Genome-wide association studies of single-fiber phenotypes uncover distinct genetic bases for fiber and seed coat neps that lower cotton quality and value

Fiber neps (FN), composed of entangled fibers, and seed coat neps (SCN), consisting of fiber-entangled seed coat fragments, are critical raw fiber defects that significantly reduce the quality and market value of fibers and downstream textiles. Despite the textile industry's need for solutions, the genetic bases for FN and SCN formation remain poorly understood. This study explored the genetic bases of FN and SCN by analyzing a 550-member multi-parent advanced generation inter-cross (MAGIC) population of upland cotton ( Gossypium hirsutum L.), cultivated under three environmental conditions. By employing both Advanced Fiber Information System (AFIS) single-fiber and High Volume Instrument (HVI) bundle fiber phenotyping, the study revealed that FN and SCN exhibit differential environmental responses and have distinct relationships with a standard fiber trait, suggesting independent biological origins. Furthermore, results demonstrated that post-ginning nep-removal processes cause a substantial decline in overall fiber quality, reinforcing the necessity of genetic-based control strategies. Genome-wide association study (GWAS), utilizing 1,481,252 single nucleotide polymorphisms (SNPs), identified stable genomic loci associated with FN on chromosome (Chr.) D13, and SCN on Chr. A03 and A07. Further functional annotation and expression profiling prioritized candidate genes involved in fiber maturation, seed coat integrity, and mechanical strength within these loci. These results clarify the complex genetic basis of cotton nep formation, providing foundational knowledge essential for causal gene discovery and the development of targeted breeding programs aimed at enhancing cotton fiber quality and production efficiency.