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Genome and Genetics, Plant breeding.
The allotetraploid species Brassica juncea (mustard) is grown worldwide as oilseed and vegetable crops; the yellow seed-color trait is particularly important for oilseed crops. Here, to examine the factors affecting seed coat color, we performed a metabolic and transcriptomic analysis of yellow- and dark-seeded B. juncea seeds. In this study, we identified 236 compounds, including 31 phenolic acids, 47 flavonoids, 17 glucosinolates, 38 lipids, 69 other hydroxycinnamic acid compounds, and 34 novel unknown compounds. Of these, 36 compounds (especially epicatechin and its derivatives) accumulated significantly different levels during the development of yellow- and dark-seeded B. juncea. In addition, the transcript levels of BjuDFR, BjuANS,BjuBAN, BjuTT8, and BjuTT19 were closely associated with changes to epicatechin and its derivatives during seed development, implicating this pathway in the seed coat color determinant in B. juncea. Furthermore, we found numerous variations of sequences in the TT8A genes that may be associated with the stability of seed coat color in B. rapa, B. napus, and B. juncea, which might have undergone functional differentiation during polyploidization in the Brassica species. The results provide valuable information for understanding the accumulation of metabolites in the seed coat color of B. juncea and lay a foundation for exploring the underlying mechanism.
Shulin Shen; Yunshan Tang; Chao Zhang; Nengwen Yin; Yuanyi Mao; Fujun Sun; Si Chen; Ran Hu; Xueqin Liu; GuoXia Shang; Liezhao Liu; Kun Lu; Jiana Li; Cunmin Qu. Metabolite Profiling and Transcriptome Analysis Provide Insight into Seed Coat Color in Brassica juncea. International Journal of Molecular Sciences 2021, 22, 7215 .
AMA StyleShulin Shen, Yunshan Tang, Chao Zhang, Nengwen Yin, Yuanyi Mao, Fujun Sun, Si Chen, Ran Hu, Xueqin Liu, GuoXia Shang, Liezhao Liu, Kun Lu, Jiana Li, Cunmin Qu. Metabolite Profiling and Transcriptome Analysis Provide Insight into Seed Coat Color in Brassica juncea. International Journal of Molecular Sciences. 2021; 22 (13):7215.
Chicago/Turabian StyleShulin Shen; Yunshan Tang; Chao Zhang; Nengwen Yin; Yuanyi Mao; Fujun Sun; Si Chen; Ran Hu; Xueqin Liu; GuoXia Shang; Liezhao Liu; Kun Lu; Jiana Li; Cunmin Qu. 2021. "Metabolite Profiling and Transcriptome Analysis Provide Insight into Seed Coat Color in Brassica juncea." International Journal of Molecular Sciences 22, no. 13: 7215.
The YABBY family of plant-specific transcription factors play important regulatory roles during the development of leaves and floral organs, but their functions in Brassica species are incompletely understood. Here, we identified 79 YABBY genes from Arabidopsis thaliana and five Brassica species (B. rapa, B. nigra, B. oleracea, B. juncea, and B. napus). A phylogenetic analysis of YABBY proteins separated them into five clusters (YAB1–YAB5) with representatives from all five Brassica species, suggesting a high degree of conservation and similar functions within each subfamily. We determined the gene structure, chromosomal location, and expression patterns of the 21 BnaYAB genes identified, revealing extensive duplication events and gene loss following polyploidization. Changes in exon–intron structure during evolution may have driven differentiation in expression patterns and functions, combined with purifying selection, as evidenced by Ka/Ks values below 1. Based on transcriptome sequencing data, we selected nine genes with high expression at the flowering stage. qRT-PCR analysis further indicated that most BnaYAB family members are tissue-specific and exhibit different expression patterns in various tissues and organs of B. napus. This preliminary study of the characteristics of the YABBY gene family in the Brassica napus genome provides theoretical support and reference for the later functional identification of the family genes.
Jichun Xia; Dong Wang; Yuzhou Peng; Wenning Wang; Qianqian Wang; Yang Xu; Tongzhou Li; Kai Zhang; Jiana Li; Xinfu Xu. Genome-Wide Analysis of the YABBY Transcription Factor Family in Rapeseed (Brassica napus L.). Genes 2021, 12, 981 .
AMA StyleJichun Xia, Dong Wang, Yuzhou Peng, Wenning Wang, Qianqian Wang, Yang Xu, Tongzhou Li, Kai Zhang, Jiana Li, Xinfu Xu. Genome-Wide Analysis of the YABBY Transcription Factor Family in Rapeseed (Brassica napus L.). Genes. 2021; 12 (7):981.
Chicago/Turabian StyleJichun Xia; Dong Wang; Yuzhou Peng; Wenning Wang; Qianqian Wang; Yang Xu; Tongzhou Li; Kai Zhang; Jiana Li; Xinfu Xu. 2021. "Genome-Wide Analysis of the YABBY Transcription Factor Family in Rapeseed (Brassica napus L.)." Genes 12, no. 7: 981.
Mitogen-activated protein kinase (MAPK) cascades are common and conserved signal transduction pathways and play important roles in various biotic and abiotic stress responses and growth and developmental processes in plants. With the advancement of sequencing technology, more systematic genetic information is being explored. The work presented here focuses on two protein families in Brassica species: MAPK kinases (MKKs) and their phosphorylation substrates MAPKs. Forty-seven MKKs and ninety-two MAPKs were identified and extensively analyzed from two tetraploid (B. juncea and B. napus) and three diploid (B. nigra, B. oleracea, and B. rapa) Brassica species. Phylogenetic relationships clearly distinguished both MKK and MAPK families into four groups, labeled A–D, which were also supported by gene structure and conserved protein motif analysis. Furthermore, their spatial and temporal expression patterns and response to stresses (cold, drought, heat, and shading) were analyzed, indicating that BnaMKK and BnaMAPK transcript levels were generally modulated by growth, development, and stress signals. In addition, several protein interaction pairs between BnaMKKs and C group BnaMAPKs were detected by yeast two-hybrid assays, in which BnaMKK3 and BnaMKK9 showed strong interactions with BnaMAPK1/2/7, suggesting that interaction between BnaMKKs and C group BnaMAPKs play key roles in the crosstalk between growth and development processes and abiotic stresses. Taken together, our data provide a deeper foundation for the evolutionary and functional characterization of MKK and MAPK gene families in Brassica species, paving the way for unraveling the biological roles of these important signaling molecules in plants.
Zhen Wang; Yuanyuan Wan; Xiaojing Meng; Xiaoli Zhang; Mengnan Yao; Wenjie Miu; Dongming Zhu; Dashuang Yuan; Kun Lu; Jiana Li; Cunmin Qu; Ying Liang. Genome-Wide Identification and Analysis of MKK and MAPK Gene Families in Brassica Species and Response to Stress in Brassica napus. International Journal of Molecular Sciences 2021, 22, 544 .
