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Zhang L, Duan Y, Zhang Z, Zhang L, Chen S, Cai C, Duan S, Zhang K, Li G, Cheng F. OcBSA: An NGS-based bulk segregant analysis tool for outcross populations. MOLECULAR PLANT 2024; 17:648-657. [PMID: 38369755 DOI: 10.1016/j.molp.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
Constructing inbred lines for self-incompatible species and species with long generation times is challenging, making the use of F1 outcross/segregating populations the main strategy for genetic studies of such species. However, there is a lack of dedicated algorithms/tools for rapid quantitative trait locus (QTL) mapping using the F1 populations. To this end, we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 populations. OcBSA transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 population. Testing of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and accuracy. In addition, the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple, pear, peach, citrus, grape, tea, and rice. We also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this study. The OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene, which regulates potato flower color. Taken together, these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing species. For ease of use, we have developed both Windows and Linux versions of OcBSA, which are freely available at: https://gitee.com/Bioinformaticslab/OcBSA.
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Affiliation(s)
- Lingkui Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanfeng Duan
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zewei Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lei Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shumin Chen
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chengcheng Cai
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shaoguang Duan
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kang Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guangcun Li
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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2
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Manickam S, Rajagopalan VR, Kambale R, Rajasekaran R, Kanagarajan S, Muthurajan R. Plant Metabolomics: Current Initiatives and Future Prospects. Curr Issues Mol Biol 2023; 45:8894-8906. [PMID: 37998735 PMCID: PMC10670879 DOI: 10.3390/cimb45110558] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
Plant metabolomics is a rapidly advancing field of plant sciences and systems biology. It involves comprehensive analyses of small molecules (metabolites) in plant tissues and cells. These metabolites include a wide range of compounds, such as sugars, amino acids, organic acids, secondary metabolites (e.g., alkaloids and flavonoids), lipids, and more. Metabolomics allows an understanding of the functional roles of specific metabolites in plants' physiology, development, and responses to biotic and abiotic stresses. It can lead to the identification of metabolites linked with specific traits or functions. Plant metabolic networks and pathways can be better understood with the help of metabolomics. Researchers can determine how plants react to environmental cues or genetic modifications by examining how metabolite profiles change under various crop stages. Metabolomics plays a major role in crop improvement and biotechnology. Integrating metabolomics data with other omics data (genomics, transcriptomics, and proteomics) provides a more comprehensive perspective of plant biology. This systems biology approach enables researchers to understand the complex interactions within organisms.
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Affiliation(s)
- Sudha Manickam
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.M.); (V.R.R.); (R.K.); (R.R.)
| | - Veera Ranjani Rajagopalan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.M.); (V.R.R.); (R.K.); (R.R.)
| | - Rohit Kambale
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.M.); (V.R.R.); (R.K.); (R.R.)
| | - Raghu Rajasekaran
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.M.); (V.R.R.); (R.K.); (R.R.)
| | - Selvaraju Kanagarajan
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, 234 22 Lomma, Sweden
| | - Raveendran Muthurajan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.M.); (V.R.R.); (R.K.); (R.R.)
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3
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Jhingan S, Harloff HJ, Abbadi A, Welsch C, Blümel M, Tasdemir D, Jung C. Reduced glucosinolate content in oilseed rape (Brassica napus L.) by random mutagenesis of BnMYB28 and BnCYP79F1 genes. Sci Rep 2023; 13:2344. [PMID: 36759657 PMCID: PMC9911628 DOI: 10.1038/s41598-023-28661-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
The presence of anti-nutritive compounds like glucosinolates (GSLs) in the rapeseed meal severely restricts its utilization as animal feed. Therefore, reducing the GSL content to < 18 µmol/g dry weight in the seeds is a major breeding target. While candidate genes involved in the biosynthesis of GSLs have been described in rapeseed, comprehensive functional analyses are missing. By knocking out the aliphatic GSL biosynthesis genes BnMYB28 and BnCYP79F1 encoding an R2R3 MYB transcription factor and a cytochrome P450 enzyme, respectively, we aimed to reduce the seed GSL content in rapeseed. After expression analyses on single paralogs, we used an ethyl methanesulfonate (EMS) treated population of the inbred winter rapeseed 'Express617' to detect functional mutations in the two gene families. Our results provide the first functional analysis by knock-out for the two GSL biosynthesis genes in winter rapeseed. We demonstrate that independent knock-out mutants of the two genes possessed significantly reduced seed aliphatic GSLs, primarily progoitrin. Compared to the wildtype Express617 control plants (36.3 µmol/g DW), progoitrin levels were decreased by 55.3% and 32.4% in functional mutants of BnMYB28 (16.20 µmol/g DW) and BnCYP79F1 (24.5 µmol/g DW), respectively. Our study provides a strong basis for breeding rapeseed with improved meal quality in the future.
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Affiliation(s)
- Srijan Jhingan
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Hans-Joachim Harloff
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Amine Abbadi
- NPZ Innovation GmbH, Hohenlieth-Hof, 24363, Holtsee, Germany
| | - Claudia Welsch
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel Kanal 44, 24106, Kiel, Germany
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel Kanal 44, 24106, Kiel, Germany
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel Kanal 44, 24106, Kiel, Germany
- Christian-Albrechts-University of Kiel, Christian-Albrechts-Platz 4, 24118, Kiel, Germany
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany.
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Tang Y, Zhang G, Jiang X, Shen S, Guan M, Tang Y, Sun F, Hu R, Chen S, Zhao H, Li J, Lu K, Yin N, Qu C. Genome-Wide Association Study of Glucosinolate Metabolites (mGWAS) in Brassica napus L. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12030639. [PMID: 36771722 PMCID: PMC9921834 DOI: 10.3390/plants12030639] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/18/2023] [Accepted: 01/27/2023] [Indexed: 06/12/2023]
Abstract
Glucosinolates (GSLs) are secondary plant metabolites that are enriched in rapeseed and related Brassica species, and they play important roles in defense due to their anti-nutritive and toxic properties. Here, we conducted a genome-wide association study of six glucosinolate metabolites (mGWAS) in rapeseed, including three aliphatic glucosinolates (m145 gluconapin, m150 glucobrassicanapin and m151 progoitrin), one aromatic glucosinolate (m157 gluconasturtiin) and two indole glucosinolates (m165 indolylmethyl glucosinolate and m172 4-hydroxyglucobrassicin), respectively. We identified 113 candidate intervals significantly associated with these six glucosinolate metabolites. In the genomic regions linked to the mGWAS peaks, 187 candidate genes involved in glucosinolate biosynthesis (e.g., BnaMAM1, BnaGGP1, BnaSUR1 and BnaMYB51) and novel genes (e.g., BnaMYB44, BnaERF025, BnaE2FC, BnaNAC102 and BnaDREB1D) were predicted based on the mGWAS, combined with analysis of differentially expressed genes. Our results provide insight into the genetic basis of glucosinolate biosynthesis in rapeseed and should facilitate marker-based breeding for improved seed quality in Brassica species.
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Affiliation(s)
- Yunshan Tang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Guorui Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Xinyue Jiang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Shulin Shen
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Mingwei Guan
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Yuhan Tang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Fujun Sun
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Ran Hu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Si Chen
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Huiyan Zhao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Nengwen Yin
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Affiliation Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
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Zhou X, Zhang H, Xie Z, Liu Y, Wang P, Dai L, Zhang X, Wang Z, Wang Z, Wan L, Yang G, Hong D. Natural variation and artificial selection at the BnaC2.MYB28 locus modulate Brassica napus seed glucosinolate. PLANT PHYSIOLOGY 2023; 191:352-368. [PMID: 36179100 PMCID: PMC9806571 DOI: 10.1093/plphys/kiac463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/20/2022] [Indexed: 05/17/2023]
Abstract
The degradation products of glucosinolates (GSLs) greatly lower the nutritional value of rapeseed (Brassica napus) meal; thus, reduction of seed GSL content (SGC) has become an important objective of rapeseed breeding. In our previous study, we finely mapped a major QTL (qGSL-C2) for SGC to a 49-kb collinear region on B. rapa chromosome A2. Here, we experimentally validated that BnaC2.MYB28, encoding an R2R3-MYB transcription factor, is the causal gene of qGSL-C2. BnaC2.MYB28 is a nucleus-localized protein mainly expressed in vegetative tissues. Knockout of BnaC2.MYB28 in the high-SGC parent G120 reduced SGC to a value lower than that in the low-SGC parent ZY50, while overexpression of BnaC2.MYB28 in both parental lines (G120 and ZY50) led to extremely high SGC, indicating that BnaC2.MYB28 acts as a positive regulator of SGC in both parents. Molecular characterization revealed that BnaC2.MYB28 forms a homodimer and specifically interacts with BnaMYC3. Moreover, BnaC2.MYB28 can directly activate the expression of GSL biosynthesis genes. Differential expression abundance resulting from the polymorphic promoter sequences, in combination with the different capability in activating downstream genes involved in aliphatic GSL biosynthesis, caused the functional divergence of BnaC2.MYB28 in SGC regulation between the parents. Natural variation of BnaC2.MYB28 was highly associated with SGC in natural germplasm and has undergone artificial selection in modern low-GSL breeding. This study provides important insights into the core function of BnaC2.MYB28 in regulating SGC and a promising strategy for manipulating SGC in rapeseed.
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Affiliation(s)
- Xianming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops Hainan University, Hainan University, Haikou 570288, China
| | - Haiyan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops Hainan University, Hainan University, Haikou 570288, China
| | - Zhaoqi Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Liu
- 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
| | - Lihong Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaohui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhaoyang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhuanrong Wang
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Lili Wan
- Institute of Crops, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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6
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Chao H, Li H, Yan S, Zhao W, Chen K, Wang H, Raboanatahiry N, Huang J, Li M. Further insight into decreases in seed glucosinolate content based on QTL mapping and RNA-seq in Brassica napus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2969-2991. [PMID: 35841418 DOI: 10.1007/s00122-022-04161-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
The QTL hotspots determining seed glucosinolate content instead of only four HAG1 loci and elucidation of a potential regulatory model for rapeseed SGC variation. Glucosinolates (GSLs) are amino acid-derived, sulfur-rich secondary metabolites that function as biopesticides and flavor compounds, but the high seed glucosinolate content (SGC) reduces seed quality for rapeseed meal. To dissect the genetic mechanism and further reduce SGC in rapeseed, QTL mapping was performed using an updated high-density genetic map based on a doubled haploid (DH) population derived from two parents that showed significant differences in SGC. In 15 environments, a total of 162 significant QTLs were identified for SGC and then integrated into 59 consensus QTLs, of which 32 were novel QTLs. Four QTL hotspot regions (QTL-HRs) for SGC variation were discovered on chromosomes A09, C02, C07 and C09, including seven major QTLs that have previously been reported and four novel major QTLs in addition to HAG1 loci. SGC was largely determined by superimposition of advantage allele in the four QTL-HRs. Important candidate genes directly related to GSL pathways were identified underlying the four QTL-HRs, including BnaC09.MYB28, BnaA09.APK1, BnaC09.SUR1 and BnaC02.GTR2a. Related differentially expressed candidates identified in the minor but environment stable QTLs indicated that sulfur assimilation plays an important rather than dominant role in SGC variation. A potential regulatory model for rapeseed SGC variation constructed by combining candidate GSL gene identification and differentially expressed gene analysis based on RNA-seq contributed to a better understanding of the GSL accumulation mechanism. This study provides insights to further understand the genetic regulatory mechanism of GSLs, as well as the potential loci and a new route to further diminish the SGC in rapeseed.
