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Thudi M, Chitikineni A, Liu X, He W, Roorkiwal M, Yang W, Jian J, Doddamani D, Gaur PM, Rathore A, Samineni S, Saxena RK, Xu D, Singh NP, Chaturvedi SK, Zhang G, Wang J, Datta SK, Xu X, Varshney RK. Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.). Sci Rep 2016; 6:38636. [PMID: 27982107 PMCID: PMC5159902 DOI: 10.1038/srep38636] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/10/2016] [Indexed: 12/18/2022] Open
Abstract
In order to understand the impact of breeding on genetic diversity and gain insights into temporal trends in diversity in chickpea, a set of 100 chickpea varieties released in 14 countries between 1948 and 2012 were re-sequenced. For analysis, the re-sequencing data for 29 varieties available from an earlier study was also included. Copy number variations and presence absence variations identified in the present study have potential to drive phenotypic variations for trait improvement. Re-sequencing of a large number of varieties has provided opportunities to inspect the genetic and genomic changes reflecting the history of breeding, which we consider as breeding signatures and the selected loci may provide targets for crop improvement. Our study also reports enhanced diversity in both desi and kabuli varieties as a result of recent chickpea breeding efforts. The current study will aid the explicit efforts to breed for local adaptation in the context of anticipated climate changes.
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Affiliation(s)
- Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Xin Liu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | | | - Dadakhalandar Doddamani
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pooran M. Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Srinivasan Samineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Narendra P. Singh
- All India Coordinated Research Project (AICRP) on Chickpea, Indian Council of Agricultural Research (ICAR), New Delhi, India
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, India
| | - Sushil K. Chaturvedi
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, India
| | | | | | | | | | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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202
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Sun C, Hu Z, Zheng T, Lu K, Zhao Y, Wang W, Shi J, Wang C, Lu J, Zhang D, Li Z, Wei C. RPAN: rice pan-genome browser for ∼3000 rice genomes. Nucleic Acids Res 2016; 45:597-605. [PMID: 27940610 PMCID: PMC5314802 DOI: 10.1093/nar/gkw958] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 10/02/2016] [Accepted: 10/24/2016] [Indexed: 11/14/2022] Open
Abstract
A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k.
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Affiliation(s)
- Chen Sun
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai Center for Bioinformation Technology, Shanghai 201203, China
| | - Zhiqiang Hu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai Center for Bioinformation Technology, Shanghai 201203, China
| | - Tianqing Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kuangchen Lu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yue Zhao
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wensheng Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunchao Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinyuan Lu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chaochun Wei
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China .,Shanghai Center for Bioinformation Technology, Shanghai 201203, China
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203
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Munasinghe M, Price AH. Genetic and root phenotype diversity in Sri Lankan rice landraces may be related to drought resistance. RICE (NEW YORK, N.Y.) 2016; 9:24. [PMID: 27189009 PMCID: PMC5396129 DOI: 10.1186/s12284-016-0092-7] [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: 11/18/2015] [Accepted: 04/23/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND The development of relatively cheap and high throughput methods of genotyping and phenotyping plants offers the opportunity to explore local germplasm more thoroughly than before and should accelerate the identification of sources of genetic variation suitable for breeding. In this study, 135 Sri Lankan accessions, mostly identified as landraces, for which data was available at the International Rice Research Institute on drought scores were genotyped using a 384 SNP array and assessed for root depth using a newly developed buried herbicide method. Roots of 36 accessions were assessed using hydroponics and 12 using soil-filled rhizotrons to establish if variation in herbicide score could be attributed to root traits. RESULTS Population structure based on the SNPs using STRUCTURE revealed six groups, being tropical japonica, aus and four indica subpopulations. Three of these indica subpopulations do not seem to be represented in the Rice Diversity Panel I (RDP1) of 372 global rice accessions and appear to represent genetic diversity so far poorly studied by the global scientific community. The herbicide score was highly discriminatory between landraces and correlated very strongly with hydroponic and rhizotron root traits. The mean herbicide score strongly differentiated between landraces according to the province and the latitude from which they were collected. It also differed between subpopulations, being high in indica 2 and tropical japonica and low in indica 1 and aus. Drought scores suggest that indica 2 is more drought resistant than the other groups. Correlations indicate that those landraces with high herbicide scores are more drought resistant in the vegetative stage. The landrace Niyan Wee, whose name in Sinhalese means "drought rice" belongs to the indica 2 subgroup, has high herbicide scores and deep roots. CONCLUSIONS Niyan Wee and other cultivars within the indica 2 subgroup should be a valuable source of breeding for drought resistance at least partly because of their superior root traits, not normally associated with the indica rice cultivars.
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Affiliation(s)
- Mayuri Munasinghe
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
- Current address: University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Adam H Price
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK.
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204
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Groen SC, Purugganan MD. Systems genetics of plant adaptation to environmental stresses. AMERICAN JOURNAL OF BOTANY 2016; 103:2019-2021. [PMID: 27864265 DOI: 10.3732/ajb.1600340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 10/19/2016] [Indexed: 05/22/2023]
Affiliation(s)
- Simon C Groen
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York 10003 USA
| | - Michael D Purugganan
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, New York 10003 USA
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205
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Liang Z, Wang L, Pan Q. A New Recessive Gene Conferring Resistance Against Rice Blast. RICE (NEW YORK, N.Y.) 2016; 9:47. [PMID: 27637926 PMCID: PMC5025421 DOI: 10.1186/s12284-016-0120-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 09/10/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Rice blast (causative pathogen Magnaporthe oryzae) represents a major biotic constraint over rice production. While numerous genes for resistance have been found in both japonica and indica germplasm, as yet the diversity harbored by aus germplasm has not been widely exploited. RESULTS The blast resistance present in the aus type cultivar AS20-1 was shown, via an analysis of segregation in the F2 generation bred from a cross with the highly blast susceptible cultivar Aichi Asahi, to be due to the action of a single recessive gene, denoted pi66(t). The presence of pi66(t) gave an intermediate level control to plants infected with the blast pathogen isolate EHL0635. A bulked segregant analysis indicated that four microsatellite loci (SSRs) mapping to chromosome 3 were probably linked to pi66(t). Localized mapping using chromosome 3-based SSRs and Indels defined a genetic window for pi66(t), flanked by the markers F04-j2 and M19-i12, which physically equals to 27.7 and 49.0 kb, respectively, in the reference genomes of cultivars Nipponbare and 93-11. This physical interval does not harbor any major gene currently associated with disease resistance. CONCLUSION pi66(t) is one of just three recessive genes controlling rice blast, and is the first major gene for resistance to be mapped to chromosome 3.
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Affiliation(s)
- Zhijian Liang
- State Key laboratory for Conservation and Utilization of Subtropic Agrobioresurces, Guangdong Provincial Key Laboratory for Crop Molecular Breeding, Rice Blast Research Center, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
| | - Ling Wang
- State Key laboratory for Conservation and Utilization of Subtropic Agrobioresurces, Guangdong Provincial Key Laboratory for Crop Molecular Breeding, Rice Blast Research Center, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
| | - Qinghua Pan
- State Key laboratory for Conservation and Utilization of Subtropic Agrobioresurces, Guangdong Provincial Key Laboratory for Crop Molecular Breeding, Rice Blast Research Center, South China Agricultural University, Guangzhou, 510642 People’s Republic of China
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206
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Reig-Valiente JL, Viruel J, Sales E, Marqués L, Terol J, Gut M, Derdak S, Talón M, Domingo C. Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions. RICE (NEW YORK, N.Y.) 2016; 9:58. [PMID: 27766601 PMCID: PMC5073090 DOI: 10.1186/s12284-016-0130-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 10/13/2016] [Indexed: 05/29/2023]
Abstract
BACKGROUND After its domestication, rice cultivation expanded from tropical regions towards northern latitudes with temperate climate in a progressive process to overcome limiting photoperiod and temperature conditions. This process has originated a wide range of diversity that can be regarded as a valuable resource for crop improvement. In general, current rice breeding programs have to deal with a lack of both germplasm accessions specifically adapted to local agro-environmental conditions and adapted donors carrying desired agronomical traits. Comprehensive maps of genome variability and population structure would facilitate genome-wide association studies of complex traits, functional gene investigations and the selection of appropriate donors for breeding purposes. RESULTS A collection of 217 rice varieties mainly cultivated in temperate regions was generated. The collection encompasses modern elite and old cultivars, as well as traditional landraces covering a wide genetic diversity available for rice breeders. Whole Genome Sequencing was performed on 14 cultivars representative of the collection and the genomic profiles of all cultivars were constructed using a panel of 2697 SNPs with wide coverage throughout the rice genome, obtained from the sequencing data. The population structure and genetic relationship analyses showed a strong substructure in the temperate rice population, predominantly based on grain type and the origin of the cultivars. Dendrogram also agrees population structure results. CONCLUSIONS Based on SNP markers, we have elucidated the genetic relationship and the degree of genetic diversity among a collection of 217 temperate rice varieties possessing an enormous variety of agromorphological and physiological characters. Taken together, the data indicated the occurrence of relatively high gene flow and elevated rates of admixture between cultivars grown in remote regions, probably favoured by local breeding activities. The results of this study significantly expand the current genetic resources available for temperate varieties of rice, providing a valuable tool for future association mapping studies.
