151
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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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152
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Xiao N, Pan C, Li Y, Wu Y, Cai Y, Lu Y, Wang R, Yu L, Shi W, Kang H, Zhu Z, Huang N, Zhang X, Chen Z, Liu J, Yang Z, Ning Y, Li A. Genomic insight into balancing high yield, good quality, and blast resistance of japonica rice. Genome Biol 2021; 22:283. [PMID: 34615543 PMCID: PMC8493723 DOI: 10.1186/s13059-021-02488-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Balancing the yield, quality and resistance to disease is a daunting challenge in crop breeding due to the negative relationship among these traits. Large-scale genomic landscape analysis of germplasm resources is considered to be an efficient approach to dissect the genetic basis of the complex traits. Central China is one of the main regions where the japonica rice is produced. However, dozens of high-yield rice varieties in this region still exist with low quality or susceptibility to blast disease, severely limiting their application in rice production. RESULTS Here, we re-sequence 200 japonica rice varieties grown in central China over the past 30 years and analyze the genetic structure of these cultivars using 2.4 million polymorphic SNP markers. Genome-wide association mapping and selection scans indicate that strong selection for high-yield and taste quality associated with low-amylose content may have led to the loss of resistance to the rice blast fungus Magnaporthe oryzae. By extensive bioinformatic analyses of yield components, resistance to rice blast, and taste quality, we identify several superior alleles for these traits in the population. Based on this information, we successfully introduce excellent taste quality and blast-resistant alleles into the background of two high-yield cultivars and develop two elite lines, XY99 and JXY1, with excellent taste, high yield, and broad-spectrum of blast resistance. CONCLUSIONS This is the first large-scale genomic landscape analysis of japonica rice varieties grown in central China and we demonstrate a balancing of multiple agronomic traits by genomic-based strategy.
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Affiliation(s)
- Ning Xiao
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, 225009 China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Cunhong Pan
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, 225009 China
| | - Yuhong Li
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, 225009 China
| | - Yunyu Wu
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, 225009 China
| | - Yue Cai
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, 225009 China
| | - Yue Lu
- Key Laboratory of Plant Functional Genomics, Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Ruyi Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Ling Yu
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, 225009 China
| | - Wei Shi
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, 225009 China
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Zhaobing Zhu
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, 225009 China
| | - Niansheng Huang
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, 225009 China
| | - Xiaoxiang Zhang
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, 225009 China
| | - Zichun Chen
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, 225009 China
| | - Jianju Liu
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, 225009 China
| | - Zefeng Yang
- Key Laboratory of Plant Functional Genomics, Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Aihong Li
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, 225009 China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 China
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153
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Li W, Yang B, Xu J, Peng L, Sun S, Huang Z, Jiang X, He Y, Wang Z. A genome-wide association study reveals that the 2-oxoglutarate/malate translocator mediates seed vigor in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:478-491. [PMID: 34376020 DOI: 10.1111/tpj.15455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/01/2021] [Accepted: 08/05/2021] [Indexed: 05/25/2023]
Abstract
Seed vigor is an important trait for the direct seeding of rice (Oryza sativa L.). In this study, we examined the genetic architecture of variation in the germination rate using a diverse panel of rice accessions. Four quantitative trait loci for germination rate were identified using a genome-wide association study during early germination. One candidate gene, encoding the 2-oxoglutarate/malate translocator (OsOMT), was validated for qGR11. Disruption of this gene (Osomt mutants) reduced seed vigor, including seed germination and seedling growth, in rice. Functional analysis revealed that OsOMT influences seed vigor mainly by modulating amino acid levels and glycolysis and tricarboxylic acid cycle processes. The levels of most amino acids, including the Glu family (Glu, Pro, Arg, and GABA), Asp family (Asp, Thr, Lys, Ile, and Met), Ser family (Ser, Gly, and Cys), and others (His, Ala, Leu, and Val), were significantly reduced in the mature grains and the early germinating seeds of Osomt mutants compared to wild type (WT). The glucose and soluble sugar contents, as well as adenosine triphosphate levels, were significantly decreased in germinating seeds of Osomt mutants compared to WT. These results provide important insights into the role of OsOMT in seed vigor in rice.
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Affiliation(s)
- Wenjun Li
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Bin Yang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Jiangyu Xu
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Liling Peng
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Shan Sun
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zhibo Huang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Xiuhua Jiang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Yongqi He
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
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154
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Kumar A, Gupta C, Thomas J, Pereira A. Genetic Dissection of Grain Yield Component Traits Under High Nighttime Temperature Stress in a Rice Diversity Panel. FRONTIERS IN PLANT SCIENCE 2021; 12:712167. [PMID: 34650575 PMCID: PMC8508263 DOI: 10.3389/fpls.2021.712167] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
To dissect the genetic complexity of rice grain yield (GY) and quality in response to heat stress at the reproductive stage, a diverse panel of 190 rice accessions in the United States Department of Agriculture (USDA) rice mini-core collection (URMC) diversity panel were treated with high nighttime temperature (HNT) stress at the reproductive stage of panicle initiation. The quantifiable yield component response traits were then measured. The traits, panicle length (PL), and number of spikelets per panicle (NSP) were evaluated in subsets of the panel comprising the rice subspecies Oryza sativa ssp. Indica and ssp. Japonica. Under HNT stress, the Japonica ssp. exhibited lower reductions in PL and NSP and a higher level of genetic variation compared with the other subpopulations. Whole genome sequencing identified 6.5 million single nucleotide polymorphisms (SNPs) that were used for the genome-wide association studies (GWASs) of the PL and NSP traits. The GWAS analysis in the Combined, Indica, and Japonica populations under HNT stress identified 83, 60, and 803 highly significant SNPs associated with PL, compared to the 30, 30, and 11 highly significant SNPs associated with NSP. Among these trait-associated SNPs, 140 were coincident with genomic regions previously reported for major GY component quantitative trait loci (QTLs) under heat stress. Using extents of linkage disequilibrium in the rice populations, Venn diagram analysis showed that the highest number of putative candidate genes were identified in the Japonica population, with 20 putative candidate genes being common in the Combined, Indica and Japonica populations. Network analysis of the genes linked to significant SNPs associated with PL and NSP identified modules that were involved in primary and secondary metabolisms. The findings in this study could be useful to understand the pathways/mechanisms involved in rice GY and its components under HNT stress for the acceleration of rice-breeding programs and further functional analysis by molecular geneticists.
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155
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Sun Y, Hu Z, Wang X, Shen X, Hu S, Yan Y, Kant S, Xu G, Xue Y, Sun S. Overexpression of OsPHR3 improves growth traits and facilitates nitrogen use efficiency under low phosphate condition. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:712-722. [PMID: 34214781 DOI: 10.1016/j.plaphy.2021.06.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 05/20/2023]
Abstract
Phosphorus (P) and nitrogen (N) are both essential macronutrients for maintaining plant growth and development. In rice (Oryza sativa L.), OsPHR3 is one of the four paralogs of PHR1, which acts as a central regulator of phosphate (Pi) homeostasis, as well being involved in N homeostasis. However, the functions of OsPHR3 in N utilization under different Pi conditions have yet to be fully studied. In this study, we aimed to dissect the effect of OsPHR3-overexpression on N utilization under Pi deficient regimes. Biochemical, molecular and physiological assays were performed to determine the N-influx, translocation, and accumulation in OsPHR3-overexpressing rice lines, grown under Pi-sufficient and -deficient conditions, in both hydroponic and soil systems. Furthermore, important agronomic traits of these plants were also evaluated. The overexpression of OsPHR3 increased N uptake under Pi stress regimes. Increased N uptake also elevated total N concentrations in these plants by inducing N transporter genes expression. Furthermore, overexpression of OsPHR3 increased N use efficiency, 1000-grain weight and grain yield under different Pi conditions. We established new findings that OsPHR3-overexpression facilitates N utilization under Pi deficient conditions. This will help achieving higher yields by coordinating the utilization of N and P.
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Affiliation(s)
- Yafei Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China; Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, 201403, China
| | - Zhi Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaowen Wang
- Landscape Architecture Department, College of Horticulture, Nanjing Agricultural University, 210095, China
| | - Xing Shen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
| | - Siwen Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Yan
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, 95616, USA
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, 3400, Australia
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yong Xue
- Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, 201403, China.
| | - Shubin Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China.
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156
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Zhang F, Hu Z, Wu Z, Lu J, Shi Y, Xu J, Wang X, Wang J, Zhang F, Wang M, Shi X, Cui Y, Vera Cruz C, Zhuo D, Hu D, Li M, Wang W, Zhao X, Zheng T, Fu B, Ali J, Zhou Y, Li Z. Reciprocal adaptation of rice and Xanthomonas oryzae pv. oryzae: cross-species 2D GWAS reveals the underlying genetics. THE PLANT CELL 2021; 33:2538-2561. [PMID: 34467412 PMCID: PMC8408478 DOI: 10.1093/plcell/koab146] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 05/15/2021] [Indexed: 05/23/2023]
Abstract
A 1D/2D genome-wide association study strategy was adopted to investigate the genetic systems underlying the reciprocal adaptation of rice (Oryza sativa) and its bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo) using the whole-genome sequencing and large-scale phenotyping data of 701 rice accessions and 23 diverse Xoo strains. Forty-seven Xoo virulence-related genes and 318 rice quantitative resistance genes (QR-genes) mainly located in 41 genomic regions, and genome-wide interactions between the detected virulence-related genes and QR genes were identified, including well-known resistance genes/virulence genes plus many previously uncharacterized ones. The relationship between rice and Xoo was characterized by strong differentiation among Xoo races corresponding to the subspecific differentiation of rice, by strong shifts toward increased resistance/virulence of rice/Xoo populations and by rich genetic diversity at the detected rice QR-genes and Xoo virulence genes, and by genome-wide interactions between many rice QR-genes and Xoo virulence genes in a multiple-to-multiple manner, presumably resulting either from direct protein-protein interactions or from genetic epistasis. The observed complex genetic interaction system between rice and Xoo likely exists in other crop-pathogen systems that would maintain high levels of diversity at their QR-loci/virulence-loci, resulting in dynamic coevolutionary consequences during their reciprocal adaptation.
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Affiliation(s)
- Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Zhiqiang Hu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Zhichao Wu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Jialing Lu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063009, China
| | - Jinpeng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063009, China
| | - Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Mingming Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Xiaorong Shi
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Yanru Cui
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Casiana Vera Cruz
- International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines
| | - Dalong Zhuo
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Dandan Hu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Min Li
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Wensheng Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Xiuqin Zhao
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Tianqing Zheng
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Binying Fu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Jauhar Ali
- International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines
| | - Yongli Zhou
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
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157
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Panahabadi R, Ahmadikhah A, McKee LS, Ingvarsson PK, Farrokhi N. Genome-Wide Association Mapping of Mixed Linkage (1,3;1,4)-β-Glucan and Starch Contents in Rice Whole Grain. FRONTIERS IN PLANT SCIENCE 2021; 12:665745. [PMID: 34512678 PMCID: PMC8424012 DOI: 10.3389/fpls.2021.665745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/28/2021] [Indexed: 05/27/2023]
Abstract
The glucan content of rice is a key factor defining its nutritional and economic value. Starch and its derivatives have many industrial applications such as in fuel and material production. Non-starch glucans such as (1,3;1,4)-β-D-glucan (mixed-linkage β-glucan, MLG) have many benefits in human health, including lowering cholesterol, boosting the immune system, and modulating the gut microbiome. In this study, the genetic variability of MLG and starch contents were analyzed in rice (Oryza sativa L.) whole grain, by performing a new quantitative analysis of the polysaccharide content of rice grains. The 197 rice accessions investigated had an average MLG content of 252 μg/mg, which was negatively correlated with the grain starch content. A new genome-wide association study revealed seven significant quantitative trait loci (QTLs) associated with the MLG content and two QTLs associated with the starch content in rice whole grain. Novel genes associated with the MLG content were a hexose transporter and anthocyanidin 5,3-O-glucosyltransferase. Also, the novel gene associated with the starch content was a nodulin-like domain. The data pave the way for a better understanding of the genes involved in determining both MLG and starch contents in rice grains and should facilitate future plant breeding programs.