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Affiliation(s)
- Hongbo Chao
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Huaixin Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shuxiang Yan
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Weiguo Zhao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Kang Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jinyong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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7
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Shang G, Zhao H, Tong L, Yin N, Hu R, Jiang H, Kamal F, Zhao Z, Xu L, Lu K, Li J, Qu C, Du D. Genome-Wide Association Study of Phenylalanine Derived Glucosinolates in Brassica rapa. PLANTS (BASEL, SWITZERLAND) 2022; 11:1274. [PMID: 35567275 PMCID: PMC9104335 DOI: 10.3390/plants11091274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/05/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022]
Abstract
Glucosinolates (GSLs) are sulfur-containing bioactive compounds usually present in Brassicaceae plants and are usually responsible for a pungent flavor and reduction of the nutritional values of seeds. Therefore, breeding rapeseed varieties with low GSL levels is an important breeding objective. Most GSLs in Brassica rapa are derived from methionine or tryptophan, but two are derived from phenylalanine, one directly (benzylGSL) and one after a round of chain elongation (phenethylGSL). In the present study, two phenylalanine (Phe)-derived GSLs (benzylGSL and phenethylGSL) were identified and quantified in seeds by liquid chromatography and mass spectrometry (LC-MS) analysis. Levels of benzylGSL were low but differed among investigated low and high GSL genotypes. Levels of phenethylGSL (also known as 2-phenylethylGSL) were high but did not differ among GSL genotypes. Subsequently, a genome-wide association study (GWAS) was conducted using 159 B. rapa accessions to demarcate candidate regions underlying 43 and 59 QTNs associated with benzylGSL and phenethylGSL that were distributed on 10 chromosomes and 9 scaffolds, explaining 0.56% to 70.86% of phenotypic variations, respectively. Furthermore, we find that 15 and 18 known or novel candidate genes were identified for the biosynthesis of benzylGSL and phenethylGSL, including known regulators of GSL biosynthesis, such as BrMYB34, BrMYB51, BrMYB28, BrMYB29 and BrMYB122, and novel regulators or structural genes, such as BrMYB44/BrMYB77 and BrMYB60 for benzylGSL and BrCYP79B2 for phenethylGSL. Finally, we investigate the expression profiles of the biosynthetic genes for two Phe-derived GSLs by transcriptomic analysis. Our findings provide new insight into the complex machinery of Phe-derived GSLs in seeds of B. rapa and help to improve the quality of Brassicaceae plant breeding.
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Affiliation(s)
- Guoxia Shang
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key Laboratory of Spring Rape Genetic Improvement, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China; (G.S.); (Z.Z.); (L.X.)
| | - Huiyan Zhao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
| | - Linhui Tong
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
| | - Nengwen Yin
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
| | - Ran Hu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
| | - Haiyan Jiang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
| | - Farah Kamal
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
| | - Zhi Zhao
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key Laboratory of Spring Rape Genetic Improvement, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China; (G.S.); (Z.Z.); (L.X.)
| | - Liang Xu
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key Laboratory of Spring Rape Genetic Improvement, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China; (G.S.); (Z.Z.); (L.X.)
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (H.Z.); (L.T.); (N.Y.); (R.H.); (H.J.); (F.K.); (K.L.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Dezhi Du
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Key Laboratory of Spring Rape Genetic Improvement, Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China; (G.S.); (Z.Z.); (L.X.)
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Raza A. Metabolomics: a systems biology approach for enhancing heat stress tolerance in plants. PLANT CELL REPORTS 2022; 41:741-763. [PMID: 33251564 DOI: 10.1007/s00299-020-02635-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/09/2020] [Indexed: 05/22/2023]
Abstract
Comprehensive metabolomic investigations provide a large set of stress-related metabolites and metabolic pathways, advancing crops under heat stress conditions. Metabolomics-assisted breeding, including mQTL and mGWAS boosted our understanding of improving numerous quantitative traits under heat stress. During the past decade, metabolomics has emerged as a fascinating scientific field that includes documentation, evaluation of metabolites, and chemical methods for cell monitoring programs in numerous plant species. A comprehensive metabolome profiling allowed the investigator to handle the comprehensive data groups of metabolites and the equivalent metabolic pathways in an extraordinary manner. Metabolomics, together with transcriptomics, plays an influential role in discovering connections between stress and genes/metabolite, phenotyping, and biomarkers documentation. Further, it helps to decode several metabolic systems connected with heat stress (HS) tolerance in plants. Heat stress is a critical environmental factor that is globally affecting the growth and productivity of plants. Thus, there is an urgent need to exploit modern breeding and biotechnological tools like metabolomics to develop cultivars with improved HS tolerance. Several studies have reported that amino acids, carbohydrates, nitrogen metabolisms, etc. and metabolites involved in the biosynthesis and catalyzing actions play a game-changing role in HS response and help plants to cope with the HS. The use of metabolomics-assisted breeding (MAB) allows a well-organized transmission of higher yield and HS tolerance at the metabolome level with specific properties. Progressive metabolomics systematic techniques have accelerated metabolic profiling. Nonetheless, continuous developments in bioinformatics, statistical tools, and databases are allowing us to produce ever-progressing, comprehensive insights into the biochemical configuration of plants and by what means this is inclined by genetic and environmental cues. Currently, assimilating metabolomics with post-genomic platforms has allowed a significant division of genetic-phenotypic connotation in several plant species. This review highlights the potential of a state-of-the-art plant metabolomics approach for the improvement of crops under HS. The development of plants with specific properties using integrated omics (metabolomics and transcriptomics) and MAB can provide new directions for future research to enhance HS tolerance in plants to achieve a goal of "zero hunger".
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Affiliation(s)
- Ali Raza
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China.
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9
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Tan Z, Xie Z, Dai L, Zhang Y, Zhao H, Tang S, Wan L, Yao X, Guo L, Hong D. Genome- and transcriptome-wide association studies reveal the genetic basis and the breeding history of seed glucosinolate content in Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:211-225. [PMID: 34525252 PMCID: PMC8710833 DOI: 10.1111/pbi.13707] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/25/2021] [Accepted: 09/07/2021] [Indexed: 05/08/2023]
Abstract
A high content of seed glucosinolates and their degradation products imposes anti-nutritional effects on livestock; therefore, persistent efforts are made to reduce the seed GSL content to increase the commercial value of rapeseed meal. Here, we dissected the genetic structure of SGC by genome-wide association studies (GWAS) combined with transcriptome-wide association studies (TWAS). Fifteen reliable quantitative trait loci (QTLs) were identified to be associated with the reduced SGC in modern B. napus cultivars by GWAS. Analysis of the selection strength and haplotypes at these QTLs revealed that low SGC was predominantly generated by the co-selection of qGSL.A02.2, qGSL.C02.1, qGSL.A09.2, and qGSL.C09.1. Integration of the results from TWAS, comprehensive bioinformatics, and POCKET algorithm analyses indicated that BnaC02.GTR2 (BnaC02g42260D) is a candidate gene underlying qGSL.C02.1. Using CRISPR/Cas9-derived Bna.gtr2s knockout mutants, we experimentally verified that both BnaC02.GTR2 and its three paralogs positively regulate seed GSL accumulation but negatively regulated vegetative tissue GSL contents. In addition, we observed smaller seeds with higher seed oil content in these Bna.gtr2 mutants. Furthermore, both RNA-seq and correlation analyses suggested that Bna.GTR2s might play a comprehensive role in seed development, such as amino acid accumulation, GSL synthesis, sugar assimilation, and oil accumulation. This study unravels the breeding selection history of low-SGC improvement and provides new insights into the molecular function of Bna.GTR2s in both seed GSL accumulation and seed development in B. napus.
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Affiliation(s)
- Zengdong Tan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Zhaoqi Xie
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Lihong Dai
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Yuting Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Hu Zhao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Shan Tang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Lili Wan
- Institute of CropsWuhan Academy of Agricultural SciencesWuhanChina
| | - Xuan Yao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Liang Guo
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
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10
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Kourani M, Mohareb F, Rezwan FI, Anastasiadi M, Hammond JP. Genetic and Physiological Responses to Heat Stress in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:832147. [PMID: 35449889 PMCID: PMC9016328 DOI: 10.3389/fpls.2022.832147] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/04/2022] [Indexed: 05/07/2023]
Abstract
Given the current rise in global temperatures, heat stress has become a major abiotic challenge affecting the growth and development of various crops and reducing their productivity. Brassica napus, the second largest source of vegetable oil worldwide, experiences a drastic reduction in seed yield and quality in response to heat. This review outlines the latest research that explores the genetic and physiological impact of heat stress on different developmental stages of B. napus with a special attention to the reproductive stages of floral progression, organogenesis, and post flowering. Several studies have shown that extreme temperature fluctuations during these crucial periods have detrimental effects on the plant and often leading to impaired growth and reduced seed production. The underlying mechanisms of heat stress adaptations and associated key regulatory genes are discussed. Furthermore, an overview and the implications of the polyploidy nature of B. napus and the regulatory role of alternative splicing in forming a priming-induced heat-stress memory are presented. New insights into the dynamics of epigenetic modifications during heat stress are discussed. Interestingly, while such studies are scarce in B. napus, opposite trends in expression of key genetic and epigenetic components have been identified in different species and in cultivars within the same species under various abiotic stresses, suggesting a complex role of these genes and their regulation in heat stress tolerance mechanisms. Additionally, omics-based studies are discussed with emphasis on the transcriptome, proteome and metabolome of B. napus, to gain a systems level understanding of how heat stress alters its yield and quality traits. The combination of omics approaches has revealed crucial interactions and regulatory networks taking part in the complex machinery of heat stress tolerance. We identify key knowledge gaps regarding the impact of heat stress on B. napus during its yield determining reproductive stages, where in-depth analysis of this subject is still needed. A deeper knowledge of heat stress response components and mechanisms in tissue specific models would serve as a stepping-stone to gaining insights into the regulation of thermotolerance that takes place in this important crop species and support future breeding of heat tolerant crops.
