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Dr. Kun Lu is working as Professor and Vice Dean at the College of Agronomy and Biotechnology, SWU, China. His areas of interest include crop yield and polyploid evolution. He regularly lectures and publishes in international journals and has been the recipient of grants from NSFC. He is an editorial board member of Frontiers in Plant Science, PeerJ, and PLoS ONE and reviewer for the NSFC and more than 40 international journals, including Plant Cell, NP, PBJ, PJ, and Food Chem.
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.
Rapeseed (Brassica napus) is the second largest oilseed crop worldwide. Silique length and seed weight are positively correlated with its yield. Here, a rapeseed gene DEFECTIVE IN ANTHER DEHISCENCE 1 (DAD1; Bna.A05DAD1) was isolated, and its overexpression could significantly increase the SL and SW in Arabidopsis and rapeseed through the enlargement of the silique pericarp cells. Bna.A05DAD1 expression is observed in the seeds and anthers specifically, and its associated protein is localized to the chloroplast. Transcriptomic analysis revealed that the fatty acid biosynthesis and phytohormone response pathways were influenced with Bna.A05DAD1 overexpression. Since the FATTY ACID DESATURASE 2/6 (FAD2/6) and FAD3/7/8 genes were significantly higher than the wild type, the concentrations of linoleic acid and linolenic acid were increased in the DAD1-overexpressing rapeseed plants. Besides, overexpression of Bna.A05DAD1 suppressed the negative regulation of AUXIN RESPONSE FACTOR 18 (ARF18) through upregulation of jasmonate acid (JA) biosynthesis genes (ALLENE OXIDE CYCLASE 4, AOC4; ALLENE OXIDE SYNTHASE, Bna.A02AOS and OXOPHYTODIENOATE-REDUCTASE, Bna.C03OPR), resulting in activating of auxin response genes, leading the auxin to accumulate and the SL and SW increase. Our results suggest new views about the role Bna.A05DAD1 played in regulating fatty acid composition and increasing yield in rapeseed, as well as reveal an important mechanism of the crosstalk between the JA and auxin signaling pathways in the breeding of high-yielding rapeseed.
Miao Liu; Wei Chang; Mengna Yu; Yonghai Fan; GuoXia Shang; Yuanfang Xu; Yue Niu; Xumei Liu; Hong Zhu; Lishi Dai; Zhanglin Tang; Kai Zhang; Liezhao Liu; Cunmin Qu; Jiana Li; Kun Lu. Overexpression of DEFECTIVE IN ANTHER DEHISCENCE 1 increases rapeseed silique length through crosstalk between JA and auxin signaling. Industrial Crops and Products 2021, 168, 113576 .
AMA StyleMiao Liu, Wei Chang, Mengna Yu, Yonghai Fan, GuoXia Shang, Yuanfang Xu, Yue Niu, Xumei Liu, Hong Zhu, Lishi Dai, Zhanglin Tang, Kai Zhang, Liezhao Liu, Cunmin Qu, Jiana Li, Kun Lu. Overexpression of DEFECTIVE IN ANTHER DEHISCENCE 1 increases rapeseed silique length through crosstalk between JA and auxin signaling. Industrial Crops and Products. 2021; 168 ():113576.
Chicago/Turabian StyleMiao Liu; Wei Chang; Mengna Yu; Yonghai Fan; GuoXia Shang; Yuanfang Xu; Yue Niu; Xumei Liu; Hong Zhu; Lishi Dai; Zhanglin Tang; Kai Zhang; Liezhao Liu; Cunmin Qu; Jiana Li; Kun Lu. 2021. "Overexpression of DEFECTIVE IN ANTHER DEHISCENCE 1 increases rapeseed silique length through crosstalk between JA and auxin signaling." Industrial Crops and Products 168, no. : 113576.
Rapeseed (Brassica napus L.) is the second most important oilseed crop in edible vegetable oil and bioenergy; however, drought stress generally causes a decrease in rapeseed yield and oil content, especially during the reproductive stage. In our study, we measured the oil and protein contents and gibberellic acid (GA) and abscisic acid (ABA) levels in seeds that were acquired on the 30th, 40th and 50th days after flowering under control and drought treatments. RNA and protein libraries were constructed from the stressed seeds to perform transcriptome and proteome analyses, respectively. Our results demonstrated that the oil content decreased due to four primary mechanisms: downregulation of fatty acid biosynthesis‐associated genes and proteins; upregulation of fatty acid degradation‐associated genes and proteins; enhancement of protein storage due to changes in the abundances of relevant genes and proteins; upregulation of Gly‐Asp‐Ser‐Leu (GDSL) gene expression, potentially as the result of upregulating the GA biosynthesis gene GA20ox3 and downregulating the GA inactivating gene GA2ox3 and thus an increase in GA content. At maturing seeds, oil storage change may also relate to ABA content increasing as the upregulation of two members of NCED6 (9‐cis‐epoxycarotenoid dioxygenase) gene family involved in ABA biosynthesis, and the upregulation of genes involved in ABA signal transduction. These results will help to establish a foundation for breeding excellent varieties of rapeseed with high oil content for areas with frequent droughts to promote the supply of edible vegetable oil and biofuel.
