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

Authors: AMARASINGHE, PRABHA - Oak Ridge National Laboratory; PINNIKA, GANESH - Oak Ridge National Laboratory; Thyssen, Gregory; Naoumkina, Marina; Fang, David; Florane, Christopher; Li, Ping; JENKINS, JOHNIE - Retired ARS Employee; McCarty Jr, Jack; Zeng, Linghe; Campbell, Benjamin; Delhom, Christopher; JONES, DON - Cotton, Inc; Kim, Hee

Submitted to: Industrial Crops and Products
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/21/2026
Publication Date: 6/23/2026
Citation: Amarasinghe, P., Pinnika, G., Thyssen, G.N., Naoumkina, M.A., Fang, D.D., Florane, C.B., Li, P., Jenkins, J.N., Mccarty Jr, J.C., Zeng, L., Campbell, B.T., Delhom, C.D., Jones, D.J., Kim, H.J. 2026. Genome-wide association studies of single-fiber phenotypes uncover distinct genetic bases for fiber and seed coat neps that lower cotton quality and value. Industrial Crops and Products. 249. Article 123766. Genome-wide association studies of single-fiber phenotypes uncover.
DOI: https://doi.org/10.1016/j.indcrop.2026.123766

Interpretive Summary: Cotton quality is often reduced by two types of tiny, tangled knots: fiber neps, which are entangled fibers, and seed coat neps, which are seed coat fragments associated with fibers. These defects make cotton less valuable and harder to turn into high-quality clothing. Even though the textile industry struggles with these knots, scientists haven't fully understood why some cotton plants grow them more than others. To solve this, phenotypes and genotypes were studied from a massive group of 550 different cotton varieties grown in three different environments. The study discovered that fiber neps and seed coat neps indeed have different biological blueprints and react differently to the environment, meaning they are two separate problems. The study also presented how cotton fiber quality is reduced while factories try to mechanically brush or pull these knots out. By using advanced DNA testing, the team successfully mapped out the specific locations on the cotton’s chromosomes that control these knots. As results, the study identified candidate genes that affect how the fiber matures and how strong the seed coat are. This discoveries help cotton industry reducing knots while maintaining fiber quality and ultimately leading to better clothes and less waste in the future.

Technical Abstract: 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 environment 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.