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Yu H, Xie W, Li J, Zhou F, Zhang Q. A whole-genome SNP array (RICE6K) for genomic breeding in rice. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:28-37. [PMID: 24034357 DOI: 10.1111/pbi.12113] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 07/25/2013] [Accepted: 07/30/2013] [Indexed: 05/19/2023]
Abstract
The advances in genotyping technology provide an opportunity to use genomic tools in crop breeding. As compared to field selections performed in conventional breeding programmes, genomics-based genotype screen can potentially reduce number of breeding cycles and more precisely integrate target genes for particular traits into an ideal genetic background. We developed a whole-genome single nucleotide polymorphism (SNP) array, RICE6K, based on Infinium technology, using representative SNPs selected from more than four million SNPs identified from resequencing data of more than 500 rice landraces. RICE6K contains 5102 SNP and insertion-deletion (InDel) markers, about 4500 of which were of high quality in the tested rice lines producing highly repeatable results. Forty-five functional markers that are located inside 28 characterized genes of important traits can be detected using RICE6K. The SNP markers are evenly distributed on the 12 chromosomes of rice with the average density of 12 SNPs per 1 Mb and can provide information for polymorphisms between indica and japonica subspecies as well as varieties within indica and japonica groups. Application tests of RICE6K showed that the array is suitable for rice germplasm fingerprinting, genotyping bulked segregating pools, seed authenticity check and genetic background selection. These results suggest that RICE6K provides an efficient and reliable genotyping tool for rice genomic breeding.
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Affiliation(s)
- Huihui Yu
- Life Science and Technology Center, China National Seed Group Co., Ltd, Wuhan, China
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202
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Norton GJ, Douglas A, Lahner B, Yakubova E, Guerinot ML, Pinson SRM, Tarpley L, Eizenga GC, McGrath SP, Zhao FJ, Islam MR, Islam S, Duan G, Zhu Y, Salt DE, Meharg AA, Price AH. Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites. PLoS One 2014. [PMID: 24586963 DOI: 10.137/journalpone.0089685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
The mineral concentrations in cereals are important for human health, especially for individuals who consume a cereal subsistence diet. A number of elements, such as zinc, are required within the diet, while some elements are toxic to humans, for example arsenic. In this study we carry out genome-wide association (GWA) mapping of grain concentrations of arsenic, copper, molybdenum and zinc in brown rice using an established rice diversity panel of ∼ 300 accessions and 36.9 k single nucleotide polymorphisms (SNPs). The study was performed across five environments: one field site in Bangladesh, one in China and two in the US, with one of the US sites repeated over two years. GWA mapping on the whole dataset and on separate subpopulations of rice revealed a large number of loci significantly associated with variation in grain arsenic, copper, molybdenum and zinc. Seventeen of these loci were detected in data obtained from grain cultivated in more than one field location, and six co-localise with previously identified quantitative trait loci. Additionally, a number of candidate genes for the uptake or transport of these elements were located near significantly associated SNPs (within 200 kb, the estimated global linkage disequilibrium previously employed in this rice panel). This analysis highlights a number of genomic regions and candidate genes for further analysis as well as the challenges faced when mapping environmentally-variable traits in a highly genetically structured diversity panel.
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Affiliation(s)
- Gareth J Norton
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Alex Douglas
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Brett Lahner
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
| | - Elena Yakubova
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
| | - Mary Lou Guerinot
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Shannon R M Pinson
- USDA ARS, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America
| | - Lee Tarpley
- Texas A&M University System, Texas A&M AgriLife Research, Beaumont, Texas, United States of America
| | - Georgia C Eizenga
- USDA ARS, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America
| | - Steve P McGrath
- Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Fang-Jie Zhao
- Rothamsted Research, Harpenden, Hertfordshire, United Kingdom ; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - M Rafiqul Islam
- Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Shofiqul Islam
- Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Guilan Duan
- Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yongguan Zhu
- Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Andrew A Meharg
- Institute for Global Food Security, Queen's University Belfast, David Keir Building, Belfast, United Kingdom
| | - Adam H Price
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
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203
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Zhang D, Song H, Cheng H, Hao D, Wang H, Kan G, Jin H, Yu D. The acid phosphatase-encoding gene GmACP1 contributes to soybean tolerance to low-phosphorus stress. PLoS Genet 2014; 10:e1004061. [PMID: 24391523 PMCID: PMC3879153 DOI: 10.1371/journal.pgen.1004061] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 11/11/2013] [Indexed: 01/12/2023] Open
Abstract
Phosphorus (P) is essential for all living cells and organisms, and low-P stress is a major factor constraining plant growth and yield worldwide. In plants, P efficiency is a complex quantitative trait involving multiple genes, and the mechanisms underlying P efficiency are largely unknown. Combining linkage analysis, genome-wide and candidate-gene association analyses, and plant transformation, we identified a soybean gene related to P efficiency, determined its favorable haplotypes and developed valuable functional markers. First, six major genomic regions associated with P efficiency were detected by performing genome-wide associations (GWAs) in various environments. A highly significant region located on chromosome 8, qPE8, was identified by both GWAs and linkage mapping and explained 41% of the phenotypic variation. Then, a regional mapping study was performed with 40 surrounding markers in 192 diverse soybean accessions. A strongly associated haplotype (P = 10(-7)) consisting of the markers Sat_233 and BARC-039899-07603 was identified, and qPE8 was located in a region of approximately 250 kb, which contained a candidate gene GmACP1 that encoded an acid phosphatase. GmACP1 overexpression in soybean hairy roots increased P efficiency by 11-20% relative to the control. A candidate-gene association analysis indicated that six natural GmACP1 polymorphisms explained 33% of the phenotypic variation. The favorable alleles and haplotypes of GmACP1 associated with increased transcript expression correlated with higher enzyme activity. The discovery of the optimal haplotype of GmACP1 will now enable the accurate selection of soybeans with higher P efficiencies and improve our understanding of the molecular mechanisms underlying P efficiency in plants.
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Affiliation(s)
- Dan Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Department of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Haina Song
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Hao Cheng
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Derong Hao
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Hui Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Guizhen Kan
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Hangxia Jin
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- National Center of Plant Gene Research (Shanghai), Shanghai, China
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204
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Lee YW, Gould BA, Stinchcombe JR. Identifying the genes underlying quantitative traits: a rationale for the QTN programme. AOB PLANTS 2014; 6:plu004. [PMID: 24790125 PMCID: PMC4038433 DOI: 10.1093/aobpla/plu004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 01/01/2014] [Indexed: 05/19/2023]
Abstract
The goal of identifying the genes or even nucleotides underlying quantitative and adaptive traits has been characterized as the 'QTN programme' and has recently come under severe criticism. Part of the reason for this criticism is that much of the QTN programme has asserted that finding the genes and nucleotides for adaptive and quantitative traits is a fundamental goal, without explaining why it is such a hallowed goal. Here we outline motivations for the QTN programme that offer general insight, regardless of whether QTNs are of large or small effect, and that aid our understanding of the mechanistic dynamics of adaptive evolution. We focus on five areas: (i) vertical integration of insight across different levels of biological organization, (ii) genetic parallelism and the role of pleiotropy in shaping evolutionary dynamics, (iii) understanding the forces maintaining genetic variation in populations, (iv) distinguishing between adaptation from standing variation and new mutation, and (v) the role of genomic architecture in facilitating adaptation. We argue that rather than abandoning the QTN programme, we should refocus our efforts on topics where molecular data will be the most effective for testing hypotheses about phenotypic evolution.
