Добірка наукової літератури з теми "Heterozygous inbred families (HIFs)"

Cultivated diploid potatoes (2n = 2x = 24) are self-incompatible, but can be altered to become self-compatible using the Sli gene. Previously, a diploid clone 97H32–6 was selfed up to S3 using the Sli gene. To explore the usefulness of the Sli gene for the production of highly homozygous diploid potatoes, 2 S4 families from the above 97H32-6 derived S3 lines (inbred series A) and 3 S5 families by continuous selfings from a different F1 (= S0) plant (inbred series B) were developed. The level of heterozygosity and the location of heterozygous loci on the genetic map were investigated using RFLP and AFLP markers. The average heterozygosity levels of the originally heterozygous loci decreased from 100% in S0 to 10.7% in S4 and 8.6% in S5 (inbred series A and B, respectively). The average rate of reduction in heterozygosity per generation (38.4% and 38.5% for inbred series A and B, respectively) was lower than the theoretically expected rate (50%). However, none of the loci or chromosome sections was exclusively heterozygous in the advanced self-progeny. Thus, highly homozygous and seed-propagated diploid potatoes could be obtained by repeated selfing using the Sli gene.Key words: Selfing, heterozygosity, diploid potato, Sli gene, Solanum.

Chrysanthemum [Dendranthema ×grandiflora Tzvelv. (syn. Chrysanthemum ×morifolium Ramat.)] breeding programs have been selecting for reduced expression of self-incompatibility (via pseudo-self-compatibility) to create inbred families with selected genotypes to serve as parents for F1 hybrid chrysanthemum seed production. However, it is not known to what extent inbreeding is affecting fertility in this outcrossing, heterozygous species. The objective of this research was to assess male/female fertility changes (gain/loss) in successive inbred generations of chrysanthemums. Pseudo-self-compatible chrysanthemum parents (n = 41 inbred, noninbred, and recombinant inbred) were chosen for fertility analyses. As many as three generations of inbreds (I1, I2, and I3) from self-pollinations were created using rapid generation cycling. Female and male fertility levels of the parents and all derived inbred populations were assessed using outcross seed set and pollen stainability, respectively. Average seed set ranges were 0.3% to 96.1% (inbred parents), 24.5% to 38.5% (noninbred parents), and 0.9% to 85.1% (recombinant inbred parents); these began decreasing in the I1 and continued to decline steadily into the I3. Statistically significant (P < 0.05) decreases in seed set occurred in n = 23 (56.1%) inbred families; the remaining inbred families had similar or higher fertility than the parents. Pollen stainability was >50% for the parents, but began declining in some inbred families as inbreeding progressed. Fertility reductions were attributed to inbreeding depression. Lack of significant fertility losses in other inbred families demonstrates the opportunity of selection of fertile inbred parents for use in hybrid seed production.

A new mating procedure for estimating additive and dominance genetic variances in a random mating population is presented. With this procedure, m number of plants from a random mating population are selfed to produce S1 families and are also crossed to n inbreds. Subsequently, all the m × n hybrids are selfed. while keeping remnant crossed seeds for the final experiment. The final experiment comprises m × n hybrids, their m × n selfs, m S1, and m S2 families as well as n inbreds. The analysis of the data, recorded on the quantitative traits provides information for both the random mating as well as the inbred populations. Epistasis can be detected by two different tests. The analysis can be applied to F2 instead of random mating populations with less effort.Key words: random mating, genetic variance, epistasis, inbred.

The objectives of this research were to identify quantitative trait loci (QTL) for Stewart's wilt resistance from a mapping population derived from a sweet corn hybrid that is highly resistant to Pantoea stewartii and to determine if marker-based selection for those QTL could substantially improve Stewart's wilt resistance in a population derived from a cross of resistant lines and a highly susceptible sweet corn inbred. Three significant QTL for Stewart's wilt resistance on chromosomes 2 (bin 2.03), 5 (bin 5.03), and 6 (bin 6.06/6.07) explained 31% of the genetic variance in a population of 110 F3:4 families derived from the sweet corn hybrid Bonus. The three QTL appeared to be additive in their effects on Stewart's wilt ratings. Based on means of families that were either homozygous or heterozygous for marker alleles associated with the resistance QTL, the QTL on chromosomes 2 and 6 appeared to have dominant or partially dominant gene action, while the QTL on chromosome 5 appeared to be recessive. A population of 422 BC2S2 families was derived from crosses of a sweet corn inbred highly susceptible to Stewart's wilt, Green Giant Code 88 (GG88), and plants from two F3:4 families (12465 and 12467) from the Bonus mapping population that were homozygous for marker alleles associated with Stewart's wilt resistance at the three QTL. Mean Stewart's wilt ratings for BC2S2 families were significantly (P < 0.05) lower for families that were homozygous for the bnlg1902 marker allele (bin 5.03) from resistant lines 12465 or 12467 than for families that were heterozygous at this marker locus or homozygous for the bnlg1902 marker allele from GG88. Resistance associated with this QTL was expressed only if F3:5 or BC2S2 families were homozygous for marker alleles associated with the resistant inbred parent (P1). Marker alleles identified in the F3:5 mapping population that were in proximity to the resistance QTL on chromosomes 2 and 6 were not polymorphic in crosses of GG88 with 12465 and 12467. Selection for other polymorphic marker loci adjacent to these two regions did not improve Stewart's wilt resistance of BC2S2 families.

