Large-Scale Cloning and Characterization of Genes Controlling Fiber Length for Deciphering of the Molecular Basis of Fiber Quality and Development of a Gene-Based Breeding System in Cotton

Cotton (Gossypium spp.) is a leading textile crop and one of the most important oilseed crops in the world, generating one hundred billion US dollars annually. However, few genes controlling lint traits that are among the most important ones to cotton have been cloned and characterized to date. Here, we report systems analysis of a large number of genes controlling fiber length that were cloned using a newly-developed genome-wide high-throughput gene and QTL cloning system with a population of 200 F₁₀ recombinant inbred lines (RILs) derived from a cross between G. hirsutum and G. barbadense. We phenotyped eight major fiber quality and fiber yield traits, including fiber length, sequenced the full-length cDNA of all genes expressed in developing fibers, profiled the expressions of all the genes, and sequenced related genomic sequences of the 200 RILs using the next-generation sequencing technology. Integrative analysis of the datasets using the new gene/QTL cloning system has identified 469 genes controlling cotton fiber length. These fiber-length genes were found to be involved in 55 metabolism pathways. Currently, we are studying the molecular basis of fiber length and developing a gene-based breeding system for fiber length breeding. These results provide a deep understanding of the molecular basis of fiber length and toolkits enabling enhanced molecular breeding of fiber length in cotton based on the genotypes, activities, gene/gene interactions and gene/non-gene element interactions of the genes controlling the trait of interest.