Pyramiding effects of favorable haplotypes of loci on major fiber yield and quality traits in Upland Cotton (Gossypium hirsutum L.)

Enhancing both fiber yield and quality is crucial in cotton breeding programs. Typically, a negative correlation exists between fiber yield and quality, and the strategy to decouple this relationship remains obscure. In this study, we generated three multi-parent intercross populations, encompassing 2,852 F2:3 lines, which represent fiber yield potential (FY), fiber quality potential (FQ), and a combination of both potentials (FYQ), derived from sixteen diverse Upland cotton cultivars. We utilized twenty-four kompetitive allele specific PCR (KASP) molecular markers, based on previously identified loci associated with fiber quality (FL5/FS1, FL3/FS2, and FL2) and fiber yield (BW1, BW2, and LP1), for genotyping purposes. The pyramiding of favorable haplotypes from three fiber quality-associated loci resulted in an increase exceeding 10% in fiber length (FL5+FL3+FL2+LP1) and in an increase exceeding 17% in fiber strength (FL5+FL3+FL2). Notably, our findings suggest that the combination of FL3+FL2+BW1+LP1 alleles has the potential to disrupt the negative correlation between fiber yield and quality. Lines harboring these alleles simultaneously exhibited an elevated lint percentage (LP), as well as enhanced fiber length and quality. This study offers robust molecular markers for the efficient selection of superior progeny with desired phenotypes in the early stages of cotton breeding. Furthermore, the allelic combination that concurrently improves fiber quality and yield sheds light on for further exploration the molecular basis of breaking unfavorable linkages in crop breeding. [Display omitted] •The successful development of twenty-four KASP molecular markers, based on loci known to influence fiber yield and quality.•Pyramiding of favorable haplotypes from three loci related to fiber quality can significantly improve fiber quality.•The specific allelic combination appears promising in breaking the negative correlation between fiber yield and quality.