Department of Agronomy, Faculty of Agricultural, Assuit University, Asyut, Egypt.
Department of Agronomy and Horticulture, Plant Science Hall, UNL, Lincoln, NE, USA.
BMC Genomics. 2020 Jun 26;21(1):434. doi: 10.1186/s12864-020-06835-0.
Wheat (Triticum aestivium L.) is an important crop globally which has a complex genome. To identify the parents with useful agronomic characteristics that could be used in the various breeding programs, it is very important to understand the genetic diversity among global wheat genotypes. Also, understanding the genetic diversity is useful in breeding studies such as marker-assisted selection (MAS), genome-wide association studies (GWAS), and genomic selection.
To understand the genetic diversity in wheat, a set of 103 spring wheat genotypes which represented five different continents were used. These genotypes were genotyped using 36,720 genotyping-by-sequencing derived SNPs (GBS-SNPs) which were well distributed across wheat chromosomes. The tested 103-wheat genotypes contained three different subpopulations based on population structure, principle coordinate, and kinship analyses. A significant variation was found within and among the subpopulations based on the AMOVA. Subpopulation 1 was found to be the more diverse subpopulation based on the different allelic patterns (Na, Ne, I, h, and uh). No high linkage disequilibrium was found between the 36,720 SNPs. However, based on the genomic level, D genome was found to have the highest LD compared with the two other genomes A and B. The ratio between the number of significant LD/number of non-significant LD suggested that chromosomes 2D, 5A, and 7B are the highest LD chromosomes in their genomes with a value of 0.08, 0.07, and 0.05, respectively. Based on the LD decay, the D genome was found to be the lowest genome with the highest number of haplotype blocks on chromosome 2D.
The recent study concluded that the 103-spring wheat genotypes and their GBS-SNP markers are very appropriate for GWAS studies and QTL-mapping. The core collection comprises three different subpopulations. Genotypes in subpopulation 1 are the most diverse genotypes and could be used in future breeding programs if they have desired traits. The distribution of LD hotspots across the genome was investigated which provides useful information on the genomic regions that includes interesting genes.
小麦（Triticum aestivum L.）是一种在全球范围内具有重要地位的作物，其基因组十分复杂。为了鉴定具有各种有用农艺性状的亲本，以便在不同的育种计划中使用，了解全球小麦基因型之间的遗传多样性非常重要。此外，了解遗传多样性对于标记辅助选择（MAS）、全基因组关联研究（GWAS）和基因组选择等育种研究也很有用。
为了了解小麦的遗传多样性，使用了代表五个不同大陆的 103 个春小麦基因型。这些基因型使用 36720 个基于测序的基因型（GBS-SNPs）进行基因分型，这些 SNP 均匀分布在小麦染色体上。基于群体结构、主坐标和亲缘关系分析，测试的 103 个小麦基因型包含三个不同的亚群。基于 AMOVA，发现亚群内和亚群间存在显著差异。基于不同等位基因模式（Na、Ne、I、h 和 uh），发现亚群 1 是更具多样性的亚群。在 36720 个 SNP 之间没有发现高连锁不平衡。然而，基于基因组水平，与另外两个基因组 A 和 B 相比，D 基因组具有最高的 LD。显著 LD/非显著 LD 的数量比表明，染色体 2D、5A 和 7B 是其基因组中 LD 最高的染色体，其值分别为 0.08、0.07 和 0.05。基于 LD 衰减，D 基因组是在其染色体 2D 上具有最高数量的单倍型块的最低基因组。
最近的研究表明，103 个春小麦基因型及其 GBS-SNP 标记非常适合 GWAS 研究和 QTL 作图。核心集合由三个不同的亚群组成。亚群 1 中的基因型是最多样化的基因型，如果它们具有所需的性状，可用于未来的育种计划。对基因组中 LD 热点的分布进行了研究，为包含有趣基因的基因组区域提供了有用的信息。
