Mulugeta Behailu, Ortiz Rodomiro, Geleta Mulatu, Hailesilassie Teklehaimanot, Hammenhag Cecilia, Hailu Faris, Tesfaye Kassahun
Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia.
Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
Front Plant Sci. 2023 Jul 20;14:1192356. doi: 10.3389/fpls.2023.1192356. eCollection 2023.
Yanyang Liu, Henan Academy of Agricultural Sciences (HNAAS), China; Landraces are an important genetic source for transferring valuable novel genes and alleles required to enhance genetic variation. Therefore, information on the gene pool's genetic diversity and population structure is essential for the conservation and sustainable use of durum wheat genetic resources. Hence, the aim of this study was to assess genetic diversity, population structure, and linkage disequilibrium, as well as to identify regions with selection signature. Five hundred (500) individuals representing 46 landraces, along with 28 cultivars were evaluated using the Illumina Infinium 25K wheat SNP array, resulting in 8,178 SNPs for further analysis. Gene diversity (GD) and the polymorphic information content (PIC) ranged from 0.13-0.50 and 0.12-0.38, with mean GD and PIC values of 0.34 and 0.27, respectively. Linkage disequilibrium (LD) revealed 353,600 pairs of significant SNPs at a cut-off ( > 0.20, < 0.01), with an average of 0.21 for marker pairs. The nucleotide diversity (π) and Tajima's D (TD) per chromosome for the populations ranged from 0.29-0.36 and 3.46-5.06, respectively, with genome level, mean π values of 0.33 and TD values of 4.43. Genomic scan using the outlier test revealed 85 loci under selection signatures, with 65 loci under balancing selection and 17 under directional selection. Putative candidate genes co-localized with regions exhibiting strong selection signatures were associated with grain yield, plant height, host plant resistance to pathogens, heading date, grain quality, and phenolic content. The Bayesian Model (STRUCTURE) and distance-based (principal coordinate analysis, PCoA, and unweighted pair group method with arithmetic mean, UPGMA) methods grouped the genotypes into five subpopulations, where landraces from geographically non-adjoining environments were clustered in the same cluster. This research provides further insights into population structure and genetic relationships in a diverse set of durum wheat germplasm, which could be further used in wheat breeding programs to address production challenges sustainably.
刘艳阳，中国河南农业科学院；地方品种是转移增强遗传变异所需的有价值新基因和等位基因的重要遗传来源。因此，关于基因库遗传多样性和群体结构的信息对于硬粒小麦遗传资源的保护和可持续利用至关重要。因此，本研究的目的是评估遗传多样性、群体结构和连锁不平衡，以及识别具有选择特征的区域。使用Illumina Infinium 25K小麦SNP芯片对代表46个地方品种的500个个体以及28个品种进行了评估，共获得8178个SNP用于进一步分析。基因多样性（GD）和多态信息含量（PIC）范围分别为0.13 - 0.50和0.12 - 0.38，平均GD和PIC值分别为0.34和0.27。连锁不平衡（LD）在截止值（> 0.20，< 0.01）时揭示了353,600对显著的SNP，标记对的平均值为0.21。群体中每条染色体的核苷酸多样性（π）和 Tajima's D（TD）范围分别为0.29 - 0.36和3.46 - 5.06，基因组水平的平均π值为0.33，TD值为4.43。使用异常值检验的基因组扫描揭示了85个处于选择特征下的位点，其中65个位点处于平衡选择下，17个处于定向选择下。与表现出强选择特征的区域共定位的推定候选基因与籽粒产量、株高、寄主植物对病原体的抗性、抽穗期、籽粒品质和酚类含量相关。贝叶斯模型（STRUCTURE）和基于距离的方法（主坐标分析，PCoA，以及算术平均的非加权配对组方法，UPGMA）将基因型分为五个亚群，来自地理上不相邻环境的地方品种聚集在同一亚群中。本研究为不同硬粒小麦种质资源的群体结构和遗传关系提供了进一步的见解，可进一步用于小麦育种计划以可持续地应对生产挑战。
