Genetic diversity and population structure analysis of synthetic and bread wheat accessions in Western Siberia

Bhatta, Madhav; Шаманин, Владимир; Shepelev, Sergey; Baenziger, P. Stephen; Pozherukova, Violetta; Pototskaya, I. V.; Morgounov, Alexey

doi:10.1007/s13353-019-00514-x

Cited by 13 publications

(13 citation statements)

References 23 publications

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“…The fourth group comprised of 77 bread wheat lines developed by KASIB (Kazakhstan and Siberian) breeding program, where14 lines were from Kazakhstan and 63 from Siberia, Russia (Table S1). Genome-wide diversity analysis conducted in these lines showed considerable genetic diversity among lines from different breeding programs, and the population structure analysis identified that these lines can be divided into three subgroups based on the type of wheat and their geographical origin (Bhatta et al 2019b). The idea of selecting diverse germplasm from different breeding programs was to assess their adaptation and performance to a new area (Siberia) as well as to better understand the growing region from already adapted lines in the specific region.…”

Section: Methodsmentioning

confidence: 99%

“…Genotyping and SNP discovery procedures for all 143 lines were described previously (Bhatta et al 2019b). In brief, genomic DNA was extracted from 2-weeks old leaves using Biosprint 96 Plant Kit (Qiagen) protocol.…”

Section: Methodsmentioning

confidence: 99%

“…SNP discovery was performed using TASSEL v.5.2.40 GBS v2 Pipeline (Glaubitz et al 2014) with a physical alignment to the Chinese spring genome sequence (RefSeq v1.0) (International Wheat Genome Sequencing Consortium 2018). The identified SNPs with minor allele frequency (MAF) of more than 5% and missing data frequency of less than 20% were retained for the analysis (Bhatta et al 2018c, 2019b).…”

Section: Methodsmentioning

confidence: 99%

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Marker-Trait Associations for Enhancing Agronomic Performance, Disease Resistance, and Grain Quality in Synthetic and Bread Wheat Accessions in Western Siberia

Bhatta

Шаманин

Shepelev

et al. 2019

G3 Genes|Genomes|Genetics

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Exploiting genetically diverse lines to identify genes for improving crop performance is needed to ensure global food security. A genome-wide association study (GWAS) was conducted using 46,268 SNP markers on a diverse panel of 143 hexaploid bread and synthetic wheat to identify potential genes/genomic regions controlling agronomic performance (yield and 26 yield-related traits), disease resistance, and grain quality traits. From phenotypic evaluation, we found large genetic variation among the 35 traits and recommended five lines having a high yield, better quality, and multiple disease resistance for direct use in a breeding program. From a GWAS, we identified a total of 243 significant marker-trait associations (MTAs) for 35 traits that explained up to 25% of the phenotypic variance. Of these, 120 MTAs have not been reported in the literature and are potentially novel MTAs. In silico gene annotation analysis identified 116 MTAs within genes and of which, 21 MTAs were annotated as a missense variant. Furthermore, we were able to identify 23 co-located multi-trait MTAs that were also phenotypically correlated to each other, showing the possibility of simultaneous improvement of these traits. Additionally, most of the co-located MTAs were within genes. We have provided genomic fingerprinting for significant markers with favorable and unfavorable alleles in the diverse set of lines for developing elite breeding lines from useful trait-integration. The results from this study provided a further understanding of genetically complex traits and would facilitate the use of diverse wheat accessions for improving multiple traits in an elite wheat breeding program.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Marker-Trait Associations for Enhancing Agronomic Performance, Disease Resistance, and Grain Quality in Synthetic and Bread Wheat Accessions in Western Siberia

Bhatta

Шаманин

Shepelev

et al. 2019

G3 Genes|Genomes|Genetics

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“…Similarly, in this study DAPC analysis clearly divided the Triticum accessions according to their species complexity as compared to ADMIXTURE analysis. Several molecular approaches have been used to assess the population structure in the polyploid wheat population (Eltaher et al, 2018;Bhatta et al, 2019;Rufo et al, 2019;Kumar et al, 2020). However, the use of DAPC to evaluate the population structure showed better performance and provided a well-defined genotypic cluster similar to other studies (Deperi et al, 2018).…”

