Genomic loci associated with leaf abscission contribute to machine picking and environmental adaptability in upland cotton (Gossypium hirsutum L.)

•The fundamental phenotypic variations of defoliation traits among 383 cotton accessions were revealed.•The defoliants had little penalty on yield and fiber quality.•Two significantly associated loci were dissected, and key candidate genes, GhLRR and GhCYCD3;1, were clarified.•The combining of two favorable haplotypes improved sensitivity to defoliant.•The favorable haplotype frequency was generally increased in high latitudes in China for adaptation to the local environment.