Expressed genes and their new alleles identification during fibre elongation reveal the genetic factors underlying improvements of fibre length in cotton

Abstract

Summary Interspecific breeding in cotton takes advantage of genetic recombination among desirable genes from different parental lines. However, the expression new alleles (ENAs) from crossovers within genic regions and their significance in fibre length (FL) improvement are currently not understood. Here, we generated resequencing genomes of 191 interspecific backcross inbred lines derived from CRI36 (Gossypium hirsutum) × Hai7124 (Gossypium barbadense) and 277 dynamic fibre transcriptomes to identify the ENAs and extremely expressed genes (eGenes) potentially influencing FL, and uncovered the dynamic regulatory network of fibre elongation. Of 35 420 eGenes in developing fibres, 10 366 ENAs were identified and preferentially distributed in chromosomes subtelomeric regions. In total, 1056–1255 ENAs showed transgressive expression in fibres at 5–15 dpa (days post‐anthesis) of some BILs, 520 of which were located in FL‐quantitative trait locus (QTLs) and GhFLA9 (recombination allele) was identified with a larger effect for FL than GhFLA9 of CRI36 allele. Using ENAs as a type of markers, we identified three novel FL‐QTLs. Additionally, 456 extremely eGenes were identified that were preferentially distributed in recombination hotspots. Importantly, 34 of them were significantly associated with FL. Gene expression quantitative trait locus analysis identified 1286, 1089 and 1059 eGenes that were colocalized with the FL trait at 5, 10 and 15 dpa, respectively. Finally, we verified the Ghir_D10G011050 gene linked to fibre elongation by the CRISPR‐cas9 system. This study provides the first glimpse into the occurrence, distribution and expression of the developing fibres genes (especially ENAs) in an introgression population, and their possible biological significance in FL.

High‐resolution sequencing of nine elite upland cotton cultivars uncovers genic variations and breeding improvement targets

“…Some of these genes are key genes in the fiber metabolism pathway. For example, fasciclin‐like arabinogalactan protein 9 ( GhFLA9 , Ghicr24_D12G154200 ) is involved in the initial differentiation and elongation of cotton fibers (Huang et al., 2008; Huang et al., 2013) and increased expression of GhFLA9 improved fiber length (FL) (Ma et al., 2022). In this study, a 162‐bp deletion was identified to be associated with the expression of GhFLA9 (Figure S8a), which was located in the promoter region and resulted in a reduced expression of Ghicr24_D12G154200 in 15 DPA fibers (Figure S8b), ultimately leading to a decreased LP (Figure S8c).…”

Analysis of the MIR396 gene family and the role of MIR396b in regulating fiber length in cotton

“…Cotton fiber development is a complex morphological and molecular process comprised of four stages: (1) fiber initiation, (2) elongation, (3) primary and secondary wall thickening, and (4) fiber maturation. The number of fibers per ovule depends on the initiation stage, while the fiber length (FL) and strength are mainly determined by elongation together with primary and secondary wall thickening (Fang et al, 2018; Kim & Triplett, 2001; Li et al, 2009; Ma et al, 2022; Shi et al, 2006; Singh et al, 2009; Tian & Zhang, 2021; Xiao et al, 2019). At the genetic level, cotton fiber initiation and elongation are mainly regulated by genes involved in phytohormone metabolism, including auxin (Guan et al, 2014; Tian & Zhang, 2021; Zhang et al, 2011), gibberellin (Richards et al, 2001; Xiao et al, 2010; Zhang et al, 2011), ethylene (Fang et al, 2018; Shi et al, 2006; Wang et al, 2011), brassinosteroid (Sun et al, 2004; Yang et al, 2014), and cytokinins (Chen et al, 1997; Zhao et al, 2015).…”