Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus

Tang, Shan; Zhao, Hu; Lu, Shaoping; Yu, Liangqian; Zhang, Guofang; Zhang, Yuting; Yang, Qingyong; Zhou, Yongming; Wang, Xuemin; Ma, Wei; Xie, Weibo; Guo, Liang

doi:10.1016/j.molp.2020.12.003

Cited by 144 publications

(158 citation statements)

References 95 publications

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“…The most promising candidate genes were determined based on (i) their potential attributions to seed vigor in various environment conditions reported in the scientific literature, and (ii) containing highly associated SNP markers within the coding regions. In order to give a priority to the candidate genes, a comprehensive score was evaluated for each candidate gene by considering the GWAS gene internal and promoter region QTLs p-value, effect variation, and haplotype variation [86].…”

Section: Genome-wide Association Analysismentioning

confidence: 99%

Genome-Wide Association Mapping Unravels the Genetic Control of Seed Vigor under Low-Temperature Conditions in Rapeseed (Brassica napus L.)

Luo

Zhang

et al. 2021

Plants

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Low temperature inhibits rapid germination and successful seedling establishment of rapeseed (Brassica napus L.), leading to significant productivity losses. Little is known about the genetic diversity for seed vigor under low-temperature conditions in rapeseed, which motivated our investigation of 13 seed germination- and emergence-related traits under normal and low-temperature conditions for 442 diverse rapeseed accessions. The stress tolerance index was calculated for each trait based on performance under non-stress and low-temperature stress conditions. Principal component analysis of the low-temperature stress tolerance indices identified five principal components that captured 100% of the seedling response to low temperature. A genome-wide association study using ~8 million SNP (single-nucleotide polymorphism) markers identified from genome resequencing was undertaken to uncover the genetic basis of seed vigor related traits in rapeseed. We detected 22 quantitative trait loci (QTLs) significantly associated with stress tolerance indices regarding seed vigor under low-temperature stress. Scrutiny of the genes in these QTL regions identified 62 candidate genes related to specific stress tolerance indices of seed vigor, and the majority were involved in DNA repair, RNA translation, mitochondrial activation and energy generation, ubiquitination and degradation of protein reserve, antioxidant system, and plant hormone and signal transduction. The high effect variation and haplotype-based effect of these candidate genes were evaluated, and high priority could be given to the candidate genes BnaA03g40290D, BnaA06g07530D, BnaA09g06240D, BnaA09g06250D, and BnaC02g10720D in further study. These findings should be useful for marker-assisted breeding and genomic selection of rapeseed to increase seed vigor under low-temperature stress.

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Section: Genome-wide Association Analysismentioning

confidence: 99%

Genome-Wide Association Mapping Unravels the Genetic Control of Seed Vigor under Low-Temperature Conditions in Rapeseed (Brassica napus L.)

Luo

Zhang

et al. 2021

Plants

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“…The TWAS technique aims to solve this problem and is becoming a powerful tool which provides abundant expression and association data aided by improved algorithms. The fact that TWASs have been successfully implemented in cotton fiber (Li et al, 2020) and rapeseed (Tang et al, 2020) provided motivation to conduct a TWAS in cotton anther. By applying TWAS, GhHRK1 was associated with a pollen phenotype, and it is one of 75 PCgenes detected by the GWAS, suggesting that TWASs can be used to support the findings of GWAS analyses and so facilitate the identification of causal factors more precisely.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, eQTLs can be used to estimate the effects on gene expression and then be combined with physical phenotypes to conduct transcriptome‐wide association studies (TWASs) to identify pivotal expression–trait associations (Gusev et al, 2016). The TWAS algorithm has been successfully implemented in cotton fiber and rapeseed to identify causal genes for important agronomic traits (Li et al, 2020; Tang et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

A combination of genome‐wide and transcriptome‐wide association studies reveals genetic elements leading to male sterility during high temperature stress in cotton

Ling

Wang

et al. 2021

New Phytologist

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 Global warming has reduced the productivity of many field-grown crops due to effects on male sterility. The genetic regulation of high temperature (HT) response in the major crop cotton is poorly understood.  We determined the functionality and transcriptomes of anther of 218 cotton accessions grown under HT stress. By analyzing transcriptome divergence and implementing genome-wide association study (GWAS), we identified three thermal tolerance associated loci which contained 75 protein coding genes and 27 long non-coding RNAs, and provided expression quantitative trait loci (eQTLs) for 13,132 transcripts.  A transcriptome-wide association study (TWAS) confirmed six causal elements for the HT response (three genes overlapped with GWAS results), involved in protein kinase activity. The most susceptible gene, GhHRK1 was confirmed as a previously uncharacterized negative regulator of the HT response both in cotton and in Arabidopsis.  These functional variants provided new understanding of genetic basis for HT tolerance in male reproduction organs.

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“…A total of 443 lines originated in China, 28 from Europe, 10 from Japan, 5 from Canada, 6 from Australia, 3 from Korea, and 10 unknown. 24 …”

Section: Methodsmentioning

confidence: 99%

“…After extracting oil, OSR cakes and OSR meals function as an important poultry feed and fertilizer. Since the release of the B. napus reference genome, 22 dozens of agriculturally important traits have been dissected by GWAS, 23 , 24 although few studies have included B. napus seed phytate traits. In this study, a diverse panel of 505 B. napus accessions was scored for seed phytate concentration and content and 119 significant associated single nucleotide polymorphism (SNP) loci were identified by GWAS.…”

Section: Introductionmentioning

confidence: 99%

Integrating a genome-wide association study with transcriptomic data to predict candidate genes and favourable haplotypes influencing Brassica napus seed phytate

Liu

Zhang

et al. 2021

DNA Research

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Phytate is the storage form of phosphorus in angiosperm seeds and plays vitally important roles during seed development. However, in crop plants phytate decreases bioavailability of seed-sourced mineral elements for humans, livestock and poultry, and contributes to phosphate-related water pollution. However, there is little knowledge about this trait in oilseed rape (Brassica napus). Here, a panel of 505 diverse B. napus accessions was screened in a genome-wide association study (GWAS) using 3.28 × 106 single-nucleotide polymorphisms (SNPs). This identified 119 SNPs significantly associated with phytate concentration (PA_Conc) and phytate content (PA_Cont) and six candidate genes were identified. Of these, BnaA9.MRP5 represented the candidate gene for the significant SNP chrA09_5198034 (27 kb) for both PA_Cont and PA_Conc. Transcription of BnaA9.MRP5 in a low-phytate variety (LPA20) was significantly elevated compared with a high-phytate variety (HPA972). Association and haplotype analysis indicated that inbred lines carrying specific SNP haplotypes within BnaA9.MRP5 were associated with high- and low-phytate phenotypes. No significant differences in seed germination and seed yield were detected between low and high phytate cultivars examined. Candidate genes, favourable haplotypes and the low phytate varieties identified in this study will be useful for low-phytate breeding of B. napus.

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Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus

Cited by 144 publications

References 95 publications

Genome-Wide Association Mapping Unravels the Genetic Control of Seed Vigor under Low-Temperature Conditions in Rapeseed (Brassica napus L.)

Genome-Wide Association Mapping Unravels the Genetic Control of Seed Vigor under Low-Temperature Conditions in Rapeseed (Brassica napus L.)

A combination of genome‐wide and transcriptome‐wide association studies reveals genetic elements leading to male sterility during high temperature stress in cotton

Integrating a genome-wide association study with transcriptomic data to predict candidate genes and favourable haplotypes influencing Brassica napus seed phytate

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