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Affiliation(s)
- Young Wha Lee
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, CanadaM5S 3B2
| | - Billie A. Gould
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, CanadaM5S 3B2
| | - John R. Stinchcombe
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, CanadaM5S 3B2
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, CanadaM5S 3B2
- Corresponding author's e-mail address:
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205
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Abdel-Haleem H, Ji P, Boerma HR, Li Z. An R package for SNP marker-based parent-offspring tests. PLANT METHODS 2013; 9:44. [PMID: 24245988 PMCID: PMC3842643 DOI: 10.1186/1746-4811-9-44] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/05/2013] [Indexed: 05/29/2023]
Abstract
BACKGROUND With the advancement of genotyping technologies, whole genome and high-density SNP markers have been widely used for genotyping of mapping populations and for characterization of germplasm lines in many crops. Before conducting SNP data analysis, it is necessary to check the individuals to ensure the integrity of lines for further data analysis. RESULTS We have developed an R package to conduct a parent-offspring test of individuals which are genotyped with a fixed set of SNP markers for further genetic studies. The program uses monomorphic SNP loci between parents and their progeny genotypes to calculate the similarity between each offspring and their parents. Based on the similarity of parents and individual offspring, the users can determine the threshold level for the individuals to be included for further data analysis. We used an F5-derived soybean population of '5601T' x PI 157440 that was genotyped with 1,536 SNPs to illustrate the procedure and its application. CONCLUSIONS The R package 'ParentOffspring' coupled with the available SNP genotyping platforms could be used to detect the possible variants in a specific cross, as well as the potential errors in sample handling and genotyping processes. It can be used in any crop which is genotyped with a fixed set of SNP markers.
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Affiliation(s)
- Hussein Abdel-Haleem
- Institute of Plant Breeding, Genetics and Genomics & Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Rd., Athens, GA 30602, USA
| | - Pengsheng Ji
- Department of statistics, University of Georgia, 103 Statistics Building, 101 Cedar St., Athens, GA 30602, USA
| | - H Roger Boerma
- Institute of Plant Breeding, Genetics and Genomics & Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Rd., Athens, GA 30602, USA
- Georgia Seed Development Commission, 2420 S. Milledge Av., Athens, GA 30605, USA
| | - Zenglu Li
- Institute of Plant Breeding, Genetics and Genomics & Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Rd., Athens, GA 30602, USA
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206
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Kujur A, Saxena MS, Bajaj D, Laxmi, Parida SK. Integrated genomics and molecular breeding approaches for dissecting the complex quantitative traits in crop plants. J Biosci 2013; 38:971-87. [DOI: 10.1007/s12038-013-9388-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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207
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Spindel J, Wright M, Chen C, Cobb J, Gage J, Harrington S, Lorieux M, Ahmadi N, McCouch S. Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2699-716. [PMID: 23918062 DOI: 10.1007/s00122-013-2166-x] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 07/12/2013] [Indexed: 05/18/2023]
Abstract
Genotyping by sequencing (GBS) is the latest application of next-generation sequencing protocols for the purposes of discovering and genotyping SNPs in a variety of crop species and populations. Unlike other high-density genotyping technologies which have mainly been applied to general interest "reference" genomes, the low cost of GBS makes it an attractive means of saturating mapping and breeding populations with a high density of SNP markers. One barrier to the widespread use of GBS has been the difficulty of the bioinformatics analysis as the approach is accompanied by a high number of erroneous SNP calls which are not easily diagnosed or corrected. In this study, we use a 384-plex GBS protocol to add 30,984 markers to an indica (IR64) × japonica (Azucena) mapping population consisting of 176 recombinant inbred lines of rice (Oryza sativa) and we release our imputation and error correction pipeline to address initial GBS data sparsity and error, and streamline the process of adding SNPs to RIL populations. Using the final imputed and corrected dataset of 30,984 markers, we were able to map recombination hot and cold spots and regions of segregation distortion across the genome with a high degree of accuracy, thus identifying regions of the genome containing putative sterility loci. We mapped QTL for leaf width and aluminum tolerance, and were able to identify additional QTL for both phenotypes when using the full set of 30,984 SNPs that were not identified using a subset of only 1,464 SNPs, including a previously unreported QTL for aluminum tolerance located directly within a recombination hotspot on chromosome 1. These results suggest that adding a high density of SNP markers to a mapping or breeding population through GBS has a great value for numerous applications in rice breeding and genetics research.
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Affiliation(s)
- Jennifer Spindel
- Department of Plant Breeding and Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853-1901, USA,
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208
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Xia J, Yamaji N, Ma JF. A plasma membrane-localized small peptide is involved in rice aluminum tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:345-55. [PMID: 23888867 DOI: 10.1111/tpj.12296] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 07/13/2013] [Accepted: 07/18/2013] [Indexed: 05/06/2023]
Abstract
A transcription factor for Al tolerance, ART1, regulates the expression of at least 30 genes in rice. Here we functionally characterized one of the downstream genes, OsCDT3, which encodes a predicted peptide of only 53 amino acid residues rich in cysteine. Knockdown of this gene resulted in decreased tolerance to Al, but did not affect the tolerance to Cd. The aluminum (Al) content in the root residues including cell wall and the plasma membrane of knockdown lines decreased, but the Al concentration in the root cell sap increased compared with those of the wild-type rice. OsCDT3 was mainly expressed in the roots and its expression was specifically induced by Al exposure, not by low pH and other metals. There was a small genotypic variation in OsCDT3 expression level, but no correlation between Al tolerance and the OsCDT3 variation was found among 17 rice cultivars. Analysis of pOsCDT3::GFP transgenic rice showed that OsCDT3 was expressed at all cells in the root tips. Transient expression of OsCDT3 fused with GFP at both N- and C-termini showed that OsCDT3 was anchored to the plasma membrane. Expression of OsCDT3 in yeast conferred tolerance to Al, but not to Cd. Furthermore, OsCDT3 did not show transport activity for Al in yeast, but was able to directly bind Al in vitro. Taken together, our results indicate that OsCDT3 anchoring to the plasma membrane may play a role in stopping entry of Al into the root cells by binding Al, therefore, contributing to high Al tolerance in rice.