Yangyang Li; Linxue Zhang; Sheng Hu; Jinfeng Zhang; Lin Wang; Xiaoke Ping; Jia Wang; Jiana Li; Kun Lu; Zhanglin Tang; Liezhao Liu. Transcriptome and proteome analyses of the molecular mechanisms underlying changes in oil storage under drought stress in Brassica napus L. GCB Bioenergy 2021, 13, 1071 -1086.
AMA StyleYangyang Li, Linxue Zhang, Sheng Hu, Jinfeng Zhang, Lin Wang, Xiaoke Ping, Jia Wang, Jiana Li, Kun Lu, Zhanglin Tang, Liezhao Liu. Transcriptome and proteome analyses of the molecular mechanisms underlying changes in oil storage under drought stress in Brassica napus L. GCB Bioenergy. 2021; 13 (7):1071-1086.
Chicago/Turabian StyleYangyang Li; Linxue Zhang; Sheng Hu; Jinfeng Zhang; Lin Wang; Xiaoke Ping; Jia Wang; Jiana Li; Kun Lu; Zhanglin Tang; Liezhao Liu. 2021. "Transcriptome and proteome analyses of the molecular mechanisms underlying changes in oil storage under drought stress in Brassica napus L." GCB Bioenergy 13, no. 7: 1071-1086.
Petal size determines the value of ornamental plants, and thus their economic value. However, the molecular mechanisms controlling petal size remain unclear in most non-model species. To identify quantitative trait loci and candidate genes controlling petal size in rapeseed (Brassica napus), we performed a genome-wide association study (GWAS) using data from 588 accessions over three consecutive years. We detected 16 significant single nucleotide polymorphisms (SNPs) associated with petal size, with the most significant SNPs located on chromosomes A05 and C06. A combination of GWAS and transcriptomic sequencing based on two accessions with contrasting differences in petal size identified 52 differentially expressed genes (DEGs) that may control petal size variation in rapeseed. In particular, the rapeseed gene BnaA05.RAP2.2, homologous to Arabidopsis RAP2.2, may be critical to the negative control of petal size through the ethylene signaling pathway. In addition, a comparison of petal epidermal cells indicated that petal size differences between the two contrasting accessions were determined mainly by differences in cell number. Finally, we propose a model for the control of petal size in rapeseed through ethylene and cytokinin signaling pathways. Our results provide insights into the genetic mechanisms regulating petal size in flowering plants.
Mingchao Qian; Yonghai Fan; Yanhua Li; Miao Liu; Wei Sun; Huichun Duan; Mengna Yu; Wei Chang; Yue Niu; Xiaodong Li; Ying Liang; Cunmin Qu; Jiana Li; Kun Lu. Genome-wide association study and transcriptome comparison reveal novel QTL and candidate genes that control petal size in rapeseed. Journal of Experimental Botany 2021, 72, 3597 -3610.
AMA StyleMingchao Qian, Yonghai Fan, Yanhua Li, Miao Liu, Wei Sun, Huichun Duan, Mengna Yu, Wei Chang, Yue Niu, Xiaodong Li, Ying Liang, Cunmin Qu, Jiana Li, Kun Lu. Genome-wide association study and transcriptome comparison reveal novel QTL and candidate genes that control petal size in rapeseed. Journal of Experimental Botany. 2021; 72 (10):3597-3610.
Chicago/Turabian StyleMingchao Qian; Yonghai Fan; Yanhua Li; Miao Liu; Wei Sun; Huichun Duan; Mengna Yu; Wei Chang; Yue Niu; Xiaodong Li; Ying Liang; Cunmin Qu; Jiana Li; Kun Lu. 2021. "Genome-wide association study and transcriptome comparison reveal novel QTL and candidate genes that control petal size in rapeseed." Journal of Experimental Botany 72, no. 10: 3597-3610.
