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Yonemaru JI, Choi SH, Sakai H, Ando T, Shomura A, Yano M, Wu J, Fukuoka S. Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar 'Koshihikari'. BREEDING SCIENCE 2015; 65:249-56. [PMID: 26175622 PMCID: PMC4482175 DOI: 10.1270/jsbbs.65.249] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/24/2015] [Indexed: 05/06/2023]
Abstract
Insertion-deletion (indel) polymorphisms, such as simple sequence repeats, have been widely used as DNA markers to identify QTLs and genes and to facilitate rice breeding. Recently, next-generation sequencing has produced deep sequences that allow genome-wide detection of indels. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. Here, re-sequencing of 5 indica, 2 aus, and 3 tropical japonica cultivars and Japanese elite cultivar 'Koshihikari' was performed to extract regions containing large indels (10-51 bp) shared by diverse cultivars. To design indel markers for the discrimination of genomic regions between 'Koshihikari' and other diverse cultivars, we subtracted the indel regions detected in 'Koshihikari' from those shared in other cultivars. Two sets of indel markers, KNJ8-indel (shared in eight or more cultivars, including 'Khao Nam Jen' as a representative tropical japonica cultivar) and C5-indel (shared in five to eight cultivars), were established, with 915 and 9,899 indel regions, respectively. Validation of the two marker sets by using 23 diverse cultivars showed a high PCR success rate (≥95%) for 83.3% of the KNJ8-indel markers and 73.9% of the C5-indel markers. The marker sets will therefore be useful for the effective breeding of Japanese rice cultivars.
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Affiliation(s)
- Jun-ichi Yonemaru
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
- Corresponding author (e-mail: )
| | - Sun Hee Choi
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Hiroaki Sakai
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Tsuyu Ando
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Ayahiko Shomura
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Masahiro Yano
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
- NARO Institute of Crop Science,
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Jianzhong Wu
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Shuichi Fukuoka
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
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252
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Duitama J, Silva A, Sanabria Y, Cruz DF, Quintero C, Ballen C, Lorieux M, Scheffler B, Farmer A, Torres E, Oard J, Tohme J. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection. PLoS One 2015; 10:e0124617. [PMID: 25923345 PMCID: PMC4414565 DOI: 10.1371/journal.pone.0124617] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 03/02/2015] [Indexed: 01/08/2023] Open
Abstract
Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.
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Affiliation(s)
- Jorge Duitama
- Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia
- * E-mail:
| | - Alexander Silva
- Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia
| | - Yamid Sanabria
- Rice Research Station, Louisiana State University Agricultural Center, Rayne, Louisiana, United States of America
| | - Daniel Felipe Cruz
- Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia
| | - Constanza Quintero
- Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia
| | - Carolina Ballen
- Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia
| | - Mathias Lorieux
- Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement, Montpellier, France
| | - Brian Scheffler
- Genomics and Bioinformatics Research Unit, Agricultural Research Service, United States Department of Agriculture, Jamie Whitten Delta States Research Center, Stoneville, Mississippi, United States of America
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Edgar Torres
- Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia
| | - James Oard
- Rice Research Station, Louisiana State University Agricultural Center, Rayne, Louisiana, United States of America
| | - Joe Tohme
- Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia
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253
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Sreenivasulu N, Butardo VM, Misra G, Cuevas RP, Anacleto R, Kavi Kishor PB. Designing climate-resilient rice with ideal grain quality suited for high-temperature stress. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1737-48. [PMID: 25662847 PMCID: PMC4669556 DOI: 10.1093/jxb/eru544] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/15/2014] [Accepted: 12/17/2014] [Indexed: 05/18/2023]
Abstract
To ensure rice food security, the target outputs of future rice breeding programmes should focus on developing climate-resilient rice varieties with emphasis on increased head rice yield coupled with superior grain quality. This challenge is made greater by a world that is increasingly becoming warmer. Such environmental changes dramatically impact head rice and milling yield as well as increasing chalkiness because of impairment in starch accumulation and other storage biosynthetic pathways in the grain. This review highlights the knowledge gained through gene discovery via quantitative trait locus (QTL) cloning and structural-functional genomic strategies to reduce chalk, increase head rice yield, and develop stable lines with optimum grain quality in challenging environments. The newly discovered genes and the knowledge gained on the influence of specific alleles related to stability of grain quality attributes provide a robust platform for marker-assisted selection in breeding to design heat-tolerant rice varieties with superior grain quality. Using the chalkiness trait in rice as a case study, we demonstrate here that the emerging field of systems genetics can help fast-track the identification of novel alleles and gene targets that can be pyramided for the development of environmentally robust rice varieties that possess improved grain quality.