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Affiliation(s)
- Rahele Panahabadi
- Department of Plant Science and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Asadollah Ahmadikhah
- Department of Plant Science and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Lauren S. McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
- Wallenberg Wood Science Centre, Stockholm, Sweden
| | - Pär K. Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Naser Farrokhi
- Department of Plant Science and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
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158
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Liao G, Zhong M, Jiang Z, Tao J, Jia D, Qu X, Huang C, Liu Q, Xu X. Genome-Wide Association Studies Provide Insights into the Genetic Determination of Flower and Leaf Traits of Actinidia eriantha. FRONTIERS IN PLANT SCIENCE 2021; 12:730890. [PMID: 34490026 PMCID: PMC8417775 DOI: 10.3389/fpls.2021.730890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Kiwifruit (Actinidia eriantha) is a dioecious vine, and the pollen of its male cultivars has a direct effect on the quality of its fruits. In this study, to facilitate molecular breeding and gene identification, we performed genome-wide association studies (GWAS) on 11 traits of flower and leaf. A total of 946,337 highly consistent SNP markers were obtained in the whole genome. Phylogenetic tree analysis and population structure analysis showed that the 143 germplasms can be divided into two groups. The linkage disequilibrium analysis showed that A. eriantha have a relatively fast attenuation rate, and that the average attenuation distance of LD was 0.1-0.3 Kb. The MLM (QK) model was determined as best for correlation analysis, and eight and three SNPs associated with flower- and leaf-related traits were identified, respectively, at 0.01 significance level. However, SNP markers associated with stamen number per flower, pollen viability, total chlorophyll content, and total flavonoid content were not identified at the 0.01 significant level, although it is worth noting that one, one, five, and two SNPs were identified to be associated with these traits at the 0.05 significant level. This study provides insights into the complex flower- and leaf-related biology, and identifies genes controlling important traits in A. eriantha through GWAS, which extends the genetic resources and basis for facilitating molecular breeding in kiwifruits.
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Lee JS, Chebotarov D, McNally KL, Pede V, Setiyono TD, Raquid R, Hyun WJ, Jeung JU, Kohli A, Mo Y. Novel Sources of Pre-Harvest Sprouting Resistance for Japonica Rice Improvement. PLANTS (BASEL, SWITZERLAND) 2021; 10:1709. [PMID: 34451754 PMCID: PMC8401653 DOI: 10.3390/plants10081709] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 12/04/2022]
Abstract
Pre-harvest sprouting (PHS), induced by unexpected weather events, such as typhoons, at the late seed maturity stage, is becoming a serious threat to rice production, especially in the state of California, USA, Japan, and the Republic of Korea, where japonica varieties (mostly susceptible to PHS) are mainly cultivated. A projected economic loss by severe PHS in these three countries could range between 8-10 billion USD per year during the next 10 years. Here, we present promising rice germplasm with strong resistance to PHS that were selected from a diverse rice panel of accessions held in the International Rice Genebank (IRG) at the International Rice Research Institute (IRRI). To induce PHS, three panicle samples per accession were harvested at 20 and 30 days after flowering (DAF), respectively, and incubated at 100% relative humidity (RH), 30 °C in a growth chamber for 15 days. A genome-wide association (GWA) analysis using a 4.8 million single nucleotide polymorphisms (SNP) marker set was performed to identify loci and candidate genes conferring PHS resistance. Interestingly, two tropical japonica and four temperate japonica accessions showed outstanding PHS resistance as compared to tolerant indica accessions. Two major loci on chromosomes 1 and 4 were associated with PHS resistance. A priori candidate genes interactions with rice gene networks, which are based on the gene ontology (GO), co-expression, and other evidence, suggested that a key resistance mechanism is related to abscisic acid (ABA), gibberellic acid (GA), and auxin mediated signaling pathways.
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Affiliation(s)
- Jae-Sung Lee
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Dmytro Chebotarov
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Kenneth L. McNally
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Valerien Pede
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Tri Deri Setiyono
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Rency Raquid
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Woong-Jo Hyun
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (W.-J.H.); (J.-U.J.)
| | - Ji-Ung Jeung
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (W.-J.H.); (J.-U.J.)
| | - Ajay Kohli
- International Rice Research Institute, Los Baños 4031, Philippines; (J.-S.L.); (D.C.); (K.L.M.); (V.P.); (T.D.S.); (R.R.)
| | - Youngjun Mo
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (W.-J.H.); (J.-U.J.)
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju 54896, Korea
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160
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Yu J, Liu C, Lin H, Zhang B, Li X, Yuan Q, Liu T, He H, Wei Z, Ding S, Zhang C, Gao H, Guo L, Wang Q, Qian Q, Shang L. Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice. BMC PLANT BIOLOGY 2021; 21:374. [PMID: 34388987 DOI: 10.1186/s12870-021-03145-3149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 07/19/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND Cadmium (Cd) is a toxic heavy metal that is harmful to the environment and human health. Cd pollution threatens the cultivation of rice (Oryza sativa L.) in many countries. Improving rice performance under Cd stress could potentially improve rice productivity. RESULTS In this study, 9 growth traits of 188 different cultivated rice accessions under normal and Cd stress conditions were found to be highly variable during the seedling stage. Based on ~3.3 million single nucleotide polymorphisms (SNPs), 119 Cd-mediated growth response (CGR) quantitative trait loci (QTL) were identified by a genome-wide association study (GWAS), 55 of which have been validated by previously reported QTL and 64 were new CGR loci. Combined with the data from the GWAS, transcriptome analysis, gene annotations from the gene ontology (GO) Slim database, and annotations and functions of homologous genes, 148 CGR candidate genes were obtained. Additionally, several reported genes have been found to play certain roles in CGRs. Seven Cd-related cloned genes were found among the CGR genes. Natural elite haplotypes/alleles in these genes that increased Cd tolerance were identified by a haplotype analysis of a diverse mini core collection. More importantly, this study was the first to uncover the natural variations of 5 GST genes that play important roles in CGRs. CONCLUSION The exploration of Cd-resistant rice germplasm resources and the identification of elite natural variations related to Cd-resistance will help improve the tolerance of current major rice varieties to Cd, as well as provide raw materials and new genes for breeding Cd-resistant varieties.
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Affiliation(s)
- Jianping Yu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/ Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Chaolei Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Hai Lin
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bin Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaoxia Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qiaoling Yuan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Tianjiao Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Huiying He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhaoran Wei
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shilin Ding
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Chao Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hongsheng Gao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Longbiao Guo
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/ Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Quan Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China.
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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Yu J, Liu C, Lin H, Zhang B, Li X, Yuan Q, Liu T, He H, Wei Z, Ding S, Zhang C, Gao H, Guo L, Wang Q, Qian Q, Shang L. Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice. BMC PLANT BIOLOGY 2021; 21:374. [PMID: 34388987 PMCID: PMC8362254 DOI: 10.1186/s12870-021-03145-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Cadmium (Cd) is a toxic heavy metal that is harmful to the environment and human health. Cd pollution threatens the cultivation of rice (Oryza sativa L.) in many countries. Improving rice performance under Cd stress could potentially improve rice productivity. RESULTS In this study, 9 growth traits of 188 different cultivated rice accessions under normal and Cd stress conditions were found to be highly variable during the seedling stage. Based on ~3.3 million single nucleotide polymorphisms (SNPs), 119 Cd-mediated growth response (CGR) quantitative trait loci (QTL) were identified by a genome-wide association study (GWAS), 55 of which have been validated by previously reported QTL and 64 were new CGR loci. Combined with the data from the GWAS, transcriptome analysis, gene annotations from the gene ontology (GO) Slim database, and annotations and functions of homologous genes, 148 CGR candidate genes were obtained. Additionally, several reported genes have been found to play certain roles in CGRs. Seven Cd-related cloned genes were found among the CGR genes. Natural elite haplotypes/alleles in these genes that increased Cd tolerance were identified by a haplotype analysis of a diverse mini core collection. More importantly, this study was the first to uncover the natural variations of 5 GST genes that play important roles in CGRs. CONCLUSION The exploration of Cd-resistant rice germplasm resources and the identification of elite natural variations related to Cd-resistance will help improve the tolerance of current major rice varieties to Cd, as well as provide raw materials and new genes for breeding Cd-resistant varieties.
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Affiliation(s)
- Jianping Yu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/ Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Chaolei Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Hai Lin
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Bin Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaoxia Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qiaoling Yuan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Tianjiao Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Huiying He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhaoran Wei
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shilin Ding
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Chao Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hongsheng Gao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Longbiao Guo
- Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/ Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Quan Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China.
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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Niu Y, Chen T, Wang C, Chen K, Shen C, Chen H, Zhu S, Wu Z, Zheng T, Zhang F, Xu J. Identification and allele mining of new candidate genes underlying rice grain weight and grain shape by genome-wide association study. BMC Genomics 2021; 22:602. [PMID: 34362301 PMCID: PMC8349016 DOI: 10.1186/s12864-021-07901-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 07/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Grain weight and grain shape are important agronomic traits that affect the grain yield potential and grain quality of rice. Both grain weight and grain shape are controlled by multiple genes. The 3,000 Rice Genomes Project (3 K RGP) greatly facilitates the discovery of agriculturally important genetic variants and germplasm resources for grain weight and grain shape. RESULTS Abundant natural variations and distinct phenotic differentiation among the subgroups in grain weight and grain shape were observed in a large population of 2,453 accessions from the 3 K RGP. A total of 21 stable quantitative trait nucleotides (QTNs) for the four traits were consistently identified in at least two of 3-year trials by genome-wide association study (GWAS), including six new QTNs (qTGW3.1, qTGW9, qTGW11, qGL4/qRLW4, qGL10, and qRLW1) for grain weight and grain shape. We further predicted seven candidate genes (Os03g0186600, Os09g0544400, Os11g0163600, Os04g0580700, Os10g0399700, Os10g0400100 and Os01g0171000) for the six new QTNs by high-density association and gene-based haplotype analyses. The favorable haplotypes of the seven candidate genes and five previously cloned genes in elite accessions with high TGW and RLW are also provided. CONCLUSIONS Our results deepen the understanding of the genetic basis of grain weight and grain shape in rice and provide valuable information for improving rice grain yield and grain quality through molecular breeding.
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Affiliation(s)
- Yanan Niu
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
- Tasmanian Institute of Agriculture, University of Tasmania, 7250, Prospect, TAS, Australia
| | - Tianxiao Chen
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
- Tasmanian Institute of Agriculture, University of Tasmania, 7250, Prospect, TAS, Australia
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chunchao Wang
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Kai Chen
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Congcong Shen
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Huizhen Chen
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Pingxiang Institute of Agricultural Sciences, 337000, Pingxiang, China
| | - Shuangbing Zhu
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Zhichao Wu
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Tianqing Zheng
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Fan Zhang
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| | - Jianlong Xu
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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163
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Potential of rice landraces with strong culms as genetic resources for improving lodging resistance against super typhoons. Sci Rep 2021; 11:15780. [PMID: 34349177 PMCID: PMC8339031 DOI: 10.1038/s41598-021-95268-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/16/2021] [Indexed: 11/08/2022] Open
Abstract
It is generally believed that rice landraces with long culms are susceptible to lodging, and have not been utilized for breeding to improve lodging resistance. However, little is known about the structural culm strength of landraces and their beneficial genetic loci. Therefore, in this study, genome-wide association studies (GWAS) were performed using a rice population panel including Japanese rice landraces to identify beneficial loci associated with strong culms. As a result, the landraces were found to have higher structural culm strength and greater diversity than the breeding varieties. Genetic loci associated with strong culms were identified, and it was demonstrated that haplotypes with positive effects of those loci were present in a high proportion of these landraces. These results indicated that the utilization of the strong culm-associated loci present in Japanese rice landraces may further improve the lodging resistance of modern breeding varieties that have relied on semi-dwarfism.
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164
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Cobb JN, Chen C, Shi Y, Maron LG, Liu D, Rutzke M, Greenberg A, Craft E, Shaff J, Paul E, Akther K, Wang S, Kochian LV, Zhang D, Zhang M, McCouch SR. Genetic architecture of root and shoot ionomes in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2613-2637. [PMID: 34018019 PMCID: PMC8277617 DOI: 10.1007/s00122-021-03848-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/29/2021] [Indexed: 05/09/2023]
Abstract
KEY MESSAGE Association analysis for ionomic concentrations of 20 elements identified independent genetic factors underlying the root and shoot ionomes of rice, providing a platform for selecting and dissecting causal genetic variants. Understanding the genetic basis of mineral nutrient acquisition is key to fully describing how terrestrial organisms interact with the non-living environment. Rice (Oryza sativa L.) serves both as a model organism for genetic studies and as an important component of the global food system. Studies in rice ionomics have primarily focused on above ground tissues evaluated from field-grown plants. Here, we describe a comprehensive study of the genetic basis of the rice ionome in both roots and shoots of 6-week-old rice plants for 20 elements using a controlled hydroponics growth system. Building on the wealth of publicly available rice genomic resources, including a panel of 373 diverse rice lines, 4.8 M genome-wide single-nucleotide polymorphisms, single- and multi-marker analysis pipelines, an extensive tome of 321 candidate genes and legacy QTLs from across 15 years of rice genetics literature, we used genome-wide association analysis and biparental QTL analysis to identify 114 genomic regions associated with ionomic variation. The genetic basis for root and shoot ionomes was highly distinct; 78 loci were associated with roots and 36 loci with shoots, with no overlapping genomic regions for the same element across tissues. We further describe the distribution of phenotypic variation across haplotypes and identify candidate genes within highly significant regions associated with sulfur, manganese, cadmium, and molybdenum. Our analysis provides critical insight into the genetic basis of natural phenotypic variation for both root and shoot ionomes in rice and provides a comprehensive resource for dissecting and testing causal genetic variants.
