Combination of Next Generation Mapping, Transcriptome and Functional Analyses: A New Strategy to Identify Candidate Genes for Fiber Quality Traits in Upland Cotton

Fiber strength, length, maturity and fineness determine the market value of cotton fibers and the quality of spun yarn. Cotton fiber strength has been recognized as a critical quality attribute in the modern textile industry. Molecular mechanisms responsible for regulating fiber strength still remain unclear. Gossypium hirsutum near isogenic lines (NILs), MD52ne and MD90ne showing variations in fiber strength provide an opportunity for uncovering the molecular and genetic basis of superior fiber quality. Comparative transcriptome analyses of the NILs showed that the superior bundle strength of MD52ne fibers was potentially related to two signaling pathways: one is ethylene and the interconnected phytohormonal pathways that are involved in cotton fiber elongation, and the other is receptor-like kinases (RLKs) signaling pathways that are involved in maintaining cell wall integrity. A group of 27 new SNP markers generated from mapping-by-sequencing (MBS) were placed in QTL regions to improve existing maps. The QTL regions contained multiple significantly differentially expressed RLKs. SNPs that result in non-synonymous substitutions to amino acid sequences of annotated genes were identified within these differentially expressed genes, and mapped. Taken together, mapping, transcriptome and amino acid mutation analysis indicate that RLK genes that were suggested to mediate a coordination of cell elongation and SCW biosynthesis in other plants likely are candidate genes for regulating cotton fiber cell wall assembly and strength. MBS along with transcriptome analysis demonstrated a powerful strategy to elucidate candidate genes for the QTLs that control complex traits in a complex genome like tetraploid upland cotton.