Cinnamoyl-CoA reductase (CCR) is the entry point of lignin pathway and a crucial locus in dissection and manipulation of associated traits, but its functional dissection in Brassicaceae plants is largely lagged behind though Arabidopsis thaliana CCR1 has been characterized to certain extent. Here, 16 CCR genes are identified from Brassica napus and its parental species B. rapa and B. oleracea. Brassicaceae CCR genes are divided into CCR1 subfamily and CCR2 subfamily with divergent organ-specificity, yellow-seed trait participation and stresses responsiveness. CCR1 is preferential in G- and H-lignins biosynthesis and vascular development, while CCR2 has a deviation to S-lignin biosynthesis and interfascicular fiber development. CCR1 has stronger effects on lignification-related development, lodging resistance, phenylpropanoid flux control and seed coat pigmentation, whereas CCR2 controls sinapates levels. CCR1 upregulation could delay bolting and flowering time, while CCR2 upregulation weakens vascular system in leaf due to suppressed G lignin accumulation. Besides, CCR1 and CCR2 are deeply but almost oppositely linked with glucosinolates metabolism through inter-pathway crosstalk. Strangely, upregulation of both CCR1 and CCR2 could not enhance resistance to UV-B and S. sclerotiorum though CCR2 is sharply induced by them. These results provide systemic dissection on Brassica CCRs and CCR1-CCR2 divergence in Brassicaceae. Highlight Brassicaceae contains two types of Cinnamoyl-CoA reductase. As revealed in Brassica napus, they are divergently involved in lignin monomer biosynthesis, tissue lignification, phenylpropanoid flux control, and inter-pathway crosstalk with glucosinolates.
Nengwen Yin; Bo Li; Xue Liu; Ying Liang; Jianping Lian; Yufei Xue; Cunmin Qu; Kun Lu; Lijuan Wei; Rui Wang; Jiana Li; Yourong Chai. Two Types of Cinnamoyl-CoA Reductase Function Divergently in Tissue Lignification, Phenylpropanoids Flux Control, and Inter-pathway Cross-talk with Glucosinolates as Revealed in Brassica napus. 2021, 1 .
AMA StyleNengwen Yin, Bo Li, Xue Liu, Ying Liang, Jianping Lian, Yufei Xue, Cunmin Qu, Kun Lu, Lijuan Wei, Rui Wang, Jiana Li, Yourong Chai. Two Types of Cinnamoyl-CoA Reductase Function Divergently in Tissue Lignification, Phenylpropanoids Flux Control, and Inter-pathway Cross-talk with Glucosinolates as Revealed in Brassica napus. . 2021; ():1.
Chicago/Turabian StyleNengwen Yin; Bo Li; Xue Liu; Ying Liang; Jianping Lian; Yufei Xue; Cunmin Qu; Kun Lu; Lijuan Wei; Rui Wang; Jiana Li; Yourong Chai. 2021. "Two Types of Cinnamoyl-CoA Reductase Function Divergently in Tissue Lignification, Phenylpropanoids Flux Control, and Inter-pathway Cross-talk with Glucosinolates as Revealed in Brassica napus." , no. : 1.
Transcription factors (TFs) and their complex interplay are essential for directing specific genetic programs, such as responses to environmental stresses, tissue development, or cell differentiation by regulating gene expression. Knowledge regarding TF–TF cooperations could be promising in gaining insight into the developmental switches between the cultivars of Brassica napus L., namely Zhongshuang11 (ZS11), a double-low accession with high-oil- content, and Zhongyou821 (ZY821), a double-high accession with low-oil-content. In this regard, we analysed a time series RNA-seq data set of seed tissue from both of the cultivars by mainly focusing on the monotonically expressed genes (MEGs). The consideration of the MEGs enables the capturing of multi-stage progression processes that are orchestrated by the cooperative TFs and, thus, facilitates the understanding of the molecular mechanisms determining seed oil content. Our findings show that TF families, such as NAC, MYB, DOF, GATA, and HD-ZIP are highly involved in the seed developmental process. Particularly, their preferential partner choices as well as changes in their gene expression profiles seem to be strongly associated with the differentiation of the oil content between the two cultivars. These findings are essential in enhancing our understanding of the genetic programs in both cultivars and developing novel hypotheses for further experimental studies.
Abirami Rajavel; Selina Klees; Johanna-Sophie Schlüter; Hendrik Bertram; Kun Lu; Armin Schmitt; Mehmet Gültas. Unravelling the Complex Interplay of Transcription Factors Orchestrating Seed Oil Content in Brassica napus L. International Journal of Molecular Sciences 2021, 22, 1033 .
