Genetic Diversity and Population Structure of Asian and European Common Wheat Accessions Based on Genotyping-By-Sequencing

Xiu Yang; Binwen Tan; Haijiao Liu; Wei Zhu; Lili Xu; Yi Wang; Xing Fan; Lina Sha; Haiqin Zhang; Jian Zeng; Dandan Wu; Yunfeng Jiang; Xigui Hu; Guoyue Chen; Yonghong Zhou; Houyang Kang

doi:10.3389/fgene.2020.580782

Genetic Diversity and Population Structure of Asian and European Common Wheat Accessions Based on Genotyping-By-Sequencing

Front Genet. 2020 Sep 25:11:580782. doi: 10.3389/fgene.2020.580782. eCollection 2020.

Authors

Xiu Yang^{1

2}, Binwen Tan^{1

2}, Haijiao Liu^{1

2}, Wei Zhu^{1

2}, Lili Xu¹, Yi Wang^{1

2}, Xing Fan^{1

2}, Lina Sha^{1

2}, Haiqin Zhang^{1

2}, Jian Zeng³, Dandan Wu^{1

2}, Yunfeng Jiang^{1

2}, Xigui Hu⁴, Guoyue Chen^{1

2}, Yonghong Zhou^{1

2}, Houyang Kang^{1

2}

Affiliations

¹ State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
² Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
³ College of Resources, Sichuan Agricultural University, Chengdu, China.
⁴ Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China.

Abstract

Obtaining information on the genetic diversity and population structure of germplasm facilitates its use in wheat breeding programs. Recently, with the development of next-generation sequencing technology, genotyping-by-sequencing (GBS) has been used as a high-throughput and cost-effective molecular tool for examination of the genetic diversity of wheat breeding lines. In this study, GBS was used to characterize a population of 180 accessions of common wheat originating from Asia and Europe between the latitudes 30° and 45°N. In total, 24,767 high-quality single-nucleotide polymorphism (SNP) markers were used for analysis of genetic diversity and population structure. The B genome contained the highest number of SNPs, followed by the A and D genomes. The polymorphism information content was in the range of 0.1 to 0.4, with a mean of 0.26. The distribution of SNPs markers on the 21 chromosomes ranged from 243 on chromosome 4D to 2,337 on chromosome 3B. Structure and cluster analyses divided the panel of accessions into two subgroups (G1 and G2). G1 principally consisted of European and partial Asian accessions, and G2 comprised mainly accessions from the Middle East and partial Asia. Molecular analysis of variance showed that the genetic variation was greater within groups (99%) than between groups (1%). Comparison of the two subgroups indicated that G1 and G2 contained a high level of genetic diversity. The genetic diversity of G2 was slightly higher as indicated by the observed heterozygosity (H _o) = 0.23, and unbiased diversity index (uh) = 0.34. The present results will not only help breeders to understand the genetic diversity of wheat germplasm on the Eurasian continent between the latitudes of 30° and 45°N, but also provide valuable information for wheat genetic improvement through introgression of novel genetic variation in this region.

Keywords: common wheat; genetic diversity; genotyping-by-sequencing; population structure; single nucleotide polymorphisms.