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Affiliation(s)
- Mariam Kourani
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - Fady Mohareb
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
- *Correspondence: Fady Mohareb,
| | - Faisal I. Rezwan
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - Maria Anastasiadi
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - John P. Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
- John P. Hammond,
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11
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Rahman H, Kebede B. Mapping of seed quality traits in the C genome of Brassica napus by using a population carrying genome content of B. oleracea and their effect on other traits. THE PLANT GENOME 2021; 14:e20078. [PMID: 33818008 DOI: 10.1002/tpg2.20078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 11/21/2020] [Indexed: 06/12/2023]
Abstract
Increasing seed oil and protein contents and reducing the content of seed glucosinolates (GSLs) in Brassica oilseed crops are important objectives in breeding. By using an oilseed rape (B. napus L.) doubled-haploid (DH) population carrying genome content introgressed from Chinese kale (B. oleracea L.), we mapped quantitative trait loci (QTL) for these seed quality traits and investigated their effect on other traits including seed yield. A stable QTL for seed oil content was identified on chromosome C5 at 40-42 Mb position and a QTL for seed GSL content was identified on C9 at 7-8 Mb position. The C5 and C9 QTL alleles for high oil and GSL contents were derived from Chinese kale, demonstrating that high-oil QTL allele can be found in the parental species of oilseed rape. The low-GSL QTL allele of C9 exerted a significant positive effect on seed protein content, demonstrating that selection for this QTL allele contributed to higher protein content in canola seed. These two QTL were not affected by field environmental conditions and did not exert a significant effect on days to flowering and seed yield. Thus, the genomic regions and the molecular markers identified in this study should be useful in molecular breeding of the seed quality traits in oilseed rape.
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Affiliation(s)
- Habibur Rahman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Berisso Kebede
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
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12
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Kumar R, Sharma V, Suresh S, Ramrao DP, Veershetty A, Kumar S, Priscilla K, Hangargi B, Narasanna R, Pandey MK, Naik GR, Thomas S, Kumar A. Understanding Omics Driven Plant Improvement and de novo Crop Domestication: Some Examples. Front Genet 2021; 12:637141. [PMID: 33889179 PMCID: PMC8055929 DOI: 10.3389/fgene.2021.637141] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/02/2021] [Indexed: 01/07/2023] Open
Abstract
In the current era, one of biggest challenges is to shorten the breeding cycle for rapid generation of a new crop variety having high yield capacity, disease resistance, high nutrient content, etc. Advances in the "-omics" technology have revolutionized the discovery of genes and bio-molecules with remarkable precision, resulting in significant development of plant-focused metabolic databases and resources. Metabolomics has been widely used in several model plants and crop species to examine metabolic drift and changes in metabolic composition during various developmental stages and in response to stimuli. Over the last few decades, these efforts have resulted in a significantly improved understanding of the metabolic pathways of plants through identification of several unknown intermediates. This has assisted in developing several new metabolically engineered important crops with desirable agronomic traits, and has facilitated the de novo domestication of new crops for sustainable agriculture and food security. In this review, we discuss how "omics" technologies, particularly metabolomics, has enhanced our understanding of important traits and allowed speedy domestication of novel crop plants.
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Affiliation(s)
- Rakesh Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Srinivas Suresh
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | | | - Akash Veershetty
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Sharan Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Kagolla Priscilla
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | | | - Rahul Narasanna
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Manish Kumar Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | | | - Sherinmol Thomas
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University, Amarkantak, India
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13
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Metabolomics Intervention Towards Better Understanding of Plant Traits. Cells 2021; 10:cells10020346. [PMID: 33562333 PMCID: PMC7915772 DOI: 10.3390/cells10020346] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023] Open
Abstract
The majority of the most economically important plant and crop species are enriched with the availability of high-quality reference genome sequences forming the basis of gene discovery which control the important biochemical pathways. The transcriptomics and proteomics resources have also been made available for many of these plant species that intensify the understanding at expression levels. However, still we lack integrated studies spanning genomics–transcriptomics–proteomics, connected to metabolomics, the most complicated phase in phenotype expression. Nevertheless, for the past few decades, emphasis has been more on metabolome which plays a crucial role in defining the phenotype (trait) during crop improvement. The emergence of modern high throughput metabolome analyzing platforms have accelerated the discovery of a wide variety of biochemical types of metabolites and new pathways, also helped in improving the understanding of known existing pathways. Pinpointing the causal gene(s) and elucidation of metabolic pathways are very important for development of improved lines with high precision in crop breeding. Along with other-omics sciences, metabolomics studies have helped in characterization and annotation of a new gene(s) function. Hereby, we summarize several areas in the field of crop development where metabolomics studies have made its remarkable impact. We also assess the recent research on metabolomics, together with other omics, contributing toward genetic engineering to target traits and key pathway(s).
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14
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Wang W, Zou J, White PJ, Ding G, Li Y, Xu F, Shi L. Identification of QTLs associated with potassium use efficiency and underlying candidate genes by whole-genome resequencing of two parental lines in Brassica napus. Genomics 2021; 113:755-768. [PMID: 33516850 DOI: 10.1016/j.ygeno.2021.01.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/20/2020] [Accepted: 01/26/2021] [Indexed: 10/22/2022]
Abstract
Breeding crops that acquire and/or utilize potassium (K) more effectively could reduce the use of K fertilizers. Sixteen traits affecting K use efficiency (KUE) at the seedling stage were investigated in a B. napus double haploid population grown at an optimal K supply (OK) and a low K supply (LK) in a hydroponic culture system. In total, 50 and 62 QTLs associated with these traits were identified at OK and LK, respectively. A total of 25 orthologues of 23 Arabidopsis genes regulating K transport were identified in the confidence intervals of nine QTLs impacting shoot dry weight at LK, and 22 of these showed variations in coding sequences and/or exhibited significant differences in mRNA abundances in roots at LK between the two parental lines. This study provided insights to the genetic basis of KUE in B. napus, which will accelerate the breeding of K-efficient rapeseed cultivars by marker-assisted selection.
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Affiliation(s)
- Wei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinsong Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Philip J White
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; Distinguished Scientist Fellowship Program, King Saud University, Riyadh 11451, Saudi Arabia
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Yalin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China.
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15
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Wang W, Ding G, White PJ, Wang M, Zou J, Xu F, Hammond JP, Shi L. Genetic dissection of the shoot and root ionomes of Brassica napus grown with contrasting phosphate supplies. ANNALS OF BOTANY 2020; 126:119-140. [PMID: 32221530 PMCID: PMC7304470 DOI: 10.1093/aob/mcaa055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 03/26/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Mineral elements have many essential and beneficial functions in plants. Phosphorus (P) deficiency can result in changes in the ionomes of plant organs. The aims of this study were to characterize the effects of P supply on the ionomes of shoots and roots, and to identify chromosomal quantitative trait loci (QTLs) for shoot and root ionomic traits, as well as those affecting the partitioning of mineral elements between shoot and root in Brassica napus grown with contrasting P supplies. METHODS Shoot and root concentrations of 11 mineral elements (B, Ca, Cu, Fe, K, Mg, Mn, Na, P, S and Zn) were investigated by inductively coupled plasma optical emission spectrometry (ICP-OES) in a Brassica napus double haploid population grown at an optimal (OP) and a low phosphorus supply (LP) in an agar system. Shoot, root and plant contents, and the partitioning of mineral elements between shoot and root were calculated. KEY RESULTS The tissue concentrations of B, Ca, Cu, K, Mg, Mn, Na, P and Zn were reduced by P starvation, while the concentration of Fe was increased by P starvation in the BnaTNDH population. A total of 133 and 123 QTLs for shoot and root ionomic traits were identified at OP and LP, respectively. A major QTL cluster on chromosome C07 had a significant effect on shoot Mg and S concentrations at LP and was narrowed down to a 2.1 Mb region using an advanced backcross population. CONCLUSIONS The tissue concentration and partitioning of each mineral element was affected differently by P starvation. There was a significant difference in mineral element composition between shoots and roots. Identification of the genes underlying these QTLs will enhance our understanding of processes affecting the uptake and partitioning of mineral elements in Brassica napus.
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Affiliation(s)
- Wei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Philip J White
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- The James Hutton Institute, Invergowrie, Dundee, UK
| | - Meng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - John P Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
- Southern Cross Plant Science, Southern Cross University, Lismore, Australia
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
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16
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Liu S, Huang H, Yi X, Zhang Y, Yang Q, Zhang C, Fan C, Zhou Y. Dissection of genetic architecture for glucosinolate accumulations in leaves and seeds of Brassica napus by genome-wide association study. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1472-1484. [PMID: 31820843 PMCID: PMC7206990 DOI: 10.1111/pbi.13314] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/01/2019] [Accepted: 12/04/2019] [Indexed: 05/04/2023]
Abstract
Glucosinolates (GSLs), whose degradation products have been shown to be increasingly important for human health and plant defence, compose important secondary metabolites found in the order Brassicales. It is highly desired to enhance pest and disease resistance by increasing the leaf GSL content while keeping the content low in seeds of Brassica napus, one of the most important oil crops worldwide. Little is known about the regulation of GSL accumulation in the leaves. We quantified the levels of 9 different GSLs and 15 related traits in the leaves of 366 accessions and found that the seed and leaf GSL content were highly correlated (r = 0.79). A total of 78 loci were associated with GSL traits, and five common and eleven tissue-specific associated loci were related to total leaf and seed GSL content. Thirty-six candidate genes were inferred to be involved in GSL biosynthesis. The candidate gene BnaA03g40190D (BnaA3.MYB28) was validated by DNA polymorphisms and gene expression analysis. This gene was responsible for high leaf/low seed GSL content and could explain 30.62% of the total leaf GSL variation in the low seed GSL panel and was not fixed during double-low rapeseed breeding. Our results provide new insights into the genetic basis of GSL variation in leaves and seeds and may facilitate the metabolic engineering of GSLs and the breeding of high leaf/low seed GSL content in B. napus.
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Affiliation(s)
- Sheng Liu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanChina
| | - Huibin Huang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xinqi Yi
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Yuanyuan Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Qingyong Yang
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
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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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Razzaq A, Sadia B, Raza A, Khalid Hameed M, Saleem F. Metabolomics: A Way Forward for Crop Improvement. Metabolites 2019; 9:E303. [PMID: 31847393 PMCID: PMC6969922 DOI: 10.3390/metabo9120303] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/02/2019] [Accepted: 12/11/2019] [Indexed: 12/15/2022] Open
Abstract
Metabolomics is an emerging branch of "omics" and it involves identification and quantification of metabolites and chemical footprints of cellular regulatory processes in different biological species. The metabolome is the total metabolite pool in an organism, which can be measured to characterize genetic or environmental variations. Metabolomics plays a significant role in exploring environment-gene interactions, mutant characterization, phenotyping, identification of biomarkers, and drug discovery. Metabolomics is a promising approach to decipher various metabolic networks that are linked with biotic and abiotic stress tolerance in plants. In this context, metabolomics-assisted breeding enables efficient screening for yield and stress tolerance of crops at the metabolic level. Advanced metabolomics analytical tools, like non-destructive nuclear magnetic resonance spectroscopy (NMR), liquid chromatography mass-spectroscopy (LC-MS), gas chromatography-mass spectrometry (GC-MS), high performance liquid chromatography (HPLC), and direct flow injection (DFI) mass spectrometry, have sped up metabolic profiling. Presently, integrating metabolomics with post-genomics tools has enabled efficient dissection of genetic and phenotypic association in crop plants. This review provides insight into the state-of-the-art plant metabolomics tools for crop improvement. Here, we describe the workflow of plant metabolomics research focusing on the elucidation of biotic and abiotic stress tolerance mechanisms in plants. Furthermore, the potential of metabolomics-assisted breeding for crop improvement and its future applications in speed breeding are also discussed. Mention has also been made of possible bottlenecks and future prospects of plant metabolomics.
