1
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Kubo T, Yamagata Y, Matsusaka H, Toyoda A, Sato Y, Kumamaru T. MiRiQ Database: A Platform for In Silico Rice Mutant Screening. PLANT & CELL PHYSIOLOGY 2024; 65:169-174. [PMID: 37930817 PMCID: PMC10799713 DOI: 10.1093/pcp/pcad134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/15/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023]
Abstract
Genetic studies using mutant resources have significantly contributed to elucidating plant gene function. Massive mutant libraries sequenced by next-generation sequencing technology facilitate mutant identification and functional analysis of genes of interest. Here, we report the creation and release of an open-access database (https://miriq.agr.kyushu-u.ac.jp/index.php), called Mutation-induced Rice in Kyushu University (MiRiQ), designed for in silico mutant screening based on a whole-genome-sequenced mutant library. This database allows any user to easily find mutants of interest without laborious efforts such as large-scale screening by PCR. The initial version of the MiRiQ database (version 1.0) harbors a total of 1.6 million single-nucleotide variants (SNVs) and InDels of 721 M1 plants that were mutagenized by N-methyl-N-nitrosourea treatment of the rice cultivar Nipponbare (Oryza sativa ssp. japonica). The SNVs were distributed among 87% of all 35,630 annotated protein-coding genes of the Nipponbare genome and were predicted to induce missense and nonsense mutations. The MiRiQ database provides built-in tools, such as a search tool by keywords and JBrowse for mutation searches. Users can request mutant seeds in the M2 or M3 generations from a request form linked to this database. We believe that the availability of a wide range of gene mutations in this database will benefit the plant science community and breeders worldwide by accelerating functional genomic research and crop improvement.
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Affiliation(s)
- Takahiko Kubo
- Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, 819-0395 Japan
| | - Yoshiyuki Yamagata
- Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, 819-0395 Japan
| | - Hiroaki Matsusaka
- Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, 819-0395 Japan
| | - Atsushi Toyoda
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540 Japan
| | - Yutaka Sato
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540 Japan
| | - Toshihiro Kumamaru
- Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, 819-0395 Japan
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2
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Liao Q, Chebotarov D, Islam MS, Quintana MR, Natividad MA, De Ocampo M, Beredo JC, Torres RO, Zhang Z, Song H, Price AH, McNally KL, Henry A. Aus rice root architecture variation contributing to grain yield under drought suggests a key role of nodal root diameter class. PLANT, CELL & ENVIRONMENT 2022; 45:854-870. [PMID: 35099814 DOI: 10.1111/pce.14272] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
The aus rice variety group originated in stress-prone regions and is a promising source for the development of new stress-tolerant rice cultivars. In this study, an aus panel (~220 genotypes) was evaluated in field trials under well-watered and drought conditions and in the greenhouse (basket, herbicide and lysimeter studies) to investigate relationships between grain yield and root architecture, and to identify component root traits behind the composite trait of deep root growth. In the field trials, high and stable grain yield was positively related to high and stable deep root growth (r = 0.16), which may indicate response to within-season soil moisture fluctuations (i.e., plasticity). When dissecting component traits related to deep root growth (including angle, elongation and branching), the number of nodal roots classified as 'large-diameter' was positively related to deep root growth (r = 0.24), and showed the highest number of colocated genome-wide association study (GWAS) peaks with grain yield under drought. The role of large-diameter nodal roots in deep root growth may be related to their branching potential. Two candidate loci that colocated for yield and root traits were identified that showed distinct haplotype distributions between contrasting yield/stability groups and could be good candidates to contribute to rice improvement.
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Affiliation(s)
- Qiong Liao
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
| | - Dmytro Chebotarov
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
| | - Mohammad S Islam
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Marinell R Quintana
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
| | - Mignon A Natividad
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
| | - Marjorie De Ocampo
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
| | - Joseph C Beredo
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
| | - Rolando O Torres
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
| | - Zhenhua Zhang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
| | - Haixing Song
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
| | - Adam H Price
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Kenneth L McNally
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
| | - Amelia Henry
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
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3
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Cobb JN, Chen C, Shi Y, Maron LG, Liu D, Rutzke M, Greenberg A, Craft E, Shaff J, Paul E, Akther K, Wang S, Kochian LV, Zhang D, Zhang M, McCouch SR. Genetic architecture of root and shoot ionomes in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2613-2637. [PMID: 34018019 PMCID: PMC8277617 DOI: 10.1007/s00122-021-03848-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/29/2021] [Indexed: 05/09/2023]
Abstract
KEY MESSAGE Association analysis for ionomic concentrations of 20 elements identified independent genetic factors underlying the root and shoot ionomes of rice, providing a platform for selecting and dissecting causal genetic variants. Understanding the genetic basis of mineral nutrient acquisition is key to fully describing how terrestrial organisms interact with the non-living environment. Rice (Oryza sativa L.) serves both as a model organism for genetic studies and as an important component of the global food system. Studies in rice ionomics have primarily focused on above ground tissues evaluated from field-grown plants. Here, we describe a comprehensive study of the genetic basis of the rice ionome in both roots and shoots of 6-week-old rice plants for 20 elements using a controlled hydroponics growth system. Building on the wealth of publicly available rice genomic resources, including a panel of 373 diverse rice lines, 4.8 M genome-wide single-nucleotide polymorphisms, single- and multi-marker analysis pipelines, an extensive tome of 321 candidate genes and legacy QTLs from across 15 years of rice genetics literature, we used genome-wide association analysis and biparental QTL analysis to identify 114 genomic regions associated with ionomic variation. The genetic basis for root and shoot ionomes was highly distinct; 78 loci were associated with roots and 36 loci with shoots, with no overlapping genomic regions for the same element across tissues. We further describe the distribution of phenotypic variation across haplotypes and identify candidate genes within highly significant regions associated with sulfur, manganese, cadmium, and molybdenum. Our analysis provides critical insight into the genetic basis of natural phenotypic variation for both root and shoot ionomes in rice and provides a comprehensive resource for dissecting and testing causal genetic variants.
