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Chen J, Zhang Y, Wei J, Hu X, Yin H, Liu W, Li D, Tian W, Hao Y, He Z, Fernie AR, Chen W. Beyond pathways: Accelerated flavonoids candidate identification and novel exploration of enzymatic properties using combined mapping populations of wheat. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2033-2050. [PMID: 38408119 PMCID: PMC11182594 DOI: 10.1111/pbi.14323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
Although forward-genetics-metabolomics methods such as mGWAS and mQTL have proven effective in providing myriad loci affecting metabolite contents, they are somehow constrained by their respective constitutional flaws such as the hidden population structure for GWAS and insufficient recombinant rate for QTL. Here, the combination of mGWAS and mQTL was performed, conveying an improved statistical power to investigate the flavonoid pathways in common wheat. A total of 941 and 289 loci were, respectively, generated from mGWAS and mQTL, within which 13 of them were co-mapped using both approaches. Subsequently, the mGWAS or mQTL outputs alone and their combination were, respectively, utilized to delineate the metabolic routes. Using this approach, we identified two MYB transcription factor encoding genes and five structural genes, and the flavonoid pathway in wheat was accordingly updated. Moreover, we have discovered some rare-activity-exhibiting flavonoid glycosyl- and methyl-transferases, which may possess unique biological significance, and harnessing these novel catalytic capabilities provides potentially new breeding directions. Collectively, we propose our survey illustrates that the forward-genetics-metabolomics approaches including multiple populations with high density markers could be more frequently applied for delineating metabolic pathways in common wheat, which will ultimately contribute to metabolomics-assisted wheat crop improvement.
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Affiliation(s)
- Jie Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
- Yazhouwan National LaboratorySanyaChina
| | - Yueqi Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Jiaqi Wei
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
- Wuhan Academy of Agricultural SciencesWuhanChina
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Huanran Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Wei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
| | - Wenfei Tian
- National Wheat Improvement Center, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yuanfeng Hao
- National Wheat Improvement Center, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | | | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
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2
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Kaur N, Lozada DN, Bhatta M, Barchenger DW, Khokhar ES, Nourbakhsh SS, Sanogo S. Insights into the genetic architecture of Phytophthora capsici root rot resistance in chile pepper (Capsicum spp.) from multi-locus genome-wide association study. BMC PLANT BIOLOGY 2024; 24:416. [PMID: 38760676 PMCID: PMC11100198 DOI: 10.1186/s12870-024-05097-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 05/02/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND Phytophthora root rot, a major constraint in chile pepper production worldwide, is caused by the soil-borne oomycete, Phytophthora capsici. This study aimed to detect significant regions in the Capsicum genome linked to Phytophthora root rot resistance using a panel consisting of 157 Capsicum spp. genotypes. Multi-locus genome wide association study (GWAS) was conducted using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS). Individual plants were separately inoculated with P. capsici isolates, 'PWB-185', 'PWB-186', and '6347', at the 4-8 leaf stage and were scored for disease symptoms up to 14-days post-inoculation. Disease scores were used to calculate disease parameters including disease severity index percentage, percent of resistant plants, area under disease progress curve, and estimated marginal means for each genotype. RESULTS Most of the genotypes displayed root rot symptoms, whereas five accessions were completely resistant to all the isolates and displayed no symptoms of infection. A total of 55,117 SNP markers derived from GBS were used to perform multi-locus GWAS which identified 330 significant SNP markers associated with disease resistance. Of these, 56 SNP markers distributed across all the 12 chromosomes were common across the isolates, indicating association with more durable resistance. Candidate genes including nucleotide-binding site leucine-rich repeat (NBS-LRR), systemic acquired resistance (SAR8.2), and receptor-like kinase (RLKs), were identified within 0.5 Mb of the associated markers. CONCLUSIONS Results will be used to improve resistance to Phytophthora root rot in chile pepper by the development of Kompetitive allele-specific markers (KASP®) for marker validation, genomewide selection, and marker-assisted breeding.
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Affiliation(s)
- Navdeep Kaur
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
- Current address: Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Dennis N Lozada
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, 88003, USA.
| | | | | | - Ehtisham S Khokhar
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Seyed Shahabeddin Nourbakhsh
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
- Department of Extension Plant Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Soum Sanogo
- Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, 88003, USA
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3
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Yin B, Jia J, Sun X, Hu X, Ao M, Liu W, Tian Z, Liu H, Li D, Tian W, Hao Y, Xia X, Sade N, Brotman Y, Fernie AR, Chen J, He Z, Chen W. Dynamic metabolite QTL analyses provide novel biochemical insights into kernel development and nutritional quality improvement in common wheat. PLANT COMMUNICATIONS 2024; 5:100792. [PMID: 38173227 PMCID: PMC11121174 DOI: 10.1016/j.xplc.2024.100792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 12/20/2023] [Accepted: 01/01/2024] [Indexed: 01/05/2024]
Abstract
Despite recent advances in crop metabolomics, the genetic control and molecular basis of the wheat kernel metabolome at different developmental stages remain largely unknown. Here, we performed widely targeted metabolite profiling of kernels from three developmental stages (grain-filling kernels [FKs], mature kernels [MKs], and germinating kernels [GKs]) using a population of 159 recombinant inbred lines. We detected 625 annotated metabolites and mapped 3173, 3143, and 2644 metabolite quantitative trait loci (mQTLs) in FKs, MKs, and GKs, respectively. Only 52 mQTLs were mapped at all three stages, indicating the high stage specificity of the wheat kernel metabolome. Four candidate genes were functionally validated by in vitro enzymatic reactions and/or transgenic approaches in wheat, three of which mediated the tricin metabolic pathway. Metabolite flux efficiencies within the tricin pathway were evaluated, and superior candidate haplotypes were identified, comprehensively delineating the tricin metabolism pathway in wheat. Finally, additional wheat metabolic pathways were re-constructed by updating them to incorporate the 177 candidate genes identified in this study. Our work provides new information on variations in the wheat kernel metabolome and important molecular resources for improvement of wheat nutritional quality.
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Affiliation(s)
- Bo Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jingqi Jia
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xu Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Min Ao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhitao Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Wenfei Tian
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanfeng Hao
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nir Sade
- School of Plant Sciences and Food Security, The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yariv Brotman
- School of Plant Sciences and Food Security, The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv 69978, Israel
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Jie Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Yazhouwan National Laboratory, Sanya 572025, China.