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Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan; (A.R.); (B.S.)
| | - Bushra Sadia
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan; (A.R.); (B.S.)
| | - Ali Raza
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan 430062, China;
| | - Muhammad Khalid Hameed
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan; (A.R.); (B.S.)
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Li S, He Q, Peng Q, Fang X, Zhu T, Qiao T, Han S. Metabolomics responses of Bambusa pervariabilis × Dendrocalamopsis grandis varieties to Biotic (pathogenic fungus) stress. PHYTOCHEMISTRY 2019; 167:112087. [PMID: 31437664 DOI: 10.1016/j.phytochem.2019.112087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 06/10/2023]
Abstract
Bambusa pervariabilis × Dendrocalamopsis grandis blight, caused by Arthrinium phaeospermum, is one of the most common and serious diseases in bamboo and occurs in the newly born twigs. Bamboo has suffered large dead areas, including more than 3000 hm2, which greatly threatens the process of returning farmlands to forests and the construction of ecological barriers. To identify differential metabolites and metabolic pathways associated with B. pervariabilis × D. grandis to A. phaeospermum, ultra-performance liquid chromatography (UPLC) and quadrupole-time of flight (Q-TOF) Mass Spectrometry (MS) combined with a data-dependent acquisition method was used to analyse the entire sample spectrum. In total, 13223 positive ion peaks and 10616 negative ion peaks were extracted. OPLS-DA and several other analyses were performed using the original data. The OPLS-DA models showed good quality and had strong predictive power, indicating clear trends in the analyses of the treatment and control groups. Clustering and KEGG pathway analyses were used to screen the differential metabolites in the treatment and control groups from the three B. pervariabilis × D. grandis varieties and reflected their metabolic responses induced by A. phaeospermum infection. The results showed that the three B. pervariabilis × D. grandis varieties mode showed significant changes in the following six resistance-related metabolites after A. phaeospermum invasion in positive and negative ion modes: proline, glutamine, dictamnine, apigenin 7-O-neohesperidoside, glutamate, and cis-Aconitate. The following four main metabolic pathways are involved: Arginine and proline metabolism, Glyoxylate and dicarboxylate metabolism, Biosynthesis of alkaloids derived from shikimate pathway, and Flavone and flavonol biosynthesis. This study lays a foundation for the later detection of differential metabolites and metabolic pathways for targeting, and provides a theoretical basis for disease-resistant breeding and the control of B. pervariabilis × D. grandis blight.
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Affiliation(s)
- Shujiang Li
- College of Forestry, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China.
| | - Qianqian He
- College of Forestry, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China.
| | - Qi Peng
- College of Forestry, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China.
| | - Xinmei Fang
- College of Forestry, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China.
| | - Tianhui Zhu
- College of Forestry, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China.
| | - Tianmin Qiao
- College of Forestry, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China.
| | - Shan Han
- College of Forestry, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China.
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Khattak AN, Wang T, Yu K, Yang R, Wan W, Ye B, Tian E. Exploring the basis of 2-propenyl and 3-butenyl glucosinolate synthesis by QTL mapping and RNA-sequencing in Brassica juncea. PLoS One 2019; 14:e0220597. [PMID: 31626668 PMCID: PMC6799926 DOI: 10.1371/journal.pone.0220597] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/04/2019] [Indexed: 01/08/2023] Open
Abstract
Brassica juncea is used as a condiment, as vegetables and as an oilseed crop, especially in semiarid areas. In the present study, we constructed a genetic map using one recombinant inbred line (RIL) of B. juncea. A total of 304 ILP (intron length polymorphism) markers were mapped to 18 linkage groups designated LG01-LG18 in B. juncea. The constructed map covered a total genetic length of 1671.13 cM with an average marker interval of 5.50 cM. The QTLs for 2-propenyl glucosinolates (GSLs) colocalized with the QTLs for 3-butenyl GSLs between At1g26180 and BnapPIP1580 on LG08 in the field experiments of 2016 and 2017. These QTLs accounted for an average of 42.3% and 42.6% phenotypic variation for 2-propenyl and 3-butenyl GSLs, respectively. Furthermore, the Illumina RNA-sequencing technique was used to excavate the genes responsible for the synthesis of GSLs in the siliques of the parental lines of the RIL mapping population, because the bulk of the seed GSLs might originate from the siliques. Comparative analysis and annotation by gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) revealed that 324 genes were involved in GSL metabolism, among which only 24 transcripts were differentially expressed genes (DEGs). Among those DEGs, 15 genes were involved in the biosynthesis and transport of aliphatic GSLs, and their expression patterns were further validated by qRT-PCR analysis. Joint QTL mapping and RNA-sequencing analyses reveal one candidate gene of IIL1 (LOC106416451) for GSL metabolism in B. juncea. These results will be helpful for further fine mapping, gene cloning and genetic mechanisms of 2-propenyl and 3-butenyl GSLs in B. juncea.
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Affiliation(s)
- Aimal Nawaz Khattak
- Oil Crops Research Institute of Guizhou University, Agricultural College of Guizhou University, Guizhou University, Guiyang, China
| | - Tianya Wang
- Oil Crops Research Institute of Guizhou University, Agricultural College of Guizhou University, Guizhou University, Guiyang, China
| | - Kunjiang Yu
- Oil Crops Research Institute of Guizhou University, Agricultural College of Guizhou University, Guizhou University, Guiyang, China
| | - Renqin Yang
- Oil Crops Research Institute of Guizhou University, Agricultural College of Guizhou University, Guizhou University, Guiyang, China
| | - Wei Wan
- Oil Crops Research Institute of Guizhou University, Agricultural College of Guizhou University, Guizhou University, Guiyang, China
| | - Botao Ye
- Oil Crops Research Institute of Guizhou University, Agricultural College of Guizhou University, Guizhou University, Guiyang, China
| | - Entang Tian
- Oil Crops Research Institute of Guizhou University, Agricultural College of Guizhou University, Guizhou University, Guiyang, China
- * E-mail:
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Alseekh S, Bermudez L, de Haro LA, Fernie AR, Carrari F. Crop metabolomics: from diagnostics to assisted breeding. Metabolomics 2018; 14:148. [PMID: 30830402 DOI: 10.1007/s11306-018-1446-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/26/2018] [Indexed: 01/02/2023]
Abstract
BACKGROUND Until recently, plant metabolomics have provided a deep understanding on the metabolic regulation in individual plants as experimental units. The application of these techniques to agricultural systems subjected to more complex interactions is a step towards the implementation of translational metabolomics in crop breeding. AIM OF REVIEW We present here a review paper discussing advances in the knowledge reached in the last years derived from the application of metabolomic techniques that evolved from biomarker discovery to improve crop yield and quality. KEY SCIENTIFIC CONCEPTS OF REVIEW Translational metabolomics applied to crop breeding programs.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Luisa Bermudez
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Luis Alejandro de Haro
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Fernando Carrari
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (IB-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), PO Box 25, B1686WAA, Castelar, Argentina.
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, 05508-090, Brazil.
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina.
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Functional Metabolomics—A Useful Tool to Characterize Stress-Induced Metabolome Alterations Opening New Avenues towards Tailoring Food Crop Quality. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8080138] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The breeding of stress-tolerant cultivated plants that would allow for a reduction in harvest losses and undesirable decrease in quality attributes requires a new quality of knowledge on molecular markers associated with relevant agronomic traits, on quantitative metabolic responses of plants to stress challenges, and on the mechanisms controlling the biosynthesis of these molecules. By combining metabolomics with genomics, transcriptomics and proteomics datasets a more comprehensive knowledge of the composition of crop plants used for food or animal feed is possible. In order to optimize crop trait developments, to enhance crop yields and quality, as well as to guarantee nutritional and health factors that provide the possibility to create functional food or feedstuffs, knowledge about the plants’ metabolome is crucial. Next to classical metabolomics studies, this review focuses on several metabolomics-based working techniques, such as sensomics, lipidomics, hormonomics and phytometabolomics, which were used to characterize metabolome alterations during abiotic and biotic stress in order to find resistant food crops with a preferred quality or at least to produce functional food crops.
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Dyer LA, Philbin CS, Ochsenrider KM, Richards LA, Massad TJ, Smilanich AM, Forister ML, Parchman TL, Galland LM, Hurtado PJ, Espeset AE, Glassmire AE, Harrison JG, Mo C, Yoon S, Pardikes NA, Muchoney ND, Jahner JP, Slinn HL, Shelef O, Dodson CD, Kato MJ, Yamaguchi LF, Jeffrey CS. Modern approaches to study plant–insect interactions in chemical ecology. Nat Rev Chem 2018. [DOI: 10.1038/s41570-018-0009-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Kulwal PL. Trait Mapping Approaches Through Linkage Mapping in Plants. PLANT GENETICS AND MOLECULAR BIOLOGY 2018; 164:53-82. [DOI: 10.1007/10_2017_49] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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25
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Seo MS, Kim JS. Understanding of MYB Transcription Factors Involved in Glucosinolate Biosynthesis in Brassicaceae. Molecules 2017; 22:molecules22091549. [PMID: 28906468 PMCID: PMC6151624 DOI: 10.3390/molecules22091549] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 09/08/2017] [Accepted: 09/12/2017] [Indexed: 02/06/2023] Open
Abstract
Glucosinolates (GSLs) are widely known secondary metabolites that have anticarcinogenic and antioxidative activities in humans and defense roles in plants of the Brassicaceae family. Some R2R3-type MYB (myeloblastosis) transcription factors (TFs) control GSL biosynthesis in Arabidopsis. However, studies on the MYB TFs involved in GSL biosynthesis in Brassica species are limited because of the complexity of the genome, which includes an increased number of paralog genes as a result of genome duplication. The recent completion of the genome sequencing of the Brassica species permits the identification of MYB TFs involved in GSL biosynthesis by comparative genome analysis with A. thaliana. In this review, we describe various findings on the regulation of GSL biosynthesis in Brassicaceae. Furthermore, we identify 63 orthologous copies corresponding to five MYB TFs from Arabidopsis, except MYB76 in Brassica species. Fifty-five MYB TFs from the Brassica species possess a conserved amino acid sequence in their R2R3 MYB DNA-binding domain, and share close evolutionary relationships. Our analysis will provide useful information on the 55 MYB TFs involved in the regulation of GSL biosynthesis in Brassica species, which have a polyploid genome.
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Affiliation(s)
- Mi-Suk Seo
- Genomics Division, Department of Agricultural Bio-Resources, National Institute of Agricultural Sciences, Rural Development Administration, Wansan-gu, Jeonju 54874, Korea.
| | - Jung Sun Kim
- Genomics Division, Department of Agricultural Bio-Resources, National Institute of Agricultural Sciences, Rural Development Administration, Wansan-gu, Jeonju 54874, Korea.
