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Patterns of Genetic Variation in a Soybean Germplasm Collection as Characterized with Genotyping-by-Sequencing.

ABSTRACT: Genomic characterization is playing an increasing role in plant germplasm conservation and utilization, as it can provide higher resolution with genome-wide SNP markers than before to identify and analyze genetic variation. A genotyping-by-sequencing technique was applied to genotype 541 soybean accessions conserved at Plant Gene Resources of Canada and 30 soybean cultivars and breeding lines developed by the Ottawa soybean breeding program of Agriculture and Agri-Food Canada. The sequencing generated an average of 952,074 raw sequence reads per sample. SNP calling identified 43,891 SNPs across 20 soybean chromosomes and 69 scaffolds with variable levels of missing values. Based on 19,898 SNPs with up to 50% missing values, three distinct genetic groups were found in the assayed samples. These groups were a mixture of the samples that originated from different countries and the samples of known maturity groups. The samples that originated from Canada were clustered into all three distinct groups, but 30 Ottawa breeding lines fell into two groups only. Based on the average pairwise dissimilarity estimates, 40 samples with the most genetic distinctness were identified from three genetic groups with diverse sample origin and known maturity. Additionally, 40 samples with the highest genetic redundancy were detected and they consisted of different sample origins and maturity groups, largely from one genetic group. Moreover, some genetically duplicated samples were identified, but the overall level of genetic duplication was relatively low in the collection. These findings are useful for soybean germplasm management and utilization.

SUBMITTER: Fu YB

PROVIDER: S-EPMC8399144 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Raphanus has undergone a lengthy evolutionary process and has rich diversity. However, the inter- and intraspecific phylogenetic relationships and genetic diversity of this genus are not well understood. Through SSR-sequencing and multi-analysis of 939 wild, semi-wild and cultivated accessions, we discovered that the European wild radish (EWR) population is separated from cultivated radishes and has a higher genetic diversity. Frequent intraspecific genetic exchanges occurred in the whole cultivated radish (WCR) population; there was considerable genetic differentiation within the European cultivated radish (ECR) population, which could drive radish diversity formation. Among the ECR subpopulations, European primitive cultivated radishes (EPCRs) with higher genetic diversity are most closely related to the EWR population and exhibit a gene flow with rat-tail radishes (RTRs) and black radishes (BRs)/oil radishes (ORs). Among Asian cultivated radishes (ACRs), Chinese big radishes (CBRs) with a relatively high diversity are furthest from the EWR population, and most Japanese/Korean big radishes (JKBRs) are close to CBR accessions, except for a few old Japanese landraces that are closer to the EPCR. The CBR and JKBR accessions are independent of RTR accessions; however, phylogenetic analysis indicates that the RTR is sister to the clade of CBR (including JWR), which suggests that the RTR may share the most recent common ancestry with CBRs and JWRs. In addition, Japanese wild radishes (JWRs), (namely, R. sativus forma raphanistroides) are mainly scattered between CBRs and EPCRs in PCoA analysis. Moreover, JWRs have a strong gene exchange with the JKBR, OR and RTR subpopulations. American wild radishes (AWRs) are closely related to European wild and cultivated radishes, and have a gene flow with European small radishes (ESRs), suggesting that the AWR developed from natural hybridization between the EWR and the ESR. Overall, this demonstrates that Europe was the origin center of the radish, and that Europe, South Asia and East Asia appear to have been three independent domestication centers. The EPCR, AWR and JWR, as semi-wild populations, might have played indispensable transitional roles in radish evolution. Our study provides new perspectives into the origin, evolution and genetic diversity of Raphanus and facilitates the conservation and exploitation of radish germplasm resources.

Project description:BackgroundEstablish a molecular breeding program involved assembling a diverse germplasm collection and generating accurate genotypes to characterize their genetic potential and associate them with agronomic traits. In this study, we acquired over eight hundred wheat accessions from international gene banks and assessed their genetic relatedness using high-quality SNP genotypes. Understanding the scope of genomic variation in this collection allows the breeders to utilize the genetic resources efficiently while improving wheat yield and quality.ResultsA wheat diversity panel comprising 39 durum wheat, 60 spelt wheat, and 765 bread wheat accessions was genotyped on iSelect 90 K wheat SNP arrays. A total of 57,398 SNP markers were mapped to IWGSC RefSeq v2.1 assembly, over 30,000 polymorphic SNPs in the A, B, D genomes were used to analyze population structure and diversity, the results revealed the separation of the three species and the differentiation of CIMMYT improved breeding lines and landraces or widely grown cultivars. In addition, several chromosomal regions under selection were detected. A subset of 280 bread wheat accessions was evaluated for grain traits, including grain length, width, surface area, and color. Genome-wide association studies (GWAS) revealed that several chromosomal regions were significantly linked to known quantitative trait loci (QTL) controlling grain-related traits. One of the SNP peaks at the end of chromosome 7A was in strong linkage disequilibrium (LD) with WAPO-A1, a gene that governs yield components.ConclusionsHere, the most updated and accurate physical positions of SNPs on 90 K genotyping array are provided for the first time. The diverse germplasm collection and associated genotypes are available for the wheat researchers to use in their molecular breeding program. We expect these resources to broaden the genetic basis of original breeding and pre-breeding materials and ultimately identify molecular markers associated with important agronomic traits which are evaluated in diverse environmental conditions.

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Patterns of Genetic Variation in a Soybean Germplasm Collection as Characterized with Genotyping-by-Sequencing.

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