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Affiliation(s)
- Joshua N Cobb
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
- RiceTec Inc, Alvin, TX, 77511, USA
| | - Chen Chen
- Department of Statistics, Purdue University, West Lafayette, IN, 47907-2054, USA
- Ausy Consulting, Esperantolaan 8, 3001, Heverlee, Belgium
| | - Yuxin Shi
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Lyza G Maron
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Danni Liu
- Department of Statistics, Purdue University, West Lafayette, IN, 47907-2054, USA
| | - Mike Rutzke
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Anthony Greenberg
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
- Bayesic Research, LLC, 452 Sheffield Rd, Ithaca, NY, 14850, USA
| | - Eric Craft
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Jon Shaff
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, 14853-1901, USA
| | - Edyth Paul
- GeneFlow, Inc, Centreville, VA, 20120, USA
| | - Kazi Akther
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
| | - Shaokui Wang
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA
- Department of Plant Breeding, South China Agriculture University, Guangdong, 510642, China
| | - Leon V Kochian
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, 14853-1901, USA
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Dabao Zhang
- Department of Statistics, Purdue University, West Lafayette, IN, 47907-2054, USA
| | - Min Zhang
- Department of Statistics, Purdue University, West Lafayette, IN, 47907-2054, USA.
| | - Susan R McCouch
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1901, USA.
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4
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Castanera R, Vendrell-Mir P, Bardil A, Carpentier MC, Panaud O, Casacuberta JM. Amplification dynamics of miniature inverted-repeat transposable elements and their impact on rice trait variability. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:118-135. [PMID: 33866641 DOI: 10.1111/tpj.15277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 03/31/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Transposable elements (TEs) are a rich source of genetic variability. Among TEs, miniature inverted-repeat TEs (MITEs) are of particular interest as they are present in high copy numbers in plant genomes and are closely associated with genes. MITEs are deletion derivatives of class II transposons, and can be mobilized by the transposases encoded by the latter through a typical cut-and-paste mechanism. However, MITEs are typically present at much higher copy numbers than class II transposons. We present here an analysis of 103 109 transposon insertion polymorphisms (TIPs) in 738 Oryza sativa genomes representing the main rice population groups. We show that an important fraction of MITE insertions has been fixed in rice concomitantly with its domestication. However, another fraction of MITE insertions is present at low frequencies. We performed MITE TIP-genome-wide association studies (TIP-GWAS) to study the impact of these elements on agronomically important traits and found that these elements uncover more trait associations than single nucleotide polymorphisms (SNPs) on important phenotypes such as grain width. Finally, using SNP-GWAS and TIP-GWAS we provide evidence of the replicative amplification of MITEs.
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Affiliation(s)
- Raúl Castanera
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
| | - Pol Vendrell-Mir
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
| | - Amélie Bardil
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan Cedex, 66860, France
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan Cedex, 66860, France
| | - Josep M Casacuberta
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
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5
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Sani Haliru B, Rafii MY, Mazlan N, Ramlee SI, Muhammad I, Silas Akos I, Halidu J, Swaray S, Rini Bashir Y. Recent Strategies for Detection and Improvement of Brown Planthopper Resistance Genes in Rice: A Review. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9091202. [PMID: 32937908 PMCID: PMC7569854 DOI: 10.3390/plants9091202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/11/2020] [Accepted: 09/10/2020] [Indexed: 05/07/2023]
Abstract
Brown planthopper (BPH; Nilaparvata lugens Stal) is considered the main rice insect pest in Asia. Several BPH-resistant varieties of rice have been bred previously and released for large-scale production in various rice-growing regions. However, the frequent surfacing of new BPH biotypes necessitates the evolution of new rice varieties that have a wide genetic base to overcome BPH attacks. Nowadays, with the introduction of molecular approaches in varietal development, it is possible to combine multiple genes from diverse sources into a single genetic background for durable resistance. At present, above 37 BPH-resistant genes/polygenes have been detected from wild species and indica varieties, which are situated on chromosomes 1, 3, 4, 6, 7, 8, 9, 10, 11 and 12. Five BPH gene clusters have been identified from chromosomes 3, 4, 6, and 12. In addition, eight BPH-resistant genes have been successfully cloned. It is hoped that many more resistance genes will be explored through screening of additional domesticated and undomesticated species in due course.
