Zhou Tong, Wang Ning, Wang Yuan, Zhang Xian-Liang, Li Bao-Guo, Li Wei, Su Jun-Ji, Wang Cai-Xiang, Zhang Ai, Ma Xiong-Feng, Li Zhong-Hu
Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China.
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.
Front Plant Sci. 2022 Apr 15;13:873788. doi: 10.3389/fpls.2022.873788. eCollection 2022.
(upland cotton) is one of the most economically important crops worldwide, which has experienced the long terms of evolution and domestication process from wild species to cultivated accessions. However, nucleotide evolution, domestication selection, and the genetic relationship of cotton species remain largely to be studied. In this study, we used chloroplast genome sequences to determine the evolutionary rate, domestication selection, and genetic relationships of 72 cotton genotypes (36 cultivated cotton accessions, seven semi-wild races of . , and 29 wild species). Evolutionary analysis showed that the cultivated tetraploid cotton genotypes clustered into a single clade, which also formed a larger lineage with the semi-wild races. Substitution rate analysis demonstrated that the rates of nucleotide substitution and indel variation were higher for the wild species than the semi-wild and cultivated tetraploid lineages. Selection pressure analysis showed that the wild species might have experienced greater selection pressure, whereas the cultivated cotton genotypes underwent artificial and domestication selection. Population clustering analysis indicated that the cultivated cotton accessions and semi-wild races have existed the obviously genetic differentiation. The nucleotide diversity was higher in the semi-wild races compared with the cultivated genotypes. In addition, genetic introgression and gene flow occurred between the cultivated tetraploid cotton and semi-wild genotypes, but mainly historical rather than contemporary gene flow. These results provide novel molecular mechanisms insights into the evolution and domestication of economically important crop cotton species.
陆地棉是全球经济上最重要的作物之一，它经历了从野生种到栽培品种的长期进化和驯化过程。然而，棉花物种的核苷酸进化、驯化选择和遗传关系在很大程度上仍有待研究。在本研究中，我们使用叶绿体基因组序列来确定72个棉花基因型（36个栽培棉品种、7个半野生棉种和29个野生棉种）的进化速率、驯化选择和遗传关系。进化分析表明，栽培四倍体棉花基因型聚为一个单系分支，该分支也与半野生棉种形成一个更大的谱系。替换率分析表明，野生棉种的核苷酸替换率和插入缺失变异率高于半野生棉种和栽培四倍体系谱。选择压力分析表明，野生棉种可能经历了更大的选择压力，而栽培棉花基因型则经历了人工和驯化选择。群体聚类分析表明，栽培棉品种和半野生棉种存在明显的遗传分化。与栽培基因型相比，半野生棉种的核苷酸多样性更高。此外，栽培四倍体棉花和半野生基因型之间发生了基因渐渗和基因流，但主要是历史上的而非当代的基因流。这些结果为经济上重要的作物棉花物种的进化和驯化提供了新的分子机制见解。