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Affiliation(s)
- Juan L. Reig-Valiente
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV 315 Km 10,7 (Carretera Moncada – Náquera Km 4.5), 46113 Moncada, Spain
| | - Juan Viruel
- Dpto. Biología Vegetal y Ecología, SGI Herbario – Universidad de Sevilla, Edif. Celestino Mutis, Av. Reina Mercedes s/n, 41012 Sevilla, Spain
- Institut Méditerranéen de Biodiversité et d’Ecologie Marine et Continentale (IMBE), Aix Marseille Université, Chemin de la Batterie des Lions, 13007 Marseille, France
| | - Ester Sales
- Dpto. Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior, Universidad de Zaragoza, Ctra. Cuarte s/n, 22071 Huesca, Spain
| | - Luis Marqués
- Cooperativa de Productores de Semillas de Arroz, Avenida del Mar 1, 46410 Sueca, Spain
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV 315 Km 10,7 (Carretera Moncada – Náquera Km 4.5), 46113 Moncada, Spain
| | - Marta Gut
- Centre Nacional d’Anàlisi Genòmica - Centre for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sophia Derdak
- Centre Nacional d’Anàlisi Genòmica - Centre for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Manuel Talón
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV 315 Km 10,7 (Carretera Moncada – Náquera Km 4.5), 46113 Moncada, Spain
| | - Concha Domingo
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV 315 Km 10,7 (Carretera Moncada – Náquera Km 4.5), 46113 Moncada, Spain
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207
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Matsumoto T, Wu J, Itoh T, Numa H, Antonio B, Sasaki T. The Nipponbare genome and the next-generation of rice genomics research in Japan. RICE (NEW YORK, N.Y.) 2016; 9:33. [PMID: 27447712 PMCID: PMC4958085 DOI: 10.1186/s12284-016-0107-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 07/03/2016] [Indexed: 05/28/2023]
Abstract
The map-based genome sequence of the japonica rice cultivar Nipponbare remains to date as the only monocot genome that has been sequenced to a high-quality level. It has become the reference sequence for understanding the diversity among thousands of rice cultivars and its wild relatives as well as the major cereal crops that comprised the food source for the entire human race. This review focuses on the accomplishments in rice genomics in Japan encompassing the last 10 years which have led into deeper understanding of the genome, characterization of many agronomic traits, comprehensive analysis of the transcriptome, and the map-based cloning of many genes associated with agronomic traits.
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Affiliation(s)
- Takashi Matsumoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
| | - Jianzhong Wu
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Takeshi Itoh
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Hisataka Numa
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Baltazar Antonio
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Takuji Sasaki
- Nodai Research Institute, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
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208
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Mansueto L, Fuentes RR, Borja FN, Detras J, Abriol-Santos JM, Chebotarov D, Sanciangco M, Palis K, Copetti D, Poliakov A, Dubchak I, Solovyev V, Wing RA, Hamilton RS, Mauleon R, McNally KL, Alexandrov N. Rice SNP-seek database update: new SNPs, indels, and queries. Nucleic Acids Res 2016; 45:D1075-D1081. [PMID: 27899667 PMCID: PMC5210592 DOI: 10.1093/nar/gkw1135] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/14/2016] [Accepted: 11/04/2016] [Indexed: 11/16/2022] Open
Abstract
We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer. Middleware is redesigned for improved performance by using a hybrid of HDF5 and RDMS for genotype storage. Query modules for genotypes, varieties and genes are improved to handle various constraints. An integrated list manager allows the user to pass query parameters for further analysis. The SNP Annotator adds traits, ontology terms, effects and interactions to markers in a list. Web-service calls were implemented to access most data. These features enable seamless querying of SNP-Seek across various biological entities, a step toward semi-automated gene-trait association discovery. URL: http://snp-seek.irri.org.
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Affiliation(s)
- Locedie Mansueto
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
| | - Roven Rommel Fuentes
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
| | - Frances Nikki Borja
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
| | - Jeffery Detras
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
| | | | - Dmytro Chebotarov
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
| | - Millicent Sanciangco
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
| | - Kevin Palis
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.,Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85750, USA
| | - Alexandre Poliakov
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Inna Dubchak
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | | | - Rod A Wing
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.,Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85750, USA
| | | | - Ramil Mauleon
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
| | - Kenneth L McNally
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
| | - Nickolai Alexandrov
- International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines
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209
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The BIG Data Center: from deposition to integration to translation. Nucleic Acids Res 2016; 45:D18-D24. [PMID: 27899658 PMCID: PMC5210546 DOI: 10.1093/nar/gkw1060] [Citation(s) in RCA: 425] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 02/06/2023] Open
Abstract
Biological data are generated at unprecedentedly exponential rates, posing considerable challenges in big data deposition, integration and translation. The BIG Data Center, established at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, provides a suite of database resources, including (i) Genome Sequence Archive, a data repository specialized for archiving raw sequence reads, (ii) Gene Expression Nebulas, a data portal of gene expression profiles based entirely on RNA-Seq data, (iii) Genome Variation Map, a comprehensive collection of genome variations for featured species, (iv) Genome Warehouse, a centralized resource housing genome-scale data with particular focus on economically important animals and plants, (v) Methylation Bank, an integrated database of whole-genome single-base resolution methylomes and (vi) Science Wikis, a central access point for biological wikis developed for community annotations. The BIG Data Center is dedicated to constructing and maintaining biological databases through big data integration and value-added curation, conducting basic research to translate big data into big knowledge and providing freely open access to a variety of data resources in support of worldwide research activities in both academia and industry. All of these resources are publicly available and can be found at http://bigd.big.ac.cn.
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Affiliation(s)
- BIG Data Center Members
- To whom correspondence should be addressed Zhang Zhang. Tel: +86 10 8409 7261; Fax: +86 10 8409 7720;
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210
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Tatarinova TV, Chekalin E, Nikolsky Y, Bruskin S, Chebotarov D, McNally KL, Alexandrov N. Nucleotide diversity analysis highlights functionally important genomic regions. Sci Rep 2016; 6:35730. [PMID: 27774999 PMCID: PMC5075931 DOI: 10.1038/srep35730] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/30/2016] [Indexed: 12/15/2022] Open
Abstract
We analyzed functionality and relative distribution of genetic variants across the complete Oryza sativa genome, using the 40 million single nucleotide polymorphisms (SNPs) dataset from the 3,000 Rice Genomes Project (http://snp-seek.irri.org), the largest and highest density SNP collection for any higher plant. We have shown that the DNA-binding transcription factors (TFs) are the most conserved group of genes, whereas kinases and membrane-localized transporters are the most variable ones. TFs may be conserved because they belong to some of the most connected regulatory hubs that modulate transcription of vast downstream gene networks, whereas signaling kinases and transporters need to adapt rapidly to changing environmental conditions. In general, the observed profound patterns of nucleotide variability reveal functionally important genomic regions. As expected, nucleotide diversity is much higher in intergenic regions than within gene bodies (regions spanning gene models), and protein-coding sequences are more conserved than untranslated gene regions. We have observed a sharp decline in nucleotide diversity that begins at about 250 nucleotides upstream of the transcription start and reaches minimal diversity exactly at the transcription start. We found the transcription termination sites to have remarkably symmetrical patterns of SNP density, implying presence of functional sites near transcription termination. Also, nucleotide diversity was significantly lower near 3′ UTRs, the area rich with regulatory regions.
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Affiliation(s)
- Tatiana V Tatarinova
- Center for Personalized Medicine and Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Yuri Nikolsky
- Vavilov Institute of General Genetics, Moscow, Russia.,F1 Genomics, San Diego, CA, USA.,School of Systems Biology, George Mason University, VA, USA
| | | | - Dmitry Chebotarov
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines
| | - Kenneth L McNally
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines
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211
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Deng X, Song X, Wei L, Liu C, Cao X. Epigenetic regulation and epigenomic landscape in rice. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww042] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Abstract
Epigenetic regulation has been implicated in the control of complex agronomic traits in rice (Oryza sativa), a staple food crop and model monocot plant. Recent advances in high-throughput sequencing and the moderately complex genome of rice have made it possible to study epigenetic regulation in rice on a genome-wide scale. This review discusses recent advances in our understanding of epigenetic regulation in rice, with an emphasis on the roles of key epigenetic regulators, the epigenomic landscape, epigenetic variation, transposon repression, and plant development.
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Affiliation(s)
- Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liya Wei
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Chunyan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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Prakash C, Mithra SVA, Singh PK, Mohapatra T, Singh NK. Unraveling the molecular basis of oxidative stress management in a drought tolerant rice genotype Nagina 22. BMC Genomics 2016. [PMID: 27716126 DOI: 10.6084/m9.figshare.c.3624881_d3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
BACKGROUND Drought stress tolerance for crop improvement is an important goal worldwide. Drought is a complex trait, and it is vital to understand the complex physiological, biochemical, and molecular mechanisms of drought tolerance to tackle it effectively. Osmotic adjustment, oxidative stress management (OSM), and cell membrane stability (CMS) are major components of cellular tolerance under drought stress. In the current study, we explored the molecular basis of OSM in the drought tolerant rice variety, Nagina 22 and compared it with the popular drought sensitive rice variety, IR 64, under drought imposed at the reproductive stage, to understand how the parental polymorphisms correlate with the superiority of Nagina 22 and tolerant bulk populations under drought. RESULTS We generated recombinant inbred lines (RIL) from contrasting parents Nagina 22 and IR 64 and focussed on spikelet fertility (SF), in terms of its correlation with OSM, which is an important component of drought tolerance in Nagina 22. Based on SF under drought stress and its correlations with other yield related traits, we used superoxide dismutase (SOD), glutathione reductase (GR), and ascorbate peroxidase (APX) activity assays to establish the relationship between SF and OSM genes in the tolerant and sensitive lines. Among the OSM enzymes studied, GR had a significant and positive correlation with single plant yield (SPY) under drought stress. GR was also positively correlated with APX but negatively so with SOD. Interestingly, none of the enzyme-morphology correlations were significant under irrigated control (IC). Through genome-wide SNP analysis of the 21 genes encoding for OSM enzymes, we identified the functional polymorphisms between the parents and identified superior alleles. By using network analysis of OSM genes in rice, we identified the genes that are central to the OSM network. CONCLUSIONS From the biochemical and morphological data and the SNP analysis, the superiority of Nagina 22 in spikelet fertility under drought stress is because of its superior alleles for SOD (SOD2, SODCC1, SODA) and GR (GRCP2) rather than for APX, for which IR 64 had the superior allele (APX8). Nagina 22 can bypass APX8 by directly interacting with SODA. For nine of the 11 genes present in the central network, Nagina 22 had the superior alleles. We propose that Nagina 22 tolerance could mainly be because of SODA which is a reactive oxygen scavenger in mitochondria which is directly associated with spikelet fertility.
