ARS | Publication request: Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm

Submitted to: Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 29, 2008
Publication Date: October 5, 2008
Citation: Abdurakhmonov, I.Y., Kohel, R.J., Yu, J., Pepper, A.E., Abdullaev, A.A., Kushanov, F.N., Salakhutdinov, I.B., Buriev, Z.T., Saha, S., Scheffler, B.E., Jenkins, J.N., Abdukarimov, A. 2008. Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm. Genomics. 92:478-487.

Interpretive Summary: Genetic diversity in cotton germplasm is essential for improvement of this crop. Discovery and localization of quantitatively inherited traits have been a tedious process that involves the hybridization of cotton accessions and generation of segregating populations. This manuscript describes the first experiment that uses molecular markers to assess the cotton genetic diversity and fiber trait association in a new approach that exploits naturally existing variation. Upon an analysis of 285 'exotic' cotton germplasm accessions with 95 simple sequence repeat (SSR) markers, the results indicate the existence of useful genetic diversity within the exotic cotton germplasm collection and the extent of reasonable potential to apply this new method to associate markers with the traits of interest in cotton. In this germplasm set, 11-12% of SSR loci revealed a significant association with the agronomically important traits including fiber quality properties. The report opens the door to more effectively characterize and evaluate large numbers of cotton germplasm accessions for unlocking the genetic potential that is desirable in cotton improvement.

Technical Abstract: The narrow genetic base of cultivated cotton germplasm is hindering the cotton production worldwide. Although potential genetic diversity exists in Gossypium genus, it is largely 'underutilized' due to photoperiodism and the lack of innovative tools to overcome such challenges. The application of linkage disequilibrium (LD)-based association mapping is an alternative powerful molecular tool to dissect and exploit the natural genetic diversity conserved within cotton germplasm collections, greatly accelerating still 'lagging' cotton marker-assisted selection (MAS) programs. However, the extent of genome-wide linkage disequilibrium (LD) has not been determined in cotton. We report the extent of genome-wide LD and association mapping of fiber quality traits by using 95 SSR markers in a total of 285 'exotic' G. hirsutum phenotypically measured in Mexico. We demonstrated the existence of useful genetic diversity within exotic cotton germplasm. In this germplasm set, the 11-12% of SSR loci pairs revealed a significant LD. At the significance threshold (r2>0.1), a genome-wide averages of LD declines within the genetic distance at <10 cM in the landrace stocks germplasm and >30 cM in variety germplasm. Genome-wide LD at r2>0.2 was reduced to ~1-2 cM in the landrace stock germplasm and 6-8 cM in variety germplasm, providing evidence of the potential for association mapping of agronomically important traits in cotton. We observed significant population structure and relatedness in assayed germplasm. Consequently, the application of the mixed liner model (MLM), considering both kinship (K) and population structure (Q) detected between 6% and 13% of SSR markers associated with the main fiber quality traits in cotton. Our results highlight the potential and feasibility of association mapping, accounting the population structure and stratification in cotton germplasm resources. The number of SSR markers associated with fiber quality traits in diverse cotton germplasm, which broadly covered many historic meiotic events, should be useful to effectively exploit potentially new genetic variations using MAS programs.