AMA StyleZhen Wang, Yuanyuan Wan, Xiaojing Meng, Xiaoli Zhang, Mengnan Yao, Wenjie Miu, Dongming Zhu, Dashuang Yuan, Kun Lu, Jiana Li, Cunmin Qu, Ying Liang. Genome-Wide Identification and Analysis of MKK and MAPK Gene Families in Brassica Species and Response to Stress in Brassica napus. International Journal of Molecular Sciences. 2021; 22 (2):544.
Chicago/Turabian StyleZhen Wang; Yuanyuan Wan; Xiaojing Meng; Xiaoli Zhang; Mengnan Yao; Wenjie Miu; Dongming Zhu; Dashuang Yuan; Kun Lu; Jiana Li; Cunmin Qu; Ying Liang. 2021. "Genome-Wide Identification and Analysis of MKK and MAPK Gene Families in Brassica Species and Response to Stress in Brassica napus." International Journal of Molecular Sciences 22, no. 2: 544.
Main conclusion The molecular mechanism underlying white petal color inBrassica napuswas revealed by transcriptomic and metabolomic analyses. Abstract Rapeseed (Brassica napusL.) is one of the most important oilseed crops worldwide, but the mechanisms underlying flower color in this crop are known less. Here, we performed metabolomic and transcriptomic analyses of the yellow-flowered rapeseed cultivar ‘Zhongshuang 11’ (ZS11) and the white-flowered inbred line ‘White Petal’ (WP). The total carotenoid contents were 1.778-fold and 1.969-fold higher in ZS11 vs. WP petals at stages S2 and S4, respectively. Our findings suggest that white petal color in WP flowers is primarily due to decreased lutein and zeaxanthin contents. Transcriptome analysis revealed 10,116 differentially expressed genes with a fourfold or greater change in expression (P-value less than 0.001) in WP vs. ZS11 petals, including 1,209 genes that were differentially expressed at four different stages and 20 genes in the carotenoid metabolism pathway.BnNCED4b, encoding a protein involved in carotenoid degradation, was expressed at abnormally high levels in WP petals, suggesting it might play a key role in white petal formation. The results of qRT-PCR were consistent with the transcriptome data. The results of this study provide important insights into the molecular mechanisms of the carotenoid metabolic pathway in rapeseed petals, and the candidate genes identified in this study provide a resource for the creation of newB. napusgermplasms with different petal colors.
Ledong Jia; Junsheng Wang; Rui Wang; Mouzheng Duan; Cailin Qiao; Xue Chen; Guoqiang Ma; Xintong Zhou; Meichen Zhu; Fuyu Jing; Shengsen Zhang; Cunmin Qu; Jiana Li. Comparative transcriptomic and metabolomic analyses of carotenoid biosynthesis reveal the basis of white petal color in Brassica napus. Planta 2021, 253, 1 -14.
AMA StyleLedong Jia, Junsheng Wang, Rui Wang, Mouzheng Duan, Cailin Qiao, Xue Chen, Guoqiang Ma, Xintong Zhou, Meichen Zhu, Fuyu Jing, Shengsen Zhang, Cunmin Qu, Jiana Li. Comparative transcriptomic and metabolomic analyses of carotenoid biosynthesis reveal the basis of white petal color in Brassica napus. Planta. 2021; 253 (1):1-14.
Chicago/Turabian StyleLedong Jia; Junsheng Wang; Rui Wang; Mouzheng Duan; Cailin Qiao; Xue Chen; Guoqiang Ma; Xintong Zhou; Meichen Zhu; Fuyu Jing; Shengsen Zhang; Cunmin Qu; Jiana Li. 2021. "Comparative transcriptomic and metabolomic analyses of carotenoid biosynthesis reveal the basis of white petal color in Brassica napus." Planta 253, no. 1: 1-14.
The KT/HAK/KUP (HAK) family is the largest potassium (K+) transporter family in plants, which plays key roles in K+ uptake and homeostasis, stress resistance, and root and embryo development. However, the HAK family has not yet been characterized in Brassica napus. In this study, 40 putative B. napus HAK genes (BnaHAKs) are identified and divided into four groups (Groups I–III and V) on the basis of phylogenetic analysis. Gene structure analysis revealed 10 conserved intron insertion sites across different groups. Collinearity analysis demonstrated that both allopolyploidization and small-scale duplication events contributed to the large expansion of BnaHAKs. Transcription factor (TF)-binding network construction, cis-element analysis, and microRNA prediction revealed that the expression of BnaHAKs is regulated by multiple factors. Analysis of RNA-sequencing data further revealed extensive expression profiles of the BnaHAKs in groups II, III, and V, with limited expression in group I. Compared with group I, most of the BnaHAKs in groups II, III, and V were more upregulated by hormone induction based on RNA-sequencing data. Reverse transcription-quantitative polymerase reaction analysis revealed that the expression of eight BnaHAKs of groups I and V was markedly upregulated under K+-deficiency treatment. Collectively, our results provide valuable information and key candidate genes for further functional studies of BnaHAKs.
Jie Zhou; Hong-Jun Zhou; Ping Chen; Lan-Lan Zhang; Jia-Tian Zhu; Peng-Feng Li; Jin Yang; Yun-Zhuo Ke; Yong-Hong Zhou; Jia-Na Li; Hai Du. Genome-Wide Survey and Expression Analysis of the KT/HAK/KUP Family in Brassica napus and Its Potential Roles in the Response to K+ Deficiency. International Journal of Molecular Sciences 2020, 21, 9487 .
AMA StyleJie Zhou, Hong-Jun Zhou, Ping Chen, Lan-Lan Zhang, Jia-Tian Zhu, Peng-Feng Li, Jin Yang, Yun-Zhuo Ke, Yong-Hong Zhou, Jia-Na Li, Hai Du. Genome-Wide Survey and Expression Analysis of the KT/HAK/KUP Family in Brassica napus and Its Potential Roles in the Response to K+ Deficiency. International Journal of Molecular Sciences. 2020; 21 (24):9487.
Chicago/Turabian StyleJie Zhou; Hong-Jun Zhou; Ping Chen; Lan-Lan Zhang; Jia-Tian Zhu; Peng-Feng Li; Jin Yang; Yun-Zhuo Ke; Yong-Hong Zhou; Jia-Na Li; Hai Du. 2020. "Genome-Wide Survey and Expression Analysis of the KT/HAK/KUP Family in Brassica napus and Its Potential Roles in the Response to K+ Deficiency." International Journal of Molecular Sciences 21, no. 24: 9487.