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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4
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Lavoignat M, Cassan C, Pétriacq P, Gibon Y, Heumez E, Duque C, Momont P, Rincent R, Blancon J, Ravel C, Le Gouis J. Different wheat loci are associated to heritable free asparagine content in grain grown under different water and nitrogen availability. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:46. [PMID: 38332254 DOI: 10.1007/s00122-024-04551-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/07/2024] [Indexed: 02/10/2024]
Abstract
KEY MESSAGE Different wheat QTLs were associated to the free asparagine content of grain grown in four different conditions. Environmental effects are a key factor when selecting for low acrylamide-forming potential. The amount of free asparagine in grain of a wheat genotype determines its potential to form harmful acrylamide in derivative food products. Here, we explored the variation in the free asparagine, aspartate, glutamine and glutamate contents of 485 accessions reflecting wheat worldwide diversity to define the genetic architecture governing the accumulation of these amino acids in grain. Accessions were grown under high and low nitrogen availability and in water-deficient and well-watered conditions, and plant and grain phenotypes were measured. Free amino acid contents of grain varied from 0.01 to 1.02 mg g-1 among genotypes in a highly heritable way that did not correlate strongly with grain yield, protein content, specific weight, thousand-kernel weight or heading date. Mean free asparagine content was 4% higher under high nitrogen and 3% higher in water-deficient conditions. After genotyping the accessions, single-locus and multi-locus genome-wide association study models were used to identify several QTLs for free asparagine content located on nine chromosomes. Each QTL was associated with a single amino acid and growing environment, and none of the QTLs colocalised with genes known to be involved in the corresponding amino acid metabolism. This suggests that free asparagine content is controlled by several loci with minor effects interacting with the environment. We conclude that breeding for reduced asparagine content is feasible, but should be firmly based on multi-environment field trials. KEY MESSAGE Different wheat QTLs were associated to the free asparagine content of grain grown in four different conditions. Environmental effects are a key factor when selecting for low acrylamide-forming potential.
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Affiliation(s)
- Mélanie Lavoignat
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont-Ferrand, France
- AgroParisTech, 75005, Paris, France
| | - Cédric Cassan
- Université Bordeaux, INRAE, UMR 1332 BFP, 33883, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Pierre Pétriacq
- Université Bordeaux, INRAE, UMR 1332 BFP, 33883, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Yves Gibon
- Université Bordeaux, INRAE, UMR 1332 BFP, 33883, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | | | | | | | - Renaud Rincent
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Justin Blancon
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont-Ferrand, France
| | - Catherine Ravel
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont-Ferrand, France
| | - Jacques Le Gouis
- Université Clermont Auvergne, INRAE, UMR1095 GDEC, 63000, Clermont-Ferrand, France.
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5
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Ding Z, Fu L, Wang B, Ye J, Ou W, Yan Y, Li M, Zeng L, Dong X, Tie W, Ye X, Yang J, Xie Z, Wang Y, Guo J, Chen S, Xiao X, Wan Z, An F, Zhang J, Peng M, Luo J, Li K, Hu W. Metabolic GWAS-based dissection of genetic basis underlying nutrient quality variation and domestication of cassava storage root. Genome Biol 2023; 24:289. [PMID: 38098107 PMCID: PMC10722858 DOI: 10.1186/s13059-023-03137-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 12/04/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Metabolites play critical roles in regulating nutritional qualities of plants, thereby influencing their consumption and human health. However, the genetic basis underlying the metabolite-based nutrient quality and domestication of root and tuber crops remain largely unknown. RESULTS We report a comprehensive study combining metabolic and phenotypic genome-wide association studies to dissect the genetic basis of metabolites in the storage root (SR) of cassava. We quantify 2,980 metabolic features in 299 cultivated cassava accessions. We detect 18,218 significant marker-metabolite associations via metabolic genome-wide association mapping and identify 12 candidate genes responsible for the levels of metabolites that are of potential nutritional importance. Me3GT, MeMYB4, and UGT85K4/UGT85K5, which are involved in flavone, anthocyanin, and cyanogenic glucoside metabolism, respectively, are functionally validated through in vitro enzyme assays and in vivo gene silencing analyses. We identify a cluster of cyanogenic glucoside biosynthesis genes, among which CYP79D1, CYP71E7b, and UGT85K5 are highly co-expressed and their allelic combination contributes to low linamarin content. We find MeMYB4 is responsible for variations in cyanidin 3-O-glucoside and delphinidin 3-O-rutinoside contents, thus controlling SR endothelium color. We find human selection affects quercetin 3-O-glucoside content and SR weight per plant. The candidate gene MeFLS1 is subject to selection during cassava domestication, leading to decreased quercetin 3-O-glucoside content and thus increased SR weight per plant. CONCLUSIONS These findings reveal the genetic basis of cassava SR metabolome variation, establish a linkage between metabolites and agronomic traits, and offer useful resources for genetically improving the nutrition of cassava and other root crops.
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Affiliation(s)
- Zehong Ding
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Lili Fu
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Bin Wang
- Wuhan Metware Biotechnology Co., Ltd, Wuhan, China
| | - Jianqiu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wenjun Ou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yan Yan
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Meiying Li
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Liwang Zeng
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
- Institute of Scientific and Technical Information, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xuekui Dong
- Wuhan Healthcare Metabolic Biotechnology Co., Ltd, Wuhan, China
| | - Weiwei Tie
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Xiaoxue Ye
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Jinghao Yang
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Zhengnan Xie
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yu Wang
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Jianchun Guo
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Songbi Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xinhui Xiao
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Zhongqing Wan
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Feifei An
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jiaming Zhang
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Ming Peng
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Jie Luo
- Hainan Yazhou Bay Seed Laboratory, Sanya, China.
- Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, China.
| | - Kaimian Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
| | - Wei Hu
- National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
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6
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Oddy J, Chhetry M, Awal R, Addy J, Wilkinson M, Smith D, King R, Hall C, Testa R, Murray E, Raffan S, Curtis TY, Wingen L, Griffiths S, Berry S, Elmore JS, Cryer N, Moreira de Almeida I, Halford NG. Genetic control of grain amino acid composition in a UK soft wheat mapping population. THE PLANT GENOME 2023; 16:e20335. [PMID: 37138544 DOI: 10.1002/tpg2.20335] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/23/2022] [Accepted: 03/13/2023] [Indexed: 05/05/2023]
Abstract
Wheat (Triticum aestivum L.) is a major source of nutrients for populations across the globe, but the amino acid composition of wheat grain does not provide optimal nutrition. The nutritional value of wheat grain is limited by low concentrations of lysine (the most limiting essential amino acid) and high concentrations of free asparagine (precursor to the processing contaminant acrylamide). There are currently few available solutions for asparagine reduction and lysine biofortification through breeding. In this study, we investigated the genetic architecture controlling grain free amino acid composition and its relationship to other traits in a Robigus × Claire doubled haploid population. Multivariate analysis of amino acids and other traits showed that the two groups are largely independent of one another, with the largest effect on amino acids being from the environment. Linkage analysis of the population allowed identification of quantitative trait loci (QTL) controlling free amino acids and other traits, and this was compared against genomic prediction methods. Following identification of a QTL controlling free lysine content, wheat pangenome resources facilitated analysis of candidate genes in this region of the genome. These findings can be used to select appropriate strategies for lysine biofortification and free asparagine reduction in wheat breeding programs.