AMA StyleAbirami Rajavel, Selina Klees, Johanna-Sophie Schlüter, Hendrik Bertram, Kun Lu, Armin Schmitt, Mehmet Gültas. Unravelling the Complex Interplay of Transcription Factors Orchestrating Seed Oil Content in Brassica napus L. International Journal of Molecular Sciences. 2021; 22 (3):1033.
Chicago/Turabian StyleAbirami Rajavel; Selina Klees; Johanna-Sophie Schlüter; Hendrik Bertram; Kun Lu; Armin Schmitt; Mehmet Gültas. 2021. "Unravelling the Complex Interplay of Transcription Factors Orchestrating Seed Oil Content in Brassica napus L." International Journal of Molecular Sciences 22, no. 3: 1033.
Rapeseed (Brassica napus) is one of the most important oil crops worldwide; however, drought seriously curtails its growth and productivity, and identifying drought-tolerant germplasm is an efficient and low-cost strategy for addressing water shortages. Here, we phenotyped a panel of 264 B. napus accessions at the full-bloom stage using a water loss ratio (WLR) as a drought-tolerant index, and identified eight low-WLR and six high-WLR accessions, regarded as drought-tolerant and drought-sensitive, respectively. Comparing with drought-sensitive accessions at the seedling stage, drought-tolerant accessions had shown better performance in maintaining fresh and dry weights, and performed the higher expression of drought-induced marker genes under drought stress. Subsequently, a total of 139 SNPs (single nucleotide polymorphisms) were identified associated with the WLR using a genome-wide association study (GWAS) among 264 B. napus accessions, with the largest number SNPs at chromosome A10, and 13 SNPs significantly were associated with the WLR (–log10(p-value) > 6). Furthermore, four putative candidate genes (BnaC09.RPS6, BnaC09.MATE, BnaA10.PPD5, and BnaC09.Histone) were screened involving in drought tolerance in B. napus. Together, our results highlight the WLR's importance in drought tolerance and establish the foundation for improving WLR-associated drought tolerance in rapeseed.
Ali Shahzad; MinChao Qian; Bangyang Sun; Umer Mahmood; Shengting Li; Yonghai Fan; Wei Chang; Lishi Dai; Hong Zhu; Jiana Li; Cunmin Qu; Kun Lu. Genome-wide association study identifies novel loci and candidate genes for drought stress tolerance in rapeseed. Oil Crop Science 2021, 6, 12 -22.
AMA StyleAli Shahzad, MinChao Qian, Bangyang Sun, Umer Mahmood, Shengting Li, Yonghai Fan, Wei Chang, Lishi Dai, Hong Zhu, Jiana Li, Cunmin Qu, Kun Lu. Genome-wide association study identifies novel loci and candidate genes for drought stress tolerance in rapeseed. Oil Crop Science. 2021; 6 (1):12-22.
Chicago/Turabian StyleAli Shahzad; MinChao Qian; Bangyang Sun; Umer Mahmood; Shengting Li; Yonghai Fan; Wei Chang; Lishi Dai; Hong Zhu; Jiana Li; Cunmin Qu; Kun Lu. 2021. "Genome-wide association study identifies novel loci and candidate genes for drought stress tolerance in rapeseed." Oil Crop Science 6, no. 1: 12-22.
Regulatory SNPs (rSNPs) are a special class of SNPs which have a high potential to affect the phenotype due to their impact on DNA-binding of transcription factors (TFs). Thus, the knowledge about such rSNPs and TFs could provide essential information regarding different genetic programs, such as tissue development or environmental stress responses. In this study, we use a multi-omics approach by combining genomics, transcriptomics, and proteomics data of two different Brassica napus L. cultivars, namely Zhongshuang11 (ZS11) and Zhongyou821 (ZY821), with high and low oil content, respectively, to monitor the regulatory interplay between rSNPs, TFs and their corresponding genes in the tissues flower, leaf, stem, and root. By predicting the effect of rSNPs on TF-binding and by measuring their association with the cultivars, we identified a total of 41,117 rSNPs, of which 1141 are significantly associated with oil content. We revealed several enriched members of the TF families DOF, MYB, NAC, or TCP, which are important for directing transcriptional programs regulating differential expression of genes within the tissues. In this work, we provide the first genome-wide collection of rSNPs for B. napus and their impact on the regulation of gene expression in vegetative and floral tissues, which will be highly valuable for future studies on rSNPs and gene regulation.
