Journal articles on the topic 'Genotypic'
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1
Sawada, Leila, Andréia Cristina Costa Pinheiro, Daiane Locks, Adriana do Socorro Coelho Pimenta, Priscila Rocha Rezende, Deborah Maia Crespo, José Ângelo Barletta Crescente, José Alexandre Rodrigues de Lemos, and Aldemir Branco de Oliveira Filho. "Distribution of hepatitis C virus genotypes among different exposure categories in the State of Pará, Brazilian Amazon." Revista da Sociedade Brasileira de Medicina Tropical 44, no. 1 (February 2011): 8–12. http://dx.doi.org/10.1590/s0037-86822011000100003.
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INTRODUCTION: Epidemiological studies concerning HCV genotypic distribution in the Brazilian Amazon are scarce. Thus, this study determined the patterns of distribution of HCV genotypes among different exposure categories in the State of Pará, Brazilian Amazon. METHODS: A cross-sectional study was conducted on 312 HCV-infected individuals belonging to different categories of exposure, who were attended at the HEMOPA, CENPREN and a private hemodialysis clinic in Belém. They were tested for HCV antibodies using an immunoenzymatic test, RNA-HCV, using real-time PCR and HCV genotyping through phylogenetic analysis of the 5' UTR. The population groups were epidemiologically characterized according to data collected in a brief interview or medical consultation. RESULTS: Genotype 1 predominated in all the different categories of HCV exposure. HCV genotypic distribution among blood donors comprised genotypes 1 (94%) and 3 (6%). All patients with chronic hematologic diseases had HCV genotype 1. The genotypic distribution in illicit-drug users comprised genotypes 1 (59.6%) and 3 (40.4%). In patients under hemodialysis, genotypes 1 (90.1%), 2 (3.3%), and 3 (6.6%) were detected. Finally, the frequency of genotypes 1 and 3 was significantly different between the groups: BD and DU, PUH and DU, PUH and PCHD and PCHD and DU. CONCLUSIONS: The genotypic frequency and distribution of HCV in different categories of exposure in the State of Pará showed a predominance of genotype 1, regardless of the possible risk of infection.
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Filho, João de Andrade Dutra, Tercilio Calsa Júnior, Djalma Euzébio Simões Neto, Lauter Silva Souto, Anielson dos Santos Souza, Rômulo Gil de Luna, Frank Gomes-Silva, et al. "Genetic divergence for adaptability and stability in sugarcane: Proposal for a more accurate evaluation." PLOS ONE 16, no. 7 (July 15, 2021): e0254413. http://dx.doi.org/10.1371/journal.pone.0254413.
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The best agro-industrial performance presented by a crop genotype in one environment may not be reproduced in another owing to complex edaphoclimatic variations. Therefore, breeding programs are constantly attempting to obtain, through artificial hybridization, novel genotypes with high adaptability and stability potential. The objective of this study was to analyze genetic divergence in sugarcane based on the genotypic values of adaptability and stability. A total of 11 sugarcane genotypes were analyzed for eight agro-industrial traits. The genotypic values of the traits were determined using mixed model methodology, and the genetic divergence based on phenotypic and genotypic values was measured using the Mahalanobis distance. The distance matrices were correlated using the Mantel test, and the genotypes were grouped using the Tocher method. Genetic divergence is more accurate when based on genotypic values free of genotype–environment interactions and will differ from genetic divergence based on phenotypic data, changing the genotype allocations in the groups. The above methodology can be applied to assess genetic divergence to obtain novel sugarcane genotypes with higher productivity that are adapted to intensive agricultural systems using diverse technologies. This methodology can also be tested in other crops to increase accuracy in selecting the parents to be crossed.
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Utsumi, Shunsuke, Yoshino Ando, Timothy P. Craig, and Takayuki Ohgushi. "Plant genotypic diversity increases population size of a herbivorous insect." Proceedings of the Royal Society B: Biological Sciences 278, no. 1721 (March 4, 2011): 3108–15. http://dx.doi.org/10.1098/rspb.2011.0239.
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It is critical to incorporate the process of population dynamics into community genetics studies to identify the mechanisms of the linkage between host plant genetics and associated communities. We studied the effects of plant genotypic diversity of tall goldenrod Solidago altissima on the population dynamics of the aphid Uroleucon nigrotuberculatum . We found genotypic variation in plant resistance to the aphid in our experiments. To determine the impact of plant genotypic diversity on aphid population dynamics, we compared aphid densities under conditions of three treatments: single-genotype plots, mixed-genotype plots and mixed-genotype-with-cages plots. In the latter treatment plants were individually caged to prevent natural enemy attack and aphid movement among plants. The synergistic effects of genotypes on population size were demonstrated by the greater aphid population size in the mixed-genotype treatment than expected from additive effects alone. Two non-exclusive hypotheses are proposed to explain this pattern. First, there is a source–sink relationship among plant genotypes: aphids move from plant genotypes where their reproduction is high to genotypes where their reproduction is low. Second, natural enemy mortality is reduced in mixed plots in a matrix of diverse plant genotypes.
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Rezene, Yayis. "GGE-Biplot Analysis of Multi-Environment Yield Trials of Common Bean (Phaseolus vulgaris L.) in the southern Ethiopia." Journal of Plant Studies 8, no. 1 (February 12, 2019): 35. http://dx.doi.org/10.5539/jps.v8n1p35.
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The present study was conducted on thirty-six common beans (Phaseolus vulgaris L.) Genotypes across six contrasting environments defined for its different soil fertility status and located at the southern Ethiopia. The genotypes were arranged in 6 x 6 triple lattice design and executed for two successive main cropping seasons with the objectives to evaluate yield performance of common bean genotypes and identification of mega environments. GGE (i.e., G = genotype and GE = genotype by environment, interaction) bi-plot methodology was used for graphical presentation of yield data after subjecting the genotypic means of each environment to GGE Bi-plot software. The first two principal components (AXIS 1 and AXIS2) were used to display a two-dimensional GGE bi-plot. Thus, genotypic AXIS1 scores >0 classified the high yielding genotypes while AXIS2 scores <0 identified low yielding genotypes. Unlike genotypic AXIS1, genotypic AXIS2, scores near zero showed stable genotypes whereas large AXIS2 scores classified the unstable ones. The environmental AXIS1 were related to crossover nature of GEI while AXIS2 scores were associated with non-cross over GEI. The six test environments in the southern region were divided in to two distinct mega environments (Mega-1 and 2). Mega-1 constituted GOHF13, ARMF12 and ARLF13 while genotype 14 (SCR10) being the best winner, on the other hand, Mega-2 contained GOHF12 and while common bean genotype 20(SCR17) being the best winner. The results of this study indicated that breeding for specific adaptation should be taken as a breeding strategy in southern region to exploit positive GEI to increase production and productivity of common bean.
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Damé-Teixeira, Nailê, Rodrigo Alex Arthur, Clarissa Cavalcanti Fatturi Parolo, and Marisa Maltz. "Genotypic Diversity and Virulence Traits ofStreptococcus mutansIsolated from Carious Dentin after Partial Caries Removal and Sealing." Scientific World Journal 2014 (2014): 1–6. http://dx.doi.org/10.1155/2014/165201.
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The aim of this study was to compare the genotypic diversity and virulence traits ofStreptococcus mutansisolated from carious dentin before and after partial dentin caries removal (PDR) and sealing. Carious dentin samples were obtained three months before and after the PDR and cavity sealing. Up to seven isolates of each morphological type ofS. mutanswere selected and strain identity was confirmed using gtfB primer. Genotyping was performed by arbitrary primer-PCR (AP-PCR). Acidogenesis and acidurance of the genotypes were evaluated as virulence traits. A pairedt-test and a Wilcoxon test were used to compare the virulence of genotypes. A total of 48 representativeS. mutansisolates were genotyped (31 before and 17 after the sealing). At least one of the genotypes found before the sealing was also found on dentin after the sealing. The number of genotypes found before the sealing ranged from 2 to 3 and after the sealing from 1 to 2 genotypes. No difference was observed in the acidogenesis and acidurance between genotypes isolated before and after the sealing. In conclusion, genotypic diversity ofS. mutansdecreased after the PDR and sealing, but the virulence traits ofS. mutansremained unchangeable.
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Stenger, Drake C., and Carrie L. McMahon. "Genotypic Diversity of Beet Curly Top Virus Populations in the Western United States." Phytopathology® 87, no. 7 (July 1997): 737–44. http://dx.doi.org/10.1094/phyto.1997.87.7.737.
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The genotypic diversity of beet curly top virus (BCTV) present in the western United States has been examined by the analysis of 58 field isolates and eight laboratory or nursery isolates of the virus. Full-length clones for each isolate have been characterized for genotype by restriction endonuclease mapping. The results indicate that most of the genotypes examined may be classified as variants of the CFH, Worland, or Cal/Logan strains of BCTV. Two genotypes were recovered that appear to share certain genotypic markers of both Worland and CFH strains. Genotypic variants of the CFH and Worland strains and the two genotypes sharing markers of both strains were recovered from field isolates collected during 1994 and 1995. In contrast, the Cal/Logan strain was recovered only from isolates maintained in laboratories or nurseries. Comparisons of restriction endonuclease maps of cloned BCTV genomes revealed considerable variability both within and between strains. Although a total of 43 distinct genotypes of BCTV were identified, only 36 (84%) were recovered from field isolates. Of 37 field isolates for which more than a single clone was recovered, 16 (43%) contained more than a single genotype of one strain, whereas 4 (11%) harbored mixed infections of the CFH and Worland strains. A phylogenetic analysis using 43 characters derived from restriction endonuclease mapping data supported the grouping of 41 genotypes into three taxa consistent with the three currently recognized strains of BCTV. The relationships of the two genotypes sharing genotypic markers of both the Worland and CFH strains to other BCTV genotypes was unresolved in the phylogenetic analysis. Based on the mild symptom phenotype of the isolates from which these two genotypes were recovered and the presence of Worland genotypic markers in portions of the genome containing both cis- and trans-acting elements determining replication specificity, these two genotypes were tentatively considered as variants of the Worland strain.
