breed with 92.3% of them classified within the 0.5–1 Mb length group, and 19 HER islands were identified in the autosomal genome. These HER islands harbor genes involved in growth pathways, carcass weight (SDCBP), meat and carcass quality (MT2A), and marbling deposition (CISH). Despite the genetic relationship between Purunã and the founder breeds, a multi-breed genomic evaluation is likely not feasible due to their population structure and low consistency of the gametic phase among them.
44
Ramayo-Caldas, Yuliaxis, Gilles Renand, Maria Ballester, Romain Saintilan, and Dominique Rocha. "Multi-breed and multi-trait co-association analysis of meat tenderness and other meat quality traits in three French beef cattle breeds." Genetics Selection Evolution 48, no. 1 (April 23, 2016). http://dx.doi.org/10.1186/s12711-016-0216-y.
Full text
45
Rowan, Troy N., Jesse L. Hoff, Tamar E. Crum, Jeremy F. Taylor, Robert D. Schnabel, and Jared E. Decker. "A multi-breed reference panel and additional rare variants maximize imputation accuracy in cattle." Genetics Selection Evolution 51, no. 1 (December 2019). http://dx.doi.org/10.1186/s12711-019-0519-x.
Full textAbstract:
Abstract Background During the last decade, the use of common-variant array-based single nucleotide polymorphism (SNP) genotyping in the beef and dairy industries has produced an astounding amount of medium-to-low density genomic data. Although low-density assays work well in the context of genomic prediction, they are less useful for detecting and mapping causal variants and the effects of rare variants are not captured. The objective of this project was to maximize the accuracies of genotype imputation from medium- and low-density assays to the marker set obtained by combining two high-density research assays (~ 850,000 SNPs), the Illumina BovineHD and the GGP-F250 assays, which contains a large proportion of rare and potentially functional variants and for which the assay design is described here. This 850 K SNP set is useful for both imputation to sequence-level genotypes and direct downstream analysis. Results We found that a large multi-breed composite imputation reference panel that includes 36,131 samples with either BovineHD and/or GGP-F250 genotypes significantly increased imputation accuracy compared with a within-breed reference panel, particularly at variants with low minor allele frequencies. Individual animal imputation accuracies were maximized when more genetically similar animals were represented in the composite reference panel, particularly with complete 850 K genotypes. The addition of rare variants from the GGP-F250 assay to our composite reference panel significantly increased the imputation accuracy of rare variants that are exclusively present on the BovineHD assay. In addition, we show that an assay marker density of 50 K SNPs balances cost and accuracy for imputation to 850 K. Conclusions Using high-density genotypes on all available individuals in a multi-breed reference panel maximized imputation accuracy for tested cattle populations. Admixed animals or those from breeds with a limited representation in the composite reference panel were still imputed at high accuracy, which is expected to further increase as the reference panel expands. We anticipate that the addition of rare variants from the GGP-F250 assay will increase the accuracy of imputation to sequence level.
46
Sanglard, Leticia P., Warren M. Snelling, Larry A. Kuehn, R. Mark Thallman, Harvey C. Freetly, Tommy L. Wheeler, Steven D. Shackelford, D. Andy King, and Matthew L. Spangler. "Genetic and phenotypic associations of mitochondrial DNA copy number, SNP, and haplogroups with growth and carcass traits in beef cattle." Journal of Animal Science, December 25, 2022. http://dx.doi.org/10.1093/jas/skac415.
Full textAbstract:
Abstract Mitochondrial DNA copy number (mtDNA CN) is heritable and easily obtained from low-pass sequencing (LPS). This study investigated the genetic correlation of mtDNA CN with growth and carcass traits in a multi-breed and crossbred beef cattle population. Blood, leucocyte, and semen samples were obtained from 2,371 animals and subjected to LPS that resulted in nuclear DNA (nuDNA) and mtDNA sequence reads. Mitochondrial DNA CN was estimated as the ratio of mtDNA to nuDNA coverages. Variant calling was performed from mtDNA, and 11 single nucleotide polymorphisms (SNP) were identified in the population. Samples were classified in taurine haplogroups. Haplogroup and mtDNA type were further classified based on the 11 segregating SNP. Growth and carcass traits were available for between 7,249 and 60,989 individuals. Associations of mtDNA CN, mtDNA haplogroups, mtDNA types, and mtDNA SNP with growth and carcass traits were estimated with univariate animal models, and genetic correlations were estimated with a bivariate animal model based on pedigree. Mitochondrial DNA CN tended (P-value ≤ 0.08) to be associated with birth weight and weaning weight. There was no association (P-value > 0.10) between mtDNA SNP, haplogroups, or types with growth and carcass traits. Genetic correlation estimates of mtDNA CN were -0.30±0.16 with birth weight, -0.31±0.16 with weaning weight, -0.15±0.14 with post-weaning gain, -0.11±0.19 with average daily dry-matter intake, -0.04±0.22 with average daily gain, -0.29±0.13 with mature cow weight, -0.11±0.13 with slaughter weight, -0.14±0.13 with carcass weight, -0.07±0.14 with carcass backfat, 0.14±0.14 with carcass marbling, and -0.06±0.14 with ribeye area. In conclusion, mtDNA CN was negatively correlated with most traits investigated, and the genetic correlation was stronger with growth traits than with carcass traits.
