Allele and transcriptome mining in Gossypium hirsutum reveals variation in candidate genes at genetic loci affecting cotton fiber quality and textile flammability

Authors: Thyssen, Gregory; SMITH, WAYNE - Texas A&M University; Naoumkina, Marina; PINNIKA, GANESH - Oak Ridge National Laboratory; Jenkins, Johnie; McCarty Jr, Jack; Li, Ping; Florane, Christopher; JONES, DON - Cotton, Inc; Fang, David

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/25/2025
Publication Date: 3/10/2025
Citation: Thyssen, G.N., Smith, W., Naoumkina, M.A., Pinnika, G., Jenkins, J.N., Mccarty Jr, J.C., Li, P., Florane, C.B., Jones, D.C., Fang, D.D. 2025. Allele and transcriptome mining in Gossypium hirsutum reveals variation in candidate genes at genetic loci affecting cotton fiber quality and textile flammability. BMC Plant Biology. 25. Article 305. https://doi.org/10.1186/s12870-025-06306-2.
DOI: https://doi.org/10.1186/s12870-025-06306-2

Interpretive Summary: Breeding valuable traits in crop plants requires identifying diversity in the genetics of the plant lines that are likely to affect desirable characteristics. The genetic diversity of historic cultivars of cotton is a reservoir of potentially important genes for crop improvement and genetic research. Diversity in the characteristics of harvested cotton fibers affects their suitability for end-use applications. Varaints of genes have been identified that affect the length, strength, and maturity of cotton fibers which affect the quality and value of the yarn, thread and textile. Natural genetic mechanisms in the plant may also affect the flammability of the produced textiles. Here we show that a combination of allele mining DNA diversity and transcriptome analysis (RNA expression diversity) can identify candidate genes for cotton fiber traits including strength and perhaps flammability. We found novel DNA variants in fiber-expressed gene families in 132 sequenced cotton varieties and identified genes with genotype-specific RNA expression. Among these, we identified new gene variants of genes that we suggest to influence cotton fiber quality. Also we identified potential textile flammability genes that may be useful for plant biologists and cotton breeders. Candidate genes for traits like flame resistance that are likely due to the combination of many small effect QTL can benefit from this multi-mining approach. We provide information about 10,418 of the ~70,000 total cotton fiber expressed and diverse genes in the historic breeding germplasm.

Technical Abstract: Breeding valuable traits in crop plants requires identifying diverse alleles in the germplasm that are likely to affect desirable characteristics. The genetic diversity of historic cultivars of cotton is a reservoir of potentially important genes for crop improvement and genetic research. Diversity in the characteristics of harvested cotton fibers affects their suitability for end-use applications. Candidate loci and genes have been identified that affect the length, strength, and maturity of cotton fibers which affect the quality and value of the yarn, thread and textile. Natural genetic mechanisms in the plant may also affect the flammability of the produced textiles. Here we show that a combination of allele mining and transcriptome analysis can identify candidate genes for cotton fiber traits including strength and perhaps flammability. We found novel DNA variants in fiber-expressed gene families in 132 newly sequenced cotton varieties and identified genes with genotype-specific RNA expression. Among these, we identified novel variation in DNA sequence and RNA expression in genes at major QTL qD04-ELO-WLIM (JGI-Gohir.D04G160000), qA13-MIC (Gohir.A13G157500), qA07-STR (Gohir.A07G191600), supported the candidacy of qD11-UHML-KRP6 (Gohir.D11G197900) and qD13-STR (Gohir.D13G17450), and identified an additional A03-WLIM transcription factor gene (Gohir.A03G182100) and several RNA expression variant candidates of potential flammability genes that may be useful for plant biologists and cotton breeders. Candidate genes for traits like flame resistance that are likely due to the combination of many small effect QTL can benefit from this multi-mining approach. We provide an annotated variant call format (vcf) file with variations at 24,996 loci that are predicted to affect 10,418 cotton fiber genes in the historic breeding germplasm.