Transcriptome, Ectopic Expression and Genetic Population Analysis Identify Candidate Genes for Fiber Quality Improvement in Cotton

Abstract

Comparative transcriptome analysis of fiber tissues between <i>Gossypium barbadense</i> and <i>Gossypium hirsutum</i> could reveal the molecular mechanisms underlying high-quality fiber formation and identify candidate genes for fiber quality improvement. In this study, 759 genes were found to be strongly upregulated at the elongation stage in <i>G. barbadense</i>, which showed four distinct expression patterns (I-IV). Among them, the 346 genes of group IV stood out in terms of the potential to promote fiber elongation, in which we finally identified 42 elongation-related candidate genes by comparative transcriptome analysis between <i>G. barbadense</i> and <i>G. hirsutum</i>. Subsequently, we overexpressed <i>GbAAR3</i> and <i>GbTWS1</i>, two of the 42 candidate genes, in <i>Arabidopsis</i> plants and validated their roles in promoting cell elongation. At the secondary cell wall (SCW) biosynthesis stage, 2275 genes were upregulated and exhibited five different expression profiles (I-V) in <i>G. barbadense</i>. We highlighted the critical roles of the 647 genes of group IV in SCW biosynthesis and further picked out 48 SCW biosynthesis-related candidate genes by comparative transcriptome analysis. SNP molecular markers were then successfully developed to distinguish the SCW biosynthesis-related candidate genes from their <i>G. hirsutum</i> orthologs, and the genotyping and phenotyping of a BC₃F₅ population proved their potential in improving fiber strength and micronaire. Our results contribute to the better understanding of the fiber quality differences between <i>G. barbadense</i> and <i>G. hirsutum</i> and provide novel alternative genes for fiber quality improvement.