Serine/arginine-rich (SR) proteins are indispensable factors for RNA splicing, and they play important roles in development and abiotic stress responses. However, little information on SR genes in Brassica napus is available. In this study, 59 SR genes were identified and classified into seven subfamilies: SR, SCL, RS2Z, RSZ, RS, SR45, and SC. In each subfamily, the genes showed relatively conserved structures and motifs, but displayed distinct expression patterns in different tissues and under abiotic stress, which might be caused by the varied cis-acting regulatory elements among them. Transcriptome datasets from Pacbio/Illumina platforms showed that alternative splicing of SR genes was widespread in B. napus and the majority of paralogous gene pairs displayed different splicing patterns. Protein-protein interaction analysis indicated that SR proteins were involved in the regulation of the whole lifecycle of mRNA, from synthesis to decay. Moreover, the association mapping analysis suggested that 12 SR genes were candidate genes for regulating specific agronomic traits, which indicated that SR genes could affect the development and hence influence the important agronomic traits of B. napus. In summary, this study provided elaborate information on SR genes in B. napus, which will aid further functional studies and genetic improvement of agronomic traits in B. napus.
Traits related to flowering time are the most promising agronomic traits that directly impact the seed yield and oil quality of rapeseed (Brassica napus L.). Developing early flowering and maturity rapeseed varieties is an important breeding objective in B. napus. Many studies have reported on days to flowering, but few have reported on budding, bolting, and the interval between bolting and DTF. Therefore, elucidating the genetic architecture of QTLs and genes regulating flowering time, we presented an integrated investigation on SNP and haplotype-based genome-wide association study of 373 diverse B. napus germplasm, which were genotyped by the 60K SNP array and were phenotyped in the four environments. The results showed that a total of 15 and 37 QTLs were detected from SNP and haplotype-based GWAS, respectively. Among them, seven QTL clusters were identified by haplotype-based GWAS. Moreover, three and eight environmentally stable QTLs were detected by SNP-GWAS and haplotype-based GWAS, respectively. By integrating the above two approaches and by co-localizing the four traits, ten (10) genomic regions were under selection on chromosomes A03, A07, A08, A10, C06, C07, and C08. Interestingly, the genomic regions FT.A07.1, FT.A08, FT.C06, and FT.C07 were identified as novel. In these ten regions, a total of 197 genes controlling FT were detected, of which 14 highly expressed DEGs were orthologous to 13 Arabidopsis thaliana genes after integration with transcriptome results. In a nutshell, the above results uncovered the genetic architecture of important agronomic traits related to flowering time and provided a basis for multiple molecular marker-trait associations in B. napus.
Tuberculosis (TB) is one of the biggest infectious disease killers caused by Mycobacterium tuberculosis (MTB). Studying the protein-protein interactions (PPIs) between MTB and human can deepen our understanding of the pathogenesis of TB and offer new clues to the treatment against MTB infection, but the experimentally validated interactions are especially scarce in this regard. Herein we proposed an integrated framework that combined template-, domain-domain interaction-, and machine learning-based methods to predict MTB-human PPIs. As a result, we established a network composed of 13 758 PPIs including 451 MTB proteins and 3167 human proteins (). Compared to known human targets of various pathogens, our predicted human targets show a similar tendency in terms of the network topological properties and enrichment in important functional genes. Additionally, these human targets largely have longer sequence lengths, more protein domains, more disordered residues, lower evolutionary rates, and older protein ages. Functional analysis demonstrates that these proteins show strong preferences toward the phosphorylation, kinase activity, and signaling transduction processes and the disease and immune related pathways. Dissecting the cross-talk among top-ranked pathways suggests that the cancer pathway may serve as a bridge in MTB infection. Triplet analysis illustrates that the paired targets interacting with the same partner are adjacent to each other in the intraspecies network and tend to share similar expression patterns. Finally, we identified 36 potential anti-MTB human targets by integrating known drug target information and molecular properties of proteins.
Previous genome-wide association studies (GWAS) reported that the allele C of rs945270 of the kinectin 1 gene (KTN1) most significantly increased the gray matter volume (GMV) of the putamen and modestly regulated the risk for attention deficit hyperactivity disorder (ADHD). On the other hand, ADHD is known to be associated with a reduction in subcortical and cortical GMVs. Here, we examined the interrelationships of the GMVs, rs945270 alleles, and ADHD symptom scores in the same cohort of children. With data of rs945270 genotypes, GMVs of 118 brain regions, and ADHD symptom scores of 3372 boys and 3129 girls of the Adolescent Brain Cognition Development project, we employed linear regression analyses to examine the pairwise correlations adjusted for the third of the three traits and other relevant covariates, and examine their mediation effects. We found that the major allele C of rs945270 modestly increased risk for ADHD in males only when controlling for the confounding effects of the GMV of any one of the 118 cerebral regions (0.026 ≤ p ≤ 0.059: Top two: left and right putamen). This allele also significantly increased putamen GMV in males alone (left p = 2.8 × 10−5, and right p = 9.4 × 10−5; α = 2.1 × 10−4) and modestly increased other subcortical and cortical GMVs in both sexes (α < p < 0.05), whether or not adjusted for ADHD symptom scores. Both subcortical and cortical GMVs were significantly or suggestively reduced in ADHD when adjusted for rs945270 alleles, each more significantly in females (3.6 × 10−7 ≤ p < α; Top two: left pallidum and putamen) and males (3.5 × 10−6 ≤ p < α), respectively. Finally, the left and right putamen GMVs reduced 14.0% and 11.7% of the risk effects of allele C on ADHD, and allele C strengthened 4.5% (left) and 12.2% (right) of the protective effects of putamen GMVs on ADHD risk, respectively. We concluded that the rs945270-GMVs-ADHD relationships were sex-different. In males, the major allele C of rs945270 increased risk for ADHD, which was compromised by putamen GMVs; this allele also but only significantly increased putamen GMVs that then significantly protected against ADHD risk. In females, the top two GMVs significantly decreasing ADHD risk were left pallidum and putamen GMVs. Basal ganglia the left putamen in particular play the most critical role in the pathogenesis of ADHD.
Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum (S. sclerotiorum) is the main disease threat of oilseed rape (Brassica napus), resulting in huge economic losses every year. SSR resistance manifests as quantitative disease resistance (QDR), and no gene with complete SSR resistance has been cloned or reported so far. Transcriptome analysis has revealed a large number of defense-related genes and response processes. However, the similarities and differences in the defense responses of different tissues are rarely reported. In this study, we analyzed the similarities and differences of different tissues in response to S. sclerotiorum at 24 h post inoculation (hpi) by using the published transcriptome data for respective leaf and stem inoculation. At 24 hpi, large differences in gene expression exist in leaf and stem, and there are more differentially expressed genes and larger expression differences in leaf. The leaf is more sensitive to S. sclerotiorum and shows a stronger response than stem. Different defense responses appear in the leaf and stem, and the biosynthesis of lignin, callose, lectin, chitinase, PGIP, and PR protein is activated in leaf. In the stem, lipid metabolism-mediated defense responses are obviously enhanced. For the common defense responses in both leaf and stem, the chain reactions resulting from signal transduction and biological process take the primary responsibility. This research will be beneficial to exploit the potential of different tissues in plant defense and find higher resistance levels of genotypic variability in different environments. Our results are significant in the identification of resistance genes and analysis of defense mechanisms.
Black rot caused by the vascular pathogenic bacterium Xanthomonas campestris pv. campestris (Xcc) is widespread in Brassicaceae plants and an infectious disease that causes large yield losses in oil seed rape (Brassica napus L.). Improvement of resistance through breeding is a crucial strategy to prevent black rot disease in B. napus, but presently hampered by insufficient understanding of Xcc-Brassica interactions. This study compares two EMS-mutagenized B. napus lines that show contrasting resistance levels to their susceptible progenitor. Patterns of differential gene expression between these B. napus lines were evaluated at three time points post inoculation by comparative RNA-seq analysis. In line with the observed disease phenotypes, the susceptible line ZS9mXccS-1 displayed a steady amount of differentially expressed genes (DEGs) at different time points of infection, whereas the resistant line ZS9mXccR-1 displayed a gradual increase in DEGs throughout the course of infection. Weighted gene co-expression network analysis (WGCNA) pinpointed multiple defense-related hub genes with potential central roles in immunity, including the cell surface receptor genes CRK11 and BIR1, and the associated downstream regulatory genes WRKY11 and PBL30. KEGG analysis of DEGs belonging to two distinct co-expression modules revealed enriched pathways associated with defense, including Ca2+-signaling, receptor-mediated immunity, and phytohormone balance. Taken together, our comparative transcriptome analysis provides new avenues to unravel the mechanisms underlying black rot resistance in B. napus.
Alternative splicing (AS) is an important regulatory process that affects plant development and stress responses by greatly increasing the complexity of transcriptome and proteome. To understand how the AS landscape of B. napus changes in response to abiotic stresses, we investigated 26 RNA-seq libraries, including control and treatments with cold, dehydration, salt, and abscisic acid (ABA) at two different time points, to perform comparative alternative splicing analysis. Apparently, AS events increased under all stresses except dehydration for 1 h, and intron retention was the most common AS mode. In addition, a total of 357 differential alternative splicing (DAS) genes were identified under four abiotic stresses, among which 81 DAS genes existed in at least two stresses, and 276 DAS genes were presented under only one stress. A weighted gene co-expression network analysis (WGCNA) based on the splicing isoforms, rather than the genes, pinpointed out 23 co-expression modules associated with different abiotic stresses. Among them, a number of significant hub genes were also found to be DAS genes, which encode key isoforms involved in responses to single stress or multiple stresses, including RNA-binding proteins, transcription factors, and other important genes, such as RBP45C, LHY, MYB59, SCL30A, RS40, MAJ23.10, and DWF4. The splicing isoforms of candidate genes identified in this study could be a valuable resource for improving tolerance of B. napus against multiple abiotic stresses.
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