Quantitative trait locus mapping for plant height and branch number in an upland cotton recombinant inbred line with an SNP-based high-density genetic map

Cotton is one of the most important cash crops around the world, providing natural fiber for the textile industry. Agronomic traits play an important role in the mechanized harvesting of cotton. Plant height (PH) and branch number (BN) are two important traits that could affect plant architecture and ultimately, economic yield of cotton. The quantitative trait locus (QTL) for PH and BN across seven environments was identified with a high-density single nucleotide polymorphism map constructed using recombinant inbred lines from upland cotton 0–153 and sGK9708. A total of 68 QTLs for PH (nine stable) and 64 QTLs for BN (eight stable) were identified. Among these stable QTLs, three (two for PH and one for BN) have been identified in previous studies. Four hundred genes for PH and 624 genes for BN were located on the confidence intervals of these stable QTLs. Among them, 134 for PH and 224 for BN were expressed in at least one tissue of root, stem and leaf. Based on the annotation information, expression pattern and the function validated on the other species, ten genes (six for PH and four for BN) could be considered as potential candidate genes. These results could contribute to understanding the mechanism of PH and branch formation, and to improving the method of cotton breeding for molecular marker-assisted selection.