High-resolution mapping of qFL-chr1, a fiber length QTL in cotton, and characterizing its phenotypic effect in a nearly isogenic background

Structural Genomics

poster

Shen, Xinlian; Xu, Peng

Shen, Xinlian

Earlier analysis of a backcross-self mapping population derived from a cross between Gossypium hirsutum and G. barbadense revealed a QTL on chromosome 1 associated with increased fiber length (qFL-chr1), which was confirmed in three independent populations of near-isogenic introgression lines (NIILs). Here, we selected a single NIIL, R01-40-08, to develop a large population segregating for the target region. Twenty-two PCR-based polymorphic markers, which were submitted to genotype 1,672 F2 plants, identified 432 recombinants containing breakpoints across the target region. We performed substitution mapping with 141 informative recombinants to narrow down the position of qFL-chr1 to a 1.0-cM interval between SSR markers MUSS084 and CIR018. To exclude possible mapping deviation due to the Pima S-6 genetic background effect of non-target regions on fiber length, different heterozygous F3 plants carrying a Pima S-6 introgression between NAU3384 and CGR5144 were selected to develop NILs with a single introgression segment in the Tamcott 2111 background. Comparisons of their phenotype differences confirmed that qFL-chr1 is located in a 0.9-cM interval flanked by SSR markers MUSS422 and CIR018. This locus increased fiber length by approximately 1 mm in a pure genetic background. A physical map based on the G. raimondii sequence showed identical linear order with the genetic map around the target region. Gene predication of 2.81-Mb regions between MUSS422 and CGR5144 in G. raimondii suggested several candidate genes for qFL-chr1. Our results will facilitate cloning of the gene underlying this QTL and analyzing the genetic architecture leading to differences in fiber length.