An integrated omics analysis reveals molecular mechanisms that are associated with differences in seed oil content between Glycine max and Brassica napus

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.

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Development and screening of EMS mutants with altered seed oil content or fatty acid composition in Brassica napus

The Plant Journal ◽

10.1111/tpj.15003 ◽

2020 ◽

Vol 104 (5) ◽

pp. 1410-1422

Author(s):

Shan Tang ◽

Dong‐Xu Liu ◽

Shaoping Lu ◽

Liangqian Yu ◽

Yuqing Li ◽

...

Keyword(s):

Fatty Acid Composition ◽

Fatty Acid ◽

Brassica Napus ◽

Acid Composition ◽

Oil Content ◽

Seed Oil ◽

Seed Oil Content

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QTL analysis of an intervarietal set of substitution lines in Brassica napus: (i) Seed oil content and fatty acid composition

Heredity ◽

10.1038/sj.hdy.6800176 ◽

2003 ◽

Vol 90 (1) ◽

pp. 39-48 ◽

Cited By ~ 102

Author(s):

M J Burns ◽

S R Barnes ◽

J G Bowman ◽

M H E Clarke ◽

C P Werner ◽

...

Keyword(s):

Fatty Acid Composition ◽

Fatty Acid ◽

Brassica Napus ◽

Acid Composition ◽

Qtl Analysis ◽

Oil Content ◽

Seed Oil ◽

Seed Oil Content ◽

Substitution Lines

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A Novel Chimeric Mitochondrial Gene Confers Cytoplasmic Effects on Seed Oil Content in Polyploid Rapeseed (Brassica napus)

Molecular Plant ◽

10.1016/j.molp.2019.01.012 ◽

2019 ◽

Vol 12 (4) ◽

pp. 582-596 ◽

Cited By ~ 5

Author(s):

Jun Liu ◽

Wanjun Hao ◽

Jing Liu ◽

Shihang Fan ◽

Wei Zhao ◽

...

Keyword(s):

Brassica Napus ◽

Oil Content ◽

Seed Oil ◽

Mitochondrial Gene ◽

Seed Oil Content ◽

Cytoplasmic Effects

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Transcriptome profiling analysis reveals the role of silique in controlling seed oil content in Brassica napus

PLoS ONE ◽

10.1371/journal.pone.0179027 ◽

2017 ◽

Vol 12 (6) ◽

pp. e0179027 ◽

Cited By ~ 3

Author(s):

Ke-Lin Huang ◽

Mei-Li Zhang ◽

Guang-Jing Ma ◽

Huan Wu ◽

Xiao-Ming Wu ◽

...

Keyword(s):

Brassica Napus ◽

Oil Content ◽

Seed Oil ◽

Transcriptome Profiling ◽

Seed Oil Content ◽

Profiling Analysis

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Integrated Transcriptomic and Bioinformatics Analyses Reveal the Molecular Mechanisms for the Differences in Seed Oil and Starch Content Between Glycine max and Cicer arietinum

Frontiers in Plant Science ◽

10.3389/fpls.2021.743680 ◽

2021 ◽

Vol 12 ◽

Author(s):

Kun Cheng ◽

Yi-Fan Pan ◽

Lü-Meng Liu ◽

Han-Qing Zhang ◽

Yuan-Ming Zhang

Keyword(s):

Seed Development ◽

Oil Content ◽

Molecular Mechanisms ◽

Seed Oil ◽

Starch Content ◽

Development Stage ◽

Seed Oil Content ◽

Bioinformatics Analyses ◽

Oil Synthesis ◽

The Common

The seed oil and starch content of soybean are significantly different from that of chickpea. However, there are limited studies on its molecular mechanisms. To address this issue, we conducted integrated transcriptomic and bioinformatics analyses for species-specific genes and acyl-lipid-, starch-, and carbon metabolism-related genes. Among seven expressional patterns of soybean-specific genes, four were highly expressed at the middle- and late oil accumulation stages; these genes significantly enriched fatty acid synthesis and carbon metabolism, and along with common acetyl CoA carboxylase (ACCase) highly expressed at soybean middle seed development stage, common starch-degrading enzyme beta-amylase-5 (BAM5) was highly expressed at soybean early seed development stage and oil synthesis-related genes ACCase, KAS, KAR, ACP, and long-chain acyl-CoA synthetase (LACS) were co-expressed with WRI1, which may result in high seed oil content and low seed starch content in soybean. The common ADP-glucose pyrophosphorylase (AGPase) was highly expressed at chickpea middle seed development stage, along with more starch biosynthesis genes co-expressed with four-transcription-factor homologous genes in chickpea than in soybean, and the common WRI1 was not co-expressed with oil synthesis genes in chickpea, which may result in high seed starch content and low seed oil content in chickpea. The above results may be used to improve chickpea seed oil content in two ways. One is to edit CaWRI1 to co-express with oil synthesis-related genes, which may increase carbon metabolites flowing to oil synthesis, and another is to increase the expression levels of miRNA159 and miRNA319 to inhibit the expression of MYB33, which may downregulate starch synthesis-related genes, making more carbon metabolites flow into oil synthesis. Our study will provide a basis for future breeding efforts to increase the oil content of chickpea seeds.

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Comparative Transcriptome Analysis of Developing Seeds and Silique Wall Reveals Dynamic Transcription Networks for Effective Oil Production in Brassica napus L.