Cacao is a globally important crop with a long history of domestication and selective breeding. Despite the increased use of elite clones by cacao farmers, worldwide plantations are established mainly using hybrid progeny material derived from heterozygous parents, therefore displaying high tree-to-tree variability. The deliberate development of hybrids from advanced inbred lines produced by successive generations of self-pollination has not yet been fully considered in cacao breeding. This is largely due to the self-incompatibility of the species, the long generation cycles (3–5 years) and the extensive trial areas needed to accomplish the endeavor. We propose a simple and accessible approach to develop inbred lines based on accelerating the buildup of homozygosity based on regular selfing assisted by genome-wide SNP genotyping. In this study we genotyped 90 clones from the Brazilian CEPEC´s germplasm collection and 49 inbred offspring of six S1 or S2 cacao families derived from self-pollinating clones CCN-51, PS-13.19, TSH-1188 and SIAL-169. A set of 3,380 SNPs distributed across the cacao genome were interrogated on the EMBRAPA multi-species 65k Infinium chip. The 90 cacao clones showed considerable variation in genome-wide SNP homozygosity (mean 0.727± 0.182) and 19 of them with homozygosity ≥90%. By assessing the increase in homozygosity across two generations of self-pollinations, SNP data revealed the wide variability in homozygosity within and between S1 and S2 families. Even in small families (<10 sibs), individuals were identified with up to ~1.5 standard deviations above the family mean homozygosity. From baseline homozygosities of 0.476 and 0.454, offspring with homozygosities of 0.862 and 0.879 were recovered for clones TSH-1188 and CCN-51 respectively, in only two generations of selfing (81–93% increase). SNP marker assisted monitoring and selection of inbred individuals can be a practical tool to optimize and accelerate the development of inbred lines of outbred tree species. This approach will allow a faster and more accurate exploitation of hybrid breeding strategies in cacao improvement programs and potentially in other perennial fruit and forest trees.

Melanin pigment helps protect our body from broad wavelength solar radiation and skin cancer. Among other pigmentation disorders in humans, albinism is reported to manifest in both syndromic and nonsyndromic forms as well as with varying inheritance patterns. Oculocutaneous albinism (OCA), an autosomal recessive nonsyndromic form of albinism, presents as partial to complete loss of melanin in the skin, hair, and iris. OCA has been known to be caused by pathogenic variants in seven different genes, so far, according to all the currently published population studies. However, the detection rate of alleles causing OCA varies from 50% to 90%. One of the significant challenges of uncovering the pathological variant underlying disease etiology is inter- and intra-familial locus heterogeneity. This problem is especially pertinent in highly inbred populations. As examples of such familial locus heterogeneity, we present nine consanguineous Pakistani families with segregating OCA due to variants in one or two different known albinism-associated genes. All of the identified variants are predicted to be pathogenic, which was corroborated by several in silico algorithms and association with diverse clinical phenotypes. We report an individual affected with OCA carries heterozygous, likely pathogenic variants in TYR and OCA2, raising the question of a possible digenic inheritance. Altogether, our study highlights the significance of exome sequencing for the complete genetic diagnosis of inbred families and provides the ramifications of potential genetic interaction and digenic inheritance of variants in the TYR and OCA2 genes.