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Affiliation(s)
- Chandra Prakash
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012, India
| | - S V Amitha Mithra
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012, India.
| | - Praveen K Singh
- Division of Seed Science and Technology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012, India
| | - T Mohapatra
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110 001, India
| | - N K Singh
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012, India
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213
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Prakash C, Mithra SVA, Singh PK, Mohapatra T, Singh NK. Unraveling the molecular basis of oxidative stress management in a drought tolerant rice genotype Nagina 22. BMC Genomics 2016; 17:774. [PMID: 27716126 PMCID: PMC5050613 DOI: 10.1186/s12864-016-3131-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 09/27/2016] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Drought stress tolerance for crop improvement is an important goal worldwide. Drought is a complex trait, and it is vital to understand the complex physiological, biochemical, and molecular mechanisms of drought tolerance to tackle it effectively. Osmotic adjustment, oxidative stress management (OSM), and cell membrane stability (CMS) are major components of cellular tolerance under drought stress. In the current study, we explored the molecular basis of OSM in the drought tolerant rice variety, Nagina 22 and compared it with the popular drought sensitive rice variety, IR 64, under drought imposed at the reproductive stage, to understand how the parental polymorphisms correlate with the superiority of Nagina 22 and tolerant bulk populations under drought. RESULTS We generated recombinant inbred lines (RIL) from contrasting parents Nagina 22 and IR 64 and focussed on spikelet fertility (SF), in terms of its correlation with OSM, which is an important component of drought tolerance in Nagina 22. Based on SF under drought stress and its correlations with other yield related traits, we used superoxide dismutase (SOD), glutathione reductase (GR), and ascorbate peroxidase (APX) activity assays to establish the relationship between SF and OSM genes in the tolerant and sensitive lines. Among the OSM enzymes studied, GR had a significant and positive correlation with single plant yield (SPY) under drought stress. GR was also positively correlated with APX but negatively so with SOD. Interestingly, none of the enzyme-morphology correlations were significant under irrigated control (IC). Through genome-wide SNP analysis of the 21 genes encoding for OSM enzymes, we identified the functional polymorphisms between the parents and identified superior alleles. By using network analysis of OSM genes in rice, we identified the genes that are central to the OSM network. CONCLUSIONS From the biochemical and morphological data and the SNP analysis, the superiority of Nagina 22 in spikelet fertility under drought stress is because of its superior alleles for SOD (SOD2, SODCC1, SODA) and GR (GRCP2) rather than for APX, for which IR 64 had the superior allele (APX8). Nagina 22 can bypass APX8 by directly interacting with SODA. For nine of the 11 genes present in the central network, Nagina 22 had the superior alleles. We propose that Nagina 22 tolerance could mainly be because of SODA which is a reactive oxygen scavenger in mitochondria which is directly associated with spikelet fertility.
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Affiliation(s)
- Chandra Prakash
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012 India
| | - S. V. Amitha Mithra
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012 India
| | - Praveen K. Singh
- Division of Seed Science and Technology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012 India
| | - T. Mohapatra
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110 001 India
| | - N. K. Singh
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012 India
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214
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Wang J, Yu J, Sun P, Li Y, Xia R, Liu Y, Ma X, Yu J, Yang N, Lei T, Wang Z, Wang L, Ge W, Song X, Liu X, Sun S, Liu T, Jin D, Pan Y, Wang X. Comparative Genomics Analysis of Rice and Pineapple Contributes to Understand the Chromosome Number Reduction and Genomic Changes in Grasses. Front Genet 2016; 7:174. [PMID: 27757123 PMCID: PMC5047885 DOI: 10.3389/fgene.2016.00174] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/13/2016] [Indexed: 11/13/2022] Open
Abstract
Rice is one of the most researched model plant, and has a genome structure most resembling that of the grass common ancestor after a grass common tetraploidization ∼100 million years ago. There has been a standing controversy whether there had been five or seven basic chromosomes, before the tetraploidization, which were tackled but could not be well solved for the lacking of a sequenced and assembled outgroup plant to have a conservative genome structure. Recently, the availability of pineapple genome, which has not been subjected to the grass-common tetraploidization, provides a precious opportunity to solve the above controversy and to research into genome changes of rice and other grasses. Here, we performed a comparative genomics analysis of pineapple and rice, and found solid evidence that grass-common ancestor had 2n = 2x = 14 basic chromosomes before the tetraploidization and duplicated to 2n = 4x = 28 after the event. Moreover, we proposed that enormous gene missing from duplicated regions in rice should be explained by an allotetraploid produced by prominently divergent parental lines, rather than gene losses after their divergence. This means that genome fractionation might have occurred before the formation of the allotetraploid grass ancestor.
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Affiliation(s)
- Jinpeng Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
| | - Jiaxiang Yu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
| | - Pengchuan Sun
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
| | - Yuxian Li
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
| | - Ruiyan Xia
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
| | - Yinzhe Liu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
| | - Xuelian Ma
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
| | - Jigao Yu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
| | - Nanshan Yang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
| | - Tianyu Lei
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
| | - Zhenyi Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
| | - Li Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
| | - Weina Ge
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
| | - Xiaoming Song
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
| | - Xiaojian Liu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
| | - Sangrong Sun
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
| | - Tao Liu
- College of Science, North China University of Science and Technology Tangshan, China
| | - Dianchuan Jin
- College of Science, North China University of Science and Technology Tangshan, China
| | - Yuxin Pan
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
| | - Xiyin Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology Tangshan, China
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215
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Prakash C, Mithra SVA, Singh PK, Mohapatra T, Singh NK. Unraveling the molecular basis of oxidative stress management in a drought tolerant rice genotype Nagina 22. BMC Genomics 2016. [PMID: 27716126 DOI: 10.1186/s12864-016-3131-2do] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND Drought stress tolerance for crop improvement is an important goal worldwide. Drought is a complex trait, and it is vital to understand the complex physiological, biochemical, and molecular mechanisms of drought tolerance to tackle it effectively. Osmotic adjustment, oxidative stress management (OSM), and cell membrane stability (CMS) are major components of cellular tolerance under drought stress. In the current study, we explored the molecular basis of OSM in the drought tolerant rice variety, Nagina 22 and compared it with the popular drought sensitive rice variety, IR 64, under drought imposed at the reproductive stage, to understand how the parental polymorphisms correlate with the superiority of Nagina 22 and tolerant bulk populations under drought. RESULTS We generated recombinant inbred lines (RIL) from contrasting parents Nagina 22 and IR 64 and focussed on spikelet fertility (SF), in terms of its correlation with OSM, which is an important component of drought tolerance in Nagina 22. Based on SF under drought stress and its correlations with other yield related traits, we used superoxide dismutase (SOD), glutathione reductase (GR), and ascorbate peroxidase (APX) activity assays to establish the relationship between SF and OSM genes in the tolerant and sensitive lines. Among the OSM enzymes studied, GR had a significant and positive correlation with single plant yield (SPY) under drought stress. GR was also positively correlated with APX but negatively so with SOD. Interestingly, none of the enzyme-morphology correlations were significant under irrigated control (IC). Through genome-wide SNP analysis of the 21 genes encoding for OSM enzymes, we identified the functional polymorphisms between the parents and identified superior alleles. By using network analysis of OSM genes in rice, we identified the genes that are central to the OSM network. CONCLUSIONS From the biochemical and morphological data and the SNP analysis, the superiority of Nagina 22 in spikelet fertility under drought stress is because of its superior alleles for SOD (SOD2, SODCC1, SODA) and GR (GRCP2) rather than for APX, for which IR 64 had the superior allele (APX8). Nagina 22 can bypass APX8 by directly interacting with SODA. For nine of the 11 genes present in the central network, Nagina 22 had the superior alleles. We propose that Nagina 22 tolerance could mainly be because of SODA which is a reactive oxygen scavenger in mitochondria which is directly associated with spikelet fertility.
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Affiliation(s)
- Chandra Prakash
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012, India
| | - S V Amitha Mithra
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012, India.
| | - Praveen K Singh
- Division of Seed Science and Technology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012, India
| | - T Mohapatra
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110 001, India
| | - N K Singh
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012, India
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216
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Savolainen O, Lascoux M. Geography matters for Arabidopsis. Nature 2016; 537:314-315. [DOI: 10.1038/nature19466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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217
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Recent Perspective of Next Generation Sequencing: Applications in Molecular Plant Biology and Crop Improvement. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s40011-016-0770-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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218
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Zhang Q, Zheng T, Hoang L, Wang C, Nafisah, Joseph C, Zhang W, Xu J, Li Z. Joint Mapping and Allele Mining of the Rolled Leaf Trait in Rice (Oryza sativa L.). PLoS One 2016; 11:e0158246. [PMID: 27441398 PMCID: PMC4956317 DOI: 10.1371/journal.pone.0158246] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/12/2016] [Indexed: 01/01/2023] Open
Abstract
The rolled leaf trait, long considered to be a key component of plant architecture, represents an important target trait for improving plant architecture at the population level. We therefore performed linkage mapping using a set of 262 highly variable RILs from two rice cultivars (Minghui 63 and 02428) with minor differences in leaf rolling index (LRI) in conjunction with GWAS mapping of a random subset of the 1127 germplasms from the 3K Rice Genomes Project (3K Rice). A total of seven main-effect loci were found to underlie the transgressive segregation of progenies from parents with minor differences in LRI. Five of these loci were previously identified and two (qRl7b and qRl9b) are newly reported with additional evidence from GWAS mapping for qRl7b. A total of 18 QTLs were identified by GWAS, including four newly identified QTLs. Six QTLs were confirmed by linkage mapping with the above RIL population, and 83.3% were found to be consistent with previously reported loci based on comparative mapping. We also performed allele mining with representative SNPs and identified the elite germplasms for the improvement of rolled leaf trait. Most favorable alleles at the detected loci were contributed by various 3K Rice germplasms. By a re-scanning of the candidate region with more saturated SNP markers, we dissected the region harboring gRl4-2 into three subregions, in which the average effect on LRI was 3.5% with a range from 2.4 to 4.1% in the third subregion, suggesting the presence of a new locus or loci within this region. The representative SNPs for favorable alleles in the reliable QTLs which were consistently identified in both bi-parental mapping and GWAS, such as qRl4, qRl5, qRl6, qRl7a, and qRl7b will be useful for future molecular breeding programs for ideal plant type in rice.