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Luo Z, Wang M, Long Y, Huang Y, Shi L, Zhang C, Liu X, Fitt BDL, Xiang J, Mason AS, Snowdon RJ, Liu P, Meng J, Zou J. Incorporating pleiotropic quantitative trait loci in dissection of complex traits: seed yield in rapeseed as an example. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1569-1585. [PMID: 28455767 PMCID: PMC5719798 DOI: 10.1007/s00122-017-2911-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 04/19/2017] [Indexed: 05/10/2023]
Abstract
A comprehensive linkage atlas for seed yield in rapeseed. Most agronomic traits of interest for crop improvement (including seed yield) are highly complex quantitative traits controlled by numerous genetic loci, which brings challenges for comprehensively capturing associated markers/genes. We propose that multiple trait interactions underlie complex traits such as seed yield, and that considering these component traits and their interactions can dissect individual quantitative trait loci (QTL) effects more effectively and improve yield predictions. Using a segregating rapeseed (Brassica napus) population, we analyzed a large set of trait data generated in 19 independent experiments to investigate correlations between seed yield and other complex traits, and further identified QTL in this population with a SNP-based genetic bin map. A total of 1904 consensus QTL accounting for 22 traits, including 80 QTL directly affecting seed yield, were anchored to the B. napus reference sequence. Through trait association analysis and QTL meta-analysis, we identified a total of 525 indivisible QTL that either directly or indirectly contributed to seed yield, of which 295 QTL were detected across multiple environments. A majority (81.5%) of the 525 QTL were pleiotropic. By considering associations between traits, we identified 25 yield-related QTL previously ignored due to contrasting genetic effects, as well as 31 QTL with minor complementary effects. Implementation of the 525 QTL in genomic prediction models improved seed yield prediction accuracy. Dissecting the genetic and phenotypic interrelationships underlying complex quantitative traits using this method will provide valuable insights for genomics-based crop improvement.
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Affiliation(s)
- Ziliang Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Meng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yongju Huang
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire AL10 9AB UK
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiang Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Bruce D. L. Fitt
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire AL10 9AB UK
| | - Jinxia Xiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Annaliese S. Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Peifa Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
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Wang X, Long Y, Wang N, Zou J, Ding G, Broadley MR, White PJ, Yuan P, Zhang Q, Luo Z, Liu P, Zhao H, Zhang Y, Cai H, King GJ, Xu F, Meng J, Shi L. Breeding histories and selection criteria for oilseed rape in Europe and China identified by genome wide pedigree dissection. Sci Rep 2017; 7:1916. [PMID: 28507329 PMCID: PMC5432491 DOI: 10.1038/s41598-017-02188-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/13/2017] [Indexed: 12/17/2022] Open
Abstract
Selection breeding has played a key role in the improvement of seed yield and quality in oilseed rape (Brassica napus L.). We genotyped Tapidor (European), Ningyou7 (Chinese) and their progenitors with the Brassica 60 K Illumina Infinium SNP array and mapped a total of 29,347 SNP markers onto the reference genome of Darmor-bzh. Identity by descent (IBD) refers to a haplotype segment of a chromosome inherited from a shared common ancestor. IBDs identified on the C subgenome were larger than those on the A subgenome within both the Tapidor and Ningyou7 pedigrees. IBD number and length were greater in the Ningyou7 pedigree than in the Tapidor pedigree. Seventy nine QTLs for flowering time, seed quality and root morphology traits were identified in the IBDs of Tapidor and Ningyou7. Many more candidate genes had been selected within the Ningyou7 pedigree than within the Tapidor pedigree. These results highlight differences in the transfer of favorable gene clusters controlling key traits during selection breeding in Europe and China.
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Affiliation(s)
- Xiaohua Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Biotechnology Research Institute, Chinese Academy of agricultural Science, Beijing, 100081, China
| | - Nian Wang
- College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Martin R Broadley
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom
| | - Philip J White
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom
- King Saud University, Riyadh, 11451, Saudi Arabia
| | - Pan Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qianwen Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ziliang Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Peifa Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hua Zhao
- College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ying Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hongmei Cai
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Graham J King
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China.
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Chao H, Wang H, Wang X, Guo L, Gu J, Zhao W, Li B, Chen D, Raboanatahiry N, Li M. Genetic dissection of seed oil and protein content and identification of networks associated with oil content in Brassica napus. Sci Rep 2017; 7:46295. [PMID: 28393910 PMCID: PMC5385559 DOI: 10.1038/srep46295] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 03/15/2017] [Indexed: 02/07/2023] Open
Abstract
High-density linkage maps can improve the precision of QTL localization. A high-density SNP-based linkage map containing 3207 markers covering 3072.7 cM of the Brassica napus genome was constructed in the KenC-8 × N53-2 (KNDH) population. A total of 67 and 38 QTLs for seed oil and protein content were identified with an average confidence interval of 5.26 and 4.38 cM, which could explain up to 22.24% and 27.48% of the phenotypic variation, respectively. Thirty-eight associated genomic regions from BSA overlapped with and/or narrowed the SOC-QTLs, further confirming the QTL mapping results based on the high-density linkage map. Potential candidates related to acyl-lipid and seed storage underlying SOC and SPC, respectively, were identified and analyzed, among which six were checked and showed expression differences between the two parents during different embryonic developmental periods. A large primary carbohydrate pathway based on potential candidates underlying SOC- and SPC-QTLs, and interaction networks based on potential candidates underlying SOC-QTLs, was constructed to dissect the complex mechanism based on metabolic and gene regulatory features, respectively. Accurate QTL mapping and potential candidates identified based on high-density linkage map and BSA analyses provide new insights into the complex genetic mechanism of oil and protein accumulation in the seeds of rapeseed.
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Affiliation(s)
- Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Xiaodong Wang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Liangxing Guo
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jianwei Gu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Weiguo Zhao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Baojun Li
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Dengyan Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China
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Arneson D, Shu L, Tsai B, Barrere-Cain R, Sun C, Yang X. Multidimensional Integrative Genomics Approaches to Dissecting Cardiovascular Disease. Front Cardiovasc Med 2017; 4:8. [PMID: 28289683 PMCID: PMC5327355 DOI: 10.3389/fcvm.2017.00008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/09/2017] [Indexed: 12/19/2022] Open
Abstract
Elucidating the mechanisms of complex diseases such as cardiovascular disease (CVD) remains a significant challenge due to multidimensional alterations at molecular, cellular, tissue, and organ levels. To better understand CVD and offer insights into the underlying mechanisms and potential therapeutic strategies, data from multiple omics types (genomics, epigenomics, transcriptomics, metabolomics, proteomics, microbiomics) from both humans and model organisms have become available. However, individual omics data types capture only a fraction of the molecular mechanisms. To address this challenge, there have been numerous efforts to develop integrative genomics methods that can leverage multidimensional information from diverse data types to derive comprehensive molecular insights. In this review, we summarize recent methodological advances in multidimensional omics integration, exemplify their applications in cardiovascular research, and pinpoint challenges and future directions in this incipient field.
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Affiliation(s)
- Douglas Arneson
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, USA; Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Le Shu
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, USA; Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Brandon Tsai
- Department of Integrative Biology and Physiology, University of California Los Angeles , Los Angeles, CA , USA
| | - Rio Barrere-Cain
- Department of Integrative Biology and Physiology, University of California Los Angeles , Los Angeles, CA , USA
| | - Christine Sun
- Department of Integrative Biology and Physiology, University of California Los Angeles , Los Angeles, CA , USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, USA; Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA; Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
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Su ZZ, Wang T, Shrivastava N, Chen YY, Liu X, Sun C, Yin Y, Gao QK, Lou BG. Piriformospora indica promotes growth, seed yield and quality of Brassica napus L. Microbiol Res 2017; 199:29-39. [PMID: 28454707 DOI: 10.1016/j.micres.2017.02.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/19/2017] [Accepted: 02/25/2017] [Indexed: 10/20/2022]
Abstract
In current scenario, crop productivity is being challenged by decreasing soil fertility. To cope up with this problem, different beneficial microbes are explored to increase the crop productivity with value additions. In this study, Brassica napus L., an important agricultural economic oilseed crop with rich source of nutritive qualities, was interacted with Piriformospora indica, a unique root colonizing fungus with wide host range and multifunctional aspects. The fungus-treated plants showed a significant increase in agronomic parameters with plant biomass, lodging-resistance, early bolting and flowering, oil yield and quality. Nutritional analysis revealed that plants treated by P. indica had reduced erucic acid and glucosinolates contents, and increased the accumulation of N, Ca, Mg, P, K, S, B, Fe and Zn elements. Low erucic acid and glucosinolates contents are important parameters for high quality oil, because oils high in erucic acid and glucosinolates are considered undesirable for human nutrition. Furthermore, the expression profiles of two encoding enzyme genes, Bn-FAE1 and BnECR, which are responsible for regulating erucic acid biosynthesis, were down-regulated at mid- and late- life stages during seeds development in colonized plants. These results demonstrated that P. indica played an important role in enhancing plant growth, rapeseed yield and quality improvement of B. napus.
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Affiliation(s)
- Zhen-Zhu Su
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China; Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Ting Wang
- Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - Neeraj Shrivastava
- Institute of Biotechnology, Zhejiang University, Hangzhou, China; Institute of Microbial Technology, Amity University, New Delhi, India
| | - You-Yuan Chen
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaoxi Liu
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Chao Sun
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yufeng Yin
- Agricultural Technology Extension Center, Zhejiang University, Hangzhou, China
| | - Qi-Kang Gao
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Bing-Gan Lou
- Institute of Biotechnology, Zhejiang University, Hangzhou, China.
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Zou J, Zhao Y, Liu P, Shi L, Wang X, Wang M, Meng J, Reif JC. Seed Quality Traits Can Be Predicted with High Accuracy in Brassica napus Using Genomic Data. PLoS One 2016; 11:e0166624. [PMID: 27880793 PMCID: PMC5120799 DOI: 10.1371/journal.pone.0166624] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 11/01/2016] [Indexed: 11/19/2022] Open
Abstract
Improving seed oil yield and quality are central targets in rapeseed (Brassica napus) breeding. The primary goal of our study was to examine and compare the potential and the limits of marker-assisted selection and genome-wide prediction of six important seed quality traits of B. napus. Our study is based on a bi-parental population comprising 202 doubled haploid lines and a diverse validation set including 117 B. napus inbred lines derived from interspecific crosses between B. rapa and B. carinata. We used phenotypic data for seed oil, protein, erucic acid, linolenic acid, stearic acid, and glucosinolate content. All lines were genotyped with a 60k SNP array. We performed five-fold cross-validations in combination with linkage mapping and four genome-wide prediction approaches in the bi-parental population. Quantitative trait loci (QTL) with large effects were detected for erucic acid, stearic acid, and glucosinolate content, blazing the trail for marker-assisted selection. Despite substantial differences in the complexity of the genetic architecture of the six traits, genome-wide prediction models had only minor impacts on the prediction accuracies. We evaluated the effects of training population size, marker density and phenotyping intensity on the prediction accuracy. The prediction accuracy in the independent and genetically very distinct validation set still amounted to 0.14 for protein content and 0.17 for oil content reflecting the utility of the developed calibration models even in very diverse backgrounds.
