Targeted identification of association between cotton fiber quality traits and microsatellite markers

Primitive and exotic accessions of cotton are potential sources of favorable alleles for genetic improvement, enriching diversity in the genetically constricted gene pool of elite cultivars. Three exotic accessions of cotton (MDN101, MDN063 and MDN257), collected from different parts of Central America and converted to day-neutral flowering; and four elite cultivars (PD94042, DES56, PMHS200 and Acala Maxxa) representing the US cotton gene pool were used as parents to create experimental populations. The corresponding F2 and F2:3 progenies of these populations were grown in two successive years (i.e., some in 2011–2012, some in 2012–2013) and phenotypes were scored in both F2 and F2:3 progenies in all 3 years (2011–2012–2013). These populations were screened with 113 polymorphic microsatellite markers selected from “hotspots” for fiber quality quantitative trait loci in the cotton genome and single marker analyses were performed to identify significant associations of the markers with six fiber quality traits. A total of 134 nominal marker-trait associations were identified, among which 15 were significant after Bonferroni correction for multiple comparisons. In 67 of 134 nominal associations and 4 of 15 significant associations, the exotic parents contributed favorable alleles to multiple backgrounds and for multiple traits, in addition to the traits for which they were selected. These results indicate that utilization of exotic and wild accessions of cotton is useful in introducing favorable alleles into the cultivated cotton gene pool for genetic improvement.