Regional association analysis coupled with transcriptome analyses reveal candidate genes affecting seed oil accumulation in Brassica napus

2021 ◽  
Vol 134 (5) ◽  
pp. 1545-1555
Author(s):  
Min Yao ◽  
Mei Guan ◽  
Qian Yang ◽  
Luyao Huang ◽  
Xinghua Xiong ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Candidate Genes ◽  
Association Analysis ◽  
Seed Oil ◽  
Oil Accumulation ◽  
Regional Association ◽  
Transcriptome Analyses ◽  
Regional Association Analysis

scholarly journals Dynamic Transcriptome Changes Related to Oil Accumulation in Developing Soybean Seeds

2019 ◽  
Vol 20 (9) ◽  
pp. 2202 ◽  
Author(s):  
Songnan Yang ◽  
Long Miao ◽  
Jianbo He ◽  
Kai Zhang ◽  
Yan Li ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Candidate Genes ◽  
Molecular Basis ◽  
Oil Content ◽  
Seed Oil ◽  
Soybean Seed ◽  
Soybean Seeds ◽  
Seed Oil Content ◽  
Oil Accumulation ◽  
Expression Levels

Soybean is one of the most important oil crops in the world. Revealing the molecular basis and exploring key candidate genes for seed oil synthesis has great significance for soybean improvement. In this study, we found that oil accumulation rates and gene expression levels changed dynamically during soybean seed development. The expression levels of genes in metabolic pathways such as carbon fixation, photosynthesis, glycolysis, and fatty acid biosynthesis were significantly up-regulated during the rapid accumulation of oil in developing soybean seeds. Through weighted correlation network analysis, we identified six co-expression modules associated with soybean seed oil content and the pink module was the most positively correlated (r = 0.83, p = 7 × 10−4) network. Through the integration of differential expression and co-expression analysis, we predicted 124 candidate genes potentially affecting soybean seed oil content, including seven genes in lipid metabolism pathway, two genes involved in glycolysis, one gene in sucrose metabolism, and 12 genes belonged to transcription factors as well as other categories. Among these, three genes (GmABI3b, GmNFYA and GmFAD2-1B) have been shown to control oil and fatty acid content in soybean seeds, and other newly identified candidate genes would broaden our knowledge to understand the molecular basis for oil accumulation in soybean seeds.

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

2019 ◽  
Vol 20 (8) ◽  
pp. 1982 ◽  
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.

Use of Genotypes of Common Variants for Genome-Wide Regional Association Analysis

2018 ◽  
Vol 54 (2) ◽  
pp. 250-258
Author(s):  
A. V. Kirichenko ◽  
I. V. Zorkoltseva ◽  
N. M. Belonogova ◽  
T. I. Axenovich
Keyword(s):  
Association Analysis ◽  
Common Variants ◽  
Regional Association ◽  
Genome Wide ◽  
Regional Association Analysis

scholarly journals Earliness traits in rapeseed (Brassica napus): SNP loci and candidate genes identified by genome-wide association analysis

DNA Research ◽  
2017 ◽  
Vol 25 (3) ◽  
pp. 229-244 ◽  
Author(s):  
Qinghong Zhou ◽  
Depeng Han ◽  
Annaliese S Mason ◽  
Can Zhou ◽  
Wei Zheng ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Candidate Genes ◽  
Association Analysis ◽  
Genome Wide Association ◽  
Genome Wide Association Analysis ◽  
Genome Wide

scholarly journals Identification of candidate genes controlling oil content by combination of genome-wide association and transcriptome analysis in the oilseed crop Brassica napus

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhongchun Xiao ◽  
Chao Zhang ◽  
Fang Tang ◽  
Bo Yang ◽  
Liyuan Zhang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Candidate Genes ◽  
Oil Content ◽  
Seed Oil ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Oilseed Crop ◽  
Seed Oil Content ◽  
Genome Wide ◽  
A Genome

Abstract 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.

scholarly journals Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in Rice

2017 ◽  
Vol 8 ◽  
Author(s):  
Anurag V. Daware ◽  
Rishi Srivastava ◽  
Ashok K. Singh ◽  
Swarup K. Parida ◽  
Akhilesh K. Tyagi
Keyword(s):  
Grain Size ◽  
Association Analysis ◽  
Regional Association ◽  
Regional Association Analysis

Heat Stress Suppresses Brassica napus Seed Oil Accumulation by Inhibition of Photosynthesis and BnWRI1 Pathway

2019 ◽  
Vol 60 (7) ◽  
pp. 1457-1470 ◽  
Author(s):  
Ruizhi Huang ◽  
Zhihong Liu ◽  
Meiqing Xing ◽  
Yong Yang ◽  
Xuelong Wu ◽  
...  
Keyword(s):  
Heat Stress ◽  
Fatty Acid ◽  
Brassica Napus ◽  
Seed Oil ◽  
Fatty Acid Biosynthesis ◽  
De Novo ◽  
Sugar Content ◽  
Light Response ◽  
Acid Biosynthesis ◽  
Oil Accumulation

Abstract Heat stress during Brassica napus seed filling severely impairs yield and oil content. However, the mechanisms underlying heat-stress effects on B. napus seed photosynthesis and oil accumulation remain elusive. In this study, we showed that heat stress resulted in reduction of seed oil accumulation, whereas the seed sugar content was enhanced, which indicated that incorporation of carbohydrates into triacylglycerols was impaired. Photosynthesis and respiration rates, and the maximum quantum yield of photosystem II in developing seeds were inhibited by heat stress. Transcriptome analysis revealed that heat stress led to up-regulation of genes associated with high light response, providing evidence that photoinhibition was induced by heat stress. BnWRI1 and its downstream genes, including genes involved in de novo fatty acid biosynthesis pathway, were down-regulated by heat stress. Overexpression of BnWRI1 with a seed-specific promoter stabilized both oil accumulation and photosynthesis under the heat-stress condition, which suggested BnWRI1 plays an important role in mediating the effect of heat stress on fatty acid biosynthesis. A number of sugar transporter genes were inhibited by heat stress, resulting in defective integration of carbohydrates into triacylglycerols units. The results collectively demonstrated that disturbances of the seed photosynthesis machinery, impairment of carbohydrates incorporation into triacylglycerols and transcriptional deregulation of the BnWRI1 pathway by heat stress might be the major cause of decreased oil accumulation in the seed.

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