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Affiliation(s)
- Bello Sani Haliru
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia; (B.S.H.); (I.M.); (I.S.A.); (J.H.)
- Department of Crop Science, Usmanu Danfodiyo University, Sokoto P. M. B. 2346, Sokoto State, Nigeria
| | - Mohd Y. Rafii
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia; (B.S.H.); (I.M.); (I.S.A.); (J.H.)
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia; (S.I.R.); (S.S.); (Y.R.B.)
- Correspondence:
| | - Norida Mazlan
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia;
| | - Shairul Izan Ramlee
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia; (S.I.R.); (S.S.); (Y.R.B.)
| | - Isma’ila Muhammad
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia; (B.S.H.); (I.M.); (I.S.A.); (J.H.)
| | - Ibrahim Silas Akos
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia; (B.S.H.); (I.M.); (I.S.A.); (J.H.)
| | - Jamilu Halidu
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia; (B.S.H.); (I.M.); (I.S.A.); (J.H.)
| | - Senesie Swaray
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia; (S.I.R.); (S.S.); (Y.R.B.)
| | - Yusuf Rini Bashir
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia; (S.I.R.); (S.S.); (Y.R.B.)
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6
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Peng H, Wang K, Chen Z, Cao Y, Gao Q, Li Y, Li X, Lu H, Du H, Lu M, Yang X, Liang C. MBKbase for rice: an integrated omics knowledgebase for molecular breeding in rice. Nucleic Acids Res 2020; 48:D1085-D1092. [PMID: 31624841 PMCID: PMC7145604 DOI: 10.1093/nar/gkz921] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 11/25/2022] Open
Abstract
To date, large amounts of genomic and phenotypic data have been accumulated in the fields of crop genetics and genomic research, and the data are increasing very quickly. However, the bottleneck to using big data in breeding is integrating the data and developing tools for revealing the relationship between genotypes and phenotypes. Here, we report a rice sub-database of an integrated omics knowledgebase (MBKbase-rice, www.mbkbase.org/rice), which integrates rice germplasm information, multiple reference genomes with a united set of gene loci, population sequencing data, phenotypic data, known alleles and gene expression data. In addition to basic data search functions, MBKbase provides advanced web tools for genotype searches at the population level and for visually displaying the relationship between genotypes and phenotypes. Furthermore, the database also provides online tools for comparing two samples by their genotypes and finding target germplasms by genotype or phenotype information, as well as for analyzing the user submitted SNP or sequence data to find important alleles in the germplasm. A soybean sub-database is planned for release in 3 months and wheat and maize will be added in 1–2 years. The data and tools integrated in MBKbase will facilitate research in crop functional genomics and molecular breeding.
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Affiliation(s)
- Hua Peng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhuo Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yinghao Cao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiuxiu Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongwei Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Yang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Hu J, Xiao C, He Y. Recent progress on the genetics and molecular breeding of brown planthopper resistance in rice. RICE (NEW YORK, N.Y.) 2016; 9:30. [PMID: 27300326 PMCID: PMC4908088 DOI: 10.1186/s12284-016-0099-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 05/23/2016] [Indexed: 05/20/2023]
Abstract
Brown planthopper (BPH) is the most devastating pest of rice. Host-plant resistance is the most desirable and economic strategy in the management of BPH. To date, 29 major BPH resistance genes have been identified from indica cultivars and wild rice species, and more than ten genes have been fine mapped to chromosome regions of less than 200 kb. Four genes (Bph14, Bph26, Bph17 and bph29) have been cloned. The increasing number of fine-mapped and cloned genes provide a solid foundation for development of functional markers for use in breeding. Several BPH resistant introgression lines (ILs), near-isogenic lines (NILs) and pyramided lines (PLs) carrying single or multiple resistance genes were developed by marker assisted backcross breeding (MABC). Here we review recent progress on the genetics and molecular breeding of BPH resistance in rice. Prospect for developing cultivars with durable, broad-spectrum BPH resistance are discussed.
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Affiliation(s)
- Jie Hu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cong Xiao
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China.
