Submitted to: Genetica
Publication Type: Peer reviewed journal
Publication Acceptance Date: 11/17/2008
Publication Date: 5/1/2009
Citation: Abdurakhmonov, I.Y., Saha, S., Jenkins, J.N., Buriev, Z.T., Shermatov, S.E., Scheffler, B.E., Pepper, A.E., Yu, J., Kohel, R.J., Abdukarimov, A. 2009. Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm. Genetica. 136:401-417. Interpretive Summary: Linkage disequilibrium (LD)-mapping, using nonrandom associations of loci is a powerful high-resolution mapping tool for complex quantitative traits. This report represents the first in cotton on the association mapping of SSR markers with complex fiber and agronomic traits detecting genome wide LD in Upland cotton. The traditional QTL mapping using bi-parental populations is a low resolution method with few allele coverage, extremely time-consuming, high-risk, and expensive work. We reported here on the extent of genome-wide LD and association mapping of fiber quality traits using 200 microsatellite markers in 335 G. hirsutum germplasm grown in two diverse environments, Uzbekistan and Mexico. At the significance threshold (r2>0.1), a genome-wide average of LD extended up to genetic distance of 25 cM in variety accessions. An average of ~20 SSR markers was associated with each main fiber quality trait using mixed liner model (MLM). The mean genetic distance among all Upland accessions ranged from 0.005-0.26 with an average of 0.12 based on SSR marker analysis. The large number of cotton accessions in our study provided the first insight on fiber quality trait diversity in G. hirsutum germplasm. We detected several SSRs associated with the important fiber quality traits. Also these markers provided a broad scan view of variation associated with important QTL regions of the cotton genome because we used a novel approach of selecting these markers from previously published reports as a prior linked marker with important fiber QTLs.
Technical Abstract: Cotton is the world’s leading cash crop, but it lags behind other major crops for marker-assisted breeding due to limited polymorphisms and a genetic bottleneck through historic domestication. Linkage disequilibrium (LD)-mapping using nonrandom associations of loci in haplotypes is a powerful high-resolution mapping tool for complex quantitative traits. Information on the extent of genome-wide LD is not available in cotton. Here we report the extent of genome-wide LD and association mapping of fiber quality traits using 200 microsatellite markers in 335 G. hirsutum germplasm grown in two diverse environments, Uzbekistan and Mexico. We demonstrated the existence of agronomically useful genetic diversity within selected cotton germplasm. We found the 4-9 % (r2>0.05, p=0.005) of SSR loci pairs revealed a significant LD. At the significance threshold (r2>0.1), a genome-wide average of LD extended up to genetic distance of 25 cM in assayed variety accessions. Genome wide LD at r2>0.2 was reduced to ~5-6 cM, providing evidence of the potential for association mapping of agronomically important traits in cotton. Results suggest that linkage, selection, inbreeding, population stratification, and genetic drift as the potential LD-generating factors in cotton. An average of ~20 SSR markers were associated with each main fiber quality trait using mixed liner model (MLM), considering both kinship (K) and population structure (Q) to minimize spurious associations. LD-based association mapping, using the MLM approach, was found to be effective in cotton, and a number of SSR markers associated with the fiber quality traits reported herein provide insight into understanding environment-specific functions of genes controlling fiber development that increases the effectiveness of cotton marker-assisted breeding programs in similar latitudes.