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Affiliation(s)
- Qiang Zhang
- Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
- 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, 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, Beijing 100081, China
| | - Long Hoang
- 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, Beijing 100081, China
| | - Chunchao 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, Beijing 100081, China
| | - Nafisah
- 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, Beijing 100081, China
| | - Charles Joseph
- 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, Beijing 100081, China
| | - Wenzhong Zhang
- Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, 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, Beijing 100081, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Shenzhen Institute of Breeding & Innovation, Chinese Academy of Agricultural Sciences, Shenzhen 518120, 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, Beijing 100081, China
- Shenzhen Institute of Breeding & Innovation, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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219
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Alonso-Blanco C, Andrade J, Becker C, Bemm F, Bergelson J, Borgwardt KM, Cao J, Chae E, Dezwaan TM, Ding W, Ecker JR, Exposito-Alonso M, Farlow A, Fitz J, Gan X, Grimm DG, Hancock AM, Henz SR, Holm S, Horton M, Jarsulic M, Kerstetter RA, Korte A, Korte P, Lanz C, Lee CR, Meng D, Michael TP, Mott R, Muliyati NW, Nägele T, Nagler M, Nizhynska V, Nordborg M, Novikova PY, Picó FX, Platzer A, Rabanal FA, Rodriguez A, Rowan BA, Salomé PA, Schmid KJ, Schmitz RJ, Seren Ü, Sperone FG, Sudkamp M, Svardal H, Tanzer MM, Todd D, Volchenboum SL, Wang C, Wang G, Wang X, Weckwerth W, Weigel D, Zhou X. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell 2016; 166:481-491. [PMID: 27293186 PMCID: PMC4949382 DOI: 10.1016/j.cell.2016.05.063] [Citation(s) in RCA: 757] [Impact Index Per Article: 94.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/20/2016] [Accepted: 05/17/2016] [Indexed: 12/30/2022]
Abstract
Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.
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220
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Wang H, Xu X, Vieira FG, Xiao Y, Li Z, Wang J, Nielsen R, Chu C. The Power of Inbreeding: NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication. MOLECULAR PLANT 2016; 9:975-85. [PMID: 27179918 DOI: 10.1016/j.molp.2016.04.018] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 04/16/2016] [Accepted: 04/27/2016] [Indexed: 05/22/2023]
Abstract
Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in humans, due to the availability of large reference panels for genotype imputation. However, it is unclear whether this strategy can be utilized in other species without reference panels. Using simulations, we show that this approach is even more relevant in inbred species such as rice (Oryza sativa L.), which are effectively haploid, allowing easy haplotype construction and imputation-based genotype calling, even without the availability of large reference panels. We sequenced 203 rice varieties with well-characterized phenotypes from the United States Department of Agriculture Rice Mini-Core Collection at an average depth of 1.5× and used the data for mapping three traits. For the first two traits, amylose content and seed length, our approach leads to direct identification of the previously identified causal SNPs in the major-effect loci. For the third trait, pericarp color, an important trait underwent selection during domestication, we identified a new major-effect locus. Although known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice, japonica and indica, the new locus identified is unique to another domesticated rice subgroup, aus, and together with existing loci, can fully explain the major variation in pericarp color in aus. Our discovery of a unique genetic basis of white pericarp in aus provides an example of convergent evolution during rice domestication and suggests that aus may have a domestication history independent of japonica and indica.
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Affiliation(s)
- Hongru Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Yunhua Xiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facilities for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Beijing 100081, China
| | - Jun Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China.
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, CA 94720 USA.
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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221
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Kim J, Woo HR, Nam HG. Toward Systems Understanding of Leaf Senescence: An Integrated Multi-Omics Perspective on Leaf Senescence Research. MOLECULAR PLANT 2016; 9:813-25. [PMID: 27174403 DOI: 10.1016/j.molp.2016.04.017] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 04/15/2016] [Accepted: 04/27/2016] [Indexed: 05/20/2023]
Abstract
Leaf senescence is a complex but tightly regulated developmental process involving a coordinated sequence of multiple molecular events, which ultimately leads to death of the leaf. Efforts to understand the mechanistic principles underlying leaf senescence have been largely made by transcriptomic, proteomic, and metabolomic studies over the past decade. This review focuses on recent milestones in leaf senescence research obtained using multi-omics technologies, as well as future endeavors toward systems understanding of leaf senescence processes. In particular, we discuss recent advances in understanding molecular events during leaf senescence through genome-wide transcriptome analyses in Arabidopsis. We also describe comparative transcriptome analyses used to unveil the commonality and diversity of regulatory mechanisms governing leaf senescence in the plant kingdom. Finally, we provide current illustrations of epigenomic, proteomic, and metabolomic landscapes of leaf senescence. We envisage that integration of multi-omics leaf senescence data will enable us to address unresolved questions regarding leaf senescence, including determining the molecular principles that coordinate concurrent and ordered changes in biological events during leaf senescence.
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Affiliation(s)
- Jeongsik Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea
| | - Hye Ryun Woo
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea.
| | - Hong Gil Nam
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea; Department of New Biology, DGIST, Daegu, 42988, Republic of Korea.
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222
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Sempéré G, Philippe F, Dereeper A, Ruiz M, Sarah G, Larmande P. Gigwa-Genotype investigator for genome-wide analyses. Gigascience 2016; 5:25. [PMID: 27267926 PMCID: PMC4897896 DOI: 10.1186/s13742-016-0131-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/16/2016] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions. DESCRIPTION Here we present Gigwa, a web-based tool that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability properties. Gigwa can handle multiple databases and may be deployed in either single- or multi-user mode. In addition, it provides a wide range of popular export formats. CONCLUSIONS The Gigwa application is suitable for managing large amounts of genomic variation data. Its user-friendly web interface makes such processing widely accessible. It can either be simply deployed on a workstation or be used to provide a shared data portal for a given community of researchers.
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Affiliation(s)
- Guilhem Sempéré
- UMR InterTryp (CIRAD), Campus International de Baillarguet, 34398, Montpellier, Cedex 5, France.
- South Green Bioinformatics Platform, 1000 Avenue Agropolis, 34934, Montpellier, Cedex 5, France.
| | - Florian Philippe
- UMR DIADE (IRD), 911 Avenue Agropolis, 34934, Montpellier, Cedex 5, France
| | - Alexis Dereeper
- South Green Bioinformatics Platform, 1000 Avenue Agropolis, 34934, Montpellier, Cedex 5, France
- UMR IPME (IRD), 911 Avenue Agropolis, 34394, Montpellier, Cedex 5, France
| | - Manuel Ruiz
- South Green Bioinformatics Platform, 1000 Avenue Agropolis, 34934, Montpellier, Cedex 5, France
- UMR AGAP, CIRAD, 34398, Montpellier, Cedex 5, France
- Institut de Biologie Computationnelle, Université de Montpellier, 860 Rue de St Priest, 34095, Montpellier, Cedex 5, France
- Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), 6713, Cali, Colombia
| | - Gautier Sarah
- South Green Bioinformatics Platform, 1000 Avenue Agropolis, 34934, Montpellier, Cedex 5, France
- INRA, UMR AGAP, 34398, Montpellier, Cedex 5, France
| | - Pierre Larmande
- South Green Bioinformatics Platform, 1000 Avenue Agropolis, 34934, Montpellier, Cedex 5, France
- UMR DIADE (IRD), 911 Avenue Agropolis, 34934, Montpellier, Cedex 5, France
- Institut de Biologie Computationnelle, Université de Montpellier, 860 Rue de St Priest, 34095, Montpellier, Cedex 5, France
- INRIA Zenith Team, LIRMM, 161 Rue Ada, 34095, Montpellier, Cedex 5, France
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223
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Wissuwa M, Kretzschmar T, Rose TJ. From promise to application: root traits for enhanced nutrient capture in rice breeding. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3605-15. [PMID: 27036129 DOI: 10.1093/jxb/erw061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Improving nutrient uptake is an objective in crop breeding, especially in tropical areas where infertile soils dominate and farmers may not have the resources to improve soil fertility through fertilizer application. Scientific endeavors to understand the genetic basis of nutrient acquisition have mostly followed reverse genetic approaches. This has undoubtedly led to improved understanding of basic principles in root development and nutrient transport. However, little evidence suggests that the genes identified are actively utilized in breeding programs, and the bottleneck has been the failure to establish links between allelic variation for identified genes and performance in the field. Screening experiments typically reveal large genotypic variation in performance under nutrient deficiency, strongly suggesting the presence of superior alleles for genes controlling root growth and/or nutrient uptake processes. Progress in sequencing technology has enabled characterizations of allelic variation across whole genomes and an international effort has recently culminated in the sequencing of 3000 rice genomes from the International Rice Research Institute genebank. Queries of the 3000 rice sequence database offer immediate possibilities to assess the extent to which allelic variation exists for candidate genes. By selecting subsets of accessions, allelic effects can be tested, diagnostic markers developed, and new donors identified. Technological and conceptual advances in phenotyping of root traits offer improved possibilities to assure that trait-allele associations are established in ways that link to field performance. Genotype-to-phenotype relationships can thus be predicted and tested with unprecedented precision, facilitating the discovery and transfer of beneficial nutrition-related alleles and associated markers into existing breeding pipelines.
