1
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Jacott CN, Schoonbeek HJ, Sidhu GS, Steuernagel B, Kirby R, Zheng X, von Tiedermann A, Macioszek VK, Kononowicz AK, Fell H, Fitt BDL, Mitrousia GK, Stotz HU, Ridout CJ, Wells R. Pathogen lifestyle determines host genetic signature of quantitative disease resistance loci in oilseed rape (Brassica napus). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:65. [PMID: 38430276 PMCID: PMC10908622 DOI: 10.1007/s00122-024-04569-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 01/30/2024] [Indexed: 03/03/2024]
Abstract
KEY MESSAGE Using associative transcriptomics, our study identifies genes conferring resistance to four diverse fungal pathogens in crops, emphasizing key genetic determinants of multi-pathogen resistance. Crops are affected by several pathogens, but these are rarely studied in parallel to identify common and unique genetic factors controlling diseases. Broad-spectrum quantitative disease resistance (QDR) is desirable for crop breeding as it confers resistance to several pathogen species. Here, we use associative transcriptomics (AT) to identify candidate gene loci associated with Brassica napus constitutive QDR to four contrasting fungal pathogens: Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae, and Verticillium longisporum. We did not identify any shared loci associated with broad-spectrum QDR to fungal pathogens with contrasting lifestyles. Instead, we observed QDR dependent on the lifestyle of the pathogen-hemibiotrophic and necrotrophic pathogens had distinct QDR responses and associated loci, including some loci associated with early immunity. Furthermore, we identify a genomic deletion associated with resistance to V. longisporum and potentially broad-spectrum QDR. This is the first time AT has been used for several pathosystems simultaneously to identify host genetic loci involved in broad-spectrum QDR. We highlight constitutive expressed candidate loci for broad-spectrum QDR with no antagonistic effects on susceptibility to the other pathogens studies as candidates for crop breeding. In conclusion, this study represents an advancement in our understanding of broad-spectrum QDR in B. napus and is a significant resource for the scientific community.
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Affiliation(s)
- Catherine N Jacott
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Henk-Jan Schoonbeek
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Gurpinder Singh Sidhu
- Computational and Systems Biology Department, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Burkhard Steuernagel
- Computational and Systems Biology Department, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Rachel Kirby
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Xiaorong Zheng
- Department of Crop Sciences, Georg August University, 37077, Göttingen, Germany
| | | | - Violetta K Macioszek
- Department of Biology and Plant Ecology, Faculty of Biology, University of Bialystok, 15-245, Białystok, Poland
| | - Andrzej K Kononowicz
- Department of Plant Ecophysiology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237, Lodz, Poland
| | - Heather Fell
- Centre for Agriculture, Food and Environmental Management Research, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire, AL10 9AB, UK
| | - Bruce D L Fitt
- Centre for Agriculture, Food and Environmental Management Research, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire, AL10 9AB, UK
| | - Georgia K Mitrousia
- Centre for Agriculture, Food and Environmental Management Research, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire, AL10 9AB, UK
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Henrik U Stotz
- Centre for Agriculture, Food and Environmental Management Research, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire, AL10 9AB, UK
| | - Christopher J Ridout
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Rachel Wells
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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2
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Gritsenko D, Daurova A, Pozharskiy A, Nizamdinova G, Khusnitdinova M, Sapakhova Z, Daurov D, Zhapar K, Shamekova M, Kalendar R, Zhambakin K. Investigation of mutation load and rate in androgenic mutant lines of rapeseed in early generations evaluated by high-density SNP genotyping. Heliyon 2023; 9:e14065. [PMID: 36923873 PMCID: PMC10008989 DOI: 10.1016/j.heliyon.2023.e14065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/06/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Oilseed rape (Brassica napus) is an important oil crop distributed worldwide with a broad adaptation to different climate zones. The cultivation of rapeseed is one of the most commercially viable areas in crop production. Altogether 269,093 ha of rapeseed are cultivated in Kazakhstan. However, all rapeseed cultivars and lines cultivated in Kazakhstan on an industrial scale predominantly belong to the foreign breeding system. Therefore, the formation of a diverse genetic pool for breeding new, highly productive cultivars adopted to the environmental conditions of Kazakhstan is the most important goal in country selection programs. In this work, we have developed ethyl methanesulfonate (EMS) doubled haploid mutant lines from plant material of cultivars 'Galant' and 'Kris' to broad diversity of rapeseed in Kazakhstan. The development of mutant lines was performed via embryo callusogenesis or embryo secondary callusogenesis. Mutants were investigated by Brassica90k SNP array, and we were able to locate 24,657 SNPs from 26,256 SNPs filtered by quality control on the genome assembly (Bra_napus_v2.0). Only 18,831 SNPs were assigned to the available annotated genomic features. The most frequent combination of mutations according to reference controls was adenine with guanine (70%), followed by adenine with cytosine (28.8%), and only minor fractions were cytosine with guanine (0.54%) and adenine with thymine (0.59%). We revealed 5606.27 markers for 'Kris' and 4893.01 markers for 'Galant' by mutation occurrence. Most mutation occurrences were occupied by double mutations where progenitors and offspring were homozygous by different alleles, enabling the selection of appropriate genotypes in a short period of time. Regarding the biological impact of mutations, 861 variants were reported as having a low predicted impact, with 1042 as moderate and 121 as high; all others were reported as belonging to non-coding sequences, intergenic regions, and other features with the effect of modifiers. Protein encoding genes, such as wall-associated receptor kinase-like protein 5, TAO1-like disease resistance protein, receptor-like protein 12, and At5g42460-like F-box protein, contained more than two variable positions, with an impact on their biological activities. Nevertheless, the obtained mutant lines were able to survive and reproduce. Mutant lines, which include moderate and high impact mutations in encoding genes, are a perfect pool not only for MAS but also for the investigation of the fundamental basis of protein functions. For the first time, a collection of mutant lines was developed in our country to improve the selection of local rapeseed cultivars.
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Affiliation(s)
- Dilyara Gritsenko
- Dept. of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty, 050040, Kazakhstan
| | - Ainash Daurova
- Dept. of Breeding and Biotechnology, Institute of Plant Biology and Biotechnology, Almaty, 050040, Kazakhstan
| | - Alexandr Pozharskiy
- Dept. of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty, 050040, Kazakhstan
| | - Gulnaz Nizamdinova
- Dept. of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty, 050040, Kazakhstan
| | - Marina Khusnitdinova
- Dept. of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty, 050040, Kazakhstan
| | - Zagipa Sapakhova
- Dept. of Breeding and Biotechnology, Institute of Plant Biology and Biotechnology, Almaty, 050040, Kazakhstan
| | - Dias Daurov
- Dept. of Breeding and Biotechnology, Institute of Plant Biology and Biotechnology, Almaty, 050040, Kazakhstan
| | - Kuanysh Zhapar
- Dept. of Breeding and Biotechnology, Institute of Plant Biology and Biotechnology, Almaty, 050040, Kazakhstan
| | - Malika Shamekova
- Dept. of Breeding and Biotechnology, Institute of Plant Biology and Biotechnology, Almaty, 050040, Kazakhstan
| | - Ruslan Kalendar
- Dept. of Breeding and Biotechnology, Institute of Plant Biology and Biotechnology, Almaty, 050040, Kazakhstan
| | - Kabyl Zhambakin
- Dept. of Breeding and Biotechnology, Institute of Plant Biology and Biotechnology, Almaty, 050040, Kazakhstan
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3
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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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4
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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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5
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Schilbert HM, Pucker B, Ries D, Viehöver P, Micic Z, Dreyer F, Beckmann K, Wittkop B, Weisshaar B, Holtgräwe D. Mapping‑by‑Sequencing Reveals Genomic Regions Associated with Seed Quality Parameters in Brassica napus. Genes (Basel) 2022; 13:genes13071131. [PMID: 35885914 PMCID: PMC9317104 DOI: 10.3390/genes13071131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 11/21/2022] Open
Abstract
Rapeseed (Brassica napus L.) is an important oil crop and has the potential to serve as a highly productive source of protein. This protein exhibits an excellent amino acid composition and has high nutritional value for humans. Seed protein content (SPC) and seed oil content (SOC) are two complex quantitative and polygenic traits which are negatively correlated and assumed to be controlled by additive and epistatic effects. A reduction in seed glucosinolate (GSL) content is desired as GSLs cause a stringent and bitter taste. The goal here was the identification of genomic intervals relevant for seed GSL content and SPC/SOC. Mapping by sequencing (MBS) revealed 30 and 15 new and known genomic intervals associated with seed GSL content and SPC/SOC, respectively. Within these intervals, we identified known but also so far unknown putatively causal genes and sequence variants. A 4 bp insertion in the MYB28 homolog on C09 shows a significant association with a reduction in seed GSL content. This study provides insights into the genetic architecture and potential mechanisms underlying seed quality traits, which will enhance future breeding approaches in B. napus.
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Affiliation(s)
- Hanna Marie Schilbert
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (H.M.S.); (B.P.); (D.R.); (P.V.); (B.W.)
- Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Faculty of Technology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Boas Pucker
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (H.M.S.); (B.P.); (D.R.); (P.V.); (B.W.)
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Mendelssohnstraße 4, 38106 Braunschweig, Germany
| | - David Ries
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (H.M.S.); (B.P.); (D.R.); (P.V.); (B.W.)
| | - Prisca Viehöver
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (H.M.S.); (B.P.); (D.R.); (P.V.); (B.W.)
| | - Zeljko Micic
- Deutsche Saatveredelung AG, Weissenburger Straße 5, 59557 Lippstadt, Germany;
| | - Felix Dreyer
- NPZ Innovation GmbH, Hohenlieth-Hof 1, 24363 Holtsee, Germany; (F.D.); (K.B.)
| | - Katrin Beckmann
- NPZ Innovation GmbH, Hohenlieth-Hof 1, 24363 Holtsee, Germany; (F.D.); (K.B.)
| | - Benjamin Wittkop
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany;
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (H.M.S.); (B.P.); (D.R.); (P.V.); (B.W.)
