Microsatellite markers associated with lint percentage trait in cotton, Gossypium hirsutum

Molecular markers associated with fiber development traits have the potential to play a key role in understanding of cotton fiber development. Seventeen SSRs out of 304 markers tested from MGHES (EST-SSR), JESPR (genomic SSR), and TMB (BAC-derived SSR) collections showed significant linkage associations (using a Kurskal-Wallis non-parametric test) with lint percentage QTL in a set of recombinant inbred cotton lines (RILs) segregating for lint percentage. The permutation test of these potential markers associated with lint percentage QTL(s) determined that 12 SSR markers have stable estimates, exceeding empirically chosen threshold significance values at or above α = 0.01. Interval mapping demonstrated that 9 SSRs with stable critical LOD threshold values at α = 0.01 have significant QTL effect. Multiple QTL-mapping (MQM) revealed that at least, two highly significant fiber development QTLs exist around regions TMB0471 and MGHES–31 (explained about 23–59% of the phenotypic variation of lint percentage) and around markers MGHES–31 and TMB0366 (accounted for 5.4–12.5% phenotypic variation of lint percentage). These markers, in particular fiber-specific EST-SSRs, might be the possible ‘candidate’ loci contributing for fiber development in cotton. BAC-derived SSRs associated with fiber trait are the possible markers that are useful for the identification of physical genomic contigs that contain fiber development genes. Several lint percentage trait associated SSR markers have been located to chromosomes 12, 18, 23, and 26 using deletion analysis in aneuploid chromosome substitution lines. Outcomes of the work may prove useful in understanding and revealing the molecular basis of the fiber development, and the utilization of these markers for development of superior cotton cultivars through marker-assisted selection (MAS) programs. I. Y. Abdurakhmonov and S. Saha contributed equally to the work