AUTHOR=He Yizhou , Li Yan , Bai Zetao , Xie Meili , Zuo Rong , Liu Jie , Xia Jing , Cheng Xiaohui , Liu Yueying , Tong Chaobo , Zhang Yuanyuan , Liu Shengyi 

TITLE=Genome-wide identification and functional analysis of cupin_1 domain-containing members involved in the responses to Sclerotinia sclerotiorum and abiotic stress in Brassica napus

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.983786

DOI=10.3389/fpls.2022.983786

ISSN=1664-462X

ABSTRACT=<p>Cupin_1 domain-containing proteins (CDPs) are ubiquitously present in higher plants, which are known to play essential roles in various biological processes. In this study, we carried out genome-wide characterization and systematic investigation of the <italic>CDP</italic> genes in <italic>Brassica napus.</italic> A total of 96 BnCDPs, including 71 germin-like proteins (GLPs; proteins with a single cupin_1 domain) and 25 CDP bicupins (proteins with two cupin_1 domains), were identified and clustered into six distinct subfamilies (I–VI) based on the phylogenic analysis, gene structure and motif distribution. Further analysis indicated that whole-genome duplication (WGD) and segmental duplication are main contributors to the species-specific expansion of the <italic>BnCDP</italic> gene family, and all the duplicated genes subsequently underwent strong purification selection. The promoter region of <italic>BnCDPs</italic> showed enrichment of <italic>cis</italic>-regulatory elements associated with development, hormone and stress, as well as transcription factor binding sites, which validates the prediction that <italic>BnCDPs</italic> are widely involved in plant growth and biotic and abiotic stress responses. The <italic>BnCDPs</italic> in different subfamilies exhibited obvious differences in expression among 30 developmental tissues/stages of <italic>B. napus</italic>, implying that <italic>BnCDP</italic>s may be involved in tissue- and stage-specific developmental processes. Similar trends in expression of most <italic>BnCDPs</italic> were observed under <italic>Sclerotinia sclerotiorum</italic> inoculation and four abiotic stresses (dehydration, cold, ABA and salinity), particularly the <italic>BnGLPs</italic> in subfamily I and III with single cupin_1 domain, revealing that <italic>BnCDPs</italic> are of great importance in the environmental adaption of <italic>B. napus</italic>. We then performed a genome-wide association study (GWAS) of 274 <italic>B. napus</italic> core germplasms on <italic>S. sclerotiorum</italic> resistance and identified four significantly associated loci harboring five <italic>BnGLPs</italic>. The expression levels of two candidate genes, <italic>BnGLP1.A08</italic> and <italic>BnGLP1.C08</italic>, were significantly correlated with <italic>S. sclerotiorum</italic> resistance. Their functional responses to multiple stages of <italic>S. sclerotiorum</italic> inoculation and four abiotic stresses were further examined through qPCR. Overall, this study provides rich resources for research on the function and evolutionary playground of <italic>CDP</italic> genes.</p>