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Affiliation(s)
- Jixing Xia
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Japan
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209
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Liu S, Wang X, Wang H, Xin H, Yang X, Yan J, Li J, Tran LSP, Shinozaki K, Yamaguchi-Shinozaki K, Qin F. Genome-wide analysis of ZmDREB genes and their association with natural variation in drought tolerance at seedling stage of Zea mays L. PLoS Genet 2013; 9:e1003790. [PMID: 24086146 PMCID: PMC3784558 DOI: 10.1371/journal.pgen.1003790] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/26/2013] [Indexed: 12/04/2022] Open
Abstract
The worldwide production of maize (Zea mays L.) is frequently impacted by water scarcity and as a result, increased drought tolerance is a priority target in maize breeding programs. While DREB transcription factors have been demonstrated to play a central role in desiccation tolerance, whether or not natural sequence variations in these genes are associated with the phenotypic variability of this trait is largely unknown. In the present study, eighteen ZmDREB genes present in the maize B73 genome were cloned and systematically analyzed to determine their phylogenetic relationship, synteny with rice, maize and sorghum genomes; pattern of drought-responsive gene expression, and protein transactivation activity. Importantly, the association between the nucleic acid variation of each ZmDREB gene with drought tolerance was evaluated using a diverse population of maize consisting of 368 varieties from tropical and temperate regions. A significant association between the genetic variation of ZmDREB2.7 and drought tolerance at seedling stage was identified. Further analysis found that the DNA polymorphisms in the promoter region of ZmDREB2.7, but not the protein coding region itself, was associated with different levels of drought tolerance among maize varieties, likely due to distinct patterns of gene expression in response to drought stress. In vitro, protein-DNA binding assay demonstrated that ZmDREB2.7 protein could specifically interact with the target DNA sequences. The transgenic Arabidopsis overexpressing ZmDREB2.7 displayed enhanced tolerance to drought stress. Moreover, a favorable allele of ZmDREB2.7, identified in the drought-tolerant maize varieties, was effective in imparting plant tolerance to drought stress. Based upon these findings, we conclude that natural variation in the promoter of ZmDREB2.7 contributes to maize drought tolerance, and that the gene and its favorable allele may be an important genetic resource for the genetic improvement of drought tolerance in maize. Water scarcity is one of the most severe threats to maize production worldwide. Although research has demonstrated that DREB-type transcription factors play important roles in plant water stress response, whether the specific genetic variants in DREB genes contribute to plant drought tolerance is largely unknown. Taking advantages of recent technical and methodological advance, we systematically analyzed all the functional DREB genes in maize and examined their associations with the natural variation in drought tolerance of 368 maize varieties collected from tropical and temperate regions. A significant association in the ZmDREB2.7 gene with drought tolerance was detected in that the DNA polymorphisms in the gene promoter region, but not those in the protein coding region, contributed to observed variations in maize drought tolerance, probably due to the distinct gene expression patterns in response to the stress. Overexpressing ZmDREB2.7 in Arabidopsis resulted in enhanced tolerance to drought stress. Moreover, a favorable ZmDREB2.7 allele, identified from drought-tolerant varieties, was effective in improving plant tolerance to drought stress when it was introduced into a drought-sensitive background. ZmDREB2.7 and its favorable allele represent a valuable genetic resource for enhancing maize drought tolerance by marker assisted breeding and transformation technology.
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Affiliation(s)
- Shengxue Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Xianglan Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Hongwei Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Haibo Xin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jiansheng Li
- National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Kazuko Yamaguchi-Shinozaki
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Feng Qin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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210
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Garcia-Oliveira AL, Benito C, Prieto P, de Andrade Menezes R, Rodrigues-Pousada C, Guedes-Pinto H, Martins-Lopes P. Molecular characterization of TaSTOP1 homoeologues and their response to aluminium and proton (H(+)) toxicity in bread wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2013; 13:134. [PMID: 24034075 PMCID: PMC3848728 DOI: 10.1186/1471-2229-13-134] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 08/01/2013] [Indexed: 05/06/2023]
Abstract
BACKGROUND Aluminium (Al) toxicity is considered to be one of the major constraints affecting crop productivity on acid soils. Being a trait governed by multiple genes, the identification and characterization of novel transcription factors (TFs) regulating the expression of entire response networks is a very promising approach. Therefore, the aim of the present study was to clone, localize, and characterize the TaSTOP1 gene, which belongs to the zinc finger family (Cys2His2 type) transcription factor, at molecular level in bread wheat. RESULTS TaSTOP1 loci were cloned and localized on the long arm of homoeologous group 3 chromosomes [3AL (TaSTOP1-A), 3BL (TaSTOP1-B) and 3DL (TaSTOP1-D)] in bread wheat. TaSTOP1 showed four potential zinc finger domains and the homoeologue TaSTOP1-A exhibited transactivation activity in yeast. Expression profiling of TaSTOP1 transcripts identified the predominance of homoeologue TaSTOP1-A followed by TaSTOP1-D over TaSTOP1-B in root and only predominance of TaSTOP1-A in shoot tissues of two diverse bread wheat genotypes. Al and proton (H(+)) stress appeared to slightly modulate the transcript of TaSTOP1 homoeologues expression in both genotypes of bread wheat. CONCLUSIONS Physical localization of TaSTOP1 results indicated the presence of a single copy of TaSTOP1 on homoeologous group 3 chromosomes in bread wheat. The three homoeologues of TaSTOP1 have similar genomic structures, but showed biased transcript expression and different response to Al and proton (H(+)) toxicity. These results indicate that TaSTOP1 homoeologues may differentially contribute under Al or proton (H(+)) toxicity in bread wheat. Moreover, it seems that TaSTOP1-A transactivation potential is constitutive and may not depend on the presence/absence of Al at least in yeast. Finally, the localization of TaSTOP1 on long arm of homoeologous group 3 chromosomes and the previously reported major loci associated with Al resistance at chromosome 3BL, through QTL and genome wide association mapping studies suggests that TaSTOP1 could be a potential candidate gene for genomic assisted breeding for Al tolerance in bread wheat.
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Affiliation(s)
- Ana Luísa Garcia-Oliveira
- Centro de Genómica e Biotecnologia, Instituto de Biotecnologia e Bioengenharia (CGB/IBB), Universidade de Trás-os-Montes e Alto Douro (UTAD), P.O. Box 1013, 5001-801 Vila Real, Portugal
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid (UCM), Madrid 28040, Spain
- Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal
| | - César Benito
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid (UCM), Madrid 28040, Spain
| | - Pilar Prieto
- Departamento de Mejora Genética Vegetal, Instituto de Agricultura Sostenible (IAS, CSIC), Alameda del Obispo s/n., P.O. Box 4084, Córdoba 14080, Spain
| | | | | | - Henrique Guedes-Pinto
- Centro de Genómica e Biotecnologia, Instituto de Biotecnologia e Bioengenharia (CGB/IBB), Universidade de Trás-os-Montes e Alto Douro (UTAD), P.O. Box 1013, 5001-801 Vila Real, Portugal
| | - Paula Martins-Lopes
- Centro de Genómica e Biotecnologia, Instituto de Biotecnologia e Bioengenharia (CGB/IBB), Universidade de Trás-os-Montes e Alto Douro (UTAD), P.O. Box 1013, 5001-801 Vila Real, Portugal
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211
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Bryant RJ, Jackson AK, Yeater KM, Yan WG, McClung AM, Fjellstrom RG. Genetic Variation and Association Mapping of Protein Concentration in Brown Rice Using a Diverse Rice Germplasm Collection. Cereal Chem 2013. [DOI: 10.1094/cchem-09-12-0122-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rolfe J. Bryant
- U.S. Department of Agriculture–Agricultural Research Service (USDA-ARS), Dale Bumpers National Rice Research Center, 2890 Hwy 130 E., Stuttgart, AR 72160, U.S.A. Mention of a trademark or proprietary product in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. USDA is an equal opportunity provider and employer
| | - Aaron K. Jackson
- U.S. Department of Agriculture–Agricultural Research Service (USDA-ARS), Dale Bumpers National Rice Research Center, 2890 Hwy 130 E., Stuttgart, AR 72160, U.S.A. Mention of a trademark or proprietary product in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. USDA is an equal opportunity provider and employer
| | | | - Wengui G. Yan
- U.S. Department of Agriculture–Agricultural Research Service (USDA-ARS), Dale Bumpers National Rice Research Center, 2890 Hwy 130 E., Stuttgart, AR 72160, U.S.A. Mention of a trademark or proprietary product in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. USDA is an equal opportunity provider and employer
| | - Anna M. McClung
- U.S. Department of Agriculture–Agricultural Research Service (USDA-ARS), Dale Bumpers National Rice Research Center, 2890 Hwy 130 E., Stuttgart, AR 72160, U.S.A. Mention of a trademark or proprietary product in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. USDA is an equal opportunity provider and employer
| | - Robert G. Fjellstrom
- U.S. Department of Agriculture–Agricultural Research Service (USDA-ARS), Dale Bumpers National Rice Research Center, 2890 Hwy 130 E., Stuttgart, AR 72160, U.S.A. Mention of a trademark or proprietary product in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. USDA is an equal opportunity provider and employer
- Corresponding author. Phone: (870) 672-9300, ext. 223. Fax: (870) 673-7581. E-mail:
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Caballero A, García-Pereira MJ, Quesada H. Genomic distribution of AFLP markers relative to gene locations for different eukaryotic species. BMC Genomics 2013; 14:528. [PMID: 24060007 PMCID: PMC3750350 DOI: 10.1186/1471-2164-14-528] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 07/30/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Amplified fragment length polymorphism (AFLP) markers are frequently used for a wide range of studies, such as genome-wide mapping, population genetic diversity estimation, hybridization and introgression studies, phylogenetic analyses, and detection of signatures of selection. An important issue to be addressed for some of these fields is the distribution of the markers across the genome, particularly in relation to gene sequences. RESULTS Using in-silico restriction fragment analysis of the genomes of nine eukaryotic species we characterise the distribution of AFLP fragments across the genome and, particularly, in relation to gene locations. First, we identify the physical position of markers across the chromosomes of all species. An observed accumulation of fragments around (peri) centromeric regions in some species is produced by repeated sequences, and this accumulation disappears when AFLP bands rather than fragments are considered. Second, we calculate the percentage of AFLP markers positioned within gene sequences. For the typical EcoRI/MseI enzyme pair, this ranges between 28 and 87% and is usually larger than that expected by chance because of the higher GC content of gene sequences relative to intergenic ones. In agreement with this, the use of enzyme pairs with GC-rich restriction sites substantially increases the above percentages. For example, using the enzyme system SacI/HpaII, 86% of AFLP markers are located within gene sequences in A. thaliana, and 100% of markers in Plasmodium falciparun. We further find that for a typical trait controlled by 50 genes of average size, if 1000 AFLPs are used in a study, the number of those within 1 kb distance from any of the genes would be only about 1-2, and only about 50% of the genes would have markers within that distance. CONCLUSIONS The high coverage of AFLP markers across the genomes and the high proportion of markers within or close to gene sequences make them suitable for genome scans and detecting large islands of differentiation in the genome. However, for specific traits, the percentage of AFLP markers close to genes can be rather small. Therefore, genome scans directed towards the search of markers closely linked to selected loci can be a difficult task in many instances.