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (H.M.S.); (B.P.); (D.R.); (P.V.); (B.W.)
- Correspondence:
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6
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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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7
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Yang J, Wang J, Li Z, Li X, He Z, Zhang L, Sha T, Lyu X, Chen S, Gu Y, Li Z, Hu Z, He H, Bancroft I, Zhang M. Genomic signatures of vegetable and oilseed allopolyploid Brassica juncea and genetic loci controlling the accumulation of glucosinolates. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2619-2628. [PMID: 34448350 PMCID: PMC8633494 DOI: 10.1111/pbi.13687] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/15/2021] [Indexed: 05/05/2023]
Abstract
Allopolyploid Brassica juncea crops in Brassicaceae are becoming increasingly revitalized as vegetables and oilseeds owing to wide adaptability and significant economic values. However, the genomic differentiation of diversified vegetables and oilseed B. juncea and the genetic basis underlying glucosinolates accumulation have yet to be elucidated. To address this knowledge gap, we report the sequencing of pairwise genomes of vegetable and oilseed B. juncea at chromosome scale. Comparative genomics analysis unveils panoramic structural variation footprints, particularly the genetic loci of HSP20 and TGA1 associated with abiotic and biotic stresses responses between oilseed and vegetable subgroups. We anchored two major loci of MYB28 (HAG1) orthologues caused by copy number variations on A02 and A09 chromosomes using scored genomic SNPs-based GWAS that are responsible for seed oil quality-determining glucosinolates biosynthesis. These findings will provide valuable repertories of polyploidy genomic information enabling polyploidy genome evolution studies and precise genomic selections for crucial traits like functional components of glucosinolates in B. juncea crops and beyond.
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Affiliation(s)
- Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
- Yazhou Bay Science and Technology CityHainan Institute of Zhejiang UniversityYazhou District, SanyaChina
- Key Laboratory of Horticultural Plant Growth and DevelopmentMinistry of Agriculture and Rural AffairsHangzhouChina
| | - Jing Wang
- Biomarker Technologies CorporationBeijingChina
| | - Zhangping Li
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
- Yazhou Bay Science and Technology CityHainan Institute of Zhejiang UniversityYazhou District, SanyaChina
| | - Xuming Li
- Biomarker Technologies CorporationBeijingChina
| | - Zhesi He
- Department of BiologyUniversity of YorkYorkUK
| | - Lili Zhang
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Tongyun Sha
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Sheng Chen
- School of Agriculture and Environment and the UWA Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | - Yuanguo Gu
- Xinjiang Academy of Agricultural SciencesUrumqiChina
| | - Zaiyun Li
- College of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
| | - Hongju He
- Beijing Academy of Agricultural and Forestry SciencesBeijingChina
| | | | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular BreedingInstitute of Vegetable ScienceZhejiang UniversityHangzhouChina
- Yazhou Bay Science and Technology CityHainan Institute of Zhejiang UniversityYazhou District, SanyaChina
- Key Laboratory of Horticultural Plant Growth and DevelopmentMinistry of Agriculture and Rural AffairsHangzhouChina
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8
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Woodhouse S, He Z, Woolfenden H, Steuernagel B, Haerty W, Bancroft I, Irwin JA, Morris RJ, Wells R. Validation of a novel associative transcriptomics pipeline in Brassica oleracea: identifying candidates for vernalisation response. BMC Genomics 2021; 22:539. [PMID: 34256693 PMCID: PMC8278714 DOI: 10.1186/s12864-021-07805-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/08/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Associative transcriptomics has been used extensively in Brassica napus to enable the rapid identification of markers correlated with traits of interest. However, within the important vegetable crop species, Brassica oleracea, the use of associative transcriptomics has been limited due to a lack of fixed genetic resources and the difficulties in generating material due to self-incompatibility. Within Brassica vegetables, the harvestable product can be vegetative or floral tissues and therefore synchronisation of the floral transition is an important goal for growers and breeders. Vernalisation is known to be a key determinant of the floral transition, yet how different vernalisation treatments influence flowering in B. oleracea is not well understood. RESULTS Here, we present results from phenotyping a diverse set of 69 B. oleracea accessions for heading and flowering traits under different environmental conditions. We developed a new associative transcriptomics pipeline, and inferred and validated a population structure, for the phenotyped accessions. A genome-wide association study identified miR172D as a candidate for the vernalisation response. Gene expression marker association identified variation in expression of BoFLC.C2 as a further candidate for vernalisation response. CONCLUSIONS This study describes a new pipeline for performing associative transcriptomics studies in B. oleracea. Using flowering time as an example trait, it provides insights into the genetic basis of vernalisation response in B. oleracea through associative transcriptomics and confirms its characterisation as a complex G x E trait. Candidate leads were identified in miR172D and BoFLC.C2. These results could facilitate marker-based breeding efforts to produce B. oleracea lines with more synchronous heading dates, potentially leading to improved yields.
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Affiliation(s)
| | - Zhesi He
- Department of Biology, University of York, YO105DD, Heslington, York, UK
| | - Hugh Woolfenden
- Computational & Systems Biology, John Innes Centre, NR47UH, Norwich, UK
| | | | - Wilfried Haerty
- Earlham Institute, NR47UH, Norwich, UK
- School of Biological Sciences, University of East Anglia, NR47TJ, Norwich, UK
| | - Ian Bancroft
- Department of Biology, University of York, YO105DD, Heslington, York, UK
| | - Judith A Irwin
- Department of Crop Genetics, John Innes Centre, NR47UH, Norwich, UK
| | - Richard J Morris
- Computational & Systems Biology, John Innes Centre, NR47UH, Norwich, UK.
| | - Rachel Wells
- Department of Crop Genetics, John Innes Centre, NR47UH, Norwich, UK.
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9
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Yang X, Su Y, Wu J, Wan W, Chen H, Cao X, Wang J, Zhang Z, Wang Y, Ma D, Loake GJ, Jiang J. Parallel analysis of global garlic gene expression and alliin content following leaf wounding. BMC PLANT BIOLOGY 2021; 21:174. [PMID: 33838642 PMCID: PMC8035738 DOI: 10.1186/s12870-021-02948-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Allium sativum (garlic) is an economically important food source and medicinal plant rich in sulfides and other protective substances such as alliin, the precursor of allicin biosynthesis. Cysteine, serine and sulfur is the precursor of alliin biosynthesis. However, little is known about the alliin content under abiotic stress or the mechanism by which it is synthesized. RESULTS The findings revealed that the content of alliin was lowest in the garlic roots, and highest in the buds. Furthermore, alliin levels decreased in mature leaves following wounding. Transcriptome data generated over time after wounding further revealed significant up-regulation of genes integral to the biosynthetic pathways of cysteine and serine in mature garlic leaves. CONCLUSIONS The findings suggest that differential expression of cysteine, serine and sulfide-related genes underlies the accumulation of alliin and its precursors in garlic, providing a basis for further analyses of alliin biosynthesis.
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Affiliation(s)
- Xuqin Yang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Yiren Su
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Jiaying Wu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Wen Wan
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Huijian Chen
- XuZhou Nuote Chemical co., Ltd., Xuzhou, 221137, Jiangsu, China
| | - Xiaoying Cao
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Junjuan Wang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Zhong Zhang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Youzhi Wang
- XuZhou Nuote Chemical co., Ltd., Xuzhou, 221137, Jiangsu, China
| | - Deliang Ma
- XuZhou Nuote Chemical co., Ltd., Xuzhou, 221137, Jiangsu, China
| | - G J Loake
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK
| | - Jihong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China.
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10
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Mohd Saad NS, Severn-Ellis AA, Pradhan A, Edwards D, Batley J. Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment. Front Genet 2021; 12:600789. [PMID: 33679880 PMCID: PMC7930750 DOI: 10.3389/fgene.2021.600789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.
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Affiliation(s)
| | | | | | | | - Jacqueline Batley
- School of Biological Sciences Western Australia and UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
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11
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Mitreiter S, Gigolashvili T. Regulation of glucosinolate biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:70-91. [PMID: 33313802 DOI: 10.1093/jxb/eraa479] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 05/18/2023]
Abstract
Glucosinolates are secondary defense metabolites produced by plants of the order Brassicales, which includes the model species Arabidopsis and many crop species. In the past 13 years, the regulation of glucosinolate synthesis in plants has been intensively studied, with recent research revealing complex molecular mechanisms that connect glucosinolate production with responses to other central pathways. In this review, we discuss how the regulation of glucosinolate biosynthesis is ecologically relevant for plants, how it is controlled by transcription factors, and how this transcriptional machinery interacts with hormonal, environmental, and epigenetic mechanisms. We present the central players in glucosinolate regulation, MYB and basic helix-loop-helix transcription factors, as well as the plant hormone jasmonate, which together with other hormones and environmental signals allow the coordinated and rapid regulation of glucosinolate genes. Furthermore, we highlight the regulatory connections between glucosinolates, auxin, and sulfur metabolism and discuss emerging insights and open questions on the regulation of glucosinolate biosynthesis.