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Affiliation(s)
- Joshua N Cobb
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
- RiceTec Inc, Alvin, TX, 77511, USA
| | - Chen Chen
- Department of Statistics, Purdue University, West Lafayette, IN, 47907-2054, USA
- Ausy Consulting, Esperantolaan 8, 3001, Heverlee, Belgium
| | - Yuxin Shi
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Lyza G Maron
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Danni Liu
- Department of Statistics, Purdue University, West Lafayette, IN, 47907-2054, USA
| | - Mike Rutzke
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Anthony Greenberg
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
- Bayesic Research, LLC, 452 Sheffield Rd, Ithaca, NY, 14850, USA
| | - Eric Craft
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Jon Shaff
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, 14853-1901, USA
| | - Edyth Paul
- GeneFlow, Inc, Centreville, VA, 20120, USA
| | - Kazi Akther
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Shaokui Wang
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
- Department of Plant Breeding, South China Agriculture University, Guangdong, 510642, China
| | - Leon V Kochian
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, 14853-1901, USA
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Dabao Zhang
- Department of Statistics, Purdue University, West Lafayette, IN, 47907-2054, USA
| | - Min Zhang
- Department of Statistics, Purdue University, West Lafayette, IN, 47907-2054, USA.
| | - Susan R McCouch
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA.
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Meger J, Ulaszewski B, Burczyk J. Genomic signatures of natural selection at phenology-related genes in a widely distributed tree species Fagus sylvatica L. BMC Genomics 2021; 22:583. [PMID: 34332553 PMCID: PMC8325806 DOI: 10.1186/s12864-021-07907-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/20/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Diversity among phenology-related genes is predicted to be a contributing factor in local adaptations seen in widely distributed plant species that grow in climatically variable geographic areas, such as forest trees. European beech (Fagus sylvatica L.) is widespread, and is one of the most important broadleaved tree species in Europe; however, its potential for adaptation to climate change is a matter of uncertainty, and little is known about the molecular basis of climate change-relevant traits like bud burst. RESULTS We explored single nucleotide polymorphisms (SNP) at candidate genes related to bud burst in beech individuals sampled across 47 populations from Europe. SNP diversity was monitored for 380 candidate genes using a sequence capture approach, providing 2909 unlinked SNP loci. We used two complementary analytical methods to find loci significantly associated with geographic variables, climatic variables (expressed as principal components), or phenotypic variables (spring and autumn phenology, height, survival). Redundancy analysis (RDA) was used to detect candidate markers across two spatial scales (entire study area and within subregions). We revealed 201 candidate SNPs at the broadest scale, 53.2% of which were associated with phenotypic variables. Additive polygenic scores, which provide a measure of the cumulative signal across significant candidate SNPs, were correlated with a climate variable (first principal component, PC1) related to temperature and precipitation availability, and spring phenology. However, different genotype-environment associations were identified within Southeastern Europe as compared to the entire geographic range of European beech. CONCLUSIONS Environmental conditions play important roles as drivers of genetic diversity of phenology-related genes that could influence local adaptation in European beech. Selection in beech favors genotypes with earlier bud burst under warmer and wetter habitats within its range; however, selection pressures may differ across spatial scales.
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Affiliation(s)
- Joanna Meger
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Bartosz Ulaszewski
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Jaroslaw Burczyk
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland.
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166
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Woodhouse S, He Z, Woolfenden H, Steuernagel B, Haerty W, Bancroft I, Irwin JA, Morris RJ, Wells R. Validation of a novel associative transcriptomics pipeline in Brassica oleracea: identifying candidates for vernalisation response. BMC Genomics 2021; 22:539. [PMID: 34256693 PMCID: PMC8278714 DOI: 10.1186/s12864-021-07805-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/08/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Associative transcriptomics has been used extensively in Brassica napus to enable the rapid identification of markers correlated with traits of interest. However, within the important vegetable crop species, Brassica oleracea, the use of associative transcriptomics has been limited due to a lack of fixed genetic resources and the difficulties in generating material due to self-incompatibility. Within Brassica vegetables, the harvestable product can be vegetative or floral tissues and therefore synchronisation of the floral transition is an important goal for growers and breeders. Vernalisation is known to be a key determinant of the floral transition, yet how different vernalisation treatments influence flowering in B. oleracea is not well understood. RESULTS Here, we present results from phenotyping a diverse set of 69 B. oleracea accessions for heading and flowering traits under different environmental conditions. We developed a new associative transcriptomics pipeline, and inferred and validated a population structure, for the phenotyped accessions. A genome-wide association study identified miR172D as a candidate for the vernalisation response. Gene expression marker association identified variation in expression of BoFLC.C2 as a further candidate for vernalisation response. CONCLUSIONS This study describes a new pipeline for performing associative transcriptomics studies in B. oleracea. Using flowering time as an example trait, it provides insights into the genetic basis of vernalisation response in B. oleracea through associative transcriptomics and confirms its characterisation as a complex G x E trait. Candidate leads were identified in miR172D and BoFLC.C2. These results could facilitate marker-based breeding efforts to produce B. oleracea lines with more synchronous heading dates, potentially leading to improved yields.
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Affiliation(s)
| | - Zhesi He
- Department of Biology, University of York, YO105DD, Heslington, York, UK
| | - Hugh Woolfenden
- Computational & Systems Biology, John Innes Centre, NR47UH, Norwich, UK
| | | | - Wilfried Haerty
- Earlham Institute, NR47UH, Norwich, UK
- School of Biological Sciences, University of East Anglia, NR47TJ, Norwich, UK
| | - Ian Bancroft
- Department of Biology, University of York, YO105DD, Heslington, York, UK
| | - Judith A Irwin
- Department of Crop Genetics, John Innes Centre, NR47UH, Norwich, UK
| | - Richard J Morris
- Computational & Systems Biology, John Innes Centre, NR47UH, Norwich, UK.
| | - Rachel Wells
- Department of Crop Genetics, John Innes Centre, NR47UH, Norwich, UK.
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167
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Wu PY, Yang MH, Kao CH. A statistical framework for QTL hotspot detection. G3-GENES GENOMES GENETICS 2021; 11:6151767. [PMID: 33638985 PMCID: PMC8049418 DOI: 10.1093/g3journal/jkab056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/11/2021] [Indexed: 11/13/2022]
Abstract
Quantitative trait loci (QTL) hotspots (genomic locations enriched in QTL) are a common and notable feature when collecting many QTL for various traits in many areas of biological studies. The QTL hotspots are important and attractive since they are highly informative and may harbor genes for the quantitative traits. So far, the current statistical methods for QTL hotspot detection use either the individual-level data from the genetical genomics experiments or the summarized data from public QTL databases to proceed with the detection analysis. These methods may suffer from the problems of ignoring the correlation structure among traits, neglecting the magnitude of LOD scores for the QTL, or paying a very high computational cost, which often lead to the detection of excessive spurious hotspots, failure to discover biologically interesting hotspots composed of a small-to-moderate number of QTL with strong LOD scores, and computational intractability, respectively, during the detection process. In this article, we describe a statistical framework that can handle both types of data as well as address all the problems at a time for QTL hotspot detection. Our statistical framework directly operates on the QTL matrix and hence has a very cheap computational cost and is deployed to take advantage of the QTL mapping results for assisting the detection analysis. Two special devices, trait grouping and top γn,α profile, are introduced into the framework. The trait grouping attempts to group the traits controlled by closely linked or pleiotropic QTL together into the same trait groups and randomly allocates these QTL together across the genomic positions separately by trait group to account for the correlation structure among traits, so as to have the ability to obtain much stricter thresholds and dismiss spurious hotspots. The top γn,α profile is designed to outline the LOD-score pattern of QTL in a hotspot across the different hotspot architectures, so that it can serve to identify and characterize the types of QTL hotspots with varying sizes and LOD-score distributions. Real examples, numerical analysis, and simulation study are performed to validate our statistical framework, investigate the detection properties, and also compare with the current methods in QTL hotspot detection. The results demonstrate that the proposed statistical framework can effectively accommodate the correlation structure among traits, identify the types of hotspots, and still keep the notable features of easy implementation and fast computation for practical QTL hotspot detection.
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Affiliation(s)
- Po-Ya Wu
- Institute of Statistical Science, Academia Sinica, Taipei 11529, Taiwan, Republic of China
| | - Man-Hsia Yang
- Crop Science Division, Taiwan Agricultural Research Institute, Council of Agriculture, Taichung 41362, Taiwan, Republic of China
| | - Chen-Hung Kao
- Institute of Statistical Science, Academia Sinica, Taipei 11529, Taiwan, Republic of China.,Department of Agronomy, National Taiwan University, Taipei 10617, Taiwan, Republic of China
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168
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Zhang X, He Q, Zhang W, Shu F, Wang W, He Z, Xiong H, Peng J, Deng H. Genetic relationships and identification of core germplasm among rice photoperiod- and thermo-sensitive genic male sterile lines. BMC PLANT BIOLOGY 2021; 21:313. [PMID: 34215178 PMCID: PMC8252326 DOI: 10.1186/s12870-021-03062-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Harnessing heterosis is one of the major approaches to increase rice yield and has made a great contribution to food security. The identification and selection of outstanding parental genotypes especially among male sterile lines is a key step for exploiting heterosis. Two-line hybrid system is based on the discovery and application of photoperiod- and thermo-sensitive genic sensitive male sterile (PTGMS) materials. The development of wide-range of male sterile lines from a common gene pool leads to a narrower genetic diversity, which is vulnerable to biotic and abiotic stress. Hence, it is valuable to ascertain the genetic background of PTGMS lines and to understand their relationships in order to select and design a future breeding strategy. RESULTS A collection of 118 male sterile rice lines and 13 conventional breeding lines from the major rice growing regions of China was evaluated and screened against the photosensitive (pms3) and temperature sensitive male sterility (tms5) genes. The total gene pool was divided into four major populations as P1 possessing the pms3, P2 possessing tms5, P3 possessing both pms3 and tms5 genes, and P4 containing conventional breeding lines without any male sterility allele. The high genetic purity was revealed by homozygous alleles in all populations. The population admixture, principle components and the phylogenetic analysis revealed the close relations of P2 and P3 with P4. The population differentiation analysis showed that P1 has the highest differentiation coefficient. The lines from P1 were observed as the ancestors of other three populations in a phylogenetic tree, while the lines in P2 and P3 showed a close genetic relation with conventional lines. A core collection of top 10% lines with maximum within and among populations genetic diversity was constructed for future research and breeding efforts. CONCLUSION The low genetic diversity and close genetic relationship among PTGMS lines in P2, P3 and P4 populations suggest a selection sweep and they might result from a backcrossing with common ancestors including the pure lines of P1. The core collection from PTGMS panel updated with new diverse germplasm will serve best for further two-line hybrid breeding.
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Affiliation(s)
- Xianwen Zhang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- Huazhi Biotech Co. Ltd, Changsha, 410125, China
| | - Qiang He
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Wuhan Zhang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Fu Shu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Weiping Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Zhizhou He
- Huazhi Biotech Co. Ltd, Changsha, 410125, China
| | - Hairong Xiong
- School of Chemistry and Materials Science, Hunan Agricultural University, Changsha, 410128, China
| | - Junhua Peng
- Huazhi Biotech Co. Ltd, Changsha, 410125, China
| | - Huafeng Deng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
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Yang W, Zhao J, Zhang S, Chen L, Yang T, Dong J, Fu H, Ma Y, Zhou L, Wang J, Liu W, Liu Q, Liu B. Genome-Wide Association Mapping and Gene Expression Analysis Reveal the Negative Role of OsMYB21 in Regulating Bacterial Blight Resistance in Rice. RICE (NEW YORK, N.Y.) 2021; 14:58. [PMID: 34185169 PMCID: PMC8241976 DOI: 10.1186/s12284-021-00501-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 06/08/2021] [Indexed: 05/17/2023]
Abstract
BACKGROUND Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases in rice all over the world. Due to the diversity and rapid evolution of Xoo, identification and use of the non-race specific quantitative resistance QTLs has been considered the preferred strategy for effective control of this disease. Although numerous QTLs for BB resistance have been identified, they haven't been effectively used for improvement of BB resistance in rice due to their small effects and lack of knowledge on the function of genes underlying the QTLs. RESULTS In the present study, a genome-wide association study of BB resistance was performed in a rice core collection from South China. A total of 17 QTLs were identified to be associated with BB resistance. Among them, 13 QTLs were newly identified in the present study and the other 4 QTLs were co-localized with the previously reported QTLs or Xa genes that confer qualitative resistance to Xoo strains. Particularly, the qBBR11-4 on chromosome 11 explained the largest phenotypic variation in this study and was co-localized with the previously identified QTLs for BB and bacterial leaf streak (BLS) resistance against diverse strains in three studies, suggesting its broad-spectrum resistance and potential value in rice breeding. Through combined analysis of differential expression and annotations of the predicted genes within qBBR11-4 between two sets of rice accessions selected based on haplotypes and disease phenotypes, we identified the transcription factor OsMYB21 as the candidate gene for qBBR11-4. The OsMYB21 overexpressing plants exhibited decreased resistance to bacterial blight, accompanied with down-regulation of several defense-related genes compared with the wild-type plants. CONCLUSION The results suggest that OsMYB21 negatively regulates bacterial blight resistance in rice, and this gene can be a promising target in rice breeding by using the gene editing method. In addition, the potential candidate genes for the 13 novel QTLs for BB resistance were also analyzed in this study, providing a new source for cloning of genes associated with BB resistance and molecular breeding in rice.
