Systems Analysis of 1,090 GSTR Genes Reveals That Epistasis Plays Important Roles in Cotton Fiber Strength

Fiber bundle strength is one of the paramount quality traits in the world’s textile and yarn industry, and stronger fiber tenacity promises better quality yarn and thus final products. Nevertheless, little is known about the molecular mechanisms underlying fiber strength in cotton. Here we report 1,090 genes controlling fiber strength, named as GSTR for Gossypium fiber strength, cloned using a novel high-throughput gene cloning system developed in our laboratory. All of the genes have been validated and their effects on fiber bundle strength have been estimated by regulating their activities in multiple cotton lines. Each of the genes has been shown to have an effect varying from 3.64 – 14.16% on fiber strength. However, 126 (11.56%) of them led to stronger fibers, whereas 964 (88.44%) led to weaker fibers when they were turned on or up-regulated. The GSTR genes encode proteins and enzymes involved in a variety of biochemical reactions, biological processes and metabolic pathways. We show that 1,090 GSTR genes function collaboratively and constitute an integrated co-expression network with 250,202 gene x gene or epistatic interaction edges. Although every GSTR gene was maintained in the network, the interactions of the GSTR genes varied dramatically across different cotton lines and were significantly associated with fiber strength. These results suggest that fiber strength is not only determined by genes, but also largely dependent on the magnitude, composition and number of their epistatic interactions, thus providing a first insight into the molecular mechanisms of fiber strength and enabling toolkits for enhanced cotton breeding.