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Affiliation(s)
- Simon Mitreiter
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Tamara Gigolashvili
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
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12
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Plewiński P, Ćwiek-Kupczyńska H, Rudy E, Bielski W, Rychel-Bielska S, Stawiński S, Barzyk P, Krajewski P, Naganowska B, Wolko B, Książkiewicz M. Innovative transcriptome-based genotyping highlights environmentally responsive genes for phenology, growth and yield in a non-model grain legume. PLANT, CELL & ENVIRONMENT 2020; 43:2680-2698. [PMID: 32885839 DOI: 10.1111/pce.13880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/21/2020] [Accepted: 08/22/2020] [Indexed: 06/11/2023]
Abstract
The narrow-leafed lupin, Lupinus angustifolius L., is a grain legume crop, cultivated both as a green manure and as a source of protein for animal feed and human food production. During its domestication process, numerous agronomic traits were improved, however, only two trait-related genes were identified hitherto, both by linkage mapping. Genome-wide association studies (GWAS), exploiting genomic sequencing, did not select any novel candidate gene. In the present study, an innovative method of 3'-end reduced representation transcriptomic profiling, a massive analysis of cDNA ends, has been used for genotyping of 126 L. angustifolius lines surveyed by field phenotyping. Significant genotype × environment interactions were identified for all phenology and yield traits analysed. Principal component analysis of population structure evidenced European domestication bottlenecks, visualized by clustering of breeding materials and cultivars. GWAS provided contribution towards deciphering vernalization pathway in legumes, and, apart from highlighting known domestication loci (Ku/Julius and mol), designated novel candidate genes for L. angustifolius traits. Early phenology was associated with genes from vernalization, cold-responsiveness and phosphatidylinositol signalling pathways whereas high yield with genes controlling photosynthesis performance and abiotic stress (drought or heat) tolerance. PCR-based toolbox was developed and validated to enable tracking desired alleles in marker-assisted selection. Narrow-leafed lupin was genotyped with an innovative method of transcriptome profiling and phenotyped for phenology, growth and yield traits in field. Early phenology was found associated with genes from cold-response, vernalization and phosphatidylinositol signalling pathways, whereas high yield with genes running photosystem II and drought or heat stress response. Key loci were supplied with PCR-based toolbox for marker-assisted selection.
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Affiliation(s)
- Piotr Plewiński
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Hanna Ćwiek-Kupczyńska
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Elżbieta Rudy
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Wojciech Bielski
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Sandra Rychel-Bielska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Stanisław Stawiński
- Department in Przebędowo, Plant Breeding Smolice Ltd., Murowana Goślina, Poland
| | - Paweł Barzyk
- Department in Wiatrowo, Poznań Plant Breeding Ltd., Wiatrowo, Poland
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Barbara Naganowska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Bogdan Wolko
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Michał Książkiewicz
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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13
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Akhatar J, Singh MP, Sharma A, Kaur H, Kaur N, Sharma S, Bharti B, Sardana VK, Banga SS. Association Mapping of Seed Quality Traits Under Varying Conditions of Nitrogen Application in Brassica juncea L. Czern & Coss. Front Genet 2020; 11:744. [PMID: 33088279 PMCID: PMC7490339 DOI: 10.3389/fgene.2020.00744] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/22/2020] [Indexed: 12/02/2022] Open
Abstract
Indian mustard (Brassica juncea) is a major source of vegetable oil in the Indian subcontinent. The seed cake left after the oil extraction is used as livestock feed. We examined the genetic architecture of oil, protein, and glucosinolates by conducting a genome-wide association study (GWAS), using an association panel comprising 92 diverse genotypes. We conducted trait phenotyping over 2 years at two levels of nitrogen (N) application. Genotyping by sequencing was used to identify 66,835 loci, covering 18 chromosomes. Genetic diversity and phenotypic variations were high for the studied traits. Trait performances were stable when averaged over years and N levels. However, individual performances differed. General and mixed linear models were used to estimate the association between the SNP markers and the seed quality traits. Population structure, principal components (PCs) analysis, and discriminant analysis of principal components (DAPCs) were included as covariates to overcome the bias due to the population stratification. We identified 16, 23, and 27 loci associated with oil, protein, and glucosinolates, respectively. We also established LD patterns and haplotype structures for the candidate genes. The average block sizes were larger on A-genome chromosomes as compared to the B- genome chromosomes. Genetic associations differed over N levels. However, meta-analysis of GWAS datasets not only improved the power to recognize associations but also helped to identify common SNPs for oil and protein contents. Annotation of the genomic region around the identified SNPs led to the prediction of 21 orthologs of the functional candidate genes related to the biosynthesis of oil, protein, and glucosinolates. Notable among these are: LACS5 (A09), FAD6 (B05), ASN1 (A06), GTR2 (A06), CYP81G1 (B06), and MYB44 (B06). The identified loci will be very useful for marker-aided breeding for seed quality modifications in B. juncea.
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Affiliation(s)
- Javed Akhatar
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Mohini Prabha Singh
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Anju Sharma
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Harjeevan Kaur
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navneet Kaur
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Sanjula Sharma
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Baudh Bharti
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - V K Sardana
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Surinder S Banga
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
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14
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Huang Y, Hussain MA, Luo D, Xu H, Zeng C, Havlickova L, Bancroft I, Tian Z, Zhang X, Cheng Y, Zou X, Lu G, Lv Y. A Brassica napus Reductase Gene Dissected by Associative Transcriptomics Enhances Plant Adaption to Freezing Stress. FRONTIERS IN PLANT SCIENCE 2020; 11:971. [PMID: 32676095 PMCID: PMC7333310 DOI: 10.3389/fpls.2020.00971] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Cold treatment (vernalization) is required for winter crops such as rapeseed (Brassica napus L.). However, excessive exposure to low temperature (LT) in winter is also a stress for the semi-winter, early-flowering rapeseed varieties widely cultivated in China. Photosynthetic efficiency is one of the key determinants, and thus a good indicator for LT tolerance in plants. So far, the genetic basis underlying photosynthetic efficiency is poorly understood in rapeseed. Here the current study used Associative Transcriptomics to identify genetic loci controlling photosynthetic gas exchange parameters in a diversity panel comprising 123 accessions. A total of 201 significant Single Nucleotide Polymorphisms (SNPs) and 147 Gene Expression Markers (GEMs) were detected, leading to the identification of 22 candidate genes. Of these, Cab026133.1, an ortholog of the Arabidopsis gene AT2G29300.2 encoding a tropinone reductase (BnTR1), was further confirmed to be closely linked to transpiration rate. Ectopic expressing BnTR1 in Arabidopsis plants significantly increased the transpiration rate and enhanced LT tolerance under freezing conditions. Also, a much higher level of alkaloids content was observed in the transgenic Arabidopsis plants, which could help protect against LT stress. Together, the current study showed that AT is an effective approach for dissecting LT tolerance trait in rapeseed and that BnTR1 is a good target gene for the genetic improvement of LT tolerance in plant.
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Affiliation(s)
- Yong Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Laboratory of Rapeseed, The Chongqing Three Gorges Academy of Agricultural Sciences, Chongqing, China
| | - Muhammad Azhar Hussain
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dan Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hongzhi Xu
- Laboratory of Rapeseed, The Chongqing Three Gorges Academy of Agricultural Sciences, Chongqing, China
| | - Chuan Zeng
- Laboratory of Rapeseed, The Chongqing Three Gorges Academy of Agricultural Sciences, Chongqing, China
| | - Lenka Havlickova
- Centre for Novel Agricultural Products (CNAP) M119, Department of Biology, University of York, York, United Kingdom
| | - Ian Bancroft
- Centre for Novel Agricultural Products (CNAP) M119, Department of Biology, University of York, York, United Kingdom
| | - Zhitao Tian
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xuekun Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yong Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiling Zou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Guangyuan Lu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yan Lv
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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15
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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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16
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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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17
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Kittipol V, He Z, Wang L, Doheny-Adams T, Langer S, Bancroft I. Genetic architecture of glucosinolate variation in Brassica napus. JOURNAL OF PLANT PHYSIOLOGY 2019; 240:152988. [PMID: 31255878 PMCID: PMC6739596 DOI: 10.1016/j.jplph.2019.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/30/2019] [Accepted: 06/03/2019] [Indexed: 05/18/2023]
Abstract
The diverse biological activities of glucosinolate (GSL) hydrolysis products play significant biological and economical roles in the defense system and nutritional qualities of Brassica napus (oilseed rape). Yet, genomic-based study of the B. napus GSL regulatory mechanisms are scarce due to the complexity of working with polyploid species. To address these challenges, we used transcriptome-based GWAS approach, Associative Transcriptomics (AT), across a diversity panel of 288 B. napus genotypes to uncover the underlying genetic basis controlling quantitative variation of GSLs in B. napus vegetative tissues. Single nucleotide polymorphism (SNP) markers and gene expression markers (GEMs) associations identify orthologues of MYB28/HAG1 (AT5G61420), specifically the copies on chromosome A9 and C2, to be the key regulators of aliphatic GSL variation in leaves. We show that the positive correlation observed between aliphatic GSLs in seed and leaf is due to the amount synthesized, as controlled by Bna.HAG1.A9 and Bna.HAG1.C2, rather than by variation in the transport processes. In addition, AT and differential expression analysis in root tissues implicate an orthologue of MYB29/HAG3 (AT5G07690), Bna.HAG3.A3, as controlling root aromatic GSL variation. Based on the root expression data we also propose Bna.MAM3.A3 to have a role in controlling phenylalanine chain elongation for aromatic GSL biosynthesis. This work uncovers a regulator of homophenylalanine-derived aromatic GSLs and implicates the shared biosynthetic pathways between aliphatic and aromatic GSLs.