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Affiliation(s)
- Matthias Wissuwa
- Crop, Livestock and Environment Division, Japan International Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Tobias Kretzschmar
- Genotyping Services Laboratory, International Rice Research Institute, The Philippines
| | - Terry J Rose
- Southern Cross Plant Science, Southern Cross University, Australia
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Wei FJ, Tsai YC, Hsu YM, Chen YA, Huang CT, Wu HP, Huang LT, Lai MH, Kuang LY, Lo SF, Yu SM, Lin YR, Hsing YIC. Lack of Genotype and Phenotype Correlation in a Rice T-DNA Tagged Line Is Likely Caused by Introgression in the Seed Source. PLoS One 2016; 11:e0155768. [PMID: 27186981 PMCID: PMC4871347 DOI: 10.1371/journal.pone.0155768] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/03/2016] [Indexed: 01/12/2023] Open
Abstract
Rice (Oryza sativa) is one of the most important crops in the world. Several rice insertional mutant libraries are publicly available for systematic analysis of gene functions. However, the tagging efficiency of these mutant resources-the relationship between genotype and phenotype-is very low. We used whole-genome sequencing to analyze a T-DNA-tagged transformant from the Taiwan Rice Insertional Mutants (TRIM) resource. The phenomics records for M0028590, one of the TRIM lines, revealed three phenotypes-wild type, large grains, and tillering dwarf-in the 12 T1 plants. Using the sequencing data for 7 plants from three generations of this specific line, we demonstrate that introgression from an indica rice variety might occur in one generation before the seed was used for callus generation and transformation of this line. In addition, the large-grain trait came from the GS3 gene of the introgressed region and the tillering dwarf phenotype came from a single nucleotide change in the D17 gene that occurred during the callus induction to regeneration of the transformant. As well, another regenerant showed completely heterozygous single-nucleotide polymorphisms across the whole genome. In addition to the known sequence changes such as T-DNA integration, single nucleotide polymorphism, insertion, deletion, chromosome rearrangement and doubling, spontaneous outcrossing occurred in the rice field may also explain some mutated traits in a tagged mutant population. Thus, the co-segregation of an integration event and the phenotype should be checked when using these mutant populations.
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Affiliation(s)
- Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yuan-Ching Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Ming Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-An Chen
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Ching-Ting Huang
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Lin-Tzu Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agriculture Research Institute, Taichung, Taiwan
| | - Lin-Yun Kuang
- Transgenic Plant Core Facility, Academia Sinica, Taipei, Taiwan
| | - Shuen-Fang Lo
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yue-Ie Caroline Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
- * E-mail:
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225
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Haberer G, Mayer KF, Spannagl M. The big five of the monocot genomes. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:33-40. [PMID: 26866569 DOI: 10.1016/j.pbi.2016.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 01/14/2016] [Accepted: 01/21/2016] [Indexed: 06/05/2023]
Abstract
Monocots represent a monophyletic clade of the angiosperms that - based on fossil and molecular records - originated at around the Early Cretaceous from aquatic and wetland ancestors. Among their members are important crops including maize, wheat, rice, sorghum and barley, accounting for the major source for the daily calorie uptake by humans. Reflecting this importance, the partly large and complex genomes of these plants were major targets for ambitious and innovative sequencing projects, which will be discussed in this review article.
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Affiliation(s)
- Georg Haberer
- Plant Genome and Systems Biology/PGSB, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Klaus Fx Mayer
- Plant Genome and Systems Biology/PGSB, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany.
| | - Manuel Spannagl
- Plant Genome and Systems Biology/PGSB, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
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226
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Kang YJ, Lee T, Lee J, Shim S, Jeong H, Satyawan D, Kim MY, Lee SH. Translational genomics for plant breeding with the genome sequence explosion. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1057-69. [PMID: 26269219 PMCID: PMC5042036 DOI: 10.1111/pbi.12449] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/04/2015] [Accepted: 07/10/2015] [Indexed: 05/22/2023]
Abstract
The use of next-generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies.
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Affiliation(s)
- Yang Jae Kang
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Taeyoung Lee
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Jayern Lee
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Sangrea Shim
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Haneul Jeong
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Dani Satyawan
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
- Indonesian Center for Agricultural Biotechnology and Genomic resources Research and Development (ICABIOGRAD-IAARD), Bogor, Indonesia
| | - Moon Young Kim
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Suk-Ha Lee
- Department of Plant Science Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
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227
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Phung NTP, Mai CD, Hoang GT, Truong HTM, Lavarenne J, Gonin M, Nguyen KL, Ha TT, Do VN, Gantet P, Courtois B. Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam. BMC PLANT BIOLOGY 2016; 16:64. [PMID: 26964867 PMCID: PMC4785749 DOI: 10.1186/s12870-016-0747-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/26/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. RESULTS The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. CONCLUSIONS Some of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development.
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Affiliation(s)
- Nhung Thi Phuong Phung
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
| | - Chung Duc Mai
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
| | - Giang Thi Hoang
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
| | - Hue Thi Minh Truong
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
| | - Jeremy Lavarenne
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
- />IRD, LMI RICE, 00000 Hanoi, Vietnam
| | | | - Khanh Le Nguyen
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
- />IRD, LMI RICE, 00000 Hanoi, Vietnam
| | - Thuy Thi Ha
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
| | - Vinh Nang Do
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
| | - Pascal Gantet
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
- />IRD, LMI RICE, 00000 Hanoi, Vietnam
- />Université de Montpellier, UMR DIADE, 34095 Montpellier, France
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228
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Okazaki Y, Saito K. Integrated metabolomics and phytochemical genomics approaches for studies on rice. Gigascience 2016; 5:11. [PMID: 26937280 PMCID: PMC4774183 DOI: 10.1186/s13742-016-0116-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 02/06/2016] [Indexed: 01/10/2023] Open
Abstract
Metabolomics is widely employed to monitor the cellular metabolic state and assess the quality of plant-derived foodstuffs because it can be used to manage datasets that include a wide range of metabolites in their analytical samples. In this review, we discuss metabolomics research on rice in order to elucidate the overall regulation of the metabolism as it is related to the growth and mechanisms of adaptation to genetic modifications and environmental stresses such as fungal infections, submergence, and oxidative stress. We also focus on phytochemical genomics studies based on a combination of metabolomics and quantitative trait locus (QTL) mapping techniques. In addition to starch, rice produces many metabolites that also serve as nutrients for human consumers. The outcomes of recent phytochemical genomics studies of diverse natural rice resources suggest there is potential for using further effective breeding strategies to improve the quality of ingredients in rice grains.
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Affiliation(s)
- Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 Japan ; Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813 Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 Japan ; Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675 Japan
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229
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Abstract
We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements; and (3) that various classes of small RNAs help shape genomic architecture and function. We illustrate ways in which understanding these organism-level and molecular genetic processes can be used for crop plant improvement.
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Affiliation(s)
- Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA.,Division of Plant Sciences, University of Missouri-Columbia, 52 Agriculture Laboratory, Columbia, MO, 65211, USA
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, Tucson, AZ, 85750, USA.,T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Baños, Laguna, Philippines
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230
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Wang S, Gao LZ. Complete Chloroplast Genome Sequence and Annotation of the Tropical japonica Group of Asian Cultivated Rice (Oryza sativa L.). GENOME ANNOUNCEMENTS 2016; 4:e01703-15. [PMID: 26893422 PMCID: PMC4759069 DOI: 10.1128/genomea.01703-15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 12/18/2015] [Indexed: 11/23/2022]
Abstract
We announce here the first complete chloroplast genome sequence of the tropical japonica rice, along with its genome structure and functional annotation. The plant was collected from Indonesia and deposited as a germplasm accession of the International Rice GenBank Collection (IRGC 66630) at the International Rice Research Institute (IRRI). This genome provides valuable data for the future utilization of the germplasm of rice.
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Affiliation(s)
- Shuo Wang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, China Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Li-Zhi Gao
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, China Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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231
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Open access resources for genome-wide association mapping in rice. Nat Commun 2016; 7:10532. [PMID: 26842267 PMCID: PMC4742900 DOI: 10.1038/ncomms10532] [Citation(s) in RCA: 225] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 12/22/2015] [Indexed: 01/19/2023] Open
Abstract
Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement. Understanding the link between genotype and phenotype can facilitate efforts by breeders to utilize natural variation and develop new crop varieties. Here the authors present a diverse germplasm collection, a high-density genotyping array and a set of bioinformatic tools to enable association mapping in rice.
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232
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Thudi M, Khan AW, Kumar V, Gaur PM, Katta K, Garg V, Roorkiwal M, Samineni S, Varshney RK. Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.). BMC PLANT BIOLOGY 2016; 16 Suppl 1:10. [PMID: 26822060 PMCID: PMC4895712 DOI: 10.1186/s12870-015-0690-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
BACKGROUND Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in South Asia and Sub-Saharan Africa. In order to harness the untapped genetic potential available for chickpea improvement, we re-sequenced 35 chickpea genotypes representing parental lines of 16 mapping populations segregating for abiotic (drought, heat, salinity), biotic stresses (Fusarium wilt, Ascochyta blight, Botrytis grey mould, Helicoverpa armigera) and nutritionally important (protein content) traits using whole genome re-sequencing approach. RESULTS A total of 192.19 Gb data, generated on 35 genotypes of chickpea, comprising 973.13 million reads, with an average sequencing depth of ~10 X for each line. On an average 92.18 % reads from each genotype were aligned to the chickpea reference genome with 82.17 % coverage. A total of 2,058,566 unique single nucleotide polymorphisms (SNPs) and 292,588 Indels were detected while comparing with the reference chickpea genome. Highest number of SNPs were identified on the Ca4 pseudomolecule. In addition, copy number variations (CNVs) such as gene deletions and duplications were identified across the chickpea parental genotypes, which were minimum in PI 489777 (1 gene deletion) and maximum in JG 74 (1,497). A total of 164,856 line specific variations (144,888 SNPs and 19,968 Indels) with the highest percentage were identified in coding regions in ICC 1496 (21 %) followed by ICCV 97105 (12 %). Of 539 miscellaneous variations, 339, 138 and 62 were inter-chromosomal variations (CTX), intra-chromosomal variations (ITX) and inversions (INV) respectively. CONCLUSION Genome-wide SNPs, Indels, CNVs, PAVs, and miscellaneous variations identified in different mapping populations are a valuable resource in genetic research and helpful in locating genes/genomic segments responsible for economically important traits. Further, the genome-wide variations identified in the present study can be used for developing high density SNP arrays for genetics and breeding applications.
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Affiliation(s)
- Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
| | - Aamir W Khan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vinay Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pooran M Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Krishnamohan Katta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Srinivasan Samineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- The University of Western Australia (UWA), Crawley, Western Australia, Australia.