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Affiliation(s)
- Wu Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Shaohong Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Luo Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Tifeng Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Hua Fu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Yamei Ma
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Lian Zhou
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Jian Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Wei Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Qing Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
| | - Bin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640 China
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170
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Akond Z, Ahsan MA, Alam M, Mollah MNH. Robustification of GWAS to explore effective SNPs addressing the challenges of hidden population stratification and polygenic effects. Sci Rep 2021; 11:13060. [PMID: 34158546 PMCID: PMC8219685 DOI: 10.1038/s41598-021-90774-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/12/2021] [Indexed: 11/24/2022] Open
Abstract
Genome-wide association studies (GWAS) play a vital role in identifying important genes those is associated with the phenotypic variations of living organisms. There are several statistical methods for GWAS including the linear mixed model (LMM) which is popular for addressing the challenges of hidden population stratification and polygenic effects. However, most of these methods including LMM are sensitive to phenotypic outliers that may lead the misleading results. To overcome this problem, in this paper, we proposed a way to robustify the LMM approach for reducing the influence of outlying observations using the β-divergence method. The performance of the proposed method was investigated using both synthetic and real data analysis. Simulation results showed that the proposed method performs better than both linear regression model (LRM) and LMM approaches in terms of powers and false discovery rates in presence of phenotypic outliers. On the other hand, the proposed method performed almost similar to LMM approach but much better than LRM approach in absence of outliers. In the case of real data analysis, our proposed method identified 11 SNPs that are significantly associated with the rice flowering time. Among the identified candidate SNPs, some were involved in seed development and flowering time pathways, and some were connected with flower and other developmental processes. These identified candidate SNPs could assist rice breeding programs effectively. Thus, our findings highlighted the importance of robust GWAS in identifying candidate genes.
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Affiliation(s)
- Zobaer Akond
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
- Institute of Environmental Science, University of Rajshahi, Rajshahi, 6205, Bangladesh
- Agricultural Statistics and ICT Division, Bangladesh Agricultural Research Institute (BARI), Gazipur, 1701, Bangladesh
| | - Md Asif Ahsan
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Munirul Alam
- Molecular Ecology and Metagenomic Laboratory, Infectious Diseases Division, International Centre for Diarrheal Disease Research (Icddr,b), Rajshahi, Bangladesh
| | - Md Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh.
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171
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Mathew B, Léon J, Dadshani S, Pillen K, Sillanpää MJ, Naz AA. Importance of correcting genomic relationships in single-locus QTL mapping model with an advanced backcross population. G3 GENES|GENOMES|GENETICS 2021; 11:6211194. [PMID: 33822941 PMCID: PMC8495747 DOI: 10.1093/g3journal/jkab105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/18/2021] [Indexed: 11/29/2022]
Abstract
Advanced backcross (AB) populations have been widely used to identify and utilize beneficial alleles in various crops such as rice, tomato, wheat, and barley. For the development of an AB population, a controlled crossing scheme is used and this controlled crossing along with the selection (both natural and artificial) of agronomically adapted alleles during the development of AB population may lead to unbalanced allele frequencies in the population. However, it is commonly believed that interval mapping of traits in experimental crosses such as AB populations is immune to the deviations from the expected frequencies under Mendelian segregation. Using two AB populations and simulated data sets as examples, we describe the severity of the problem caused by unbalanced allele frequencies in quantitative trait loci mapping and demonstrate how it can be corrected using the linear mixed model having a polygenic effect with the covariance structure (genomic relationship matrix) calculated from molecular markers.
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Affiliation(s)
- Boby Mathew
- Institute of Crop Science and Resource Conservation, Department of Plant Breeding, University of Bonn, 53115 Bonn, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation, Department of Plant Breeding, University of Bonn, 53115 Bonn, Germany
| | - Said Dadshani
- Institute of Crop Science and Resource Conservation, Department of Plant Breeding, University of Bonn, 53115 Bonn, Germany
| | - Klaus Pillen
- Department of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | | | - Ali Ahmad Naz
- Institute of Crop Science and Resource Conservation, Department of Plant Breeding, University of Bonn, 53115 Bonn, Germany
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172
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Lee ON, Koo H, Yu JW, Park HY. Genotyping-by-Sequencing-Based Genome-Wide Association Studies of Fusarium Wilt Resistance in Radishes ( Raphanus sativus L.). Genes (Basel) 2021; 12:genes12060858. [PMID: 34205206 PMCID: PMC8228987 DOI: 10.3390/genes12060858] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 11/22/2022] Open
Abstract
Fusarium wilt (FW) is a fungal disease that causes severe yield losses in radish production. The most effective method to control the FW is the development and use of resistant varieties in cultivation. The identification of marker loci linked to FW resistance are expected to facilitate the breeding of disease-resistant radishes. In the present study, we applied an integrated framework of genome-wide association studies (GWAS) using genotyping-by-sequencing (GBS) to identify FW resistance loci among a panel of 225 radish accessions, including 58 elite breeding lines. Phenotyping was conducted by manual inoculation of seedlings with the FW pathogen, and scoring for the disease index was conducted three weeks after inoculation during two constitutive years. The GWAS analysis identified 44 single nucleotide polymorphisms (SNPs) and twenty putative candidate genes that were significantly associated with FW resistance. In addition, a total of four QTLs were identified from F2 population derived from a FW resistant line and a susceptible line, one of which was co-located with the SNPs on chromosome 7, detected in GWAS study. These markers will be valuable for molecular breeding programs and marker-assisted selection to develop FW resistant varieties of R. sativus.
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Affiliation(s)
- O New Lee
- College of Life Sciences, Sejong University, Seoul 05006, Korea;
| | - Hyunjin Koo
- Department of Agricultural Biotechnology and Research, Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea;
| | | | - Han Yong Park
- College of Life Sciences, Sejong University, Seoul 05006, Korea;
- Correspondence:
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173
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Rabara RC, Msanne J, Basu S, Ferrer MC, Roychoudhury A. Coping with inclement weather conditions due to high temperature and water deficit in rice: An insight from genetic and biochemical perspectives. PHYSIOLOGIA PLANTARUM 2021; 172:487-504. [PMID: 33179306 DOI: 10.1111/ppl.13272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/13/2020] [Accepted: 11/06/2020] [Indexed: 06/11/2023]
Abstract
Climatic fluctuations, temperature extremes, and water scarcity are becoming increasingly unpredictable with the passage of time. Such environmental atrocities have been the scourge of agriculture over the ages, bringing with them poor harvests and threat of famine. Rice production, owing to its high-water requirement for cultivation, is highly vulnerable to the threat of changing climate, particularly prolonged drought and high temperature, individually or in combination. Amidst all the abiotic stresses, heat and drought are considered as the most important concurrent stressors, largely affecting rice yield and productivity under the current scenario. Such threats heighten the need for new breeding and cultivation strategies in generating abiotic stress-resilient rice varieties with better yield potential. Responses of rice to these stresses can be categorized at the morphological, physiological and biochemical levels. This review examines the physiological and molecular mechanism, in the form of up regulation of several defense machineries of rice varieties to cope with drought stress (DS), high temperature stress (HTS), and their combination (DS-HTS). Genotypic differences among rice varieties in their tolerance ability have also been addressed. The review also appraises research studies conducted in rice regarding various phenotypic traits, genetic loci and response mechanisms to stress conditions to help craft new breeding strategies for improved tolerance to DS and HTS, singly or in combination. The review also encompasses the gene regulatory networks and transcription factors, and their cross-talks in mediating tolerance to such stresses. Understanding the epigenetic regulation, involving DNA methylation and histone modification during such hostile situations, will also play a crucial role in our comprehensive understanding of combinatorial stress responses. Taken together, this review consolidates current research and available information on promising rice cultivars with desirable traits as well as advocates synergistic and complementary approaches in molecular and systems biology to develop new rice breeds that favorably respond to DS-HTS-induced abiotic stress.
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Affiliation(s)
- Roel C Rabara
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Joseph Msanne
- New Mexico Consortium, Los Alamos, NM, New Mexico, United States of America
| | - Supratim Basu
- New Mexico Consortium, Los Alamos, NM, New Mexico, United States of America
| | - Marilyn C Ferrer
- Genetic Resources Division, Philippine Rice Research Institute, Science City of Muñoz, Nueva Ecija, Philippines
| | - Aryadeep Roychoudhury
- Department of Biotechnology, St. Xavier's College (Autonomous), Kolkata, West Bengal, India
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174
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Choi JY, Abdulkina LR, Yin J, Chastukhina IB, Lovell JT, Agabekian IA, Young PG, Razzaque S, Shippen DE, Juenger TE, Shakirov EV, Purugganan MD. Natural variation in plant telomere length is associated with flowering time. THE PLANT CELL 2021; 33:1118-1134. [PMID: 33580702 PMCID: PMC8599780 DOI: 10.1093/plcell/koab022] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/14/2021] [Indexed: 05/05/2023]
Abstract
Telomeres are highly repetitive DNA sequences found at the ends of chromosomes that protect the chromosomes from deterioration duringcell division. Here, using whole-genome re-sequencing and terminal restriction fragment assays, we found substantial natural intraspecific variation in telomere length in Arabidopsis thaliana, rice (Oryza sativa), and maize (Zea mays). Genome-wide association study (GWAS) mapping in A. thaliana identified 13 regions with GWAS-significant associations underlying telomere length variation, including a region that harbors the telomerase reverse transcriptase (TERT) gene. Population genomic analysis provided evidence for a selective sweep at the TERT region associated with longer telomeres. We found that telomere length is negatively correlated with flowering time variation not only in A. thaliana, but also in maize and rice, indicating a link between life-history traits and chromosome integrity. Our results point to several possible reasons for this correlation, including the possibility that longer telomeres may be more adaptive in plants that have faster developmental rates (and therefore flower earlier). Our work suggests that chromosomal structure itself might be an adaptive trait associated with plant life-history strategies.
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Affiliation(s)
- Jae Young Choi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003, NY, USA
- Author for correspondence: (J.Y.C), (E.V.S.) or (M.D.P.)
| | - Liliia R Abdulkina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Republic of Tatarstan 420008, Russia
| | - Jun Yin
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA
| | - Inna B Chastukhina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Republic of Tatarstan 420008, Russia
| | - John T Lovell
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Alabama 35806, USA
| | - Inna A Agabekian
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Republic of Tatarstan 420008, Russia
| | - Pierce G Young
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, USA
| | - Samsad Razzaque
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA
| | - Eugene V Shakirov
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Republic of Tatarstan 420008, Russia
- Department of Biological Sciences, College of Science, Marshall University, West Virginia 25701, USA
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, West Virginia 25755, USA
- Author for correspondence: (J.Y.C), (E.V.S.) or (M.D.P.)
| | - Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003, NY, USA
- Author for correspondence: (J.Y.C), (E.V.S.) or (M.D.P.)
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175
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McGowan MT, Zhang Z, Ficklin SP. Chromosomal characteristics of salt stress heritable gene expression in the rice genome. BMC Genom Data 2021; 22:17. [PMID: 34044788 PMCID: PMC8162008 DOI: 10.1186/s12863-021-00970-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene expression is potentially an important heritable quantitative trait that mediates between genetic variation and higher-level complex phenotypes through time and condition-dependent regulatory interactions. Therefore, we sought to explore both the genomic and condition-specific characteristics of gene expression heritability within the context of chromosomal structure. RESULTS Heritability was estimated for biological gene expression using a diverse, 84-line, Oryza sativa (rice) population under optimal and salt-stressed conditions. Overall, 5936 genes were found to have heritable expression regardless of condition and 1377 genes were found to have heritable expression only during salt stress. These genes with salt-specific heritable expression are enriched for functional terms associated with response to stimulus and transcription factor activity. Additionally, we discovered that highly and lowly expressed genes, and genes with heritable expression are distributed differently along the chromosomes in patterns that follow previously identified high-throughput chromosomal conformation capture (Hi-C) A/B chromatin compartments. Furthermore, multiple genomic hot-spots enriched for genes with salt-specific heritability were identified on chromosomes 1, 4, 6, and 8. These hotspots were found to contain genes functionally enriched for transcriptional regulation and overlaps with a previously identified major QTL for salt-tolerance in rice. CONCLUSIONS Investigating the heritability of traits, and in-particular gene expression traits, is important towards developing a basic understanding of how regulatory networks behave across a population. This work provides insights into spatial patterns of heritable gene expression at the chromosomal level.