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Affiliation(s)
- Varanya Kittipol
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Zhesi He
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Lihong Wang
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Tim Doheny-Adams
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Swen Langer
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Ian Bancroft
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
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Zhu S, Chen X, Liu X, Zhao J, Liu T. Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum). BMC Genomics 2019; 20:657. [PMID: 31419936 PMCID: PMC6698038 DOI: 10.1186/s12864-019-6025-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 08/12/2019] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Garlic bulbs are abnormal expanding axillary buds that are rarely found among vascular plants. Bulb-yield is one of the valuable agronomic traits of garlic. However, due to the large genome size and a strictly asexual life cycle in the cultivars, the genetic basis of the yield traits are poorly understood in garlic. RESULTS In the present study, we carried out an association mapping for three yield traits of garlic bulbs: bulb weight (BW), diameter (BD), and the number of garlic cloves (CN), using the recently proposed transcriptome-referenced association study. In total 25, 2, and 30 single nucleotide polymorphisms (SNPs), were identified in the transcripts to be associated with BW, BD, and CN traits, respectively. Of the transcripts with associated SNPs, the expression of 17 of them showed a significant correlation with the corresponding traits in the population, suggesting their relation to bulbs yield traits. Six transcripts were long non-coding RNAs (lncRNAs), and the others encode proteins involved mainly in carbohydrate metabolism, transcription regulation, cytokinin activity, protein degradation, etc. In addition, expression quantitative trait locus (eQTL) and expression correlation analysis have revealed that seven CN-related transcripts displayed interrelation, constituting two potential pathways. CONCLUSION This study provides novel insights into the genetic basis of the yield traits in garlic bulbs, and the identification of trait-associated SNPs/transcripts provides a basis for improving the bulb yield in garlic breeding.
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Affiliation(s)
- Siyuan Zhu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Xiaojun Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Xia Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Jian Zhao
- Novogene Bioinformatics Institute, Beijing, China
| | - Touming Liu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China.
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19
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Kittipol V, He Z, Wang L, Doheny-Adams T, Langer S, Bancroft I. Data in support of genetic architecture of glucosinolate variations in Brassica napus. Data Brief 2019; 25:104402. [PMID: 31497635 PMCID: PMC6722234 DOI: 10.1016/j.dib.2019.104402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 11/25/2022] Open
Abstract
The transcriptome-based GWAS approach, Associative Transcriptomics (AT), which was employed to uncover the genetic basis controlling quantitative variation of glucosinolates in Brassica napus vegetative tissues is described. This article includes the phenotypic data of leaf and root glucosinolate (GSL) profiles across a diversity panel of 288 B. napus genotypes, as well as information on population structure and levels of GSLs grouped by crop types. Moreover, data on genetic associations of single nucleotide polymorphism (SNP) markers and gene expression markers (GEMs) for the major GSL types are presented in detail, while Manhattan plots and QQ plots for the associations of individual GSLs are also included. Root genetic association are supported by differential expression analysis generated from root RNA-seq. For further interpretation and details, please see the related research article entitled 'Genetic architecture of glucosinolate variation in Brassica napus' (Kittipol et al., 2019).
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Affiliation(s)
- Varanya Kittipol
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Zhesi He
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Lihong Wang
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Tim Doheny-Adams
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Swen Langer
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Ian Bancroft
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
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20
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Hejna O, Havlickova L, He Z, Bancroft I, Curn V. Analysing the genetic architecture of clubroot resistance variation in Brassica napus by associative transcriptomics. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2019; 39:112. [PMID: 31396013 PMCID: PMC6647481 DOI: 10.1007/s11032-019-1021-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/08/2019] [Indexed: 06/01/2023]
Abstract
Clubroot is a destructive soil-borne pathogen of Brassicaceae that causes significant recurrent reductions in yield of cruciferous crops. Although there is some resistance in oilseed rape (a crop type of the species Brassica napus), the genetic basis of that resistance is poorly understood. In this study, we used an associative transcriptomics approach to elucidate the genetic basis of resistance to clubroot pathotype ECD 17/31/31 across a genetic diversity panel of 245 accessions of B. napus. A single nucleotide polymorphism (SNP) association analysis was performed with 256,397 SNPs distributed across the genome of B. napus and combined with transcript abundance data of 53,889 coding DNA sequence (CDS) gene models. The SNP association analysis identified two major loci (on chromosomes A2 and A3) controlling resistance and seven minor loci. Within these were a total of 86 SNP markers. Altogether, 392 genes were found in these regions. Another 21 genes were implicated as potentially involved in resistance using gene expression marker (GEM) analysis. After GO enrichment analysis and InterPro functional analysis of the identified genes, 82 candidate genes were identified as having roles in clubroot resistance. These results provide useful information for marker-assisted breeding which could lead to acceleration of pyramiding of multiple clubroot resistance genes in new varieties.
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Affiliation(s)
- Ondrej Hejna
- Biotechnological Centre, Faculty of Agriculture, University of South Bohemia, Studentska, 1668 Ceske Budejovice, Czech Republic
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - Lenka Havlickova
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - Zhesi He
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - Ian Bancroft
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - Vladislav Curn
- Biotechnological Centre, Faculty of Agriculture, University of South Bohemia, Studentska, 1668 Ceske Budejovice, Czech Republic
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Wei D, Cui Y, Mei J, Qian L, Lu K, Wang ZM, Li J, Tang Q, Qian W. Genome-wide identification of loci affecting seed glucosinolate contents in Brassica napus L. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:611-623. [PMID: 30183130 DOI: 10.1111/jipb.12717] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Glucosinolates are amino acid-derived secondary metabolites that act as chemical defense agents against pests. However, the presence of high levels of glucosinolates severely diminishes the nutritional value of seed meals made from rapeseed (Brassica napus L.). To identify the loci affecting seed glucosinolate content (SGC), we conducted genome-wide resequencing in a population of 307 diverse B. napus accessions from the three B. napus ecotype groups, namely, spring, winter, and semi-winter. These resequencing data were used for a genome-wide association study (GWAS) to identify the loci affecting SGC. In the three ecotype groups, four common and four ecotype-specific haplotype blocks (HBs) were significantly associated with SGC. To identify candidate genes controlling SGC, transcriptome analysis was carried out in 36 accessions showing extreme SGC values. Analyses of haplotypes, genomic variation, and candidate gene expression pointed to five and three candidate genes in the common and spring group-specific HBs, respectively. Our expression analyses demonstrated that additive effects of the three candidate genes in the spring group-specific HB play important roles in the SGC of B. napus.
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Affiliation(s)
- Dayong Wei
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing 400715, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jiaqin Mei
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Lunwen Qian
- Collaborative Innovation Center of Grain and Oil Crops in South China, Hunan Agricultural University, Changsha 410128, China
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Zhi-Min Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Qinglin Tang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing 400715, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
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22
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Chen X, Liu X, Zhu S, Tang S, Mei S, Chen J, Li S, Liu M, Gu Y, Dai Q, Liu T. Transcriptome-referenced association study of clove shape traits in garlic. DNA Res 2019; 25:587-596. [PMID: 30084885 PMCID: PMC6289775 DOI: 10.1093/dnares/dsy027] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 07/25/2018] [Indexed: 11/13/2022] Open
Abstract
Genome-wide association studies are a powerful approach for identifying genes related to complex traits in organisms, but are limited by the requirement for a reference genome sequence of the species under study. To circumvent this problem, we propose a transcriptome-referenced association study (TRAS) that utilizes a transcriptome generated by single-molecule long-read sequencing as a reference sequence to score population variation at both transcript sequence and expression levels. Candidate transcripts are identified when both scores are associated with a trait and their potential interactions are ascertained by expression quantitative trait loci analysis. Applying this method to characterize garlic clove shape traits in 102 landraces, we identified 22 candidate transcripts, most of which showed extensive interactions. Eight transcripts were long non-coding RNAs (lncRNAs), and the others were proteins involved mainly in carbohydrate metabolism, protein degradation, etc. TRAS, as an efficient tool for association study independent of a reference genome, extends the applicability of association studies to a broad range of species.
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Affiliation(s)
- Xiaojun Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Xia Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Siyuan Zhu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Shouwei Tang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Shiyong Mei
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jing Chen
- Novogene Bioinformatics Institute, Beijing, China
| | - Shan Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Mengdi Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Yuejiao Gu
- Novogene Bioinformatics Institute, Beijing, China
| | - Qiuzhong Dai
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Touming Liu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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24
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Zhang W, Dai X, Xu S, Zhao PX. 2D association and integrative omics analysis in rice provides systems biology view in trait analysis. Commun Biol 2018; 1:153. [PMID: 30272029 PMCID: PMC6160469 DOI: 10.1038/s42003-018-0159-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/30/2018] [Indexed: 12/28/2022] Open
Abstract
The interactions among genes and between genes and environment contribute significantly to the phenotypic variation of complex traits and may be possible explanations for missing heritability. However, to our knowledge no existing tool can address the two kinds of interactions. Here we propose a novel linear mixed model that considers not only the additive effects of biological markers but also the interaction effects of marker pairs. Interaction effect is demonstrated as a 2D association. Based on this linear mixed model, we developed a pipeline, namely PATOWAS. PATOWAS can be used to study transcriptome-wide and metabolome-wide associations in addition to genome-wide associations. Our case analysis with real rice recombinant inbred lines (RILs) at three omics levels demonstrates that 2D association mapping and integrative omics are able to provide a systems biology view into the analyzed traits, leading toward an answer about how genes, transcripts, proteins, and metabolites work together to produce an observable phenotype. Wenchao Zhang et al. developed a tool for analyzing traits using data generated from genome-wide, transcriptome-wide, and metabolome-wide association studies. They test their approach in rice, providing a systems biology view of identified traits.
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Affiliation(s)
- Wenchao Zhang
- Computational Biology and Bioinformatics Lab, Noble Research Institute, Ardmore, OK, 73401, USA
| | - Xinbin Dai
- Computational Biology and Bioinformatics Lab, Noble Research Institute, Ardmore, OK, 73401, USA
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
| | - Patrick X Zhao
- Computational Biology and Bioinformatics Lab, Noble Research Institute, Ardmore, OK, 73401, USA.
