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 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 Genome-wide association studies detects candidate genes for wool traits by re-sequencing in Chinese fine-wool sheep

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Hongchang Zhao ◽  
Tingting Guo ◽  
Zengkui Lu ◽  
Jianbin Liu ◽  
Shaohua Zhu ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Candidate Genes ◽  
Fiber Diameter ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Merino Sheep ◽  
Genome Wide ◽  
A Genome ◽  
Staple Length

Abstract Background The quality and yield of wool determine the economic value of the fine-wool sheep. Therefore, discovering markers or genes relevant to wool traits is the cornerstone for the breeding of fine-wool sheep. In this study, we used the Illumina HiSeq X Ten platform to re-sequence 460 sheep belonging to four different fine-wool sheep breeds, namely, Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Aohan fine-wool sheep (AHS) and Qinghai fine-wool sheep (QHS). Eight wool traits, including fiber diameter (FD), fiber diameter coefficient of variance (FDCV), fiber diameter standard deviation (FDSD), staple length (SL), greasy fleece weight (GFW), clean wool rate (CWR), staple strength (SS) and staple elongation (SE) were examined. A genome-wide association study (GWAS) was performed to detect the candidate genes for the eight wool traits. Results A total of 8.222 Tb of raw data was generated, with an average of approximately 8.59X sequencing depth. After quality control, 12,561,225 SNPs were available for analysis. And a total of 57 genome-wide significant SNPs and 30 candidate genes were detected for the desired wool traits. Among them, 7 SNPs and 6 genes are related to wool fineness indicators (FD, FDCV and FDSD), 10 SNPs and 7 genes are related to staple length, 13 SNPs and 7 genes are related to wool production indicators (GFW and CWR), 27 SNPs and 10 genes associated with staple elongation. Among these candidate genes, UBE2E3 and RHPN2 associated with fiber diameter, were found to play an important role in keratinocyte differentiation and cell proliferation. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results, revealed that multitude significant pathways are related to keratin and cell proliferation and differentiation, such as positive regulation of canonical Wnt signaling pathway (GO:0090263). Conclusion This is the first GWAS on the wool traits by using re-sequencing data in Chinese fine-wool sheep. The newly detected significant SNPs in this study can be used in genome-selective breeding for the fine-wool sheep. And the new candidate genes would provide a good theoretical basis for the fine-wool sheep breeding.

scholarly journals The Brassica Napus Fatty Acid Exporter FAX1-1 Contributes to Biological Yield, Seed Oil Production, and Oil Quality

2021 ◽  
Author(s):  
Zhongchun Xiao ◽  
Fang Tang ◽  
Liyuan Zhang ◽  
Shengting Li ◽  
Shufeng Wang ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Brassica Napus ◽  
Seed Yield ◽  
Oil Content ◽  
Seed Oil ◽  
Oil Quality ◽  
Oil Production ◽  
Oilseed Crop ◽  
Seed Oil Content ◽  
Biological Yield

Abstract Background: In the oilseed crop Brassica napus (rapeseed), various metabolic processes influence seed oil production, oil quality, and biological yield. However, the role of plastid membrane proteins in these traits has not been explored. Results: Our genome-wide association study (GWAS) of 520 B. napus accessions identified the chloroplast membrane protein-localized FATTY ACID EXPORTER 1-1 (FAX1-1) as a candidate associated with biological yield. Seed transcript levels of BnaFAX1-1 were higher in a cultivar with high seed oil content relative to a low-oil cultivar. BnaFAX1-1 localized to the plastid envelope. When expressed in Arabidopsis thaliana, BnaFAX1-1 enhanced biological yield (total plant dry matter), seed yield and seed oil content per plant. Likewise, in the field, B. napus BnaFAX1-1 overexpression lines (BnaFAX1-1-OE) displayed significantly enhanced biological yield, seed yield, and seed oil content compared with the wild type. BnaFAX1-1 overexpression also up-regulated gibberellic acid 4 (GA4) biosynthesis, which may contribute to biological yield improvement. Furthermore, oleic acid (C18:1) significantly increased in BnaFAX1-1 overexpression seeds. Conclusion: Our results indicated that the putative fatty acid exporter BnaFAX1-1 simultaneously improved seed oil production, oil quality and biological yield in B. napus, providing new approaches for future molecular breeding.