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Sabaghnia, Naser, Mohtasham Mohammadi, and Rahmatollah Karimizadeh. "Clustering Durum Wheat Genotypes in Multi-Environmental Trials of Rain-Fed Conditions." Plant Breeding and Seed Science 66, no. 1 (August 8, 2014): 119–37. http://dx.doi.org/10.2478/v10129-011-0063-5.
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AbstractFor durum wheat genotypes evaluation in multi-environmental trials (MET), measured seed yield is the combined result of effects of genotype (G), environment (E) and genotype by environment GE interaction. The GE interaction structure can be identified if the data are stratified into homogeneous subsets through cluster analysis. A combined analysis to assess GE interactions of 20 durum wheat genotypes across 14 environments was undertaken. The combined analysis of variance for E, G and GE interaction was significant, suggesting differential responses of the genotypes in various environments. Four cluster methods, which differ in the dissimilarity indices depending on the regression model or ANOVA model, were used. According to dendograms of regression methods there were 10 different genotypic groups based on G (intercept) and GE (line slope) sources and 3 different genotypic groups based on GE (line slope) sources. Also, the dendograms of ANOVA methods indicated 11 different genotypic groups based on G and GE sources and 13 different genotypic groups based on GE sources. The above mentioned genotypic groups were determined via F-test as an empirical stopping criterion for clustering. Due to the high values of regression’s determination coefficient which ranged from 92.6 to 99.4, using of the linear regression-based clustering was more practical. The genotypes clustering based on similarity of linear regression parameters or ANOVA model indicated that there were considerable variations among durum wheat genotypes and there are different with each other in response to environmental changes. Such an outcome could be regularly applied in the future to clattering durum wheat genotypes and other crops based on regression or ANOVA models in the Middle East and other areas of the world.
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Ul-Rahman, Aziz. "Genotypic and Sub-genotypic Diversity of Avian Paramyxoviruses 2, 4 and 6." Pakistan Veterinary Journal 41, no. 01 (March 1, 2021): 156–59. http://dx.doi.org/10.29261/pakvetj/2020.088.
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Avian paramyxoviruses (APMVs) are contagious viruses infecting multiple avian species around the globe. Subsequent to evolution, the emergence of new strains is considered to cause outbreaks worldwide. Using standard classification criteria, genotypic and sub-genotypic distribution of strains within APMV-1 is much elucidated across the globe. Nevertheless, despite a growing number of genome sequencing data for APMVs excluding those that are prototypes, there is an absolute paucity of an updated unified phylogenetic classification scheme for APMV-2, 4, and 6. Utilizing a well-recognized genetic marker (complete fusion gene), genotyping and sub-genotyping of under-studied of APMVs strains was proposed by the implementation of different reliable tools and criteria. The analysis categorized the strains of each APMV-2 and 6 into two distinct genotypes (I and II), whereas APMV-4 strains categorized into three genotypes (I, II, and III). Additionally, a total of four sub-genotypes within APMV-6 (I.1, I.2, II.1, and II.2) and five sub-genotypes (I.1, I.2, II.1, II.2, and II.3) within APMV-4 were also proposed in the current study. Though it may require a revision and update in the future with the abundance of genome sequences and subsequent analysis from wide geography, herein the outcomes are relevant to better elucidate the classification and molecular epidemiology of study-included APMVs to depict an evolution and epidemiological link among outbreaks caused by field circulatory strains.
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Arellano-Galindo, José, Dina Villanueva-García, José Luis Cruz-Ramirez, Juan Pablo Yalaupari-Mejìa, Gabriel Uribe-Gutiérrez, Norma Velazquez-Guadarrama, Margarita Nava-Frias, Onofre Munoz-Hernández, and Juan Manuel Mejía-Arangure. "Detection and gB genotyping of CMV in Mexican preterm infants in the context of maternal seropositivity." Journal of Infection in Developing Countries 8, no. 06 (June 11, 2014): 758–67. http://dx.doi.org/10.3855/jidc.3501.
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Introduction: Congenital (CI) and perinatal cytomegalovirus (CMV) infections (PI) can be linked to maternal CMV seropositivity, with fatal consequences in preterm newborns. GB genotyping has been used to analyze genotypic similarity in mothers and infants. The frequency of CMV infection in the context of maternal seropositivity and the viral gB genotypes as well as the genotypic similarity in mothers and preterm infants were investigated. Methodology: Saliva samples and dry blood spots (DBS) were taken weekly from preterm newborns from birth until the first month of life, and breast milk samples were taken from their mothers weekly during the first month of lactation. CMV IgG seroprevalence of the mothers and CI or PI in the infants were established. The gB status and genotypic similarities were established retrospectively in DBS and in the breast milk samples. Results: In total, 387 neonates and 375 mothers were enrolled. The maternal CMV-positive IgG serology was 97.3% (365/375). Neonatal CMV was found in 5.1% (20/387) of newborns, and one infant presented with CMV-compatible symptoms. CI was 2.5% and PI in the first month after birth was 11.8%. GB2 was the most prevalent genotype and was also the genotype preferentially transmitted to newborns by mothers with mixed infections. Conclusions: CMV PI and CI in preterm infants from highly seropositive mothers was high, but the rate of symptomatic infection was low. The prevalent genotype was gB2, and this genotype was preferentially transmitted to newborns by mothers with mixed infections.
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Dirac, M. Ashworth, Kris M. Weigel, Mitchell A. Yakrus, Annie L. Becker, Hui-Ling Chen, Gina Fridley, Arthur Sikora, et al. "Shared Mycobacterium avium Genotypes Observed among Unlinked Clinical and Environmental Isolates." Applied and Environmental Microbiology 79, no. 18 (July 12, 2013): 5601–7. http://dx.doi.org/10.1128/aem.01443-13.
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ABSTRACTOur understanding of the sources ofMycobacterium aviuminfection is partially based on genotypic matching of pathogen isolates from cases and environmental sources. These approaches assume that genotypic identity is rare in isolates from unlinked cases or sources. To test this assumption, a high-resolution PCR-based genotyping approach, large-sequence polymorphism (LSP)-mycobacterial interspersed repetitive unit–variable-number tandem repeat (MIRU-VNTR), was selected and used to analyze clinical and environmental isolates ofM. aviumfrom geographically diverse sources. Among 127 clinical isolates from seven locations in North America, South America, and Europe, 42 genotypes were observed. Among 12 of these genotypes, matches were seen in isolates from apparently unlinked patients in two or more geographic locations. Six of the 12 were also observed in environmental isolates. A subset of these isolates was further analyzed by alternative strain genotyping methods, pulsed-field gel electrophoresis and MIRU-VNTR, which confirmed the existence of geographically dispersed strain genotypes. These results suggest that caution should be exercised in interpreting high-resolution genotypic matches as evidence for an acquisition event.
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Krutko, V. S., L. H. Nikolaieva, T. V. Maistat, O. A. Oparin, and Anton Viktorovych Rohozhyn. "INFLUENCE OF GENOTYPIC VARIABILITY OF M. TUBERCULOSIS ON THE COURSE OF TUBERCULOSIS WITH MULTIPLE DRUG RESISTANCE." International Medical Journal, no. 1 (March 5, 2020): 68–71. http://dx.doi.org/10.37436/2308-5274-2020-1-15.
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Tuberculosis is infectious and socially dependent disease, being now one of the most pressing issues in practical health care. As well the usual types of tuberculosis infection, chemoresistant tuberculosis is spreading rapidly in the world. The WHO estimates that about 500,000 people on the planet are infected with M. tuberculosis, which is resistant to standard anti−tuberculosis drugs. The probability of successful treatment decreases with emergence of new genotypes of M. tuberculosis with total resistance. In the modern epidemiology of tuberculosis, it is important to identify genotypes on certain signs, allowing to address issues such as their origin, identification of the infection source, possible routes and factors of transmission, as well as to reveal cases and spread of resistance to anti−tuberculosis drugs. To evaluate the therapy efficiency of multidrug−resistant tuberculosis patients with revealed genotypic variability during treatment, 10 patients with chemoresistant pulmonary tuberculosis having M. tuberculosis genotypic variability were treated. In these patients, the clinical, laboratory and radiological dynamics of disease in intensive phase of treatment were studied. Analysis of treatment results for patients with chemoresistant tuberculosis with genotypic variability of M. tuberculosis was evaluated by the intoxication syndrome dynamics of, the timing of closure of the decay cavities and cessation of bacterial excretion. The study found that the genotypic variability of M. tuberculosis is characterized by the change of less virulent genotypes of M. tuberculosis to more virulent. Signs of intoxication have been shown to change from less virulent M. tuberculosis genotypes to M. tuberculosis Beijing genotypes. Genotypic variability of mycobacteria in hospital suggests that hospitalization in tuberculosis facilities is a risk of exogenous tuberculosis superinfection. Studying the influence of genotypic variability of M. tuberculosis on the course of multidrug−resistant tuberculosis requires more extensive research, being a very relevant and promising area in phthisiology. Key words: Mycobacterium tuberculosis, genotypic variability, VNTR−genotyping, treatment.
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Rosell, R., J. L. Ramirez, M. Sanchez-Ronco, D. Isla, T. Moran, M. Cobo, B. Massuti, M. Taron, D. Carbone, and I. De Aguirre. "Blood-based CHRNA3 single nucleotide polymorphisms (SNPs) and outcome in advanced non-small cell lung cancer (NSCLC) patients (p)." Journal of Clinical Oncology 27, no. 15_suppl (May 20, 2009): 8033. http://dx.doi.org/10.1200/jco.2009.27.15_suppl.8033.