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8
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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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9
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Wang Y, Wang Y, Sun X, Caiji Z, Yang J, Cui D, Cao G, Ma X, Han B, Xue D, Han L. Influence of ethnic traditional cultures on genetic diversity of rice landraces under on-farm conservation in southwest China. JOURNAL OF ETHNOBIOLOGY AND ETHNOMEDICINE 2016; 12:51. [PMID: 27788685 PMCID: PMC5084377 DOI: 10.1186/s13002-016-0120-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/07/2016] [Indexed: 05/12/2023]
Abstract
BACKGROUND Crop genetic resources are important components of biodiversity. However, with the large-scale promotion of mono-cropping, genetic diversity has largely been lost. Ex-situ conservation approaches were widely used to protect traditional crop varieties worldwide. However, this method fails to maintain the dynamic evolutionary processes of crop genetic resources in their original habitats, leading to genetic diversity reduction and even loss of the capacity of resistance to new diseases and pests. Therefore, on-farm conservation has been considered a crucial complement to ex-situ conservation. This study aimed at clarifying the genetic diversity differences between ex-situ conservation and on-farm conservation and to exploring the influence of traditional cultures on genetic diversity of rice landraces under on-farm conservation. METHODS The conservation status of rice landrace varieties, including Indica and Japonica, non-glutinous rice (Oryza sativa) and glutinous rice (Oryza sativa var. glutinosa Matsum), was obtained through ethno-biology investigation method in 12 villages of ethnic groups from Guizhou, Yunnan and Guangxi provinces of China. The genetic diversity between 24 pairs of the same rice landraces from different times were compared using simple sequence repeat (SSR) molecular markers technology. The landrace paris studied were collected in 1980 and maintained ex-situ, while 2014 samples were collected on-farm in southwest of China. RESULTS The results showed that many varieties of rice landraces have been preserved on-farm by local farmers for hundreds or thousands of years. The number of alleles (Na), effective number of alleles (Ne), Nei genetic diversity index (He) and Shannon information index (I) of rice landraces were significantly higher by 12.3-30.4 % under on-farm conservation than under ex-situ conservation. Compared with the ex-situ conservation approach, rice landraces under on-farm conservation programs had more alleles and higher genetic diversity. In every site we investigated, ethnic traditional cultures play a positive influence on rice landrace variety diversity and genetic diversity. CONCLUSION Most China's rice landraces were conserved in the ethnic areas of southwest China. On-farm conservation can effectively promote the allelic variation and increase the genetic diversity of rice landraces over the past 35 years. Moreover, ethnic traditional culture practices are a crucial foundation to increase genetic diversity of rice landraces and implement on-farm conservation.
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Affiliation(s)
- Yanjie Wang
- Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081 China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081 China
| | - Yanli Wang
- Inner Mongolia Institute of Biotechnology Research, Hohhot, 010070 China
| | - Xiaodong Sun
- Heilongjiang Institute of Sericulture Research, Harbin, 150086 China
| | - Zhuoma Caiji
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081 China
| | - Jingbiao Yang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081 China
| | - Di Cui
- Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081 China
| | - Guilan Cao
- Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081 China
| | - Xiaoding Ma
- Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081 China
| | - Bing Han
- Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081 China
| | - Dayuan Xue
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081 China
| | - Longzhi Han
- Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081 China
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10
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Ling Y, Weilin Z. Genetic and biochemical mechanisms of rice resistance to planthopper. PLANT CELL REPORTS 2016; 35:1559-72. [PMID: 26979747 DOI: 10.1007/s00299-016-1962-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 02/25/2016] [Indexed: 05/24/2023]
Abstract
This article presents a comprehensive review on the genetic and biochemical mechanisms governing rice-planthopper interactions, aiming to contribute substantial planthopper control and facilitate breeding for resistance to planthoppers in rice. The rice planthopper is the most destructive pest of rice and a substantial threat to rice production. The brown planthopper (BPH), white-backed planthopper (WBPH) and small brown planthopper (SBPH) are three species of delphacid planthoppers and important piercing-sucking pests of rice. Host-plant resistance has been recognized as the most practical, economical and environmentally friendly strategy to control planthoppers. Until now, at least 30, 14 and 34 major genes/quantitative trait loci for resistance to BPH, WBPH and SBPH have been identified, respectively. Recent inheritance and molecular mapping of gene analysis showed that some planthopper-resistance genes in rice derived from different donors aggregate in clusters, while resistance to these three species of planthoppers in a single donor is governed not by any one dominant gene but by multiple genes. Notably, Bph14, Bph26, Bph3 and Bph29 were successfully identified as BPH-resistance genes in rice. Biological and chemical studies on the feeding of planthoppers indicate that rice plants have acquired various forms of defence against planthoppers. Between the rice-planthopper interactions, rice plants defend against planthoppers through activation the salicylic acid-dependent systemic acquired resistance but not jasmonate-dependent hormone response pathways. Transgenic rice for the planthopper-resistance mechanism shows that jasmonate and its metabolites function diversely in rice's resistance to planthopper. Understanding the genetic and biochemical mechanisms underlying resistance in rice will contribute to the substantial control of such pests and facilitate breeding for rice's resistance to planthopper more efficiently.
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Affiliation(s)
- Yang Ling
- College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Blvd, Jinhua, 321004, Zhejiang, People's Republic of China
| | - Zhang Weilin
- College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Blvd, Jinhua, 321004, Zhejiang, People's Republic of China.