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Affiliation(s)
- Matthew T McGowan
- Molecular Plant Sciences Program, Washington State University, French Ad 324G, Pullman, WA, 99164, USA.
| | - Zhiwu Zhang
- Molecular Plant Sciences Program, Washington State University, French Ad 324G, Pullman, WA, 99164, USA.,Department of Crops and Soils, Washington State University, 105 Johnson Hall, Pullman, WA, 99164, USA
| | - Stephen P Ficklin
- Molecular Plant Sciences Program, Washington State University, French Ad 324G, Pullman, WA, 99164, USA.,Department of Horticulture, Washington State University, 149 Johnson Hall, Pullman, WA, 99164, USA
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176
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Kim M, Xi H, Park J. Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors. PLoS One 2021; 16:e0252181. [PMID: 34038437 PMCID: PMC8153473 DOI: 10.1371/journal.pone.0252181] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 05/11/2021] [Indexed: 12/30/2022] Open
Abstract
GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g., number of plant genomes in the Plant Genome Database (http://www.plantgenome.info/) is 2,174 originated from 713 plant species. Thus, we investigated GATA TFs of 19 Arabidopsis thaliana genome-widely to understand intraspecific features of Arabidopsis GATA TFs with the pipeline of GATA database (http://gata.genefamily.info/). Numbers of GATA genes and GATA TFs of each A. thaliana genome range from 29 to 30 and from 39 to 42, respectively. Four cases of different pattern of alternative splicing forms of GATA genes among 19 A. thaliana genomes are identified. 22 of 2,195 amino acids (1.002%) from the alignment of GATA domain amino acid sequences display variations across 19 ecotype genomes. In addition, maximally four different amino acid sequences per each GATA domain identified in this study indicate that these position-specific amino acid variations may invoke intraspecific functional variations. Among 15 functionally characterized GATA genes, only five GATA genes display variations of amino acids across ecotypes of A. thaliana, implying variations of their biological roles across natural isolates of A. thaliana. PCA results from 28 characteristics of GATA genes display the four groups, same to those defined by the number of GATA genes. Topologies of bootstrapped phylogenetic trees of Arabidopsis chloroplasts and common GATA genes are mostly incongruent. Moreover, no relationship between geographical distribution and their phylogenetic relationships was found. Our results present that intraspecific variations of GATA TFs in A. thaliana are conserved and evolutionarily neutral along with 19 ecotypes, which is congruent to the fact that GATA TFs are one of the main regulators for controlling essential mechanisms, such as seed germination and hypocotyl elongation.
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Affiliation(s)
- Mangi Kim
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
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177
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Li J, Wang Z, Fernando R, Cheng H. Tests of association based on genomic windows can lead to spurious associations when using genotype panels with heterogeneous SNP densities. Genet Sel Evol 2021; 53:45. [PMID: 34039266 PMCID: PMC8157676 DOI: 10.1186/s12711-021-00638-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/11/2021] [Indexed: 11/10/2022] Open
Abstract
Dense single nucleotide polymorphism (SNP) panels are widely used for genome-wide association studies (GWAS). In these panels, SNPs within a genomic segment tend to be highly correlated. Thus, association studies based on testing the significance of single SNPs are not very effective, and genomic-window based tests have been proposed to address this problem. However, when the SNP density on the genotype panel is not homogeneous, genomic-window based tests can lead to the detection of spurious associations by declaring effects of genomic windows that explain a large proportion of genetic variance as significant. We propose two methods to solve this problem.
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Affiliation(s)
- Jinghui Li
- Department of Animal Science, University of California, Davis, USA
| | - Zigui Wang
- Department of Animal Science, University of California, Davis, USA
| | - Rohan Fernando
- Department of Animal Science, Iowa State Univeristy, Ames, USA
| | - Hao Cheng
- Department of Animal Science, University of California, Davis, USA.
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178
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Mores A, Borrelli GM, Laidò G, Petruzzino G, Pecchioni N, Amoroso LGM, Desiderio F, Mazzucotelli E, Mastrangelo AM, Marone D. Genomic Approaches to Identify Molecular Bases of Crop Resistance to Diseases and to Develop Future Breeding Strategies. Int J Mol Sci 2021; 22:5423. [PMID: 34063853 PMCID: PMC8196592 DOI: 10.3390/ijms22115423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/30/2021] [Accepted: 05/15/2021] [Indexed: 12/16/2022] Open
Abstract
Plant diseases are responsible for substantial crop losses each year and affect food security and agricultural sustainability. The improvement of crop resistance to pathogens through breeding represents an environmentally sound method for managing disease and minimizing these losses. The challenge is to breed varieties with a stable and broad-spectrum resistance. Different approaches, from markers to recent genomic and 'post-genomic era' technologies, will be reviewed in order to contribute to a better understanding of the complexity of host-pathogen interactions and genes, including those with small phenotypic effects and mechanisms that underlie resistance. An efficient combination of these approaches is herein proposed as the basis to develop a successful breeding strategy to obtain resistant crop varieties that yield higher in increasing disease scenarios.
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Affiliation(s)
- Antonia Mores
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Grazia Maria Borrelli
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giovanni Laidò
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giuseppe Petruzzino
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | | | - Francesca Desiderio
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Daniela Marone
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
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179
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Ahmadi N, Ramanantsoanirina A, Santos JD, Frouin J, Radanielina T. Evolutionary Processes Involved in the Emergence and Expansion of an Atypical O. sativa Group in Madagascar. RICE (NEW YORK, N.Y.) 2021; 14:44. [PMID: 34014423 PMCID: PMC8137759 DOI: 10.1186/s12284-021-00479-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Understanding crops genetic diversity and the evolutionary processes that accompanied their worldwide spread is useful for designing effective breeding strategies. Madagascar Island was one of the last major Old World areas where human settlement brought the introduction of Oryza sativa. Early studies in the island had reported the presence of a rice group specific to Madagascar. Using 24 K SNP, we compared diversity patterns at the whole genome and at haplotype (30 SNP-long segments along the genome) levels, between 620 Malagasy and 1929 Asian rice accessions. The haplotype level analysis aimed at identifying local genotypic variations, relative to the whole genome level, using a group assignment method that relies on kernel density estimation in a Principal Component Analysis feature space. Migration bottleneck had resulted in 10-25% reduction of diversity among the Malagasy representatives of indica and japonica populations. Compared to their Asian counterpart, they showed slightly lower indica and japonica introgressions, suggesting the two populations had undergone less recombination when migration to the island occurred. The origins of the Malagasy indica and japonica groups were delineated to indica subpopulation from the Indian subcontinent and to tropical japonica from the Malay Archipelago, respectively. The Malagasy-specific group (Gm) had a rather high gene diversity and an original haplotype pattern: much lower share of indica haplotypes, and much higher share of Aus and japonica haplotypes than indica. Its emergence and expansion are most probably due to inter-group recombination facilitated by sympatry between indica-Aus admixes and "Bulu" type landraces of japonica in the central high plateaux of Madagascar, and to human selection for adaptation to the lowland rice cultivation. Pattern of rice genetic diversity was also tightly associated with the history of human settlement in the island. Emergence of the Gm group is associated with the latest arrivals of Austronesians, who founded the Merina kingdom in the high plateaux and developed lowland rice cultivation. As an intermediary form between Aus, indica and japonica, the three pillars of O. sativa domestication, Gm represents a very valuable genetic resource in breeding for adaptation to cold tolerance in tropical highlands. We proposed the name Rojo for this new rice group.
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Affiliation(s)
- Nourollah Ahmadi
- CIRAD, UMR AGAP, TA-A 108/03, Avenue Agropolis, F-34398, Montpellier Cedex 5, France.
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
| | | | - João D Santos
- CIRAD, UMR AGAP, TA-A 108/03, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
| | - Julien Frouin
- CIRAD, UMR AGAP, TA-A 108/03, Avenue Agropolis, F-34398, Montpellier Cedex 5, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Tendro Radanielina
- Université de Antananarivo, département de biologie et écologie végétale, Antananarivo, Madagascar
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180
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Selvaraj R, Singh AK, Singh VK, Abbai R, Habde SV, Singh UM, Kumar A. Superior haplotypes towards development of low glycemic index rice with preferred grain and cooking quality. Sci Rep 2021; 11:10082. [PMID: 33980871 PMCID: PMC8115083 DOI: 10.1038/s41598-021-87964-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/19/2021] [Indexed: 02/03/2023] Open
Abstract
Increasing trends in the occurrence of diabetes underline the need to develop low glycemic index (GI) rice with preferred grain quality. In the current study, a diverse set of 3 K sub-panel of rice consisting of 150 accessions was evaluated for resistant starch and predicted glycemic index, including nine other quality traits under transplanted situation. Significant variations were noticed among the accessions for the traits evaluated. Trait associations had shown that amylose content possess significant positive and negative association with resistant starch and predicted glycemic index. Genome-wide association studies with 500 K SNPs based on MLM model resulted in a total of 41 marker-trait associations (MTAs), which were further confirmed and validated with mrMLM multi-locus model. We have also determined the allelic effect of identified MTAs for 11 targeted traits and found favorable SNPs for 8 traits. A total of 11 genes were selected for haplo-pheno analysis to identify the superior haplotypes for the target traits where haplotypes ranges from 2 (Os10g0469000-GC) to 15 (Os06g18720-AC). Superior haplotypes for RS and PGI, the candidate gene Os06g11100 (H4-3.28% for high RS) and Os08g12590 (H13-62.52 as intermediate PGI). The identified superior donors possessing superior haplotype combinations may be utilized in Haplotype-based breeding to developing next-generation tailor-made high quality healthier rice varieties suiting consumer preference and market demand.
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Affiliation(s)
- Ramchander Selvaraj
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Arun Kumar Singh
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Vikas Kumar Singh
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Ragavendran Abbai
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Sonali Vijay Habde
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India
| | - Uma Maheshwar Singh
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India
| | - Arvind Kumar
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India.
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India.
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181
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Lou G, Chen P, Zhou H, Li P, Xiong J, Wan S, Zheng Y, Alam M, Liu R, Zhou Y, Yang H, Tian Y, Bai J, Rao W, Tan X, Gao H, Li Y, Gao G, Zhang Q, Li X, Liu C, He Y. FLOURY ENDOSPERM19 encoding a class I glutamine amidotransferase affects grain quality in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:36. [PMID: 37309330 PMCID: PMC10236042 DOI: 10.1007/s11032-021-01226-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/27/2021] [Indexed: 06/14/2023]
Abstract
As a staple food for more than half of the world's population, the importance of rice is self-evident. Compared with ordinary rice, rice cultivars with superior eating quality and appearance quality are more popular with consumers due to their unique taste and ornamental value, even if their price is much higher. Appearance quality and CEQ (cooking and eating quality) are two very important aspects in the evaluation of rice quality. Here, we performed a genome-wide association study on floury endosperm in a diverse panel of 533 cultivated rice accessions. We identified a batch of potential floury genes and prioritize one (LOC_Os03g48060) for functional analyses. Two floury outer endosperm mutants (flo19-1 and flo19-2) were generated through editing LOC_Os03g48060 (named as FLO19 in this study), which encodes a class I glutamine amidotransferase. The different performances of the two mutants in various storage substances directly led to completely different changes in CEQ. The mutation of FLO19 gene caused the damage of carbon and nitrogen metabolism in rice, which affected the normal growth and development of rice, including decreased plant height and yield loss by decreased grain filling rate. Through haplotype analysis, we identified a haplotype of FLO19 that can improve both CEQ and appearance quality of rice, Hap2, which provides a selection target for rice quality improvement, especially for high-yield indica rice varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01226-z.
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Affiliation(s)
- Guangming Lou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Pingli Chen
- Guangdong Key Laboratory of New Technology in Rice Breeding, The Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Hao Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Pingbo Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Jiawang Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Shanshan Wan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yuanyuan Zheng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Mufid Alam
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Rongjia Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yin Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Hanyuan Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yahong Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Jingjing Bai
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Wenting Rao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xuan Tan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Haozhou Gao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yanhua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Chuanguang Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, The Rice Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
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182
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Yu H, Du Q, Campbell M, Yu B, Walia H, Zhang C. Genome-wide discovery of natural variation in pre-mRNA splicing and prioritising causal alternative splicing to salt stress response in rice. THE NEW PHYTOLOGIST 2021; 230:1273-1287. [PMID: 33453070 PMCID: PMC8048671 DOI: 10.1111/nph.17189] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/04/2021] [Indexed: 05/14/2023]
Abstract
Pre-mRNA splicing is an essential step for the regulation of gene expression. In order to specifically capture splicing variants in plants for genome-wide association studies (GWAS), we developed a software tool to quantify and visualise Variations of Splicing in Population (VaSP). VaSP can quantify splicing variants from short-read RNA-seq datasets and discover genotype-specific splicing (GSS) events, which can be used to prioritise causal pre-mRNA splicing events in GWAS. We applied our method to an RNA-seq dataset with 328 samples from 82 genotypes from a rice diversity panel exposed to optimal and saline growing conditions. In total, 764 significant GSS events were identified in salt stress conditions. GSS events were used as markers for a GWAS with the shoot Na+ accumulation, which identified six GSS events in five genes significantly associated with the shoot Na+ content. Two of these genes, OsNUC1 and OsRAD23 emerged as top candidate genes with splice variants that exhibited significant divergence between the variants for shoot growth under salt stress conditions. VaSP is a versatile tool for alternative splicing analysis in plants and a powerful tool for prioritising candidate causal pre-mRNA splicing and corresponding genomic variations in GWAS.
