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

Abstract

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 CDP genes in Brassica napus. 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 BnCDP gene family, and all the duplicated genes subsequently underwent strong purification selection. The promoter region of BnCDPs showed enrichment of cis-regulatory elements associated with development, hormone and stress, as well as transcription factor binding sites, which validates the prediction that BnCDPs are widely involved in plant growth and biotic and abiotic stress responses. The BnCDPs in different subfamilies exhibited obvious differences in expression among 30 developmental tissues/stages of B. napus, implying that BnCDPs may be involved in tissue- and stage-specific developmental processes. Similar trends in expression of most BnCDPs were observed under Sclerotinia sclerotiorum inoculation and four abiotic stresses (dehydration, cold, ABA and salinity), particularly the BnGLPs in subfamily I and III with single cupin_1 domain, revealing that BnCDPs are of great importance in the environmental adaption of B. napus. We then performed a genome-wide association study (GWAS) of 274 B. napus core germplasms on S. sclerotiorum resistance and identified four significantly associated loci harboring five BnGLPs. The expression levels of two candidate genes, BnGLP1.A08 and BnGLP1.C08, were significantly correlated with S. sclerotiorum resistance. Their functional responses to multiple stages of S. sclerotiorum 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 CDP genes.

Identification and characterization of the cupin_1 domain-containing proteins in ma bamboo (Dendrocalamus latiflorus) and their potential role in rhizome sprouting

“…Among them, the bicupins in DlCDP family all belong to the branch VII b, and these members have longer exon lengths (Figure 2). This may be due to the number of cupin_1 domains greatly affects the exon length and motif type of DlCDPs, which was also observed in rapeseed (He et al, 2022). Accordingly, the expression pattern of DlCDPs showed that bicupin member DlCDP49 had a low expression level in well-developed tissues (Figure 7).…”

“…CDP family includes GLP members that contain a single cupin_1 domain, which are related to hormone-mediated development processes ( Murphy and Peer, 2022 ). GLPs have been identified in multiple species ( Davidson et al., 2010 ; Cheng et al., 2014 ; Li et al., 2016 ; Zhang et al., 2022 ; Li et al., 2023 ), and whole CDP family members have also been identified in B. napus ( He et al., 2022 ). In our cognition, the distribution and functional diversity of CDP family in ma bamboo have not been studied.…”

“…It belongs to the cupin superfamily, which harbors one or more cupin_1 domains (Y. He et al., 2022 ). This domain is a conserved structural domain with the capacity to bind metal ions, which contains two conserved motifs of β-strands separated by a less conserved region consisting of another two β-strands with a variable loop in between ( Rocha et al., 2021 ).…”

“…Nevertheless, most studies have not simultaneously identified and characterized bicupins or muticupins that contain two or more cupin_1 domains. Recently, all members of the CDP family in Brassica napus were identified and characterized, and two BnCDPs were found to commonly respond to multiple stresses ( He et al., 2022 ). This laid a foundation for a comprehensive understanding of the functions of the CDP family and set a precedent for further studies on this topic.…”

Characterization and Potential Function Analysis of the SRS Gene Family in Brassica napus

“…Transcriptome data were obtained from the previous studies that included a total of 32 tissues containing bud, callus, leaf, stamen, new pistil, blossomy pistil, wilting pistil, stem, sepal, ovule, 11 time-course seeds and silique walls (0, 4,8,12,16,20,24,28,32,40,48), and five stress conditions (Sclerotinia sclerotiorum (S. sclerotiorum), dehydration, salt, cold, and abscisic acid) [45][46][47]. These data were aligned to the reference genome by software hisat2 with the following parameters: -t -p 40-min-intronlen 20-max-intronlen 20,000-dta [48], and the expression quantity based on the transcripts per kilobase million (TPM) normalization method was calculated by software Stringtie with the setting: -e -B -p 30 -f 0.1 [49].…”