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11
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Kashima K, Yuki Y, Mejima M, Kurokawa S, Suzuki Y, Minakawa S, Takeyama N, Fukuyama Y, Azegami T, Tanimoto T, Kuroda M, Tamura M, Gomi Y, Kiyono H. Good manufacturing practices production of a purification-free oral cholera vaccine expressed in transgenic rice plants. PLANT CELL REPORTS 2016; 35:667-79. [PMID: 26661780 DOI: 10.1007/s00299-015-1911-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/11/2015] [Accepted: 11/25/2015] [Indexed: 05/03/2023]
Abstract
The first Good Manufacturing Practices production of a purification-free rice-based oral cholera vaccine (MucoRice-CTB) from transgenic plants in a closed cultivation system yielded a product meeting regulatory requirements. Despite our knowledge of their advantages, plant-based vaccines remain unavailable for human use in both developing and industrialized countries. A leading, practical obstacle to their widespread use is producing plant-based vaccines that meet governmental regulatory requirements. Here, we report the first production according to current Good Manufacturing Practices of a rice-based vaccine, the cholera vaccine MucoRice-CTB, at an academic institution. To this end, we established specifications and methods for the master seed bank (MSB) of MucoRice-CTB, which was previously generated as a selection-marker-free line, evaluated its propagation, and given that the stored seeds must be renewed periodically. The production of MucoRice-CTB incorporated a closed hydroponic system for cultivating the transgenic plants, to minimize variations in expression and quality during vaccine manufacture. This type of molecular farming factory can be operated year-round, generating three harvests annually, and is cost- and production-effective. Rice was polished to a ratio of 95 % and then powdered to produce the MucoRice-CTB drug substance, and the identity, potency, and safety of the MucoRice-CTB product met pre-established release requirements. The formulation of MucoRice-CTB made by fine-powdering of drug substance and packaged in an aluminum pouch is being evaluated in a physician-initiated phase I study.
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Affiliation(s)
- Koji Kashima
- Division of Mucosal Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
- Engineering Headquarters, Asahi Kogyosha Co., Ltd., 3-13-12, Mita, Minato-ku, Tokyo, 108-0073, Japan
| | - Yoshikazu Yuki
- Division of Mucosal Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
- International Research and Development Center for Mucosal Vaccine, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
| | - Mio Mejima
- Division of Mucosal Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
- Seto Center, Kanonji Institute, The Research Foundation for Microbial Diseases of Osaka University, 4-1-70, Seto-Cho, Kanonji, Kagawa, 768-0065, Japan
| | - Shiho Kurokawa
- Division of Mucosal Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
- Seto Center, Kanonji Institute, The Research Foundation for Microbial Diseases of Osaka University, 4-1-70, Seto-Cho, Kanonji, Kagawa, 768-0065, Japan
| | - Yuji Suzuki
- Division of Mucosal Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
- Seto Center, Kanonji Institute, The Research Foundation for Microbial Diseases of Osaka University, 4-1-70, Seto-Cho, Kanonji, Kagawa, 768-0065, Japan
| | - Satomi Minakawa
- Division of Mucosal Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
- Seto Center, Kanonji Institute, The Research Foundation for Microbial Diseases of Osaka University, 4-1-70, Seto-Cho, Kanonji, Kagawa, 768-0065, Japan
| | - Natsumi Takeyama
- Division of Mucosal Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
- Research Department, Nippon Institute for Biological Science, 9-2221-1, Shin-machi, Ome, Tokyo, 198-0024, Japan
| | - Yoshiko Fukuyama
- Division of Mucosal Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Tatsuhiko Azegami
- Division of Mucosal Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Takeshi Tanimoto
- Seto Center, Kanonji Institute, The Research Foundation for Microbial Diseases of Osaka University, 4-1-70, Seto-Cho, Kanonji, Kagawa, 768-0065, Japan
| | - Masaharu Kuroda
- Crop Development Division, NARO Agriculture Research Center, 1-2-1, Inada, Joetsu-shi, Niigata, 943-0193, Japan
| | - Minoru Tamura
- Engineering Headquarters, Asahi Kogyosha Co., Ltd., 3-13-12, Mita, Minato-ku, Tokyo, 108-0073, Japan
| | - Yasuyuki Gomi
- Seto Center, Kanonji Institute, The Research Foundation for Microbial Diseases of Osaka University, 4-1-70, Seto-Cho, Kanonji, Kagawa, 768-0065, Japan
| | - Hiroshi Kiyono
- Division of Mucosal Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
- International Research and Development Center for Mucosal Vaccine, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
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12
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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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13
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Alexandrov N, Tai S, Wang W, Mansueto L, Palis K, Fuentes RR, Ulat VJ, Chebotarov D, Zhang G, Li Z, Mauleon R, Hamilton RS, McNally KL. SNP-Seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Res 2014; 43:D1023-7. [PMID: 25429973 PMCID: PMC4383887 DOI: 10.1093/nar/gku1039] [Citation(s) in RCA: 209] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes project with the Nipponbare genome. The SNPs and allele information are organized into a SNP-Seek system (http://www.oryzasnp.org/iric-portal/), which consists of Oracle database having a total number of rows with SNP genotypes close to 60 billion (20 M SNPs × 3 K rice lines) and web interface for convenient querying. The database allows quick retrieving of SNP alleles for all varieties in a given genome region, finding different alleles from predefined varieties and querying basic passport and morphological phenotypic information about sequenced rice lines. SNPs can be visualized together with the gene structures in JBrowse genome browser. Evolutionary relationships between rice varieties can be explored using phylogenetic trees or multidimensional scaling plots.
