Transcript profiling by microarray and marker analysis of the short cotton (Gossypium hirsutum L.) fiber mutant Ligon lintless-1 (Li1)

Authors: Gilbert, Matthew; Turley, Rickie; Kim, Hee-Jin; Li, Ping; Thyssen, Gregory; TANG, YUHONG - Samuel Roberts Noble Foundation, Inc; Delhom, Christopher - Chris; Naoumkina, Marina; Fang, David

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/12/2013
Publication Date: 6/16/2013
Publication URL: http://handle.nal.usda.gov/10113/57005
Citation: Gilbert, M.K., Turley, R.B., Kim, H.J., Li, P., Thyssen, G.N., Tang, Y., Delhom, C.D., Naoumkina, M.A., Fang, D.D. 2013. Transcript profiling by microarray and marker analysis of the short cotton (Gossypium hirsutum L.) fiber mutant Ligon lintless-1 (Li1). Biomed Central (BMC) Genomics. 14:403.

Interpretive Summary: Cotton fiber length is very important to the quality of textiles. Understanding the genetics and physiology of cotton fiber length development can provide valuable tools to the cotton industry by targeting specific genes or other molecules responsible for fiber elongation. Ligon Lintless-1 (Li1) is a cotton mutant which has very short fibers (< 6mm) at maturity. This presents an excellent model system for studying the molecular and cellular processes involved with cotton fiber elongation. In this research, physical and morphological measurements of the Li1 mutant fibers were conducted, including measurement of the cellulose content during development. Microarrays (a chip containing tens of thousands DNA molecules) were used to analyze the gene expression profiles of Li1 mutant and its wild type. The results indicated that Li1 mutation caused severe disruption to key hormonal and other pathways related to fiber development, especially pertaining to the transition stage from elongation to secondary cell wall synthesis. Gene Ontology enrichment analysis identified several key pathways at the transition stage that exhibited altered regulation. Genes involved in ethylene biosynthesis and primary cell wall rearrangement were affected, and a primary cell wall-related cellulose synthase was repressed. Linkage mapping using a population of 2,553 F2 individuals identified DNA markers associated with the Li1 genetic locus on chromosome 22. Linkage mapping in combination with utilizing the diploid G. raimondii genome sequences permitted additional analysis of the region containing the Li1 gene.

Technical Abstract: Cotton fiber length is very important to the quality of textiles. Understanding the genetics and physiology of cotton fiber elongation can provide valuable tools to the cotton industry by targeting genes or other molecules responsible for fiber elongation. Ligon Lintless-1 (Li1) is a monogenic mutant in Upland cotton (Gossypium hirsutum) which exhibits an early cessation of fiber elongation resulting in very short fibers (< 6mm) at maturity. This presents an excellent model system for studying the underlying molecular and cellular processes involved with cotton fiber elongation. Previous reports have characterized Li1 at early cell wall elongation and during later secondary cell wall synthesis, however there has been very limited analysis of the transition period between these developmental time points. Physical and morphological measurements of the Li1 mutant fibers were conducted, including measurement of the cellulose content during development. Affymetrix microarrays were used to analyze transcript profiles at the critical developmental time points of 3 days post anthesis (DPA), the late elongation stage of 12 DPA and the early secondary cell wall synthesis stage of 16 DPA. The results indicated severe disruption to key hormonal and other pathways related to fiber development, especially pertaining to the transition stage from elongation to secondary cell wall synthesis. Gene Ontology enrichment analysis identified several key pathways at the transition stage that exhibited altered regulation. Genes involved in ethylene biosynthesis and primary cell wall rearrangement were affected, and a primary cell wall-related cellulose synthase was transcriptionally repressed. Linkage mapping using a population of 2,553 F2 individuals identified SSR markers associated with the Li1 genetic locus on chromosome 22. Linkage mapping in combination with utilizing the diploid G. raimondii genome sequences permitted additional analysis of the region containing the Li1 gene. The early termination of fiber elongation in the Li1 mutant is likely controlled by an early upstream regulatory factor resulting in the altered regulation of hundreds of downstream genes. Several elongation-related genes that exhibited altered expression profiles in the Li1 mutant were identified. Molecular markers closely associated with the Li1 locus were developed. Results presented here will lay the foundation for further investigation of the genetic and molecular mechanisms of fiber elongation.