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Genomic Patterns of Introgression in Interspecific Populations Created by Crossing Wheat with Its Wild Relative.

ABSTRACT: Introgression from wild relatives is a valuable source of novel allelic diversity for breeding. We investigated the genomic patterns of introgression from Aegilops tauschii, the diploid ancestor of the wheat D genome, into winter wheat (Triticum aestivum) cultivars. The population of 351 BC1F3:5 lines was selected based on phenology from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. SNP markers developed for this population and a diverse panel of 116 Ae. tauschii accessions by complexity-reduced genome sequencing were used to detect introgression based on the identity-by-descent analysis. Overall, introgression frequency positively correlated with recombination rate, with a high incidence of introgression at the ends of chromosomes and low in the pericentromeric regions, and was negatively related to sequence divergence between the parental genomes. Reduced introgression in the pericentromeric low-recombining regions spans nearly 2/3 of each chromosome arm, suggestive of the polygenic nature of introgression barriers that could be associated with multilocus negative epistasis between the alleles of wild and cultivated wheat. On the contrary, negative selection against the wild allele of Tg, controlling free-threshing trait and located in the high-recombining chromosomal region, led to reduced introgression only within ?10 Mbp region around Tg These results are consistent with the effect of selection on linked variation described by the Hill-Robertson effect, and offer insights into the introgression population development for crop improvement to maximize retention of introgressed diversity across entire genome.

SUBMITTER: Nyine M

PROVIDER: S-EPMC7534432 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Genomic Patterns of Introgression in Interspecific Populations Created by Crossing Wheat with Its Wild Relative.

Nyine Moses M Adhikari Elina E Clinesmith Marshall M Jordan Katherine W KW Fritz Allan K AK Akhunov Eduard E

G3 (Bethesda, Md.) 20201005 10

Introgression from wild relatives is a valuable source of novel allelic diversity for breeding. We investigated the genomic patterns of introgression from Aegilops tauschii, the diploid ancestor of the wheat D genome, into winter wheat (Triticum aestivum) cultivars. The population of 351 BC1F3:5 lines was selected based on phenology from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. SNP markers developed for ...[more]

PMID: 32737066

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Project description:BackgroundEvidence of introgression, the transfer of genetic material, between crops and their wild relatives through spontaneous hybridization and subsequent backcrossing has been documented; however, the evolutionary patterns and consequences of introgression and its influence on the processes of crop domestication and varietal diversification are poorly understood.ResultsWe investigate the genomic landscape and evolution of putative crop-wild-relative introgression by analyzing the nuclear and chloroplast genomes from a panel of wild (Glycine soja) and domesticated (Glycine max) soybeans. Our data suggest that naturally occurring introgression between wild and domesticated soybeans was widespread and that introgressed variation in both wild and domesticated soybeans was selected against throughout the genomes and preferentially removed from the genomic regions underlying selective sweeps and domestication quantitative trait locus (QTL). In both taxa, putative introgression was preferentially retained in recombination-repressed pericentromeric regions that exhibit lower gene densities, reflecting potential roles of recombination in purging introgression. Despite extensive removal of introgressed variation by recurrent selection for domestication-related QTL and associated genomic regions, spontaneous interspecific hybridization during soybean domestication appear to have contributed to a rapid varietal diversification with high levels of genetic diversity and asymmetric evolution between the nuclear and chloroplast genomes.ConclusionsThis work reveals the evolutionary forces, patterns, and consequences of putative genomic introgression between crops and their wild relatives, and the effects of introgression on the processes of crop domestication and varietal diversification. We envision that interspecific introgression serves as an important mechanism for counteracting the reduction of genetic diversity in domesticated crops, particularly the ones under single domestication.

Project description:Agronomically important traits generally have complex genetic architecture, where many genes have a small and largely additive effect. Genomic prediction has been demonstrated to increase genetic gain and efficiency in plant breeding programs beyond marker-assisted selection and phenotypic selection. The objective of this study was to evaluate the impact of allelic origin, marker density, training population size, and cross-validation schemes on the accuracy of genomic prediction models in an interspecific soybean nested association mapping (NAM) panel. Three cross-validation schemes were used: (a) Within-Family (WF): training population and predictions are made exclusively within each family; (b) Across All families (AF): all the individuals from the three families were randomly assigned to either the training or validation set; (c) Leave one Family out (LFO): each family is predicted using a training set that contains the other two families. Predictive abilities increased with training population size up to 350 individuals, but no significant gains were noted beyond 250 individuals in the training population. The number of markers had a limited impact on the observed predictive ability across traits; increasing markers used in the model above 1000 revealed no significant increases in prediction accuracy. Predictive abilities for AF were not significantly different from the WF method, and predictive abilities across populations for the WF method had a range of 0.58 to 0.70 for maturity, protein, meal, and oil. Our results also showed encouraging prediction accuracies for grain yield (0.58–0.69) using the WF method. Partitioning genomic prediction between G. max and G. soja alleles revealed useful information to select material with a larger allele contribution from both parents and could accelerate allele introgression from exotic germplasm into the elite soybean gene pool. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01203-6.

Project description:Tritcum urartu (2n = 2x = 14, AuAu), the A genome donor of wheat, is an important source for new genetic variation for wheat improvement due to its high photosynthetic rate and disease resistance. By facilitating the generation of genome-wide introgressions leading to a variety of different wheat-T. urartu translocation lines, T. urartu can be practically utilized in wheat improvement. Previous studies that have generated such introgression lines have been unable to successfully use cytological methods to detect the presence of T. urartu in these lines. Many have, thus, used a variety of molecular markers with limited success due to the low-density coverage of these markers and time-consuming nature of the techniques rendering them unsuitable for large-scale breeding programs. In this study, we report the generation of a resource of single nucleotide polymorphic (SNP) markers, present on a high-throughput SNP genotyping array, that can detect the presence of T. urartu in a hexaploid wheat background making it a potentially valuable tool in wheat pre-breeding programs. A whole genome introgression approach has resulted in the transfer of different chromosome segments from T. urartu into wheat which have then been detected and characterized using these SNP markers. The molecular analysis of these wheat-T. urartu recombinant lines has resulted in the generation of a genetic map of T. urartu containing 368 SNP markers, spread across all seven chromosomes of T. urartu. Comparative analysis of the genetic map of T. urartu and the physical map of the hexaploid wheat genome showed that synteny between the two species is highly conserved at the macro-level and confirmed the presence of the 4/5 translocation in T. urartu also present in the A genome of wheat. A panel of 17 wheat-T. urartu recombinant lines, which consisted of introgressed segments that covered the whole genome of T. urartu, were also selected for self-fertilization to provide a germplasm resource for future trait analysis. This valuable resource of high-density molecular markers specifically designed for detecting wild relative chromosomes and a panel of stable interspecific introgression lines will greatly enhance the efficiency of wheat improvement through wild relative introgressions.

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Genomic Patterns of Introgression in Interspecific Populations Created by Crossing Wheat with Its Wild Relative.

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Genomic Patterns of Introgression in Interspecific Populations Created by Crossing Wheat with Its Wild Relative.

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