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Affiliation(s)
- Nickolai Alexandrov
- T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines
| | | | - Wensheng Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081
| | - Locedie Mansueto
- T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines
| | - Kevin Palis
- T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines
| | | | - Victor Jun Ulat
- T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines
| | - Dmytro Chebotarov
- T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines
| | | | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081
| | - Ramil Mauleon
- T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines
| | | | - Kenneth L McNally
- T.T.Chang Genetic Resources Center, IRRI, Los Baños, Laguna 4031, Philippines
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14
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Abstract
Artificial hybridization has probably been practiced since ancient time; however, the science of genetics did not initiate until Gregor Mendel conducted a series of crosses between different pure lines of garden pea and made careful observations and systematical analyses of their offspring. Artificial hybridization or crossing between carefully chosen parents has been and still is the primary way to transfer genes from different germplasm for self-pollinated rice. Through gene recombination, novel genetic variation is created by different arrangements of genes existing in parental lines. Procedures of artificial hybridization involve the selection of appropriate panicles from representative plants of the female parents, the emasculation of female parents, and the pollination of emasculated panicles with abundant pollens of selected male parents. Of the numerous proposed methods, hot water and vacuum emasculation have proven to be the most robust and reliable ones. A successful and efficient hybridization program also relies on the knowledge of parental lines or germplasm, the reproductive biology and development of rice, the conditions needed to promote flowering and seed development, and the techniques to synchronize flowering of diverse parents.
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Affiliation(s)
- Xueyan Sha
- Rice Research Station, Louisiana State University Agricultural Center, Crowley, LA, USA.
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15
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Barding GA, Fukao T, Béni S, Bailey-Serres J, Larive CK. Differential Metabolic Regulation Governed by the Rice SUB1A Gene during Submergence Stress and Identification of Alanylglycine by 1H NMR Spectroscopy. J Proteome Res 2011; 11:320-30. [DOI: 10.1021/pr200919b] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Gregory A. Barding
- Department of Chemistry, University of California −Riverside, California, United States
- Center for Plant Cell Biology, University of California −Riverside, California, United States
| | - Takeshi Fukao
- Center for Plant Cell Biology, University of California −Riverside, California, United States
- Department of Botany and Plant Sciences, University of California −Riverside, California, United States
| | - Szabolcs Béni
- Department of Chemistry, University of California −Riverside, California, United States
- Department of Pharmaceutical Chemistry, Semmelweis University, Budapest, Hungary
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, University of California −Riverside, California, United States
- Department of Botany and Plant Sciences, University of California −Riverside, California, United States
| | - Cynthia K. Larive
- Department of Chemistry, University of California −Riverside, California, United States
- Center for Plant Cell Biology, University of California −Riverside, California, United States
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16
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Ammiraju JSS, Fan C, Yu Y, Song X, Cranston KA, Pontaroli AC, Lu F, Sanyal A, Jiang N, Rambo T, Currie J, Collura K, Talag J, Bennetzen JL, Chen M, Jackson S, Wing RA. Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 63:430-42. [PMID: 20487382 DOI: 10.1111/j.1365-313x.2010.04251.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Despite knowledge that polyploidy is widespread and a major evolutionary force in flowering plant diversification, detailed comparative molecular studies on polyploidy have been confined to only a few species and families. The genus Oryza is composed of 23 species that are classified into ten distinct 'genome types' (six diploid and four polyploid), and is emerging as a powerful new model system to study polyploidy. Here we report the identification, sequence and comprehensive comparative annotation of eight homoeologous genomes from a single orthologous region (Adh1-Adh2) from four allopolyploid species representing each of the known Oryza genome types (BC, CD, HJ and KL). Detailed comparative phylogenomic analyses of these regions within and across species and ploidy levels provided several insights into the spatio-temporal dynamics of genome organization and evolution of this region in 'natural' polyploids of Oryza. The major findings of this study are that: (i) homoeologous genomic regions within the same nucleus experience both independent and parallel evolution, (ii) differential lineage-specific selection pressures do not occur between polyploids and their diploid progenitors, (iii) there have been no dramatic structural changes relative to the diploid ancestors, (iv) a variation in the molecular evolutionary rate exists between the two genomes in the BC complex species even though the BC and CD polyploid species appear to have arisen <2 million years ago, and (v) there are no clear distinctions in the patterns of genome evolution in the diploid versus polyploid species.