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25
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Werner CR, Voss-Fels KP, Miller CN, Qian W, Hua W, Guan CY, Snowdon RJ, Qian L. Effective Genomic Selection in a Narrow-Genepool Crop with Low-Density Markers: Asian Rapeseed as an Example. THE PLANT GENOME 2018; 11. [PMID: 30025015 DOI: 10.3835/plantgenome2017.09.0084] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Genomic selection (GS) has revolutionized breeding for quantitative traits in plants, offering potential to optimize resource allocation in breeding programs and increase genetic gain per unit of time. Modern high-density single nucleotide polymorphism (SNP) arrays comprising up to several hundred thousand markers provide a user-friendly technology to characterize the genetic constitution of whole populations and for implementing GS in breeding programs. However, GS does not build upon detailed genotype profiling facilitated by maximum marker density. With extensive genome-wide linkage disequilibrium (LD) being a common characteristic of breeding pools, fewer representative markers from available high-density genotyping platforms could be sufficient to capture the association between a genomic region and a phenotypic trait. To examine the effects of reduced marker density on genomic prediction accuracy, we collected data on three traits across 2 yr in a panel of 203 homozygous Chinese semiwinter rapeseed ( L.) inbred lines, broadly encompassing allelic variability in the Asian genepool. We investigated two approaches to selecting subsets of markers: a trait-dependent strategy based on genome-wide association study (GWAS) significance thresholds and a trait-independent method to detect representative tag SNPs. Prediction accuracies were evaluated using cross-validation with ridge-regression best linear unbiased predictions (rrBLUP). With semiwinter rapeseed as a model species, we demonstrate that low-density marker sets comprising a few hundred to a few thousand markers enable high prediction accuracies in breeding populations with strong LD comparable to those achieved with high-density arrays. Our results are valuable for facilitating routine application of cost-efficient GS in breeding programs.
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26
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Wang B, Wu Z, Li Z, Zhang Q, Hu J, Xiao Y, Cai D, Wu J, King GJ, Li H, Liu K. Dissection of the genetic architecture of three seed-quality traits and consequences for breeding in Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1336-1348. [PMID: 29265559 PMCID: PMC5999192 DOI: 10.1111/pbi.12873] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/20/2017] [Accepted: 12/12/2017] [Indexed: 05/08/2023]
Abstract
Genome-wide association studies (GWASs) combining high-throughput genome resequencing and phenotyping can accelerate the dissection of genetic architecture and identification of genes for plant complex traits. In this study, we developed a rapeseed genomic variation map consisting of 4 542 011 SNPs and 628 666 INDELs. GWAS was performed for three seed-quality traits, including erucic acid content (EAC), glucosinolate content (GSC) and seed oil content (SOC) using 3.82 million polymorphisms in an association panel. Six, 49 and 17 loci were detected to be associated with EAC, GSC and SOC in multiple environments, respectively. The mean total contribution of these loci in each environment was 94.1% for EAC and 87.9% for GSC, notably higher than that for SOC (40.1%). A high correlation was observed between phenotypic variance and number of favourable alleles for associated loci, which will contribute to breeding improvement by pyramiding these loci. Furthermore, candidate genes were detected underlying associated loci, based on functional polymorphisms in gene regions where sequence variation was found to correlate with phenotypic variation. Our approach was validated by detection of well-characterized FAE1 genes at each of two major loci for EAC on chromosomes A8 and C3, along with MYB28 genes at each of three major loci for GSC on chromosomes A9, C2 and C9. Four novel candidate genes were detected by correlation between GSC and SOC and observed sequence variation, respectively. This study provides insights into the genetic architecture of three seed-quality traits, which would be useful for genetic improvement of B. napus.
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Affiliation(s)
- Bo Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Zhikun Wu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Zhaohong Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Jianlin Hu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Dongfang Cai
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Jiangsheng Wu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Graham J. King
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreNSWAustralia
| | - Haitao Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Kede Liu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
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Chan HY, Sultana R, Yeo SJ, Chia SL, Pang HN, Lo NN. Comparison of outcome measures from different pathways following total knee arthroplasty. Singapore Med J 2018; 59:476-486. [PMID: 29372260 DOI: 10.11622/smedj.2018011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
INTRODUCTION The benefits of extended inpatient rehabilitation following total knee arthroplasty (TKA) in local community hospitals (CHs) are unproven. Our study compared functional outcomes between patients discharged home and to CHs following TKA. METHODS A case-control study was conducted of patients undergoing primary unilateral TKA. Consecutive patients (n = 1,065) were retrospectively reviewed using the Knee Society Clinical Rating System (KSCRS), 36-item Short Form Health Survey (SF-36) and Oxford Knee Score (OKS) preoperatively, and at the six-month and two-year follow-ups. RESULTS Overall, 967 (90.8%) patients were discharged home and 98 (9.2%) to CHs. CH patients were older (mean age 70.7 vs. 67.2 years; p < 0.0001), female (86.7% vs. 77.5%; p = 0.0388) and less educated (primary education and above: 61.7% vs. 73.8%; p = 0.0081). Median CH length of stay was 23.0 (range 17.0-32.0) days. Significant predictors of discharge destination were older age, female gender, lower education, and poorer ambulatory status and physical health. Preoperatively, CH patients had worse KSCRS Function (49.2 ± 19.5 vs. 54.4 ± 16.8; p = 0.0201), SF-36 Physical Functioning (34.3 ± 22.6 vs. 40.4 ± 22.2; p = 0.0017) and Social Functioning (48.2 ± 35.1 vs. 56.0 ± 35.6; p = 0.0447) scores. CH patients had less improvement for all scores at all follow-ups. Regardless of preoperative confounders, with repeated analysis of variance, discharge destination was significantly associated with KSCRS, SF-36 and OKS scores. CONCLUSION Older, female and less educated patients with poorer preoperative functional scores were more likely to be discharged to CHs after TKA. At the two-year follow-up, patients in CHs had less improvement in functional outcomes than those discharged home.
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Affiliation(s)
- Hiok Yang Chan
- Department of Orthopaedic Surgery, Singapore General Hospital, Singapore
| | - Rehena Sultana
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore
| | - Seng Jin Yeo
- Department of Orthopaedic Surgery, Singapore General Hospital, Singapore
| | - Shi-Lu Chia
- Department of Orthopaedic Surgery, Singapore General Hospital, Singapore
| | - Hee Nee Pang
- Department of Orthopaedic Surgery, Singapore General Hospital, Singapore
| | - Ngai Nung Lo
- Department of Orthopaedic Surgery, Singapore General Hospital, Singapore
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Guan M, Huang X, Xiao Z, Jia L, Wang S, Zhu M, Qiao C, Wei L, Xu X, Liang Y, Wang R, Lu K, Li J, Qu C. Association Mapping Analysis of Fatty Acid Content in Different Ecotypic Rapeseed Using mrMLM. FRONTIERS IN PLANT SCIENCE 2018; 9:1872. [PMID: 30662447 PMCID: PMC6328494 DOI: 10.3389/fpls.2018.01872] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/04/2018] [Indexed: 05/06/2023]
Abstract
Brassica napus L. is a widely cultivated oil crop and provides important resources of edible vegetable oil, and its quality is determined by fatty acid composition and content. To explain the genetic basis and identify more minor loci for fatty acid content, the multi-locus random-SNP-effect mixed linear model (mrMLM) was used to identify genomic regions associated with fatty acid content in a genetically diverse population of 435 rapeseed accessions, including 77 winter-type, 55 spring-type, and 303 semi-winter-type accessions grown in different environments. A total of 149 quantitative trait nucleotides (QTNs) were found to be associated with fatty acid content and composition, including 34 QTNs that overlapped with the previously reported loci, and 115 novel QTNs. Of these, 35 novel QTNs, located on chromosome A01, A02, A03, A05, A06, A09, A10, and C02, respectively, were repeatedly detected across different environments. Subsequently, we annotated 95 putative candidate genes by BlastP analysis using sequences from Arabidopsis thaliana homologs of the identified regions. The candidate genes included 34 environmentally-insensitive genes (e.g., CER4, DGK2, KCS17, KCS18, MYB4, and TT16) and 61 environment-sensitive genes (e.g., FAB1, FAD6, FAD7, KCR1, KCS9, KCS12, and TT1) as well as genes invloved in the fatty acid biosynthesis. Among these, BnaA08g08280D and BnaC03g60080D differed in genomic sequence between the high- and low-oleic acid lines, and might thus be the novel alleles regulating oleic acid content. Furthermore, RT-qPCR analysis of these genes showed differential expression levels during seed development. Our results highlight the practical and scientific value of mrMLM or QTN detection and the accuracy of linking specific QTNs to fatty acid content, and suggest a useful strategy to improve the fatty acid content of B. napus seeds by molecular marker-assisted breeding.
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Affiliation(s)
- Mingwei Guan
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xiaohu Huang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Zhongchun Xiao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Ledong Jia
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Shuxian Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Meichen Zhu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Cailin Qiao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Lijuan Wei
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xinfu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Ying Liang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Rui Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- *Correspondence: Jiana Li
| | - Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Cunmin Qu
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Wang X, Xu P, Yin L, Ren Y, Li S, Shi Y, Alcock TD, Xiong Q, Qian W, Chi X, Pandey MK, Varshney RK, Yuan M. Genomic and Transcriptomic Analysis Identified Gene Clusters and Candidate Genes for Oil Content in Peanut (Arachis hypogaea L.). PLANT MOLECULAR BIOLOGY REPORTER 2018; 36:518-529. [PMID: 30100671 PMCID: PMC6061501 DOI: 10.1007/s11105-018-1088-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Peanut (Arachis hypogaea), a major source of vegetable oil in many Asian countries, has become an integral part of human diet globally due to its high nutritional properties and option to consume in different forms. In order to meet the demand of vegetable oil, many peanut breeding programs of China have intensified their efforts in increasing oil content in newly bred varieties for reducing the import of edible oils in China. In this context, transcriptome sequencing data generated on 49 peanut cultivars were analyzed to identify candidate genes and develop molecular markers for seed oil content across multiple environments. Transcriptome analysis identified 5458 differentially expressed genes (DEGs) including 2243 positive DEGs and 3215 negative DEGs involved in oil synthesis process. Genome-wide association study identified 48 significant insertion/deletion (InDel) markers associated with seed oil content across five environments. A comparative genomics and transcriptomics analysis detected a total of 147 common gene clusters located in 17 chromosomes. Interestingly, an InDel cluster associated with seed oil content on A03 chromosome was detected in three different environments. Candidate genes identified on A03 form a haplotype, in which variable alleles were found to be different in oil content in an independent population. This locus is important for understanding the genetic control of peanut oil content and may be useful for marker-assisted selection in peanut breeding programs.