Section: Population Genomic Differentiationmentioning

confidence: 99%

“…However, species discrimination with a combination of nuclear-and chloroplastspecific DNA barcodes failed to discriminate T. aestivum and T. turgidum species (Raveendar et al, 2019). Moreover, unfortunately relatively few evolutionary studies have been performed on wheat species discrimination and none of the studies so far reported the efficient identification of wheat genotypes, as all other studies have only reported on genetic diversity in the landrace or cultivars (Alipour et al, 2017;Eltaher et al, 2018;Rimbert et al, 2018;Bhatta et al, 2019;Rufo et al, 2019). In the present study, Bayesian analysis revealed that the polyploid wheat species are divided into groups according to the presence of A, B, D, and G genomes (Figure 3), in which all 17 Triticum species and subspecies could be discriminated.…”

Section: Species-specific Markers For Genebank Managementmentioning

confidence: 99%

Genotyping-by-Sequencing Derived Single Nucleotide Polymorphisms Provide the First Well-Resolved Phylogeny for the Genus Triticum (Poaceae)

et al. 2020

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Wheat (Triticum spp.) has been an important staple food crop for mankind since the beginning of agriculture. The genus Triticum L. is composed of diploid, tetraploid, and hexaploid species, majority of which have not yet been discriminated clearly, and hence their phylogeny and classification remain unresolved. Genotyping-by-sequencing (GBS) is an easy and affordable method that allows us to generate genome-wide single nucleotide polymorphism (SNP) markers. In this study, we used GBS to obtain SNPs covering all seven chromosomes from 283 accessions of Triticum-related genera. After filtering low-quality and redundant SNPs based on haplotype information, the GBS assay provided 14,188 high-quality SNPs that were distributed across the A (71%), B (26%), and D (2.4%) genomes. Cluster analysis and discriminant analysis of principal components (DAPC) allowed us to distinguish six distinct groups that matched well with Triticum species complexity. We constructed a Bayesian phylogenetic tree using 14,188 SNPs, in which 17 Triticum species and subspecies were discriminated. Dendrogram analysis revealed that the polyploid wheat species could be divided into groups according to the presence of A, B, D, and G genomes with strong nodal support and provided new insight into the evolution of spelt wheat. A total of 2,692 speciesspecific SNPs were identified to discriminate the common (T. aestivum) and durum (T. turgidum) wheat cultivar and landraces. In principal component analysis grouping, the two wheat species formed individual clusters and the SNPs were able to distinguish up to nine groups of 10 subspecies. This study demonstrated that GBS-derived SNPs could be used efficiently in genebank management to classify Triticum species and subspecies that are very difficult to distinguish by their morphological characters.

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Gene Flow Between Tetraploid and Hexaploid Wheat for Breeding Innovation

Mazzucotelli,

Mastrangelo,

Desiderio

et al. 2023

Compendium of Plant Genomes

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Durum and bread wheat are two related species with different ploidy levels but a high similarity between the common A and B genomes. This feature, which allows a continuous gene flow between the two species, can be exploited in breeding programs to improve key traits in both crops. Therefore, durum wheat, despite covering only 5% of cultivated wheat worldwide, also represents an asset for the genetic improvement of bread wheat. Tetraploid wheat, with a very large availability of wild and domesticated accessions, durum landraces, and cultivars, offers a large gene reservoir to increase the genetic diversity of A and B genomes in bread wheat. Moreover, thanks to the possibility of crossing durum wheat with Aegilops tauschii, synthetic hexaploid lines are generated which show a much larger genetic diversity also in the D genome compared to common wheat. The genome sequences of wild emmer, durum, and bread wheat provide power tools for gene cloning and comparative genomics that will also facilitate the shuttling of genes between tetraploid and hexaploid wheats.

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Genetic diversity and population structure analysis of synthetic and bread wheat accessions in Western Siberia

Cited by 13 publications

References 23 publications

Marker-Trait Associations for Enhancing Agronomic Performance, Disease Resistance, and Grain Quality in Synthetic and Bread Wheat Accessions in Western Siberia

Marker-Trait Associations for Enhancing Agronomic Performance, Disease Resistance, and Grain Quality in Synthetic and Bread Wheat Accessions in Western Siberia

Genotyping-by-Sequencing Derived Single Nucleotide Polymorphisms Provide the First Well-Resolved Phylogeny for the Genus Triticum (Poaceae)

Gene Flow Between Tetraploid and Hexaploid Wheat for Breeding Innovation

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