Genetic dissection and optimal cross design for early maturity and yield traits in upland cotton (Gossypium hirsutum L.) based on RTM-GWAS

Breeding of early-maturing and high-yield cotton varieties is important for simultaneous promotion of cotton production and multiple-crop systems. The present study used a restricted two-stage multi-locus genome-wide association study (RTM-GWAS) approach to elucidate the genetic basis of major early maturity and yield traits in upland cotton ( Gossypium hirsutum L.), and to determine the optimal cross design. For five target traits (first fruiting branch node, height of the first fruiting branch node, boll number per plant, boll weight, and lint percentage), 139 quantitative trait loci (QTLs) and 67 QTL–environment interactions (QEIs) were detected. Among these, 74 QTLs and 37 QEIs were validated as stable via haplotype and multi-environment phenotypic difference analyses, respectively. QTL-allele matrices were constructed on the basis of stable QTLs. The recombination potential of all 83,028 possible single crosses among 408 parental accessions was predicted. When only single traits were targeted as breeding objectives, the progeny of the top 10 crosses for all traits exhibited high superiority to the high-value parent and the parental population mean. For simultaneous improvement of multiple traits, three strategies were implemented. When early maturity was prioritized, three crosses (A24/A49, A24/A45, and A3/A418) were identified as optimal. When yield was prioritized, four optimal crosses (A420/A268, A420/A259, A420/A241, and A420/A254) were identified. For the strategy balancing early maturity and yield, the screened crosses may provide a reference for balance selection. The results provide novel insights into the genetic architecture of early maturity and yield traits, and support their synergistic improvement via molecular design breeding in cotton.