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Affiliation(s)
- Huihui Yu
- School of Biological SciencesUniversity of NebraskaLincolnNE68588USA
| | - Qian Du
- School of Biological SciencesUniversity of NebraskaLincolnNE68588USA
| | - Malachy Campbell
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNE68583USA
- Department of Plant BiologyCornell UniversityIthacaNY14850USA
| | - Bin Yu
- School of Biological SciencesUniversity of NebraskaLincolnNE68588USA
- Center for Plant Science and InnovationUniversity of NebraskaLincolnNE68588USA
| | - Harkamal Walia
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNE68583USA
- Center for Plant Science and InnovationUniversity of NebraskaLincolnNE68588USA
| | - Chi Zhang
- School of Biological SciencesUniversity of NebraskaLincolnNE68588USA
- Center for Plant Science and InnovationUniversity of NebraskaLincolnNE68588USA
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183
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Zhang J, Liu F, Reif JC, Jiang Y. On the use of GBLUP and its extension for GWAS with additive and epistatic effects. G3-GENES GENOMES GENETICS 2021; 11:6237487. [PMID: 33871030 PMCID: PMC8495923 DOI: 10.1093/g3journal/jkab122] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/04/2021] [Indexed: 11/29/2022]
Abstract
Genomic best linear unbiased prediction (GBLUP) is the most widely used model for genome-wide predictions. Interestingly, it is also possible to perform genome-wide association studies (GWAS) based on GBLUP. Although the estimated marker effects in GBLUP are shrunken and the conventional test based on such effects has low power, it was observed that a modified test statistic can be produced and the result of test was identical to a standard GWAS model. Later, a mathematical proof was given for the special case that there is no fixed covariate in GBLUP. Since then, the new approach has been called “GWAS by GBLUP”. Nevertheless, covariates such as environmental and subpopulation effects are very common in GBLUP. Thus, it is necessary to confirm the equivalence in the general case. Recently, the concept was generalized to GWAS for epistatic effects and the new approach was termed rapid epistatic mixed-model association analysis (REMMA) because it greatly improved the computational efficiency. However, the relationship between REMMA and the standard GWAS model has not been investigated. In this study, we first provided a general mathematical proof of the equivalence between “GWAS by GBLUP” and the standard GWAS model for additive effects. Then, we compared REMMA with the standard GWAS model for epistatic effects by a theoretical investigation and by empirical data analyses. We hypothesized that the similarity of the two models is influenced by the relative contribution of additive and epistatic effects to the phenotypic variance, which was verified by empirical and simulation studies.
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Affiliation(s)
- Jie Zhang
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Stadt Seeland, Germany
| | - Fang Liu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Stadt Seeland, Germany
| | - Jochen C Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Stadt Seeland, Germany
| | - Yong Jiang
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Stadt Seeland, Germany
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Yadav AK, Kumar A, Grover N, Ellur RK, Bollinedi H, Krishnan SG, Bhowmick PK, Vinod KK, Nagarajan M, Singh AK. Genome-Wide Association Study Reveals Marker-Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice. PLANTS (BASEL, SWITZERLAND) 2021; 10:559. [PMID: 33809618 PMCID: PMC8000697 DOI: 10.3390/plants10030559] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 11/16/2022]
Abstract
Rice germplasm is a rich resource for discovering genes associated with salt tolerance. In the current study, a set of 96 accessions were evaluated for seedling stage salinity tolerance and its component traits. Significant phenotypic variation was observed among the genotypes for all the measured traits and eleven accessions with high level of salt tolerance at seedling stage were identified. The germplasm set comprised of three sub-populations and genome-wide association study (GWAS) identified a total of 23 marker-trait associations (MTAs) for traits studied. These MTAs were located on rice chromosomes 1, 2, 5, 6, 7, 9, and 12 and explained the trait phenotypic variances ranging from 13.98 to 29.88 %. Twenty-one MTAs identified in this study were located either in or near the previously reported quantitative trait loci (QTLs), while two MTAs namely, qSDW2.1 and qSNC5 were novel. A total of 18 and 13 putative annotated candidate genes were identified in a genomic region spanning ~200 kb around the MTAs qSDW2.1 and qSNC5, respectively. Some of the important genes underlying the novel MTAs were OsFBA1,OsFBL7, and mTERF which are known to be associated with salinity tolerance in crops. These MTAs pave way for combining salinity tolerance with high yield in rice genotypes through molecular breeding.
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Affiliation(s)
- Ashutosh Kumar Yadav
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
- Amity Institute of Biotechnology, Amity University, Noida 201303, India;
| | - Aruna Kumar
- Amity Institute of Biotechnology, Amity University, Noida 201303, India;
| | - Nitasha Grover
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Ranjith Kumar Ellur
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Haritha Bollinedi
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Subbaiyan Gopala Krishnan
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Prolay Kumar Bhowmick
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Kunnummal Kurungara Vinod
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
| | - Mariappan Nagarajan
- Rice Breeding and Genetics Research Centre, ICAR—Indian Agricultural Research Institute, Aduthurai 612101, Tamil Nadu, India;
| | - Ashok Kumar Singh
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.Y.); (N.G.); (R.K.E.); (H.B.); (S.G.K.); (P.K.B.); (K.K.V.)
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185
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Liu Q, Lan G, Zhu Y, Chen K, Shen C, Zhao X, Zhang F, Xu J, Li Z. Genome-Wide Association Study on Resistance to Rice Black-Streaked Dwarf Disease Caused by Rice black-streaked dwarf virus. PLANT DISEASE 2021; 105:607-615. [PMID: 32830595 DOI: 10.1094/pdis-10-19-2263-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Rice black-streaked dwarf disease caused by Rice black-streaked dwarf virus (RBSDV) is one of the most destructive viral diseases of rice. Thus, it is imperative that resistant rice germplasms are screened for novel RBSDV-resistant genes. RBSDV resistance of a diverse global collection comprising 1,953 rice accessions was evaluated under natural conditions across 3 years. The average disease incidences of the Xian/indica (XI) subgroup were significantly lower than those of the Geng/japonica (GJ) subgroup. Interestingly, most XI-1A accessions in the Xian subgroup were significantly more susceptible than XI-1B accessions, even though XI-1A and XI-1B have a close phylogenetic relationship. Four Xian accessions stably and highly resistant to RBSDV were consistently identified in 2 years. Ten genomic regions (GRs) with 147 single nucleotide polymorphisms associated with RBSDV resistance were detected by a single-locus genome-wide association study (GWAS), of which five were repeatedly identified in a multilocus GWAS. Two previously reported GRs, grRBSDV-6.1 and grRBSDV-6.3, which were repeatedly detected as stably and highly associated with RBSDV resistance, contained 17 and seven genes, respectively, with significant differences of resistance among haplotypes. Haplotype analyses of the candidate genes LOC_Os06g03150 in grRBSDV-6.1 and LOC_Os06g31190 in grRBSDV-6.3 suggested that the former gene is mainly associated with the differentiation of resistance within the Xian subgroup and the latter gene mainly explains the difference in the resistance between Xian and Geng. Another three novel resistance GRs (grRBSDV-1.1, grRBSDV-7.1, and grRBSDV-9.1) were identified. Our findings may enhance the application of disease-resistant rice germplasms for breeding RBSDV-resistant varieties.
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Affiliation(s)
- Qing Liu
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guofang Lan
- Key Laboratory of Plant Functional Genomics of Ministry of Education/College of Bioscience and Biotechnology, Yangzhou University, 225009 Yangzhou, China
- Changshu Institute of Agricultural Science, Changshu 215500, China
| | - Yajun Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Kai Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Congcong Shen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiuqin Zhao
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fan Zhang
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianlong Xu
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhikang Li
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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186
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Pawar S, Pandit E, Mohanty IC, Saha D, Pradhan SK. Population genetic structure and association mapping for iron toxicity tolerance in rice. PLoS One 2021; 16:e0246232. [PMID: 33647046 PMCID: PMC7920388 DOI: 10.1371/journal.pone.0246232] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 11/11/2020] [Indexed: 02/01/2023] Open
Abstract
Iron (Fe) toxicity is a major abiotic stress which severely reduces rice yield in many countries of the world. Genetic variation for this stress tolerance exists in rice germplasms. Mapping of gene(s)/QTL controlling the stress tolerance and transfer of the traits into high yielding rice varieties are essential for improvement against the stress. A panel population of 119 genotypes from 352 germplasm lines was constituted for detecting the candidate gene(s)/QTL through association mapping. STRUCTURE, GenAlEx and Darwin softwares were used to classify the population. The marker-trait association was detected by considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) analyses. Wide genetic variation was observed among the genotypes present in the panel population for the stress tolerance. Linkage disequilibrium was detected in the population for iron toxicity tolerance. The population was categorized into three genetic structure groups. Marker-trait association study considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) showed significant association of leaf browning index (LBI) with markers RM471, RM3, RM590 and RM243. Three novel QTL controlling Fe-toxicity tolerance were detected and designated as qFeTox4.3, qFeTox6.1 and qFeTox10.1. A QTL reported earlier in the marker interval of C955-C885 on chromosome 1 is validated using this panel population. The present study showed that QTL controlling Fe-toxicity tolerance to be co-localized with the QTL for Fe-biofortification of rice grain indicating involvement of common pathway for Fe toxicity tolerance and Fe content in rice grain. Fe-toxicity tolerance QTL qFeTox6.1 was co-localized with grain Fe-biofortification QTLs qFe6.1 and qFe6.2 on chromosome 6, whereas qFeTox10.1 was co-localized with qFe10.1 on chromosome 10. The Fe-toxicity tolerance QTL detected from this mapping study will be useful in marker-assisted breeding programs.
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Affiliation(s)
- S. Pawar
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - E. Pandit
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India
- Department of Bio-Science and Bio-Technology, Fakir Mohan University, Balasore, Odisha, India
| | - I. C. Mohanty
- Department of Biotechnology, College of Agriculture, OUAT, Bhubaneswar, Odisha, India
| | - D. Saha
- Department of Biotechnology, College of Agriculture, OUAT, Bhubaneswar, Odisha, India
| | - S. K. Pradhan
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India
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187
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Lu J, Wang C, Zeng D, Li J, Shi X, Shi Y, Zhou Y. Genome-Wide Association Study Dissects Resistance Loci against Bacterial Blight in a Diverse Rice Panel from the 3000 Rice Genomes Project. RICE (NEW YORK, N.Y.) 2021; 14:22. [PMID: 33638765 PMCID: PMC7914325 DOI: 10.1186/s12284-021-00462-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 02/12/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastating bacterial diseases of rice in temperate and tropical regions. Breeding and deployment of resistant cultivars carrying major resistance (R) genes has been the most effective approach for BB management. However, because of specific interaction of each R gene with the product of the corresponding pathogen avirulence or effector gene, new pathogen strains that can overcome the deployed resistance often emerge rapidly. To deal with ever-evolving Xoo, it is necessary to identify novel R genes and resistance quantitative trait loci (QTL). RESULTS BB resistance of a diverse panel of 340 accessions from the 3000 Rice Genomes Project (3 K RGP) was evaluated by artificial inoculation with four representative Xoo strains, namely Z173 (C4), GD1358 (C5), V from China and PXO339 (P9a) from Philippines. Using the 3 K RG 4.8mio filtered SNP Dataset, a total of 11 QTL associated with BB resistance on chromosomes 4, 5, 11 and 12 were identified through a genome-wide association study (GWAS). Among them, eight resistance loci, which were narrowed down to relatively small genomic intervals, coincided with previously reported QTL or R genes, e.g. xa5, xa25, xa44(t). The other three QTL were putative novel loci associated with BB resistance. Linear regression analysis showed a dependence of BB lesion length on the number of favorable alleles, suggesting that pyramiding QTL using marker-assisted selection would be an effective approach for improving resistance. In addition, the Hap2 allele of LOC_Os11g46250 underlying qC5-11.1 was validated as positively regulating resistance against strain C5. CONCLUSIONS Our findings provide valuable information for the genetic improvement of BB resistance and application of germplasm resources in rice breeding programs.