Selina Klees; Thomas Lange; Hendrik Bertram; Abirami Rajavel; Johanna-Sophie Schlüter; Kun Lu; Armin Schmitt; Mehmet Gültas. In Silico Identification of the Complex Interplay between Regulatory SNPs, Transcription Factors, and Their Related Genes in Brassica napus L. Using Multi-Omics Data. International Journal of Molecular Sciences 2021, 22, 789 .
AMA StyleSelina Klees, Thomas Lange, Hendrik Bertram, Abirami Rajavel, Johanna-Sophie Schlüter, Kun Lu, Armin Schmitt, Mehmet Gültas. In Silico Identification of the Complex Interplay between Regulatory SNPs, Transcription Factors, and Their Related Genes in Brassica napus L. Using Multi-Omics Data. International Journal of Molecular Sciences. 2021; 22 (2):789.
Chicago/Turabian StyleSelina Klees; Thomas Lange; Hendrik Bertram; Abirami Rajavel; Johanna-Sophie Schlüter; Kun Lu; Armin Schmitt; Mehmet Gültas. 2021. "In Silico Identification of the Complex Interplay between Regulatory SNPs, Transcription Factors, and Their Related Genes in Brassica napus L. Using Multi-Omics Data." International Journal of Molecular Sciences 22, no. 2: 789.
Rapeseed (Brassica napus) is one of the most important oil crops worldwide; however, drought seriously curtails its growth and productivity. Identifying drought-tolerant germplasm is an efficient strategy for addressing water shortages. Here, we phenotyped a panel of 264 B. napus accessions at full-bloom stage using water loss ratio (WLR) as drought-tolerant index. It identified 8 low-WLR and 6 high-WLR accessions, regarded as drought-tolerant and drought-sensitive, respectively. Comparing with drought-sensitive accessions at the seedling stage, drought-tolerant accessions had shown better performance in maintaining fresh and dry weights, and performed the higher expression of drought-induced marker genes under drought stress. Subsequently, a total of 139 SNPs (single nucleotide polymorphisms) were identified associated with the WLR using a genome-wide association study (GWAS) among 264 B. napus accessions, with the largest number SNPs at chromosome A10, and 13 SNPs significantly were associated with the WLR (–log10(p-value) > 6). Furthermore, 4 putative candidate genes (BnaC09.RPS6, BnaC09.MATE, BnaA10.PPD5 and BnaC09.Histone) were screened involving in drought tolerance in B. napus. Together, our results highlight the WLR's importance in drought tolerance and establish the foundation for improving WLR-associated drought tolerance in rapeseed.
Ali Shahzad; MinChao Qian; Bangyang Sun; Umer Mahmood; Shengting Li; Yonghai Fan; Wei Chang; Lishi Dai; Hong Zhu; Jiana Li; Cunmin Qu; Kun Lu. WITHDRAWN: Genome-wide association study identifies novel loci and candidate genes for drought stress tolerance in rapeseed. Oil Crop Science 2021, 1 .
AMA StyleAli Shahzad, MinChao Qian, Bangyang Sun, Umer Mahmood, Shengting Li, Yonghai Fan, Wei Chang, Lishi Dai, Hong Zhu, Jiana Li, Cunmin Qu, Kun Lu. WITHDRAWN: Genome-wide association study identifies novel loci and candidate genes for drought stress tolerance in rapeseed. Oil Crop Science. 2021; ():1.
Chicago/Turabian StyleAli Shahzad; MinChao Qian; Bangyang Sun; Umer Mahmood; Shengting Li; Yonghai Fan; Wei Chang; Lishi Dai; Hong Zhu; Jiana Li; Cunmin Qu; Kun Lu. 2021. "WITHDRAWN: Genome-wide association study identifies novel loci and candidate genes for drought stress tolerance in rapeseed." Oil Crop Science , no. : 1.
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.
Polygalacturonase (PG) is a hydrolase that participates in pectin degradation, pod shattering and fruit softening. Here, we identified 2786 PG genes across 54 plants, which could be divided into three groups. Evolutionary analysis suggested that PG family originated from the charophyte green algae, and Subgroups A2–A4 evolved from the Subgroup A1 after the tracheophyte–angiosperm split. Whole-genome duplication was the major force leading to PG gene expansion. Interestingly, the PG genes continuously expanded in eudicots, whereas it contracted in monocots after the eudicot–monocot split. PG genes in Group A are expressed at high levels in floral organs, whereas genes in Groups B and C are expressed at high levels in various tissues. Moreover, three BnaPG15 members were found for their potential possibility in pod shattering in Brassica napus. Our results provide new insight into the evolutionary history of PG family, and their potentially functional role in plants.