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Affiliation(s)
| | | | - Rajani Awal
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | | | | | | | | | | | | | | | - Luzie Wingen
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - J Stephen Elmore
- Department of Food & Nutritional Sciences, University of Reading, Reading, UK
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7
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Kaur N, Halford NG. Reducing the Risk of Acrylamide and Other Processing Contaminant Formation in Wheat Products. Foods 2023; 12:3264. [PMID: 37685197 PMCID: PMC10486470 DOI: 10.3390/foods12173264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/23/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023] Open
Abstract
Wheat is a staple crop, consumed worldwide as a major source of starch and protein. Global intake of wheat has increased in recent years, and overall, wheat is considered to be a healthy food, particularly when products are made from whole grains. However, wheat is almost invariably processed before it is consumed, usually via baking and/or toasting, and this can lead to the formation of toxic processing contaminants, including acrylamide, 5-hydroxymethylfurfural (HMF) and polycyclic aromatic hydrocarbons (PAHs). Acrylamide is principally formed from free (soluble, non-protein) asparagine and reducing sugars (glucose, fructose and maltose) within the Maillard reaction and is classified as a Group 2A carcinogen (probably carcinogenic to humans). It also has neurotoxic and developmental effects at high doses. HMF is also generated within the Maillard reaction but can also be formed via the dehydration of fructose or caramelisation. It is frequently found in bread, biscuits, cookies, and cakes. Its molecular structure points to genotoxicity and carcinogenic risks. PAHs are a large class of chemical compounds, many of which are genotoxic, mutagenic, teratogenic and carcinogenic. They are mostly formed during frying, baking and grilling due to incomplete combustion of organic matter. Production of these processing contaminants can be reduced with changes in recipe and processing parameters, along with effective quality control measures. However, in the case of acrylamide and HMF, their formation is also highly dependent on the concentrations of precursors in the grain. Here, we review the synthesis of these contaminants, factors impacting their production and the mitigation measures that can be taken to reduce their formation in wheat products, focusing on the role of genetics and agronomy. We also review the risk management measures adopted by food safety authorities around the world.
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8
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Kumari J, Lakhwani D, Jakhar P, Sharma S, Tiwari S, Mittal S, Avashthi H, Shekhawat N, Singh K, Mishra KK, Singh R, Yadav MC, Singh GP, Singh AK. Association mapping reveals novel genes and genomic regions controlling grain size architecture in mini core accessions of Indian National Genebank wheat germplasm collection. FRONTIERS IN PLANT SCIENCE 2023; 14:1148658. [PMID: 37457353 PMCID: PMC10345843 DOI: 10.3389/fpls.2023.1148658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/11/2023] [Indexed: 07/18/2023]
Abstract
Wheat (Triticum aestivum L.) is a staple food crop for the global human population, and thus wheat breeders are consistently working to enhance its yield worldwide. In this study, we utilized a sub-set of Indian wheat mini core germplasm to underpin the genetic architecture for seed shape-associated traits. The wheat mini core subset (125 accessions) was genotyped using 35K SNP array and evaluated for grain shape traits such as grain length (GL), grain width (GW), grain length, width ratio (GLWR), and thousand grain weight (TGW) across the seven different environments (E1, E2, E3, E4, E5, E5, E6, and E7). Marker-trait associations were determined using a multi-locus random-SNP-effect Mixed Linear Model (mrMLM) program. A total of 160 non-redundant quantitative trait nucleotides (QTNs) were identified for four grain shape traits using two or more GWAS models. Among these 160 QTNs, 27, 36, 38, and 35 QTNs were associated for GL, GW, GLWR, and TGW respectively while 24 QTNs were associated with more than one trait. Of these 160 QTNs, 73 were detected in two or more environments and were considered reliable QTLs for the respective traits. A total of 135 associated QTNs were annotated and located within the genes, including ABC transporter, Cytochrome450, Thioredoxin_M-type, and hypothetical proteins. Furthermore, the expression pattern of annotated QTNs demonstrated that only 122 were differentially expressed, suggesting these could potentially be related to seed development. The genomic regions/candidate genes for grain size traits identified in the present study represent valuable genomic resources that can potentially be utilized in the markers-assisted breeding programs to develop high-yielding varieties.
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Affiliation(s)
- Jyoti Kumari
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Deepika Lakhwani
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Preeti Jakhar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Shivani Sharma
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Shailesh Tiwari
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Shikha Mittal
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
- Jaypee University of Information Technology, Solan, India
| | | | - Neelam Shekhawat
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Jodhpur, Jodhpur, India
| | - Kartar Singh
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Jodhpur, Jodhpur, India
| | | | - Rakesh Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Mahesh C. Yadav
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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9
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Zhao C, Tong J, Gao Z, Liu J, Hao Y, Xia X, He Z, Zhang Y, Tian W. Genome-wide association study of alkylresorcinols content in 161 wheat cultivars. J Cereal Sci 2023. [DOI: 10.1016/j.jcs.2023.103679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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10
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Chen J, Zhang Y, Yin H, Liu W, Hu X, Li D, Lan C, Gao L, He Z, Cui F, Fernie AR, Chen W. The pathway of melatonin biosynthesis in common wheat (Triticum aestivum). J Pineal Res 2023; 74:e12841. [PMID: 36396897 PMCID: PMC10078269 DOI: 10.1111/jpi.12841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/25/2022] [Accepted: 11/12/2022] [Indexed: 11/19/2022]
Abstract
Melatonin (Mel) is a multifunctional biomolecule found in both animals and plants. In plants, the biosynthesis of Mel from tryptophan (Trp) has been delineated to comprise of four consecutive reactions. However, while the genes encoding these enzymes in rice are well characterized no systematic evaluation of the overall pathway has, as yet, been published for wheat. In the current study, the relative contents of six Mel-pathway-intermediates including Trp, tryptamine (Trm), serotonin (Ser), 5-methoxy tryptamine (5M-Trm), N-acetyl serotonin (NAS) and Mel, were determined in 24 independent tissues spanning the lifetime of wheat. These studies indicated that Trp was the most abundant among the six metabolites, followed by Trm and Ser. Next, the candidate genes expressing key enzymes involved in the Mel pathway were explored by means of metabolite-based genome-wide association study (mGWAS), wherein two TDC genes, a T5H gene and one SNAT gene were identified as being important for the accumulation of Mel pathway metabolites. Moreover, a 463-bp insertion within the T5H gene was discovered that may be responsible for variation in Ser content. Finally, a ASMT gene was found via sequence alignment against its rice homolog. Validations of these candidate genes were performed by in vitro enzymatic reactions using proteins purified following recombinant expression in Escherichia coli, transient gene expression in tobacco, and transgenic approaches in wheat. Our results thus provide the first comprehensive investigation into the Mel pathway metabolites, and a swift candidate gene identification via forward-genetics strategies, in common wheat.
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Affiliation(s)
- Jie Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yueqi Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Huanran Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Wei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | | | - Lifeng Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fa Cui
- Wheat Molecular Breeding Innovation Research Group, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, School of Agriculture, Ludong University, Yantai, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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11
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Alamin M, Sultana MH, Lou X, Jin W, Xu H. Dissecting Complex Traits Using Omics Data: A Review on the Linear Mixed Models and Their Application in GWAS. PLANTS (BASEL, SWITZERLAND) 2022; 11:3277. [PMID: 36501317 PMCID: PMC9739826 DOI: 10.3390/plants11233277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Genome-wide association study (GWAS) is the most popular approach to dissecting complex traits in plants, humans, and animals. Numerous methods and tools have been proposed to discover the causal variants for GWAS data analysis. Among them, linear mixed models (LMMs) are widely used statistical methods for regulating confounding factors, including population structure, resulting in increased computational proficiency and statistical power in GWAS studies. Recently more attention has been paid to pleiotropy, multi-trait, gene-gene interaction, gene-environment interaction, and multi-locus methods with the growing availability of large-scale GWAS data and relevant phenotype samples. In this review, we have demonstrated all possible LMMs-based methods available in the literature for GWAS. We briefly discuss the different LMM methods, software packages, and available open-source applications in GWAS. Then, we include the advantages and weaknesses of the LMMs in GWAS. Finally, we discuss the future perspective and conclusion. The present review paper would be helpful to the researchers for selecting appropriate LMM models and methods quickly for GWAS data analysis and would benefit the scientific society.
