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

Authors: WEST, DALTON - University Of Georgia; LUBBERS, EDWARD - University Of Georgia; WAN, S - University Of Georgia; KHANAL, SAMEER - University Of Georgia; Davis, Richard; JONES, DON - Cotton, Inc; KUMAR, PAWAN - Bayer Cropscience; SINGH, R - University Of Georgia; SUASSUNA, NELSON - Embrapa; PATERSON, ANDREW - University Of Georgia; CHEE, PENG - University Of Georgia

Submitted to: Industrial Crops and Products
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/17/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary: The Southern root-knot nematode (Meloidogyne incognita; RKN) is the most economically important pathogen affecting cotton production in the United States and worldwide. While commercial cultivars with high levels of resistance to RKN have been available for some time, they are not widely adopted by U.S. producers, possibly due to lower yield potential compared to susceptible varieties. Resistance to RKN is conferred by two major sections of genetic code (DNA) known as quantitative trait loci (QTLs), qMi-C11 and qMi-C14, which originate from an obsolete cultivar and wild accession. These resistance loci may introduce deleterious effects when transferred into elite germplasm. The objective of this study was to determine whether qMi-C11 and qMi-C14 are associated with negative effects on agronomic and fiber quality traits. Eight resistant experimental lines and two near-isogenic lines (nearly genetically identical except for the resistance QTLs) carrying these resistance QTLs were compared to their susceptible parents. The results showed no substantial evidence of linkage drag affecting lint yield and fiber quality traits. However, the resistance QTLs may have a slight negative effect on lint percentage, which can be mitigated through breeding efforts. Overall, the experimental lines exhibited high levels of RKN resistance in both field and greenhouse trials 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 future breeding efforts.

Technical Abstract: The Southern root-knot nematode (Meloidogyne incognita RKN) is the most economically important pathogen affecting cotton (Gossypium hirsutum L.) production in the United States and worldwide. While commercial cultivars with high levels of resistance to Southern root-knot nematode have been available for some time, they are not widely adopted by U.S. producers, possibly due to lower yield potential compared to susceptible varieties. Resistance to RKN is conferred by two major quantitative trait loci (QTLs), qMi-C11 and qMi-C14, which originate from an obsolete cultivar and wild accession. These resistant loci may be associated with deleterious effects when introduced into elite germplasm. The objective of this study was to determine whether qMi-C11 and qMi-C14 are associated with negative effects on agronomic and fiber quality traits. Eight resistant experimental lines and two near-isogenic lines carrying these resistance QTLs were compared to their susceptible parents. The results showed no substantial evidence of linkage drag affecting lint yield and fiber quality traits. However, the resistance QTLs may have a slight negative effect on lint percentage, which can be mitigated through breeding efforts. Overall, the experimental lines exhibited high levels of RKN resistance in both field and greenhouse trials 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 future breeding efforts.