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Yang Z, Wang S, Wei L, Huang Y, Liu D, Jia Y, Luo C, Lin Y, Liang C, Hu Y, Dai C, Guo L, Zhou Y, Yang QY. BnIR: A multi-omics database with various tools for Brassica napus research and breeding. MOLECULAR PLANT 2023; 16:775-789. [PMID: 36919242 DOI: 10.1016/j.molp.2023.03.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/15/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
In the post-genome-wide association study 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 report 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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Affiliation(s)
- Zhiquan Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Shengbo Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Lulu Wei
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiming Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Dongxu Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yupeng Jia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Chengfang Luo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuchen Lin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Congyuan Liang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yue Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
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Liu Y, Zhou X, Yan M, Wang P, Wang H, Xin Q, Yang L, Hong D, Yang G. Fine mapping and candidate gene analysis of a seed glucosinolate content QTL, qGSL-C2, in rapeseed (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:479-490. [PMID: 31832742 DOI: 10.1007/s00122-019-03479-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
QTL mapping and candidate gene analysis indicate that allelic variations in BnaC2.MYB28 resulted from homeologous exchange and determine difference in seed glucosinolate content. A low seed glucosinolate content has long been an important breeding objective in rapeseed improvement. However, the molecular mechanisms underlying seed GSL content variations remain to be elucidated in allotetraploid Brassica napus. Here, we developed a double haploid population from a cross between two B. napus accessions that possess relatively low, but significantly different seed GSL contents and identified a major QTL, qGSL-C2, on chromosome C02 that explains 30.88-72.87% of the phenotypic variation observed in five environments. Using near-isogenic lines, we further delimited qGSL-C2 to a physical region of 49 kb on the B. rapa chromosome A02 which is highly homologous to the target C02 interval. Among five candidate genes, BnaC2.MYB28, a homologue of the Arabidopsis MYB28 encoding a putative R2R3-MYB-type transcription factor functioning in aliphatic methionine-derived GSL synthesis, was most likely to be the target gene underlying the QTL. Sequence analysis revealed multiple insertion/deletion and SNP variations in the genomic region between the alleles of the NILs. Furthermore, the allelic variations in BnaC2.MYB28 in the natural B. napus population were significantly associated with seed GSL content. Remarkably, the phylogenetic analysis and sequence comparison suggested that while the BnaC2.MYB28 allele from the parental line G120 was inherited from B. oleracea BolC2.MYB28, its counterpart from the other parent, 9172, most likely evolved from B. rapa BraA2.MYB28 via possible homeologous exchange. Our study promotes greater understanding of the molecular regulation of seed GSL content and provides useful molecular markers for seed GSL improvement in B. napus.
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Affiliation(s)
- Ying Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Min Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiang Xin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liyong Yang
- Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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Kittipol V, He Z, Wang L, Doheny-Adams T, Langer S, Bancroft I. Genetic architecture of glucosinolate variation in Brassica napus. JOURNAL OF PLANT PHYSIOLOGY 2019; 240:152988. [PMID: 31255878 PMCID: PMC6739596 DOI: 10.1016/j.jplph.2019.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/30/2019] [Accepted: 06/03/2019] [Indexed: 05/18/2023]
Abstract
The diverse biological activities of glucosinolate (GSL) hydrolysis products play significant biological and economical roles in the defense system and nutritional qualities of Brassica napus (oilseed rape). Yet, genomic-based study of the B. napus GSL regulatory mechanisms are scarce due to the complexity of working with polyploid species. To address these challenges, we used transcriptome-based GWAS approach, Associative Transcriptomics (AT), across a diversity panel of 288 B. napus genotypes to uncover the underlying genetic basis controlling quantitative variation of GSLs in B. napus vegetative tissues. Single nucleotide polymorphism (SNP) markers and gene expression markers (GEMs) associations identify orthologues of MYB28/HAG1 (AT5G61420), specifically the copies on chromosome A9 and C2, to be the key regulators of aliphatic GSL variation in leaves. We show that the positive correlation observed between aliphatic GSLs in seed and leaf is due to the amount synthesized, as controlled by Bna.HAG1.A9 and Bna.HAG1.C2, rather than by variation in the transport processes. In addition, AT and differential expression analysis in root tissues implicate an orthologue of MYB29/HAG3 (AT5G07690), Bna.HAG3.A3, as controlling root aromatic GSL variation. Based on the root expression data we also propose Bna.MAM3.A3 to have a role in controlling phenylalanine chain elongation for aromatic GSL biosynthesis. This work uncovers a regulator of homophenylalanine-derived aromatic GSLs and implicates the shared biosynthetic pathways between aliphatic and aromatic GSLs.
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Affiliation(s)
- Varanya Kittipol
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Zhesi He
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Lihong Wang
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Tim Doheny-Adams
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Swen Langer
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Ian Bancroft
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
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