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Affiliation(s)
- Md. Alamin
- Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | | | - Xiangyang Lou
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Wenfei Jin
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Haiming Xu
- Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
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12
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Kumar J, Kumar A, Sen Gupta D, Kumar S, DePauw RM. Reverse genetic approaches for breeding nutrient-rich and climate-resilient cereal and food legume crops. Heredity (Edinb) 2022; 128:473-496. [PMID: 35249099 PMCID: PMC9178024 DOI: 10.1038/s41437-022-00513-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/21/2022] Open
Abstract
In the last decade, advancements in genomics tools and techniques have led to the discovery of many genes. Most of these genes still need to be characterized for their associated function and therefore, such genes remain underutilized for breeding the next generation of improved crop varieties. The recent developments in different reverse genetic approaches have made it possible to identify the function of genes controlling nutritional, biochemical, and metabolic traits imparting drought, heat, cold, salinity tolerance as well as diseases and insect-pests. This article focuses on reviewing the current status and prospects of using reverse genetic approaches to breed nutrient-rich and climate resilient cereal and food legume crops.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sachin Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Ron M DePauw
- Advancing Wheat Technologies, 118 Strathcona Rd SW, Calgary, AB, T3H 1P3, Canada
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13
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Tong J, Zhao C, Sun M, Fu L, Song J, Liu D, Zhang Y, Zheng J, Pu Z, Liu L, Rasheed A, Li M, Xia X, He Z, Hao Y. High Resolution Genome Wide Association Studies Reveal Rich Genetic Architectures of Grain Zinc and Iron in Common Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:840614. [PMID: 35371186 PMCID: PMC8966881 DOI: 10.3389/fpls.2022.840614] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/28/2022] [Indexed: 05/02/2023]
Abstract
Biofortification is a sustainable strategy to alleviate micronutrient deficiency in humans. It is necessary to improve grain zinc (GZnC) and iron concentrations (GFeC) in wheat based on genetic knowledge. However, the precise dissection of the genetic architecture underlying GZnC and GFeC remains challenging. In this study, high-resolution genome-wide association studies were conducted for GZnC and GFeC by three different models using 166 wheat cultivars and 373,106 polymorphic markers from the wheat 660K and 90K single nucleotide polymorphism (SNP) arrays. Totally, 25 and 16 stable loci were detected for GZnC and GFeC, respectively. Among them, 17 loci for GZnC and 8 for GFeC are likely to be new quantitative trait locus/loci (QTL). Based on gene annotations and expression profiles, 28 promising candidate genes were identified for Zn/Fe uptake (8), transport (11), storage (3), and regulations (6). Of them, 11 genes were putative wheat orthologs of known Arabidopsis and rice genes related to Zn/Fe homeostasis. A brief model, such as genes related to Zn/Fe homeostasis from root uptake, xylem transport to the final seed storage was proposed in wheat. Kompetitive allele-specific PCR (KASP) markers were successfully developed for two major QTL of GZnC on chromosome arms 3AL and 7AL, respectively, which were independent of thousand kernel weight and plant height. The 3AL QTL was further validated in a bi-parental population under multi-environments. A wheat multidrug and toxic compound extrusion (MATE) transporter TraesCS3A01G499300, the ortholog of rice gene OsPEZ2, was identified as a potential candidate gene. This study has advanced our knowledge of the genetic basis underlying GZnC and GFeC in wheat and provides valuable markers and candidate genes for wheat biofortification.
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Affiliation(s)
- Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cong Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengjing Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Luping Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yelun Zhang
- The Key Laboratory of Crop Genetics and Breeding of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Jianmin Zheng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Zongjun Pu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Lianzheng Liu
- Research Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Awais Rasheed
- International Maize and Wheat Improvement Center (CIMMYT) China Office, Beijing, China
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ming Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianchun Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, Beijing, China
- *Correspondence: Zhonghu He,
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Yuanfeng Hao,
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14
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Lai R, Ikram M, Li R, Xia Y, Yuan Q, Zhao W, Zhang Z, Siddique KHM, Guo P. Identification of Novel Quantitative Trait Nucleotides and Candidate Genes for Bacterial Wilt Resistance in Tobacco ( Nicotiana tabacum L.) Using Genotyping-by-Sequencing and Multi-Locus Genome-Wide Association Studies. FRONTIERS IN PLANT SCIENCE 2021; 12:744175. [PMID: 34745174 PMCID: PMC8566715 DOI: 10.3389/fpls.2021.744175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/22/2021] [Indexed: 05/17/2023]
Abstract
Tobacco bacterial wilt (TBW) is a devastating soil-borne disease threatening the yield and quality of tobacco. However, its genetic foundations are not fully understood. In this study, we identified 126,602 high-quality single-nucleotide polymorphisms (SNPs) in 94 tobacco accessions using genotyping-by-sequencing (GBS) and a 94.56 KB linkage disequilibrium (LD) decay rate for candidate gene selection. The population structure analysis revealed two subpopulations with 37 and 57 tobacco accessions. Four multi-locus genome-wide association study (ML-GWAS) approaches identified 142 quantitative trait nucleotides (QTNs) in E1-E4 and the best linear unbiased prediction (BLUP), explaining 0.49-22.52% phenotypic variance. Of these, 38 novel stable QTNs were identified across at least two environments/methods, and their alleles showed significant TBW-DI differences. The number of superior alleles associated with TBW resistance for each accession ranged from 4 to 24; eight accessions had more than 18 superior alleles. Based on TBW-resistant alleles, the five best cross combinations were predicted, including MC133 × Ruyuan No. 1 and CO258 × ROX28. We identified 52 candidate genes around 38 QTNs related to TBW resistance based on homologous functional annotation and KEGG enrichment analysis, e.g., CYCD3;2, BSK1, Nitab4.5_0000641g0050, Nitab4.5_0000929g0030. To the best of our knowledge, this is the first comprehensive study to identify QTNs, superior alleles, and their candidate genes for breeding TBW-resistant tobacco varieties. The results provide further insight into the genetic architecture, marker-assisted selection, and functional genomics of TBW resistance, improving future breeding efforts to increase crop productivity.
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Affiliation(s)
- Ruiqiang Lai
- International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Muhammad Ikram
- International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yanshi Xia
- International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Qinghua Yuan
- Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Weicai Zhao
- Nanxiong Research Institute of Guangdong Tobacco Co., Ltd., Nanxiong, China
| | - Zhenchen Zhang
- Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, China
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15
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Breeding Canola ( Brassica napus L.) for Protein in Feed and Food. PLANTS 2021; 10:plants10102220. [PMID: 34686029 PMCID: PMC8539702 DOI: 10.3390/plants10102220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/03/2021] [Accepted: 10/11/2021] [Indexed: 01/12/2023]
Abstract
Interest in canola (Brassica napus L.). In response to this interest, scientists have been tasked with altering and optimizing the protein production chain to ensure canola proteins are safe for consumption and economical to produce. Specifically, the role of plant breeders in developing suitable varieties with the necessary protein profiles is crucial to this interdisciplinary endeavour. In this article, we aim to provide an overarching review of the canola protein chain from the perspective of a plant breeder, spanning from the genetic regulation of seed storage proteins in the crop to advancements of novel breeding technologies and their application in improving protein quality in canola. A review on the current uses of canola meal in animal husbandry is presented to underscore potential limitations for the consumption of canola meal in mammals. General discussions on the allergenic potential of canola proteins and the regulation of novel food products are provided to highlight some of the challenges that will be encountered on the road to commercialization and general acceptance of canola protein as a dietary protein source.