Background NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER (NRT1/PTR) family (NPF) members are essential transporters for many substrates in plants, including nitrate, hormones, peptides, and secondary metabolites. Here, we report the global characterization of NPF in the important oil crop Brassica napus, including that for phylogeny, gene/protein structures, duplications, and expression patterns. Results A total of 199 B. napus (BnaNPFs) NPF-coding genes were identified. Phylogenetic analyses categorized these genes into 11 subfamilies, including three new ones. Sequence feature analysis revealed that members of each subfamily contain conserved gene and protein structures. Many hormone−/abiotic stress-responsive cis-acting elements and transcription factor binding sites were identified in BnaNPF promoter regions. Chromosome distribution analysis indicated that BnaNPFs within a subfamily tend to cluster on one chromosome. Syntenic relationship analysis showed that allotetraploid creation by its ancestors (Brassica rapa and Brassica oleracea) (57.89%) and small-scale duplication events (39.85%) contributed to rapid BnaNPF expansion in B. napus. A genome-wide spatiotemporal expression survey showed that NPF genes of each Arabidopsis and B. napus subfamily have preferential expression patterns across developmental stages, most of them are expressed in a few organs. RNA-seq analysis showed that many BnaNPFs (32.66%) have wide exogenous hormone-inductive profiles, suggesting important hormone-mediated patterns in diverse bioprocesses. Homologs in a clade or branch within a given subfamily have conserved organ/spatiotemporal and hormone-inductive profiles, indicating functional conservation during evolution. qRT-PCR-based comparative expression analysis of the 12 BnaNPFs in the NPF2–1 subfamily between high- and low-glucosinolate (GLS) content B. napus varieties revealed that homologs of AtNPF2.9 (BnaNPF2.12, BnaNPF2.13, and BnaNPF2.14), AtNPF2.10 (BnaNPF2.19 and BnaNPF2.20), and AtNPF2.11 (BnaNPF2.26 and BnaNPF2.28) might be involved in GLS transport. qRT-PCR further confirmed the hormone-responsive expression profiles of these putative GLS transporter genes. Conclusion We identified 199 B. napus BnaNPFs; these were divided into 11 subfamilies. Allopolyploidy and small-scale duplication events contributed to the immense expansion of BnaNPFs in B. napus. The BnaNPFs had preferential expression patterns in different tissues/organs and wide hormone-induced expression profiles. Four BnaNPFs in the NPF2–1 subfamily may be involved in GLS transport. Our results provide an abundant gene resource for further functional analysis of BnaNPFs.
Jing Wen; Peng-Feng Li; Feng Ran; Peng-Cheng Guo; Jia-Tian Zhu; Jin Yang; Lan-Lan Zhang; Ping Chen; Jia-Na Li; Hai Du. Genome-wide characterization, expression analyses, and functional prediction of the NPF family in Brassica napus. BMC Genomics 2020, 21, 1 -17.
AMA StyleJing Wen, Peng-Feng Li, Feng Ran, Peng-Cheng Guo, Jia-Tian Zhu, Jin Yang, Lan-Lan Zhang, Ping Chen, Jia-Na Li, Hai Du. Genome-wide characterization, expression analyses, and functional prediction of the NPF family in Brassica napus. BMC Genomics. 2020; 21 (1):1-17.
Chicago/Turabian StyleJing Wen; Peng-Feng Li; Feng Ran; Peng-Cheng Guo; Jia-Tian Zhu; Jin Yang; Lan-Lan Zhang; Ping Chen; Jia-Na Li; Hai Du. 2020. "Genome-wide characterization, expression analyses, and functional prediction of the NPF family in Brassica napus." BMC Genomics 21, no. 1: 1-17.
In crops there are quantitative trait loci (QTLs) in which some of the causal quantitative trait genes (QTGs) have not been functionally characterized even in the model plant Arabidopsis. We propose an approach to delineate QTGs in rapeseed by coordinating expression of genes located within QTLs and known orthologs related to traits from Arabidopsis. Using this method in developing siliques 15 d after pollination in 71 lines of rapeseed, we established an acyl-lipid metabolism co-expression network with 21 modules composed of 270 known acyl-lipid genes and 3503 new genes. The core module harbored 76 known genes involved in fatty acid and triacylglycerol biosynthesis and 671 new genes involved in sucrose transport, carbon metabolism, amino acid metabolism, seed storage protein processes, seed maturation, and phytohormone metabolism. Moreover, the core module closely associated with the modules of photosynthesis and carbon metabolism. From the co-expression network, we selected 12 hub genes to identify their putative Arabidopsis orthologs. These putative orthologs were functionally analysed using Arabidopsis knockout and overexpression lines. Four knockout mutants exhibited lower seed oil content, while the seed oil content in 10 overexpression lines was significantly increased. Therefore, combining gene co-expression network analysis and QTL mapping, this study provides new insights into the detection of QTGs and into acyl-lipid metabolism in rapeseed.
Yixin Cui; Xiao Zeng; Qing Xiong; Dayong Wei; Jinghang Liao; Yang Xu; Guanqun Chen; Yonghong Zhou; Hongli Dong; Huafang Wan; Zhi Liu; Jiana Li; Liang Guo; Christian Jung; Yajun He; Wei Qian. Combining quantitative trait locus and co-expression analysis allowed identification of new candidates for oil accumulation in rapeseed. Journal of Experimental Botany 2020, 72, 1649 -1660.
AMA StyleYixin Cui, Xiao Zeng, Qing Xiong, Dayong Wei, Jinghang Liao, Yang Xu, Guanqun Chen, Yonghong Zhou, Hongli Dong, Huafang Wan, Zhi Liu, Jiana Li, Liang Guo, Christian Jung, Yajun He, Wei Qian. Combining quantitative trait locus and co-expression analysis allowed identification of new candidates for oil accumulation in rapeseed. Journal of Experimental Botany. 2020; 72 (5):1649-1660.
Chicago/Turabian StyleYixin Cui; Xiao Zeng; Qing Xiong; Dayong Wei; Jinghang Liao; Yang Xu; Guanqun Chen; Yonghong Zhou; Hongli Dong; Huafang Wan; Zhi Liu; Jiana Li; Liang Guo; Christian Jung; Yajun He; Wei Qian. 2020. "Combining quantitative trait locus and co-expression analysis allowed identification of new candidates for oil accumulation in rapeseed." Journal of Experimental Botany 72, no. 5: 1649-1660.
