Genome-wide identification and comparative analysis of CLE family in rapeseed and its diploid progenitors

• Published in: Frontiers in plant science Vol. 13; p. 998082
• Main Authors: Xie, Meili, Zhao, Chuanji, Song, Min, Xiang, Yang, Tong, Chaobo
• Format: Journal Article
• Language: English
• Published: Frontiers Media S.A 20.10.2022
• Subjects: association mapping analysis; Brassica napus; CLE peptide; diploid progenitor; expression pattern; orthologous pairs; Plant Science
• ISSN: 1664-462X; 1664-462X
• DOI: 10.3389/fpls.2022.998082

Crop genomics and breeding CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) proteins belong to a small peptide family in plants. During plant development, CLE gene family members play a pivotal role in regulating cell-to-cell communication and stem cell maintenance. However, the evolutionary process and functional importance of CLE s are unclear in Brassicaceae. In this study, a total of 70 BnCLE s were identified in Brassica napus (2n = 4x = 38, A n C n ): 32 from the A n subgenome, 36 from the C n subgenome, and 2 from the unanchored subgenome. Meanwhile, 29 BrCLE and 32 BoCLE genes were explored in Brassica rapa (2n = 2x = 20, A r ) and Brassica oleracea (2n = 2x = 18, C o ). Phylogenetic analysis revealed that 163 CLE s derived from three Brassica species and Arabidopsis thaliana can be divided into seven subfamilies. Homology and synteny analyses indicated whole-genome triplication (WGT) and segmental duplication may be the major contributors to the expansion of CLE family. In addition, RNA-seq and qPCR analysis indicated that 19 and 16 BnCLE s were more highly expressed in immature seeds and roots than in other tissues. Some CLE gene pairs exhibited different expression patterns in the same tissue, which indicated possible functional divergence. Furthermore, genetic variations and regional association mapping analysis indicated that 12 BnCLE s were potential genes for regulating important agronomic traits. This study provided valuable information to understand the molecular evolution and biological function of CLE s in B. napus and its diploid progenitors, which will be helpful for genetic improvement of high-yield breeding in B. napus .