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Affiliation(s)
- Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Peifa Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaohua Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Meng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jochen Christoph Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Borpatragohain P, Rose TJ, King GJ. Fire and Brimstone: Molecular Interactions between Sulfur and Glucosinolate Biosynthesis in Model and Crop Brassicaceae. FRONTIERS IN PLANT SCIENCE 2016; 7:1735. [PMID: 27917185 PMCID: PMC5116641 DOI: 10.3389/fpls.2016.01735] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/03/2016] [Indexed: 05/20/2023]
Abstract
Glucosinolates (GSLs) represent one of the most widely studied classes of plant secondary metabolite, and have a wide range of biological activities. Their unique properties also affect livestock and human health, and have been harnessed for food and other end-uses. Since GSLs are sulfur (S)-rich there are many lines of evidence suggesting that plant S status plays a key role in determining plant GSL content. However, there is still a need to establish a detailed knowledge of the distribution and remobilization of S and GSLs throughout the development of Brassica crops, and to represent this in terms of primary and secondary sources and sinks. The increased genome complexity, gene duplication and divergence within brassicas, together with their ontogenetic plasticity during crop development, appear to have a marked effect on the regulation of S and GSLs. Here, we review the current understanding of inorganic S (sulfate) assimilation into organic S forms, including GSLs and their precursors, the intracellular and inter-organ transport of inorganic and organic S forms, and the accumulation of GSLs in specific tissues. We present this in the context of overlapping sources and sinks, transport processes, signaling molecules and their associated molecular interactions. Our analysis builds on recent insights into the molecular regulation of sulfate uptake and transport by different transporters, transcription factors and miRNAs, and the role that these may play in GSL biosynthesis. We develop a provisional model describing the key processes that could be targeted in crop breeding programs focused on modifying GSL content.
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Affiliation(s)
| | - Terry J. Rose
- Southern Cross Plant Science, Southern Cross University, LismoreNSW, Australia
- Southern Cross GeoScience, Southern Cross University, LismoreNSW, Australia
| | - Graham J. King
- Southern Cross Plant Science, Southern Cross University, LismoreNSW, Australia
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35
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Zou C, Wang P, Xu Y. Bulked sample analysis in genetics, genomics and crop improvement. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1941-55. [PMID: 26990124 PMCID: PMC5043468 DOI: 10.1111/pbi.12559] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/09/2016] [Accepted: 03/12/2016] [Indexed: 05/18/2023]
Abstract
Biological assay has been based on analysis of all individuals collected from sample populations. Bulked sample analysis (BSA), which works with selected and pooled individuals, has been extensively used in gene mapping through bulked segregant analysis with biparental populations, mapping by sequencing with major gene mutants and pooled genomewide association study using extreme variants. Compared to conventional entire population analysis, BSA significantly reduces the scale and cost by simplifying the procedure. The bulks can be built by selection of extremes or representative samples from any populations and all types of segregants and variants that represent wide ranges of phenotypic variation for the target trait. Methods and procedures for sampling, bulking and multiplexing are described. The samples can be analysed using individual markers, microarrays and high-throughput sequencing at all levels of DNA, RNA and protein. The power of BSA is affected by population size, selection of extreme individuals, sequencing strategies, genetic architecture of the trait and marker density. BSA will facilitate plant breeding through development of diagnostic and constitutive markers, agronomic genomics, marker-assisted selection and selective phenotyping. Applications of BSA in genetics, genomics and crop improvement are discussed with their future perspectives.
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Affiliation(s)
- Cheng Zou
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pingxi Wang
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunbi Xu
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
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36
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Gokul A, Roode E, Klein A, Keyster M. Exogenous 3,3'-diindolylmethane increases Brassica napus L. seedling shoot growth through modulation of superoxide and hydrogen peroxide content. JOURNAL OF PLANT PHYSIOLOGY 2016; 196-197:93-8. [PMID: 27100938 DOI: 10.1016/j.jplph.2016.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 01/25/2016] [Accepted: 03/24/2016] [Indexed: 05/27/2023]
Abstract
Brassica napus L. (cv. AV Garnet) seeds were pre-treated with 15μM 3,3'-diindolylmethane (DIM) to investigate whether DIM could enhance seed germination. Further treatment of seedlings with 15μM DIM for 14days explored the effects on seedling shoot growth. Exogenous DIM led to improved germination percentage, increased seedling shoot lengths, and increased fresh and dry weights. Furthermore, DIM triggered induction of superoxide radical (O2(-)) and hydrogen peroxide (H2O2) content however, no change in malondialdehyde (MDA) content and cell death (assessed with Evans Blue assay) was detected for both the control and DIM treated seedling shoots. We also observed increases in superoxide dismutase (SOD) activity and ascorbate peroxidase (APX) activity in response to exogenous DIM, two fundamental enzymes in the control of reactive oxygen species (ROS) in plants. These results indicate that exogenous DIM treatment enhances seed germination and improves seedling shoot growth through possible activation of a reactive oxygen species signalling pathway involving O2(-) and H2O2 in B. napus.
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Affiliation(s)
- Arun Gokul
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa
| | - Enrico Roode
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa
| | - Ashwil Klein
- Proteomics Research Unit, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa
| | - Marshall Keyster
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa.
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Hong J, Yang L, Zhang D, Shi J. Plant Metabolomics: An Indispensable System Biology Tool for Plant Science. Int J Mol Sci 2016; 17:ijms17060767. [PMID: 27258266 PMCID: PMC4926328 DOI: 10.3390/ijms17060767] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/04/2016] [Accepted: 05/06/2016] [Indexed: 11/16/2022] Open
Abstract
As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plant behavior under both normal and stressed conditions. Hereby, we summarize the current knowledge on the genetic and biochemical mechanisms underlying plant growth, development, and stress responses, focusing further on the contributions of metabolomics to practical applications in crop quality improvement and food safety assessment, as well as plant metabolic engineering. We also highlight the current challenges and future perspectives in this inspiring area, with the aim to stimulate further studies leading to better crop improvement of yield and quality.
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Affiliation(s)
- Jun Hong
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Litao Yang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
- Plant Genomics Center, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia.
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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38
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Fletcher RS, Herrmann D, Mullen JL, Li Q, Schrider DR, Price N, Lin J, Grogan K, Kern A, McKay JK. Identification of Polymorphisms Associated with Drought Adaptation QTL in Brassica napus by Resequencing. G3 (BETHESDA, MD.) 2016; 6:793-803. [PMID: 26801646 PMCID: PMC4825650 DOI: 10.1534/g3.115.021279] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/17/2016] [Indexed: 11/24/2022]
Abstract
Brassica napus is a globally important oilseed for which little is known about the genetics of drought adaptation. We previously mapped twelve quantitative trait loci (QTL) underlying drought-related traits in a biparental mapping population created from a cross between winter and spring B. napus cultivars. Here we resequence the genomes of the mapping population parents to identify genetic diversity across the genome and within QTL regions. We sequenced each parental cultivar on the Illumina HiSeq platform to a minimum depth of 23 × and performed a reference based assembly in order to describe the molecular variation differentiating them at the scale of the genome, QTL and gene. Genome-wide patterns of variation were characterized by an overall higher single nucleotide polymorphism (SNP) density in the A genome and a higher ratio of nonsynonymous to synonymous substitutions in the C genome. Nonsynonymous substitutions were used to categorize gene ontology terms differentiating the parent genomes along with a list of putative functional variants contained within each QTL. Marker assays were developed for several of the discovered polymorphisms within a pleiotropic QTL on chromosome A10. QTL analysis with the new, denser map showed the most associated marker to be that developed from an insertion/deletion polymorphism located in the candidate gene Bna.FLC.A10, and it was the only candidate within the QTL interval with observed polymorphism. Together, these results provide a glimpse of genome-wide variation differentiating annual and biennial B. napus ecotypes as well as a better understanding of the genetic basis of root and drought phenotypes.
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Affiliation(s)
| | - David Herrmann
- Cargill Specialty Seeds & Oils, Fort Collins, Colorado 80525
| | - Jack L Mullen
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523
| | - Qinfei Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
| | - Daniel R Schrider
- Department of Genetics, Rutgers University, Piscataway, New Jersey 08854
| | - Nicholas Price
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523
| | - Junjiang Lin
- Department of Computer Science, University of Toronto, Ontario M5S 2J7, Canada
| | - Kelsi Grogan
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523
| | - Andrew Kern
- Department of Genetics, Rutgers University, Piscataway, New Jersey 08854
| | - John K McKay
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523
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39
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Elahi N, Duncan RW, Stasolla C. Modification of oil and glucosinolate content in canola seeds with altered expression of Brassica napus LEAFY COTYLEDON1. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 100:52-63. [PMID: 26773545 DOI: 10.1016/j.plaphy.2015.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/24/2015] [Accepted: 12/31/2015] [Indexed: 05/08/2023]
Abstract
Over the last few decades, research focusing on canola (Brassica napus L.) seed oil content and composition has expanded. Oil production and accumulation are influenced by genes participating in embryo and seed development. The Arabidopsis LEAFY COTYLEDON1 (LEC1) is a well characterized regulator of embryo development that also enhances the expression of genes involved in fatty acid (FA) synthesis. B. napus lines over-expressing or down-regulating BnLEC1 were successfully generated by Agrobacterium-mediated transformation. The constitutive expression of BnLEC1 in B. napus var. Polo, increased seed oil content by 7-16%, while the down-regulation of BnLEC1 in B. napus var. Topas reduced oil content by 9-12%. Experimental manipulation of BnLEC1 caused transcriptional changes in enzymes participating in sucrose metabolism, glycolysis, and FA biosynthesis, suggesting an enhanced carbon flux towards FA biosynthesis in tissues over-expressing BnLEC1. The increase in oil content induced by BnLEC1 was not accompanied by alterations in FA composition, oil nutritional value or glucosinolate (GLS) levels. Suppression of BnLEC1 reduced seed oil accumulation and elevated the level of GLS possibly through the transcriptional regulation of BnST5a (Sulphotransferase5a), the last GLS biosynthetic enzyme. Collectively, these findings demonstrate that experimental alterations of BnLEC1 expression can be used to influence oil production and quality in B. napus.
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Affiliation(s)
- Nosheen Elahi
- Dept. Plant Science, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Robert W Duncan
- Dept. Plant Science, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Claudio Stasolla
- Dept. Plant Science, University of Manitoba, Winnipeg, R3T 2N2, Canada.