Umer Mahmood; Yonghai Fan; Siyu Wei; Yue Niu; Yanhua Li; Hualei Huang; Yuling Chen; Zhanglin Tang; Liezhao Liu; Cunmin Qu; Kai Zhang; Jiana Li; Kun Lu. Comprehensive analysis of polygalacturonase genes offers new insights into their origin and functional evolution in land plants. Genomics 2020, 113, 1096 -1108.
AMA StyleUmer Mahmood, Yonghai Fan, Siyu Wei, Yue Niu, Yanhua Li, Hualei Huang, Yuling Chen, Zhanglin Tang, Liezhao Liu, Cunmin Qu, Kai Zhang, Jiana Li, Kun Lu. Comprehensive analysis of polygalacturonase genes offers new insights into their origin and functional evolution in land plants. Genomics. 2020; 113 (1):1096-1108.
Chicago/Turabian StyleUmer Mahmood; Yonghai Fan; Siyu Wei; Yue Niu; Yanhua Li; Hualei Huang; Yuling Chen; Zhanglin Tang; Liezhao Liu; Cunmin Qu; Kai Zhang; Jiana Li; Kun Lu. 2020. "Comprehensive analysis of polygalacturonase genes offers new insights into their origin and functional evolution in land plants." Genomics 113, no. 1: 1096-1108.
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.
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.
Although the leaf is the most important photosynthetic organ in most plants, many of the molecular mechanisms underlying leaf developmental dynamics remain to be explored. To better understand the transcriptional regulatory mechanisms involved in leaf development, we conducted comparative transcriptomic and metabolomic analysis of leaves from seven positions on tobacco (Nicotiana tabacum) plants. A total of 35,622 unique differentially expressed genes and 79 metabolites were identified. A time-series expression analysis detected two interesting transcriptional profiles, one comprising 10,197 genes that displayed continual up-regulation during leaf development and another comprising 4696 genes that displayed continual down-regulation. Combining these data with co-expression network results identified four important regulatory networks involved in photorespiration and the tricarboxylic acid cycle; these networks may regulate carbon/nitrogen balance during leaf development. We also found that the transcription factor NtGATA5 acts as a hub associated with C and N metabolism and chloroplast development during leaf development through regulation of phytohormones. Furthermore, we investigated the transcriptional dynamics of genes involved in the auxin, cytokinin, and jasmonic acid biosynthesis and signaling pathways during tobacco leaf development. Overall, our study greatly expands the understanding of the regulatory network controlling developmental dynamics in plant leaves.
Wei Chang; Huina Zhao; Shizhou Yu; Jing Yu; Kai Cai; Wei Sun; Xumei Liu; Xiaodong Li; Mengna Yu; Shahzad Ali; Kai Zhang; Cunmin Qu; Bo Lei; Kun Lu. Comparative transcriptome and metabolomic profiling reveal the complex mechanisms underlying the developmental dynamics of tobacco leaves. Genomics 2020, 112, 4009 -4022.
AMA StyleWei Chang, Huina Zhao, Shizhou Yu, Jing Yu, Kai Cai, Wei Sun, Xumei Liu, Xiaodong Li, Mengna Yu, Shahzad Ali, Kai Zhang, Cunmin Qu, Bo Lei, Kun Lu. Comparative transcriptome and metabolomic profiling reveal the complex mechanisms underlying the developmental dynamics of tobacco leaves. Genomics. 2020; 112 (6):4009-4022.
Chicago/Turabian StyleWei Chang; Huina Zhao; Shizhou Yu; Jing Yu; Kai Cai; Wei Sun; Xumei Liu; Xiaodong Li; Mengna Yu; Shahzad Ali; Kai Zhang; Cunmin Qu; Bo Lei; Kun Lu. 2020. "Comparative transcriptome and metabolomic profiling reveal the complex mechanisms underlying the developmental dynamics of tobacco leaves." Genomics 112, no. 6: 4009-4022.
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.