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Affiliation(s)
- Xiaohua Wang
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Ping Xu
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Liang Yin
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Yan Ren
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Shuangling Li
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Yanmao Shi
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Thomas D. Alcock
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Qing Xiong
- College of Computer and Information Science, Southwest University, Chongqing, 400715 China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Xiaoyuan Chi
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Manish K. Pandey
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
| | - Rajeev K. Varshney
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
| | - Mei Yuan
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
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30
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Alcock TD, Havlickova L, He Z, Wilson L, Bancroft I, White PJ, Broadley MR, Graham NS. Species-Wide Variation in Shoot Nitrate Concentration, and Genetic Loci Controlling Nitrate, Phosphorus and Potassium Accumulation in Brassica napus L. FRONTIERS IN PLANT SCIENCE 2018; 9:1487. [PMID: 30386356 PMCID: PMC6198146 DOI: 10.3389/fpls.2018.01487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/25/2018] [Indexed: 05/06/2023]
Abstract
Large nitrogen, phosphorus and potassium fertilizer inputs are used in many crop systems. Identifying genetic loci controlling nutrient accumulation may be useful in crop breeding strategies to increase fertilizer use efficiency and reduce financial and environmental costs. Here, variation in leaf nitrate concentration across a diversity population of 383 genotypes of Brassica napus was characterized. Genetic loci controlling variation in leaf nitrate, phosphorus and potassium concentration were then identified through Associative Transcriptomics using single nucleotide polymorphism (SNP) markers and gene expression markers (GEMs). Leaf nitrate concentration varied over 8-fold across the diversity population. A total of 455 SNP markers were associated with leaf nitrate concentration after false-discovery-rate (FDR) correction. In linkage disequilibrium of highly associated markers are a number of known nitrate transporters and sensors, including a gene thought to mediate expression of the major nitrate transporter NRT1.1. Several genes influencing root and root-hair development co-localize with chromosomal regions associated with leaf P concentration. Orthologs of three ABC-transporters involved in suberin synthesis in roots also co-localize with association peaks for both leaf nitrate and phosphorus. Allelic variation at nearby, highly associated SNPs confers large variation in leaf nitrate and phosphorus concentration. A total of five GEMs associated with leaf K concentration after FDR correction including a GEM that corresponds to an auxin-response family protein. Candidate loci, genes and favorable alleles identified here may prove useful in marker-assisted selection strategies to improve fertilizer use efficiency in B. napus.
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Affiliation(s)
- Thomas D. Alcock
- Plant and Crop Sciences Division, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | | | - Zhesi He
- Department of Biology, University of York, York, United Kingdom
| | - Lolita Wilson
- Plant and Crop Sciences Division, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Ian Bancroft
- Department of Biology, University of York, York, United Kingdom
| | - Philip J. White
- The James Hutton Institute, Dundee, United Kingdom
- Distinguished Scientist Fellowship Program, King Saud University, Riyadh, Saudi Arabia
| | - Martin R. Broadley
- Plant and Crop Sciences Division, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Neil S. Graham
- Plant and Crop Sciences Division, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
- *Correspondence: Neil S. Graham
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Havlickova L, He Z, Wang L, Langer S, Harper AL, Kaur H, Broadley MR, Gegas V, Bancroft I. Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:181-192. [PMID: 29124814 PMCID: PMC5767744 DOI: 10.1111/tpj.13767] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/06/2017] [Accepted: 10/30/2017] [Indexed: 05/21/2023]
Abstract
An updated platform was developed to underpin association genetics studies in the polyploid crop species Brassica napus (oilseed rape). Based on 1.92 × 1012 bases of leaf mRNAseq data, functional genotypes, comprising 355 536 single-nucleotide polymorphism markers and transcript abundance were scored across a genetic diversity panel of 383 accessions using a transcriptome reference comprising 116 098 ordered coding DNA sequence (CDS) gene models. The use of the platform for Associative Transcriptomics was first tested by analysing the genetic architecture of variation in seed erucic acid content, as high-erucic rapeseed oil is highly valued for a variety of applications in industry. Known loci were identified, along with a previously undetected minor-effect locus. The platform was then used to analyse variation for the relative proportions of tocopherol (vitamin E) forms in seeds, and the validity of the most significant markers was assessed using a take-one-out approach. Furthermore, the analysis implicated expression variation of the gene Bo2g050970.1, an orthologue of VTE4 (which encodes a γ-tocopherol methyl transferase converting γ-tocopherol into α-tocopherol) associated with the observed trait variation. The establishment of the first full-scale Associative Transcriptomics platform for B. napus enables rapid progress to be made towards an understanding of the genetic architecture of trait variation in this important species, and provides an exemplar for other crops.
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Affiliation(s)
| | - Zhesi He
- Department of BiologyUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Lihong Wang
- Department of BiologyUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Swen Langer
- Department of BiologyUniversity of YorkHeslingtonYorkYO10 5DDUK
| | | | - Harjeevan Kaur
- Department of BiologyUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Martin R. Broadley
- Plant and Crop Sciences DivisionSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughboroughLE12 5RDUK
| | - Vasilis Gegas
- Limagrain UK Ltd.Joseph Nickerson Research CentreRothwellLN7 6DTUK
| | - Ian Bancroft
- Department of BiologyUniversity of YorkHeslingtonYorkYO10 5DDUK
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Wei D, Cui Y, He Y, Xiong Q, Qian L, Tong C, Lu G, Ding Y, Li J, Jung C, Qian W. A genome-wide survey with different rapeseed ecotypes uncovers footprints of domestication and breeding. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4791-4801. [PMID: 28992309 PMCID: PMC5853444 DOI: 10.1093/jxb/erx311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Rapeseed (Brassica napus L.) is an important oilseed crop. Despite a short period of domestication and breeding, rapeseed has formed three diverse ecotype groups, namely spring, winter, and semi-winter. However, the genetic changes among the three ecotype groups have remained largely unknown. To detect selective signals, a set of 327 accessions from a worldwide collection were genotyped using a Brassica array, producing 33 186 high-quality single nucleotide polymorphisms (SNPs). Linkage disequilibrium (LD) was unevenly distributed across the genome. A total of 705 (78.2%) weak LD regions were found in the A subgenome, whereas 445 (72.6%) strong LD regions were in the C subgenome. By calculating the nucleotide diversity and population differentiation indices, a total of 198 selective sweeps were identified across ecotype groups, spanning 5.91% (37.9 Mb) of the genome. Within these genome regions, a few known functional genes or loci were found to be in association with environmental adaptability and yield-related traits. In particular, all 12 SNPs detected in significant association with flowering time among accessions were in the selection regions between ecotype groups. These findings provide new insights into the structure of the B. napus genome and uncover the footprints of domestication and breeding.
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Affiliation(s)
- Dayong Wei
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yajun He
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Qing Xiong
- School of Computer and Information Science, Southwest University, Chongqing 400715, China
| | - Lunwen Qian
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Chaobo Tong
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Guangyuan Lu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yijuan Ding
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Christian Jung
- Plant Breeding Institute, Christian Albrechts University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Correspondence:
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Carbohydrate microarrays and their use for the identification of molecular markers for plant cell wall composition. Proc Natl Acad Sci U S A 2017; 114:6860-6865. [PMID: 28607074 DOI: 10.1073/pnas.1619033114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genetic improvement of the plant cell wall has enormous potential to increase the quality of food, fibers, and fuels. However, the identification and characterization of genes involved in plant cell wall synthesis is far from complete. Association mapping is one of the few techniques that can help identify candidate genes without relying on our currently incomplete knowledge of cell wall synthesis. However, few cell wall phenotyping methodologies have proven sufficiently precise, robust, or scalable for association mapping to be conducted for specific cell wall polymers. Here, we created high-density carbohydrate microarrays containing chemically extracted cell wall polysaccharides collected from 331 genetically diverse Brassica napus cultivars and used them to obtain detailed, quantitative information describing the relative abundance of selected noncellulosic polysaccharide linkages and primary structures. We undertook genome-wide association analysis of data collected from 57 carbohydrate microarrays and identified molecular markers reflecting a diversity of specific xylan, xyloglucan, pectin, and arabinogalactan moieties. These datasets provide a detailed insight into the natural variations in cell wall carbohydrate moieties between B. napus genotypes and identify associated markers that could be exploited by marker-assisted breeding. The identified markers also have value beyond B. napus for functional genomics, facilitated by the close genetic relatedness to the model plant Arabidopsis Together, our findings provide a unique dissection of the genetic architecture that underpins plant cell wall biosynthesis and restructuring.
