Integration of NIRS and GWAS identifies GhMYB86 as a potential regulator of cottonseed protein content with pleiotropic effects on fiber strength

Abstract

Abstract Cottonseed is rich in protein and oil, making the improvement of its nutritional quality essential for global food security. In this study, high-accuracy near-infrared spectroscopy (NIRS) models were developed for predicting cottonseed protein and oil content using least absolute shrinkage and selection operator (LASSO) regression, achieving validation R 2 values of 0.969 and 0.972, respectively. Using these models, 249 upland cotton accessions were phenotyped across five environments and subjected to a genome-wide association study (GWAS) based on a 10K liquid-phase SNP array, resulting in the identification of 24 significant loci. A novel stable QTL, qPO-A07-1 , was detected, within which GhMYB86 was prioritized as a candidate gene. This gene exhibited higher expression in high protein varieties during ovule development. Functional validation demonstrated that heterologous overexpression in Arabidopsis thaliana increased seed protein content by 2.61% – 3.34%, whereas expression in Saccharomyces cerevisiae reduced triglyceride content by 30.72% relative to the control. These results demonstrate that GhMYB86 positively regulates protein accumulation while negatively affecting oil content. A kompetitive allele-specific PCR (KASP) marker targeting a promoter A/T polymorphism revealed that the AA allele was associated with higher protein content, lower oil content, and increased fiber strength across both mapping and validation populations. Furthermore, the protein- and fiber strength-favorable allele has undergone positive selection during breeding. This study provides robust phenotyping tools, reliable genetic resources and molecular markers for cottonseed nutritional quality breeding, laying a foundation for the synergistic improvement of both fiber quality and nutritional quality in cotton.

Plant phenotyping relevance

NIRSによる綿実タンパク質・油分の非破壊推定モデルを開発・検証し、多数系統の表現型取得に用いており、植物形質の取得法が実質的な中心要素である。

Code and data availability

The supplied blocks describe NIRS models, GWAS phenotyping of 249 accessions, and supplementary tables (S1–S10), but contain no public deposit, availability statement, or authors' URL for phenotype datasets, spectra, sequencing data, or analysis code. The only URLs mentioned (NCBI Primer-BLAST, SNPway) are generic web-

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