Genome-wide identification and comparative analysis of CLE family in rapeseed and its diploid progenitors
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...
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Published in | Frontiers in plant science Vol. 13; p. 998082 |
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Main Authors | , , , , |
Format | Journal Article |
Language | English |
Published |
Frontiers Media S.A
20.10.2022
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Subjects | |
Online Access | Get full text |
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Summary: | 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
. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 This article was submitted to Functional and Applied Plant Genomics, a section of the journal Frontiers in Plant Science Reviewed by: Kumar Paritosh, University of Delhi, India; Yinbo Ma, Yangzhou University, China Edited by: Xiangshu Dong, Yunnan University, China These authors have contributed equally to this work |
ISSN: | 1664-462X 1664-462X |
DOI: | 10.3389/fpls.2022.998082 |