Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium

Authors: Yurchenko, Olga; PARK, SUNJUNG - University Of North Texas; ILUT, DAN - Cornell University; Inmon, Jay; Millhollon, Jonathan; LEICHTY, ZACH - Brigham Young University; PAGE, JUSTIN - Brigham Young University; JENKS, MATTHEW - West Virginia University; CHAPMAN, KENT - University Of North Texas; UDALL, JOSHUA - Brigham Young University; GORE, MICHAEL - Cornell University; Dyer, John

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/28/2014
Publication Date: 11/18/2014
Publication URL: http://handle.nal.usda.gov/10113/59984
Citation: Yurchenko, O., Park, S., Ilut, D., Inmon, J.J., Millhollon, J.C., Leichty, Z., Page, J.T., Jenks, M.A., Chapman, K.D., Udall, J.A., Gore, M.A., Dyer, J.M. 2014. Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium. Biomed Central (BMC) Plant Biology. 14:312-315. doi: 10.1186/s12870-014-0312-5.

Interpretive Summary: In the US, upland cotton is planted at various times throughout the year, and the beginning and end of the growing seasons often include sub-optimal growth temperatures and environmental conditions. For instance, heat and drought can cause significant reductions in crop yield during the latter parts of the growing season. In addition, exposure of cotton seedlings to sudden episodes of cold temperature during the early parts of the growing season can also significantly reduce crop yields. Development of upland cotton varieties with improved tolerance to temperature-related abiotic stress could significantly impact the cotton industry. In this manuscript, ARS scientists, in collaboration with scientists at the University of North Texas, Cornell University, Brigham Young University, and West Virginia University, identified and characterized a large gene family in cotton that is responsible for production of omega-3 fatty acids. Omega-3 fatty acids are involved in both heat and drought adaptation as well as development of chilling tolerance in plants, and knowledge of this gene family in cotton provides key insight to the genes that underlie these processes in commercially important varieties. Notably, a single cotton gene was identified whose expression was upregulated during both drought and cold temperature response. This information will underpin future efforts to develop abiotic stress tolerant cotton germplasm using molecular breeding approaches.

Technical Abstract: Background The majority of commercial cotton varieties planted worldwide are derived from Gossypium hirsutum, which is a naturally occurring allotetraploid produced by interspecific hybridization of A- and D-genome diploid progenitor species. While most cotton species are adapted to warm, semi-arid tropical and subtropical regions, and thus perform well in these geographical areas, cotton seedlings are sensitive to cold temperature, which can significantly reduce crop yields. One of the common biochemical responses of plants to cold temperatures is an increase in omega-3 fatty acids, which protects cellular function by maintaining membrane integrity. The purpose of our study was to identify and characterize the omega-3 fatty acid desaturase (FAD) gene family in G. hirsutum, with an emphasis on identifying omega-3 FADs involved in cold temperature adaptation. Results Eleven omega-3 FAD genes were identified in G. hirsutum, and characterization of the gene family in extant A and D diploid species (G. herbaceum and G. raimondii, respectively) allowed for unambiguous genome assignment of all homoeologs in tetraploid G. hirsutum. The omega-3 FAD family of cotton includes five distinct genes, two of which encode endoplasmic reticulum-type enzymes (FAD3-1 and FAD3-2) and three that encode chloroplast-type enzymes (FAD7/8-1, FAD7/8-2, and FAD7/8-3). The FAD3-2 gene was duplicated in the A genome progenitor species after the evolutionary split from the D progenitor, but before the interspecific hybridization event that gave rise to modern tetraploid cotton. RNA-seq analysis revealed conserved, gene-specific expression patterns in various organs and cell types and semi-quantitative RT-PCR further revealed that FAD7/8-1 was specifically induced during cold temperature treatment of G. hirsutum seedlings. Conclusions The omega-3 FAD gene family in cotton was characterized at the genome-wide level in three species, showing relatively ancient establishment of the gene family prior to the split of A and D diploid progenitor species. The FAD genes are differentially expressed in various organs and cell types, including fiber, and expression of the FAD7/8-1 gene was induced by drought and cold temperature. Collectively, these data define the genetic and functional genomic properties of this important gene family in cotton and provide a foundation for future efforts to improve cotton abiotic stress tolerance through molecular breeding.