Dataset Information

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

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.

SUBMITTER: Xiao Z

PROVIDER: S-EPMC6737612 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Identification of candidate genes controlling oil content by combination of genome-wide association and transcriptome analysis in the oilseed crop <i>Brassica napus</i>.

Xiao Zhongchun Z Zhang Chao C Tang Fang F Yang Bo B Zhang Liyuan L Liu Jingsen J Huo Qiang Q Wang Shufeng S Li Shengting S Wei Lijuan L Du Hai H Qu Cunmin C Lu Kun K Li Jiana J Li Nannan N

Biotechnology for biofuels 20190910

<h4>Background</h4>Increasing seed oil content is one of the most important targets for rapeseed (<i>Brassica napus</i>) breeding. However, genetic mechanisms of mature seed oil content in <i>Brassica napus</i> (<i>B. napus</i>) remain little known. To identify oil content-related genes, a genome-wide association study (GWAS) was performed using 588 accessions.<h4>Results</h4>High-throughput genome resequencing resulted in 385,692 high-quality single nucleotide polymorphism (SNPs) with a minor a ...[more]

PMID: 31528204

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Project description:Background:Brassica napus provides approximately 13-16% of global vegetable oil for human consumption and biodiesel production. Plant height (PH) is a key trait that affects plant architecture, seed yield and harvest index. However, the genetic mechanism of PH in B. napus is poorly understood. Results:A dwarf mutant df59 was isolated from a large-scale screening of an ethyl methanesulphonate-mutagenized rapeseed variety Ningyou 18. A genetic analysis showed that the dwarfism phenotype was controlled by one semi-dominant gene, which was mapped on C9 chromosome by quantitative trait loci sequencing analysis and designated as BnaDwf.C9. To fine-map BnaDwf.C9, two F2 populations were constructed from crosses between conventional rapeseed cultivars (Zhongshuang 11 and Holly) and df59. BnaDwf.C9 was fine-mapped to the region between single-nucleotide polymorphism (SNP) markers M14 and M4, corresponding to a 120.87-kb interval of the B. napus 'Darmor-bzh' genome. Within this interval, seven, eight and nine annotated or predicted genes were identified in "Darmor-bzh", "Ningyou 7" and "Zhongshuang 11" reference genomes, respectively. In addition, a comparative transcriptome analysis was performed using stem tips from Ningyou 18 and df59 at the stem elongation stage. In total, 3995 differentially expressed genes (DEGs) were identified. Among them, 118 DEGs were clustered in plant hormone-related signal transduction pathways, including 81 DEGs were enriched in auxin signal transduction. Combining the results of fine-mapping and transcriptome analyses, BnaC09g20450D was considered a candidate gene for BnaDwf.C9, which contains a SNP that co-segregated in 4746 individuals. Finally, a PCR-based marker was developed based on the SNP in BnaC09g20450D. Conclusions:The combination of quantitative trait loci sequencing, fine-mapping and genome-wide transcriptomic analysis revealed one candidate gene located within the confidence interval of 120.87-kb region. This study provides a new genetic resource for semi-dwarf breeding and new insights into understanding the genetic architecture of PH in B. napus.

Dataset Information

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

Publications

Identification of candidate genes controlling oil content by combination of genome-wide association and transcriptome analysis in the oilseed crop <i>Brassica napus</i>.

Similar Datasets

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