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233
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Dievart A, Perin C, Hirsch J, Bettembourg M, Lanau N, Artus F, Bureau C, Noel N, Droc G, Peyramard M, Pereira S, Courtois B, Morel JB, Guiderdoni E. The phenome analysis of mutant alleles in Leucine-Rich Repeat Receptor-Like Kinase genes in rice reveals new potential targets for stress tolerant cereals. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:240-249. [PMID: 26566841 DOI: 10.1016/j.plantsci.2015.06.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 06/17/2015] [Accepted: 06/22/2015] [Indexed: 05/08/2023]
Abstract
Plants are constantly exposed to a variety of biotic and abiotic stresses that reduce their fitness and performance. At the molecular level, the perception of extracellular stimuli and the subsequent activation of defense responses require a complex interplay of signaling cascades, in which protein phosphorylation plays a central role. Several studies have shown that some members of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) family are involved in stress and developmental pathways. We report here a systematic analysis of the role of the members of this gene family by mutant phenotyping in the monocotyledon model plant rice, Oryza sativa. We have then targeted 176 of the ∼320 LRR-RLK genes (55.7%) and genotyped 288 mutant lines. Position of the insertion was confirmed in 128 lines corresponding to 100 LRR-RLK genes (31.6% of the entire family). All mutant lines harboring homozygous insertions have been screened for phenotypes under normal conditions and under various abiotic stresses. Mutant plants have been observed at several stages of growth, from seedlings in Petri dishes to flowering and grain filling under greenhouse conditions. Our results show that 37 of the LRR-RLK rice genes are potential targets for improvement especially in the generation of abiotic stress tolerant cereals.
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Affiliation(s)
- Anne Dievart
- CIRAD, UMR AGAP, 34398 Montpellier cedex 5, France.
| | | | - Judith Hirsch
- INRA, UMR BGPI, INRA-CIRAD-SupAgro, TA 54/K, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
| | | | - Nadège Lanau
- CIRAD, UMR AGAP, 34398 Montpellier cedex 5, France
| | | | | | - Nicolas Noel
- CIRAD, UMR AGAP, 34398 Montpellier cedex 5, France
| | - Gaétan Droc
- CIRAD, UMR AGAP, 34398 Montpellier cedex 5, France
| | | | - Serge Pereira
- INRA, UMR BGPI, INRA-CIRAD-SupAgro, TA 54/K, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
| | | | - Jean-Benoit Morel
- INRA, UMR BGPI, INRA-CIRAD-SupAgro, TA 54/K, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
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234
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Rebolledo MC, Peña AL, Duitama J, Cruz DF, Dingkuhn M, Grenier C, Tohme J. Combining Image Analysis, Genome Wide Association Studies and Different Field Trials to Reveal Stable Genetic Regions Related to Panicle Architecture and the Number of Spikelets per Panicle in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:1384. [PMID: 27703460 PMCID: PMC5029283 DOI: 10.3389/fpls.2016.01384] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 08/30/2016] [Indexed: 05/19/2023]
Abstract
Number of spikelets per panicle (NSP) is a key trait to increase yield potential in rice (O. sativa). The architecture of the rice inflorescence which is mainly determined by the length and number of primary (PBL and PBN) and secondary (SBL and SBN) branches can influence NSP. Although several genes controlling panicle architecture and NSP in rice have been identified, there is little evidence of (i) the genetic control of panicle architecture and NSP in different environments and (ii) the presence of stable genetic associations with panicle architecture across environments. This study combines image phenotyping of 225 accessions belonging to a genetic diversity array of indica rice grown under irrigated field condition in two different environments and Genome Wide Association Studies (GWAS) based on the genotyping of the diversity panel, providing 83,374 SNPs. Accessions sown under direct seeding in one environement had reduced Panicle Length (PL), NSP, PBN, PBL, SBN, and SBL compared to those established under transplanting in the second environment. Across environments, NSP was significantly and positively correlated with PBN, SBN and PBL. However, the length of branches (PBL and SBL) was not significantly correlated with variables related to number of branches (PBN and SBN), suggesting independent genetic control. Twenty- three GWAS sites were detected with P ≤ 1.0E-04 and 27 GWAS sites with p ≤ 5.9E-04. We found 17 GWAS sites related to NSP, 10 for PBN and 11 for SBN, 7 for PBL and 11 for SBL. This study revealed new regions related to NSP, but only three associations were related to both branching number (PBN and SBN) and NSP. Two GWAS sites associated with SBL and SBN were stable across contrasting environments and were not related to genes previously reported. The new regions reported in this study can help improving NSP in rice for both direct seeded and transplanted conditions. The integrated approach of high-throughput phenotyping, multi-environment field trials and GWAS has the potential to dissect complex traits, such as NSP, into less complex traits and to match single nucleotide polymorphisms with relevant function under different environments, offering a potential use for molecular breeding.
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Affiliation(s)
- Maria C. Rebolledo
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
- *Correspondence: Maria C. Rebolledo
| | - Alexandra L. Peña
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
| | - Jorge Duitama
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
| | - Daniel F. Cruz
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
| | - Michael Dingkuhn
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
- Agricultural Research for Development - CIRAD, Unités Mixtes de Recherche - Amélioration Génétique et Adaptation des PlantesMontpellier, France
| | - Cecile Grenier
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
- Agricultural Research for Development - CIRAD, Unités Mixtes de Recherche - Amélioration Génétique et Adaptation des PlantesMontpellier, France
| | - Joe Tohme
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
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235
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Hori K. Detection of Genetic Factors Responsible for Grain Quality and Cooking Characteristics of Japanese Rice Cultivars. J JPN SOC FOOD SCI 2016. [DOI: 10.3136/nskkk.63.484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Kiyosumi Hori
- National Agriculture and Food Research Organization (NARO) Institute of Crop Science
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236
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González-Schain N, Dreni L, Lawas LMF, Galbiati M, Colombo L, Heuer S, Jagadish KSV, Kater MM. Genome-Wide Transcriptome Analysis During Anthesis Reveals New Insights into the Molecular Basis of Heat Stress Responses in Tolerant and Sensitive Rice Varieties. PLANT & CELL PHYSIOLOGY 2016; 57:57-68. [PMID: 26561535 DOI: 10.1093/pcp/pcv174] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/04/2015] [Indexed: 05/19/2023]
Abstract
Rice is one of the main food crops in the world. In the near future, yield is expected to be under pressure due to unfavorable climatic conditions, such as increasing temperatures. Therefore, improving rice germplasm in order to guarantee rice production under harsh environmental conditions is of top priority. Although many physiological studies have contributed to understanding heat responses during anthesis, the most heat-sensitive stage, molecular data are still largely lacking. In this study, an RNA-sequencing approach of heat- and control-treated reproductive tissues during anthesis was carried out using N22, one of the most heat-tolerant rice cultivars known to date. This analysis revealed that expression of genes encoding a number of transcription factor families, together with signal transduction and metabolic pathway genes, is repressed. On the other hand, expression of genes encoding heat shock factors and heat shock proteins was highly activated. Many of these genes are predominantly expressed at late stages of anther development. Further physiological experiments using heat-tolerant N22 and two sensitive cultivars suggest that reduced yield in heat-sensitive plants may be associated with poor pollen development or production in anthers prior to anthesis. In parallel, induction levels of a set of heat-responsive genes in these tissues correlated well with heat tolerance. Altogether, these findings suggest that proper expression of protective chaperones in anthers is needed before anthesis to overcome stress damage and to ensure fertilization. Genes putatively controlling this process were identified and are valuable candidates to consider for molecular breeding of highly productive heat-tolerant cultivars.
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Affiliation(s)
- Nahuel González-Schain
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milan, Italy Present address: Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario, CONICET, Ocampo y Esmeralda, Rosario 2000, Argentina
| | - Ludovico Dreni
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milan, Italy Present address: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lovely M F Lawas
- Crop and Environmental Sciences Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines Present address: Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam, Germany
| | - Massimo Galbiati
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milan, Italy
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milan, Italy
| | - Sigrid Heuer
- Australian Centre for Plant Functional Genomics (ACPFG), Adelaide, Australia
| | - Krishna S V Jagadish
- Crop and Environmental Sciences Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines Present address: Department of Agronomy, 2004 Throckmorton Plant Science Center, Kansas State University, Manhattan, KS 66506, USA
| | - Martin M Kater
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milan, Italy
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237
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Abstract
The SIFT (sorting intolerant from tolerant) algorithm helps bridge the gap between mutations and phenotypic variations by predicting whether an amino acid substitution is deleterious. SIFT has been used in disease, mutation and genetic studies, and a protocol for its use has been previously published with Nature Protocols. This updated protocol describes SIFT 4G (SIFT for genomes), which is a faster version of SIFT that enables practical computations on reference genomes. Users can get predictions for single-nucleotide variants from their organism of interest using the SIFT 4G annotator with SIFT 4G's precomputed databases. The scope of genomic predictions is expanded, with predictions available for more than 200 organisms. Users can also run the SIFT 4G algorithm themselves. SIFT predictions can be retrieved for 6.7 million variants in 4 min once the database has been downloaded. If precomputed predictions are not available, the SIFT 4G algorithm can compute predictions at a rate of 2.6 s per protein sequence. SIFT 4G is available from http://sift-dna.org/sift4g.
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238
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Travis AJ, Norton GJ, Datta S, Sarma R, Dasgupta T, Savio FL, Macaulay M, Hedley PE, McNally KL, Sumon MH, Islam MR, Price AH. Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal. RICE (NEW YORK, N.Y.) 2015; 8:35. [PMID: 26626493 PMCID: PMC4667538 DOI: 10.1186/s12284-015-0068-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/18/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND Genetic diversity among rice cultivars from Bangladesh and North East India was assessed using a custom 384-SNP microarray assay. A total of 511 cultivars were obtained from several sources, choosing landraces likely to be from the aus subpopulation and modern improved cultivars from Bangladesh. Cultivars from the OryzaSNP set and Rice Diversity Panel 1 (RDP1) were also included for reference. RESULTS The population analysis program STRUCTURE was used to infer putative population groups in the panel, revealing four groups: indica (76 cultivars), japonica (55) and two distinct groups within the aus subpopulation (aus-1 = 99, aus-2 = 151). Principal Component Analysis was used to confirm the four population groups identified by STRUCTURE. The analysis revealed cultivars that belonged to neither aus-1 nor aus-2 but which are clearly aus based on the combined probabilities of their membership of the two aus groups which have been termed aus-admix (96). Information obtained from the panel of 511 cultivars was used to assign rice groups to 74 additional landraces obtained from Assam and West Bengal. While both the aus-1 and aus-2 groups were represented approximately equally in India, aus-2 (which includes cultivar N 22) was more common in Bangladesh, but was not found at all in West Bengal. CONCLUSIONS Examining the distribution of landrace names within theaus-1 and aus-2 groups suggests that aus-1 is associated with the term "boro", a word used to describe a winter growing season in Bangladesh and Assam. The information described here has been used to select a population of 300 cultivars for Genome Wide Association studies of the aus rice subpopulation.