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Affiliation(s)
- Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidade de Vigo, 36310 Vigo, Spain.
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Upadhyaya HD, Wang YH, Gowda CLL, Sharma S. Association mapping of maturity and plant height using SNP markers with the sorghum mini core collection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2003-15. [PMID: 23649651 DOI: 10.1007/s00122-013-2113-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 04/26/2013] [Indexed: 05/20/2023]
Abstract
Plant height and maturity are two critical traits in sorghum breeding. To develop molecular tools and to identify genes underlying the traits for molecular breeding, we developed 14,739 SNP markers used to genotype the complete sorghum [Sorghum bicolor (L.) Moench] mini core collection. The collection was evaluated in four rainy and three post-rainy season environments for plant height and maturity. Association analysis identified six marker loci linked to height and ten to maturity in at least two environments with at least two SNPs in each locus. Of these, 14 were in close proximity to previously mapped height/maturity QTL in sorghum. Candidate genes for maturity or plant height close to the marker loci include a sugar transporter (SbSUC9), an auxin response factor (SbARF3), an FLC and FT regulator (SbMED12), and a photoperiod response gene (SbPPR1) for maturity and peroxidase 53, and an auxin transporter (SbLAX4) for plant height. Linkage disequilibrium analysis showed that SbPPR1 and SbARF3 were in regions with reduced sequence variation among early-maturing accessions, suggestive of past purifying selection. We also found a linkage disequilibrium block that existed only among the accessions with short plant height in rainy season environments. The block contains a gene homologous to the Arabidopsis flowering time gene, LUMINIDEPENDENS (LD). Functional LD promotes early maturity while mutation delays maturity, affecting plant height. Previous studies also found reduced sequence variations within this gene. These newly-mapped SNP markers will facilitate further efforts to identify plant height or maturity genes in sorghum.
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Affiliation(s)
- Hari D Upadhyaya
- Gene Bank, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Andhra Pradesh, India
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214
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Cai S, Wu D, Jabeen Z, Huang Y, Huang Y, Zhang G. Genome-wide association analysis of aluminum tolerance in cultivated and Tibetan wild barley. PLoS One 2013; 8:e69776. [PMID: 23922796 PMCID: PMC3724880 DOI: 10.1371/journal.pone.0069776] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 06/05/2013] [Indexed: 11/19/2022] Open
Abstract
Tibetan wild barley (Hordeum vulgare L. ssp. spontaneum), originated and grown in harsh enviroNment in Tibet, is well-known for its rich germpalsm with high tolerance to abiotic stresses. However, the genetic variation and genes involved in Al tolerance are not totally known for the wild barley. In this study, a genome-wide association analysis (GWAS) was performed by using four root parameters related with Al tolerance and 469 DArT markers on 7 chromosomes within or across 110 Tibetan wild accessions and 56 cultivated cultivars. Population structure and cluster analysis revealed that a wide genetic diversity was present in Tibetan wild barley. Linkage disequilibrium (LD) decayed more rapidly in Tibetan wild barley (9.30 cM) than cultivated barley (11.52 cM), indicating that GWAS may provide higher resolution in the Tibetan group. Two novel Tibetan group-specific loci, bpb-9458 and bpb-8524 were identified, which were associated with relative longest root growth (RLRG), located at 2H and 7H on barely genome, and could explain 12.9% and 9.7% of the phenotypic variation, respectively. Moreover, a common locus bpb-6949, localized 0.8 cM away from a candidate gene HvMATE, was detected in both wild and cultivated barleys, and showed significant association with total root growth (TRG). The present study highlights that Tibetan wild barley could provide elite germplasm novel genes for barley Al-tolerant improvement.
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Affiliation(s)
- Shengguan Cai
- Agronomy Department, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Dezhi Wu
- Agronomy Department, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Zahra Jabeen
- Agronomy Department, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Yuqing Huang
- Agronomy Department, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Yechang Huang
- Agronomy Department, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Guoping Zhang
- Agronomy Department, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
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215
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Zhang B, Shi W, Li W, Chang X, Jing R. Efficacy of pyramiding elite alleles for dynamic development of plant height in common wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2013; 32:327-338. [PMID: 23976874 PMCID: PMC3748324 DOI: 10.1007/s11032-013-9873-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 04/18/2013] [Indexed: 05/28/2023]
Abstract
Plant height is an important botanical feature closely related to yield. Two populations consisting of 118 and 262 accessions respectively were used to identify elite alleles for plant height and to validate their allelic effects. Plant height was measured from the early booting to the flowering stages. Simple sequence repeat markers for candidate quantitative trait locus (QTL) regions with large effects identified in a doubled haploid (DH) population (Hanxuan 10 × Lumai 14) were selected for further verification by association analysis. Nine loci significantly (P < 0.001) associated with plant height were detected 13 times in the population with 118 accessions. Three loci (Xgwm11-1B, Xwmc349-4B and Xcfd23-4D) were identified in three, two and two periods of plant height growth, respectively. Markers Xbarc168-2D, Xgwm249-2D, Xwmc349-4B, Xcfd23-4D and Xgwm410-5A located at or near additive QTL regions in the DH population proved to coincide with known Rht loci. The results showed a consistency between linkage analysis and association mapping, and also confirmed the value of fine mapping of QTL through combined linkage and association analyses. For final plant height, the alleles Xgwm11-1B208 , Xwmc349-4B103 and Xcfd23-4D202 exhibited negative effects, i.e. reducing plant height; Xwmc349-4B101 and Xcfd23-4D205 showed significant positive effects. A second larger population (262 accessions) was used to validate the effects of these large-effect alleles and the efficacy of pyramiding in eight environments (year × site × water regime combinations). Strong correlations between final plant height and numbers of large-effect alleles indicated that the alleles contributed additively to plant height. The additive effects showed that pyramiding elite alleles for target traits has significant potential for wheat breeding.