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40
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Cai G, Yang Q, Chen H, Yang Q, Zhang C, Fan C, Zhou Y. Genetic dissection of plant architecture and yield-related traits in Brassica napus. Sci Rep 2016; 6:21625. [PMID: 26880301 PMCID: PMC4754947 DOI: 10.1038/srep21625] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/27/2016] [Indexed: 01/01/2023] Open
Abstract
An optimized plant architecture (PA) is fundamental for high-yield breeding but the genetic control of the important trait is largely unknown in rapeseed. Here plant architecture factors (PAFs) were proposed to consist of main inflorescence length proportion (MILP), branch height proportion (BHP), and branch segment proportion (BSP). Comparison of different genotypes in a DH population grown in diverse environments showed that an optimized PAF performance with MILP and BHP between 0.3–0.4 was important for high yield potential. In total, 163 unique quantitative trait loci (QTLs) for PA- and plant yield (PY)-related traits were mapped onto a high-density genetic map. Furthermore, 190 PA-related candidate genes for 91 unique PA QTLs and 2350 PY epistatic interaction loci-pairs were identified, which explain 2.8–51.8% and 5.2–23.6% of phenotypic variation, respectively. Three gene categories, transcription factor, auxin/IAA, and gibberellin, comprise the largest proportions of candidate genes for PA-related QTLs. The effectiveness of QTL candidate genes prediction was demonstrated by cloning of three candidate genes, Bna.A02.CLV2, Bna.A09.SLY2, and Bna.C07.AHK4. The study thus outlines a gene network for control of PA-related traits and provides novel information for understanding the establishment of ideal PA and for developing effective breeding strategies for yield improvement in rapeseed and other crops.
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Affiliation(s)
- Guangqin Cai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingyong Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qian Yang
- Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunyu Zhang
- Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, Huazhong Agricultural University, Wuhan 430070, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, Huazhong Agricultural University, Wuhan 430070, China
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Comparative transcriptomic analysis uncovers the complex genetic network for resistance to Sclerotinia sclerotiorum in Brassica napus. Sci Rep 2016; 6:19007. [PMID: 26743436 PMCID: PMC4705546 DOI: 10.1038/srep19007] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 12/02/2015] [Indexed: 01/24/2023] Open
Abstract
Sclerotinia stem rot caused by Sclerotinia sclerotiorum is one of the most devastating diseases in many important crops including Brassica napus worldwide. Quantitative resistance is the only source for genetic improvement of Sclerotinia-resistance in B. napus, but the molecular basis for such a resistance is largely unknown. Here, we performed dynamic transcriptomic analyses to understand the differential defense response to S. sclerotiorum in a resistant line (R-line) and a susceptible line (S-line) of B. napus at 24, 48 and 96 h post-inoculation. Both the numbers of and fold changes in differentially expressed genes in the R-line were larger than those in the S-line. We identified 9001 relative differentially expressed genes in the R-line compared with the S-line. The differences between susceptibility and resistance were associated with the magnitude of expression changes in a set of genes involved in pathogen recognition, MAPK signaling cascade, WRKY transcription regulation, jasmonic acid/ethylene signaling pathways, and biosynthesis of defense-related protein and indolic glucosinolate. The results were supported by quantitation of defense-related enzyme activity and glucosinolate contents. Our results provide insights into the complex molecular mechanism of the defense response to S. sclerotiorum in B. napus and for development of effective strategies in Sclerotinia-resistance breeding.
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Körber N, Bus A, Li J, Parkin IAP, Wittkop B, Snowdon RJ, Stich B. Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:386. [PMID: 27066036 PMCID: PMC4814720 DOI: 10.3389/fpls.2016.00386] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/14/2016] [Indexed: 05/18/2023]
Abstract
In Brassica napus breeding, traits related to commercial success are of highest importance for plant breeders. However, such traits can only be assessed in an advanced developmental stage. Molecular markers genetically linked to such traits have the potential to accelerate the breeding process of B. napus by marker-assisted selection. Therefore, the objectives of this study were to identify (i) genome regions associated with the examined agronomic and seed quality traits, (ii) the interrelationship of population structure and the detected associations, and (iii) candidate genes for the revealed associations. The diversity set used in this study consisted of 405 B. napus inbred lines which were genotyped using a 6K single nucleotide polymorphism (SNP) array and phenotyped for agronomic and seed quality traits in field trials. In a genome-wide association study, we detected a total of 112 associations between SNPs and the seed quality traits as well as 46 SNP-trait associations for the agronomic traits with a P < 1.28e-05 (Bonferroni correction of α = 0.05) for the inbreds of the spring and winter trial. For the seed quality traits, a single SNP-sulfur concentration in seeds (SUL) association explained up to 67.3% of the phenotypic variance, whereas for the agronomic traits, a single SNP-blossom color (BLC) association explained up to 30.2% of the phenotypic variance. In a basic local alignment search tool (BLAST) search within a distance of 2.5 Mbp around these SNP-trait associations, 62 hits of potential candidate genes with a BLAST-score of ≥100 and a sequence identity of ≥70% to A. thaliana or B. rapa could be found for the agronomic SNP-trait associations and 187 hits of potential candidate genes for the seed quality SNP-trait associations.
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Affiliation(s)
- Niklas Körber
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- Plant Breeding and Biotechnology, Institute of Crop Science and Resource Conservation, University of BonnBonn, Germany
- *Correspondence: Niklas Körber
| | - Anja Bus
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- Plant Breeding and Biotechnology, Institute of Crop Science and Resource Conservation, University of BonnBonn, Germany
| | - Jinquan Li
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | | | - Benjamin Wittkop
- Department of Plant Breeding, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig UniversityGiessen, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig UniversityGiessen, Germany
| | - Benjamin Stich
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- Benjamin Stich
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Zhang W, Kwon ST, Chen F, Kliebenstein DJ. Isolate Dependency of Brassica rapa Resistance QTLs to Botrytis cinerea. FRONTIERS IN PLANT SCIENCE 2016; 7:161. [PMID: 26925079 PMCID: PMC4756292 DOI: 10.3389/fpls.2016.00161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/30/2016] [Indexed: 05/04/2023]
Abstract
Generalist necrotrophic pathogens including Botrytis cinerea cause significant yield and financial losses on Brassica crops. However, there is little knowledge about the mechanisms underlying the complex interactions encoded by both host and pathogen genomes in this interaction. This potentially includes multiple layers of plant defense and pathogen virulence mechanisms that could complicate in breeding broad spectrum resistance within Brassica species. Glucosinolates (GSLs) are a diverse group of defense metabolites that play a key role in interaction between Brassica and biotic attackers. In this study, we utilized a collection of diverse B. cinerea isolates to investigate resistance within the Brassica rapa R500 × IMB211 recombinant inbred line population. We tested variation on lesion development and glucosinolate accumulation in parental lines and all population lines. We then mapped quantitative trait loci (QTL) for both resistances to B. cinerea and defense metabolites in this population. Phenotypic analysis and QTL mapping demonstrate that the genetic basis of resistance to B. cinerea in B. rapa is isolate specific and polygenic with transgressive segregation that both parents contribute resistance alleles. QTLs controlling defensive GSLs are highly dependent on pathogen infection. An overlap of two QTLs identified between resistance to B. cinerea and defense metabolites also showed isolate specific effects. This work suggests that directly searching for resistance loci may not be the best approach at improving resistance in B. rapa to necrotrophic pathogen.
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Affiliation(s)
- Wei Zhang
- Department of Plant Sciences, University of California, Davis, DavisCA, USA
- National and Local Joint Engineering Laboratory for Energy Plant Bio-oil Production and Application, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan UniversityChengdu, China
| | - Soon-Tae Kwon
- Department of Plant Sciences, University of California, Davis, DavisCA, USA
- Department of Horticulture and Breeding, Andong National UniversityAndong, South Korea
| | - Fang Chen
- National and Local Joint Engineering Laboratory for Energy Plant Bio-oil Production and Application, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan UniversityChengdu, China
| | - Daniel J. Kliebenstein
- Department of Plant Sciences, University of California, Davis, DavisCA, USA
- DynaMo Center of Excellence, University of CopenhagenCopenhagen, Denmark
- *Correspondence: Daniel J. Kliebenstein,
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Overexpression of Three Glucosinolate Biosynthesis Genes in Brassica napus Identifies Enhanced Resistance to Sclerotinia sclerotiorum and Botrytis cinerea. PLoS One 2015; 10:e0140491. [PMID: 26465156 PMCID: PMC4605783 DOI: 10.1371/journal.pone.0140491] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 09/25/2015] [Indexed: 01/27/2023] Open
Abstract
Sclerotinia sclerotiorum and Botrytis cinerea are notorious plant pathogenic fungi with an extensive host range including Brassica crops. Glucosinolates (GSLs) are an important group of secondary metabolites characteristic of the Brassicales order, whose degradation products are proving to be increasingly important in plant protection. Enhancing the defense effect of GSL and their associated degradation products is an attractive strategy to strengthen the resistance of plants by transgenic approaches. We generated the lines of Brassica napus with three biosynthesis genes involved in GSL metabolic pathway (BnMAM1, BnCYP83A1 and BnUGT74B1), respectively. We then measured the foliar GSLs of each transgenic lines and inoculated them with S. sclerotiorum and B. cinerea. Compared with the wild type control, over-expressing BnUGT74B1 in B. napus increased the aliphatic and indolic GSL levels by 1.7 and 1.5 folds in leaves respectively; while over-expressing BnMAM1 or BnCYP83A1 resulted in an approximate 1.5-fold higher only in the aliphatic GSL level in leaves. The results of plant inoculation demonstrated that BnUGT74B1-overexpressing lines showed less severe disease symptoms and tissue damage compared with the wild type control, but BnMAM1 or BnCYP83A1-overexpressing lines showed no significant difference in comparison to the controls. These results suggest that the resistance to S. sclerotiorum and B. cinerea in B. napus could be enhanced through tailoring the GSL profiles by transgenic approaches or molecular breeding, which provides useful information to assist plant breeders to design improved breeding strategies.
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Wang X, Wang H, Long Y, Liu L, Zhao Y, Tian J, Zhao W, Li B, Chen L, Chao H, Li M. Dynamic and comparative QTL analysis for plant height in different developmental stages of Brassica napus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1175-92. [PMID: 25796183 DOI: 10.1007/s00122-015-2498-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 03/10/2015] [Indexed: 05/04/2023]
Abstract
This report describes a dynamic QTL analysis for plant height at various stages using a large doubled haploid population and performs a QTL comparison between different populations in Brassica napus. Plant height (PH) not only plays an important role in determining plant architecture, but is also an important character related to yield. The process of determining PH occurs through a series of steps; however, no studies have focused on developmental behavior factors affecting PH in Brassica napus. In the present study, KN DH, a large doubled haploid population containing 348 lines was used for a dynamic quantitative trait locus (QTL) analysis for PH in six experiments. In all, 20 QTLs were identified at maturity, whereas 50 QTLs were detected by conditional m apping method and the same number was identified by unconditional mapping strategies. Interestingly, five unconditional QTLs ucPH.A2-2, ucPH.A3-2, ucPH.C5-1, ucPH.C6-2 and ucPH.C6-3 were identified that were consistent over the all growth stages of one or two particular experiments, and one conditional QTL cPH.A2-3 was expressed throughout the entire growth process in one experiment. A total of 70 QTLs were obtained after combining QTLs identified at maturity, by conditional and unconditional mapping strategies, in which 25 showed opposite genetic effects in different periods/stages and experiments. A consensus map containing 1357 markers was constructed to compare QTLs identified in the KN population with five previously mapped populations. Alignment of the QTLs detected in different populations onto the consensus map showed that 27 were repeatedly detected in different genetic backgrounds. These findings will enhance our understanding of the genetic control of PH regulation in B. napus, and will be useful for rapeseed genetic manipulation through molecular marker-assisted selection.
