Dynamic Expression Analysis and Introgressive Gene Identification of Fiber Length Using Chromosome Segment Substitution Lines from G. hirsutum �G. barbadense

Abstract

Fiber length is a critical trait that principally determines cotton spinning quality, while Upland cotton as the most widely cultivated Gossypium species around the world subjects to the relatively ordinary fiber performance. Chromosome segment substitution lines (CSSLs) have been introduced in cotton breeding to take full advantages of superior fiber quality and high yield from Sea Island and Upland cotton, respectively, which serve as ideal materials for elucidating the genetic mechanism of complex quantitative traits. Here, three CSSLs derived from CCRI45 (G. hirsutum) × Hai1 (G. barbadense), two superior (MBI7561 and MBI7747) and one (MBI7285) with ordinary fiber-quality, were subjected to transcriptome sequencing during fiber elongation together with their recurrent parent CCRI45, and 471.425 million clean reads were obtained with 91.47% average Q30 and 45.23% mean GC content. In total, 5,673 differentially expressed genes (DEGs) were identified from multi-sample comparisons, which were mainly involved in the oxidation-reduction process, protein phosphorylation, regulation of transcription, DNA template, and carbohydrate metabolic process. Eight temporal expression patterns were monitored on the DEGs of different lines, of which the significantly enriched profile revealed higher similarities between two superior CSSLs or the ordinary CSSL and CCRI45 with respect to fiber performance. Based on the intersection between the predicted introgressive genes from RNAseq data and the published gene information from the G. barbadense genome, 1,535 introgressive genes were identified in three CSSLs. Further analysis of the three common introgressive sections in superior CSSLs revealed eight candidate genes that were identified to be involved in fiber development, namely, O-fucosyltransferase family protein (GB_A02G0240), glutamine synthetase 2 (GB_A02G0272), Ankyrin repeat family protein (GB_A02G0264), beta-6 tubulin (GB_D03G1742), WRKY DNA-binding protein 2 (GB_D03G1655), quinolinate synthase (GB_D07G0623), nuclear factor Y, subunit B13 (GB_D07G0631), and leucine-rich repeat transmembrane protein kinase (GB_D07G0797). Our results provide novel insights into the mechanism underlying fiber formation and lay a solid foundation for further high-efficiency determination of candidate genes by combining RNA-seq data and pivotal chromosome regions.