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Affiliation(s)
- Bin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Wei Shi
- National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Weiyu Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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216
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Hu Z, Zhang H, Kan G, Ma D, Zhang D, Shi G, Hong D, Zhang G, Yu D. Determination of the genetic architecture of seed size and shape via linkage and association analysis in soybean (Glycine max L. Merr.). Genetica 2013; 141:247-54. [PMID: 23754189 DOI: 10.1007/s10709-013-9723-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 06/03/2013] [Indexed: 10/26/2022]
Abstract
Seed-size traits, which are controlled by multiple genes in soybean, play an important role in determining seed yield, quality and appearance. However, the molecular mechanisms controlling the size of soybean seeds remain unclear, and little research has been done to investigate these mechanisms. In this study, we performed a genetic analysis to determine the genetic architecture of soybean seed size and shape via linkage and association analyses. We used 184 recombinant inbred lines (RILs) and 219 cultivated soybean accessions to evaluate seed length, seed width and seed height as seed-size traits, and their ratios of these values as seed-shape traits. Our results showed that all six traits had high heritability ranging from 92.46 to 98.47 %. Linkage analysis in the RILs identified 12 quantitative traits loci (QTLs), with five of these QTLs being associated with seed size, five with seed shape and two with the two first principal components of our principal component analysis (PCA). Association analysis in the 219 accessions detected 41 single nucleotide polymorphism (SNP)-trait associations, with 20 of these SNPs being associated with seed-size traits, seven with seed-shape traits and 14 with the two first principal components of our PCA. This analysis reveals that seed-size and seed-shape may be controlled by different genetic factors. Our results provide a greater understanding of phenotypic structure and genetic architecture of soybean seed, and the QTLs detected in this study form a basis for future fine mapping, quantitative trait gene cloning and molecular breeding in soybean.
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Affiliation(s)
- Zhenbin Hu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
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217
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Upadhyaya HD, Wang YH, Sharma R, Sharma S. Identification of genetic markers linked to anthracnose resistance in sorghum using association analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1649-57. [PMID: 23463493 DOI: 10.1007/s00122-013-2081-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/23/2013] [Indexed: 05/20/2023]
Abstract
Anthracnose in sorghum caused by Colletotrichum sublineolum is one of the most destructive diseases affecting sorghum production under warm and humid conditions. Markers and genes linked to resistance to the disease are important for plant breeding. Using 14,739 SNP markers, we have mapped eight loci linked to resistance in sorghum through association analysis of a sorghum mini-core collection consisting of 242 diverse accessions evaluated for anthracnose resistance for 2 years in the field. The mini-core was representative of the International Crops Research Institute for the Semi-Arid Tropics' world-wide sorghum landrace collection. Eight marker loci were associated with anthracnose resistance in both years. Except locus 8, disease resistance-related genes were found in all loci based on their physical distance from linked SNP markers. These include two NB-ARC class of R genes on chromosome 10 that were partially homologous to the rice blast resistance gene Pib, two hypersensitive response-related genes: autophagy-related protein 3 on chromosome 1 and 4 harpin-induced 1 (Hin1) homologs on chromosome 8, a RAV transcription factor that is also part of R gene pathway, an oxysterol-binding protein that functions in the non-specific host resistance, and homologs of menthone:neomenthol reductase (MNR) that catalyzes a menthone reduction to produce the antimicrobial neomenthol. These genes and markers may be developed into molecular tools for genetic improvement of anthracnose resistance in sorghum.
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Affiliation(s)
- Hari D Upadhyaya
- International Crops Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, Andhra Pradesh, India
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218
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Schroeder JI, Delhaize E, Frommer WB, Guerinot ML, Harrison MJ, Herrera-Estrella L, Horie T, Kochian LV, Munns R, Nishizawa NK, Tsay YF, Sanders D. Using membrane transporters to improve crops for sustainable food production. Nature 2013; 497:60-6. [PMID: 23636397 PMCID: PMC3954111 DOI: 10.1038/nature11909] [Citation(s) in RCA: 276] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 01/11/2013] [Indexed: 02/05/2023]
Abstract
With the global population predicted to grow by at least 25 per cent by 2050, the need for sustainable production of nutritious foods is critical for human and environmental health. Recent advances show that specialized plant membrane transporters can be used to enhance yields of staple crops, increase nutrient content and increase resistance to key stresses, including salinity, pathogens and aluminium toxicity, which in turn could expand available arable land.
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Affiliation(s)
- Julian I Schroeder
- Division of Biological Sciences, Food and Fuel for the 21st Century Center, University of California San Diego, La Jolla, California 92093-0116, USA.
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219
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Chen H, He H, Zhou F, Yu H, Deng XW. Development of genomics-based genotyping platforms and their applications in rice breeding. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:247-54. [PMID: 23706659 DOI: 10.1016/j.pbi.2013.04.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 03/29/2013] [Accepted: 04/25/2013] [Indexed: 05/26/2023]
Abstract
Breeding by design has been an aspiration of researchers in the plant sciences for a decade. With the rapid development of genomics-based genotyping platforms and available of hundreds of functional genes/alleles in related to important traits, however, it may now be possible to turn this enduring ambition into a practical reality. Rice has a relatively simple genome comparing to other crops, and its genome composition and genetic behavior have been extensively investigated. Recently, rice has been taken as a model crop to perform breeding by design. The essential process of breeding by design is to integrate functional genes/alleles in an ideal genetic background, which requires high throughput genotyping platforms to screen for expected genotypes. With large amount of genome resequencing data and high-throughput genotyping technologies available, quite a number of genomics-based genotyping platforms have been developed. These platforms are widely used in genetic mapping, integration of target traits via marker-assisted backcrossing (MABC), pyramiding, recurrent selection (MARS) or genomic selection (GS). Here, we summarize and discuss recent exciting development of rice genomics-based genotyping platforms and their applications in molecular breeding.
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Affiliation(s)
- Haodong Chen
- Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China.
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220
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Cadic E, Coque M, Vear F, Grezes-Besset B, Pauquet J, Piquemal J, Lippi Y, Blanchard P, Romestant M, Pouilly N, Rengel D, Gouzy J, Langlade N, Mangin B, Vincourt P. Combined linkage and association mapping of flowering time in Sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1337-56. [PMID: 23435733 DOI: 10.1007/s00122-013-2056-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 01/20/2013] [Indexed: 05/20/2023]
Abstract
Association mapping and linkage mapping were used to identify quantitative trait loci (QTL) and/or causative mutations involved in the control of flowering time in cultivated sunflower Helianthus annuus. A panel of 384 inbred lines was phenotyped through testcrosses with two tester inbred lines across 15 location × year combinations. A recombinant inbred line (RIL) population comprising 273 lines was phenotyped both per se and through testcrosses with one or two testers in 16 location × year combinations. In the association mapping approach, kinship estimation using 5,923 single nucleotide polymorphisms was found to be the best covariate to correct for effects of panel structure. Linkage disequilibrium decay ranged from 0.08 to 0.26 cM for a threshold of 0.20, after correcting for structure effects, depending on the linkage group (LG) and the ancestry of inbred lines. A possible hitchhiking effect is hypothesized for LG10 and LG08. A total of 11 regions across 10 LGs were found to be associated with flowering time, and QTLs were mapped on 11 LGs in the RIL population. Whereas eight regions were demonstrated to be common between the two approaches, the linkage disequilibrium approach did not detect a documented QTL that was confirmed using the linkage mapping approach.
