Elucidation of sequence polymorphism in fuzzless-seed cotton lines

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

Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/9/2020
Publication Date: 11/3/2020
Citation: Naoumkina, M.A., Thyssen, G.N., Fang, D.D., Li, P., Florane, C.B. 2020. Elucidation of sequence polymorphism in fuzzless-seed cotton lines. Molecular Genetics and Genomics. 296(1):193–206. https://doi.org/10.1007/s00438-020-01736-z.
DOI: https://doi.org/10.1007/s00438-020-01736-z

Interpretive Summary: Most commercially produced cotton cultivars have two types of fibers on the seed coat, short fuzz and long lint. Lint fiber is used in the textile industry, while fuzz is considered an undesirable trait. Both types of fibers are believed to be controlled by the same regulators; however, their mechanisms of actions are still obscure. Cotton fiber mutants provide an excellent system to study the genes that regulate fiber development. Here we described four uncharacterized and three previously reported cotton mutants with fuzzless seed phenotypes. We sequenced whole genomic DNA of seven mutants and wild type varieties and identified multiple changes among the tested genes previously associated with fuzzless phenotype. We have mapped the locus of the causative fuzzless-dominant N1 mutation. Further, we have identified the causative fuzzless-recessive n2 mutations by analyzing the sequence data and previously reported mapping data. We did not detect mutations among the tested genes for the nt4 fuzzless-tufted line that suggests involvement of additional unknown gene(s) in fiber initiation. The key genes and possible mechanisms of fiber differentiation are discussed in this study.

Technical Abstract: Most commercially produced cotton cultivars have two types of fibers on the seed coat, short fuzz and long lint. Lint fiber is used in the textile industry, while fuzz is considered an undesirable trait. Both types of fibers are believed to be controlled by the same regulators; however, their mechanisms of actions are still obscure. Cotton fiber mutants provide an excellent system to study the genes that regulate fiber development. Here we described four uncharacterized and three previously reported cotton mutants with fuzzless seed phenotypes. To evaluate whether or not the genes previously associated with fuzzless seed phenotypes have mutations we sequenced whole genomic DNA of seven mutants and wild type varieties. We identified multiple polymorphic changes among the tested genes. Non-synonymous SNPs in the coding region of the MML3-A gene was common in the six mutant lines tested in this study, showing both dominant and recessive fuzzless phenotypes. We have mapped the locus of the causative N1 mutation downstream of MML3-A using an F2 population that originated from a cross between the dominant fuzzless mutant and a wild type. Further, we have identified the causative n2 mutations by analyzing the sequence data and previously reported mapping data. We did not detect mutations among the tested genes for the nt4 fuzzless-tufted line that suggests involvement of additional unknown gene(s) in fiber initiation. The key genes and possible mechanisms of fiber differentiation are discussed in this study.