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34
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Qu C, Jia L, Fu F, Zhao H, Lu K, Wei L, Xu X, Liang Y, Li S, Wang R, Li J. Genome-wide association mapping and Identification of candidate genes for fatty acid composition in Brassica napus L. using SNP markers. BMC Genomics 2017; 18:232. [PMID: 28292259 PMCID: PMC5351109 DOI: 10.1186/s12864-017-3607-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 03/03/2017] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND B. napus (oilseed) is an important source of edible vegetable oil, and its nutritional and economic value is determined by its fatty acid composition and content. RESULTS Using the Brassica 60 K SNP array, we performed a genome-wide association study of fatty acid composition in a population of 520 genetically diverse oilseed accessions. Using the PCA + K model in TASSEL 5.2.1, we identified 62 genomic regions that were significantly associated with the composition of seven fatty acids, and five consensus regions that mapped to the A2, A8, A9, C1, and C3 chromosomes, respectively, of the Brassica napus Darmor-bzh genome. We then identified 24 orthologs of the functional candidate genes involved in fatty acid biosynthesis, excluding BnaA.FAE1 and BnaC.FAE1 on the A8 and C3 homologous genome blocks, which are known to have critical roles in the fatty acid biosynthesis pathway, and potential orthologs of these genes (e.g., LACS9, KCR1, FAB1, LPAT4, KCS17, CER4, TT16, and ACBP5). CONCLUSIONS Our results demonstrate the power of association mapping in identifying genes of interest in B. napus and provide insight into the genetic basis of fatty acid biosynthesis in B. napus. Furthermore, our findings may facilitate marker-based breeding efforts aimed at improving fatty acid composition and quality in B. napus.
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Affiliation(s)
- Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing, 400716, China
| | - Ledong Jia
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing, 400716, China
| | - Fuyou Fu
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907-2054, USA
| | - Huiyan Zhao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing, 400716, China
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing, 400716, China
| | - Lijuan Wei
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing, 400716, China
| | - Xinfu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing, 400716, China
| | - Ying Liang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing, 400716, China
| | - Shimeng Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing, 400716, China
| | - Rui Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China. .,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing, 400716, China.
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China. .,Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing, 400716, China.
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35
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Reduction of antinutritional glucosinolates in Brassica oilseeds by mutation of genes encoding transporters. Nat Biotechnol 2017; 35:377-382. [DOI: 10.1038/nbt.3823] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 01/27/2017] [Indexed: 12/31/2022]
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36
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Alcock TD, Havlickova L, He Z, Bancroft I, White PJ, Broadley MR, Graham NS. Identification of Candidate Genes for Calcium and Magnesium Accumulation in Brassica napus L. by Association Genetics. FRONTIERS IN PLANT SCIENCE 2017; 8:1968. [PMID: 29187860 PMCID: PMC5694822 DOI: 10.3389/fpls.2017.01968] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 10/31/2017] [Indexed: 05/07/2023]
Abstract
Calcium (Ca) and magnesium (Mg) are essential plant nutrients and vital for human and animal nutrition. Biofortification of crops has previously been suggested to alleviate widespread human Ca and Mg deficiencies. In this study, new candidate genes influencing the leaf accumulation of Ca and Mg were identified in young Brassica napus plants using associative transcriptomics of ionomics datasets. A total of 247 and 166 SNP markers were associated with leaf Ca and Mg concentration, respectively, after false discovery rate correction and removal of SNPs with low second allele frequency. Gene expression markers at similar positions were also associated with leaf Ca and Mg concentration, including loci on chromosomes A10 and C2, within which lie previously identified transporter genes ACA8 and MGT7. Further candidate genes were selected from seven loci and the mineral composition of whole Arabidopsis thaliana shoots were characterized from lines mutated in orthologous genes. Four and two mutant lines had reduced shoot Ca and Mg concentration, respectively, compared to wild type plants. Three of these mutations were found to have tissue specific effects; notably reduced silique Ca in all three such mutant lines. This knowledge could be applied in targeted breeding, with the possibility of increasing Ca and Mg in plant tissue for improving human and livestock nutrition.
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Affiliation(s)
- Thomas D. Alcock
- Plant and Crop Sciences Division, University of Nottingham, Loughborough, United Kingdom
| | | | - Zhesi He
- Department of Biology, University of York, York, United Kingdom
| | - Ian Bancroft
- Department of Biology, University of York, York, United Kingdom
| | - Philip J. White
- The James Hutton Institute, Dundee, United Kingdom
- Distinguished Scientist Fellowship Program, King Saud University, Riyadh, Saudi Arabia
| | - Martin R. Broadley
- Plant and Crop Sciences Division, University of Nottingham, Loughborough, United Kingdom
| | - Neil S. Graham
- Plant and Crop Sciences Division, University of Nottingham, Loughborough, United Kingdom
- *Correspondence: Neil S. Graham,
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37
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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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38
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Li L, Luo Y, Chen B, Xu K, Zhang F, Li H, Huang Q, Xiao X, Zhang T, Hu J, Li F, Wu X. A Genome-Wide Association Study Reveals New Loci for Resistance to Clubroot Disease in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1483. [PMID: 27746804 PMCID: PMC5044777 DOI: 10.3389/fpls.2016.01483] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 09/20/2016] [Indexed: 05/19/2023]
Abstract
Rapeseed (Brassica napus L.) is one of the most important oil crops in the world. However, the yield and quality of rapeseed were largely decreased by clubroot (Plasmodiophora brassicae Woronin). Therefore, it is of great importance for screening more resistant germplasms or genes and improving the resistance to P. brassicae in rapeseed breeding. In this study, a massive resistant identification for a natural global population was conducted in two environments with race/pathotype 4 of P. brassicae which was the most predominant in China, and a wide range of phenotypic variation was found in the population. In addition, a genome-wide association study of 472 accessions for clubroot resistance (CR) was performed with 60K Brassica Infinium SNP arrays for the first time. In total, nine QTLs were detected, seven of which were novel through integrative analysis. Furthermore, additive effects in genetic control of CR in rapeseed among the above loci were found. By bioinformatic analyses, the candidate genes of these loci were predicted, which indicated that TIR-NBS gene family might play an important role in CR. It is believable that the results presented in our study could provide valuable information for understanding the genetic mechanism and molecular regulation of CR.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute – Chinese Academy of Agricultural SciencesWuhan, China
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Li L, Luo Y, Chen B, Xu K, Zhang F, Li H, Huang Q, Xiao X, Zhang T, Hu J, Li F, Wu X. A Genome-Wide Association Study Reveals New Loci for Resistance to Clubroot Disease in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1483. [PMID: 27746804 DOI: 10.3389/fpls.2015.01483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 09/20/2016] [Indexed: 05/26/2023]
Abstract
Rapeseed (Brassica napus L.) is one of the most important oil crops in the world. However, the yield and quality of rapeseed were largely decreased by clubroot (Plasmodiophora brassicae Woronin). Therefore, it is of great importance for screening more resistant germplasms or genes and improving the resistance to P. brassicae in rapeseed breeding. In this study, a massive resistant identification for a natural global population was conducted in two environments with race/pathotype 4 of P. brassicae which was the most predominant in China, and a wide range of phenotypic variation was found in the population. In addition, a genome-wide association study of 472 accessions for clubroot resistance (CR) was performed with 60K Brassica Infinium SNP arrays for the first time. In total, nine QTLs were detected, seven of which were novel through integrative analysis. Furthermore, additive effects in genetic control of CR in rapeseed among the above loci were found. By bioinformatic analyses, the candidate genes of these loci were predicted, which indicated that TIR-NBS gene family might play an important role in CR. It is believable that the results presented in our study could provide valuable information for understanding the genetic mechanism and molecular regulation of CR.
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Affiliation(s)
- Lixia Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Yujie Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Biyun Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Kun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Fugui Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Hao Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Qian Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Xin Xiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Tianyao Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Jihong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Feng Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
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Genome-Wide Association Study Dissecting the Genetic Architecture Underlying the Branch Angle Trait in Rapeseed (Brassica napus L.). Sci Rep 2016; 6:33673. [PMID: 27646167 PMCID: PMC5028734 DOI: 10.1038/srep33673] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 08/31/2016] [Indexed: 12/04/2022] Open
Abstract
The rapeseed branch angle is an important morphological trait because an adequate branch angle enables more efficient light capture under high planting densities. Here, we report that the average angle of the five top branches provides a reliable representation of the average angle of all branches. Statistical analyses revealed a significantly positive correlation between the branch angle and multiple plant-type and yield-related traits. The 60 K Brassica Infinium® single nucleotide polymorphism (SNP) array was utilized to genotype an association panel with 520 diverse accessions. A genome-wide association study was performed to determine the genetic architecture of branch angle, and 56 loci were identified as being significantly associated with the branch angle trait via three models, including a robust, novel, nonparametric Anderson-Darling (A-D) test. Moreover, these loci explained 51.1% of the phenotypic variation when a simple additive model was applied. Within the linkage disequilibrium (LD) decay ranges of 53 loci, we observed plausible candidates orthologous to documented Arabidopsis genes, such as LAZY1, SGR2, SGR4, SGR8, SGR9, PIN3, PIN7, CRK5, TIR1, and APD7. These results provide insight into the genetic basis of the branch angle trait in rapeseed and might facilitate marker-based breeding for improvements in plant architecture.
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Recent Perspective of Next Generation Sequencing: Applications in Molecular Plant Biology and Crop Improvement. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s40011-016-0770-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Wei L, Jian H, Lu K, Filardo F, Yin N, Liu L, Qu C, Li W, Du H, Li J. Genome-wide association analysis and differential expression analysis of resistance to Sclerotinia stem rot in Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1368-80. [PMID: 26563848 DOI: 10.1111/pbi.12501] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 10/08/2015] [Accepted: 10/13/2015] [Indexed: 05/20/2023]
Abstract
Brassica napus is one of the most important oil crops in the world, and stem rot caused by the fungus Sclerotinia sclerotiorum results in major losses in yield and quality. To elucidate resistance genes and pathogenesis-related genes, genome-wide association analysis of 347 accessions was performed using the Illumina 60K Brassica SNP (single nucleotide polymorphism) array. In addition, the detached stem inoculation assay was used to select five highly resistant (R) and susceptible (S) B. napus lines, 48 h postinoculation with S. sclerotiorum for transcriptome sequencing. We identified 17 significant associations for stem resistance on chromosomes A8 and C6, five of which were on A8 and 12 on C6. The SNPs identified on A8 were located in a 409-kb haplotype block, and those on C6 were consistent with previous QTL mapping efforts. Transcriptome analysis suggested that S. sclerotiorum infection activates the immune system, sulphur metabolism, especially glutathione (GSH) and glucosinolates in both R and S genotypes. Genes found to be specific to the R genotype related to the jasmonic acid pathway, lignin biosynthesis, defence response, signal transduction and encoding transcription factors. Twenty-four genes were identified in both the SNP-trait association and transcriptome sequencing analyses, including a tau class glutathione S-transferase (GSTU) gene cluster. This study provides useful insight into the molecular mechanisms underlying the plant's response to S. sclerotiorum.
