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Research Project: Molecular Approaches for More Efficient Breeding to Improve Cotton Fiber Quality Traits

Location: Cotton Fiber Bioscience Research

Title: Mapping-by-sequencing of Ligon-lintless-1 (Li1) reveals a cluster of neighboring genes with correlated expression in developing fibers of Upland cotton (Gossypium hirsutum L.)

Author
item Thyssen, Gregory
item Fang, David
item Turley, Rickie
item Florane, Christopher
item Li, Ping
item Naoumkina, Marina

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/11/2015
Publication Date: 5/29/2015
Citation: Thyssen, G.N., Fang, D.D., Turley, R.B., Florane, C.B., Li, P., Naoumkina, M.A. 2015. Mapping-by-sequencing of Ligon-lintless-1 (Li1) reveals a cluster of neighboring genes with correlated expression in developing fibers of Upland cotton (Gossypium hirsutum L.). Journal of Theoretical and Applied Genetics. 128:1703-1712.

Interpretive Summary: The identification of the genes that control fiber elongation and development is important to cotton breeders and will enable the development of superior cotton varieties. The Ligon-lintless-1 (Li1) mutant of cotton (Gossypium hirsutum L.) has been studied as a model for cotton fiber development since its identification in 1929; however, the causative mutation has not yet been identified. We took advantage of the incompletely dominant dwarf phenotype of Li1 plants to identify homozygotes in a mapping population which we bulked and deep sequenced. Although the genome of cultivated cotton has not yet been sequenced, we were able to use next generation sequencing technologies to identify a cluster of sixteen neighboring gene that may be responsible for controlling fiber elongation. Interestingly, nearly all genes at the candidate locus showed a high degree of co-expression. One of the most highly expressed genes at the Li1 locus in wild-type fiber cells is 40-fold under-expressed when fibers initiate in Li1 and is part of the large family of proteins that includes auxin and sugar transporters. Further characterization is required to determine if transport of hormones or carbohydrates is involved in both the dwarf and lintless phenotypes of Li1 plants.

Technical Abstract: The Ligon-lintless-1 (Li1) mutant of cotton (Gossypium hirsutum L.) has been studied as a model for cotton fiber development since its identification in 1929; however, the causative mutation has not been identified yet. Here we report the fine genetic mapping of the mutation to a 255-kb region that contains only 16 annotated genes in the reference Gossypium raimondii genome. We took advantage of the incompletely dominant dwarf vegetative phenotype to identify 100 Li1 and wild-type homozygotes from a mapping population of 2,567 F2 plants, which we bulked and deep sequenced. Since only homozygotes were sequenced, we were able to use a high stringency in SNP calling to rapidly identify the introgressed region and design subgenome-specific SNP markers to test the population. We characterized the expression of all sixteen genes in the resulting genetic interval by RNA sequencing of elongating fibers and by RT-qPCR at seven time points spanning fiber development. Interestingly, nearly all genes at the candidate locus were most highly expressed at the day of anthesis (DOA) and showed a high degree of co-expression. One of the most highly expressed genes at the Li1 locus in wild-type fiber cells is 40-fold under-expressed at DOA in Li1 and is a major facilitator superfamily protein, part of the large family of proteins that includes auxin and sugar transporters. Further characterization is required to determine if transport of hormones or carbohydrates is involved in both the dwarf and lintless phenotypes of Li1 plants.