Genomic analysis of marker-associated fiber development genes in Upland cotton (Gossypium hirsutum L)

Authors: Yu, John; GERVERS, KYLE - Oregon State University

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/1/2019
Publication Date: 4/1/2019
Citation: Yu, J., Gervers, K. 2019. Genomic analysis of marker-associated fiber development genes in Upland cotton (Gossypium hirsutum L). Euphytica. 215:74. https://doi.org/10.1007/s10681-019-2388-3.
DOI: https://doi.org/10.1007/s10681-019-2388-3

Interpretive Summary: Upland cotton is the most widely grown fiber crop in the world. Genetic improvement of this cash crop is needed to meet the demands of the competitive textile industry. Although the cotton fiber is single-celled, its development and growth is controlled by a very complex genetic network that involves large numbers of genes or genetic elements. This study analyzed a sample of several thousand so-called Unigenes in recombination-active regions of the Upland cotton genome. By use of a consensus genetic map and a sequence assembly of this cotton genome that consists of two partially homologous subgenomes, Unigenes responsible for fiber initiation (IN), fiber elongation (EL) and secondary cell wall deposition (SCWD) as well as non-fiber (NF) traits were located to the 26 chromosomes of the two cotton subgenomes. Analysis of predicted coding sequences (CDS) showed that some Unigenes may be specific to individual fiber development stages while others may function across multiple stages. Further studies on the structure and function of such fiber Unigenes in the Upland cotton will provide plant breeders with new knowledge to efficiently exploit genetic variation for the development of cotton cultivars with improved fiber yield and quality.

Technical Abstract: Understanding genetic control of fiber development is essential for cotton improvement. This study analyzed several thousand fiber Unigenes in Upland cotton (Gossypium hirsutum). They included 2,423 Unigenes for fiber initiation (IN), 1,841 for fiber elongation (EL) and 86 for secondary cell wall deposition (SCWD). These Unigenes were located on recombination hotspots between At and Dt subgenomes with nearly equal frequency (51% vs 49%). Sequence analysis with Upland cotton TM-1 genome assembly showed that 477 IN, 464 EL, 20 SCWD and 367 non-fiber (NF) Unigenes intersect with predicted coding sequences (CDS). There were 140 IN, 118 EL and one SCWD Unigenes that do not overlap between individual stages of fiber development. Annotation of top scoring Unigenes with Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated mitochondrial biogenesis for IN Unigene #18205, conversion of PRPP to histidine for IN #25329, and spliceosome pathways for IN #24380. EL Unigene #11669 appeared to be responsible for septum site-determining protein, EL #11916 for vacuolar protein, and EL #17251 for protein trichome birefringence-like 33. One SCWD Unigene #190099 was responsible for legumin A-like protein. In addition, Unigene #03070 overlapped three fiber development stages and involved in fatty acid biosynthesis. Unigenes that shared same genomic positions for all fiber stages are of particular interest as they may have possible pleiotropic function. On the other hand, Unigenes from one fiber development stage that did not share with any other stage may have stage-specific function. The information would be useful for plant breeders to exploit fiber genes in cotton breeding programs.