The AINTEGUMENTA-like (AIL) proteins, which belong to the AP2 family, play important roles in regulating the growth and development of plant organs. The AIL family has not yet been comprehensively studied in rapeseed (Brassica napus), an allotetraploid and model organism for the study of polyploid evolution. In the present study, 99 AIL family genes were identified and characterized from B. rapa, B. oleracea, B. napus, B. juncea, and B. nigra using a comprehensive genome-wide study, including analyses of phylogeny, gene structure, chromosomal localization, and expression pattern. Using a phylogenetic analysis, the AIL genes were divided into eight groups, which were closely related to the eight AtAIL genes, and which shared highly conserved structural features within the same subfamily. The non-synonymous/synonymous substitution ratios of the paralogs and orthologs were less than 1, suggesting that the AIL genes mainly experienced purifying selection during evolution. In addition, the RNA sequencing data and qRT-PCR analysis revealed that the B. napus AIL genes exhibited organ- and developmental stage-specific expression patterns. Certain genes were highly expressed in the developing seeds (BnaAIL1, BnaAIL2, BnaAIL5, and BnaAIL6), the roots (BnaANT, BnaAIL5, and BnaAIL6), and the stem (BnaAIL7B). Our results provide valuable information for further functional analysis of the AIL family in B. napus and related Brassica species.
Shulin Shen; Fujun Sun; Meichen Zhu; Si Chen; Mingwei Guan; Rui Chen; Fang Tang; Nengwen Yin; Xinfu Xu; Zhanglin Tang; Jiana Li; Kun Lu; Cunmin Qu. Genome-wide identification AINTEGUMENTA-like (AIL) genes in Brassica species and expression patterns during reproductive development in Brassica napus L. PLOS ONE 2020, 15, e0234411 .
AMA StyleShulin Shen, Fujun Sun, Meichen Zhu, Si Chen, Mingwei Guan, Rui Chen, Fang Tang, Nengwen Yin, Xinfu Xu, Zhanglin Tang, Jiana Li, Kun Lu, Cunmin Qu. Genome-wide identification AINTEGUMENTA-like (AIL) genes in Brassica species and expression patterns during reproductive development in Brassica napus L. PLOS ONE. 2020; 15 (6):e0234411.
Chicago/Turabian StyleShulin Shen; Fujun Sun; Meichen Zhu; Si Chen; Mingwei Guan; Rui Chen; Fang Tang; Nengwen Yin; Xinfu Xu; Zhanglin Tang; Jiana Li; Kun Lu; Cunmin Qu. 2020. "Genome-wide identification AINTEGUMENTA-like (AIL) genes in Brassica species and expression patterns during reproductive development in Brassica napus L." PLOS ONE 15, no. 6: e0234411.
Background Brassica rapa is an important oilseed and vegetable crop species and is the A subgenome donor of two important oilseed Brassica crops, Brassica napus and Brassica juncea. Although seed size (SZ), seed color (SC), and oil content (OC) substantially affect seed yield and quality, the mechanisms regulating these traits in Brassica crops remain unclear. Results We collected seeds from a pair of B. rapa accessions with significantly different SZ, SC, and OC at seven seed developmental stages (every 7 days from 7 to 49 days after pollination), and identified 28,954 differentially expressed genes (DEGs) from seven pairwise comparisons between accessions at each developmental stage. K-means clustering identified a group of cell cycle-related genes closely connected to variation in SZ of B. rapa. A weighted correlation analysis using the WGCNA package in R revealed two important co-expression modules comprising genes whose expression was positively correlated with SZ increase and negatively correlated with seed yellowness, respectively. Upregulated expression of cell cycle-related genes in one module was important for the G2/M cell cycle transition, and the transcription factor Bra.A05TSO1 seemed to positively stimulate the expression of two CYCB1;2 genes to promote seed development. In the second module, a conserved complex regulated by the transcription factor TT8 appear to determine SC through downregulation of TT8 and its target genes TT3, TT18, and ANR. In the third module, WRI1 and FUS3 were conserved to increase the seed OC, and Bra.A03GRF5 was revealed as a key transcription factor on lipid biosynthesis. Further, upregulation of genes involved in triacylglycerol biosynthesis and storage in the seed oil body may increase OC. We further validated the accuracy of the transcriptome data by quantitative real-time PCR of 15 DEGs. Finally, we used our results to construct detailed models to clarify the regulatory mechanisms underlying variations in SZ, SC, and OC in B. rapa. Conclusions This study provides insight into the regulatory mechanisms underlying the variations of SZ, SC, and OC in plants based on transcriptome comparison. The findings hold great promise for improving seed yield, quality and OC through genetic engineering of critical genes in future molecular breeding.
Yue Niu; Limin Wu; Yanhua Li; Hualei Huang; Mingchao Qian; Wei Sun; Hong Zhu; Yuanfang Xu; Yonghai Fan; Umer Mahmood; Benbo Xu; Kai Zhang; Cunmin Qu; Jiana Li; Kun Lu. Deciphering the transcriptional regulatory networks that control size, color, and oil content in Brassica rapa seeds. Biotechnology for Biofuels 2020, 13, 1 -20.
