Eltaher Shamseldeen, Sallam Ahmed, Belamkar Vikas, Emara Hamdy A, Nower Ahmed A, Salem Khaled F M, Poland Jesse, Baenziger Peter S
Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States.
Department of Plant Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat, Egypt.
Front Genet. 2018 Mar 12;9:76. doi: 10.3389/fgene.2018.00076. eCollection 2018.
The availability of information on the genetic diversity and population structure in wheat ( L.) breeding lines will help wheat breeders to better use their genetic resources and manage genetic variation in their breeding program. The recent advances in sequencing technology provide the opportunity to identify tens or hundreds of thousands of single nucleotide polymorphism (SNPs) in large genome species (e.g., wheat). These SNPs can be utilized for understanding genetic diversity and performing genome wide association studies (GWAS) for complex traits. In this study, the genetic diversity and population structure were investigated in a set of 230 genotypes (F) derived from various crosses as a prerequisite for GWAS and genomic selection. Genotyping-by-sequencing provided 25,566 high-quality SNPs. The polymorphism information content (PIC) across chromosomes ranged from 0.09 to 0.37 with an average of 0.23. The distribution of SNPs markers on the 21 chromosomes ranged from 319 on chromosome 3D to 2,370 on chromosome 3B. The analysis of population structure revealed three subpopulations (G1, G2, and G3). Analysis of molecular variance identified 8% variance among and 92% within subpopulations. Of the three subpopulations, G2 had the highest level of genetic diversity based on three genetic diversity indices: Shannon's information index () = 0.494, diversity index () = 0.328 and unbiased diversity index (uh) = 0.331, while G3 had lowest level of genetic diversity ( = 0.348, = 0.226 and uh = 0.236). This high genetic diversity identified among the subpopulations can be used to develop new wheat cultivars.
了解小麦（L.）育种系的遗传多样性和群体结构信息，将有助于小麦育种者更好地利用其遗传资源，并在育种计划中管理遗传变异。测序技术的最新进展为在大型基因组物种（如小麦）中鉴定数万或数十万个单核苷酸多态性（SNP）提供了机会。这些SNP可用于了解遗传多样性，并对复杂性状进行全基因组关联研究（GWAS）。在本研究中，作为GWAS和基因组选择的前提条件，对一组来自不同杂交组合的230个基因型（F）的遗传多样性和群体结构进行了研究。简化基因组测序提供了25,566个高质量SNP。各染色体上的多态性信息含量（PIC）范围为0.09至0.37，平均为0.23。SNP标记在21条染色体上的分布范围从3D染色体上的319个到3B染色体上的2,370个。群体结构分析揭示了三个亚群（G1、G2和G3）。分子方差分析确定亚群间方差为8%，亚群内方差为92%。在这三个亚群中，基于三个遗传多样性指数，G2具有最高水平的遗传多样性：香农信息指数（）= 0.494，多样性指数（）= 0.328，无偏多样性指数（uh）= 0.331，而G3的遗传多样性水平最低（ = 0.348， = 0.226，uh = 0.236）。在亚群间鉴定出的这种高遗传多样性可用于培育新的小麦品种。