International Journal of Molecular Sciences ◽

10.3390/ijms20081982 ◽

2019 ◽

Vol 20 (8) ◽

pp. 1982 ◽

Cited By ~ 11

Author(s):

Muhammad Shahid ◽

Guangqin Cai ◽

Feng Zu ◽

Qing Zhao ◽

Muhammad Uzair Qasim ◽

...

Keyword(s):

Brassica Napus ◽

Seed Development ◽

Vegetable Oil ◽

Oil Content ◽

Seed Oil ◽

Seed Oil Content ◽

Oil Accumulation ◽

Developing Seeds ◽

Oil Biosynthesis ◽

Oil Crops

Vegetable oil is an essential constituent of the human diet and renewable raw material for industrial applications. Enhancing oil production by increasing seed oil content in oil crops is the most viable, environmentally friendly, and sustainable approach to meet the continuous demand for the supply of vegetable oil globally. An in-depth understanding of the gene networks involved in oil biosynthesis during seed development is a prerequisite for breeding high-oil-content varieties. Rapeseed (Brassica napus) is one of the most important oil crops cultivated on multiple continents, contributing more than 15% of the world’s edible oil supply. To understand the phasic nature of oil biosynthesis and the dynamic regulation of key pathways for effective oil accumulation in B. napus, comparative transcriptomic profiling was performed with developing seeds and silique wall (SW) tissues of two contrasting inbred lines with ~13% difference in seed oil content. Differentially expressed genes (DEGs) between high- and low-oil content lines were identified across six key developmental stages, and gene enrichment analysis revealed that genes related to photosynthesis, metabolism, carbohydrates, lipids, phytohormones, transporters, and triacylglycerol and fatty acid synthesis tended to be upregulated in the high-oil-content line. Differentially regulated DEG patterns were revealed for the control of metabolite and photosynthate production in SW and oil biosynthesis and accumulation in seeds. Quantitative assays of carbohydrates and hormones during seed development together with gene expression profiling of relevant pathways revealed their fundamental effects on effective oil accumulation. Our results thus provide insights into the molecular basis of high seed oil content (SOC) and a new direction for developing high-SOC rapeseed and other oil crops.

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Maternal control of seed oil content in Brassica napus: the role of silique wall photosynthesis

The Plant Journal ◽

10.1111/j.1365-313x.2011.04802.x ◽

2011 ◽

Vol 69 (3) ◽

pp. 432-444 ◽

Cited By ~ 77

Author(s):

Wei Hua ◽

Rong-Jun Li ◽

Gao-Miao Zhan ◽

Jing Liu ◽

Jun Li ◽

...

Keyword(s):

Brassica Napus ◽

Oil Content ◽

Seed Oil ◽

Seed Oil Content ◽

Maternal Control

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Genome-wide association study and identification of candidate genes for seed oil content in Brassica napus

Euphytica ◽

10.1007/s10681-021-02783-2 ◽

2021 ◽

Vol 217 (4) ◽

Author(s):

Lalit Pal ◽

Surinder K. Sandhu ◽

Dharminder Bhatia

Keyword(s):

Brassica Napus ◽

Association Study ◽

Candidate Genes ◽

Oil Content ◽

Seed Oil ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Seed Oil Content ◽

Genome Wide

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Genome-wide association study reveals a patatin-like lipase relating to the reduction of seed oil content in Brassica napus

BMC Plant Biology ◽

10.1186/s12870-020-02774-w ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Haoyi Wang ◽

Qian Wang ◽

Haksong Pak ◽

Tao Yan ◽

Mingxun Chen ◽

...

Keyword(s):

Brassica Napus ◽

In Silico ◽

Oil Content ◽

Seed Oil ◽

Genome Wide Association Study ◽

In Silico Analysis ◽

Genome Wide Association ◽

Seed Oil Content ◽

Genome Wide ◽

Silico Analysis

Abstract Background Rapeseed (Brassica napus L.) is an important oil crop world-widely cultivated, and seed oil content (SOC) is one of the most important traits for rapeseed. To increase SOC, many efforts for promoting the function of genes on lipid biosynthesis pathway have been previously made. However, seed oil formation is a dynamic balance between lipid synthesis and breakdown. It is, therefore, also reasonable to weaken or eliminate the function of genes involved in lipid degradation for a higher final SOC. Results We applied a genome-wide association study (GWAS) on SOC in a collection of 290 core germplasm accessions. A total of 2,705,480 high-quality SNPs were used in the GWAS, and we identified BnaC07g30920D, a patatin-like lipase (PTL) gene, that was associated with SOC. In particular, six single-nucleotide-polymorphisms (SNPs) in the promoter region of BnaC07g30920D were associated with the significant reduction of SOC, leading to a 4.7–6.2% reduction of SOCs. We performed in silico analysis to show a total of 40 PTLs, which were divided into four clades, evenly distributed on the A and C subgenomes of Brassica napus. RNA-seq analysis unveiled that BnPTLs were preferentially expressed in reproductive tissues especially maturing seeds. Conclusions We identified BnaC07g30920D, a BnPTL gene, that was associated with SOC using GWAS and performed in silico analysis of 40 PTLs in Brassica napus. The results enrich our knowledge about the SOC formation in rapeseed and facilitate the future study in functional characterization of BnPTL genes.

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