AMA StyleYue Niu, Limin Wu, Yanhua Li, Hualei Huang, Mingchao Qian, Wei Sun, Hong Zhu, Yuanfang Xu, Yonghai Fan, Umer Mahmood, Benbo Xu, Kai Zhang, Cunmin Qu, Jiana Li, Kun Lu. Deciphering the transcriptional regulatory networks that control size, color, and oil content in Brassica rapa seeds. Biotechnology for Biofuels. 2020; 13 (1):1-20.
Chicago/Turabian StyleYue Niu; Limin Wu; Yanhua Li; Hualei Huang; Mingchao Qian; Wei Sun; Hong Zhu; Yuanfang Xu; Yonghai Fan; Umer Mahmood; Benbo Xu; Kai Zhang; Cunmin Qu; Jiana Li; Kun Lu. 2020. "Deciphering the transcriptional regulatory networks that control size, color, and oil content in Brassica rapa seeds." Biotechnology for Biofuels 13, no. 1: 1-20.
Background: Brassica rapa is an important oilseed and vegetable crop species and is the A subgenome donor of two important oilseed Brassica crops, Brassica napus and Brassica juncea. Although seed size (SZ), seed color (SC), and oil content (OC) substantially affect seed yield and quality, the mechanisms regulating these traits in Brassica crops remain unclear.Results: We collected seeds from a pair of B. rapa accessions with significantly different SZ, SC, and OC at seven seed developmental stages (every 7 days from 7 to 49 days after pollination), and identified 28,954 differentially expressed genes (DEGs) from seven pairwise comparisons between accessions at each developmental stage. K-means clustering identified a group of cell cycle-related genes closely connected to variation in SZ of B. rapa. A weighted correlation analysis using the WGCNA package in R revealed two important co-expression modules comprising genes whose expression was positively correlated with SZ increase and negatively correlated with seed yellowness, respectively. Upregulated expression of cell cycle-related genes in one module was important for the G2/M cell cycle transition, and the transcription factor Bra.A05TSO1 seemed to positively stimulate the expression of two CYCB1;2 genes to promote seed development. In the second module, a conserved complex regulated by the transcription factor TT8 appear to determine SC through downregulation of TT8 and its target genes TT3, TT18, and ANR. In the third module, WRI1 and FUS3 were conserved to increase the seed OC, and Bra.A03GRF5 was revealed as a key transcription factor on lipid biosynthesis. Further, upregulation of genes involved in triacylglycerol biosynthesis and storage in the seed oil body may increase OC. We further validated the accuracy of the transcriptome data by quantitative real-time PCR of 15 DEGs. Finally, we used our results to construct detailed models to clarify the regulatory mechanisms underlying variations in SZ, SC, and OC in B. rapa.Conclusions: This study provides insight into the regulatory mechanisms underlying the variations of SZ, SC, and OC in plants based on transcriptome comparison. The findings hold great promise for improving seed yield, quality and OC through genetic engineering of critical genes in future molecular breeding.
Yue Niu; Limin Wu; Yanhua Li; Hualei Huang; Mingchao Qian; Wei Sun; Hong Zhu; Yuanfang Xu; Yonghai Fan; Umer Mahmood; Benbo Xu; Kai Zhang; Cunmin Qu; Jiana Li; Kun Lu. Deciphering the transcriptional regulatory networks that control size, color, and oil content in Brassica rapa seeds. 2020, 1 .
AMA StyleYue Niu, Limin Wu, Yanhua Li, Hualei Huang, Mingchao Qian, Wei Sun, Hong Zhu, Yuanfang Xu, Yonghai Fan, Umer Mahmood, Benbo Xu, Kai Zhang, Cunmin Qu, Jiana Li, Kun Lu. Deciphering the transcriptional regulatory networks that control size, color, and oil content in Brassica rapa seeds. . 2020; ():1.
Chicago/Turabian StyleYue Niu; Limin Wu; Yanhua Li; Hualei Huang; Mingchao Qian; Wei Sun; Hong Zhu; Yuanfang Xu; Yonghai Fan; Umer Mahmood; Benbo Xu; Kai Zhang; Cunmin Qu; Jiana Li; Kun Lu. 2020. "Deciphering the transcriptional regulatory networks that control size, color, and oil content in Brassica rapa seeds." , no. : 1.