National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
Plant J. 2019 Aug;99(3):494-505. doi: 10.1111/tpj.14339. Epub 2019 May 16.
Recombination breaks up ancestral linkage disequilibrium, creates combinations of alleles, affects the efficiency of natural selection, and plays a major role in crop domestication and improvement. However, there is little knowledge regarding the variation in the population-scaled recombination rate in cotton. We constructed recombination maps and characterized the difference in the genomic landscape of the population-scaled recombination rate between Gossypium hirsutum and G. arboreum and sub-genomes based on the 381 sequenced G. hirsutum and 215 G. arboreum accessions. Comparative genomics identified large structural variations and syntenic genes in the recombination regions, suggesting that recombination was related to structural variation and occurred preferentially in the distal chromosomal regions. Correlation analysis indicated that recombination was only slightly affected by geographical distribution and breeding period. A genome-wide association study (GWAS) was performed with 15 agronomic traits using 267 cotton accessions and identified 163 quantitative trait loci (QTL) and an important candidate gene (Ghir_COL2) for early maturity traits. Comparative analysis of recombination and a GWAS revealed that the QTL of fibre quality traits tended to be more common in high-recombination regions than were those of yield and early maturity traits. These results provide insights into the population-scaled recombination landscape, suggesting that recombination contributed to the domestication and improvement of cotton, which provides a useful reference for studying recombination in other species.
重组打破了祖先的连锁不平衡，创造了等位基因的组合，影响了自然选择的效率，在作物驯化和改良中发挥了重要作用。然而，关于棉花群体规模重组率的变异，我们知之甚少。我们构建了重组图谱，并基于 381 个已测序的陆地棉和 215 个亚洲棉的品系，对陆地棉和亚洲棉以及亚基因组之间的群体规模重组率的基因组景观差异进行了特征描述。比较基因组学在重组区域识别到了大量的结构变异和同源基因，表明重组与结构变异有关，并且优先发生在染色体的远端区域。相关性分析表明，重组仅受到地理分布和选育期的轻微影响。对 267 个棉花品系的 15 个农艺性状进行了全基因组关联研究（GWAS），鉴定出 163 个数量性状位点（QTL）和一个早期成熟性状的重要候选基因（Ghir_COL2）。重组和 GWAS 的比较分析表明，纤维品质性状的 QTL 比产量和早期成熟性状的 QTL 更倾向于出现在高重组区域。这些结果为群体规模的重组景观提供了深入的了解，表明重组促进了棉花的驯化和改良，为研究其他物种的重组提供了有用的参考。
