A genome-wide association study reveals novel elite allelic variations in seed oil content of Brassica napus

2016 ◽  
Vol 129 (6) ◽  
pp. 1203-1215 ◽  
Author(s):  
Sheng Liu ◽  
Chuchuan Fan ◽  
Jiana Li ◽  
Guangqin Cai ◽  
Qingyong Yang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Association Study ◽  
Oil Content ◽  
Seed Oil ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Seed Oil Content ◽  
Genome Wide ◽  
A Genome ◽  
Allelic Variations

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

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.

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 A genome-wide association study of seed protein and oil content in soybean

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 1 ◽  
Author(s):  
Eun-Young Hwang ◽  
Qijian Song ◽  
Gaofeng Jia ◽  
James E Specht ◽  
David L Hyten ◽  
...  
Keyword(s):  
Association Study ◽  
Oil Content ◽  
Seed Protein ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

Integration of RNA-Seq profiling with genome-wide association study predicts candidate genes for oil accumulation in soybean

2020 ◽  
Vol 71 (12) ◽  
pp. 996
Author(s):  
Yuan Niu ◽  
Guoliang Zhang ◽  
Faxiang Wan ◽  
Yuan-Ming Zhang
Keyword(s):  
Oleic Acid ◽  
Association Study ◽  
Acid Content ◽  
Oil Content ◽  
Seed Oil ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Rna Seq ◽  
Oil Accumulation ◽  
Genome Wide

The most important objectives of soybean (Glycine max (L.) Merr.) breeding are to increase oil content and to improve oil quality. Although the biochemical processes of oil accumulation in oilseeds are very clear, knowledge of their underlying genetic mechanisms and regulation is limited. We performed RNA-Seq of soybean seeds from six accessions with high, medium and low seed oil contents. Through comparative genome analysis, promoter-enrichment study, and protein–protein interaction (PPI) analysis, 80 lipid-metabolism-related genes and 31 transcription factors were detected. The pathways of fatty acid elongation, desaturation and export from plastid (P = 2.53E-4), and triacylglycerol biosynthesis (P = 2.31E-8), were significantly over-represented in accessions with high total oil content. Further, in an integration analysis of RNA-Seq and a genome-wide association study (GWAS) database, 62 candidate genes were found to be associated with seed oil content, 73 with oleic acid content, and 83 with linolenic acid content. Of these, 60 genes were found to be involved mainly in metabolism of lipids (25), carbohydrates (24), and amino acids (11). Thirty are known oil-synthesis-related genes; LOX1, CYP93D1 and GPT2 for oil content, SAD and FAD2 for oleic acid, and FAD2, CYP89A6 and GPT2 for linolenic acid were detected twice. There were 22 genes found to be associated with at least two oil-related traits, and of 154 pairs of PPIs, two genes for each pair of 95 PPIs (62%) were found to be associated with various oil-related traits, indicating the genetic foundations of oil-related traits. Three transcription factor genes were found to be associated with oil-related traits: HRE2 (Glyma.10G016500), ERF12 (Glyma.13G236600) and WRKY6 (Glyma.15G110300). This study provides an efficient strategy for further discovery of mechanisms of oil composition and accumulation.

scholarly journals A combination of genome-wide association study and transcriptome analysis in leaf epidermis identifies candidate genes involved in cuticular wax biosynthesis in Brassica napus

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Shurong Jin ◽  
Shuangjuan Zhang ◽  
Yuhua Liu ◽  
Youwei Jiang ◽  
Yanmei Wang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Association Study ◽  
Stress Tolerance ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Cuticular Waxes ◽  
Biochemical Basis ◽  
Genome Wide ◽  
A Genome ◽  
Wax Load

Abstract Background Brassica napus L. is one of the most important oil crops in the world. However, climate-change-induced environmental stresses negatively impact on its yield and quality. Cuticular waxes are known to protect plants from various abiotic/biotic stresses. Dissecting the genetic and biochemical basis underlying cuticular waxes is important to breed cultivars with improved stress tolerance. Results Here a genome-wide association study (GWAS) of 192 B. napus cultivars and inbred lines was used to identify single-nucleotide polymorphisms (SNPs) associated with leaf waxes. A total of 202 SNPs was found to be significantly associated with 31 wax traits including total wax coverage and the amounts of wax classes and wax compounds. Next, epidermal peels from leaves of both high-wax load (HW) and low-wax load (LW) lines were isolated and used to analyze transcript profiles of all GWAS-identified genes. Consequently, 147 SNPs were revealed to have differential expressions between HW and LW lines, among which 344 SNP corresponding genes exhibited up-regulated while 448 exhibited down-regulated expressions in LW when compared to those in HW. According to the gene annotation information, some differentially expressed genes were classified into plant acyl lipid metabolism, including fatty acid-related pathways, wax and cutin biosynthesis pathway and wax secretion. Some genes involved in cell wall formation and stress responses have also been identified. Conclusions Combination of GWAS with transcriptomic analysis revealed a number of directly or indirectly wax-related genes and their associated SNPs. These results could provide clues for further validation of SNPs for marker-assisted breeding and provide new insights into the genetic control of wax biosynthesis and improving stress tolerance of B. napus.

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