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16
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Khan SU, Saeed S, Khan MHU, Fan C, Ahmar S, Arriagada O, Shahzad R, Branca F, Mora-Poblete F. Advances and Challenges for QTL Analysis and GWAS in the Plant-Breeding of High-Yielding: A Focus on Rapeseed. Biomolecules 2021; 11:1516. [PMID: 34680149 PMCID: PMC8533950 DOI: 10.3390/biom11101516] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Yield is one of the most important agronomic traits for the breeding of rapeseed (Brassica napus L), but its genetic dissection for the formation of high yield remains enigmatic, given the rapid population growth. In the present review, we review the discovery of major loci underlying important agronomic traits and the recent advancement in the selection of complex traits. Further, we discuss the benchmark summary of high-throughput techniques for the high-resolution genetic breeding of rapeseed. Biparental linkage analysis and association mapping have become powerful strategies to comprehend the genetic architecture of complex agronomic traits in crops. The generation of improved crop varieties, especially rapeseed, is greatly urged to enhance yield productivity. In this sense, the whole-genome sequencing of rapeseed has become achievable to clone and identify quantitative trait loci (QTLs). Moreover, the generation of high-throughput sequencing and genotyping techniques has significantly enhanced the precision of QTL mapping and genome-wide association study (GWAS) methodologies. Furthermore, this study demonstrates the first attempt to identify novel QTLs of yield-related traits, specifically focusing on ovule number per pod (ON). We also highlight the recent breakthrough concerning single-locus-GWAS (SL-GWAS) and multi-locus GWAS (ML-GWAS), which aim to enhance the potential and robust control of GWAS for improved complex traits.
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Affiliation(s)
- Shahid Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Sumbul Saeed
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Muhammad Hafeez Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3465548, Chile;
| | - Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile;
| | - Raheel Shahzad
- Department of Biotechnology, Faculty of Science & Technology, Universitas Muhammadiyah Bandung, Bandung 40614, Indonesia;
| | - Ferdinando Branca
- Department of Agriculture, Food and Environment (Di3A), University of Catania, 95123 Catania, Italy;
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3465548, Chile;
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17
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Berhe M, Dossa K, You J, Mboup PA, Diallo IN, Diouf D, Zhang X, Wang L. Genome-wide association study and its applications in the non-model crop Sesamum indicum. BMC PLANT BIOLOGY 2021; 21:283. [PMID: 34157965 PMCID: PMC8218510 DOI: 10.1186/s12870-021-03046-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 05/17/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Sesame is a rare example of non-model and minor crop for which numerous genetic loci and candidate genes underlying features of interest have been disclosed at relatively high resolution. These progresses have been achieved thanks to the applications of the genome-wide association study (GWAS) approach. GWAS has benefited from the availability of high-quality genomes, re-sequencing data from thousands of genotypes, extensive transcriptome sequencing, development of haplotype map and web-based functional databases in sesame. RESULTS In this paper, we reviewed the GWAS methods, the underlying statistical models and the applications for genetic discovery of important traits in sesame. A novel online database SiGeDiD ( http://sigedid.ucad.sn/ ) has been developed to provide access to all genetic and genomic discoveries through GWAS in sesame. We also tested for the first time, applications of various new GWAS multi-locus models in sesame. CONCLUSIONS Collectively, this work portrays steps and provides guidelines for efficient GWAS implementation in sesame, a non-model crop.
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Affiliation(s)
- Muez Berhe
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China
- Humera Agricultural Research Center of Tigray Agricultural Research Institute, Humera, Tigray, Ethiopia
| | - Komivi Dossa
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China.
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal.
- Laboratory of Genetics, Horticulture and Seed Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526, Cotonou, Republic of Benin.
| | - Jun You
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Pape Adama Mboup
- Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal
| | - Idrissa Navel Diallo
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal
- Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Linhai Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China.
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18
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Goto T, Shimamoto S, Takaya M, Sato S, Takahashi K, Nishimura K, Morii Y, Kunishige K, Ohtsuka A, Ijiri D. Impact on genetic differences among various chicken breeds on free amino acid contents of egg yolk and albumen. Sci Rep 2021; 11:2270. [PMID: 33500483 PMCID: PMC7838262 DOI: 10.1038/s41598-021-81660-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
Eggs play important roles as food resources and nutraceuticals, to alleviate malnutrition and to improve health status in the world. Since free amino acids contribute to the nutritional values and food tastes, we investigated a total of 81 eggs from five chicken breeds, which are Australorp, Nagoya (NGY), Rhode Island Red (RIR), Shamo (SHA), Ukokkei, and two F1 hybrids (NGYxRIR and SHAxRIR) to test impact on genetic differences in 10 egg traits, 20 yolk amino acid traits, and 18 albumen amino acid traits. One-way ANOVA revealed significant breed effects on 10 egg traits, 20 yolk amino acid traits, and 15 albumen amino acid traits. Moreover, a significant heterosis effect on yolk aspartic acid was identified. In addition, positive correlations were found broadly among traits within each trait category (egg traits, yolk amino acid traits, and albumen amino acid traits), whereas there were basically no or weak correlations among the trait categories. These results suggest that almost all traits can be dramatically modified by genetic factor, and there will be partially independent production systems of amino acids into yolk and albumen. Since there will be typical quantitative genetic architecture of egg contents, further genetic analyses will be needed.
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Affiliation(s)
- Tatsuhiko Goto
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan. .,Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan.
