Linkage drag associated with introgression of Meloidogyne incognita resistant genes from wild relatives into upland cotton

The Southern root-knot nematode (RKN, Meloidogyne incognita ) is the most economically important pathogen affecting cotton ( Gossypium hirsutum L.) production in the United States and worldwide. While commercial cultivars with high RKN resistance have been available for some time, they are not widely adopted by U.S. producers, possibly due to lower yield potential and fiber quality penalties associated with linkage drag. Resistance to RKN is conferred by two major quantitative trait loci (QTLs), qMi-C11 and qMi-C14 , originated from an obsolete cultivar and wild accession. This study evaluated whether these QTLs negatively impact agronomic and fiber quality traits. Eight resistant experimental lines and two near-isogenic lines carrying the QTLs were evaluated along with their susceptible parents in field trials across two locations over three years. Data collected included yield, fiber quality traits, and nematode population density. No substantial linkage drag was observed for lint yield and fiber quality traits. Near-isogenic lines CH11 and CH14 showed lower lint percentages than the recurrent parent, suggesting a minor linkage drag. However, five experimental lines had lint percentages equivalent to or higher than their donor parent, indicating this negative association can be mitigated through breeding. Overall, the experimental lines exhibited high RKN resistance in both field and greenhouse conditions while maintaining excellent lint yield and fiber quality. The top-performing RKN resistant experimental lines, which combine high yield potential with superior fiber quality, will be publicly released to support in future cotton breeding efforts. • The study investigated whether the RKN resistance QTLs, qMi-C11 and qMi-C14 , negatively impact yield and fiber quality. • Results showed no substantial linkage drag associated with the resistant QTLs for lint yield or fiber quality traits. • Only a reduction in lint percentage was observed in lines carrying resistance QTLs. • RKN resistant lines, with high yield and superior fiber quality, will be valuable in future cotton breeding efforts.