The objective of this study was to identify restriction fragment length polymorphism (RFLP) markers linked to QTLs that control aluminum (Al) tolerance in maize. The strategy used was bulked segregant analysis (BSA) and the genetic material utilized was an F2 population derived from a cross between the Al-susceptible inbred line L53 and Al-tolerant inbred line L1327. Both lines were developed at the National Maize and Sorghum Research Center - CNPMS/EMBRAPA. The F2 population of 1554 individuals was evaluated in a nutrient solution containing a toxic concentration of Al and relative seminal root length (RSRL) was used as a phenotypic measure of tolerance. The RSRL frequency distribution was continuous, but skewed towards Al-susceptible individuals. Seedlings of the F2 population which scored the highest and the lowest RSRL values were transplanted to the field and subsequently selfed to obtain F3 families. Thirty F3 families (15 Al-susceptible and 15 Al-tolerant) were evaluated in nutrient solution, using an incomplete block design, to identify those with the smallest variances for aluminum tolerance and susceptibility. Six Al-susceptible and five Al-tolerant F3 families were chosen to construct one pool of Al-susceptible individuals, and another of Al-tolerant, herein referred as "bulks", based on average values of RSRL and genetic variance. One hundred and thirteen probes were selected, with an average interval of 30 cM, covering the 10 maize chromosomes. These were tested for their ability to discriminate the parental lines. Fifty-four of these probes were polymorphic, with 46 showing codominance. These probes were hybridized with DNA from the two contrasting bulks. Three RFLPs on chromosome 8 distinguished the bulks on the basis of band intensity. DNA of individuals from the bulks was hybridized with these probes and showed the presence of heterozygous individuals in each bulk. These results suggest that in maize there is a region related to aluminum tolerance on chromosome 8

Approximately 10% of newborns with congenital hypothyroidism are unable to convert iodide into organic iodine. This iodide organification defect has a prevalence of 1 in 40,000 newborns and may be caused by defects in the thyroid peroxidase enzyme (TPO), the hydrogen peroxide-generating system, the TPO substrate thyroglobulin, or inhibitors of TPO. We identified a high incidence of severe hypothyroidism due to a complete iodide organification defect in the youngest generation of five nuclear families belonging to an inbred Amish kindred. Genealogical records permitted us to trace their origin to an ancestral couple 7–8 generations back and to identify an autosomal recessive pattern of inheritance. Initial studies of homozygosity by descent using two polymorphic markers within the TPO gene showed no linkage to the phenotype. In fact, 4 of 15 affected siblings from 2 of the nuclear families were heterozygous, resulting in homozygosity values of 73% and 53% in affected and unaffected family members, respectively. A genome-wide homozygosity screen using DNA pools from affected and unaffected family members localized the defect to a locus close to the TPO gene. Linkage analysis using 4 additional polymorphic markers within the TPO gene reduced the number of homozygous unaffected siblings to zero without altering the percent homozygosity initially found in the affected. Sequencing of the TPO gene revealed 2 missense mutations, E799K and R648Q. TPO 779K was found in both alleles of the 11 affected homozygotes, both mutations were present in each of the 3 affected compound heterozygotes, and there were no TPO mutations in 1 subject with hypothyroidism of different etiology. These results demonstrate the power of the DNA pooling strategy in the localization of a defective gene and the pitfalls of linkage analysis when 2 relatively rare mutations coexist in an inbred population.

Amplified fragment length polymorphisms (AFLPs) are a widely used marker system: the technique is very cost-effective, easy and rapid, and reproducibly generates hundreds of markers. Unfortunately, AFLP alleles are typically scored as the presence or absence of a band and, thus, heterozygous and dominant homozygous genotypes cannot be distinguished. This results in a significant loss of information, especially as regards mapping of quantitative trait loci (QTLs). We present a Monte Carlo Markov Chain method that allows us to compute the identity by descent probabilities (IBD) in a general pedigree whose individuals have been typed for dominant markers. The method allows us to include the information provided by the fluorescent band intensities of the markers, the rationale being that homozygous individuals have on average higher band intensities than heterozygous individuals, as well as information from linked markers in each individual and its relatives. Once IBD probabilities are obtained, they can be combined into the QTL mapping strategy of choice. We illustrate the method with two simulated populations: an outbred population consisting of full sib families, and an F2 cross between inbred lines. Two marker spacings were considered, 5 or 20 cM, in the outbred population. There was almost no difference, for the practical purpose of QTL estimation, between AFLPs and biallelic codominant markers when the band density is taken into account, especially at the 5 cM spacing. The performance of AFLPs every 5 cM was also comparable to that of highly polymorphic markers (microsatellites) spaced every 20 cM. In economic terms, QTL mapping with a dense map of AFLPs is clearly better than microsatellite QTL mapping and little is lost in terms of accuracy of position. Nevertheless, at low marker densities, AFLPs or other biallelic markers result in very inaccurate estimates of QTL position.