Background Anthracnose is a damaging disease of sorghum caused by the fungal pathogenColletotrichum sublineolum.Genome-wide mRNA and microRNA (miRNA) profiles of resistant and susceptible sorghum genotypes were studied to understand components of immune responses, and fungal induced miRNA and target gene networks. Results A total of 18 mRNA and 12 miRNA libraries from resistant and susceptible sorghum lines were sequenced prior to and after inoculation withC. sublineolum. Significant differences in transcriptomes of the susceptible and resistant genotypes were observed with dispersion distance and hierarchical cluster tree analyses. Of the total 33,032 genes predicted in the sorghum genome, 19,593 were induced byC. sublineolum,and 15,512 were differentially expressed (DEGs) between the two genotypes. The resistant line was marked by significant reprogramming of the transcriptome at 24 h post inoculation (hpi), and a decrease at 48 hpi, whereas the susceptible line displayed continued changes in gene expression concordant with elevated fungal growth in the susceptible genotype. DEGs encode proteins implicated in diverse functions including photosynthesis, synthesis of tetrapyrrole, carbohydrate and secondary metabolism, immune signaling, and chitin binding. Genes encoding immune receptors, MAPKs, pentatricopeptide repeat proteins, and WRKY transcription factors were induced in the resistant genotype. In a parallel miRNA profiling, the susceptible line displayed greater number of differentially expressed miRNAs than the resistant line indicative of a widespread suppression of gene expression. Interestingly, we found 75 miRNAs, including 36 novel miRNAs, which were differentially expressed in response to fungal inoculation. The expression of 50 miRNAs was significantly different between resistant and susceptible lines. Subsequently, for 35 differentially expressed miRNAs, the corresponding 149 target genes were identified. Expression of 56 target genes were significantly altered after inoculation, showing inverse expression with the corresponding miRNAs. Conclusions We provide insights into genome wide dynamics of mRNA and miRNA profiles, biological and cellular processes underlying host responses to fungal infection in sorghum. Resistance is correlated with early transcriptional reprogramming of genes in various pathways. Fungal induced genes, miRNAs and their targets with a potential function in host responses to anthracnose were identified, opening avenues for genetic dissection of resistance mechanisms.
Fuyou Fu; Gezahegn Girma; Tesfaye Mengiste. Global mRNA and microRNA expression dynamics in response to anthracnose infection in sorghum. BMC Genomics 2020, 21, 1 -16.
AMA StyleFuyou Fu, Gezahegn Girma, Tesfaye Mengiste. Global mRNA and microRNA expression dynamics in response to anthracnose infection in sorghum. BMC Genomics. 2020; 21 (1):1-16.
Chicago/Turabian StyleFuyou Fu; Gezahegn Girma; Tesfaye Mengiste. 2020. "Global mRNA and microRNA expression dynamics in response to anthracnose infection in sorghum." BMC Genomics 21, no. 1: 1-16.
Background Diacylglycerol kinases (DGKs) are signaling enzymes that play pivotal roles in response to abiotic and biotic stresses by phosphorylating diacylglycerol (DAG) to form phosphatidic acid (PA). However, no comprehensive analysis of the DGK gene family had previously been reported in B. napus and its diploid progenitors (B. rapa and B. oleracea). Results In present study, we identified 21, 10, and 11 DGK genes from B. napus, B. rapa, and B. oleracea, respectively, which all contained conserved catalytic domain and were further divided into three clusters. Molecular evolutionary analysis showed that speciation and whole-genome triplication (WGT) was critical for the divergence of duplicated DGK genes. RNA-seq transcriptome data revealed that, with the exception of BnaDGK4 and BnaDGK6, BnaDGK genes have divergent expression patterns in most tissues. Furthermore, some DGK genes were upregulated or downregulated in response to hormone treatment and metal ion (arsenic and cadmium) stress. Quantitative real-time PCR analysis revealed that different BnaDGK genes contribute to seed oil content. Conclusions Together, our results indicate that DGK genes have diverse roles in plant growth and development, hormone response, and metal ion stress, and in determining seed oil content, and lay a foundation for further elucidating the roles of DGKs in Brassica species.
Fang Tang; Zhongchun Xiao; Fujun Sun; Shulin Shen; Si Chen; Rui Chen; Meichen Zhu; Qianwei Zhang; Hai Du; Kun Lu; Jiana Li; Cunmin Qu. Genome-wide identification and comparative analysis of diacylglycerol kinase (DGK) gene family and their expression profiling in Brassica napus under abiotic stress. BMC Plant Biology 2020, 20, 1 -17.
AMA StyleFang Tang, Zhongchun Xiao, Fujun Sun, Shulin Shen, Si Chen, Rui Chen, Meichen Zhu, Qianwei Zhang, Hai Du, Kun Lu, Jiana Li, Cunmin Qu. Genome-wide identification and comparative analysis of diacylglycerol kinase (DGK) gene family and their expression profiling in Brassica napus under abiotic stress. BMC Plant Biology. 2020; 20 (1):1-17.
Chicago/Turabian StyleFang Tang; Zhongchun Xiao; Fujun Sun; Shulin Shen; Si Chen; Rui Chen; Meichen Zhu; Qianwei Zhang; Hai Du; Kun Lu; Jiana Li; Cunmin Qu. 2020. "Genome-wide identification and comparative analysis of diacylglycerol kinase (DGK) gene family and their expression profiling in Brassica napus under abiotic stress." BMC Plant Biology 20, no. 1: 1-17.
Carotenoid cleavage dioxygenase (CCD), a key enzyme in carotenoid metabolism, cleaves carotenoids to form apo-carotenoids, which play a major role in plant growth and stress responses. CCD genes had not previously been systematically characterized in Brassica napus (rapeseed), an important oil crop worldwide. In this study, we identified 30 BnCCD genes and classified them into nine subgroups based on a phylogenetic analysis. We identified the chromosomal locations, gene structures, and cis-promoter elements of each of these genes and performed a selection pressure analysis to identify residues under selection. Furthermore, we determined the subcellular localization, physicochemical properties, and conserved protein motifs of the encoded proteins. All the CCD proteins contained a retinal pigment epithelial membrane protein (RPE65) domain. qRT-PCR analysis of expression of 20 representative BnCCD genes in 16 tissues of the B. napus cultivar Zhong Shuang 11 (‘ZS11’) revealed that members of the BnCCD gene family possess a broad range of expression patterns. This work lays the foundation for functional studies of the BnCCD gene family.
Xin-Tong Zhou; Le-Dong Jia; Mou-Zheng Duan; Xue Chen; Cai-Lin Qiao; Jin-Qi Ma; Chao Zhang; Fu-Yu Jing; Sheng-Sen Zhang; Bo Yang; Li-Yuan Zhang; Jia-Na Li. Genome-wide identification and expression profiling of the carotenoid cleavage dioxygenase (CCD) gene family in Brassica napus L. PLOS ONE 2020, 15, e0238179 .
