Mapping of cotton fiber length and strength quantitative trait loci using microsatellites

There is a need to improve fiber characteristics of upland (Gossypium hirsutum L.) cotton cultivars to meet market and textile demands. Polymorphic microsatellite markers, derived from several sources, were identified and used to map chromosomal regions, genes and quantitative trait loci (QTLs), that influence cotton fiber length and strength characteristics. Microsatellites (350) derived from three separate sources provided 88 polymorphic loci for development of a linkage map for QTL analysis. In addition, three cleaved amplified polymorphic sequence (CAPS) markers were incorporated. A segregating F₂ population consisting of 98 individuals derived from the cross of G. hirsutum cv Tamcot SP37 × G. barbadense cv Pima S-7 were phenotyped for fiber length and strength utilizing individual instruments. The F₂ distribution of both traits indicated polygenic inheritance. Single-point analysis identified 13 markers strongly associated with fiber length with four of these being assigned to chromosomes 26 and 27. Twelve of these markers attributed increased fiber length to Pima S-7. The phytochrome A (PHYA1) CAPS marker exhibited the strongest linkage (p < .00001) to fiber length accounting for 20% of the observed variation in fiber length and a significant QTL (LOD 4) was identified on linkage group 18 following QTL analysis. A second QTL was identified on chromosome 25. CM13, located on chromosome 25, was linked to a fiber length QTL. This accounted for 10% of the variation in fiber length and attributed the positive allele to Tamcot SP37. Eleven markers had significant linkage associations to fiber strength where four were assigned to chromosomes 10s, 20, and 26. PHYA1 was also associated with fiber strength. Two markers, CM30 and CM27, contributed increased fiber strength alleles from TamCot SP37 with the rest associated with positive alleles from Pima S-7. The PHYA1 CAPS marker significantly influences fiber length characteristics and will be useful for marker-assisted selection (MAS). Microsatellites identified in this study will provide a useful base from which additional markers can be identified, and will aid cotton breeders in moving desirable alleles related to fiber quality into elite cotton cultivars.