| | - Saki Shimamoto
- Department of Biochemical Science and Technology, Kagoshima University, Korimoto, Kagoshima, 890-0065, Japan.,Graduate School of Science and Technology, Niigata University, Niigata, 950-2181, Japan
| | - Masahiro Takaya
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan.,Hokkaido Tokachi Area Regional Food Processing Technology Center, Tokachi Foundation, Obihiro, Hokkaido, 080-2462, Japan
| | - Shun Sato
- Agricultural Research Department, Animal Research Center, Hokkaido Research Organization, Shintoku, Hokkaido, 081-0038, Japan
| | - Kanna Takahashi
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan
| | - Kenji Nishimura
- Department of Life and Food Sciences, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan
| | - Yasuko Morii
- Agricultural Research Department, Animal Research Center, Hokkaido Research Organization, Shintoku, Hokkaido, 081-0038, Japan
| | - Kyoko Kunishige
- Agricultural Research Department, Animal Research Center, Hokkaido Research Organization, Shintoku, Hokkaido, 081-0038, Japan
| | - Akira Ohtsuka
- Department of Biochemical Science and Technology, Kagoshima University, Korimoto, Kagoshima, 890-0065, Japan
| | - Daichi Ijiri
- Department of Biochemical Science and Technology, Kagoshima University, Korimoto, Kagoshima, 890-0065, Japan
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19
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Li S, Zhang C, Yang D, Lu M, Qian Y, Jin F, Liu X, Wang Y, Liu W, Li X. Detection of QTNs for kernel moisture concentration and kernel dehydration rate before physiological maturity in maize using multi-locus GWAS. Sci Rep 2021; 11:1764. [PMID: 33469070 PMCID: PMC7815807 DOI: 10.1038/s41598-020-80391-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 12/21/2020] [Indexed: 11/10/2022] Open
Abstract
Maize is China’s largest grain crop. Mechanical grain harvesting is the key technology in maize production, and the kernel moisture concentration (KMC) is the main controlling factor in mechanical maize harvesting in China. The kernel dehydration rate (KDR) is closely related to the KMC. Thus, it is important to conduct genome-wide association studies (GWAS) of the KMC and KDR in maize, detect relevant quantitative trait nucleotides (QTNs), and mine relevant candidate genes. Here, 132 maize inbred lines were used to measure the KMC every 5 days from 10 to 40 days after pollination (DAP) in order to calculate the KDR. These lines were genotyped using a maize 55K single-nucleotide polymorphism array. QTNs for the KMC and KDR were detected based on five methods (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, and ISIS EM-BLASSO) in the package mrMLM. A total of 334 significant QTNs were found for both the KMC and KDR, including 175 QTNs unique to the KMC and 178 QTNs unique to the KDR; 116 and 58 QTNs were detected among the 334 QTNs by two and more than two methods, respectively; and 9 and 5 QTNs among 58 QTNs were detected in 2 and 3 years, respectively. A significant enrichment in cellular component was revealed by Gene Ontology enrichment analysis of candidate genes in the intervals adjacent to the 14 QTNs and this category contained five genes. The information provided in this study may be useful for further mining of genes associated with the KMC and KDR in maize.
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Affiliation(s)
- Shufang Li
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China
| | - Chunxiao Zhang
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China
| | - Deguang Yang
- College of Agronomy, Northeast Agricultural University, Harbin, 150030, China
| | - Ming Lu
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Yiliang Qian
- Maize Research Center, Anhui Academy of Agricultural Science, Hefei, 230001, China
| | - Fengxue Jin
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China
| | - Xueyan Liu
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China
| | - Yu Wang
- Gongzhuling Meteorological Bureau, Gongzhuling, 136100, China
| | - Wenguo Liu
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China.
| | - Xiaohui Li
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Kemaoxi Street 303, Gongzhuling, 136100, Jilin Province, China.
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20
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Lin Y, Zhou K, Hu H, Jiang X, Yu S, Wang Q, Li C, Ma J, Chen G, Yang Z, Liu Y. Multi-Locus Genome-Wide Association Study of Four Yield-Related Traits in Chinese Wheat Landraces. FRONTIERS IN PLANT SCIENCE 2021; 12:665122. [PMID: 34484253 PMCID: PMC8415402 DOI: 10.3389/fpls.2021.665122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 07/20/2021] [Indexed: 05/13/2023]
Abstract
Wheat (Triticum aestivum L.) is one of the most important crops in the world. Here, four yield-related traits, namely, spike length, spikelets number, tillers number, and thousand-kernel weight, were evaluated in 272 Chinese wheat landraces in multiple environments. Five multi-locus genome-wide association studies (FASTmrEMMA, ISIS EN-BLASSO, mrMLM, pKWmEB, and pLARmEB) were performed using 172,711 single-nucleotide polymorphisms (SNPs) to identify yield-related quantitative trait loci (QTL). A total of 27 robust QTL were identified by more than three models. Nine of these QTL were consistent with those in previous studies. The remaining 18 QTL may be novel. We identified a major QTL, QTkw.sicau-4B, with up to 18.78% of phenotypic variation explained. The developed kompetitive allele-specific polymerase chain reaction marker for QTkw.sicau-4B was validated in two recombinant inbred line populations with an average phenotypic difference of 16.07%. After combined homologous function annotation and expression analysis, TraesCS4B01G272300 was the most likely candidate gene for QTkw.sicau-4B. Our findings provide new insights into the genetic basis of yield-related traits and offer valuable QTL to breed wheat cultivars via marker-assisted selection.
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Affiliation(s)
- Yu Lin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Kunyu Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Haiyan Hu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Xiaojun Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shifan Yu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Caixia Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Zisong Yang
- College of Resources and Environment, Aba Teachers University, Wenchuan, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Yaxi Liu, , orcid.org/0000-0001-6814-7218
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21
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An Y, Chen L, Li YX, Li C, Shi Y, Zhang D, Li Y, Wang T. Genome-wide association studies and whole-genome prediction reveal the genetic architecture of KRN in maize. BMC PLANT BIOLOGY 2020; 20:490. [PMID: 33109077 PMCID: PMC7590725 DOI: 10.1186/s12870-020-02676-x] [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: 05/31/2020] [Accepted: 09/24/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Kernel row number (KRN) is an important trait for the domestication and improvement of maize. Exploring the genetic basis of KRN has great research significance and can provide valuable information for molecular assisted selection. RESULTS In this study, one single-locus method (MLM) and six multilocus methods (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB and ISIS EM-BLASSO) of genome-wide association studies (GWASs) were used to identify significant quantitative trait nucleotides (QTNs) for KRN in an association panel including 639 maize inbred lines that were genotyped by the MaizeSNP50 BeadChip. In three phenotyping environments and with best linear unbiased prediction (BLUP) values, the seven GWAS methods revealed different numbers of KRN-associated QTNs, ranging from 11 to 177. Based on these results, seven important regions for KRN located on chromosomes 1, 2, 3, 5, 9, and 10 were identified by at least three methods and in at least two environments. Moreover, 49 genes from the seven regions were expressed in different maize tissues. Among the 49 genes, ARF29 (Zm00001d026540, encoding auxin response factor 29) and CKO4 (Zm00001d043293, encoding cytokinin oxidase protein) were significantly related to KRN, based on expression analysis and candidate gene association mapping. Whole-genome prediction (WGP) of KRN was also performed, and we found that the KRN-associated tagSNPs achieved a high prediction accuracy. The best strategy was to integrate all of the KRN-associated tagSNPs identified by all GWAS models. CONCLUSIONS These results aid in our understanding of the genetic architecture of KRN and provide useful information for genomic selection for KRN in maize breeding.
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Affiliation(s)
- Yixin An
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lin Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yong-Xiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yunsu Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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22
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Chen J, Hu X, Shi T, Yin H, Sun D, Hao Y, Xia X, Luo J, Fernie AR, He Z, Chen W. Metabolite-based genome-wide association study enables dissection of the flavonoid decoration pathway of wheat kernels. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1722-1735. [PMID: 31930656 PMCID: PMC7336285 DOI: 10.1111/pbi.13335] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/29/2019] [Indexed: 05/02/2023]
Abstract
The marriage of metabolomic approaches with genetic design has proven a powerful tool in dissecting diversity in the metabolome and has additionally enhanced our understanding of complex traits. That said, such studies have rarely been carried out in wheat. In this study, we detected 805 metabolites from wheat kernels and profiled their relative contents among 182 wheat accessions, conducting a metabolite-based genome-wide association study (mGWAS) utilizing 14 646 previously described polymorphic SNP markers. A total of 1098 mGWAS associations were detected with large effects, within which 26 candidate genes were tentatively designated for 42 loci. Enzymatic assay of two candidates indicated they could catalyse glucosylation and subsequent malonylation of various flavonoids and thereby the major flavonoid decoration pathway of wheat kernel was dissected. Moreover, numerous high-confidence genes associated with metabolite contents have been provided, as well as more subdivided metabolite networks which are yet to be explored within our data. These combined efforts presented the first step towards realizing metabolomics-associated breeding of wheat.