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8033 Background: Nicotonic acetylcholine receptors (nAChRs) are associated with resistance to gemcitabine (gem), cisplatin (cis) and paclitaxel in NSCLC cell lines. Three SNPs of CHRNA3, CHRNA5 and LOC123688 increase lung cancer risk. These SNPs may have influenced outcome in p treated in our phase III trial (Cobo et al. J Clin Oncol 2007;25:2747–54). Methods: Stage IV NSCLC p were treated with customized chemotherapy based on ERCC1 mRNA expression. p in the control arm received docetaxel (doc)/cis; p in the genotypic arm with low ERCC1 levels (low genotypic group [LG]) received doc/cis; p in the genotypic arm with high ERCC1 levels (high genotypic group [HG]) received doc/gem. DNA was extracted from lymphocytes, and CHRNA3 (rs1051730), CHRNA5 (rs16969968) and LOC123688 (rs8034191) SNPs were genotyped with the Taqman allele discrimination assay. Results: A significant interaction was found for CHRNA3 and PS (P = 0.02). In p with PS 0, CT p had a better response than both CC (P = 0.01) and TT (P = 0.02) p, and LG p also had a better response (P = 0.01). When the CHRNA3 genotype was added in the multivariate analysis for progression-free survival (PFS), an improvement was observed in the LG in PS 0 p (P = 0.02). PS 0 p in the LG with the CT genotype attained an 84% response, 12.1-month PFS, and 19-month median survival (MS) ( Table ). Conclusions: CHRNA3 genotyping can improve customized chemotherapy based on tumor ERCC1 mRNA in stage IV NSCLC p with PS 0. [Table: see text] No significant financial relationships to disclose.
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Tai, G. C. C. "Canonical variate analysis of genotype × environment interactions." Canadian Journal of Plant Science 79, no. 3 (July 1, 1999): 427–31. http://dx.doi.org/10.4141/p98-073.
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The additive main effects and multiplicative interaction (AMMI) model is used to investigate genotype × environment interactions often encountered in variety trials. Interaction effects are accounted for by several multiplicative terms in the model, with each consisting of a genotypic and an environmental parameter. These effects are estimated using principal-component analysis. An alternative method is presented to estimate the genotypic and environmental parameters in the multiplicative terms of the AMMI model by canonical variate analysis. The number of significant interactive terms can be easily determined using the χ2 test. Each of the multiplicative terms include a unitless coefficient measuring genotypic response and an environmental effect in terms of the physical unit of the concerned trait. Biplots can be used with the scores of both genotypes and environments for graphic examination of analytic results. Total tuber-yield data from potato genotypes tested in a series of international trials are used to illustrate the new analytic procedure. Key words: Genotype × environment interactions, AMMI, canonical variate analysis, potato
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Lee, Hong-Kee, Lionel D. Lewis, Gregory J. Tsongalis, Bernard C. Schur, Paul J. Jannetto, Steven H. Wong, and Kiang-Teck J. Yeo. "Validation of a CYP2D6 Genotyping Panel on the NanoChip Molecular Biology Workstation." Clinical Chemistry 53, no. 5 (May 1, 2007): 823–28. http://dx.doi.org/10.1373/clinchem.2006.081539.
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Abstract Background: CYP2D6 is a highly polymorphic phase I enzyme that metabolizes 20%–25% of clinically used drugs. The objective of this study was to validate a CYP2D6 genotyping assay with the NanoChip® Molecular Biology Workstation. Methods: We genotyped 200 anonymized human DNA samples with the Pyrosequencing® platform at the Medical College of Wisconsin and with the NanoChip platform at Dartmouth Medical School. We compared CYP2D6 genotypes and resolved samples with genotypic discrepancies with the Jurilab CYP2D6 duplication/deletion assay or with traditional DNA sequencing. The Jurilab assay is a long-range PCR assay used to evaluate sequence structures 3′ of the CYP2D7 and CYP2D6 coding regions. For the NanoChip platform, we performed multipad addressing and duplicate runs to test the intra- and intercartridge precision, within- and between-run precision, and reproducibility of the defined genotypes. Results: We used both platforms to genotype all 200 DNA samples for CYP2D6*3, *4, *5, *6, *7, *8, and gene duplication. The 2 methods showed 99.4% concordance in the genotyping results; we found only 8 discrepant genotypes among 1400 DNA analyses. Confirmatory molecular analysis of the discrepant genotypes revealed that the NanoChip assay showed better agreement. The imprecision of the NanoChip method (CV) was 8.9%–17.7%. Conclusions: This validation study of the NanoChip electronic microarray–based CYP2D6 genotyping assay revealed a CV <20% and good concordance with the Pyrosequencing method and a confirmatory sequencing method.
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Pei, Jen-Sheng, Chao-Chun Chen, Wen-Shin Chang, Yun-Chi Wang, Jaw-Chyun Chen, Yu-Chen Hsiau, Pei-Chen Hsu, Yuan-Nian Hsu, Chia-Wen Tsai, and Da-Tian Bau. "Significant Associations of lncRNA H19 Genotypes with Susceptibility to Childhood Leukemia in Taiwan." Pharmaceuticals 14, no. 3 (March 8, 2021): 235. http://dx.doi.org/10.3390/ph14030235.
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The purpose of our study was to investigate whether genetic variations in lncRNA H19 were associated with susceptibility to childhood leukemia. Two hundred and sixty-six childhood leukemia patients and 266 healthy controls were enrolled in Taiwan, and two single nucleotide polymorphisms (SNPs), rs2839698 and rs217727, in H19 were genotyped and analyzed. There was a significant difference in the genotypic distribution of rs2839698 between patients and healthy controls (p = 0.0277). Compared to the wild-type CC genotype, the heterozygous variant CT and homozygous variant TT genotypes were associated with significantly increased risks of childhood leukemia with an adjusted odd ratio (OR) of 1.46 (95% confidence interval (CI), 1.08–2.14, p = 0.0429) and 1.94 (95%CI, 1.15–3.31, p = 0.0169), respectively (pfor tread = 0.0277). The difference in allelic frequencies between childhood leukemia patients and controls was also significant (T versus C, adjusted OR = 1.53, 95%CI, 1.13–1.79, p = 0.0077). There were no significant differences in the genotypic and allelic distributions of rs217727 between cases and controls. Interestingly, the average level of H19 rs2839698 was statistically significantly higher for patients with CT and TT genotypes than from those with the CC genotype (p < 0.0001). Our results indicate that H19 SNP rs2839698, but not rs217727, may serve as a novel susceptibility marker for childhood leukemia.
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Grünwald, Niklaus J., Stephen B. Goodwin, Michael G. Milgroom, and William E. Fry. "Analysis of Genotypic Diversity Data for Populations of Microorganisms." Phytopathology® 93, no. 6 (June 2003): 738–46. http://dx.doi.org/10.1094/phyto.2003.93.6.738.
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Estimation of genotypic diversity is an important component of the analysis of the genetic structure of plant pathogen and microbial populations. Estimates of genotypic diversity are a function of both the number of genotypes observed in a sample (genotype richness) and the evenness of distribution of genotypes within the sample. Currently used measures of genotypic diversity have inherent problems that could lead to incorrect conclusions, particularly when diversity is low or sample sizes differ. The number of genotypes observed in a sample depends on the technique used to assay for genetic variation; each technique will affect the maximum number of genotypes that can be detected. We developed an approach to analysis of genotypic diversity in plant pathology that makes specific reference to the techniques used for identifying genotypes. Preferably, populations that are being compared should be very similar in sample size. In this case, the number of genotypes observed can be used directly for comparing richness. In most cases, sample sizes differ and use of the rarefaction method to calculate richness is more appropriate. In all cases, scaling either Stoddart and Taylor's G or Shannon and Wiener's H' by sample size should be avoided. Under those circumstances where it might be important to distinguish whether richness or evenness contribute more to diversity, a bootstrapping approach, where confidence intervals are calculated for indices of diversity and evenness, is recommended.
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Balestre, Marcio, Vanderley Borges dos Santos, Antonio Alves Soares, and Moisés Souza Reis. "Stability and adaptability of upland rice genotypes." Crop Breeding and Applied Biotechnology 10, no. 4 (December 2010): 357–63. http://dx.doi.org/10.1590/s1984-70332010000400011.
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The aim of this study was to identify upland rice genotypes with high stability and adaptability by the GGE biplot method based on the predicted genotypic and phenotypic values. Of the 20 genotypes evaluated, 14 were lines developed by the cooperative program for rice improvement of Minas Gerais and six were controls. The GGE biplot analysis showed that cultivar BRS Pepita and MG1097 were closest to the ideal genotype. In the comparison of the fixed with the random models (% G + GE, prediction error sum of squares and correlation), it was observed that the use of phenotypic means in all comparative parameters indicated a lower predictive potential under simulated imbalance than the use of predicted genotypic values. The conclusion was drawn that BRS Pepita and MG1097 are ideal genotypes for southern Minas Gerais and that the predictive power of the phenotypic means underlying the study of stability and adaptability is lower than of genotypic means.
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Farias Neto, João Tomé de, Elisa Ferreira Moura, Marcos Deon Vilela de Resende, Pedro Celestino Filho, and Sebastião Geraldo Augusto. "Genetic parameters and simultaneous selection for root yield, adaptability and stability of cassava genotypes." Pesquisa Agropecuária Brasileira 48, no. 12 (December 2013): 1562–68. http://dx.doi.org/10.1590/s0100-204x2013001200005.
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The objective of this work was to estimate genetic parameters and to evaluate simultaneous selection for root yield and for adaptability and stability of cassava genotypes. The effects of genotypes were assumed as fixed and random, and the mixed model methodology (REML/Blup) was used to estimate genetic parameters and the harmonic mean of the relative performance of genotypic values (HMRPGV), for simultaneous selection purposes. Ten genotypes were analyzed in a complete randomized block design, with four replicates. The experiment was carried out in the municipalities of Altamira, Santarém, and Santa Luzia do Pará in the state of Pará, Brazil, in the growing seasons of 2009/2010, 2010/2011, and 2011/2012. Roots were harvested 12 months after planting, in all tested locations. Root yield had low coefficients of genotypic variation (4.25%) and broad-sense heritability of individual plots (0.0424), which resulted in low genetic gain. Due to the low genotypic correlation (0.15), genotype classification as to root yield varied according to the environment. Genotypes CPATU 060, CPATU 229, and CPATU 404 stood out as to their yield, adaptability, and stability.
