QTL mapping and candidate gene identification of lint percentage based on a recombinant inbred line population of upland cotton

Abstract

Lint percentage is a major yield component in cotton breeding programmes. To identify quantitative trait loci (QTLs) and candidate genes related to lint percentage, we used an intraspecific recombinant inbred line population of 137 lines derived from Gossypium hirsutum cv. CCRI36 and G. hirsutum acc. G2005 for QTL mapping of lint percentage. Based on a high-density genetic map and phenotype data collected in four growing environments, we identified a total of 28 QTLs for lint percentage. Three stable QTLs (qLP-At5-2, qLP-Dt7-1 and qLP-Dt7-2) were detected in at least two environments. Two genes (Gh_A05G1584 and Gh_A05G1689) containing nonsynonymous single nucleotide polymorphisms (SNPs) were identified by association analysis using published data. The quantitative real-time PCR results showed that the expression levels of Gh_A05G1584 were higher in cv. CCRI36 than in acc. G2005 during all fibre development stages; Gh_A05G1689 was mainly expressed in 15 and 25 days post-anthesis fibres and its expression level was higher in cv. CCRI36. These results suggest candidate genes for lint percentage and provide molecular information for use in cotton breeding programmes aimed at improving yield.