scholarly journals The Brassica napus fatty acid exporter FAX1-1 contributes to biological yield, seed oil content, and oil quality

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Zhongchun Xiao ◽  
Fang Tang ◽  
Liyuan Zhang ◽  
Shengting Li ◽  
Shufeng Wang ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Brassica Napus ◽  
Seed Yield ◽  
Oil Content ◽  
Seed Oil ◽  
Genome Wide Association Study ◽  
Oil Quality ◽  
Oilseed Crop ◽  
Seed Oil Content ◽  
Biological Yield

Abstract Background In the oilseed crop Brassica napus (rapeseed), various metabolic processes influence seed oil content, oil quality, and biological yield. However, the role of plastid membrane proteins in these traits has not been explored. Results Our genome-wide association study (GWAS) of 520 B. napus accessions identified the chloroplast membrane protein-localized FATTY ACID EXPORTER 1-1 (FAX1-1) as a candidate associated with biological yield. Seed transcript levels of BnaFAX1-1 were higher in a cultivar with high seed oil content relative to a low-oil cultivar. BnaFAX1-1 was localized to the plastid envelope. When expressed in Arabidopsis thaliana, BnaFAX1-1 enhanced biological yield (total plant dry matter), seed yield and seed oil content per plant. Likewise, in the field, B. napus BnaFAX1-1 overexpression lines (BnaFAX1-1-OE) displayed significantly enhanced biological yield, seed yield, and seed oil content compared with the wild type. BnaFAX1-1 overexpression also up-regulated gibberellic acid 4 (GA4) biosynthesis, which may contribute to biological yield improvement. Furthermore, oleic acid (C18:1) significantly increased in BnaFAX1-1 overexpression seeds. Conclusion Our results indicated that the putative fatty acid exporter BnaFAX1-1 may simultaneously improve seed oil content, oil quality and biological yield in B. napus, providing new approaches for future molecular breeding.

scholarly journals Genome-wide association analysis uncovers candidate genes for forage quality traits in Brassica napus stems

2020 ◽  
Author(s):  
lijuan wei ◽  
Ruiying Liu ◽  
Wen Xu ◽  
Yan Zhu ◽  
Jinqi Ma ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Candidate Genes ◽  
Animal Feed ◽  
Forage Quality ◽  
Neutral Detergent Fiber ◽  
Genome Wide Association ◽  
Oilseed Crop ◽  
Quality Traits ◽  
Genome Wide ◽  
Genes Encoding

Abstract Background Brassica napus (rapeseed) is an important oilseed crop and its leaves and stems can also be used as animal feed. Lignocellulose content is closely related to the nutritional quality and palatability of animal feed. However, quantitative trait loci (QTLs) associated with acid detergent fiber (ADF) and neutral detergent fiber (NDF) contents in rapeseed stems have not yet been mapped. Results In this study, we used 494 B. napus accessions to perform genome-wide association studies (GWAS) of ADF and NDF contents. Ninety-two single-nucleotide polymorphisms (SNP) and 35 simple-sequence repeat (SSR) loci were significantly correlated with ADF and NDF contents, respectively, and six genetic loci associated with ADF and NDF contents were detected using both types of markers. We identified three candidate genes on chromosome A05 related to ADF content, including genes encoding chitinase-like protein 2 (CTL2) and two trichome birefringence-like 41 s (TBL41s). Seven genes on chromosomes A03 and A04 were related to NDF content, including genes encoding glycosyl hydrolase (GH), reversibly glycosylated polypeptide 1 (RGP), irregular xylem 12 (IRX12), trichome birefringence-like 34 (TBL34), galacturonosyltransferase 7 (GAUT7), cytokinesis defective 1 (CYT1), and LOB domain-containing protein 15 (LBD15). These candidate genes encode factors that likely participate in secondary cell wall formation and lignocellulose biosynthesis. Conclusions These findings lay the foundation for identifying genes related to forage quality traits and improving the efficiency of forage utilization in rapeseed, which will be beneficial for breeding new varieties for high-quality forage with low lignocellulose content.

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