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Raugi, Dana N., Robert S. Nixon, Sally Leong, Khadim Faye, Jean Phillipe Diatta, Fatima Sall, Robert A. Smith, et al. "HIV-2 Drug Resistance Genotyping from Dried Blood Spots." Journal of Clinical Microbiology 59, no. 1 (October 14, 2020): e02303-20. http://dx.doi.org/10.1128/jcm.02303-20.
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ABSTRACTThe treatment of HIV-2 in resource-limited settings (RLS) is complicated by the limited availability of HIV-2-active antiretroviral drugs and inadequate access to HIV-2 viral load and drug resistance testing. Dried blood spots (DBS)-based drug resistance testing, widely studied for HIV-1, has not been reported for HIV-2 and could present an opportunity to improve care for HIV-2-infected individuals. We selected 150 DBS specimens from ongoing studies of antiretroviral therapy (ART) for HIV-2 infection in Senegal and subjected them to genotypic drug resistance testing. Total nucleic acid was extracted from DBS, reverse transcribed, PCR amplified, and analyzed by population-based Sanger sequencing, and major drug resistance-associated mutations (RAM) were identified. Parallel samples from plasma and peripheral blood mononuclear cells (PBMC) were also genotyped. We obtained 58 protease/reverse transcriptase genotypes. Plasma viral load was significantly correlated with genotyping success (P < 0.001); DBS samples with corresponding plasma viral load >250 copies/ml had a success rate of 86.8%. In paired DBS-plasma genotypes, 83.8% of RAM found in plasma were also found in DBS, and replicate DBS genotyping revealed that a single test detected 86.7% of known RAM. These findings demonstrate that DBS-based genotypic drug resistance testing for HIV-2 is feasible and can be deployed in RLS with limited infrastructure.
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Morales, Nicolas, Guillaume J. Bauchet, Titima Tantikanjana, Adrian F. Powell, Bryan J. Ellerbrock, Isaak Y. Tecle, and Lukas A. Mueller. "High density genotype storage for plant breeding in the Chado schema of Breedbase." PLOS ONE 15, no. 11 (November 11, 2020): e0240059. http://dx.doi.org/10.1371/journal.pone.0240059.
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Modern breeding programs routinely use genome-wide information for selecting individuals to advance. The large volumes of genotypic information required present a challenge for data storage and query efficiency. Major use cases require genotyping data to be linked with trait phenotyping data. In contrast to phenotyping data that are often stored in relational database schemas, next-generation genotyping data are traditionally stored in non-relational storage systems due to their extremely large scope. This study presents a novel data model implemented in Breedbase (https://breedbase.org/) for uniting relational phenotyping data and non-relational genotyping data within the open-source PostgreSQL database engine. Breedbase is an open-source, web-database designed to manage all of a breeder’s informatics needs: management of field experiments, phenotypic and genotypic data collection and storage, and statistical analyses. The genotyping data is stored in a PostgreSQL data-type known as binary JavaScript Object Notation (JSONb), where the JSON structures closely follow the Variant Call Format (VCF) data model. The Breedbase genotyping data model can handle different ploidy levels, structural variants, and any genotype encoded in VCF. JSONb is both compressed and indexed, resulting in a space and time efficient system. Furthermore, file caching maximizes data retrieval performance. Integration of all breeding data within the Chado database schema retains referential integrity that may be lost when genotyping and phenotyping data are stored in separate systems. Benchmarking demonstrates that the system is fast enough for computation of a genomic relationship matrix (GRM) and genome wide association study (GWAS) for datasets involving 1,325 diploid Zea mays, 314 triploid Musa acuminata, and 924 diploid Manihot esculenta samples genotyped with 955,690, 142,119, and 287,952 genotype-by-sequencing (GBS) markers, respectively.
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Feng, Yue, Jieyu Ran, Yue-Mei Feng, Jing Miao, Yue Zhao, Yuanyuan Jia, Zheng Li, Wei Yue, and Xueshan Xia. "Genetic diversity of hepatitis B virus in Yunnan, China: identification of novel subgenotype C17, an intergenotypic B/I recombinant, and B/C recombinants." Journal of General Virology 101, no. 9 (September 1, 2020): 972–81. http://dx.doi.org/10.1099/jgv.0.001147.
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Yunnan is considered to be a geographical hotspot for the introduction, mutation and recombination of several viruses in China. However, there are limited data regarding the genotypic profiles of hepatitis B virus (HBV) in this region. In this study, we characterized 206 HBV strains isolated from chronic hepatitis B patients in Yunnan, China. Initial genotyping based on 1.5 kb sequences revealed that genotype C was the most prevalent at 52.4 % (108/206), followed by genotype B at 30.6 % (63/206) and unclassified genotypes at 17.0 % (35/206). To characterize the 35 unclassified strains, 32 complete HBV genomes were amplified and analysed; 17 isolates were classified within a known subgenotype, 8 were classified as B/C recombinants, 1 was classified as a B/I recombinant and 6 constituted a potentially novel C subgenotype that we designated as C17, based on the characteristics of a monophyletic cluster, >4 % genetic distances, no significant evidence of recombination and no epidemiological link among individuals. Thus, multiple subgenotypes – namely B1, B2, B4, C1, C2, C3, C4, C8 and C17 – and two distinct intergenotypic recombinants exist in Yunnan, China, highlighting the complex and diverse distribution pattern of HBV genotypic profiles.
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Santana, Alice, Alison Uberti, João Romero Rocha, Adriana Lugaresi, Newton Alex Mayer, and Clevison Luiz Giacobbo. "Simultaneous selection of peach rootstocks by mixed models." Comunicata Scientiae 11 (August 24, 2020): e3357. http://dx.doi.org/10.14295/cs.v11i.3357.
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The term adaptability refers to the ability of a genotype to respond favorably to environmental spur, while stability is the predictability of genotypic behavior. Therefore, the objective was to select Prunus rootstock cultivars with greater adaptability and genotypic stability for subtropical environmental conditions using the HMPRVG method. The experiment was conducted in Chapecó, Santa Catarina State, Brazil. Twenty-one rootstock genotypes were evaluated under the ‘BRS-Libra’ canopy cultivar and one genotype from self-rooted seedlings. The 22 genotypes were evaluated for canopy volume, yield, fruit diameter and fruit set in the growing seasons 2015/16, 2016/17, 2017/18 and 2018/19. Adaptability and stability were measured by means of the harmonic mean relative performance of genotypic values (HMRPGV). In addition, genetic parameters for heritability and ratio test were measured. According to the results, the self-rooted, ‘De Guia’, ‘I-67-52-4’, ‘Mexico Row 1’ and ‘Rosaflor’ genotypes coincided most frequently in the ranking of the three most adaptable and stable genotypes. On the other hand, the ‘P. mandshurica’, ‘Rigitano’ and ‘Santa Rosa’ genotypes corresponded to the lowest adaptability and stability values, thus constituting low quality genetic materials for cultivation. It can be concluded that under the tested conditions the HMPRVG method is efficient for the Prunus rootstock selection cultivars and the ‘BRS-Libra’ grafted on ‘Mexico Row 1’, ‘Rosaflor’ rootstocks and trees from self-rooted seedlings have greater adaptability and phenotypic stability under the subtropical cultivation conditions.
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Teodoro, Paulo Eduardo, Camila Ferreira Azevedo, Francisco José Correia Farias, Rodrigo Silva Alves, Leonardo de Azevedo Peixoto, Larissa Pereira Ribeiro, Luiz Paulo de Carvalho, and Leonardo Lopes Bhering. "Adaptability of cotton (Gossypium hirsutum) genotypes analysed using a Bayesian AMMI model." Crop and Pasture Science 70, no. 7 (2019): 615. http://dx.doi.org/10.1071/cp18318.
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Cotton (Gossypium spp.) provides ~90% of the world’s textile fibre. The aim of this study was to use the principal additive effects and multiplicative interaction (AMMI) model under the Bayesian approach to recommend cotton genotypes for the Central-West region of Brazil. Eight trials with upland cotton genotypes were conducted during the 2008–09 harvest in the State of Mato Grosso, Brazil. The experiment included a randomised block design with 16 genotypes. The genotypes were evaluated for fibre yield, length and strength. Chains were simulated via the Markov chain Monte Carlo method with 300000 iterations for the parameters of the Bayesian AMMI model. From the chains generated, the first 20000 burn-in observations were discarded and samples were taken by jumping every 20 observations (thin). Bayesian analysis provided additional results to those obtained by the frequentist approach, highlighting the credibility regions in the biplot for the genotypic and environmental scores. Bayesian AMMI model allowed identification of a genotype that can be widely recommended; this genotype has genotypic values above the overall mean for the three evaluated traits and did not contribute to the genotype × environment interactions observed in these traits. In addition, adaptability of genotypes to specific environments was observed, which makes it possible to capitalise the positive effect of the genotype × environment interaction.
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Hadincová, Věroslava, Hana Skálová, and Zuzana Münzbergová. "Genotypic diversity and genotype identity of resident species drive community composition." Journal of Plant Ecology 13, no. 2 (February 4, 2020): 224–32. http://dx.doi.org/10.1093/jpe/rtaa004.
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Abstract Aims Species-rich plant communities are more resistant to invasions. In the past decade it was demonstrated that genetic variation also has many ecological effects. In our study we aimed to test whether the patterns of response to the genetic diversity of a resident species differ between colonizing species of different growth forms and whether the response is affected by soil nutrients. Methods We established experimental stands of a common grass, Festuca rubra, harbouring three levels of genetic diversity (1, 6 or 18 clonal genotypes, referred to as genotypic diversity) under two soil nutrient levels. In the fourth year after the stands were established, we sowed a mixture of four colonizers into the stands: a stoloniferous legume (Trifolium repens), a broad-leaf tussock grass (Anthoxanthum odoratum), a large-rosette forb (Plantago lanceolata) and a small-rosette forb (Campanula rotundifolia). We observed species establishment and growth over 3 years. We tested whether colonization success depended on genotypic diversity, specific Festuca genotypes, soil nutrients and colonizer growth form. Important Findings The colonization success and biomass of the colonizers were significantly affected by the genotypic diversity and the genotype identity of the resident clonal grass. The response, however, differed between the colonizers. The strongest response to the genotypic diversity of the resident species was observed in the tussock grass with a growth form and architecture similar to the resident species. The large-rosette species responded in early stages of growth whereas the stoloniferous legume did not respond at all. The intraspecific genotypic diversity and genotype identity of the resident species play an important role in the assembly of plant communities.