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Affiliation(s)
- Xiaodong Wang
- College of Life Science and Technology, Key Laboratory of Molecular Biology, Physics of Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, China
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46
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Cai G, Yang Q, Yi B, Fan C, Zhang C, Edwards D, Batley J, Zhou Y. A bi-filtering method for processing single nucleotide polymorphism array data improves the quality of genetic map and accuracy of quantitative trait locus mapping in doubled haploid populations of polyploid Brassica napus. BMC Genomics 2015; 16:409. [PMID: 26018616 PMCID: PMC4445301 DOI: 10.1186/s12864-015-1559-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 04/20/2015] [Indexed: 01/01/2023] Open
Abstract
Background Single nucleotide polymorphism (SNP) markers have a wide range of applications in crop genetics and genomics. Due to their polyploidy nature, many important crops, such as wheat, cotton and rapeseed contain a large amount of repeat and homoeologous sequences in their genomes, which imposes a huge challenge in high-throughput genotyping with sequencing and/or array technologies. Allotetraploid Brassica napus (AACC, 2n = 4x = 38) comprises of two highly homoeologous sub-genomes derived from its progenitor species B. rapa (AA, 2n = 2x = 20) and B. oleracea (CC, 2n = 2x = 18), and is an ideal species to exploit methods for reducing the interference of extensive inter-homoeologue polymorphisms (mHemi-SNPs and Pseudo-simple SNPs) between closely related sub-genomes. Results Based on a recent B. napus 6K SNP array, we developed a bi-filtering procedure to identify unauthentic lines in a DH population, and mHemi-SNPs and Pseudo-simple SNPs in an array data matrix. The procedure utilized both monomorphic and polymorphic SNPs in the DH population and could effectively distinguish the mHemi-SNPs and Pseudo-simple SNPs that resulted from superposition of the signals from multiple SNPs. Compared with conventional procedure for array data processing, the bi-filtering method could minimize the pseudo linkage relationship caused by the mHemi-SNPs and Pseudo-simple SNPs, thus improving the quality of SNP genetic map. Furthermore, the improved genetic map could increase the accuracies of mapping of QTLs as demonstrated by the ability to eliminate non-real QTLs in the mapping population. Conclusions The bi-filtering analysis of the SNP array data represents a novel approach to effectively assigning the multi-loci SNP genotypes in polyploid B. napus and may find wide applications to SNP analyses in polyploid crops. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1559-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guangqin Cai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. .,Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Qingyong Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. .,Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - David Edwards
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD, Australia.
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD, Australia.
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. .,Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, Huazhong Agricultural University, Wuhan, 430070, China.
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Rout K, Sharma M, Gupta V, Mukhopadhyay A, Sodhi YS, Pental D, Pradhan AK. Deciphering allelic variations for seed glucosinolate traits in oilseed mustard (Brassica juncea) using two bi-parental mapping populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:657-66. [PMID: 25628164 DOI: 10.1007/s00122-015-2461-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 01/10/2015] [Indexed: 05/21/2023]
Abstract
QTL mapping by two DH mapping populations deciphered allelic variations for five different seed glucosinolate traits in B. juncea. Allelic variations for five different seed glucosinolate (GS) traits, namely % propyl, % butyl, % pentyl, aliphatics and total GS content were studied through QTL analysis using two doubled haploid (DH) mapping populations. While the high GS parents in two populations differed in their profiles of seed aliphatic GS, the low GS parents were similar. Phenotypic data of seed GS traits from three environments of the two populations were subjected to QTL analysis. The first population (referred to as DE population) detected a total of 60 QTL from three environments which upon intra-population meta-QTL analysis were merged to 17 S-QTL (Stable QTL) and 15 E-QTL (Environment QTL). The second population (referred to as VH population) detected 58 QTL from the three environments that were merged to 15S-QTL and 16E-QTL. In both the populations, majority of S-QTL were detected as major QTL. Inter-population meta-analysis identified three C-QTL (consensus QTL) formed by merging major QTL from the two populations. Candidate genes of GS pathway were co-localized to the QTL regions either through genetic mapping or through in silico comparative analysis. Parental allelic variants of QTL or of the co-mapped candidate gene(s) were determined on the basis of the significantly different R (2) values of the component QTL from the two populations which were merged to form C-QTL. The results of the study are significant for marker-assisted transfer of the low GS trait and also for developing lines with lower GS than are present in Brassica juncea.
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Affiliation(s)
- Kadambini Rout
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
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48
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Lu G, Harper AL, Trick M, Morgan C, Fraser F, O'Neill C, Bancroft I. Associative transcriptomics study dissects the genetic architecture of seed glucosinolate content in Brassica napus. DNA Res 2014; 21:613-25. [PMID: 25030463 PMCID: PMC4263295 DOI: 10.1093/dnares/dsu024] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/16/2014] [Indexed: 11/12/2022] Open
Abstract
Breeding new varieties with low seed glucosinolate (GS) concentrations has long been a prime target in Brassica napus. In this study, a novel association mapping methodology termed 'associative transcriptomics' (AT) was applied to a panel of 101 B. napus lines to define genetic regions and also candidate genes controlling total seed GS contents. Over 100,000 informative single-nucleotide polymorphisms (SNPs) and gene expression markers (GEMs) were developed for AT analysis, which led to the identification of 10 SNP and 7 GEM association peaks. Within these peaks, 26 genes were inferred to be involved in GS biosynthesis. A weighted gene co-expression network analysis provided additional 40 candidate genes. The transcript abundance in leaves of two candidate genes, BnaA.GTR2a located on chromosome A2 and BnaC.HAG3b on C9, was correlated with seed GS content, explaining 18.8 and 16.8% of phenotypic variation, respectively. Resequencing of genomic regions revealed six new SNPs in BnaA.GTR2a and four insertions or deletions in BnaC.HAG3b. These deletion polymorphisms were then successfully converted into polymerase chain reaction-based diagnostic markers that can, due to high linkage disequilibrium observed in these regions of the genome, be used for marker-assisted breeding for low seed GS lines.
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Affiliation(s)
- Guangyuan Lu
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, UK Oil Crops Research Institute, CAAS, Wuhan 430062, Hubei, China
| | - Andrea L Harper
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Martin Trick
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
| | - Colin Morgan
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
| | - Fiona Fraser
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
| | - Carmel O'Neill
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
| | - Ian Bancroft
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, UK
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Dolferus R. To grow or not to grow: a stressful decision for plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 229:247-261. [PMID: 25443851 DOI: 10.1016/j.plantsci.2014.10.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/06/2014] [Accepted: 10/09/2014] [Indexed: 05/18/2023]
Abstract
Progress in improving abiotic stress tolerance of crop plants using classic breeding and selection approaches has been slow. This has generally been blamed on the lack of reliable traits and phenotyping methods for stress tolerance. In crops, abiotic stress tolerance is most often measured in terms of yield-capacity under adverse weather conditions. "Yield" is a complex trait and is determined by growth and developmental processes which are controlled by environmental signals throughout the life cycle of the plant. The use of model systems has allowed us to gradually unravel how plants grow and develop, but our understanding of the flexibility and opportunistic nature of plant development and its capacity to adapt growth to environmental cues is still evolving. There is genetic variability for the capacity to maintain yield and productivity under abiotic stress conditions in crop plants such as cereals. Technological progress in various domains has made it increasingly possible to mine that genetic variability and develop a better understanding about the basic mechanism of plant growth and abiotic stress tolerance. The aim of this paper is not to give a detailed account of all current research progress, but instead to highlight some of the current research trends that may ultimately lead to strategies for stress-proofing crop species. The focus will be on abiotic stresses that are most often associated with climate change (drought, heat and cold) and those crops that are most important for human nutrition, the cereals.
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Affiliation(s)
- Rudy Dolferus
- CSIRO, Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia.
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50
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Chalhoub B, Denoeud F, Liu S, Parkin IAP, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VHD, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CHD, Wang X, Canaguier A, Chauveau A, Bérard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang X, Meng J, Ma J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 2014; 345:950-3. [PMID: 25146293 DOI: 10.1126/science.1253435] [Citation(s) in RCA: 1408] [Impact Index Per Article: 140.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
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Affiliation(s)
- Boulos Chalhoub
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France.
| | - France Denoeud
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France. Université d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada.
| | - Haibao Tang
- J. Craig Venter Institute, Rockville, MD 20850, USA. Center for Genomics and Biotechnology, Fujian Agriculture and Forestry, University, Fuzhou 350002, Fujian Province, China
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. Center of Genomics and Computational Biology, School of Life Sciences, Hebei United University, Tangshan, Hebei 063000, China
| | - Julien Chiquet
- Laboratoire de Mathématiques et Modélisation d'Evry-UMR 8071 CNRS/Université d'Evry val d'Essonne-USC INRA, Evry, France
| | - Harry Belcram
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Birgit Samans
- Department of Plant Breeding, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Margot Corréa
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Jérémy Just
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Cyril Falentin
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Chu Shin Koh
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Isabelle Le Clainche
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Maria Bernard
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Pascal Bento
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Benjamin Noel
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Adriana Alberti
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Mathieu Charles
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Dominique Arnaud
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Hui Guo
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91000 Evry, France
| | - Salman Alamery
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Kamel Jabbari
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France. Cologne Center for Genomics, University of Cologne, Weyertal 115b, 50931 Köln, Germany
| | - Meixia Zhao
- Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, IN 47907, USA
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Houda Chelaifa
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - David Tack
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Gilles Lassalle
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Imen Mestiri
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Nicolas Schnel
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Marie-Christine Le Paslier
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Guangyi Fan
- Beijing Genome Institute-Shenzhen, Shenzhen 518083, China
| | - Victor Renault
- Fondation Jean Dausset-Centre d'Étude du Polymorphisme Humain, 27 rue Juliette Dodu, 75010 Paris, France
| | - Philippe E Bayer
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Agnieszka A Golicz
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Sahana Manoli
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Tae-Ho Lee
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Vinh Ha Dinh Thi
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Smahane Chalabi
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Qiong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Reece Tollenaere
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Yunhai Lu
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Christophe Battail
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | | | - Xinfa Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Aurélie Canaguier
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Aurélie Chauveau
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Aurélie Bérard
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Gwenaëlle Deniot
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Mei Guan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Zhongsong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Fengming Sun
- Beijing Genome Institute-Shenzhen, Shenzhen 518083, China
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon-305764, South Korea
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, USA
| | | | - Ian Bancroft
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianxin Ma
- Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, IN 47907, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Dominique Brunel
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Régine Delourme
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Michel Renard
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Keith L Adams
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Jacqueline Batley
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia
| | - Rod J Snowdon
- Department of Plant Breeding, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91000 Evry, France
| | - David Edwards
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia.
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wei Hua
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
| | - Chunyun Guan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France. Université d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France.
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