AMA StyleXin-Tong Zhou, Le-Dong Jia, Mou-Zheng Duan, Xue Chen, Cai-Lin Qiao, Jin-Qi Ma, Chao Zhang, Fu-Yu Jing, Sheng-Sen Zhang, Bo Yang, Li-Yuan Zhang, Jia-Na Li. Genome-wide identification and expression profiling of the carotenoid cleavage dioxygenase (CCD) gene family in Brassica napus L. PLOS ONE. 2020; 15 (9):e0238179.
Chicago/Turabian StyleXin-Tong Zhou; Le-Dong Jia; Mou-Zheng Duan; Xue Chen; Cai-Lin Qiao; Jin-Qi Ma; Chao Zhang; Fu-Yu Jing; Sheng-Sen Zhang; Bo Yang; Li-Yuan Zhang; Jia-Na Li. 2020. "Genome-wide identification and expression profiling of the carotenoid cleavage dioxygenase (CCD) gene family in Brassica napus L." PLOS ONE 15, no. 9: e0238179.
The multidrug and toxic compound extrusion (MATE) protein family is important in the export of toxins and other substrates, but detailed information on this family in the Brassicaceae has not yet been reported compared to Arabidopsis thaliana. In this study, we identified 57, 124, 81, 85, 130, and 79 MATE genes in A. thaliana, Brassica napus, Brassica oleracea, Brassica rapa, Brassica juncea, and Brassica nigra, respectively, which were unevenly distributed on chromosomes owing to both tandem and segmental duplication events. Phylogenetic analysis showed that these genes could be classified into four subgroups, shared high similarity and conservation within each group, and have evolved mainly through purifying selection. Furthermore, numerous B. napusMATE genes showed differential expression between tissues and developmental stages and between plants treated with heavy metals or hormones and untreated control plants. This differential expression was especially pronounced for the Group 2 and 3 BnaMATE genes, indicating that they may play important roles in stress tolerance and hormone induction. Our results provide a valuable foundation for the functional dissection of the different BnaMATE homologs in B. napus and its parental lines, as well as for the breeding of more stress-tolerant B. napus genotypes.
Cailin Qiao; Jing Yang; Yuanyuan Wan; Sirou Xiang; Mingwei Guan; Hai Du; Zhanglin Tang; Kun Lu; Jiana Li; Cunmin Qu. A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling their Expression Profiles under Abiotic Stress in Rapeseed. Plants 2020, 9, 1072 .
AMA StyleCailin Qiao, Jing Yang, Yuanyuan Wan, Sirou Xiang, Mingwei Guan, Hai Du, Zhanglin Tang, Kun Lu, Jiana Li, Cunmin Qu. A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling their Expression Profiles under Abiotic Stress in Rapeseed. Plants. 2020; 9 (9):1072.
Chicago/Turabian StyleCailin Qiao; Jing Yang; Yuanyuan Wan; Sirou Xiang; Mingwei Guan; Hai Du; Zhanglin Tang; Kun Lu; Jiana Li; Cunmin Qu. 2020. "A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling their Expression Profiles under Abiotic Stress in Rapeseed." Plants 9, no. 9: 1072.
The genus Brassica contains several economically important crops, including rapeseed (Brassica napus, 2n = 38, AACC), the second largest source of seed oil and protein meal worldwide. However, research in rapeseed is hampered because it is complicated and time-consuming for researchers to access different types of expression data. We therefore developed the Brassica Expression Database (BrassicaEDB) for the research community. In the current BrassicaEDB, we only focused on the transcriptome level in rapeseed. We conducted RNA sequencing (RNA-Seq) of 103 tissues from rapeseed cultivar ZhongShuang11 (ZS11) at seven developmental stages (seed germination, seedling, bolting, initial flowering, full-bloom, podding, and maturation). We determined the expression patterns of 101,040 genes via FPKM analysis and displayed the results using the eFP browser. We also analyzed transcriptome data for rapeseed from 70 BioProjects in the SRA database and obtained three types of expression level data (FPKM, TPM, and read counts). We used this information to develop the BrassicaEDB, including “eFP”, “Treatment”, “Coexpression”, and “SRA Project” modules based on gene expression profiles and “Gene Feature”, “qPCR Primer”, and “BLAST” modules based on gene sequences. The BrassicaEDB provides comprehensive gene expression profile information and a user-friendly visualization interface for rapeseed researchers. Using this database, researchers can quickly retrieve the expression level data for target genes in different tissues and in response to different treatments to elucidate gene functions and explore the biology of rapeseed at the transcriptome level.
Haoyu Chao; Tian Li; Chaoyu Luo; Hualei Huang; Yingfei Ruan; Xiaodong Li; Yue Niu; Yonghai Fan; Wei Sun; Kai Zhang; Jiana Li; Cunmin Qu; Kun Lu. BrassicaEDB: A Gene Expression Database for Brassica Crops. International Journal of Molecular Sciences 2020, 21, 5831 .
AMA StyleHaoyu Chao, Tian Li, Chaoyu Luo, Hualei Huang, Yingfei Ruan, Xiaodong Li, Yue Niu, Yonghai Fan, Wei Sun, Kai Zhang, Jiana Li, Cunmin Qu, Kun Lu. BrassicaEDB: A Gene Expression Database for Brassica Crops. International Journal of Molecular Sciences. 2020; 21 (16):5831.
Chicago/Turabian StyleHaoyu Chao; Tian Li; Chaoyu Luo; Hualei Huang; Yingfei Ruan; Xiaodong Li; Yue Niu; Yonghai Fan; Wei Sun; Kai Zhang; Jiana Li; Cunmin Qu; Kun Lu. 2020. "BrassicaEDB: A Gene Expression Database for Brassica Crops." International Journal of Molecular Sciences 21, no. 16: 5831.
Background Brassica napus is one of the most important oilseed crops, and also an important biofuel plant due to its low air pollution and renewability. Growth period are important traits that affect yield and are crucial for its adaptation to different environments in B. napus. Results To elucidate the genetic basis of growth period traits, genome-wide association analysis (GWAS) and linkage mapping were employed to detect the quantitative trait loci (QTL) for days to initial flowering (DIF), days to final flowering (DFF), flowering period (FP), maturity time (MT), and whole growth period (GP). A total of 146 SNPs were identified by association mapping, and 83 QTLs were identified by linkage mapping using the RIL population. Among these QTLs, 19 were pleiotropic SNPs related to multiple traits, and six (q18DFF.A03-2, q18MT.A03-2, q17DFF.A05-1, q18FP.C04, q17DIF.C05 and q17GP.C09) were consistently detected using both mapping methods. Additionally, we performed RNA sequencing to analyze the differential expression of gene (DEG) transcripts between early- and late-flowering lines selected from the RIL population, and the DEGs were integrated with association mapping and linkage analysis to confirm their roles in the growth period. Consequently, 12 candidate genes associated with growth period traits were identified in B. napus. Among these genes, seven have polymorphic sites in the coding sequence and the upstream 2-kb sequence based on the resequencing data. The haplotype BnaSOC1.A05-Haplb and BnaLNK2.C06-Hapla showed more favorable phenotypic traits. Conclusions The candidate genes identified in this study will contribute to our genetic understanding of growth period traits and can be used as targets for target mutations or marker-assisted breeding for rapeseed adapted to different environments.
