Abdullaev Alisher A, Salakhutdinov Ilkhom B, Egamberdiev Sharof S, Khurshut Ernest E, Rizaeva Sofiya M, Ulloa Mauricio, Abdurakhmonov Ibrokhim Y
Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan.
Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan.
PLoS One. 2017 Nov 14;12(11):e0188125. doi: 10.1371/journal.pone.0188125. eCollection 2017.
Limited polymorphism and narrow genetic base, due to genetic bottleneck through historic domestication, highlight a need for comprehensive characterization and utilization of existing genetic diversity in cotton germplasm collections. In this study, 288 worldwide Gossypium barbadense L. cotton germplasm accessions were evaluated in two diverse environments (Uzbekistan and USA). These accessions were assessed for genetic diversity, population structure, linkage disequilibrium (LD), and LD-based association mapping (AM) of fiber quality traits using 108 genome-wide simple sequence repeat (SSR) markers. Analyses revealed structured population characteristics and a high level of intra-variability (67.2%) and moderate interpopulation differentiation (32.8%). Eight percent and 4.3% of markers revealed LD in the genome of the G. barbadense at critical values of r2 ≥ 0.1 and r2 ≥ 0.2, respectively. The LD decay was on average 24.8 cM at the threshold of r2 ≥ 0.05. LD retained on average distance of 3.36 cM at the threshold of r2 ≥ 0.1. Based on the phenotypic evaluations in the two diverse environments, 100 marker loci revealed a strong association with major fiber quality traits using mixed linear model (MLM) based association mapping approach. Fourteen marker loci were found to be consistent with previously identified quantitative trait loci (QTLs), and 86 were found to be new unreported marker loci. Our results provide insights into the breeding history and genetic relationship of G. barbadense germplasm and should be helpful for the improvement of cotton cultivars using molecular breeding and omics-based technologies.
由于历史驯化过程中的遗传瓶颈，棉花的多态性有限且遗传基础狭窄，这凸显了全面表征和利用棉花种质资源库中现有遗传多样性的必要性。在本研究中，对288份来自世界各地的海岛棉（Gossypium barbadense L.）种质材料在两个不同环境（乌兹别克斯坦和美国）中进行了评估。使用108个全基因组简单序列重复（SSR）标记，对这些种质材料的遗传多样性、群体结构、连锁不平衡（LD）以及纤维品质性状的基于LD的关联作图（AM）进行了分析。分析揭示了结构化的群体特征、高水平的内部变异性（67.2%）和中等程度的群体间分化（32.8%）。分别有8%和4.3%的标记在海岛棉基因组中r2≥0.1和r2≥0.2的临界值下显示出LD。在r2≥0.05的阈值下，LD衰减平均为24.8厘摩。在r2≥0.1的阈值下，LD平均保留距离为3.36厘摩。基于在两个不同环境中的表型评估，使用基于混合线性模型（MLM）的关联作图方法，100个标记位点与主要纤维品质性状显示出强关联。发现14个标记位点与先前鉴定的数量性状位点（QTL）一致，86个是新的未报道的标记位点。我们的结果为海岛棉种质的育种历史和遗传关系提供了见解，并且应该有助于利用分子育种和基于组学的技术改良棉花品种。
