Skip to main content
ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Publications at this Location » Publication #394815

Research Project: Advanced Genomic and Bioinformatic Tools for Accelerated Cotton Genetic Improvement

Location: Crop Germplasm Research

Title: The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication

item RAMARAJ, THIRUVARANGAN - Depaul University
item GROVER, CORRINE - Iowa State University
item AZALEA, MENDOZA - Depaul University
item ARICK II, MARK - Mississippi State University
item JARECZEK, JOSEF - Iowa State University
item LEACH, ALEXIS - Iowa State University
item PETERSON, DANIEL - Mississippi State University
item WENDEL, JONATHAN - Iowa State University
item Udall, Joshua - Josh

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/23/2022
Publication Date: 12/1/2022
Citation: Ramaraj, T., Grover, C.E., Azalea, M., Arick II, M.A., Jareczek, J., Leach, A., Peterson, D., Wendel, J.F., Udall, J.A. 2022. The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication. G3, Genes/Genomes/Genetics. 13(2).

Interpretive Summary: This work describes a new genome sequence of diploid African cotton. This cotton species is cultivated in the African continent because of its environmental hardiness, yet it lacks significant fiber quality. The genome sequence provides the building blocks to further investigate the genetic control and development of cotton fiber, as well as identification of genes that are tolerant to abiotic stresses. A genome sequence of the species has been previously published, but it was of a wild accession. This genome sequence is from an old, but popular, cultivar of G. herbaceum. The genome sequence provides the blueprint for further investigations to the evolution and genetics of the cotton genus.

Technical Abstract: Gossypium herbaceum is a species of cotton native to Africa and Asia that is one of the two domesticated diploids. Together with its sister-species G. arboreum, these A-genome taxa represent models of the extinct A-genome donor of modern polyploid cotton, which provide about 95% of cotton grown worldwide. As part of a larger effort to characterize variation and improve resources among diverse diploid and polyploid cotton genomes, we sequenced and assembled the genome of G. herbaceum cultivar (cv) Wagad, representing the first domesticated accession for this species. This chromosome-level genome was generated using a combination of PacBio long-read technology, HiC, and Bionano optical mapping and compared to existing genome sequences in cotton. We compare the genome of this cultivar to the existing genome of wild G. herbaceum subspecies africanum to elucidate changes in the G. herbaceum genome concomitant with domestication, and extend these analyses to gene expression using available RNA-seq. Our results demonstrate the utility of the G. herbaceum cv Wagad genome in understanding domestication in the diploid species, which could inform modern breeding programs.