Genome-wide analysis of the serine carboxypeptidase-like (SCPL) proteins in Brassica napus L.

The serine carboxypeptidase-like protein (SCPL) family plays a key part in plant growth, development and stress responses. However, the serine carboxypeptidase-like (SCPL) proteins in Brassica napus L. (B. napus) have not been reported yet. Here, we identified a total of 117 putative SCPL genes in B. napus, which were unevenly distributed on all 19 chromosomes and were divided into three groups (carboxypeptidase Ⅰ to Ⅲ) according to their phylogenetic relationships. Synteny and duplication analysis revealed that the SCPL gene family of B. napus was amplified during allopolyploidization, in which the whole genome triplication and dispersed duplication played critical roles. After the separation of Brassica and Arabidopsis lineages, orthologous gene analysis showed that many SCPL genes were lost during the evolutionary process in B. rapa, B. oleracea and B. napus. Subsequently, the analyses of the gene structure, conserved motifs, cis-element and expression patterns showed that the members in the same group were highly conserved. Furthermore, candidate gene based association study suggested the role of BnSCPL52 in controlling seed number per silique, seed weight and silique length and a CAPS marker was developed to distinguish different haplotypes. Our results provide an overview of rapeseed SCPL genes that enable us for further functional research and benefit the marker-assisted breeding in Brassica napus.

Identification of Candidate Genes for Clubroot-Resistance in Brassica oleracea Using Quantitative Trait Loci-Sequencing.

Clubroot caused by Plasmodiophora brassicae is a devastating disease of cabbage (Brassica oleracea). To identify quantitative trait loci (QTLs) for clubroot resistance (CR) in B. oleracea, genomic resequencing was carried out in two sets of extreme pools, group I and group II, which were constructed separately from 110 and 74 F2 cloned lines derived from the cross between clubroot-resistant (R) cabbage "GZ87" (against race 4) and susceptible (S) cabbage "263." Based on the QTL-sequencing (QTL-Seq) analysis of group I and group II, three QTLs (i.e., qCRc7-2, qCRc7-3, and qCRc7-4) were determined on the C07 chromosome. RNA-Seq and qRT-PCR were conducted in the extreme pools of group II before and after inoculation, and two potential candidate genes (i.e., Bol037115 and Bol042270), which exhibiting upregulation after inoculation in the R pool but downregulation in the S pool, were identified from the three QTLs on C07. A functional marker "SWU-OA" was developed from qCRc7-4 on C07, exhibiting ∼95% accuracy in identifying CR in 56 F2 lines. Our study will provide valuable information on resistance genes against P. brassicae and may accelerate the breeding process of B. oleracea with CR.