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Hartley, RA, RJ Lawn, and DE Byth. "Genotypic variation in growth and seed yield of soybean (Glycine max (L.) Merr.) in saturated soil culture." Australian Journal of Agricultural Research 44, no. 4 (1993): 689. http://dx.doi.org/10.1071/ar9930689.
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Studies were conducted over several years at field sites in south east Queensland to evaluate the response of diverse soybean genotypes to saturated soil culture (SSC), relative to that in conventional irrigation (CI). In an initial study at Dalby, 56 accessions from 12 countries were tested, and all exhibited the ability to acclimate to, and grow in SSC. The chance occurrence of residual picloram herbicide on the site confounded interpretation of differential genotypic responses, but highlighted the potential vulnerability of the SSC system to chemical residues in the surface soil. In more detailed studies with representative subsets of lines at Lawes, there was large genotypic variation in relative responsiveness (RR, defined as {[Response in SSC-Response in CI]/Response in CI}) of yield to SSC, with seed yields reduced by up to 52%, enhanced by up to 37%, or unchanged, depending on genotype and agronomic management. Genotypic variation in RR was generally consistent across seasons, and was variously associated with genotypic differences in phenology when grown under CI. In general, the most positively responsive genotypes were those that started flowering late enough for the plants to have already acclimated to SSC, and that then flowered for a longer duration. Negatively responsive genotypes were those in which the pre-flowering period was sufficiently short for flowering to have commenced before acclimation was complete, i.e. where the acclimation phase intruded into reproductive ontogeny. Very late genotypes were also less responsive, perhaps because of greater lodging under the very favourable growth conditions provided by SSC. The studies indicated the potential for predicting responsiveness to SSC from knowledge of genotypic responses under conventional irrigation.
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_, Anas, Meddy Rachmadi, and Mansyur _. "PHENOTYPIC AND GENOTYPIC VARIANCE AND HERITABILITY OF STAY GREEN CHARACTER AMONG 22 ELITE SORGHUM (Sorghum bicolor (L.) Moench) GENOTYPES." KnE Life Sciences 2, no. 1 (September 20, 2015): 318. http://dx.doi.org/10.18502/kls.v2i1.166.
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<p>Delaying of leaf senescence (stay green) is an effective strategy for increasing of crop yield, particularly under water-limited conditions. Study of genotypic variance of stay green is very useful for breeding program of stay green character. Replicated field experiment was carried out in Farm Experimental Station, Faculty of Agriculture Padjadjaran University during dry season. The objectives of this study were: i) to estimate genotypic and phenotypic variances of stay green character; ii) to evaluate and investigate stay green performance of the 22 elite sorghum genotypes. High genotypic and phenotypic variances were observed for plant morphology (plant height, stem diameter), leaf morphology (leaf number, leaf width, leaf length and total leaf area) and yield component (panicle length) and were supported by high estimation of heritability value. Corresponding heritability ranged between 0.77 and 0.94. Genotypic variance of stay green characters was narrow and estimation of broad sense heritability was low. Stay green characters in sorghum might be a quantitative character that was controlled by many genes. Unpad 1.3, Unpad 1.1 and 1090 genotype showed good performance for stay green character. These genotypes can be recommended as stay green parental in breeding program.</p><p><br /><strong>Keywords</strong>: Genotypic variance, Heritability, Phenotypic variance, Sorghum, Stay green</p>
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Zhang, Dapeng, Wanda W. Collins, and Maria Andrade. "Estimation of Genetic Variance of Starch Digestibility in Sweetpotato." HortScience 30, no. 2 (April 1995): 348–49. http://dx.doi.org/10.21273/hortsci.30.2.348.
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Two experiments that included 25 sweetpotato [Ipomoea batatas (L.) Lam] genotypes were planted in various environments across North Carolina, and an in vitro screening method was used to investigate genotypic and environmental variance and genotype × environment (G × E) interactions of starch digestibility in sweetpotato. Significant genotypic variation of starch digestibility was found in both experiments. Some clones have starch digestibility equivalent to that of corn. Variance analysis from both experiments indicated that genotypic variance was the dominant component in starch digestibility. G × E interaction only accounted for 6.8% of the phenotypic variance in one experiment and for 5.9% in the other one. These results suggested that starch digestibility of sweetpotato could be improved to a level as that of corn through conventional breeding.
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Hucl, P., and R. J. Graf. "Variation in spike harvest index among diverse genotypes of spring wheat and triticale." Canadian Journal of Plant Science 72, no. 1 (January 1, 1992): 257–61. http://dx.doi.org/10.4141/cjps92-030.
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Genotypes of spring wheat and triticale exhibited significant differences in spike harvest index (SPHI). SPHI averaged 78% over genotypes and experiments. Genotype SPHI differed by up to 13% units. SPHI, however, was not correlated with either plot harvest index, or grain yield.Key words: Spike harvest index, genotypic differences, spring wheat, Triticum aestivum L.
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Xu, Jianping, Cynthia M. Boyd, Elizabeth Livingston, Wieland Meyer, John F. Madden, and Thomas G. Mitchell. "Species and Genotypic Diversities and Similarities of Pathogenic Yeasts Colonizing Women †." Journal of Clinical Microbiology 37, no. 12 (1999): 3835–43. http://dx.doi.org/10.1128/jcm.37.12.3835-3843.1999.
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We examined the patterns of strain relatedness among pathogenic yeasts from within and among groups of women to determine whether there were significant associations between genotype and host condition or body site. A total of 80 yeast strains were isolated, identified, and genotyped from 49 female volunteers, who were placed in three groups: (i) 19 women with AIDS, (ii) 11 pregnant women without human immunodeficiency virus (HIV) infection, and (iii) 19 women who were neither pregnant nor infected with HIV. Seven yeast species were recovered, including 59 isolates of Candida albicans, 9 isolates of Candida parapsilosis, 5 isolates ofCandida krusei, 3 isolates of Candida glabrata, 2 isolates of Saccharomyces cerevisiae, and 1 isolate each of Candida tropicalis and Candida lusitaniae. Seventy unique genotypes were identified by PCR fingerprinting with the M13 core sequence and by random amplified polymorphic DNA analysis. Of the nine shared genotypes, isolates from three different hosts were of one genotype and pairs of strains from different body sites of the same host shared each of the other eight genotypes. Genetic similarities among groups of strains were calculated and compared. We found no significant difference in the patterns of relatedness of strains from the three body sites (oral cavity, vagina, and rectum), regardless of host conditions. The yeast microflora of all three host groups had similar species and genotypic diversities. Furthermore, a single host can be colonized with multiple species or multiple genotypes of the same species at the same or different body sites, indicating dynamic processes of yeast colonization on women.
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Otyama, Paul I., Roshan Kulkarni, Kelly Chamberlin, Peggy Ozias-Akins, Ye Chu, Lori M. Lincoln, Gregory E. MacDonald, et al. "Genotypic Characterization of the U.S. Peanut Core Collection." G3: Genes|Genomes|Genetics 10, no. 11 (September 4, 2020): 4013–26. http://dx.doi.org/10.1534/g3.120.401306.
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Cultivated peanut (Arachis hypogaea) is an important oil, food, and feed crop worldwide. The USDA peanut germplasm collection currently contains 8,982 accessions. In the 1990s, 812 accessions were selected as a core collection on the basis of phenotype and country of origin. The present study reports genotyping results for the entire available core collection. Each accession was genotyped with the Arachis_Axiom2 SNP array, yielding 14,430 high-quality, informative SNPs across the collection. Additionally, a subset of 253 accessions was replicated, using between two and five seeds per accession, to assess heterogeneity within these accessions. The genotypic diversity of the core is mostly captured in five genotypic clusters, which have some correspondence with botanical variety and market type. There is little genetic clustering by country of origin, reflecting peanut’s rapid global dispersion in the 18th and 19th centuries. A genetic cluster associated with the hypogaea/aequatoriana/peruviana varieties, with accessions coming primarily from Bolivia, Peru, and Ecuador, is consistent with these having been the earliest landraces. The genetics, phenotypic characteristics, and biogeography are all consistent with previous reports of tetraploid peanut originating in Southeast Bolivia. Analysis of the genotype data indicates an early genetic radiation, followed by regional distribution of major genetic classes through South America, and then a global dissemination that retains much of the early genetic diversity in peanut. Comparison of the genotypic data relative to alleles from the diploid progenitors also indicates that subgenome exchanges, both large and small, have been major contributors to the genetic diversity in peanut.
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Dutilleul, P., and C. Potvin. "Among-environment heteroscedasticity and genetic autocorrelation: implications for the study of phenotypic plasticity." Genetics 139, no. 4 (April 1, 1995): 1815–29. http://dx.doi.org/10.1093/genetics/139.4.1815.
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Abstract The impact of among-environment heteroscedasticity and genetic autocorrelation on the analysis of phenotypic plasticity is examined. Among-environment heteroscedasticity occurs when genotypic variances differ among environments. Genetic autocorrelation arises whenever the responses of a genotype to different environments are more or less similar than expected for observations randomly associated. In a multivariate analysis-of-variance model, three transformations of genotypic profiles (reaction norms), which apply to the residuals of the model while preserving the mean responses within environments, are derived. The transformations remove either among-environment heteroscedasticity, genetic autocorrelation or both. When both nuisances are not removed, statistical tests are corrected in a modified univariate approach using the sample covariance matrix of the genotypic profiles. Methods are illustrated on a Chlamydomonas reinhardtii data set. When heteroscedasticity was removed, the variance component associated with the genotype-by-environment interaction increased proportionally to the genotype variance component. As a result, the genetic correlation rg was altered. Genetic autocorrelation was responsible for statistical significance of the genotype-by-environment interaction and genotype main effects on raw data. When autocorrelation was removed, the ranking of genotypes according to their stability index dramatically changed. Evolutionary implications of our methods and results are discussed.