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Affiliation(s)
- Anthony J Travis
- 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
| | - Sutapa Datta
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
- Department of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ramendra Sarma
- Department of Plant Breeding and Genetics, Assam Agricultural University, Jorhat, 785013, Assam, India
| | - Tapash Dasgupta
- Department of Genetics and Plant Breeding, Calcutta University, 35 B.C. Road, Kolkata, 700 019, West Bengal, India
| | - Filipe L Savio
- Luiz de Queiroz College of Agriculture, University of São Paulo, Avenida Pádua Dias, 11, Bairro Agronomia, Piracicaba, São Paulo, Brazil
| | - Malcolm Macaulay
- Cell & Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Peter E Hedley
- Cell & Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Kenneth L McNally
- International Rice Research Institute (IRRI), DAPO 7777, Metro Manila, 1031, The Philippines
| | - Mahmud H Sumon
- Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - M Rafiqul Islam
- Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Adam H Price
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK.
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239
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Leung H, Raghavan C, Zhou B, Oliva R, Choi IR, Lacorte V, Jubay ML, Cruz CV, Gregorio G, Singh RK, Ulat VJ, Borja FN, Mauleon R, Alexandrov NN, McNally KL, Sackville Hamilton R. Allele mining and enhanced genetic recombination for rice breeding. RICE (NEW YORK, N.Y.) 2015; 8:34. [PMID: 26606925 PMCID: PMC4659784 DOI: 10.1186/s12284-015-0069-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/20/2015] [Indexed: 05/17/2023]
Abstract
Traditional rice varieties harbour a large store of genetic diversity with potential to accelerate rice improvement. For a long time, this diversity maintained in the International Rice Genebank has not been fully used because of a lack of genome information. The publication of the first reference genome of Nipponbare by the International Rice Genome Sequencing Project (IRGSP) marked the beginning of a systematic exploration and use of rice diversity for genetic research and breeding. Since then, the Nipponbare genome has served as the reference for the assembly of many additional genomes. The recently completed 3000 Rice Genomes Project together with the public database (SNP-Seek) provides a new genomic and data resource that enables the identification of useful accessions for breeding. Using disease resistance traits as case studies, we demonstrated the power of allele mining in the 3,000 genomes for extracting accessions from the GeneBank for targeted phenotyping. Although potentially useful landraces can now be identified, their use in breeding is often hindered by unfavourable linkages. Efficient breeding designs are much needed to transfer the useful diversity to breeding. Multi-parent Advanced Generation InterCross (MAGIC) is a breeding design to produce highly recombined populations. The MAGIC approach can be used to generate pre-breeding populations with increased genotypic diversity and reduced linkage drag. Allele mining combined with a multi-parent breeding design can help convert useful diversity into breeding-ready genetic resources.
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Affiliation(s)
- Hei Leung
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines.
| | - Chitra Raghavan
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Bo Zhou
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Ricardo Oliva
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Il Ryong Choi
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Vanica Lacorte
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Mona Liza Jubay
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Casiana Vera Cruz
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Glenn Gregorio
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Rakesh Kumar Singh
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Victor Jun Ulat
- T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines
| | - Frances Nikki Borja
- T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines
| | - Ramil Mauleon
- T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines
| | - Nickolai N Alexandrov
- T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines
| | - Kenneth L McNally
- T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines
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240
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Evans J, Crisovan E, Barry K, Daum C, Jenkins J, Kunde-Ramamoorthy G, Nandety A, Ngan CY, Vaillancourt B, Wei CL, Schmutz J, Kaeppler SM, Casler MD, Buell CR. Diversity and population structure of northern switchgrass as revealed through exome capture sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:800-15. [PMID: 26426343 DOI: 10.1111/tpj.13041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/31/2015] [Accepted: 09/03/2015] [Indexed: 05/11/2023]
Abstract
Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype, composed of tetraploid and octoploid accessions, and a southern lowland ecotype, composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single-nucleotide polymorphisms (SNPs), of which 1 590 653 high-confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype-restricted, non-synonymous SNPs that are predicted to affect the protein function of CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering, which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up-CNVs), 112 630 genes present in fewer copies than in the reference genome (down-CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland-specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.
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Affiliation(s)
- Joseph Evans
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Emily Crisovan
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Kerrie Barry
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Chris Daum
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - Aruna Nandety
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Chew Yee Ngan
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Brieanne Vaillancourt
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Chia-Lin Wei
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Shawn M Kaeppler
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Michael D Casler
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- USDA-ARS, U.S. Dairy Forage Research Center, 1925 Linden Dr., Madison, WI, 53706-1108, USA
| | - Carol Robin Buell
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
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241
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Abstract
Rice is the most important staple food for a large part of the world's human population and also a key model organism for plant research. Here, we present Information Commons for Rice (IC4R; http://ic4r.org), a rice knowledgebase featuring adoption of an extensible and sustainable architecture that integrates multiple omics data through community-contributed modules. Each module is developed and maintained by different committed groups, deals with data collection, processing and visualization, and delivers data on-demand via web services. In the current version, IC4R incorporates a variety of rice data through multiple committed modules, including genome-wide expression profiles derived entirely from RNA-Seq data, resequencing-based genomic variations obtained from re-sequencing data of thousands of rice varieties, plant homologous genes covering multiple diverse plant species, post-translational modifications, rice-related literatures and gene annotations contributed by the rice research community. Unlike extant related databases, IC4R is designed for scalability and sustainability and thus also features collaborative integration of rice data and low costs for database update and maintenance. Future directions of IC4R include incorporation of other omics data and association of multiple omics data with agronomically important traits, dedicating to build IC4R into a valuable knowledgebase for both basic and translational researches in rice.
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242
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Dixit S, Kumar Biswal A, Min A, Henry A, Oane RH, Raorane ML, Longkumer T, Pabuayon IM, Mutte SK, Vardarajan AR, Miro B, Govindan G, Albano-Enriquez B, Pueffeld M, Sreenivasulu N, Slamet-Loedin I, Sundarvelpandian K, Tsai YC, Raghuvanshi S, Hsing YIC, Kumar A, Kohli A. Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL. Sci Rep 2015; 5:15183. [PMID: 26507552 PMCID: PMC4623671 DOI: 10.1038/srep15183] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/21/2015] [Indexed: 02/06/2023] Open
Abstract
Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs over gene families, biosynthetic pathways or certain traits represent functional gene-clusters of genes of the same gene ontology (GO). Gene-clusters containing genes of different GO have not been elaborated, except in silico as coexpressed genes within QTLs. Here we demonstrate the requirement of multiple intra-QTL genes for the full impact of QTL qDTY12.1 on rice yield under drought. Multiple evidences are presented for the need of the transcription factor 'no apical meristem' (OsNAM12.1) and its co-localized target genes of separate GO categories for qDTY12.1 function, raising a regulon-like model of genetic architecture. The molecular underpinnings of qDTY12.1 support its effectiveness in further improving a drought tolerant genotype and for its validity in multiple genotypes/ecosystems/environments. Resolving the combinatorial value of OsNAM12.1 with individual intra-QTL genes notwithstanding, identification and analyses of qDTY12.1has fast-tracked rice improvement towards food security.
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Affiliation(s)
- Shalabh Dixit
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Akshaya Kumar Biswal
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Aye Min
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Amelia Henry
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Rowena H. Oane
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Manish L. Raorane
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Toshisangba Longkumer
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Isaiah M. Pabuayon
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Sumanth K. Mutte
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Adithi R. Vardarajan
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Berta Miro
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Ganesan Govindan
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Blesilda Albano-Enriquez
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Mandy Pueffeld
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 03, 06466 Gatersleben, Germany
| | - Nese Sreenivasulu
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 03, 06466 Gatersleben, Germany
| | - Inez Slamet-Loedin
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | | | - Yuan-Ching Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Yue-Ie C. Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Arvind Kumar
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
| | - Ajay Kohli
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO 7777, Metro Manila-1226, Philippines
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243
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Lau WCP, Rafii MY, Ismail MR, Puteh A, Latif MA, Ramli A. Review of functional markers for improving cooking, eating, and the nutritional qualities of rice. FRONTIERS IN PLANT SCIENCE 2015; 6:832. [PMID: 26528304 PMCID: PMC4604308 DOI: 10.3389/fpls.2015.00832] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/22/2015] [Indexed: 05/16/2023]
Abstract
After yield, quality is one of the most important aspects of rice breeding. Preference for rice quality varies among cultures and regions; therefore, rice breeders have to tailor the quality according to the preferences of local consumers. Rice quality assessment requires routine chemical analysis procedures. The advancement of molecular marker technology has revolutionized the strategy in breeding programs. The availability of rice genome sequences and the use of forward and reverse genetics approaches facilitate gene discovery and the deciphering of gene functions. A well-characterized gene is the basis for the development of functional markers, which play an important role in plant genotyping and, in particular, marker-assisted breeding. In addition, functional markers offer advantages that counteract the limitations of random DNA markers. Some functional markers have been applied in marker-assisted breeding programs and have successfully improved rice quality to meet local consumers' preferences. Although functional markers offer a plethora of advantages over random genetic markers, the development and application of functional markers should be conducted with care. The decreasing cost of sequencing will enable more functional markers for rice quality improvement to be developed, and application of these markers in rice quality breeding programs is highly anticipated.