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Affiliation(s)
- Jialing Lu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Chunchao Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Dan Zeng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jianmin Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiaorong Shi
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 China
| | - Yongli Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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188
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Zhao J, Yang B, Li W, Sun S, Peng L, Feng D, Li L, Di H, He Y, Wang Z. A genome-wide association study reveals that the glucosyltransferase OsIAGLU regulates root growth in rice. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1119-1134. [PMID: 33130882 DOI: 10.1093/jxb/eraa512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/26/2020] [Indexed: 05/18/2023]
Abstract
Good root growth in the early post-germination stages is an important trait for direct seeding in rice, but its genetic control is poorly understood. In this study, we examined the genetic architecture of variation in primary root length using a diverse panel of 178 accessions. Four QTLs for root length (qRL3, qRL6, qRL7, and qRL11) were identified using genome-wide association studies. One candidate gene was validated for the major QTL qRL11, namely the glucosyltransferase OsIAGLU. Disruption of this gene in Osiaglu mutants reduced the primary root length and the numbers of lateral and crown roots. The natural allelic variations of OsIAGLU contributing to root growth were identified. Functional analysis revealed that OsIAGLU regulates root growth mainly via modulating multiple hormones in the roots, including levels of auxin, jasmonic acid, abscisic acid, and cytokinin. OsIAGLU also influences the expression of multiple hormone-related genes associated with root growth. The regulation of root growth through multiple hormone pathways by OsIAGLU makes it a potential target for future rice breeding for crop improvement.
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Affiliation(s)
- Jia Zhao
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Bin Yang
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, People's Republic of China
| | - Wenjun Li
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Shan Sun
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Liling Peng
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Defeng Feng
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Li Li
- Huzhou Agricultural Science and Technology Development Center, Huzhou, People's Republic of China
| | - Hong Di
- Northeast Agricultural University, Harbin, People's Republic of China
| | - Yongqi He
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, Guangdong Laboratory of Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, People's Republic of China
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189
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Frontini M, Boisnard A, Frouin J, Ouikene M, Morel JB, Ballini E. Genome-wide association of rice response to blast fungus identifies loci for robust resistance under high nitrogen. BMC PLANT BIOLOGY 2021; 21:99. [PMID: 33602120 PMCID: PMC7893971 DOI: 10.1186/s12870-021-02864-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 02/01/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND Nitrogen fertilization is known to increase disease susceptibility, a phenomenon called Nitrogen-Induced Susceptibility (NIS). In rice, this phenomenon has been observed in infections with the blast fungus Magnaporthe oryzae. A previous classical genetic study revealed a locus (NIS1) that enhances susceptibility to rice blast under high nitrogen fertilization. In order to further address the underlying genetics of plasticity in susceptibility to rice blast after fertilization, we analyzed NIS under greenhouse-controlled conditions in a panel of 139 temperate japonica rice strains. A genome-wide association analysis was conducted to identify loci potentially involved in NIS by comparing susceptibility loci identified under high and low nitrogen conditions, an approach allowing for the identification of loci validated across different nitrogen environments. We also used a novel NIS Index to identify loci potentially contributing to plasticity in susceptibility under different nitrogen fertilization regimes. RESULTS A global NIS effect was observed in the population, with the density of lesions increasing by 8%, on average, under high nitrogen fertilization. Three new QTL, other than NIS1, were identified. A rare allele of the RRobN1 locus on chromosome 6 provides robust resistance in high and low nitrogen environments. A frequent allele of the NIS2 locus, on chromosome 5, exacerbates blast susceptibility under the high nitrogen condition. Finally, an allele of NIS3, on chromosome 10, buffers the increase of susceptibility arising from nitrogen fertilization but increases global levels of susceptibility. This allele is almost fixed in temperate japonicas, as a probable consequence of genetic hitchhiking with a locus involved in cold stress adaptation. CONCLUSIONS Our results extend to an entire rice subspecies the initial finding that nitrogen increases rice blast susceptibility. We demonstrate the usefulness of estimating plasticity for the identification of novel loci involved in the response of rice to the blast fungus under different nitrogen regimes.
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Affiliation(s)
- Mathias Frontini
- BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Julien Frouin
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Malika Ouikene
- Groupe de Valorisation des Produits Agricoles (GVAPRO), Alger, Algeria
| | - Jean Benoit Morel
- BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Elsa Ballini
- BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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190
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Norton GJ, Travis A, Ruang-areerate P, Nicol GW, Adeosun AA, Hossain M, Islam MR, Douglas A, Price AH. Genetic loci regulating cadmium content in rice grains. EUPHYTICA: NETHERLANDS JOURNAL OF PLANT BREEDING 2021; 217:35. [PMID: 33627887 PMCID: PMC7875855 DOI: 10.1007/s10681-020-02752-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
UNLABELLED It has been estimated that up to 90% of human exposure to cadmium is through food, and that cadmium within rice grains can be a major contributor to that dietary source. In this study genome wide association mapping was conducted on the Bengal and Assam Aus Panel (BAAP) of rice to identify quantitative trait loci and candidate genes for lowering grain cadmium. Field experiments were conducted over two years under two different irrigation systems: continually flooded and alternate wetting and drying (AWD). There was significant effects of water treatment, genotype, and genotype by water treatment interaction. Importantly, AWD increased grain cadmium, on average, by 49.6% and 108.8% in year 1 and 2 respectively. There was between 4.6 and 28 fold variation in cadmium concentration. A total of 58 QTLs were detected but no loci are clearly specific to one water regime despite approximately 20% of variation attributable to genotype by water regime interaction. A number of QTLs were consistent across most water treatments and years. These included QTLs on chromosome 7 (7.23-7.61, 8.93-9.04, and 29.12-29.14 Mbp), chromosome 5 (8.66-8.72 Mbp), and chromosome 9 (11.46-11.64 Mbp). Further analysis of the loci on chromosome 7 (8.93-9.04 Mbp), identified the candidate gene OsNRAMP1, where cultivars with a deletion upstream of the gene had higher concentrations of cadmium compared to the cultivars that did not have the deletion. The distribution of alleles within the BAAP suggest this QTL is easily detected in this population because it is composed of aus cultivars. Local genome cluster analysis suggest high Cd alleles are uncommon, but should be avoided in breeding. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at (10.1007/s10681-020-02752-1).
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Affiliation(s)
- Gareth J. Norton
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU UK
| | - Anthony Travis
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU UK
| | - Panthita Ruang-areerate
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU UK
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120 Thailand
| | - Graeme W. Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue, 69134 Ecully Cedex, France
| | - Ayotunde A. Adeosun
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU UK
| | - Mahmud Hossain
- Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - M. Rafiq Islam
- Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Alex Douglas
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU UK
| | - Adam H. Price
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU UK
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191
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Wei X, Qiu J, Yong K, Fan J, Zhang Q, Hua H, Liu J, Wang Q, Olsen KM, Han B, Huang X. A quantitative genomics map of rice provides genetic insights and guides breeding. Nat Genet 2021; 53:243-253. [PMID: 33526925 DOI: 10.1038/s41588-020-00769-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 12/11/2020] [Indexed: 02/07/2023]
Abstract
Extensive allelic variation in agronomically important genes serves as the basis of rice breeding. Here, we present a comprehensive map of rice quantitative trait nucleotides (QTNs) and inferred QTN effects based on eight genome-wide association study cohorts. Population genetic analyses revealed that domestication, local adaptation and heterosis are all associated with QTN allele frequency changes. A genome navigation system, RiceNavi, was developed for QTN pyramiding and breeding route optimization, and implemented in the improvement of a widely cultivated indica variety. This work presents an efficient platform that bridges ever-increasing genomic knowledge and diverse improvement needs in rice.
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Affiliation(s)
- Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Kaicheng Yong
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jiongjiong Fan
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Qi Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Hua Hua
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jie Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Qin Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Kenneth M Olsen
- Department of Biology, Washington University in St Louis, St Louis, MO, USA
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.
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192
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Thudi M, Palakurthi R, Schnable JC, Chitikineni A, Dreisigacker S, Mace E, Srivastava RK, Satyavathi CT, Odeny D, Tiwari VK, Lam HM, Hong YB, Singh VK, Li G, Xu Y, Chen X, Kaila S, Nguyen H, Sivasankar S, Jackson SA, Close TJ, Shubo W, Varshney RK. Genomic resources in plant breeding for sustainable agriculture. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153351. [PMID: 33412425 PMCID: PMC7903322 DOI: 10.1016/j.jplph.2020.153351] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 05/19/2023]
Abstract
Climate change during the last 40 years has had a serious impact on agriculture and threatens global food and nutritional security. From over half a million plant species, cereals and legumes are the most important for food and nutritional security. Although systematic plant breeding has a relatively short history, conventional breeding coupled with advances in technology and crop management strategies has increased crop yields by 56 % globally between 1965-85, referred to as the Green Revolution. Nevertheless, increased demand for food, feed, fiber, and fuel necessitates the need to break existing yield barriers in many crop plants. In the first decade of the 21st century we witnessed rapid discovery, transformative technological development and declining costs of genomics technologies. In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants for climate resilience and global food security. In this review we focus on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic stress tolerant and high nutrition varieties in six major cereals (rice, maize, wheat, barley, sorghum and pearl millet), and six major legumes (soybean, groundnut, cowpea, common bean, chickpea and pigeonpea). We further provide a perspective and way forward to use genomic breeding approaches including marker-assisted selection, marker-assisted backcrossing, haplotype based breeding and genomic prediction approaches coupled with machine learning and artificial intelligence, to speed breeding approaches. The overall goal is to accelerate genetic gains and deliver climate resilient and high nutrition crop varieties for sustainable agriculture.
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Affiliation(s)
- Mahendar Thudi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; University of Southern Queensland, Toowoomba, Australia
| | - Ramesh Palakurthi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Emma Mace
- Agri-Science Queensland, Department of Agriculture & Fisheries (DAF), Warwick, Australia
| | - Rakesh K Srivastava
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - C Tara Satyavathi
- Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Damaris Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | | | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Yan Bin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Vikas K Singh
- South Asia Hub, International Rice Research Institute (IRRI), Hyderabad, India
| | - Guowei Li
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yunbi Xu
- International Maize and Wheat Improvement Center (CYMMIT), Mexico DF, Mexico; Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sanjay Kaila
- Department of Biotechnology, Ministry of Science and Technology, Government of India, India
| | - Henry Nguyen
- National Centre for Soybean Research, University of Missouri, Columbia, USA
| | - Sobhana Sivasankar
- Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | | | | | - Wan Shubo
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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Zhu F, Paul P, Hussain W, Wallman K, Dhatt BK, Sandhu J, Irvin L, Morota G, Yu H, Walia H. SeedExtractor: An Open-Source GUI for Seed Image Analysis. FRONTIERS IN PLANT SCIENCE 2021; 11:581546. [PMID: 33597957 PMCID: PMC7882627 DOI: 10.3389/fpls.2020.581546] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Accurate measurement of seed size parameters is essential for both breeding efforts aimed at enhancing yields and basic research focused on discovering genetic components that regulate seed size. To address this need, we have developed an open-source graphical user interface (GUI) software, SeedExtractor that determines seed size and shape (including area, perimeter, length, width, circularity, and centroid), and seed color with capability to process a large number of images in a time-efficient manner. In this context, our application takes ∼2 s for analyzing an image, i.e., significantly less compared to the other tools. As this software is open-source, it can be modified by users to serve more specific needs. The adaptability of SeedExtractor was demonstrated by analyzing scanned seeds from multiple crops. We further validated the utility of this application by analyzing mature-rice seeds from 231 accessions in Rice Diversity Panel 1. The derived seed-size traits, such as seed length, width, were used for genome-wide association analysis. We identified known loci for regulating seed length (GS3) and width (qSW5/GW5) in rice, which demonstrates the accuracy of this application to extract seed phenotypes and accelerate trait discovery. In summary, we present a publicly available application that can be used to determine key yield-related traits in crops.
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Affiliation(s)
- Feiyu Zhu
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Waseem Hussain
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Kyle Wallman
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Balpreet K. Dhatt
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Jaspreet Sandhu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Larissa Irvin
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Gota Morota
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Hongfeng Yu
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
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194
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Gao Y, Yang Z, Yang W, Yang Y, Gong J, Yang QY, Niu X. Plant-ImputeDB: an integrated multiple plant reference panel database for genotype imputation. Nucleic Acids Res 2021; 49:D1480-D1488. [PMID: 33137192 PMCID: PMC7779032 DOI: 10.1093/nar/gkaa953] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/23/2020] [Accepted: 10/08/2020] [Indexed: 12/21/2022] Open
Abstract
Genotype imputation is a process that estimates missing genotypes in terms of the haplotypes and genotypes in a reference panel. It can effectively increase the density of single nucleotide polymorphisms (SNPs), boost the power to identify genetic association and promote the combination of genetic studies. However, there has been a lack of high-quality reference panels for most plants, which greatly hinders the application of genotype imputation. Here, we developed Plant-ImputeDB (http://gong_lab.hzau.edu.cn/Plant_imputeDB/), a comprehensive database with reference panels of 12 plant species for online genotype imputation, SNP and block search and free download. By integrating genotype data and whole-genome resequencing data of plants from various studies and databases, the current Plant-ImputeDB provides high-quality reference panels of 12 plant species, including ∼69.9 million SNPs from 34 244 samples. It also provides an easy-to-use online tool with the option of two popular tools specifically designed for genotype imputation. In addition, Plant-ImputeDB accepts submissions of different types of genomic variations, and provides free and open access to all publicly available data in support of related research worldwide. In general, Plant-ImputeDB may serve as an important resource for plant genotype imputation and greatly facilitate the research on plant genetic research.