Tengyue Wang; Lijuan Wei; Jia Wang; Ling Xie; Yang Yang Li; Shuyao Ran; Lanyang Ren; Kun Lu; Jiana Li; Michael P. Timko; Liezhao Liu. Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.). Biotechnology for Biofuels 2020, 13, 1 -19.
AMA StyleTengyue Wang, Lijuan Wei, Jia Wang, Ling Xie, Yang Yang Li, Shuyao Ran, Lanyang Ren, Kun Lu, Jiana Li, Michael P. Timko, Liezhao Liu. Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.). Biotechnology for Biofuels. 2020; 13 (1):1-19.
Chicago/Turabian StyleTengyue Wang; Lijuan Wei; Jia Wang; Ling Xie; Yang Yang Li; Shuyao Ran; Lanyang Ren; Kun Lu; Jiana Li; Michael P. Timko; Liezhao Liu. 2020. "Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)." Biotechnology for Biofuels 13, no. 1: 1-19.
Yellow seed coat color is a desirable characteristic in rapeseed (Brassica napus), as it is associated with higher oil content and higher quality of meal. Alternative splicing (AS) is a vital post-transcriptional regulatory process contributing to plant cell differentiation and organ development. To identify novel transcripts and differences at the isoform level that are associated with seed color in B. napus, we compared 31 RNA-seq libraries of yellow- and black-seeded B. napus at five different developmental stages. AS events in the different samples were highly similar, and intron retention accounted for a large proportion of the observed AS pattern. AS mainly occurred in the early and middle stage of seed development. Weighted gene co-expression network analysis (WGCNA) identified 23 co-expression modules composed of differentially spliced genes, and we picked out two of the modules whose functions were highly associated with seed color. In the two modules, we found candidate DAS (differentially alternative splicing) genes related to the flavonoid pathway, such as TT8 (BnaC09g24870D), TT5 (BnaA09g34840D and BnaC08g26020D), TT12 (BnaC06g17050D and BnaA07g18120D), AHA10 (BnaA08g23220D and BnaC08g17280D), CHI (BnaC09g50050D), BAN (BnaA03g60670D) and DFR (BnaC09g17150D). Gene BnaC03g23650D, encoding RNA-binding family protein, was also identified. The splicing of the candidate genes identified in this study might be used to develop stable, yellow-seeded B. napus. This study provides insight into the formation of seed coat color in B. napus.
Ai Lin; Jinqi Ma; Fei Xu; Wen Xu; Huanhuan Jiang; Haoran Zhang; Cunmin Qu; Lijuan Wei; Jiana Li. Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed. Plants 2020, 9, 977 .
AMA StyleAi Lin, Jinqi Ma, Fei Xu, Wen Xu, Huanhuan Jiang, Haoran Zhang, Cunmin Qu, Lijuan Wei, Jiana Li. Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed. Plants. 2020; 9 (8):977.
Chicago/Turabian StyleAi Lin; Jinqi Ma; Fei Xu; Wen Xu; Huanhuan Jiang; Haoran Zhang; Cunmin Qu; Lijuan Wei; Jiana Li. 2020. "Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed." Plants 9, no. 8: 977.
Alternative splicing (AS) is a post-transcriptional level of gene expression regulation that increases transcriptome and proteome diversity. How the AS landscape of rapeseed (Brassica napus L.) changes in response to the fungal pathogen Sclerotinia sclerotiorum is unknown. Here, we analyzed 18 RNA-seq libraries of mock-inoculated and S. sclerotiorum-inoculated susceptible and tolerant B. napus plants. We found that infection increased AS, with intron retention being the main AS event. To determine the key genes functioning in the AS response, we performed a differential AS (DAS) analysis. We identified 79 DAS genes, including those encoding splicing factors, defense response proteins, crucial transcription factors and enzymes. We generated coexpression networks based on the splicing isoforms, rather than the genes, to explore the genes’ diverse functions. Using this weighted gene coexpression network analysis alongside a gene ontology enrichment analysis, we identified 11 modules putatively involved in the pathogen defense response. Within these regulatory modules, six DAS genes (ascorbate peroxidase 1, ser/arg-rich protein 34a, unknown function 1138, nitrilase 2, v-atpase f, and amino acid transporter 1) were considered to encode key isoforms involved in the defense response. This study provides insight into the post-transcriptional response of B. napus to S. sclerotiorum infection.
Jin-Qi Ma; Wen Xu; Fei Xu; Ai Lin; Wei Sun; Huan-Huan Jiang; Kun Lu; Jia-Na Li; Li-Juan Wei. Differential Alternative Splicing Genes and Isoform Regulation Networks of Rapeseed (Brassica napus L.) Infected with Sclerotinia sclerotiorum. Genes 2020, 11, 784 .
AMA StyleJin-Qi Ma, Wen Xu, Fei Xu, Ai Lin, Wei Sun, Huan-Huan Jiang, Kun Lu, Jia-Na Li, Li-Juan Wei. Differential Alternative Splicing Genes and Isoform Regulation Networks of Rapeseed (Brassica napus L.) Infected with Sclerotinia sclerotiorum. Genes. 2020; 11 (7):784.
Chicago/Turabian StyleJin-Qi Ma; Wen Xu; Fei Xu; Ai Lin; Wei Sun; Huan-Huan Jiang; Kun Lu; Jia-Na Li; Li-Juan Wei. 2020. "Differential Alternative Splicing Genes and Isoform Regulation Networks of Rapeseed (Brassica napus L.) Infected with Sclerotinia sclerotiorum." Genes 11, no. 7: 784.
Sugars are important throughout a plant’s lifecycle. Monosaccharide transporters (MST) are essential sugar transporters that have been identified in many plants, but little is known about the evolution or functions of MST genes in rapeseed (Brassica napus). In this study, we identified 175 MST genes in B. napus, 87 in Brassica oleracea, and 83 in Brassica rapa. These genes were separated into the sugar transport protein (STP), polyol transporter (PLT), vacuolar glucose transporter (VGT), tonoplast monosaccharide transporter (TMT), inositol transporter (INT), plastidic glucose transporter (pGlcT), and ERD6-like subfamilies, respectively. Phylogenetic and syntenic analysis indicated that gene redundancy and gene elimination have commonly occurred in Brassica species during polyploidization. Changes in exon-intron structures during evolution likely resulted in the differences in coding regions, expression patterns, and functions seen among BnMST genes. In total, 31 differentially expressed genes (DEGs) were identified through RNA-seq among materials with high and low harvest index (HI) values, which were divided into two categories based on the qRT-PCR results, expressed more highly in source or sink organs. We finally identified four genes, including BnSTP5, BnSTP13, BnPLT5, and BnERD6-like14, which might be involved in monosaccharide uptake or unloading and further affect the HI of rapeseed. These findings provide fundamental information about MST genes in Brassica and reveal the importance of BnMST genes to high HI in B. napus.