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Donnik, Irina, Irina Donnik, Ramil Vafin, Ramil Vafin, Aram Galstyan, Aram Galstyan, Anna Krivonogova, et al. "Genetic identification of bovine leukaemia virus." Foods and Raw Materials 6, no. 2 (December 20, 2018): 314–24. http://dx.doi.org/10.21603/2308-4057-2018-2-314-324.
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Molecular genetic research methods make it possible to evaluate the genetic diversity of bovine leukemia virus (BLV) and are the most informative approaches to its genetic identification. Molecular genetic research methods work well for the phylogenetic analysis of sequenced nucleotide DNA sequences of the provirus, as well as for the polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP) according to the phylogenetic classification of the pathogen. The purpose of the research was to study the scientific and methodological approaches to the genetic identification of bovine leukemia virus, integrated into the molecular monitoring of infection of cattle with BLV genotypes. The authors used PCR-RFLP-genotyping and comparative phylogenetic analysis of aligned nucleotide sequences of the env gene fragment of the BLV provirus isolates to detect the genotypic affiliation of the cattle from twenty-one livestock farms of the Republic of Tatarstan. As a result, isolates of four out of ten BLV genotypes were found in the Tatarstani cattle, namely genotypes 1, 4, 7, and 8. The research involved a comparative analysis of 505 nucleotide sequences of a fragment of the BLV env gene, including those deposited in GenBank NCBI. The analysis confirms the inconsistency of several earlier PCR-RFLP typing strategies with the current approach in assessing the genotypic diversity by phylogenetic analysis. The improved strategy of PCR-RFLP genotyping of BLV corresponds with its modern phylogenetic classification. The strategy makes it possible to identify all the known genotypes of the viral pathogen. Its validity has been proved by in silico modelling of restrictogrammes and a phylogenetic analysis of the env gene fragment of 57 reference isolates of ten BLV genotypes that generate 57 genotype-associated combinations of diagnostically significant PCR-RFLP profiles.
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Merkle, S. A., W. T. Adams, and R. K. Campbell. "Multivariate analysis of allozyme variation patterns in coastal Douglas-fir from southwest Oregon." Canadian Journal of Forest Research 18, no. 2 (February 1, 1988): 181–87. http://dx.doi.org/10.1139/x88-028.
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Isozyme data collected from megagametophytes of coastal Douglas-fir (Pseudotsugamenziesii (Mirb.) Franco var. menziesii) parent trees, representing 22 southwest Oregon breeding zones, were analyzed by multivariate techniques to describe the distribution of genotypic variation among and within breeding zones and to relate genotypic and environmental variation. Data entered were mean haploid genotype scores obtained by averaging two haploid genotype scores from each parent tree. Haploid genotype scores were created from 27-locus haploid genotypes of two megagametophytes collected from each of 1230 parent trees. Although principal components analysis did not indicate the presence of linkage disequilibria among loci, canonical discriminant analysis suggested that much more genotypic variation may be accounted for by breeding-zone differences than was evident from single-locus techniques. The first two canonical variables, which accounted for ~25% of the genotypic variation, appeared to separate breeding zones on the basis of geographic and elevational differences among zones. Regressing canonical variable scores against location variables failed to provide a model attributing > 10% of genotypic variation to latitude, elevation, or distance from the ocean. Although canonical correlation analysis of mean haploid genotype scores with the same location variables produced two significant canonical variables accounting for 39% of the variation, little of the variation accounted for by the canonical variables was related to location variables. Although these results may be due to the small geographic scale of the study, the region covered is characterized by extreme environmental heterogeneity, to which variability in seedling quantitative traits has been strongly correlated in a companion common garden study. In sum, multivariate techniques were not markedly better than single-locus techniques in providing evidence that allozyme variation is adaptive in the coastal Douglas-fir breeding zones studied. Consequently, multivariate techniques cannot be expected to improve the use of allozymes for certifying seed or for designating breeding zones in this region.
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MOGHADDAM, M. J., and S. S. POURDAD. "Comparison of parametric and non-parametric methods for analysing genotype×environment interactions in safflower (Carthamus tinctorius L.)." Journal of Agricultural Science 147, no. 5 (June 18, 2009): 601–12. http://dx.doi.org/10.1017/s0021859609990050.
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SUMMARYGenotype×environment interaction (GEI) is a major factor in the development of stable and high-yielding safflower cultivars under rain-fed conditions. In order to quantify GEI effects on the seed yield of 17 safflower genotypes and to identify stable genotypes, multi-environment yield trials (multi-environment trials (MET)) were conducted for four consecutive years in 33 different environments (year–location combinations) during 2003–06. The results indicated that GEI was significant using the Hildebrand (1980) procedure for non-crossover interaction (no change in genotypic rank) and by the Azzalini & Cox (1984) and the De Kroon & Van Der Laan (1981) tests for crossover interaction (change in genotypic rank). The rank-interaction was not significant when assessed using the Bredenkamp (1974) method. Fifteen univariate stability methods measuring different aspects of stability were used to determine stable genotypes. A principal component analysis based on rank correlation matrix separated those methods based on a dynamic concept of yield stability (change in genotypic performance corresponds to the predicted level for each environment) from those which are based on a static one (the lowest changes in genotypic performance across environments). The methods could be grouped into three distinct classes: (i) those which were associated with yield level and the dynamic concept of stability; (ii) those which were associated with environmental variance, which represents static stability; and (iii) those which were grouped with non-parametric stability statistics, which also represent static stability. The superiority index of cultivar performance, coefficient of regression, Rank-Sum (sum of ranks of yield and stability variance) and TOP (number of environments at which the cultivar occurred in the top third of the ranks) defined the dynamic stability.In this MET, the genotype PI-537598 was identified as the genotype with the highest yield and high stability of yield.
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Pieralisi, F. J. S., M. R. Rodrigues, V. G. Segura, S. M. Maciel, F. B. A. Ferreira, J. E. Garcia, and R. C. Poli-Frederico. "Genotypic Diversity ofStreptococcus mutansin Caries-Free and Caries-Active Preschool Children." International Journal of Dentistry 2010 (2010): 1–5. http://dx.doi.org/10.1155/2010/824976.
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Aim. The aim of the present paper was to evaluate the genotypic diversity ofS. mutansin caries-free and caries-active preschool children in Brazil.Design. Twenty-eight preschool children were examined regarding caries experience by the dmft index. DNA from 280 isolates ofS. mutanswas extracted.S. mutansevaluated using to the PCR method, with primers for the glucosyltransferase gene. The genetic diversity ofS. mutansisolates was analyzed by arbitrary primed-PCR (AP-PCR) reactions. The differences between the diversity genotypic and dmft/caries experience were evaluated by test and Spearman's correlation.Results. The Spearman correlation test showed a strong association between genotypic diversity and caries experience (; ). There were moreS. mutansgenotypes in the group of preschool children with dental caries, compared with the caries-free group. Among the children with more than 1 genotype, 13 had dental caries (2 to 5 genotypes) and 4 were caries-free (only 2 genotypes).Conclusion. Our results support the previous findings of genetic diversity ofS. mutansin preschool children being associated with dental caries. The investigation of such populations may be important for directing the development of programs for caries prevention worldwide.
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Gambín, Brenda L., and Lucas Borrás. "Adding genotypic differences in reproductive partitioning and grain set efficiency for estimating sorghum grain number." Crop and Pasture Science 64, no. 1 (2013): 9. http://dx.doi.org/10.1071/cp13013.
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Current models of sorghum crop growth predict grain number using a calculated plant growth rate around flowering and a genotype-dependent parameter that describes the relationship between both traits. Few values for this parameter have been reported, being similar within triple-dwarf or single-dwarf sorghum genotypes. This approach narrows genotypic differences in grain number determination mostly to differences in traits affecting biomass production. Relevant traits such as biomass partitioning to reproductive structures and grain-set efficiency are not specifically considered, but both vary across genotypes and could improve grain number estimations. We first explored variation for these traits (CGR, crop growth rate around flowering; PR, biomass partitioning to reproductive structures during this period; EG, grain set per unit of accumulated reproductive biomass) for a set a sorghum commercial hybrids and inbred lines growing under different conditions. Later, we used a second set of experiments to test whether considering genotype-specific PR and EG improved estimates of grain number compared with the current approach used in crop simulation models. Grain number variations (14–63 × 103 grains m–2) due to genotype and environment were a consequence of significant differences (P < 0.05) in all analysed traits (CGR, PR, EG). Biomass partitioning and grain set per unit of accumulated reproductive biomass showed consistent genotypic differences (P < 0.001); however, they also showed significant environment or genotype × environment effects. When these specific genotypic parameters dealing with biomass partitioning and grain-set efficiency were used for estimating grain number in other non-related experiments, the predicted accuracy improved (r2 = 0.47, P < 0.05, RMSE = 7029 grains m–2) relative to the general approach using a constant parameter for most genotypes (r2 = 0.14, P < 0.28, RMSE = 12 630 grains m–2) or a calculated parameter for each genotype (r2 = 0.38, P < 0.10, RMSE = 8919 grains m–2). We propose that these traits (PR and EG) need to be considered and included in sorghum crop growth models, as they help predict grain number performance of different genotypes in different growth environments.
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Al-Taweel, M. "ESTIMATINON GENOTYPIC PHENOTYPIC VARIANCES FOR BARLEY GENOTYPES." Mesopotamia Journal of Agriculture 41, no. 2 (July 28, 2013): 248–58. http://dx.doi.org/10.33899/magrj.2013.81128.
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Serra, J. J., M. Ellis, and C. S. Haley. "Genetic components of carcass and meat quality traits in Meishan and Large White pigs and their reciprocal crosses." Animal Science 54, no. 1 (February 1992): 117–27. http://dx.doi.org/10.1017/s0003356100020638.