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Affiliation(s)
- Jetty S S Ammiraju
- Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USABiodiversity Synthesis Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USADepartment of Genetics, University of Georgia, Athens, GA 30602-7223, USAState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, ChinaDepartment of Agronomy, Purdue University, West Lafayette, IN 47907-2054, USADepartment of Horticulture, Michigan State University, East Lansing, MI 48823, USA
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17
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Chen Y, Lübberstedt T. Molecular basis of trait correlations. TRENDS IN PLANT SCIENCE 2010; 15:454-61. [PMID: 20542719 DOI: 10.1016/j.tplants.2010.05.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2009] [Revised: 05/05/2010] [Accepted: 05/13/2010] [Indexed: 05/20/2023]
Abstract
Trait correlations are common phenomena in biology. Plant breeders need to consider trait correlations to either improve correlated traits simultaneously or to reduce undesirable side effects when improving only one of the correlated traits. Pleiotropy or close linkage are the two major reasons for genetic trait correlations and are often confounded at the level of quantitative trait loci or genes. With the progress of genetic and genomic approaches, discrimination of intragenic linkage from true pleiotropy is increasingly possible. This will substantially impact breeding strategies and will be helpful to understand the nature of trait correlations.
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Affiliation(s)
- Yongsheng Chen
- Department of Agronomy, Iowa State University, Ames, IA 50011-1010, USA
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18
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Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, York TL, Polato NR, Olsen KM, Nielsen R, McCouch SR, Bustamante CD, Purugganan MD. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet 2007; 3:1745-56. [PMID: 17907810 PMCID: PMC1994709 DOI: 10.1371/journal.pgen.0030163] [Citation(s) in RCA: 349] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Accepted: 08/06/2007] [Indexed: 11/18/2022] Open
Abstract
Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models to explain contemporary patterns of polymorphisms in rice, including a (i) selectively neutral population bottleneck model, (ii) bottleneck plus migration model, (iii) multiple selective sweeps model, and (iv) bottleneck plus selective sweeps model. We find that a simple bottleneck model, which has been the dominant demographic model for domesticated species, cannot explain the derived nucleotide polymorphism site frequency spectrum in rice. Instead, a bottleneck model that incorporates selective sweeps, or a more complex demographic model that includes subdivision and gene flow, are more plausible explanations for patterns of variation in domesticated rice varieties. If selective sweeps are indeed the explanation for the observed nucleotide data of domesticated rice, it suggests that strong selection can leave its imprint on genome-wide polymorphism patterns, contrary to expectations that selection results only in a local signature of variation.
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Affiliation(s)
- Ana L Caicedo
- Department of Genetics, North Carolina State University, Raleigh, North Carolina, USA
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19
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Brar D, Khush G. Cytogenetic Manipulation and Germplasm Enhancement of Rice (Oryza sativa L.). GENETIC RESOURCES, CHROMOSOME ENGINEERING, AND CROP IMPROVEMENT 2006. [DOI: 10.1201/9780203489260.ch5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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20
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Gao L, McCarthy EM, Ganko EW, McDonald JF. Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences. BMC Genomics 2004; 5:18. [PMID: 15040813 PMCID: PMC373447 DOI: 10.1186/1471-2164-5-18] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2003] [Accepted: 03/02/2004] [Indexed: 12/03/2022] Open
Abstract
Background LTR Retrotransposons transpose through reverse transcription of an RNA intermediate and are ubiquitous components of all eukaryotic genomes thus far examined. Plant genomes, in particular, have been found to be comprised of a remarkably high number of LTR retrotransposons. There is a significant body of direct and indirect evidence that LTR retrotransposons have contributed to gene and genome evolution in plants. Results To explore the evolutionary history of long terminal repeat (LTR) retrotransposons and their impact on the genome of Oryza sativa, we have extended an earlier computer-based survey to include all identifiable full-length, fragmented and solo LTR elements in the rice genome database as of April 2002. A total of 1,219 retroelement sequences were identified, including 217 full-length elements, 822 fragmented elements, and 180 solo LTRs. In order to gain insight into the chromosomal distribution of LTR-retrotransposons in the rice genome, a detailed examination of LTR-retrotransposon sequences on Chromosome 10 was carried out. An average of 22.3 LTR-retrotransposons per Mb were detected in Chromosome 10. Conclusions Gypsy-like elements were found to be >4 × more abundant than copia-like elements. Eleven of the thirty-eight investigated LTR-retrotransposon families displayed significant subfamily structure. We estimate that at least 46.5% of LTR-retrotransposons in the rice genome are older than the age of the species (< 680,000 years). LTR-retrotransposons present in the rice genome range in age from those just recently inserted up to nearly 10 million years old. Approximately 20% of LTR retrotransposon sequences lie within putative genes. The distribution of elements across chromosome 10 is non-random with the highest density (48 elements per Mb) being present in the pericentric region.
