An EMS-induced mutation in a tetratricopeptide repeat-like superfamily protein gene (Ghir_A12G008870) on chromosome A12 is responsible for the liy short fiber phenotype in cotton

Authors: Fang, David; Naoumkina, Marina; Thyssen, Gregory; Bechere, Efrem; Li, Ping; Florane, Christopher

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/7/2019
Publication Date: 10/17/2020
Publication URL: https://handle.nal.usda.gov/10113/6808414
Citation: Fang, D.D., Naoumkina, M.A., Thyssen, G.N., Bechere, E., Li, P., Florane, C.B. 2020. An EMS-induced mutation in a tetratricopeptide repeat-like superfamily protein gene (Ghir_A12G008870) on chromosome A12 is responsible for the liy short fiber phenotype in cotton. Journal of Theoretical and Applied Genetics. 133(1):271-282. https://doi.org/10.1007/s00122-019-03456-4.
DOI: https://doi.org/10.1007/s00122-019-03456-4

Interpretive Summary: A short fiber mutant was created through treating the cotton seeds with ethyl methanesulfonate (EMS), a chemical with mutagenesis effect. The mutation is controlled by a single recessive locus designated liy. Whole genome sequencing analysis located the liy locus on chromosome A12. Genetic mapping mapped the liy locus within a genomic region of 1.18Mb. In this region, there is only one gene, i.e., Ghir_A12G008870 encoding a tetratricopeptide repeat (TPR)-like superfamily protein, that has a non-synonymous mutation between the liy mutant and its WT. Analysis of a SNP marker representing this gene in the F2 and F3 progeny plants demonstrated its complete linkage with the phenotype. In addition, the mutant allele of this gene is absent in all 384 cotton varieties. Virus-induced gene silencing of the gene Ghir_A12G008870 significantly reduced the fiber length of the WT cotton line MD15. Taken together, our results suggest that the gene Ghir_A12G008870 is involved in the cotton fiber cell elongation process and is a promising candidate gene responsible for the liy short fiber phenotype. Our findings enrich our understanding of the molecular mechanisms of fiber elongation and may facilitate the development of cotton varieties with longer fiber.

Technical Abstract: A short fiber mutant Ligon-lintless-y was created through treating the seeds of the cotton line MD15 with ethyl methanesulfonate (EMS). Genetic analysis indicated that the mutation is controlled by a single recessive locus designated liy. From F2 mapping populations derived from crosses between the mutant and its wild type (WT), we selected 132 short fiber progeny (liy/liy), and made two DNA bulks. We sequenced these DNA bulks along with the two parents of the population. The liy locus was located on chromosome A12. Using multiple F2 populations and F3 progeny plants, we mapped the liy locus within a genomic region of 1.18Mb. In this region, there is only one gene, i.e., Ghir_A12G008870 encoding a tetratricopeptide repeat (TPR)-like superfamily protein, that has a non-synonymous mutation between the liy mutant and its WT. Analysis of a SNP marker representing this gene in the F2 and F3 progeny plants demonstrated its complete linkage with the liy phenotype. We further analyzed this SNP marker in a panel of 384 cotton varieties. The mutant allele is absent in all 384 cotton varieties. RNAseq and RT-qPCR analysis of the gene Ghir_A12G008870 during fiber development showed a significant expression difference between the liy mutant and its WT in developing fiber cells beginning at 12 days post anthesis. Virus-induced gene silencing of the gene Ghir_A12G008870 significantly reduced the fiber length of the WT cotton line MD15. Taken together, our results suggest that the gene Ghir_A12G008870 is involved in the cotton fiber cell elongation process and is a promising candidate gene responsible for the liy short fiber phenotype. Our findings enrich our understanding of the molecular mechanisms of fiber elongation and may facilitate the development of cotton varieties with longer fiber.