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Affiliation(s)
- Elena Cadic
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, 31326 Castanet-Tolosan, France.
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Delourme R, Falentin C, Fomeju BF, Boillot M, Lassalle G, André I, Duarte J, Gauthier V, Lucante N, Marty A, Pauchon M, Pichon JP, Ribière N, Trotoux G, Blanchard P, Rivière N, Martinant JP, Pauquet J. High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L. BMC Genomics 2013; 14:120. [PMID: 23432809 PMCID: PMC3600037 DOI: 10.1186/1471-2164-14-120] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 02/11/2013] [Indexed: 11/30/2022] Open
Abstract
Background High density genetic maps built with SNP markers that are polymorphic in various genetic backgrounds are very useful for studying the genetics of agronomical traits as well as genome organization and evolution. Simultaneous dense SNP genotyping of segregating populations and variety collections was applied to oilseed rape (Brassica napus L.) to obtain a high density genetic map for this species and to study the linkage disequilibrium pattern. Results We developed an integrated genetic map for oilseed rape by high throughput SNP genotyping of four segregating doubled haploid populations. A very high level of collinearity was observed between the four individual maps and a large number of markers (>59%) was common to more than two maps. The precise integrated map comprises 5764 SNP and 1603 PCR markers. With a total genetic length of 2250 cM, the integrated map contains a density of 3.27 markers (2.56 SNP) per cM. Genotyping of these mapped SNP markers in oilseed rape collections allowed polymorphism level and linkage disequilibrium (LD) to be studied across the different collections (winter vs spring, different seed quality types) and along the linkage groups. Overall, polymorphism level was higher and LD decayed faster in spring than in “00” winter oilseed rape types but this was shown to vary greatly along the linkage groups. Conclusions Our study provides a valuable resource for further genetic studies using linkage or association mapping, for marker assisted breeding and for Brassica napus sequence assembly and genome organization analyses.
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Clark RT, Famoso AN, Zhao K, Shaff JE, Craft EJ, Bustamante CD, McCouch SR, Aneshansley DJ, Kochian LV. High-throughput two-dimensional root system phenotyping platform facilitates genetic analysis of root growth and development. PLANT, CELL & ENVIRONMENT 2013; 36:454-66. [PMID: 22860896 DOI: 10.1111/j.1365-3040.2012.02587.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
High-throughput phenotyping of root systems requires a combination of specialized techniques and adaptable plant growth, root imaging and software tools. A custom phenotyping platform was designed to capture images of whole root systems, and novel software tools were developed to process and analyse these images. The platform and its components are adaptable to a wide range root phenotyping studies using diverse growth systems (hydroponics, paper pouches, gel and soil) involving several plant species, including, but not limited to, rice, maize, sorghum, tomato and Arabidopsis. The RootReader2D software tool is free and publicly available and was designed with both user-guided and automated features that increase flexibility and enhance efficiency when measuring root growth traits from specific roots or entire root systems during large-scale phenotyping studies. To demonstrate the unique capabilities and high-throughput capacity of this phenotyping platform for studying root systems, genome-wide association studies on rice (Oryza sativa) and maize (Zea mays) root growth were performed and root traits related to aluminium (Al) tolerance were analysed on the parents of the maize nested association mapping (NAM) population.
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Affiliation(s)
- Randy T Clark
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
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223
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Tovkach A, Ryan PR, Richardson AE, Lewis DC, Rathjen TM, Ramesh S, Tyerman SD, Delhaize E. Transposon-mediated alteration of TaMATE1B expression in wheat confers constitutive citrate efflux from root apices. PLANT PHYSIOLOGY 2013; 161:880-92. [PMID: 23204428 PMCID: PMC3561026 DOI: 10.1104/pp.112.207142] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 11/27/2012] [Indexed: 05/02/2023]
Abstract
The TaMATE1B gene (for multidrug and toxic compound extrusion) from wheat (Triticum aestivum) was isolated and shown to encode a citrate transporter that is located on the plasma membrane. TaMATE1B expression in roots was induced by iron deficiency but not by phosphorus deficiency or aluminum treatment. The coding region of TaMATE1B was identical in a genotype showing citrate efflux from root apices (cv Carazinho) to one that lacked citrate efflux (cv Egret). However, sequence upstream of the coding region differed between these two genotypes in two ways. The first difference was a single-nucleotide polymorphism located approximately 2 kb upstream from the start codon in cv Egret. The second difference was an 11.1-kb transposon-like element located 25 bp upstream of the start codon in cv Carazinho that was absent from cv Egret. The influence of these polymorphisms on TaMATE1B expression was investigated using fusions to green fluorescent protein expressed in transgenic lines of rice (Oryza sativa). Fluorescence measurements in roots of rice indicated that 1.5- and 2.3-kb regions upstream of TaMATE1B in cv Carazinho (which incorporated 3' regions of the transposon-like element) generated 20-fold greater expression in the apical 1 mm of root compared with the native promoter in cv Egret. By contrast, fluorescence in more mature tissues was similar in both cultivars. The presence of the single-nucleotide polymorphism alone consistently generated 2-fold greater fluorescence than the cv Egret promoter. We conclude that the transposon-like element in cv Carazinho extends TaMATE1B expression to the root apex, where it confers citrate efflux and enhanced aluminum tolerance.
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Affiliation(s)
- Andriy Tovkach
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2601, Australia (A.T., P.R.R., A.E.R., D.C.L., T.M.R., E.D.); and School of Agriculture, Food, and Wine, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia (S.R., S.D.T.)
| | - Peter R. Ryan
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2601, Australia (A.T., P.R.R., A.E.R., D.C.L., T.M.R., E.D.); and School of Agriculture, Food, and Wine, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia (S.R., S.D.T.)
| | - Alan E. Richardson
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2601, Australia (A.T., P.R.R., A.E.R., D.C.L., T.M.R., E.D.); and School of Agriculture, Food, and Wine, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia (S.R., S.D.T.)
| | - David C. Lewis
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2601, Australia (A.T., P.R.R., A.E.R., D.C.L., T.M.R., E.D.); and School of Agriculture, Food, and Wine, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia (S.R., S.D.T.)
| | - Tina M. Rathjen
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2601, Australia (A.T., P.R.R., A.E.R., D.C.L., T.M.R., E.D.); and School of Agriculture, Food, and Wine, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia (S.R., S.D.T.)
| | - Sunita Ramesh
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2601, Australia (A.T., P.R.R., A.E.R., D.C.L., T.M.R., E.D.); and School of Agriculture, Food, and Wine, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia (S.R., S.D.T.)
| | - Stephen D. Tyerman
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2601, Australia (A.T., P.R.R., A.E.R., D.C.L., T.M.R., E.D.); and School of Agriculture, Food, and Wine, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia (S.R., S.D.T.)
| | - Emmanuel Delhaize
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, Australian Capital Territory 2601, Australia (A.T., P.R.R., A.E.R., D.C.L., T.M.R., E.D.); and School of Agriculture, Food, and Wine, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia (S.R., S.D.T.)