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AbstractThe prospect that genes from the Chinese Meishan pig will be used to improve reproductive performance of European pigs requires that the Meishan is evaluated for traits of economic importance and the genetics of any breed effects investigated. Entire male and female pigs of four genotypes; purebred Meishan (MS) and Large White (LW) pigs and both reciprocal Fl crossbred genotypes (MS ♂ × LW ♀and LW ♂ × MS ♀), were fed ad libitum and slaughtered at about 70 kg. After slaughter, carcass weight, dimensions and conformation were recorded and fat depths at the shoulder, mid back and loin were measured on the carcass, together with fat depths and eye muscle dimensions recorded on a section cut at the last rib position. Drip loss, muscle reflectance and pH were measured and subjective assessments of fat firmness, fat separation, muscle marbling and muscle colour were made. Genotypic means and genetic crossbreeding effects (direct additive and heterosis effects and maternal additive effects) were estimated using restricted maximum likelihood procedures. When compared with the LW, MS carcasses had a similar killing-out proportion but were shorter with a poorer conformation. MS carcasses had substantially greater fat depths and reduced eye muscle dimensions in comparison with the LW. Differences between genotypes for fat depths and muscle dimensions were largely controlled by direct additive gene action, there was little evidence of direct heterosis and hence Fl crosses were intermediate between the purebreds. Significant genotype × sex interaction meant that genotypic differences for these traits were much greater in females than in males. Significant direct additive genetic differences between female genotypes were found for fat firmness, fat separation and drip loss, but these effects may in part have been a consequence of subcutaneous fat depth differences between genotypes. The degree of marbling was greater in MS females than in females of the other three genotypes and these genotypic differences did not seem to be associated with subcutaneous fat depth. Muscle from MS males was darker in colour with a lower reflectance than that from LW males. Genotype × sex interaction was such that genotypic differences for meat and fat quality traits differed between sexes.
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James, A. T., R. J. Lawn, and M. Cooper. "Genotypic variation for drought stress response traits in soybean. II. Inter-relations between epidermal conductance, osmotic potential, relative water content, and plant survival." Australian Journal of Agricultural Research 59, no. 7 (2008): 670. http://dx.doi.org/10.1071/ar07160.
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As part of a project exploring the potential for using leaf physiological traits to improve drought tolerance in soybean, studies were conducted to explore whether epidermal conductance (ge), osmotic potential (π), and relative water content (RWC) influenced turgor maintenance and ultimately the survival of droughted plants. In a glasshouse study, plants of 8 soybean genotypes that showed different expression of the traits were grown in well watered soil-filled beds for 21 days and then exposed to terminal water deficit stress. The trends in each trait were then monitored periodically until plant death. Genotypic differences were observed in the rate of decline in RWC as the soil dried, in the temporal patterns of change in ge and π, in the duration of survival after watering ceased, and in the critical relative water content (RWCC) at which plants died. In general, ge became smaller and π became more negative as RWC declined and plants acclimated to the increasing stress. Genotypic differences in ge remained broadly consistent as RWC declined. In contrast, the genotypic rankings for π in stressed plants were poorly correlated with those for well watered plants, indicating differential genotypic capacity for osmotic adjustment (OA) in response to stress. Survival times among genotypes after stress commenced ranged from 27 to 41 days, while RWCC ranged from 49% down to 41%. The differences in survival time among the genotypes were able to be explained by genotypic differences in the rate of decline in RWC and in the RWCC, using a multiple linear regression relationship (R 2 = 0.94**). In turn, genotypic differences in the rate of decline in RWC were positively correlated (r = 0.75*) with ge at 70% RWC, and with OA over the drying period (r = 0.98**). In a second study in a controlled environment facility, leaf area retention at 90% soil water extraction was greatest in the one genotype that combined low ge, high OA, and low RWCC. Overall, the responses from the two studies were consistent with the hypothesis that turgor maintenance and ultimately leaf and plant survival of different genotypes during advanced stages of drought stress are enhanced by low ge, high OA capacity, and low RWCC.
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Knight, Noel L., Niloofar Vaghefi, Zachariah R. Hansen, Julie R. Kikkert, and Sarah J. Pethybridge. "Temporal Genetic Differentiation of Cercospora beticola Populations in New York Table Beet Fields." Plant Disease 102, no. 11 (November 2018): 2074–82. http://dx.doi.org/10.1094/pdis-01-18-0175-re.
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Annual epidemics of Cercospora leaf spot (CLS), caused by the fungus Cercospora beticola, can result in substantial defoliation in table beet fields in New York. High allelic and genotypic diversity have been described within C. beticola populations; however, information on the temporal stability of populations is lacking. C. beticola isolates were obtained from symptomatic leaves in three table beet fields in successive years. Two of the fields were organic mixed-cropping farms and the third was managed conventionally in a broad-acre cropping system. C. beticola isolates (n = 304) were genotyped using 12 microsatellite markers. Genotypic diversity (Simpson’s complement index = 0.178 to 0.990), allele frequencies, and indices of differentiation between years varied. Pairwise index of differentiation values ranged from 0.02 to 0.25 for clone-corrected data, and indicated significant genetic differentiation at Farm 2. No multilocus genotype was shared between years. The shift in multilocus genotypes between years questions the role of clonally reproducing primary inoculum. Collectively, these results suggest that a dominant inoculum source for initiating annual CLS epidemics is external to the field of interest. These findings have implications for CLS disease management in conventional and organic table beet production.
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El-Hendawy, Salah E., Yuncai Hu, and Urs Schmidhalter. "Growth, ion content, gas exchange, and water relations of wheat genotypes differing in salt tolerances." Australian Journal of Agricultural Research 56, no. 2 (2005): 123. http://dx.doi.org/10.1071/ar04019.
Full textAbstract:
Although the mechanisms of salt tolerance in plants have received much attention for many years, genotypic differences influencing salt tolerance still remain uncertain. To investigate the key physiological factors associated with genotypic differences in salt tolerance of wheat and their relationship to salt stress, 13 wheat genotypes from Egypt, Australia, India, and Germany, that differ in their salt tolerances, were grown in a greenhouse in soils of 4 different salinity levels (control, 50, 100, and 150 mm NaCl). Relative growth rate (RGR), net assimilation rate (NAR), leaf area ratio (LAR), photosynthesis, chlorophyll content (SPAD value), and leaf water relations were measured at Days 45 and 60 after sowing. Mineral nutrient content in leaves and stems was determined at Day 45 and final harvest. Salinity reduced RGR, NAR, photosynthetic rate, stomatal conductance, water and osmotic potentials, and K+ and Ca2+ content in stems and leaves at all times, whereas it increased leaf respiration, and Na+ and Cl– content in leaves and stems. LAR was not affected by salinity and the effect of salinity on SPAD value was genotype-dependent. Growth of salt-tolerant genotypes (Sakha 8, Sakha 93, and Kharchia) was affected by salinity primarily due to a decline in photosynthetic capacity rather than a reduction in leaf area, whereas NAR was the more important factor in determining RGR of moderately tolerant and salt-sensitive genotypes. We conclude that Na+ and Cl– exclusion did not always reflect the salt tolerance, whereas K+ in the leaves and Ca2+ in the leaves and stems were closely associated with genotypic differences in salt tolerance among the 13 genotypes even at Day 45. Calcium content showed a greater difference in salt tolerance among the genotypes than did K+ content. The genotypic variation in salt tolerance was also observed for the parameters involved in photosynthesis, and water and osmotic potentials, but not for turgor pressure.
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Oduwaye, O. A., D. K. Ojo, J. Mkumbira, C. O. Alake, O. Adenuga, and E. F. Mapayi. "Genetic Assessment of 23 Cassava, Manihot Esculenta Crantz, Genotypes at Two Agro-Climatic Zones in Nigeria." Plant Breeding and Seed Science 67, no. 1 (August 8, 2014): 103–14. http://dx.doi.org/10.2478/v10129-011-0073-3.
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Abstract This study investigated genetic diversity among 23 cassava genotypes in two-agro-ecological zones (Ibadan and Mokwa), Nigeria. The experiment was conducted using a randomized complete block design with three replicates. The cassava genotypes were evaluated for tuber yield, fresh weight of tuber, number of tubers, tuber girth and length, dry matter and chlorophyll concentration. The data collected were subjected to analysis of variance and differences among the genotypes were computed using Duncan’s multiple range test. Single linkage cluster and FASTCLUS analysis were used to group the cassava genotypes. Genotypic and phenotypic coefficient of variability, heritability and genetic advance were also evaluated. Genotype, environment and genotype × environment interaction (GEI) were significant (P < 0.01) for most of the traits evaluated. The magnitude of the environment was higher compared to genotype and GEI. Comparative mean performance varied from location to location. Tuber yield ranged from 0.32 for 92/0325 to 0.90 kg for 99/3073 with mean of 0.58 kg, and 0.16 kg for 82/00058 to 0.67 kg for 98/0581 with mean of 0.35 kg in Mokwa. Higher genotypic and phenotypic coefficients of variability were observed in Ibadan than Mokwa, for most of the characters. The interrelationships among the characters revealed the superiority of some cassava genotypes for a character in one location and not in the other location. However, breeding potentials exists among the cassava genotypes across the two environments.
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Condon, AG, and RA Richards. "Broad sense heritability and genotype × environment interaction for carbon isotope discrimination in field-grown wheat." Australian Journal of Agricultural Research 43, no. 5 (1992): 921. http://dx.doi.org/10.1071/ar9920921.