47
Purfield, D. C., R. D. Evans, and D. P. Berry. "Reaffirmation of known major genes and the identification of novel candidate genes associated with carcass-related metrics based on whole genome sequence within a large multi-breed cattle population." BMC Genomics 20, no. 1 (September 18, 2019). http://dx.doi.org/10.1186/s12864-019-6071-9.
Full textAbstract:
Abstract Background The high narrow sense heritability of carcass traits suggests that the underlying additive genetic potential of an individual should be strongly correlated with both animal carcass quality and quantity, and therefore, by extension, carcass value. Therefore, the objective of the present study was to detect genomic regions associated with three carcass traits, namely carcass weight, conformation and fat cover, using imputed whole genome sequence in 28,470 dairy and beef sires from six breeds with a total of 2,199,926 phenotyped progeny. Results Major genes previously associated with carcass performance were identified, as well as several putative novel candidate genes that likely operate both within and across breeds. The role of MSTN in carcass performance was re-affirmed with the segregating Q204X mutation explaining 1.21, 1.11 and 5.95% of the genetic variance in carcass weight, fat and conformation, respectively in the Charolais population. In addition, a genomic region on BTA6 encompassing the NCAPG/LCORL locus, which is a known candidate locus associated with body size, was associated with carcass weight in Angus, Charolais and Limousin. Novel candidate genes identified included ZFAT in Angus, and SLC40A1 and the olfactory gene cluster on BTA15 in Charolais. Although the majority of associations were breed specific, associations that operated across breeds included SORCS1 on BTA26, MCTP2 on BTA21 and ARL15 on BTA20; these are of particular interest due to their potential informativeness in across-breed genomic evaluations. Genomic regions affecting all three carcass traits were identified in each of the breeds, although these were mainly concentrated on BTA2 and BTA6, surrounding MSTN and NCAPG/LCORL, respectively. This suggests that although major genes may be associated with all three carcass traits, the majority of genes containing significant variants (unadjusted p-value < 10− 4) may be trait specific associations of small effect. Conclusions Although plausible novel candidate genes were identified, the proportion of variance explained by these candidates was minimal thus reaffirming that while carcass performance may be affected by major genes in the form of MSTN and NCAPG/LCORL, the majority of variance is attributed to the additive (and possibly multiplicative) effect of many polymorphisms of small effect.
48
Fernandes, G. M., R. P. Savegnago, L. A. Freitas, L. El Faro, V. M. Roso, and C. C. P. de Paz. "Multi-trait selection index and cluster analyses in Angus cattle." Journal of Agricultural Science, August 3, 2021, 1–8. http://dx.doi.org/10.1017/s0021859621000575.
Full textAbstract:
Abstract In breeding programmes, the genetic selection process is based on the prediction of animal breeding values, and its results may vary according to the employed selection method. The current study developed an economic selection index for animals of the Angus breed; performed cluster analyses using the breeding values in order to evaluate the genetic profile of the animals candidates to selection, and compared the obtained results between the economic selection index and the cluster analyses. The evaluated traits included weaning weight, 18-month weight, scrotal circumference, fat thickness and ribeye area. Economic values were obtained using bioeconomic modelling, simulating a complete cycle production system of beef cattle breeds in Brazil, and the selection objective were the weaning rate and slaughter weight. The chosen selection index was composed of all of the traits used as selection criteria for the simulated production system. During the cluster analyses, the population was divided into two to four groups, in which the groupings containing potential animals were assessed. The animals of the grouping which was used for comparison with the selection index were identified, and most of the bulls that were included in the index were among the best in the analysed group. These results suggest that the cluster analyses can be used as a tool for the selection of animals to be used as parents for future generations.