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Affiliation(s)
- Nese Sreenivasulu
- Grain Quality and Nutrition Center, International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
| | - Vito M Butardo
- Grain Quality and Nutrition Center, International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
| | - Gopal Misra
- Grain Quality and Nutrition Center, International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
| | - Rosa Paula Cuevas
- Grain Quality and Nutrition Center, International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
| | - Roslen Anacleto
- Grain Quality and Nutrition Center, International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
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254
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Huang X, Yang S, Gong J, Zhao Y, Feng Q, Gong H, Li W, Zhan Q, Cheng B, Xia J, Chen N, Hao Z, Liu K, Zhu C, Huang T, Zhao Q, Zhang L, Fan D, Zhou C, Lu Y, Weng Q, Wang ZX, Li J, Han B. Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis. Nat Commun 2015; 6:6258. [PMID: 25651972 PMCID: PMC4327311 DOI: 10.1038/ncomms7258] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 01/09/2015] [Indexed: 01/08/2023] Open
Abstract
Exploitation of heterosis is one of the most important applications of genetics in agriculture. However, the genetic mechanisms of heterosis are only partly understood, and a global view of heterosis from a representative number of hybrid combinations is lacking. Here we develop an integrated genomic approach to construct a genome map for 1,495 elite hybrid rice varieties and their inbred parental lines. We investigate 38 agronomic traits and identify 130 associated loci. In-depth analyses of the effects of heterozygous genotypes reveal that there are only a few loci with strong overdominance effects in hybrids, but a strong correlation is observed between the yield and the number of superior alleles. While most parental inbred lines have only a small number of superior alleles, high-yielding hybrid varieties have several. We conclude that the accumulation of numerous rare superior alleles with positive dominance is an important contributor to the heterotic phenomena.
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Affiliation(s)
- Xuehui Huang
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Shihua Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Junyi Gong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Yan Zhao
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qi Feng
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Hao Gong
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Wenjun Li
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qilin Zhan
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Benyi Cheng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Junhui Xia
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Neng Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Zhongna Hao
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Kunyan Liu
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Chuanrang Zhu
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Tao Huang
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qiang Zhao
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Lei Zhang
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Danlin Fan
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Congcong Zhou
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yiqi Lu
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qijun Weng
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Zi-Xuan Wang
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Jiayang Li
- National Center for Plant Gene Research, State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Han
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
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255
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Chen LY, Shi DQ, Zhang WJ, Tang ZS, Liu J, Yang WC. The Arabidopsis alkaline ceramidase TOD1 is a key turgor pressure regulator in plant cells. Nat Commun 2015; 6:6030. [PMID: 25591940 PMCID: PMC4309442 DOI: 10.1038/ncomms7030] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 12/04/2014] [Indexed: 11/09/2022] Open
Abstract
Turgor pressure plays pivotal roles in the growth and movement of walled cells that make up plants and fungi. However, the molecular mechanisms regulating turgor pressure and the coordination between turgor pressure and cell wall remodelling for cell growth remain poorly understood. Here, we report the characterization of Arabidopsis TurgOr regulation Defect 1 (TOD1), which is preferentially expressed in pollen tubes and silique guard cells. We demonstrate that TOD1 is a Golgi-localized alkaline ceramidase. tod1 mutant pollen tubes have higher turgor than wild type and show growth retardation both in pistils and in agarose medium. In addition, tod1 guard cells are insensitive to abscisic acid (ABA)-induced stomatal closure, whereas sphingosine-1-phosphate, a putative downstream component of ABA signalling and product of alkaline ceramidases, promotes closure in both wild type and tod1. Our data suggest that TOD1 acts in turgor pressure regulation in both guard cells and pollen tubes.
