Genetic analysis of the transition from wild to domesticated cotton (G. hirsutum L.)

Authors: GROVER, CORRINNE - Iowa State University; YOO, MI-JEONG - University Of Florida; LIN, MENG - Cornell University; MURPHY, MATTHEW - University Of Illinois; HARKER, DAVID - University Of Texas Southwestern Medical Center; BYERS, ROBERT - Brigham Young University; LIPKA, ALEXANDER - University Of Illinois; HU, GUANJING - Iowa State University; YUAN, DAOJUN - Iowa State University; CONOVER, JUSTIN - Iowa State University; Udall, Joshua - Josh; PATERSON, ANDREW - University Of Georgia; GORE, MICHAEL - Cornell University; WENDEL, JONATHAN - Iowa State University

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/5/2019
Publication Date: 2/1/2020
Citation: Grover, C.E., Yoo, M., Lin, M., Murphy, M.D., Harker, D.B., Byers, R.L., Lipka, A.E., Hu, G., Yuan, D., Conover, J., Udall, J.A., Paterson, A.H., Gore, M.A., Wendel, J. 2020. Genetic analysis of the transition from wild to domesticated cotton (G. hirsutum L.). G3, Genes/Genomes/Genetics. 10(2):731-754. https://doi.org/10.1534/g3.119.400909.
DOI: https://doi.org/10.1534/g3.119.400909

Interpretive Summary: This publication contains details regarding the construction of a genetic map of cotton and its association with cotton fiber traits. Cotton fiber traits are often quantitative. Quantitative traits are mapped to the chromosomes using Quantitative Trait Loci (QTL) mapping. The results of this work indicate regions of the cotton genome that control cotton fiber quantitative traits. Results of this work reflect a significant contribution to ongoing efforts by cotton scientists to use modern genetics/genomics techniques to improve cotton productivity by and profitability for U.S. farmers.

Technical Abstract: The evolution and domestication of cotton is of great interest from both economic and evolutionary standpoints. Although many genetic and genomic resources have been generated for cotton, the genetic underpinnings of the transition from wild to domesticated cotton remain poorly known. Here we generated an intraspecific QTL mapping population specifically targeting the domesticated cotton fiber phenotype. We used 465 F2 individuals derived from an intraspecific cross between the wild Gossypium hirsutum var. yucatanense (TX2094) and the elite cultivar G. hirsutum cv. Acala Maxxa, in two environments, to identify 68 QTL associated with phenotypic changes under domestication. These QTL average approximately 46 Mbp in size, and together represent 29% (647 Mbp) of the 2,260 Mbp genome. Although over 70% of QTL were recovered from the A-subgenome, many key fiber QTL were detected in the D-subgenome, which was derived from a species with unspinnable fiber. We found that many QTL are environmentally labile, with only 41% shared between the two environments, indicating that QTL associated with G. hirsutum domestication are genomically clustered but environmentally labile. Possible candidate genes were recovered and discussed in the context of the phenotype. We found some support for the previously noted biased recruitment under domestication of factors from one of the two co-resident genomes of allopolyploid cotton. We conclude that the evolutionary forces that shape intraspecific divergence and domestication in cotton are complex, and that phenotypic transformations likely involved multiple interacting and environmentally responsive factors.