Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA.
USDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA.
Sci Rep. 2017 Jan 27;7:41285. doi: 10.1038/srep41285.
Use of 10,129 singleton SNPs of known genomic location in tetraploid cotton provided unique opportunities to characterize genome-wide diversity among 440 Gossypium hirsutum and 219 G. barbadense cultivars and landrace accessions of widespread origin. Using the SNPs distributed genome-wide, we examined genetic diversity, haplotype distribution and linkage disequilibrium patterns in the G. hirsutum and G. barbadense genomes to clarify population demographic history. Diversity and identity-by-state analyses have revealed little sharing of alleles between the two cultivated allotetraploid genomes, with a few exceptions that indicated sporadic gene flow. We found a high number of new alleles, representing increased nucleotide diversity, on chromosomes 1 and 2 in cultivated G. hirsutum as compared with low nucleotide diversity on these chromosomes in landrace G. hirsutum. In contrast, G. barbadense chromosomes showed negative Tajima's D on several chromosomes for both cultivated and landrace types, which indicate that speciation of G. barbadense itself, might have occurred with relatively narrow genetic diversity. The presence of conserved linkage disequilibrium (LD) blocks and haplotypes between G. hirsutum and G. barbadense provides strong evidence for comparable patterns of evolution in their domestication processes. Our study illustrates the potential use of population genetic techniques to identify genomic regions for domestication.
利用已知基因组位置的 10129 个单体型 SNP，为广泛起源的 440 个陆地棉和 219 个海岛棉品种和地方品种提供了表征全基因组多样性的独特机会。利用分布在全基因组的 SNP，我们研究了陆地棉和海岛棉基因组中的遗传多样性、单倍型分布和连锁不平衡模式，以阐明种群的历史动态。多样性和等位基因状态分析表明，两个栽培的同源四倍体基因组之间很少有等位基因共享，只有少数例外表明存在零星的基因流。与地方品种陆地棉的低核苷酸多样性相比，我们发现栽培陆地棉的 1 号和 2 号染色体上有大量新的等位基因，代表核苷酸多样性增加。相比之下，陆地棉和地方品种的几个染色体上都出现了负的 Tajima's D，表明海岛棉本身的物种形成可能发生在相对狭窄的遗传多样性中。陆地棉和海岛棉之间存在保守的连锁不平衡（LD）块和单倍型，这为它们在驯化过程中的类似进化模式提供了有力证据。我们的研究说明了利用群体遗传技术鉴定驯化相关基因组区域的潜力。