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Carbon isotope discrimination (-) has been proposed as a possible selection criterion for greater water use efficiency in breeding programs for water-limited environments because it provides an integrative assessment of genotypic variation in leaf transpiration efficiency. Considerable genotypic variation for - has been demonstrated in wheat, but environmental factors may cause even larger changes in the value of - measured in plant dry matter, which could compromise the effective use of - in breeding programs. In this study we assess broad-sense heritability of - and the significance of genotype x environment interaction for - in field-grown wheat. Another objective was to identify the most effective growth stage or plant part to characterize genotypic variation in -. Experiments were done using several large sets of genotypes (between 8 and 40, usually c. 20) grown in a range of field environments spanning the southern Australian wheat-belt. Carbon isotope discrimination was determined on unreplicated grain samples from seven Interstate Wheat Variety trials grown in 1983 and 1984 and on several plant parts taken from replicated experiments conducted at four locations in south-west New South Wales from 1985 to 1988. From these replicated experiments broad-sense heritabilities for - were calculated on a genotype mean basis h2-M) and on a single-plot basis (h2-P). In dry matter sampled from several environments, site-mean - ranged from 21.0 x 10-3 to 18.9 x 10-3 for early-formed dry matter and from 16.4 x 10-3 to 13.4 x 10-3 for grain. When followed in a single environment, the value of - fell from c. 20 x 10-3 in early-formed leaves to 15.4 x 10-3 in the grain. Variation among genotypes in - of different plant parts was always significant, and was typically c. 2 x 10-3 . Among Australian wheats, low values of - (implying greater transpiration efficiency) were strongly associated with the WW15 genetic background. Estimates of broad-sense heritability for - averaged over 95%, on a genotype mean basis, in experiments where common genotypes were grown in numerous environments. In individual trials, heritability was lowest for plant material sampled near anthesis (average value for h2-M, 83% and for h2-p, 62%) and greatest for dry matter laid down before or during early stem elongation (average value for h2-M, 95% and for h2-P 88%). Even though heritability for grain - was also relatively high (average value for h2-M, 92% and for h2-P, 79%), genotypic differences in grain - are difficult to interpret because of the likelihood of some changes in genotype ranking for - resulting from differences among genotypes in the degree of water stress encountered during grain filling. As well, the contribution of remobilized carbon to grain - may vary between environments and genotypes. We conclude that, for wheat, assessment of genotypic variation in - should be most effective under well-watered conditions using dry matter laid down early in plant development.
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Helms, Theodore C. "Probability of a recombinant inbred diploid plant for two linked genes." Canadian Journal of Plant Science 87, no. 3 (July 1, 2007): 489–92. http://dx.doi.org/10.4141/p06-156.
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For some discreet traits, breeders may need to break genetic linkage between a desirable trait and an undesirable trait. Breeders need to be able to determine the minimum number of plants to grow to have a specified probability of identifying at least one plant that is recombinant between two linked loci. Since 1931, recurrence equations have been available to determine the genotypic frequencies of each genotype when two loci are linked as the level of inbreeding changes. However, these genotypic frequencies have not been published in a tabular form that would be helpful to the applied plant breeder. The objectives are to: (1) provide genotypic proportions as the intensity of linkage and the level of inbreeding increases; (2) determine the most efficient method of identifying a homozygous recombinant genotype as the level of inbreeding and linkage intensity are varied. Numerical examples and formula are provided to determine the number of plants that must be grown to have a given probability of success of identifying a specified number of recombinant types. For close linkage, the number of plants that must be genotyped is greatly decreased by waiting until the population is highly inbred. Key words: Genetic recombination, inbreeding
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Jahan, Eisrat, Jeffrey S. Amthor, Graham D. Farquhar, Richard Trethowan, and Margaret M. Barbour. "Variation in mesophyll conductance among Australian wheat genotypes." Functional Plant Biology 41, no. 6 (2014): 568. http://dx.doi.org/10.1071/fp13254.
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CO2 diffusion from substomatal intercellular cavities to sites of carboxylation in chloroplasts (mesophyll conductance; gm) limits photosynthetic rate and influences leaf intrinsic water-use efficiency (A/gsw). We investigated genotypic variability of gm and effects of gm on A/gsw among eleven wheat (Triticum aestivum L.) genotypes under light-saturated conditions and at either 2 or 21% O2. Significant variation in gm and A/gsw was found between genotypes at both O2 concentrations, but there was no significant effect of O2 concentration on gm. Further, gm was correlated with photosynthetic rate among the 11 genotypes, but was unrelated to stomatal conductance. The effect of leaf age differed between genotypes, with gm being lower in older leaves for one genotype but not another. This study demonstrates a high level of variation in gm between wheat genotypes; 0.5 to 1.0 μmol m−2 s−1 bar−1. Further, leaf age effects indicate that great care must be taken to choose suitable leaves in studies of genotypic variation in gm and water-use efficiency.
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Owen, H. R., R. E. Veilleux, D. Levy, and D. L. Ochs. "Environmental, genotypic, and ploidy effects on endopolyploidization within a genotype of Solanum phureja and its derivatives." Genome 30, no. 4 (August 1, 1988): 506–10. http://dx.doi.org/10.1139/g88-085.
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Flow-cytometric analyses of DNA content were performed on chopped in vivo, in vitro, and protoplast-derived in vitro nuclei of Solanum phureja. An anther-derived monoploid genotype and a diploid and tetraploid clone, derived from callus culture of the monoploid genotype, were used to characterize the influence of in vivo and in vitro environment and explant ploidy level on the extent of endopolyploidization. In addition, protoplast-derived nuclei, from nine anther-derived monoploid genotypes, were examined for genotypic influences on endopolyploidization. DNA distributions of the anther-derived monoploid and callus-derived clones in vivo contained peaks corresponding to 1C, 2C, and 4C DNA levels. By comparison, diploid and tetraploid clones cultured in vitro did not contain 1C DNA peaks. Nuclear DNA content beyond the 4C level was not observed in any of the samples tested. The frequency of monoploid nuclei did not vary significantly among protoplast-derived nuclei from the monoploid genotypes; however, significant differences were detected between replications over time. Variability among the monoploid genotypes was shown for frequency of endoreplicated (4C) nuclei, indicating a genotypic influence on monoploid stability.Key words: potato, monoploid, anther culture, callus culture, protoplast culture, flow cytometry.
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Lee, So-Young, Sung-Seok Lee, Young S. Lyoo, and Hee-Myung Park. "DNA Detection and Genotypic Identification of Potentially Human-Pathogenic Microsporidia from Asymptomatic Pet Parrots in South Korea as a Risk Factor for Zoonotic Emergence." Applied and Environmental Microbiology 77, no. 23 (September 30, 2011): 8442–44. http://dx.doi.org/10.1128/aem.05343-11.
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ABSTRACTWe detected and identified genotypes of human-pathogenic microsporidia in fecal samples from 51 asymptomatic captive-bred pet parrots in South Korea. Microsporidia were identified in 8 samples (15.7%); 7 parrots tested positive forEncephalitozoon hellem, and 1 parrot tested positive for bothE. hellemandEncephalitozoon cuniculi. In genotypic identifications,E. hellemwas present in genotypes 1A and 2B andE. cuniculiwas present in genotype II. Pet parrots might be a source of human microsporidian infection.
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van Eeuwijk, Fred A., Marcos Malosetti, Xinyou Yin, Paul C. Struik, and Piet Stam. "Statistical models for genotype by environment data: from conventional ANOVA models to eco-physiological QTL models." Australian Journal of Agricultural Research 56, no. 9 (2005): 883. http://dx.doi.org/10.1071/ar05153.
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To study the performance of genotypes under different growing conditions, plant breeders evaluate their germplasm in multi-environment trials. These trials produce genotype × environment data. We present statistical models for the analysis of such data that differ in the extent to which additional genetic, physiological, and environmental information is incorporated into the model formulation. The simplest model in our exposition is the additive 2-way analysis of variance model, without genotype × environment interaction, and with parameters whose interpretation depends strongly on the set of included genotypes and environments. The most complicated model is a synthesis of a multiple quantitative trait locus (QTL) model and an eco-physiological model to describe a collection of genotypic response curves. Between those extremes, we discuss linear-bilinear models, whose parameters can only indirectly be related to genetic and physiological information, and factorial regression models that allow direct incorporation of explicit genetic, physiological, and environmental covariables on the levels of the genotypic and environmental factors. Factorial regression models are also very suitable for the modelling of QTL main effects and QTL × environment interaction. Our conclusion is that statistical and physiological models can be fruitfully combined for the study of genotype × environment interaction.
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HENSHALL, JOHN M., BRUCE TIER, and RICHARD J. KERR. "Estimating genotypes with independently sampled descent graphs." Genetical Research 78, no. 3 (December 2001): 281–88. http://dx.doi.org/10.1017/s0016672301005316.
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A method for estimating genotypic and identity-by-descent probabilities in complex pedigrees is described. The method consists of an algorithm for drawing independent genotype samples which are consistent with the pedigree and observed genotype. The probability distribution function for samples obtained using the algorithm can be evaluated up to a normalizing constant, and combined with the likelihood to produce a weight for each sample. Importance sampling is then used to estimate genotypic and identity-by-descent probabilities. On small but complex pedigrees, the genotypic probability estimates are demonstrated to be empirically unbiased. On large complex pedigrees, while the algorithm for obtaining genotype samples is feasible, importance sampling may require an infeasible number of samples to estimate genotypic probabilities with accuracy.
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Lopes-da-Silva, Marcelo, and Luiz Gonzaga Esteves Vieira. "Temporal genotypic diversity of Schizaphis graminum (Rondani 1852) (Hemiptera: Aphididae) in a black oats (Avena strigosa) field." Brazilian Archives of Biology and Technology 53, no. 4 (August 2010): 911–16. http://dx.doi.org/10.1590/s1516-89132010000400021.
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The aim of this work was to analyze the clonal diversity variation in Schizaphis graminum during a complete phenological cycle of black oats (Avena strigosa). RAPD markers were used for detection of DNA polymorphisms of each clonal lineage, derived from a single clone collected weekly during a period of four months, in a crop field of black oats, Londrina, Paraná, Brazil. The monthly genotypic diversity was estimated by Shannon Information Index (H). Only four genotypes were distinguished from 122 specimens, with one of them overly predominant in all sampling dates (>60%). Another genotype, apparently a later colonizer, rapidly reached greater frequency than other genotypes on the second and third month. The results of this work suggested that temporal genotypic diversity of S. graminum assessed by RAPD markers was small and less variable than the genetic variation found at geographical scale.