49
Karaman, Emre, Guosheng Su, Iola Croue, and Mogens S. Lund. "Genomic prediction using a reference population of multiple pure breeds and admixed individuals." Genetics Selection Evolution 53, no. 1 (May 31, 2021). http://dx.doi.org/10.1186/s12711-021-00637-y.
Full textAbstract:
Abstract Background In dairy cattle populations in which crossbreeding has been used, animals show some level of diversity in their origins. In rotational crossbreeding, for instance, crossbred dams are mated with purebred sires from different pure breeds, and the genetic composition of crossbred animals is an admixture of the breeds included in the rotation. How to use the data of such individuals in genomic evaluations is still an open question. In this study, we aimed at providing methodologies for the use of data from crossbred individuals with an admixed genetic background together with data from multiple pure breeds, for the purpose of genomic evaluations for both purebred and crossbred animals. A three-breed rotational crossbreeding system was mimicked using simulations based on animals genotyped with the 50 K single nucleotide polymorphism (SNP) chip. Results For purebred populations, within-breed genomic predictions generally led to higher accuracies than those from multi-breed predictions using combined data of pure breeds. Adding admixed population’s (MIX) data to the combined pure breed data considering MIX as a different breed led to higher accuracies. When prediction models were able to account for breed origin of alleles, accuracies were generally higher than those from combining all available data, depending on the correlation of quantitative trait loci (QTL) effects between the breeds. Accuracies varied when using SNP effects from any of the pure breeds to predict the breeding values of MIX. Using those breed-specific SNP effects that were estimated separately in each pure breed, while accounting for breed origin of alleles for the selection candidates of MIX, generally improved the accuracies. Models that are able to accommodate MIX data with the breed origin of alleles approach generally led to higher accuracies than models without breed origin of alleles, depending on the correlation of QTL effects between the breeds. Conclusions Combining all available data, pure breeds’ and admixed population’s data, in a multi-breed reference population is beneficial for the estimation of breeding values for pure breeds with a small reference population. For MIX, such an approach can lead to higher accuracies than considering breed origin of alleles for the selection candidates, and using breed-specific SNP effects estimated separately in each pure breed. Including MIX data in the reference population of multiple breeds by considering the breed origin of alleles, accuracies can be further improved. Our findings are relevant for breeding programs in which crossbreeding is systematically applied, and also for populations that involve different subpopulations and between which exchange of genetic material is routine practice.
50
Al Kalaldeh, Mohammad, Marimuthu Swaminathan, Yuvraj Gaundare, Sachin Joshi, Hassan Aliloo, Eva M. Strucken, Vincent Ducrocq, and John P. Gibson. "Genomic evaluation of milk yield in a smallholder crossbred dairy production system in India." Genetics Selection Evolution 53, no. 1 (September 10, 2021). http://dx.doi.org/10.1186/s12711-021-00667-6.
Full textAbstract:
Abstract Background India is the largest milk producer globally, with the largest proportion of cattle milk production coming from smallholder farms with an average herd size of less than two milking cows. These cows are mainly undefined multi-generation crosses between exotic dairy breeds and indigenous Indian cattle, with no performance or pedigree recording. Therefore, implementing genetic improvement based on genetic evaluation has not yet been possible. We present the first results from a large smallholder performance recording program in India, using single nucleotide polymorphism (SNP) genotypes to estimate genetic parameters for monthly test-day (TD) milk records and to obtain and validate genomic estimated breeding values (GEBV). Results The average TD milk yield under the high, medium, and low production environments were 9.64, 6.88, and 4.61 kg, respectively. In the high production environment, the usual profile of a lactation curve was evident, whereas it was less evident in low and medium production environments. There was a clear trend of an increasing milk yield with an increasing Holstein Friesian (HF) proportion in the high production environment, but no increase above intermediate grades in the medium and low production environments. Trends for Jersey were small but yield estimates had a higher standard error than HF. Heritability estimates for TD yield across the lactation ranged from 0.193 to 0.250, with an average of 0.230. The additive genetic correlations between TD yield at different times in lactation were high, ranging from 0.846 to 0.998. The accuracy of phenotypic validation of GEBV from the method that is believed to be the least biased was 0.420, which was very similar to the accuracy obtained from the average prediction error variance of the GEBV. Conclusions The results indicate strong potential for genomic selection to improve milk production of smallholder crossbred cows in India. The performance of cows with different breed compositions can be determined in different Indian environments, which makes it possible to provide better advice to smallholder farmers on optimum breed composition for their environment.