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Affiliation(s)
- Lijuan Wei
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Hongju Jian
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Fiona Filardo
- Queensland Department of Agriculture and Fisheries (QDAF), Ecosciences Precinct, Brisbane, Old, Australia
| | - Nengwen Yin
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Liezhao Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Wei Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Hai Du
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
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Liu J, Wang W, Mei D, Wang H, Fu L, Liu D, Li Y, Hu Q. Characterizing Variation of Branch Angle and Genome-Wide Association Mapping in Rapeseed (Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2016; 7:21. [PMID: 26870051 PMCID: PMC4740498 DOI: 10.3389/fpls.2016.00021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/08/2016] [Indexed: 05/20/2023]
Abstract
Changes in the rapeseed branch angle alter plant architecture, allowing more efficient light capture as planting density increases. In this study, a natural population of rapeseed was grown in three environments and evaluated for branch angle trait to characterize their phenotypic patterns and genotype with a 60K Brassica Infinium SNP array. Significant phenotypic variation was observed from 20 to 70°. As a result, 25 significant quantitative trait loci (QTL) associated with branch angle were identified on chromosomes A2, A3, A7, C3, C5, and C7 by the MLM model in TASSEL 4.0. Orthologs of the functional candidate genes involved in branch angle were identified. Among the key QTL, the peak SNPs were close to the key orthologous genes BnaA.Lazy1 and BnaC.Lazy1 on A3 and C3 homologous genome blocks. With the exception of Lazy (LA) orthologous genes, SQUMOSA PROMOTER BINDING PROTEIN LIKE 14 (SPL14) and an auxin-responsive GRETCHEN HAGEN 3 (GH3) genes from Arabidopsis thaliana were identified close to two clusters of SNPs on the A7 and C7 chromosomes. These findings on multiple novel loci and candidate genes of branch angle will be useful for further understanding and genetic improvement of plant architecture in rapeseed.
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Affiliation(s)
- Jia Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Wenxiang Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Desheng Mei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Hui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Li Fu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Daoming Liu
- Agricultural Sciences Institute of Lu'an MunicipalLu'an, China
| | - Yunchang Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Qiong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
- *Correspondence: Qiong Hu
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Li F, Chen B, Xu K, Gao G, Yan G, Qiao J, Li J, Li H, Li L, Xiao X, Zhang T, Nishio T, Wu X. A genome-wide association study of plant height and primary branch number in rapeseed (Brassica napus). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:169-177. [PMID: 26566834 DOI: 10.1016/j.plantsci.2015.05.012] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/14/2015] [Accepted: 05/17/2015] [Indexed: 05/18/2023]
Abstract
Crop plant architecture plays a highly important role in its agronomic performance. Plant height (PH) and primary branch number (PB) are two major factors that affect the plant architecture of rapeseed (Brassica napus). Previous studies have shown that these two traits are controlled by multiple quantitative trait loci (QTL); however, QTLs have not been delimited to regions less than 10cM. Genome-wide association study (GWAS) is a highly efficient approach for identifying genetic loci controlling traits at relatively high resolution. In this study, variations in PH and PB of a panel of 472 rapeseed accessions that had previously been analyzed by a 60k SNP array were investigated for three consecutive years and studied by GWAS. Eight QTLs on chromosome A03, A05, A07 and C07 were identified for PH, and five QTLs on A01, A03, A07 and C07 were identified for PB. Although most QTLs have been detected in previous studies based on linkage analyses, the two QTLs of PH on A05 and the QTL of PB on C07 were novel. In the genomic regions close to the GWAS peaks, orthologs of the genes involved in flower development, phytohormone biosynthesis, metabolism and signaling in Arabidopsis were identified.
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Affiliation(s)
- Feng Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Biyun Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Kun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Guizhen Gao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Guixin Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jiangwei Qiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Hao Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Lixia Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Xin Xiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Tianyao Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
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Kopriva S, Calderwood A, Weckopp SC, Koprivova A. Plant sulfur and Big Data. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 241:1-10. [PMID: 26706053 DOI: 10.1016/j.plantsci.2015.09.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/26/2015] [Accepted: 09/17/2015] [Indexed: 05/20/2023]
Abstract
Sulfur is an essential mineral nutrient for plants, therefore, the pathways of its uptake and assimilation have been extensively studied. Great progress has been made in elucidation of the individual genes and enzymes and their regulation. Sulfur assimilation has been intensively investigated by -omics technologies and has been target of several genome wide genetic approaches. This brought a significant step in our understanding of the regulation of the pathway and its integration in cellular metabolism. However, the large amount of information derived from other experiments not directly targeting sulfur has also brought new and exciting insights into processes affecting sulfur homeostasis. In this review we will integrate the findings of the targeted experiments with those that brought unintentional progress in sulfur research, and will discuss how to synthesize the large amount of information available in various repositories into a meaningful dissection of the regulation of a specific metabolic pathway. We then speculate how this might be used to further advance knowledge on control of sulfur metabolism and what are the main questions to be answered.
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Affiliation(s)
- Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany.
| | | | - Silke C Weckopp
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany
| | - Anna Koprivova
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany
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Qu CM, Li SM, Duan XJ, Fan JH, Jia LD, Zhao HY, Lu K, Li JN, Xu XF, Wang R. Identification of Candidate Genes for Seed Glucosinolate Content Using Association Mapping in Brassica napus L. Genes (Basel) 2015; 6:1215-29. [PMID: 26593950 PMCID: PMC4690036 DOI: 10.3390/genes6041215] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 10/22/2015] [Accepted: 11/06/2015] [Indexed: 12/18/2022] Open
Abstract
Rapeseed contains glucosinolates, a toxic group of sulfur-containing glucosides, which play critical roles in defense against herbivores and microbes. However, the presence of glucosinolates in rapeseed reduces the value of the meal as feed for livestock. We performed association mapping of seed glucosinolate (GS) content using the 60K Brassica Infinium single nucleotide polymorphism (SNP) array in 520 oilseed rape accessions. A total of 11 peak SNPs significantly associated with GS content were detected in growing seasons of 2013 and 2014 and were located on B. napus chromosomes A08, A09, C03, and C09, respectively. Two associated regions of GS content covered by these markers were further verified, and three B. napus homologous genes involved in the biosynthesis and accumulation of GS were identified. These genes were multigene family members and were distributed on different chromosomes. Moreover, two genes (BnGRT2 and BnMYB28) associated with GS content were validated by the qRT-PCR analysis of their expression profiles. The further identification and functionalization of these genes will provide useful insight into the mechanism underlying GS biosynthesis and allocation in B. napus, and the associated SNPs markers could be helpful for molecular maker-assisted breeding for low seed GS in B. napus.
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Affiliation(s)
- Cun-Min Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China.
- Food and Bioproduct Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada.
| | - Shi-Meng Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China.
| | - Xiu-Jian Duan
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China.
| | - Jin-Hua Fan
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China.
| | - Le-Dong Jia
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China.
| | - Hui-Yan Zhao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China.
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China.
| | - Jia-Na Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China.
| | - Xin-Fu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China.
| | - Rui Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400716, China.
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, China.
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Hirschmann F, Papenbrock J. The fusion of genomes leads to more options: A comparative investigation on the desulfo-glucosinolate sulfotransferases of Brassica napus and homologous proteins of Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 91:10-9. [PMID: 25827495 DOI: 10.1016/j.plaphy.2015.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 03/25/2015] [Indexed: 05/11/2023]
Abstract
Sulfotransferases (SOTs) (EC 2.8.2.-) play a crucial role in the glucosinolate (Gl) biosynthesis, by catalyzing the final step of the core glucosinolate formation. In Arabidopsis thaliana the three desulfo (ds)-Gl SOTs AtSOT16, AtSOT17 and AtSOT18 were previously characterized, showing different affinities to ds-Gls. But can the knowledge about these SOTs be generally transferred to other Gl-synthesizing plants? It was investigated how many SOTs are present in the economically relevant crop plant Brassica napus L., and if it is possible to predict their characteristics by sequence analysis. The recently sequenced B. napus is a hybrid of Brassica rapa and Brassica oleracea. By database research, 71 putative functional BnSOT family members were identified and at least eleven of those are putative ds-Gl SOTs. Besides the homologs of AtSOT16 - 18, phylogenetic analyses revealed new subfamilies of ds-Gl SOTs, which are not present in A. thaliana. Three of the B. napus ds-Gl SOT proteins were expressed and purified, and characterized by determining the substrate affinities to different ds-Gls. Two of them, BnSOT16-a and BnSOT16-b, showed a significantly higher affinity to an indolic ds-Gl, similarly to AtSOT16. Additionally, BnSOT17-a was characterized and showed a higher affinity to long chained aliphatic Gls, similarly to AtSOT17. Identification of homologs to AtSOT18 was less reliable, because putative SOT18 sequences are more heterogeneous and confirmation of similar characteristics was not possible.
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Affiliation(s)
- Felix Hirschmann
- Institute of Botany, Leibniz University Hannover, Herrenhäuserstr. 2, D-30419 Hannover, Germany
| | - Jutta Papenbrock
- Institute of Botany, Leibniz University Hannover, Herrenhäuserstr. 2, D-30419 Hannover, Germany.
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