Genome-wide identification of the pectate lyase (PEL) gene family in Malvaceae and their contribution to cotton fiber quality

Abstract

Pectin is a major constituent of the plant cell wall. Pectate lyase (PEL, EC 4.2.2.2) use anti-β-elimination chemistry to cleave the α-1,4 glycosidic linkage in the homogalacturonan region of pectin. However, there is limited information available on the comprehensive and evolutionary analysis of PELs in the Malvaceae. In this study, we identified 597 PEL genes from 10 Malvaceae species. Phylogenetic and motif analyses revealed that PELs are classified into six subfamilies: Clade I, II, III, IV, Va, and Vb. The two largest subfamilies Clade I and II contained 237 and 222 PEL members, respectively. Members of Clade Va and Vb only contained four or five motifs, much less than other subfamilies. Gene duplication analysis showed that segmental duplication played a crucial role in the expansion of the PEL gene family in Gossypium species. The PELs from Clade I, IV, Va, and Vb were expressed during the fiber elongation stage, but nearly all PEL genes from Clade II and III showed no expression in all of the investigated fiber developmental stages. We further performed single-gene haplotype association analysis in 2001 G. hirsutum accessions and 229 G. barbadense accessions. Interestingly, 14 PELs were significantly associated with fiber length and strength traits in G. barbadense with superior fiber quality, while only 8 GhPEL genes were identified to be significantly associated with fiber quality traits in G. hirsutum. Our findings provide important information for further evolutionary and functional research of the PEL gene family and their potential utilization value for fiber quality improvement in cotton.