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Affiliation(s)
- Lizhi Gao
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Eugene M McCarthy
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Eric W Ganko
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - John F McDonald
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
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21
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Lee KS, Rasabandith S, Angeles ER, Khush GS. Inheritance of resistance to bacterial blight in 21 cultivars of rice. PHYTOPATHOLOGY 2003; 93:147-52. [PMID: 18943128 DOI: 10.1094/phyto.2003.93.2.147] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
ABSTRACT Genetic analysis for resistance to bacterial blight (Xanthomonas oryzae pv. oryzae) of 21 rice (Oryza sativa L.) cultivars was carried out. These cultivars were divided into two groups based on their reactions to Philippine races of bacterial blight. Cultivars of group 1 were resistant to race 1 and those of group 2 were susceptible to race 1 but resistant to race 2. All the cultivars were crossed with TN1, which is susceptible to all the Philippine races of X. oryzae pv. oryzae. F(1) and F(2) populations of hybrids of group 1 cultivars were evaluated using race 1 and F(1) and F(2) populations of hybrids of group 2 cultivars were evaluated using race 2. All the cultivars showed monogenic inheritance of resistance. Allelic relationships of the genes were investigated by crossing these cultivars with different testers having single genes for resistance. Three cultivars have Xa4, another three have xa5, one has xa8, two have Xa3, eight have Xa10, and one has Xa4 as well as Xa10. Three cultivars have new, as yet undescribed, genes. Nep Bha Bong To has a new recessive gene for moderate resistance to races 1, 2, and 3 and resistance to race 5. This gene is designated xa26(t). Arai Raj has a dominant gene for resistance to race 2 which segregates independently of Xa10. This gene is designated as Xa27(t). Lota Sail has a recessive gene for resistance to race 2 which segregates independently of Xa10. This gene is designated as xa28(t).
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Ford-Lloyd BV, Newbury HJ, Jackson MT, Virk PS. Genetic basis for co-adaptive gene complexes in rice (Oryza sativa L.) landraces. Heredity (Edinb) 2001; 87:530-6. [PMID: 11869343 DOI: 10.1046/j.1365-2540.2001.00937.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One hundred and twenty-two AFLP markers were mapped using an IR64 x Azucena rice doubled-haploid (DH) population. The distribution of these mapped markers was monitored across a set of 48 diverse landraces of rice. Strong statistical associations were observed between 960 of the 7381 possible pairs of markers across the diverse material. These 960 strongly associated pairs of markers mapped to the same chromosomes in only 111 cases. The remaining 849 pairs were the result of association between markers found on different chromosomes. More than 21% of these genetically unlinked but strongly associated markers are not randomly distributed across the genome but instead occupy blocks of DNA on different rice chromosomes. Amongst associated blocks, there has clearly been maintenance of combinations of marker alleles across very diverse germplasm. Analyses have also revealed that markers are found in association with performance for each of four quantitative traits in both the diverse landrace material and a DH mapping population. It is proposed that the present data provide strong evidence for the co-adaptation of geographically distinct landraces and that this has resulted over time in the maintenance of 'adaptive gene complexes' involving agronomically important quantitative traits.
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Affiliation(s)
- B V Ford-Lloyd
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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Jana S. Some recent issues on the conservation of crop genetic resources in developing countries. Genome 1999. [DOI: 10.1139/g99-051] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Crop genetic resources (CGRs) are renewable resources. These resources are enriched rather than depleted by their use in research and plant breeding. Both at the time of Vavilov and, later, in the early 1970s, when concerted international efforts to collect and preserve CGRs started with the initiatives of the International Board for Plant Genetic Resources (IBPGR), CGRs were considered to be the common heritage of humankind. Now, they are widely accepted as "national heritage." Possible impacts of this nationalization on the utilization and enrichment of global crop genetic diversity and, consequently, on global food security are issues of great significance. At present, efficient management and adequate use of CGRs are more important concerns than their further exploration and collection. To increase the use of preserved CGRs in plant breeding, the formation of core collections, by selecting representative subsets from large ex situ collections of CGRs, was recommended in 1984. Since then, the core-collection strategy has been further justified as a practical approach to genetic resources management, as well as to their conservation. As a cost-saving germplasm-management strategy, the core-collection concept has considerable merit. However, the rapidly increasing popularity of core collections may undermine the genetic wealth stored in national gene banks of both developed and developing countries. Distinction is made between subsets of working collections and core collections. When a small number of CGRs is required for specific plant breeding purposes, a properly formed working collection is more useful than a representative collection. Despite the relative abundance of genetic diversity in crop plants in traditional agroecosystems, maintenance of these agroecosystems is not a realistic long-term alternative for preserving crop genetic diversity and ensuring global food security. What is needed in the "gene-rich" developing countries is the adoption of "biodiversity friendly" plant breeding and agricultural practices.Key words: crop genetic resources, core collection, germplasm conservation, in situ conservation, ex situ conservation, modern landraces.
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