利用基于全基因组 DArTseq 的 SNP 标记对鹰嘴豆（L.）基因型进行全基因组多样性、群体结构和连锁不平衡分析。
Whole Genome Diversity, Population Structure, and Linkage Disequilibrium Analysis of Chickpea ( L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers.
机构信息
Department of Plant Protection, Varamin-Pishva Branch, Islamic Azad University, Varamin, P.O.Box: 33817-74895, Iran.
Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan P.O. Box: 8415683111, Iran.
出版信息
Genes (Basel). 2019 Sep 4;10(9):676. doi: 10.3390/genes10090676.
Characterization of genetic diversity, population structure, and linkage disequilibrium is a prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes, including advanced "" breeding lines and Iranian landrace "" chickpea genotypes, were genotyped using DArTseq-Based single nucleotide polymorphism (SNP) markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that was covered by SNPs varied from 16,236.36 kbp (LG8) to 67,923.99 kbp (LG5), while LG4 showed a higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6, and LG8 showed higher mean PIC value than average. Unweighted neighbor joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and discriminant analysis of principal component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r ≥ 0.8, while 2961 pairs of markers showed complete LD (r = 1), and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggest the presence of a high genetic diversity among the studied chickpea genotypes. This study also demonstrates the efficiency of DArTseq-based SNP genotyping for large-scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits, such as seed yield, abiotic, and biotic stresses, and therefore can be efficiently used in breeding programs to improve chickpea.
遗传多样性、群体结构和连锁不平衡的特征分析是合理管理育种计划和保护遗传资源的前提。本研究利用 DArTseq 基于的单核苷酸多态性（SNP）标记对 186 份鹰嘴豆基因型进行了基因分型，包括先进的“育种系”和伊朗地方品种“鹰嘴豆基因型”。在 3339 个 SNP 中，选择了 1152 个具有已知染色体位置的标记用于基因组多样性分析。标记的映射数量从 52 个（LG8）到 378 个（LG4）不等，每个连锁群平均有 144 个 SNP。SNP 覆盖的染色体大小从 16236.36 kbp（LG8）到 67923.99 kbp（LG5）不等，而 LG4 显示出更多的 SNP，平均每个 Mbp 有 6.56 个 SNP。SNP 标记的多态信息含量（PIC）值范围为 0.05 至 0.50，平均值为 0.32，而 LG4、LG6 和 LG8 上的标记平均 PIC 值较高。非加权邻接聚类分析和基于贝叶斯的模型群体结构将鹰嘴豆基因型分为四个不同的聚类。主成分分析（PCoA）和主成分判别分析（DAPC）的结果与聚类和群体结构分析一致。连锁不平衡（LD）广泛存在，鹰嘴豆种质的 LD 衰减相对较低。少数标记显示 r≥0.8，而 2961 对标记显示完全 LD（r=1），并且在 LG4 上观察到一个巨大的 LD 块。基因型之间的遗传多样性高且亲缘关系值低表明，研究的鹰嘴豆基因型之间存在较高的遗传多样性。本研究还证明了 DArTseq 基于 SNP 基因分型在鹰嘴豆大规模基因组分析中的效率。提供的基因型标记与不同性状（如种子产量、非生物和生物胁迫）的表型数据结合使用时，对于各种关联图谱研究非常有用，因此可以有效地用于育种计划，以提高鹰嘴豆的产量。
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