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Affiliation(s)
- Wendy C. P. Lau
- Department of Crop Science, Faculty of Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Mohd Y. Rafii
- Department of Crop Science, Faculty of Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Mohd R. Ismail
- Department of Crop Science, Faculty of Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Adam Puteh
- Department of Crop Science, Faculty of Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | | | - Asfaliza Ramli
- Rice and Industrial Crops Research Centre, Malaysian Agricultural Research and Development InstituteSeberang Perai, Malaysia
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Vikram P, Swamy BPM, Dixit S, Singh R, Singh BP, Miro B, Kohli A, Henry A, Singh NK, Kumar A. Drought susceptibility of modern rice varieties: an effect of linkage of drought tolerance with undesirable traits. Sci Rep 2015; 5:14799. [PMID: 26458744 PMCID: PMC4602206 DOI: 10.1038/srep14799] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/02/2015] [Indexed: 12/15/2022] Open
Abstract
Green Revolution (GR) rice varieties are high yielding but typically drought sensitive. This is partly due to the tight linkage between the loci governing plant height and drought tolerance. This linkage is illustrated here through characterization of qDTY1.1, a QTL for grain yield under drought that co-segregates with the GR gene sd1 for semi-dwarf plant height. We report that the loss of the qDTY1.1 allele during the GR was due to its tight linkage in repulsion with the sd1 allele. Other drought-yield QTLs (qDTY) also showed tight linkage with traits rejected in GR varieties. Genetic diversity analysis for 11 different qDTY regions grouped GR varieties separately from traditional drought-tolerant varieties, and showed lower frequency of drought tolerance alleles. The increased understanding and breaking of the linkage between drought tolerance and undesirable traits has led to the development of high-yielding drought-tolerant dwarf lines with positive qDTY alleles and provides new hope for extending the benefits of the GR to drought-prone rice-growing regions.
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Affiliation(s)
- Prashant Vikram
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - B. P. Mallikarjuna Swamy
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Shalabh Dixit
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Renu Singh
- National Research Center for Plant Biology, Indian Agricultural Research Institute, New Delhi, India 110012
| | - Bikram P. Singh
- National Research Center for Plant Biology, Indian Agricultural Research Institute, New Delhi, India 110012
| | - Berta Miro
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Ajay Kohli
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Amelia Henry
- Crop and Environmental Sciences Division, International Rice Research Institute, Los Baños, Philippines
| | - N. K. Singh
- National Research Center for Plant Biology, Indian Agricultural Research Institute, New Delhi, India 110012
| | - Arvind Kumar
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
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Wachsman G, Sparks EE, Benfey PN. Genes and networks regulating root anatomy and architecture. THE NEW PHYTOLOGIST 2015; 208:26-38. [PMID: 25989832 DOI: 10.1111/nph.13469] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 04/20/2015] [Indexed: 05/05/2023]
Abstract
The root is an excellent model for studying developmental processes that underlie plant anatomy and architecture. Its modular structure, the lack of cell movement and relative accessibility to microscopic visualization facilitate research in a number of areas of plant biology. In this review, we describe several examples that demonstrate how cell type-specific developmental mechanisms determine cell fate and the formation of defined tissues with unique characteristics. In the last 10 yr, advances in genome-wide technologies have led to the sequencing of thousands of plant genomes, transcriptomes and proteomes. In parallel with the development of these high-throughput technologies, biologists have had to establish computational, statistical and bioinformatic tools that can deal with the wealth of data generated by them. These resources provide a foundation for posing more complex questions about molecular interactions, and have led to the discovery of new mechanisms that control phenotypic differences. Here we review several recent studies that shed new light on developmental processes, which are involved in establishing root anatomy and architecture. We highlight the power of combining large-scale experiments with classical techniques to uncover new pathways in root development.
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Affiliation(s)
- Guy Wachsman
- Department of Biology and Center for Systems Biology, Duke University, Durham, NC, 27708, USA
| | - Erin E Sparks
- Department of Biology and Center for Systems Biology, Duke University, Durham, NC, 27708, USA
| | - Philip N Benfey
- Department of Biology and Center for Systems Biology, Duke University, Durham, NC, 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA
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Abstract
A rapid and cost-effective approach has been developed to harvest and map the dispensable genome, that is, population-level natural sequence variation within a species that is not present in static genome assemblies. See related Research article: http://www.genomebiology.com/2015/16/1/187.
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Yao W, Li G, Zhao H, Wang G, Lian X, Xie W. Exploring the rice dispensable genome using a metagenome-like assembly strategy. Genome Biol 2015; 16:187. [PMID: 26403182 PMCID: PMC4583175 DOI: 10.1186/s13059-015-0757-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 08/20/2015] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The dispensable genome of a species, consisting of the dispensable sequences present only in a subset of individuals, is believed to play important roles in phenotypic variation and genome evolution. However, construction of the dispensable genome is costly and labor-intensive at present, and so the influence of the dispensable genome in genetic and functional genomic studies has not been fully explored. RESULTS We construct the dispensable genome of rice through a metagenome-like de novo assembly strategy based on low-coverage (1-3×) sequencing data of 1483 cultivated rice (Oryza sativa L.) accessions. Thousands of protein-coding genes are successfully assembled, including most of the known agronomically important genes absent from the Nipponbare rice reference genome. We develop an integration approach based on alignment and linkage disequilibrium, which is able to assign genomic positions relative to the reference genome for more than 78.2 % of the dispensable sequences. We carry out association mapping studies for rice grain width and 840 metabolic traits using 0.46 million polymorphisms between the dispensable sequences of different rice accessions. About 23.5 % of metabolic traits have more significant association signals with polymorphisms from dispensable sequences than with SNPs from the reference genome, and 41.6 % of trait-associated SNPs have concordant genomic locations with associated dispensable sequences. CONCLUSIONS Our results suggest the feasibility of building a species' dispensable genome using low-coverage population sequencing data. The constructed sequences will be helpful for understanding the rice dispensable genome and are complementary to the reference genome for identifying candidate genes associated with phenotypic variation.
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Affiliation(s)
- Wen Yao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Guangwei Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China.
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
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248
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Yang H, Jian J, Li X, Renshaw D, Clements J, Sweetingham MW, Tan C, Li C. Application of whole genome re-sequencing data in the development of diagnostic DNA markers tightly linked to a disease-resistance locus for marker-assisted selection in lupin (Lupinus angustifolius). BMC Genomics 2015; 16:660. [PMID: 26329386 PMCID: PMC4557927 DOI: 10.1186/s12864-015-1878-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/24/2015] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Molecular marker-assisted breeding provides an efficient tool to develop improved crop varieties. A major challenge for the broad application of markers in marker-assisted selection is that the marker phenotypes must match plant phenotypes in a wide range of breeding germplasm. In this study, we used the legume crop species Lupinus angustifolius (lupin) to demonstrate the utility of whole genome sequencing and re-sequencing on the development of diagnostic markers for molecular plant breeding. RESULTS Nine lupin cultivars released in Australia from 1973 to 2007 were subjected to whole genome re-sequencing. The re-sequencing data together with the reference genome sequence data were used in marker development, which revealed 180,596 to 795,735 SNP markers from pairwise comparisons among the cultivars. A total of 207,887 markers were anchored on the lupin genetic linkage map. Marker mining obtained an average of 387 SNP markers and 87 InDel markers for each of the 24 genome sequence assembly scaffolds bearing markers linked to 11 genes of agronomic interest. Using the R gene PhtjR conferring resistance to phomopsis stem blight disease as a test case, we discovered 17 candidate diagnostic markers by genotyping and selecting markers on a genetic linkage map. A further 243 candidate diagnostic markers were discovered by marker mining on a scaffold bearing non-diagnostic markers linked to the PhtjR gene. Nine out from the ten tested candidate diagnostic markers were confirmed as truly diagnostic on a broad range of commercial cultivars. Markers developed using these strategies meet the requirements for broad application in molecular plant breeding. CONCLUSIONS We demonstrated that low-cost genome sequencing and re-sequencing data were sufficient and very effective in the development of diagnostic markers for marker-assisted selection. The strategies used in this study may be applied to any trait or plant species. Whole genome sequencing and re-sequencing provides a powerful tool to overcome current limitations in molecular plant breeding, which will enable plant breeders to precisely pyramid favourable genes to develop super crop varieties to meet future food demands.
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Affiliation(s)
- Huaan Yang
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia.
| | - Jianbo Jian
- Beijing Genome Institute - Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Xuan Li
- Beijing Genome Institute - Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Daniel Renshaw
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia.
| | - Jonathan Clements
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia.
| | - Mark W Sweetingham
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia.
| | - Cong Tan
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, 6150, Australia.
| | - Chengdao Li
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia.
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, 6150, Australia.
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Kretzschmar T, Pelayo MAF, Trijatmiko KR, Gabunada LFM, Alam R, Jimenez R, Mendioro MS, Slamet-Loedin IH, Sreenivasulu N, Bailey-Serres J, Ismail AM, Mackill DJ, Septiningsih EM. A trehalose-6-phosphate phosphatase enhances anaerobic germination tolerance in rice. NATURE PLANTS 2015; 1:15124. [PMID: 27250677 DOI: 10.1038/nplants.2015.124] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/24/2015] [Indexed: 05/04/2023]
Abstract
Global socioeconomic developments create strong incentives for farmers to shift from transplanted to direct-seeded rice (DSR) as a means of intensification and economization(1). Rice production must increase to ensure food security(2) and the bulk of this increase will have to be achieved through intensification of cultivation, because expansion of cultivated areas is reaching sustainable limits(3). Anaerobic germination tolerance, which enables uniform germination and seedling establishment under submergence(4), is a key trait for the development of tropical DSR varieties(5,6). Here, we identify a trehalose-6-phosphate phosphatase gene, OsTPP7, as the genetic determinant in qAG-9-2, a major quantitative trait locus (QTL) for anaerobic germination tolerance(7). OsTPP7 is involved in trehalose-6-phosphate (T6P) metabolism, central to an energy sensor that determines anabolism or catabolism depending on local sucrose availability(8,9). OsTPP7 activity may increase sink strength in proliferating heterotrophic tissues by indicating low sugar availability through increased T6P turnover, thus enhancing starch mobilization to drive growth kinetics of the germinating embryo and elongating coleoptile, which consequently enhances anaerobic germination tolerance.
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Affiliation(s)
- Tobias Kretzschmar
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | | | | | - Lourd Franz M Gabunada
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - Rejbana Alam
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, California 92521, USA
| | - Rosario Jimenez
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | | | | | - Nese Sreenivasulu
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, California 92521, USA
| | - Abdelbagi M Ismail
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - David J Mackill
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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