#$%^&*AU2020100969A420200716.pdf#####ABSTRACT The present invention discloses a method for selecting multi-target trait-associated haplotypes of cotton and use thereof. The method includes the following steps: (1) collecting tender leaves of a plurality of upland cotton materials from a field to extract total DNAs thereof； (2) hybridizing the foregoing DNAs with Illumina Cotton SNP Chips； (3) mapping SNP marker genotypes of the upland cotton materials and genomes thereof, and obtaining distances of linkage disequilibrium decay of 26 chromosomes of upland cotton genomes； (4) obtaining the information on haplotype drafts of upland cotton genomes and tag markers thereof； (5) obtaining SNP markers significantly associated with different phenotypes of target traits of the cotton； and finally obtaining haplotypes associated with a plurality of different traits of the cotton. Further, the haplotypes are used for synergistic improvement of cotton yield, quality, maturity, and disease resistance. The present invention is of significance in creating new, high-yield, high-quality, and multi-resistant cotton breeding materials and cultivating new high-yield, quality, and multi-resistant cotton cultivars.
