Development of Gossypium hirsutum–Gossypium raimondii introgression lines and their use in QTL mapping of agricultural traits

Gossypium raimondii (2n=2x=26, D₅), an untapped wild species, is the putative progenitor of the D-subgenome of G. hirsutum (2n=4x=52, AD₁), an extensively cultivated species. Here, we developed a G. hirsutum (recipient)–G. raimondii (donor) introgression population to exploit the favorable QTLs/genes and mapped potential quantitative trait loci (QTLs) from wild cotton species. The introgression population consisted of 256 lines with an introgression rate of 52.33% for the G. raimondii genome. The introgression segment length range was 0.03–19.12 Mb, with an average of 1.22 Mb. The coverage of total introgression fragments from G. raimondii was 386.98 Mb. Further genome-wide association analysis (Q+K+MLM) and QTL mapping (RSTEP-LRT) identified 59 common QTLs, including 14 stable QTLs and six common QTL (co-QTL) clusters, and one hotspot of micronaire (MIC). The common QTLs for seed index all showed positive additive effects, while the common QTLs for boll weight all had negative additive effects, indicating that the linkage between seed index and boll weight could be broken. QTLs for lint percentage showed positive effects and could be beneficial for improving cotton yield. Most QTLs for fiber quality had negative additive effects, implying these QTLs were domesticated/improved in G. hirsutum. A few fiber quality QTLs showed positive additive effects, so they could be used to improve cotton fiber quality. The introgression lines developed could be useful for molecular marker-assisted breeding and mapping QTLs precisely for mining desirable genes from the wild species G. raimondii. Such genes can improve cultivated cotton in the future through a design-breeding approach.