Liyuan Zhang; Chao Zhang; Bo Yang; Zhongchun Xiao; Jinqi Ma; Jingsen Liu; Hongju Jian; Cunmin Qu; Kun Lu; Jiana Li. Genome-Wide Identification and Expression Profiling of Monosaccharide Transporter Genes Associated with High Harvest Index Values in Rapeseed (Brassica napus L.). Genes 2020, 11, 653 .
AMA StyleLiyuan Zhang, Chao Zhang, Bo Yang, Zhongchun Xiao, Jinqi Ma, Jingsen Liu, Hongju Jian, Cunmin Qu, Kun Lu, Jiana Li. Genome-Wide Identification and Expression Profiling of Monosaccharide Transporter Genes Associated with High Harvest Index Values in Rapeseed (Brassica napus L.). Genes. 2020; 11 (6):653.
Chicago/Turabian StyleLiyuan Zhang; Chao Zhang; Bo Yang; Zhongchun Xiao; Jinqi Ma; Jingsen Liu; Hongju Jian; Cunmin Qu; Kun Lu; Jiana Li. 2020. "Genome-Wide Identification and Expression Profiling of Monosaccharide Transporter Genes Associated with High Harvest Index Values in Rapeseed (Brassica napus L.)." Genes 11, no. 6: 653.
MYB proteins are involved in diverse important biological processes in plants. Herein, we obtained the MYB superfamily from the allotetraploid Brassica napus, which contains 227 MYB-related (BnMYBR/Bn1R-MYB), 429 R2R3-MYB (Bn2R-MYB), 22 R1R2R3-MYB (Bn3R-MYB), and two R1R2R2R1/2-MYB (Bn4R-MYB) genes. Phylogenetic analysis classified the Bn2R-MYBs into 43 subfamilies, and the BnMYBRs into five subfamilies. Sequence characteristics and exon/intron structures within each subfamily of the Bn2R-MYBs and BnMYBRs were highly conserved. The whole superfamily was unevenly distributed on 19 chromosomes and underwent unbalanced expansion in B. napus. Allopolyploidy between B. oleracea and B. rapa mainly contributed to the expansion in their descendent B. napus, in which B. rapa-derived genes were more retained. Comparative phylogenetic analysis of 2R-MYB proteins from nine Brassicaceae and seven non-Brassicaceae species identified five Brassicaceae-specific subfamilies and five subfamilies that are lacking from the examined Brassicaceae species, which provided an example for the adaptive evolution of the 2R-MYB gene family alongside angiosperm diversification. Ectopic expression of four Bn2R-MYBs under the control of the viral CaMV35S and/or native promoters could rescue the lesser root hair phenotype of the Arabidopsis thaliana wer mutant plants, proving the conserved negative roles of the 2R-MYBs of the S15 subfamily in root hair development. RNA-sequencing data revealed that the Bn2R-MYBs and BnMYBRs had diverse transcript profiles in roots in response to the treatments with various hormones. Our findings provide valuable information for further functional characterizations of B. napus MYB genes.
Pengfeng Li; Jing Wen; Ping Chen; Pengcheng Guo; Yunzhuo Ke; Mangmang Wang; Mingming Liu; Lam-Son Phan Tran; Jiana Li; Hai Du. MYB Superfamily in Brassica napus: Evidence for Hormone-Mediated Expression Profiles, Large Expansion, and Functions in Root Hair Development. Biomolecules 2020, 10, 875 .
AMA StylePengfeng Li, Jing Wen, Ping Chen, Pengcheng Guo, Yunzhuo Ke, Mangmang Wang, Mingming Liu, Lam-Son Phan Tran, Jiana Li, Hai Du. MYB Superfamily in Brassica napus: Evidence for Hormone-Mediated Expression Profiles, Large Expansion, and Functions in Root Hair Development. Biomolecules. 2020; 10 (6):875.
Chicago/Turabian StylePengfeng Li; Jing Wen; Ping Chen; Pengcheng Guo; Yunzhuo Ke; Mangmang Wang; Mingming Liu; Lam-Son Phan Tran; Jiana Li; Hai Du. 2020. "MYB Superfamily in Brassica napus: Evidence for Hormone-Mediated Expression Profiles, Large Expansion, and Functions in Root Hair Development." Biomolecules 10, no. 6: 875.
Phosphorus transporter (PHT) genes encode H2PO4−/H+ co-transporters that absorb and transport inorganic nutrient elements required for plant development and growth and protect plants from heavy metal stress. However, little is known about the roles of PHTs in Brassica compared to Arabidopsis thaliana. In this study, we identified and extensively analyzed 336 PHTs from three diploid (B. rapa, B. oleracea, and B. nigra) and two allotetraploid (B. juncea and B. napus) Brassica species. We categorized the PHTs into five phylogenetic clusters (PHT1–PHT5), including 201 PHT1 homologs, 15 PHT2 homologs, 40 PHT3 homologs, 54 PHT4 homologs, and 26 PHT5 homologs, which are unevenly distributed on the corresponding chromosomes of the five Brassica species. All PHT family genes from Brassica are more closely related to Arabidopsis PHTs in the same vs. other clusters, suggesting they are highly conserved and have similar functions. Duplication and synteny analysis revealed that segmental and tandem duplications led to the expansion of the PHT gene family during the process of polyploidization and that members of this family have undergone purifying selection during evolution based on Ka/Ks values. Finally, we explored the expression profiles of BnaPHT family genes in specific tissues, at various developmental stages, and under heavy metal stress via RNA-seq analysis and qRT-PCR. BnaPHTs that were induced by heavy metal treatment might mediate the response of rapeseed to this important stress. This study represents the first genome-wide analysis of PHT family genes in Brassica species. Our findings improve our understanding of PHT family genes and provide a basis for further studies of BnaPHTs in plant tolerance to heavy metal stress.
Yuanyuan Wan; Zhen Wang; Jichun Xia; Shulin Shen; Mingwei Guan; Meichen Zhu; Cailin Qiao; Fujun Sun; Ying Liang; Jiana Li; Kun Lu; Cunmin Qu. Genome-Wide Analysis of Phosphorus Transporter Genes in Brassica and Their Roles in Heavy Metal Stress Tolerance. International Journal of Molecular Sciences 2020, 21, 2209 .
