Summary
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 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.