Identification of resistance (R) genes to races of Magnaporthe oryzae in rice (Oryza sativa) germplasm is essential for the development of rice cultivars with long-lasting blast resistance. In the present study, one major quantitative trait locus, qPi93-3, was fine mapped using a recombinant inbred line (RIL), F8 RIL171, derived from the cross between ‘Nipponbare’ and ‘93-11’. RIL171 contained a heterozygous qPi93-3 allele which was found to be resistant against nine U.S. common races—ID1, IA1, IB49, IE1, IA45, IB1, IC17, IB45, and IH1—of M. oryzae. An F2 mapping population consisting of 2,381 individuals derived from RIL171 was evaluated with a field isolate (race) ARB82 (IA1) of M. oryzae under greenhouse conditions. Disease reaction of a resistant/susceptible ratio of 3:1 was identified with F2:F3 families. In total, 12 simple sequence repeat markers spanning qPi93-3 were used for fine mapping. Consequently, qPi93-3 was delimited to 4.2 Mb between RM3246 and RM7102. Three insertion-deletion (InDel) markers located between RM3246 and RM7102, that had previously used to map Pi61(t), showed that qPi93-3 was Pi61(t). The existence of Pi61(t) in 136 rice germplasm lines from the United States Department of Agriculture rice core collection was evaluated using Pi61(t)-specific InDel markers. Pi61(t) was identified as a source of resistance in 5 of the 136 lines. The characterized germplasm will be useful for rice breeders to use for improving blast resistance.

Crop productivity in many wheat cultivation areas is severely affected by dry and hot conditions, increasing the yield gap between potential and actual yield. To close this gap, the identification of genes contributing to yield in stressed conditions is one key to the breeding of tolerant cultivars. However, due to low stability across environments, no genes have yet been identified for yield variation. In this project, we focussed on the positional cloning of a quantitative trait locus (QTL), qYDH.3BL, located on the wheat chromosome arm 3BL. The QTL has been identified by the multi-environment analysis of the double-haploid (DH) population of the cross from the drought tolerant line RAC875 and the susceptible variety Kukri. The QTL was constitutively expressed in the Mexican environment with the positive allele from RAC875 associated with an increase in yield, thousand grain weight and early vigour under dry and hot conditions. Greater allele effect dependent on temperature has been observed at qYDH.3BL, suggesting that the QTL is heat related. To fine map qYDH.3BL, we developed a deep-soil platform using 1 m deep wheelie bins placed in the polytunnel to increase temperature. We confirmed the expression of qYDH.3BL using a set of RAC875 x Kukri RILs. Single marker analysis showed the positive allele from RAC875 associated with spike length and biomass, early vigour and stem biomass. The development of a high-density genetic map of qYDH.3BL in RAC875, combined with the deep-platform experiment, narrowed the QTL interval to a 690 kbp sequence. The anchoring of the interval in the physical assembly of the wheat cv. Chinese Spring reference genome (IWGSC Ref 1.0) identified 12 candidate genes. The study of the allelic diversity at qYDH.3BL in a wheat diversity panel of 808 accessions identified four haplotypes. Haplotype I, the RAC875 allele was over-represented in the CIMMYT germplasm suggesting that the allele may have been selected for yield in a Mexican environment-type. To study the physiological mechanisms under qYDH.3BL control, we developed heterozygous inbred families (HIF). The lines were phenotyped in the deep soil platform. The lines with the RAC875 allele among the HIFs increased biomass, single grain weight and number of spikelets per spike. Water use was also measured in the deep soil platform using sap flow sensors. RAC875 had an increased water use compared to Kukri. A similar pattern was observed in the HIFs, the lines with the RAC875 allele had a higher water use compared to those with the Kukri allele. As qYDH.3BL was constitutively expressed in the Mexican environments characterised by a deep soil and RAC875 was shown to have a lower root conductivity than Kukri due to its root anatomy, we also phenotyped the roots of the HIFs. We did not identify root traits that could contribute to the heat tolerance mechanism associated with qYDH.3BL. Finally, we studied the expression of the 12 candidate genes within the 690 kbp interval in the HIFs. Expression analysis identified a strong candidate gene, Seven in absentia (TaSINA). The gene was up-regulated in Kukri compared to RAC875 and in the HIFs containing the Kukri allele compared to those with the RAC875 allele. TaSINA is annotated as an E3 ubiquitin ligase protein, a family involved in ubiquitin pathway. To study the role of TaSINA in drought and heat tolerance, we screened the Gladius TILLING population and identified two missense variants. Study of the phylogenetic relationship of TaSINA with published SINA genes in plants and animals revealed that TaSINA is specific to the Triticeae. This is the first report of a wheat SINA gene and a gene associated to yield variation under heat in wheat. Discovery of new alleles of TaSINA could lead to the breeding of new varieties able to maintain yield under heat stress conditions.
Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 2018