AMA StyleYuanyuan Wan, Zhen Wang, Jichun Xia, Shulin Shen, Mingwei Guan, Meichen Zhu, Cailin Qiao, Fujun Sun, Ying Liang, Jiana Li, Kun Lu, Cunmin Qu. Genome-Wide Analysis of Phosphorus Transporter Genes in Brassica and Their Roles in Heavy Metal Stress Tolerance. International Journal of Molecular Sciences. 2020; 21 (6):2209.
Chicago/Turabian StyleYuanyuan Wan; Zhen Wang; Jichun Xia; Shulin Shen; Mingwei Guan; Meichen Zhu; Cailin Qiao; Fujun Sun; Ying Liang; Jiana Li; Kun Lu; Cunmin Qu. 2020. "Genome-Wide Analysis of Phosphorus Transporter Genes in Brassica and Their Roles in Heavy Metal Stress Tolerance." International Journal of Molecular Sciences 21, no. 6: 2209.
Background The basic helix-loop-helix (bHLH) gene family is one of the largest transcription factor families in plants and is functionally characterized in diverse species. However, less is known about its functions in the economically important allopolyploid oil crop, Brassica napus. Results We identified 602 potential bHLHs in the B. napus genome (BnabHLHs) and categorized them into 35 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure, and exon-intron organization analysis. The intron insertion patterns of this gene family were analyzed and a total of eight types were identified in the bHLH regions of BnabHLHs. Chromosome distribution and synteny analyses revealed that hybridization between Brassica rapa and Brassica oleracea was the main expansion mechanism for BnabHLHs. Expression analyses showed that BnabHLHs were widely in different plant tissues and formed seven main patterns, suggesting they may participate in various aspects of B. napus development. Furthermore, when roots were treated with five different hormones (IAA, auxin; GA3, gibberellin; 6-BA, cytokinin; ABA, abscisic acid and ACC, ethylene), the expression profiles of BnabHLHs changed significantly, with many showing increased expression. The induction of five candidate BnabHLHs was confirmed following the five hormone treatments via qRT-PCR. Up to 246 BnabHLHs from nine subfamilies were predicted to have potential roles relating to root development through the joint analysis of their expression profiles and homolog function. Conclusion The 602 BnabHLHs identified from B. napus were classified into 35 subfamilies, and those members from the same subfamily generally had similar sequence motifs. Overall, we found that BnabHLHs may be widely involved in root development in B. napus. Moreover, this study provides important insights into the potential functions of the BnabHLHs super gene family and thus will be useful in future gene function research.
Yun-Zhuo Ke; Yun-Wen Wu; Hong-Jun Zhou; Ping Chen; Mang-Mang Wang; Ming-Ming Liu; Peng-Feng Li; Jin Yang; Jia-Na Li; Hai Du. Genome-wide survey of the bHLH super gene family in Brassica napus. BMC Plant Biology 2020, 20, 1 -16.
AMA StyleYun-Zhuo Ke, Yun-Wen Wu, Hong-Jun Zhou, Ping Chen, Mang-Mang Wang, Ming-Ming Liu, Peng-Feng Li, Jin Yang, Jia-Na Li, Hai Du. Genome-wide survey of the bHLH super gene family in Brassica napus. BMC Plant Biology. 2020; 20 (1):1-16.
Chicago/Turabian StyleYun-Zhuo Ke; Yun-Wen Wu; Hong-Jun Zhou; Ping Chen; Mang-Mang Wang; Ming-Ming Liu; Peng-Feng Li; Jin Yang; Jia-Na Li; Hai Du. 2020. "Genome-wide survey of the bHLH super gene family in Brassica napus." BMC Plant Biology 20, no. 1: 1-16.
Background Increasing seed oil content is one of the most important targets for rapeseed (Brassica napus) breeding. However, genetic mechanisms of mature seed oil content in Brassica napus (B. napus) remain little known. To identify oil content-related genes, a genome-wide association study (GWAS) was performed using 588 accessions. Results High-throughput genome resequencing resulted in 385,692 high-quality single nucleotide polymorphism (SNPs) with a minor allele frequency (MAF) > 0.05. We identified 17 loci that were significantly associated with seed oil content, among which 12 SNPs were distributed on the A3 (11 loci) and A1 (one loci) chromosomes, and five novel significant SNPs on the C5 (one loci) and C7 (four loci) chromosomes, respectively. Subsequently, we characterized differentially expressed genes (DEGs) between the seeds and silique pericarps on main florescences and primary branches of extremely high- and low-oil content accessions (HO and LO). A total of 64 lipid metabolism-related DEGs were identified, 14 of which are involved in triacylglycerols (TAGs) biosynthesis and assembly. Additionally, we analyzed differences in transcription levels of key genes involved in de novo fatty acid biosynthesis in the plastid, TAGs assembly and lipid droplet packaging in the endoplasmic reticulum (ER) between high- and low-oil content B. napus accessions. Conclusions The combination of GWAS and transcriptome analyses revealed seven candidate genes located within the confidence intervals of significant SNPs. Current findings provide valuable information for facilitating marker-based breeding for higher seed oil content in B. napus.
Zhongchun Xiao; Chao Zhang; Fang Tang; Bo Yang; Liyuan Zhang; Jingsen Liu; Qiang Huo; Shufeng Wang; Shengting Li; Lijuan Wei; Hai Du; Cunmin Qu; Kun Lu; Jiana Li; Nannan Li. Identification of candidate genes controlling oil content by combination of genome-wide association and transcriptome analysis in the oilseed crop Brassica napus. Biotechnology for Biofuels 2019, 12, 1 -16.
AMA StyleZhongchun Xiao, Chao Zhang, Fang Tang, Bo Yang, Liyuan Zhang, Jingsen Liu, Qiang Huo, Shufeng Wang, Shengting Li, Lijuan Wei, Hai Du, Cunmin Qu, Kun Lu, Jiana Li, Nannan Li. Identification of candidate genes controlling oil content by combination of genome-wide association and transcriptome analysis in the oilseed crop Brassica napus. Biotechnology for Biofuels. 2019; 12 (1):1-16.
Chicago/Turabian StyleZhongchun Xiao; Chao Zhang; Fang Tang; Bo Yang; Liyuan Zhang; Jingsen Liu; Qiang Huo; Shufeng Wang; Shengting Li; Lijuan Wei; Hai Du; Cunmin Qu; Kun Lu; Jiana Li; Nannan Li. 2019. "Identification of candidate genes controlling oil content by combination of genome-wide association and transcriptome analysis in the oilseed crop Brassica napus." Biotechnology for Biofuels 12, no. 1: 1-16.