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Affiliation(s)
- Jie Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Taotao Shi
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Huanran Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Dongfa Sun
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yuanfeng Hao
- National Wheat Improvement CenterInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xianchun Xia
- National Wheat Improvement CenterInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
| | | | - Zhonghu He
- National Wheat Improvement CenterInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
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23
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Yang Y, Chai Y, Zhang X, Lu S, Zhao Z, Wei D, Chen L, Hu YG. Multi-Locus GWAS of Quality Traits in Bread Wheat: Mining More Candidate Genes and Possible Regulatory Network. FRONTIERS IN PLANT SCIENCE 2020; 11:1091. [PMID: 32849679 PMCID: PMC7411135 DOI: 10.3389/fpls.2020.01091] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/02/2020] [Indexed: 05/20/2023]
Abstract
In wheat breeding, improved quality traits, including grain quality and dough rheological properties, have long been a critical goal. To understand the genetic basis of key quality traits of wheat, two single-locus and five multi-locus GWAS models were performed for six grain quality traits and three dough rheological properties based on 19, 254 SNPs in 267 bread wheat accessions. As a result, 299 quantitative trait nucleotides (QTNs) within 105 regions were identified to be associated with these quality traits in four environments. Of which, 40 core QTN regions were stably detected in at least three environments, 19 of which were novel. Compared with the previous studies, these novel QTN regions explained smaller phenotypic variation, which verified the advantages of the multi-locus GWAS models in detecting important small effect QTNs associated with complex traits. After characterization of the function and expression in-depth, 67 core candidate genes involved in protein/sugar synthesis, histone modification and the regulation of transcription factor were observed to be associated with the formation of grain quality, which showed that multi-level regulations influenced wheat grain quality. Finally, a preliminary network of gene regulation that may affect wheat quality formation was inferred. This study verified the power and reliability of multi-locus GWAS methods in wheat quality trait research, and increased the understanding of wheat quality formation mechanisms. The detected QTN regions and candidate genes in this study could be further used for gene cloning and marker-assisted selection in high-quality breeding of bread wheat.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Yongmao Chai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Xuan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Shan Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Zhangchen Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Di Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Liang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Yin-Gang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- Institute of Water Saving Agriculture in Arid Regions of China, Northwest A&F University, Yangling, China
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24
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Navrotskyi S, Belamkar V, Baenziger PS, Rose DJ. Insights into the Genetic Architecture of Bran Friability and Water Retention Capacity, Two Important Traits for Whole Grain End-Use Quality in Winter Wheat. Genes (Basel) 2020; 11:E838. [PMID: 32717821 PMCID: PMC7466047 DOI: 10.3390/genes11080838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 11/16/2022] Open
Abstract
Bran friability (particle size distribution after milling) and water retention capacity (WRC) impact wheat bran functionality in whole grain milling and baking applications. The goal of this study was to identify genomic regions and underlying genes that may be responsible for these traits. The Hard Winter Wheat Association Mapping Panel, which comprised 299 lines from breeding programs in the Great Plains region of the US, was used in a genome-wide association study. Bran friability ranged from 34.5% to 65.9% (median, 51.1%) and WRC ranged from 159% to 458% (median, 331%). Two single-nucleotide polymorphisms (SNPs) on chromosome 5D were significantly associated with bran friability, accounting for 11-12% of the phenotypic variation. One of these SNPs was located within the Puroindoline-b gene, which is known for influencing endosperm texture. Two SNPs on chromosome 4A were tentatively associated with WRC, accounting for 4.6% and 4.4% of phenotypic variation. The favorable alleles at the SNP sites were present in only 15% (friability) and 34% (WRC) of lines, indicating a need to develop new germplasm for these whole-grain end-use quality traits. Validation of these findings in independent populations will be useful for breeding winter wheat cultivars with improved functionality for whole grain food applications.
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Affiliation(s)
- Sviatoslav Navrotskyi
- Department of Food Science & Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Vikas Belamkar
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA;
| | - P. Stephen Baenziger
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA;
| | - Devin J. Rose
- Department of Food Science & Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA;
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25
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Safdar LB, Andleeb T, Latif S, Umer MJ, Tang M, Li X, Liu S, Quraishi UM. Genome-Wide Association Study and QTL Meta-Analysis Identified Novel Genomic Loci Controlling Potassium Use Efficiency and Agronomic Traits in Bread Wheat. FRONTIERS IN PLANT SCIENCE 2020; 11:70. [PMID: 32133017 PMCID: PMC7041172 DOI: 10.3389/fpls.2020.00070] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/17/2020] [Indexed: 05/21/2023]
Abstract
Potassium use efficiency, a complex trait, directly impacts the yield potential of crop plants. Low potassium efficiency leads to a high use of fertilizers, which is not only farmer unfriendly but also deteriorates the environment. Genome-wide association studies (GWAS) are widely used to dissect complex traits. However, most studies use single-locus one-dimensional GWAS models which do not provide true information about complex traits that are controlled by multiple loci. Here, both single-locus GWAS (MLM) and multi-locus GWAS (pLARmEB, FASTmrMLM, mrMLM, FASTmrEMMA) models were used with genotyping from 90 K Infinium SNP array and phenotype derived from four normal and potassium-stress environments, which identified 534 significant marker-trait associations (MTA) for agronomic and potassium related traits: pLARmEB = 279, FASTmrMLM = 213, mrMLM = 35, MLM = 6, FASTmrEMMA = 1. Further screening of these MTA led to the detection of eleven stable loci: q1A, q1D, q2B-1, q2B-2, q2D, q4D, q5B-1, q5B-2, q5B-3, q6D, and q7A. Moreover, Meta-QTL (MQTL) analysis of four independent QTL studies for potassium deficiency in bread wheat located 16 MQTL on 13 chromosomes. One locus identified in this study (q5B-1) colocalized with an MQTL (MQTL_11 ), while the other ten loci were novel associations. Gene ontology of these loci identified 20 putative candidate genes encoding functional proteins involved in key pathways related to stress tolerance, sugar metabolism, and nutrient transport. These findings provide potential targets for breeding potassium stress resistant wheat cultivars and advocate the advantages of multi-locus GWAS models for studying complex traits.