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Affiliation(s)
- Yingjie Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Zhiquan Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Wenqian Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Yanbo Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Jing Gong
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China.,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Qing-Yong Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China.,College of Agriculture, Shihezi University, Xinjiang 832003, P.R. China
| | - Xiaohui Niu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
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195
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Lin YL, Wu DH, Wu CC, Huang YF. Explore the genetics of weedy traits using rice 3K database. BOTANICAL STUDIES 2021; 62:2. [PMID: 33432466 PMCID: PMC7801593 DOI: 10.1186/s40529-020-00309-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Weedy rice, a conspecific weedy counterpart of the cultivated rice (Oryza sativa L.), has been problematic in rice-production area worldwide. Although we started to know about the origin of some weedy traits for some rice-growing regions, an overall assessment of weedy trait-related loci was not yet available. On the other hand, the advances in sequencing technologies, together with community efforts, have made publicly available a large amount of genomic data. Given the availability of public data and the need of "weedy" allele mining for a better management of weedy rice, the objective of the present study was to explore the genetic architecture of weedy traits based on publicly available data, mainly from the 3000 Rice Genome Project (3K-RGP). RESULTS Based on the results of population structure analysis, we have selected 1378 individuals from four sub-populations (aus, indica, temperate japonica, tropical japonica) without admixed genomic composition for genome-wide association analysis (GWAS). Five traits were investigated: awn color, seed shattering, seed threshability, seed coat color, and seedling height. GWAS was conducted for each sub-population × trait combination and we have identified 66 population-specific trait-associated SNPs. Eleven significant SNPs fell into an annotated gene and four other SNPs were close to a putative candidate gene (± 25 kb). SNPs located in or close to Rc were particularly predictive of the occurrence of seed coat color and our results showed that different sub-populations required different SNPs for a better seed coat color prediction. We compared the data of 3K-RGP to a publicly available weedy rice dataset. The profile of allele frequency, phenotype-genotype segregation of target SNP, as well as GWAS results for the presence and absence of awns diverged between the two sets of data. CONCLUSIONS The genotype of trait-associated SNPs identified in this study, especially those located in or close to Rc, can be developed to diagnostic SNPs to trace the origin of weedy trait occurred in the field. The difference of results from the two publicly available datasets used in this study emphasized the importance of laboratory experiments to confirm the allele mining results based on publicly available data.
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Affiliation(s)
- Yu-Lan Lin
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Da'an Dist., Taipei, 10617, Taiwan
| | - Dong-Hong Wu
- Taiwan Agricultural Research Institute, Council of Agriculture, Executive Yuan, No. 189, Zhongzheng Rd, Wufeng Dist, Taichung City, 41362, Taiwan
| | - Cheng-Chieh Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Institute of Plant Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Da'an Dist., Taipei, 10617, Taiwan
| | - Yung-Fen Huang
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Da'an Dist., Taipei, 10617, Taiwan.
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196
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Wambugu PW, Ndjiondjop MN, Henry R. Genetics and Genomics of African Rice (Oryza glaberrima Steud) Domestication. RICE (NEW YORK, N.Y.) 2021; 14:6. [PMID: 33415579 PMCID: PMC7790969 DOI: 10.1186/s12284-020-00449-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
African rice (Oryza glaberrima Steud) is one of the two independently domesticated rice species, the other one being Asian rice (Oryza sativa L.). Despite major progress being made in understanding the evolutionary and domestication history of African rice, key outstanding issues remain controversial. There appears to be an underlying difficulty in identifying the domestication centre and number of times the crop has been domesticated. Advances in genomics have provided unprecedented opportunities for understanding the genetic architecture of domestication related traits. For most of the domestication traits, the underlying genes and mutations have been identified. Comparative analysis of domestication genes between Asian and African rice has revealed that the two species went through an independent but convergent evolution process. The genetic and developmental basis of some of the domestic traits are conserved not only between Asian and African rice but also with other domesticated crop species. Analysis of genome data and its interpretation is emerging as a major challenge facing studies of domestication in African rice as key studies continue giving contradictory findings and conclusions. Insights obtained on the domestication of this species are vital for guiding crop improvement efforts.
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Affiliation(s)
- Peterson W. Wambugu
- Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, P.O. Box 30148, Nairobi, 00100 Kenya
| | - Marie-Noelle Ndjiondjop
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551 Bouaké 01, Côte d’Ivoire
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia
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197
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Su L, Yang J, Li D, Peng Z, Xia A, Yang M, Luo L, Huang C, Wang J, Wang H, Chen Z, Guo T. Dynamic genome-wide association analysis and identification of candidate genes involved in anaerobic germination tolerance in rice. RICE (NEW YORK, N.Y.) 2021; 14:1. [PMID: 33409869 PMCID: PMC7788155 DOI: 10.1186/s12284-020-00444-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 12/06/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND In Asian rice production, an increasing number of countries now choose the direct seeding mode because of rising costs, labour shortages and water shortages. The ability of rice seeds to undergo anaerobic germination (AG) plays an important role in the success of direct seeding. RESULTS In this study, we used 2,123,725 single nucleotide polymorphism (SNP) markers based on resequencing to conduct a dynamic genome-wide association study (GWAS) of coleoptile length (CL) and coleoptile diameter (CD) in 209 natural rice populations. A total of 26 SNP loci were detected in these two phenotypes, of which 5 overlapped with previously reported loci (S1_ 39674301, S6_ 20797781, S7_ 18722403, S8_ 9946213, S11_ 19165397), and two sites were detected repeatedly at different time points (S3_ 24689629 and S5_ 27918754). We suggest that these 7 loci (-log10 (P) value > 7.3271) are the key sites that affect AG tolerance. To screen the candidate genes more effectively, we sequenced the transcriptome of the flooding-tolerant variety R151 in six key stages, including anaerobic (AN) and the oxygen conversion point (AN-A), and obtained high-quality differential expression profiles. Four reliable candidate genes were identified: Os01g0911700 (OsVP1), Os05g0560900 (OsGA2ox8), Os05g0562200 (OsDi19-1) and Os06g0548200. Then qRT-PCR and LC-MS/ MS targeting metabolite detection technology were used to further verify that the up-regulated expression of these four candidate genes was closely related to AG. CONCLUSION The four novel candidate genes were associated with gibberellin (GA) and abscisic acid (ABA) regulation and cell wall metabolism under oxygen-deficiency conditions and promoted coleoptile elongation while avoiding adverse effects, allowing the coleoptile to obtain oxygen, escape the low-oxygen environment and germinate rapidly. The results of this study improve our understanding of the genetic basis of AG in rice seeds, which is conducive to the selection of flooding-tolerant varieties suitable for direct seeding.
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Affiliation(s)
- Ling Su
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Jing Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Dandan Li
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Ziai Peng
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Aoyun Xia
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Meng Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Lixin Luo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Cuihong Huang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Jiafeng Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642 China
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198
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Mandozai A, Moussa AA, Zhang Q, Qu J, Du Y, Anwari G, Al Amin N, Wang P. Genome-Wide Association Study of Root and Shoot Related Traits in Spring Soybean ( Glycine max L.) at Seedling Stages Using SLAF-Seq. FRONTIERS IN PLANT SCIENCE 2021; 12:568995. [PMID: 34394134 PMCID: PMC8355526 DOI: 10.3389/fpls.2021.568995] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/08/2021] [Indexed: 05/19/2023]
Abstract
Root systems can display variable genetic architectures leading to nutrient foraging or improving abiotic stress tolerance. Breeding for new soybean varieties with efficient root systems has tremendous potential in enhancing resource use efficiency and plant adaptation for challenging climates. In this study, root related traits were analyzed in a panel of 260 spring soybean with genome-wide association study (GWAS). Genotyping was done with specific locus amplified fragment sequencing (SLAF-seq), and five GWAS models (GLM, MLM, CMLM, FaST-LMM, and EMMAX) were used for analysis. A total of 179,960 highly consistent SNP markers distributed over the entire genome with an inter-marker distance of 2.36 kb was used for GWAS analysis. Overall, 27 significant SNPs with a phenotypic contribution ranging from 20 to 72% and distributed on chromosomes 2, 6, 8, 9, 13, 16 and 18 were identified and two of them were found to be associated with multiple root-related traits. Based on the linkage disequilibrium (LD) distance of 9.5 kb for the different chromosomes, 11 root and shoot regulating genes were detected based on LD region of a maximum 55-bp and phenotypic contribution greater than 22%. Expression analysis revealed an association between expression levels of those genes and the degree of root branching number. The current study provides new insights into the genetic architecture of soybean roots, and the underlying SNPs/genes could be critical for future breeding of high-efficient root system in soybean.
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199
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Al-Tamimi N, Oakey H, Tester M, Negrão S. Assessing Rice Salinity Tolerance: From Phenomics to Association Mapping. Methods Mol Biol 2021; 2238:339-375. [PMID: 33471343 DOI: 10.1007/978-1-0716-1068-8_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rice is the most salt-sensitive cereal, suffering yield losses above 50% with soil salinity of 6 dS/m. Thus, understanding the mechanisms of rice salinity tolerance is key to address food security. In this chapter, we provide guidelines to assess rice salinity tolerance using a high-throughput phenotyping platform (HTP) with digital imaging at seedling/early tillering stage and suggest improved analysis methods using stress indices. The protocols described here also include computer scripts for users to improve their experimental design, run genome-wide association studies (GWAS), perform multi-testing corrections, and obtain the Manhattan plots, enabling the identification of loci associated with salinity tolerance. Notably, the computer scripts provided here can be used for any stress or GWAS experiment and independently of HTP.
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Affiliation(s)
- Nadia Al-Tamimi
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena Oakey
- School of Agriculture Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Mark Tester
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sónia Negrão
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
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200
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Yadav CB, Tokas J, Yadav D, Winters A, Singh RB, Yadav R, Gangashetty PI, Srivastava RK, Yadav RS. Identifying Anti-Oxidant Biosynthesis Genes in Pearl Millet [ Pennisetum glaucum (L.) R. Br.] Using Genome-Wide Association Analysis. FRONTIERS IN PLANT SCIENCE 2021; 12:599649. [PMID: 34122460 PMCID: PMC8194398 DOI: 10.3389/fpls.2021.599649] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 04/19/2021] [Indexed: 05/05/2023]
Abstract
Pearl millet [Pennisetum glaucum (L.) R Br.] is an important staple food crop in the semi-arid tropics of Asia and Africa. It is a cereal grain that has the prospect to be used as a substitute for wheat flour for celiac patients. It is an important antioxidant food resource present with a wide range of phenolic compounds that are good sources of natural antioxidants. The present study aimed to identify the total antioxidant content of pearl millet flour and apply it to evaluate the antioxidant activity of its 222 genotypes drawn randomly from the pearl millet inbred germplasm association panel (PMiGAP), a world diversity panel of this crop. The total phenolic content (TPC) significantly correlated with DPPH (1,1-diphenyl-2-picrylhydrazyl) radical scavenging activity (% inhibition), which ranged from 2.32 to 112.45% and ferric-reducing antioxidant power (FRAP) activity ranging from 21.68 to 179.66 (mg ascorbic acid eq./100 g). Genome-wide association studies (GWAS) were conducted using 222 diverse accessions and 67 K SNPs distributed across all the seven pearl millet chromosomes. Approximately, 218 SNPs were found to be strongly associated with DPPH and FRAP activity at high confidence [-log (p) > 3.0-7.4]. Furthermore, flanking regions of significantly associated SNPs were explored for candidate gene harvesting. This identified 18 candidate genes related to antioxidant pathway genes (flavanone 7-O-beta-glycosyltransferase, GDSL esterase/lipase, glutathione S-transferase) residing within or near the association signal that can be selected for further functional characterization. Patterns of genetic variability and the associated genes reported in this study are useful findings, which would need further validation before their utilization in molecular breeding for high antioxidant-containing pearl millet cultivars.
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Affiliation(s)
- Chandra Bhan Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Jayanti Tokas
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Devvart Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Ana Winters
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Ram B. Singh
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Rama Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | | | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Rattan S. Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- *Correspondence: Rattan S. Yadav
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