Interspecific genomic variation can provide a genetic basis for local adaptation and domestication. A series of studies have presented its role of interspecific haplotypes and introgressions in adaptive traits, but few studies have addressed their role in improving agronomic character. Two allotetraploid Gossypium species, Gossypium barbadense (Gb) and G. hirsutum (Gh) originating from the Americas, are cultivated independently. Here, through sequencing and the comparison of one GWAS panel in 229 Gb accessions and two GWAS panels in 491 Gh accessions, we found that most associated loci or functional haplotypes for agronomic traits were highly divergent, representing the strong divergent improvement between Gb and Gh. Using a comprehensive interspecific haplotype map, we revealed that six interspecific introgressions from Gh to Gb were significantly associated with the phenotypic performance of Gb, which could explain 5%–40% of phenotypic variation in yield and fibre qualities. In addition, three introgressions overlapped with six associated loci in Gb, indicating that these introgression regions were under further selection and stabilized during improvement. A single interspecific introgression often possessed yield-increasing potential but decreased fibre qualities, or the opposite, making it difficult to simultaneously improve yield and fibre qualities. Our study not only has proved the importance of interspecific functional haplotypes or introgressions in the divergent improvement of Gb and Gh, but also supports their potential value in further human-mediated hybridization or precision breeding.

中文翻译：

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两个栽培异源四倍体棉花品种的发散改良

种间基因组变异可为当地适应和驯化提供遗传基础。一系列研究提出了种间单倍型和基因渗入在适应性性状中的作用，但很少有研究讨论它们在改善农艺性状方面的作用。两个异源四倍体棉属物种，海岛棉（千兆）和陆地棉（Gh的来自美洲）始发，独立地栽培。在这里，通过测序和比较 229 Gb 种质中的一个 GWAS 面板和 491 Gh 中的两个 GWAS 面板加入后，我们发现农艺性状的大多数相关基因座或功能单倍型高度不同，代表Gb和Gh之间的强烈差异改进。使用全面间单倍型图，我们发现，从六个间渐渗Gh的到千兆均显著用的表型性能相关千兆，这可能在产率和纤维品质解释5％-40表型变异的％。此外，三个基因渗入与Gb 中的六个相关基因座重叠，表明这些基因渗入区域正在进一步选择并在改进过程中稳定下来。单个种间基因渗入通常具有增加产量的潜力，但会降低纤维质量，或相反，难以同时提高产量和纤维质量。我们的研究不仅证明了种间功能单倍型或基因渗入在Gb和Gh的不同改进中的重要性，而且还支持它们在进一步人类介导的杂交或精确育种中的潜在价值。