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Affiliation(s)
- Luqman Bin Safdar
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Tayyaba Andleeb
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sadia Latif
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Jawad Umer
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Minqiang Tang
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xiang Li
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
- *Correspondence: Shengyi Liu, ; Umar Masood Quraishi,
| | - Umar Masood Quraishi
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- *Correspondence: Shengyi Liu, ; Umar Masood Quraishi,
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Qin J, Shi A, Song Q, Li S, Wang F, Cao Y, Ravelombola W, Song Q, Yang C, Zhang M. Genome Wide Association Study and Genomic Selection of Amino Acid Concentrations in Soybean Seeds. FRONTIERS IN PLANT SCIENCE 2019; 10:1445. [PMID: 31803203 PMCID: PMC6873630 DOI: 10.3389/fpls.2019.01445] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/17/2019] [Indexed: 05/15/2023]
Abstract
Soybean is a major source of protein for human consumption and animal feed. Releasing new cultivars with high nutritional value is one of the major goals in soybean breeding. To achieve this goal, genome-wide association studies of seed amino acid contents were conducted based on 249 soybean accessions from China, US, Japan, and South Korea. The accessions were evaluated for 15 amino acids and genotyped by sequencing. Significant genetic variation was observed for amino acids among the accessions. Among the 231 single nucleotide polymorphisms (SNPs) significantly associated with variations in amino acid contents, fifteen SNPs localized near 14 candidate genes involving in amino acid metabolism. The amino acids were classified into two groups with five in one group and seven amino acids in the other. Correlation coefficients among the amino acids within each group were high and positive, but the correlation coefficients of amino acids between the two groups were negative. Twenty-five SNP markers associated with multiple amino acids can be used to simultaneously improve multi-amino acid concentration in soybean. Genomic selection analysis of amino acid concentration showed that selection efficiency of amino acids based on the markers significantly associated with all 15 amino acids was higher than that based on random markers or markers only associated with individual amino acid. The identified markers could facilitate selection of soybean varieties with improved seed quality.
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Affiliation(s)
- Jun Qin
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Laboratory of Crop Genetics and Breeding of Hebei, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Qijian Song
- Soybean Genomics and Improvement Lab, USDA-ARS, Beltsville, MD, United States
| | - Song Li
- Crop and Soil Environmental Science, Virginia Tech, Blacksburg, VA, United States
| | - Fengmin Wang
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Laboratory of Crop Genetics and Breeding of Hebei, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Yinghao Cao
- Bioinformatics Center, Allife Medical Science and Technology Co., Ltd, Beijing, China
| | - Waltram Ravelombola
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Qi Song
- Crop and Soil Environmental Science, Virginia Tech, Blacksburg, VA, United States
| | - Chunyan Yang
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Laboratory of Crop Genetics and Breeding of Hebei, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Mengchen Zhang
- National Soybean Improvement Center Shijiazhuang Sub-Center, North China Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Laboratory of Crop Genetics and Breeding of Hebei, Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
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Haplotype Networking of GWAS Hits for Citrulline Variation Associated with the Domestication of Watermelon. Int J Mol Sci 2019; 20:ijms20215392. [PMID: 31671884 PMCID: PMC6862219 DOI: 10.3390/ijms20215392] [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: 09/17/2019] [Revised: 10/21/2019] [Accepted: 10/26/2019] [Indexed: 12/30/2022] Open
Abstract
Watermelon is a good source of citrulline, a non-protein amino acid. Citrulline has several therapeutic and clinical implications as it produces nitric oxide via arginine. In plants, citrulline plays a pivotal role in nitrogen transport and osmoprotection. The purpose of this study was to identify single nucleotide polymorphism (SNP) markers associated with citrulline metabolism using a genome-wide association study (GWAS) and understand the role of citrulline in watermelon domestication. A watermelon collection consisting of 187 wild, landraces, and cultivated accessions was used to estimate citrulline content. An association analysis involved a total of 12,125 SNPs with a minor allele frequency (MAF) >0.05 in understanding the population structure and phylogeny in light of citrulline accumulation. Wild egusi types and landraces contained low to medium citrulline content, whereas cultivars had higher content, which suggests that obtaining higher content of citrulline is a domesticated trait. GWAS analysis identified candidate genes (ferrochelatase and acetolactate synthase) showing a significant association of SNPs with citrulline content. Haplotype networking indicated positive selection from wild to domesticated watermelon. To our knowledge, this is the first study showing genetic regulation of citrulline variation in plants by using a GWAS strategy. These results provide new insights into the citrulline metabolism in plants and the possibility of incorporating high citrulline as a trait in watermelon breeding programs.
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Su J, Wang C, Hao F, Ma Q, Wang J, Li J, Ning X. Genetic Detection of Lint Percentage Applying Single-Locus and Multi-Locus Genome-Wide Association Studies in Chinese Early-Maturity Upland Cotton. FRONTIERS IN PLANT SCIENCE 2019; 10:964. [PMID: 31428110 PMCID: PMC6688134 DOI: 10.3389/fpls.2019.00964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/10/2019] [Indexed: 05/28/2023]
Abstract
Upland cotton (Gossypium hirsutum L.) is the most important source of natural fiber in the world. Early-maturity upland cotton varieties are commonly planted in China. Nevertheless, lint yield of early-maturity upland cotton varieties is strikingly lower than that of middle- and late-maturity ones. How to effectively improve lint yield of early maturing cotton, becomes a focus of cotton research. Here, based on 72,792 high-quality single nucleotide polymorphisms of 160 early-maturing upland cotton accessions, we performed genome-wide association studies (GWASs) for lint percentage (LP), one of the most lint-yield component traits, applying one single-locus method and six multi-locus methods. A total of 4 and 45 significant quantitative trait nucleotides (QTNs) were respectively identified to be associated with LP. Interestingly, in two of four planting environments, two of these QTNs (A02_74713290 and A02_75551547) were simultaneously detected via both one single-locus and three or more multi-locus GWAS methods. Among the 42 genes within a genomic region (A02: 74.31-75.95 Mbp) containing the above two peak QTNs, Gh_A02G1269, Gh_A02G1280, and Gh_A02G1295 had the highest expression levels in ovules during seed development from 20 to 25 days post anthesis, whereas Gh_A02G1278 was preferentially expressed in the fibers rather than other organs. These results imply that the four potential candidate genes might be closely related to cotton LP by regulating the proportion of seed weight and fiber yield. The QTNs and potential candidate genes for LP, identified in this study, provide valuable resource for cultivating novel cotton varieties with earliness and high lint yield in the future.
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Affiliation(s)
- Junji Su
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Caixiang Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Fushun Hao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng, China
| | - Qi Ma
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Ji Wang
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng, China
| | - Jilian Li
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Xinzhu Ning
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
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Fang C, Luo J, Wang S. The Diversity of Nutritional Metabolites: Origin, Dissection, and Application in Crop Breeding. FRONTIERS IN PLANT SCIENCE 2019; 10:1028. [PMID: 31475024 PMCID: PMC6706459 DOI: 10.3389/fpls.2019.01028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/23/2019] [Indexed: 05/21/2023]
Abstract
The chemical diversity of plants is very high, and plant-based foods provide almost all the nutrients necessary for human health, either directly or indirectly. With advancements in plant metabolomics studies, the concept of nutritional metabolites has been expanded and updated. Because the concentration of many nutrients is usually low in plant-based foods, especially those from crops, metabolome-assisted breeding techniques using molecular markers associated with the synthesis of nutritional metabolites have been developed and used to improve nutritional quality of crops. Here, we review the origins of the diversity of nutrient metabolites from a genomic perspective and the role of gene duplication and divergence. In addition, we systematically review recent advances in the metabolomic and genetic basis of metabolite production in major crops. With the development of genome sequencing and metabolic detection technologies, multi-omic integrative analysis of genomes, transcriptomes, and metabolomes has greatly facilitated the deciphering of the genetic basis of metabolic pathways and the diversity of nutrient metabolites. Finally, we summarize the application of nutrient diversity in crop breeding and discuss the future development of a viable alternative to metabolome-assisted breeding techniques that can be used to improve crop nutrient quality.
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Affiliation(s)
- Chuanying Fang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shouchuang Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
- *Correspondence: Shouchuang Wang,
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30
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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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