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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (3): 597-607.doi: 10.3724/SP.J.1006.2022.14023

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genome wide analysis of BnAPs gene family in Brassica napus

HUANG Cheng(), LIANG Xiao-Mei, DAI Cheng, WEN Jing, YI Bin, TU Jin-Xing, SHEN Jin-Xiong, FU Ting-Dong, MA Chao-Zhi*()   

  1. National Key Laboratory of Crop Genetic Improvement/National Engineering Research Center of Rapeseed, Huazhong Agricultural University, Wuhan 430070, Hubei, China
  • Received:2021-02-02 Accepted:2021-06-16 Online:2021-07-14 Published:2021-07-14
  • Contact: MA Chao-Zhi E-mail:822075664@qq.com;yuanbeauty@mail.hzau.edu.cn
  • Supported by:
    Key Research and Development Program in Hubei Province(2020BBB061);National Key Research and Development Program of China(2016YFD100803)

Abstract:

Aspartate protease (AP) is one of the four major proteolytic enzymes and plays an important role in protein processing, signal transduction, and stress response. Brassica napus is an important oil crop in China. We identified 154 APs coding genes in Brassica napu by protein homology analysis, which encoded typical, atypical, and nucellar aspartate proteases, respectively. Gene structure analysis showed that most BnAPs genes contained 1-4 exons and the motif distribution of the same type of aspartic protease was similar. Collinearity analysis revealed that there was a large number of homologous genes between Brassica napus and Brassica rape, Brassica oleracea and Arabidopsis thaliana, and about 89% of BnAPs genes came from genome-wide replication events. Transcriptional analysis demonstrated that BnAPs gene family was expressed in all tissues. The stigma of BnAP30.A05.1/ A05.2/C05.1/C05.2, BnAP36.A04/C08, and BnAP39.A06/C03 increased significantly after pollination. Cis-element analysis in the promoter region of BnAPs gene presented that stress-related cis regulatory elements were significantly enriched. We further verify that the relative expression levels of these genes rich in stress-related cis regulatory elements changed significantly after stress (ABA, NaCl, or 4℃), suggesting that these BnAPs genes may be involved in response to stress in Brassica napus. Compared with Arabidopsis homologous genes, about 24% of BnAPs had the same expression pattern as their homologous AtAPs. This study laid a foundation for further understanding the biological function of aspartic protease family in Brassica napus.

Key words: Brassica napus, aspartic protease, collinearity analysis, expression patterns, RT-qPCR

Fig. 1

Phylogenetic relationships of APs proteins in Brassica napus and Arabidopsis thaliana The different colors indicate different subgroups of the APs family members."

Fig. 2

Phylogenetic tree, gene structure, and motif composition analysis of the AP family in Brassica napus"

Fig. 3

Collinearity analysis of BnAPs gene family in Brassica napus and Brassica plants A: the gray lines indicate all synteny blocks in B. napus genome, and the red lines indicate duplicated BnAPs gene pairs. B: the gray line background shows the collinear regions in the genomes of Brassica napus and other plants, and the color line region highlights the collinear APs gene pairs with different species."

Fig. 4

Relative expression pattern of BnAPs in the different tissue at different developmental stages a: the expression patterns of BnAPs gene at five different growth stages (root, stem, leaf, flower, and seed). b: the expression pattern of BnAPs gene during flower development and in stigma before and after pollination. c: the relative expression pattern of BnAP30/36/39 in stigmas before and after pollination. UP: unpollination; AP: after pollination."

Fig. 5

Analysis of co-expression pattern of BnAPs and AtAPs The relative expression patterns of BnAPs and AtAPs at five growth stages (root, stem, leaf, flower, and seed); red and green represent BnAPs and AtAPs, respectively."

Fig. 6

Relative expression patterns of BnAPs under abscisic acid (ABA), NaCl, and 4℃ treatment"

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