The Molecular Mechanisms of Crop Quality: Cloning and Systems Analysis of 474 Genes Controlling Fiber Length in Cotton, Gossypium hirsutum L. and G. barbadense L.

Cotton is one of the most important textile and oil seed crops in the world. Fiber length is one of the most economically valuable quality traits in cotton. We have recently cloned 474 genes controlling fiber length (named GFL) using a newly-developed high-throughput gene and QTL cloning system. The function and effect of each GFL gene were confirmed through replicated field trials, showing that each of them has an effect ranging from 2.64% to 7.92%. Of the 474 GFL genes, 88.6% decreased fiber length while 11.4% increased fiber length, when turned on or up-regulated in the field conditions. The GFL genes are involved in a variety of biochemical reactions, biological processes and metabolic pathways. Systems analysis showed that the 474 GFL genes interact in action, forming an integrated network, and the content of the network varied significantly among cotton lines with different lengths. Twenty of the 474 GFL genes were found to be the key players in the determination of fiber length. It is also shown that the interactions among the GFL genes of the network played paramount roles in the variation of fiber length. Therefore, cotton fiber length is a consequence of the interaction between genetics (genes) and epigenetics (gene x gene interactions). These results, for the first time worldwide, reveal the molecular mechanisms underlying crop quality, using fiber length as a model system, from such a large number of cloned genes controlling the trait and provide knowledge and toolkits enabling gene-based fiber breeding and fiber production in cotton.