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Chen C, DeClerck G, Tian F, Spooner W, McCouch S, Buckler E. PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants. PLoS One 2012; 7:e46596. [PMID: 23144785 PMCID: PMC3492367 DOI: 10.1371/journal.pone.0046596] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 09/04/2012] [Indexed: 01/28/2023] Open
Abstract
PICARA is an analytical pipeline designed to systematically summarize observed SNP/trait associations identified by genome wide association studies (GWAS) and to identify candidate genes involved in the regulation of complex trait variation. The pipeline provides probabilistic inference about a priori candidate genes using integrated information derived from genome-wide association signals, gene homology, and curated gene sets embedded in pathway descriptions. In this paper, we demonstrate the performance of PICARA using data for flowering time variation in maize – a key trait for geographical and seasonal adaption of plants. Among 406 curated flowering time-related genes from Arabidopsis, we identify 61 orthologs in maize that are significantly enriched for GWAS SNP signals, including key regulators such as FT (Flowering Locus T) and GI (GIGANTEA), and genes centered in the Arabidopsis circadian pathway, including TOC1 (Timing of CAB Expression 1) and LHY (Late Elongated Hypocotyl). In addition, we discover a regulatory feature that is characteristic of these a priori flowering time candidates in maize. This new probabilistic analytical pipeline helps researchers infer the functional significance of candidate genes associated with complex traits and helps guide future experiments by providing statistical support for gene candidates based on the integration of heterogeneous biological information.
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Affiliation(s)
- Charles Chen
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America.
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225
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Ma Y, Qin F, Tran LSP. Contribution of genomics to gene discovery in plant abiotic stress responses. MOLECULAR PLANT 2012; 5:1176-8. [PMID: 22930735 DOI: 10.1093/mp/sss085] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Affiliation(s)
- Yun Ma
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100039, China
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226
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Li X, Acharya A, Farmer AD, Crow JA, Bharti AK, Kramer RS, Wei Y, Han Y, Gou J, May GD, Monteros MJ, Brummer EC. Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing. BMC Genomics 2012; 13:568. [PMID: 23107476 PMCID: PMC3533575 DOI: 10.1186/1471-2164-13-568] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 10/18/2012] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Alfalfa, a perennial, outcrossing species, is a widely planted forage legume producing highly nutritious biomass. Currently, improvement of cultivated alfalfa mainly relies on recurrent phenotypic selection. Marker assisted breeding strategies can enhance alfalfa improvement efforts, particularly if many genome-wide markers are available. Transcriptome sequencing enables efficient high-throughput discovery of single nucleotide polymorphism (SNP) markers for a complex polyploid species. RESULT The transcriptomes of 27 alfalfa genotypes, including elite breeding genotypes, parents of mapping populations, and unimproved wild genotypes, were sequenced using an Illumina Genome Analyzer IIx. De novo assembly of quality-filtered 72-bp reads generated 25,183 contigs with a total length of 26.8 Mbp and an average length of 1,065 bp, with an average read depth of 55.9-fold for each genotype. Overall, 21,954 (87.2%) of the 25,183 contigs represented 14,878 unique protein accessions. Gene ontology (GO) analysis suggested that a broad diversity of genes was represented in the resulting sequences. The realignment of individual reads to the contigs enabled the detection of 872,384 SNPs and 31,760 InDels. High resolution melting (HRM) analysis was used to validate 91% of 192 putative SNPs identified by sequencing. Both allelic variants at about 95% of SNP sites identified among five wild, unimproved genotypes are still present in cultivated alfalfa, and all four US breeding programs also contain a high proportion of these SNPs. Thus, little evidence exists among this dataset for loss of significant DNA sequence diversity from either domestication or breeding of alfalfa. Structure analysis indicated that individuals from the subspecies falcata, the diploid subspecies caerulea, and the tetraploid subspecies sativa (cultivated tetraploid alfalfa) were clearly separated. CONCLUSION We used transcriptome sequencing to discover large numbers of SNPs segregating in elite breeding populations of alfalfa. Little loss of SNP diversity was evident between unimproved and elite alfalfa germplasm. The EST and SNP markers generated from this study are publicly available at the Legume Information System ( http://medsa.comparative-legumes.org/) and can contribute to future alfalfa research and breeding applications.
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Affiliation(s)
- Xuehui Li
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Ananta Acharya
- Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - John A Crow
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Arvind K Bharti
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Robin S Kramer
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Yanling Wei
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Yuanhong Han
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Jiqing Gou
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Gregory D May
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Maria J Monteros
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - E Charles Brummer
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
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227
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Tsutsui T, Yamaji N, Huang CF, Motoyama R, Nagamura Y, Ma JF. Comparative genome-wide transcriptional analysis of Al-responsive genes reveals novel Al tolerance mechanisms in rice. PLoS One 2012; 7:e48197. [PMID: 23110212 PMCID: PMC3482186 DOI: 10.1371/journal.pone.0048197] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 09/20/2012] [Indexed: 11/18/2022] Open
Abstract
Rice (Oryza sativa) is the most aluminum (Al)-tolerant crop among small-grain cereals, but the mechanism underlying its high Al resistance is still not well understood. To understand the mechanisms underlying high Al-tolerance, we performed a comparative genome-wide transcriptional analysis by comparing expression profiling between the Al-tolerance cultivar (Koshihikari) and an Al-sensitive mutant star1 (SENSITIVE TO AL RHIZOTOXICITY 1) in both the root tips and the basal roots. Exposure to 20 µM AlCl(3) for 6 h resulted in up-regulation (higher than 3-fold) of 213 and 2015 genes including 185 common genes in the root tips of wild-type and the mutant, respectively. On the other hand, in the basal root, genes up-regulated by Al were 126 and 2419 including 76 common genes in the wild-type and the mutant, respectively. These results indicate that Al-response genes are not only restricted to the root tips, but also in the basal root region. Analysis with genes up- or down-regulated only in the wild-type reveals that there are other mechanisms for Al-tolerance except for a known transcription factor ART1-regulated one in rice. These mechanisms are related to nitrogen assimilation, secondary metabolite synthesis, cell-wall synthesis and ethylene synthesis. Although the exact roles of these putative tolerance genes remain to be examined, our data provide a platform for further work on Al-tolerance in rice.
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Affiliation(s)
- Tomokazu Tsutsui
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Naoki Yamaji
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Chao Feng Huang
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Ritsuko Motoyama
- Genome Resource Center, Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Yoshiaki Nagamura
- Genome Resource Center, Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Jian Feng Ma
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
- * E-mail:
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228
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Chen ZC, Yamaji N, Motoyama R, Nagamura Y, Ma JF. Up-regulation of a magnesium transporter gene OsMGT1 is required for conferring aluminum tolerance in rice. PLANT PHYSIOLOGY 2012; 159:1624-33. [PMID: 22732245 PMCID: PMC3425201 DOI: 10.1104/pp.112.199778] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Magnesium (Mg)-mediated alleviation of aluminum (Al) toxicity has been observed in a number of plant species, but the mechanisms underlying the alleviation are still poorly understood. When a putative rice (Oryza sativa) Mg transporter gene, Oryza sativa MAGNESIUM TRANSPORTER1 (OsMGT1), was knocked out, the tolerance to Al, but not to cadmium and lanthanum, was decreased. However, this inhibition could be rescued by addition of 10 μm Mg, but not by the same concentration of barium or strontium. OsMGT1 was expressed in both the roots and shoots in the absence of Al, but the expression only in the roots was rapidly up-regulated by Al. Furthermore, the expression did not respond to low pH and other metals including cadmium and lanthanum, and was regulated by an Al-responsive transcription factor, AL RESISTANCE TRANSCRIPTION FACTOR1. An investigation of subcellular localization showed that OsMGT1 was localized to the plasma membrane. A short-term (30 min) uptake experiment with stable isotope (25)Mg showed that knockout of OsMGT1 resulted in decreased Mg uptake, but that the uptake in the wild type was enhanced by Al. Mg concentration in the cell sap of the root tips was also increased in the wild-type rice, but not in the knockout lines in the presence of Al. A microarray analysis showed that transcripts of genes related to stress were more up- and down-regulated in the knockout lines. Taken together, our results indicate that OsMGT1 is a transporter for Mg uptake in the roots and that up-regulation of this gene is required for conferring Al tolerance in rice by increasing Mg concentration in the cell.
