BnVIR: bridging the genotype-phenotype gap to accelerate mining of candidate variations underlying agronomic traits in Brassica napus

Yang, Zhiquan; Liang, Congyuan; Wei, Lulu; Wang, Shengbo; Yin, Feifan; Li, Dongxu; Guo, Liang; Zhou, Yongming; Yang, Qingyong

doi:10.1016/j.molp.2022.02.002

Cited by 17 publications

(12 citation statements)

References 12 publications

(16 reference statements)

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“…As a result, they shared the same causal variant (PPH 4 = 0.99), suggesting that BnaC09.MYB28a and BnaC09.MYB28b are candidate genes associated with SGC (Figure 4F and G). In addition, frameshift mutation (GCTA/-) may be the casual variation, which has been analyzed in our previous research (Wang et al ., 2018; Yang et al ., 2022a) (Figure 4F and G).…”

Section: Resultsmentioning

confidence: 99%

“…The previous BnVIR database integrated 10,090,561 genetic variations and 21 phenotypes of 2,311 core B. napus accessions (Yang et al, 2022a). On this basis, we newly collected 216 published phenotype datasets from 13 studies (Bus et al, 2011; Sun et al, 2016b; Sun et al, 2016a; Chen et al, 2018; Kittipol et al, 2019; Wu et al, 2019; Song et al, 2020; Xuan et al, 2020; Liu et al, 2021c; Liu et al, 2021b; Wang et al, 2021; Zhang et al ., 2021; Zhang et al ., 2022a) (Supplementary Table S3).…”

Section: Resultsmentioning

confidence: 99%

“…Metabolome datasets were retrieved from two previous studies (Geng et al, 2017; Clement et al, 2018). Genetic variation datasets of 2,311 accessions from BnVIR were also integrated into BnIR (Yang et al ., 2022a).…”

Section: Methodsmentioning

confidence: 99%

“…However, the identification is still rather time-consuming, and the regulatory mechanisms of most identified candidate loci or genes on phenotypes remain elusive. In our recent work, we have constructed and released several databases, including BnPIR (Song et al, 2021) (http://cbi.hzau.edu.cn/bnapus/), BnTIR (Liu et al, 2021a) (http://yanglab.hzau.edu.cn/BnTIR/) and BnVIR (Yang et al, 2022a) (http://yanglab.hzau.edu.cn/BnVIR/), by collecting multi-omics data including genome, transcriptome and population genetic variations and developing related omics tools. These databases have been widely applied to facilitate related research work.…”

Section: Introductionmentioning

confidence: 99%

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BnIR: a multi-omics database with various tools for Brassica napus research and breeding

Yang

Wang

et al. 2023

Preprint

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In the post-GWAS era, multi-omics techniques have shown great power and potential for candidate gene mining and functional genomics research. However, due to the lack of effective data integration and multi-omics analysis platforms, such techniques have not still been applied widely in rapeseed, an important oil crop worldwide. Here, we constructed a rapeseed multi-omics database (BnIR; http://yanglab.hzau.edu.cn/BnIR), which provides datasets of six omics including genomics, transcriptomics, variomics, epigenetics, phenomics and metabolomics, as well as numerous "variation-gene expression-phenotype" associations by using multiple statistical methods. In addition, a series of multi-omics search and analysis tools are integrated to facilitate the browsing and application of these datasets. BnIR is the most comprehensive multi-omics database for rapeseed so far, and two case studies demonstrated its power to mine candidate genes associated with specific traits and analyze their potential regulatory mechanisms.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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BnIR: a multi-omics database with various tools for Brassica napus research and breeding

Yang

Wang

et al. 2023

Preprint

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“…All the sequences of the annotated genes from the candidate regions were downloaded from the B. napus reference genome, ZS11 ( and accessed on 10 March 2022) [ 65 , 66 ], and aligned against the genome sequence of Arabidopsis by local BLAST analysis.…”

Section: Methodsmentioning

confidence: 99%

Mapping of Two Major QTLs Controlling Flowering Time in Brassica napus Using a High-Density Genetic Map

Chen

Lei

et al. 2022

Plants

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Research on the flowering habit of rapeseed is important for the selection of varieties adapted to specific ecological environments. Here, quantitative trait loci (QTL) for the days-to-flowering trait were identified using a doubled haploid population of 178 lines derived from a cross between the winter type SGDH284 and the semi-winter type 158A. A linkage map encompassing 3268.01 cM was constructed using 2777 bin markers obtained from next-generation sequencing. The preliminary mapping results revealed 56 QTLs for the days to flowering in the six replicates in the three environments. Twelve consensus QTLs were identified by a QTL meta-analysis, two of which (cqDTF-C02 and cqDTF-C06) were designated as major QTLs. Based on the micro-collinearity of the target regions between B. napus and Arabidopsis, four genes possibly related to flowering time were identified in the cqDTF-C02 interval, and only one gene possibly related to flowering time was identified in the cqDTF-C06 interval. A tightly linked insertion–deletion marker for the cqFT-C02 locus was developed. These findings will aid the breeding of early maturing B. napus varieties.

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Genomic and transcriptome analyses reveal potential contributors to erucic acid biosynthesis in seeds of rapeseed (Brassica napus)

Xu,

Chen,

Cai

et al. 2024

Theor Appl Genet

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BnVIR: bridging the genotype-phenotype gap to accelerate mining of candidate variations underlying agronomic traits in Brassica napus

Cited by 17 publications

References 12 publications

BnIR: a multi-omics database with various tools for Brassica napus research and breeding

BnIR: a multi-omics database with various tools for Brassica napus research and breeding

Mapping of Two Major QTLs Controlling Flowering Time in Brassica napus Using a High-Density Genetic Map

Genomic and transcriptome analyses reveal potential contributors to erucic acid biosynthesis in seeds of rapeseed (Brassica napus)

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