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229
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Delhaize E, Ma JF, Ryan PR. Transcriptional regulation of aluminium tolerance genes. TRENDS IN PLANT SCIENCE 2012; 17:341-8. [PMID: 22459757 DOI: 10.1016/j.tplants.2012.02.008] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 02/24/2012] [Accepted: 02/27/2012] [Indexed: 05/19/2023]
Abstract
Trivalent aluminium (Al(3+)) is the major toxin encountered by plants on acid soils. These cations inhibit root growth by damaging cells at the root apex. The physiology and genetics of Al(3+) tolerance mechanisms involving organic anion efflux from roots have now been investigated in a range of species. Over the past decade, genes encoding these and other newly discovered mechanisms of tolerance have been cloned. In this review, we describe the genes controlling the genotypic variation in Al(3+) tolerance for several important crop species. We focus on recent insights into the transcriptional regulation of these and other genes involved in Al(3+) tolerance and discuss the pathways coordinating their expression in Arabidopsis and rice.
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230
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Advances in biotechnology and linking outputs to variation in complex traits: Plant and Animal Genome meeting January 2012. Funct Integr Genomics 2012; 12:1-9. [DOI: 10.1007/s10142-012-0270-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 02/07/2012] [Indexed: 12/22/2022]
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231
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McCouch SR, McNally KL, Wang W, Sackville Hamilton R. Genomics of gene banks: A case study in rice. AMERICAN JOURNAL OF BOTANY 2012; 99:407-23. [PMID: 22314574 DOI: 10.3732/ajb.1100385] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Only a small fraction of the naturally occurring genetic diversity available in the world's germplasm repositories has been explored to date, but this is expected to change with the advent of affordable, high-throughput genotyping and sequencing technology. It is now possible to examine genome-wide patterns of natural variation and link sequence polymorphisms with downstream phenotypic consequences. In this paper, we discuss how dramatic changes in the cost and efficiency of sequencing and genotyping are revolutionizing the way gene bank scientists approach the responsibilities of their job. Sequencing technology provides a set of tools that can be used to enhance the quality, efficiency, and cost-effectiveness of gene bank operations, the depth of scientific knowledge of gene bank holdings, and the level of public interest in natural variation. As a result, gene banks have the chance to take on new life. Previously seen as "warehouses" where seeds were diligently maintained, but evolutionarily frozen in time, gene banks could transform into vibrant research centers that actively investigate the genetic potential of their holdings. In this paper, we will discuss how genotyping and sequencing can be integrated into the activities of a modern gene bank to revolutionize the way scientists document the genetic identity of their accessions; track seed lots, varieties, and alleles; identify duplicates; and rationalize active collections, and how the availability of genomics data are likely to motivate innovative collaborations with the larger research and breeding communities to engage in systematic and rigorous phenotyping and multilocation evaluation of the genetic resources in gene banks around the world. The objective is to understand and eventually predict how variation at the DNA level helps determine the phenotypic potential of an individual or population. Leadership and vision are needed to coordinate the characterization of collections and to integrate genotypic and phenotypic information in ways that will illuminate the value of these resources. Genotyping of collections represents a powerful starting point that will enable gene banks to become more effective as stewards of crop biodiversity.
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Affiliation(s)
- Susan R McCouch
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NewYork 14853-1901, USA.
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Genome-wide association study identifies candidate genes that affect plant height in Chinese elite maize (Zea mays L.) inbred lines. PLoS One 2011; 6:e29229. [PMID: 22216221 PMCID: PMC3247246 DOI: 10.1371/journal.pone.0029229] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 11/22/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The harvest index for many crops can be improved through introduction of dwarf stature to increase lodging resistance, combined with early maturity. The inbred line Shen5003 has been widely used in maize breeding in China as a key donor line for the dwarf trait. Also, one major quantitative trait locus (QTL) controlling plant height has been identified in bin 5.05-5.06, across several maize bi-parental populations. With the progress of publicly available maize genome sequence, the objective of this work was to identify the candidate genes that affect plant height among Chinese maize inbred lines with genome wide association studies (GWAS). METHODS AND FINDINGS A total of 284 maize inbred lines were genotyped using over 55,000 evenly spaced SNPs, from which a set of 41,101 SNPs were filtered with stringent quality control for further data analysis. With the population structure controlled in a mixed linear model (MLM) implemented with the software TASSEL, we carried out a genome-wide association study (GWAS) for plant height. A total of 204 SNPs (P≤0.0001) and 105 genomic loci harboring coding regions were identified. Four loci containing genes associated with gibberellin (GA), auxin, and epigenetic pathways may be involved in natural variation that led to a dwarf phenotype in elite maize inbred lines. Among them, a favorable allele for dwarfing on chromosome 5 (SNP PZE-105115518) was also identified in six Shen5003 derivatives. CONCLUSIONS The fact that a large number of previously identified dwarf genes are missing from our study highlights the discovery of the consistently significant association of the gene harboring the SNP PZE-105115518 with plant height (P=8.91e-10) and its confirmation in the Shen5003 introgression lines. Results from this study suggest that, in the maize breeding schema in China, specific alleles were selected, that have played important roles in maize production.
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233
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Brachi B, Morris GP, Borevitz JO. Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol 2011; 12:232. [PMID: 22035733 PMCID: PMC3333769 DOI: 10.1186/gb-2011-12-10-232] [Citation(s) in RCA: 304] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Genome-wide association studies (GWAS) have been even more successful in plants than in humans. Mapping approaches can be extended to dissect adaptive genetic variation from structured background variation in an ecological context.
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Affiliation(s)
- Benjamin Brachi
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
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234
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Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, McClung AM, Bustamante CD, McCouch SR. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2011; 2:467. [PMID: 21915109 PMCID: PMC3195253 DOI: 10.1038/ncomms1467] [Citation(s) in RCA: 787] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 08/02/2011] [Indexed: 01/31/2023] Open
Abstract
Asian rice, Oryza sativa is a cultivated, inbreeding species that feeds over half of the world's population. Understanding the genetic basis of diverse physiological, developmental, and morphological traits provides the basis for improving yield, quality and sustainability of rice. Here we show the results of a genome-wide association study based on genotyping 44,100 SNP variants across 413 diverse accessions of O. sativa collected from 82 countries that were systematically phenotyped for 34 traits. Using cross-population-based mapping strategies, we identified dozens of common variants influencing numerous complex traits. Significant heterogeneity was observed in the genetic architecture associated with subpopulation structure and response to environment. This work establishes an open-source translational research platform for genome-wide association studies in rice that directly links molecular variation in genes and metabolic pathways with the germplasm resources needed to accelerate varietal development and crop improvement.
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Affiliation(s)
- Keyan Zhao
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Chih-Wei Tung
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Georgia C. Eizenga
- USDA ARS, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160, USA
| | - Mark H. Wright
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - M. Liakat Ali
- Rice Research and Extension Center, University of Arkansas, Stuttgart, Arkansas 72160, USA
| | - Adam H. Price
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - Gareth J. Norton
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - M. Rafiqul Islam
- Department of Soil Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Andy Reynolds
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Jason Mezey
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Anna M. McClung
- USDA ARS, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160, USA
| | - Carlos D. Bustamante
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Susan R. McCouch
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14850, USA
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