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Affiliation(s)
- Li-Yu Chen
- 1] State Key Laboratory of Molecular Developmental Biology and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong-Qiao Shi
- State Key Laboratory of Molecular Developmental Biology and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen-Juan Zhang
- 1] State Key Laboratory of Molecular Developmental Biology and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuo-Shun Tang
- State Key Laboratory of Molecular Developmental Biology and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Liu
- State Key Laboratory of Molecular Developmental Biology and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei-Cai Yang
- 1] State Key Laboratory of Molecular Developmental Biology and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China [2] Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200433, China
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Ahmadi N, Audebert A, Bennett MJ, Bishopp A, de Oliveira AC, Courtois B, Diedhiou A, Diévart A, Gantet P, Ghesquière A, Guiderdoni E, Henry A, Inukai Y, Kochian L, Laplaze L, Lucas M, Luu DT, Manneh B, Mo X, Muthurajan R, Périn C, Price A, Robin S, Sentenac H, Sine B, Uga Y, Véry AA, Wissuwa M, Wu P, Xu J. The roots of future rice harvests. RICE (NEW YORK, N.Y.) 2014; 7:29. [PMID: 26224558 PMCID: PMC4884021 DOI: 10.1186/s12284-014-0029-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 10/12/2014] [Indexed: 05/05/2023]
Abstract
Rice production faces the challenge to be enhanced by 50% by year 2030 to meet the growth of the population in rice-eating countries. Whereas yield of cereal crops tend to reach plateaus and a yield is likely to be deeply affected by climate instability and resource scarcity in the coming decades, building rice cultivars harboring root systems that can maintain performance by capturing water and nutrient resources unevenly distributed is a major breeding target. Taking advantage of gathering a community of rice root biologists in a Global Rice Science Partnership workshop held in Montpellier, France, we present here the recent progresses accomplished in this area and focal points where an international network of laboratories should direct their efforts.
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Affiliation(s)
| | | | - Malcolm J Bennett
- />Centre for Plant Integrative Biology, University of Nottingham, Loughborough, LE12 5RD UK
| | - Anthony Bishopp
- />Centre for Plant Integrative Biology, University of Nottingham, Loughborough, LE12 5RD UK
| | | | | | - Abdala Diedhiou
- />Université Cheikh Anta Diop (UCAD), Département de Biologie Végétale, Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Centre de Recherche de Bel Air - BP 1386, CP 18524 Dakar, Sénégal
- />Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air - BP 1386, CP 18524 Dakar, Sénégal
| | - Anne Diévart
- />CIRAD, UMR AGAP, Montpellier Cedex 5, 34398 France
| | - Pascal Gantet
- />Université Montpellier 2, UMR DIADE, Montpellier, France
- />IRD, LMI RICE, USTH, Agronomical Genetics Institute, Hanoi, Vietnam
| | | | | | | | - Yoshiaki Inukai
- />International Cooperation Center for Agricultural Education (ICCAE), Nagoya University, Furo-cho, Chikusa 464-8601 Nagoya, Japan
| | - Leon Kochian
- />Robert W. Holley Center for Agriculture and Health, USDA-ARS and Department of Plant Biology, Cornell University, Ithaca, 14853 NY USA
| | - Laurent Laplaze
- />Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air - BP 1386, CP 18524 Dakar, Sénégal
- />IRD, UMR DIADE, Montpellier, France
| | | | - Doan Trung Luu
- />Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/386 INRA/Montpellier SupAgro/Université Montpellier 2, F-34060 Montpellier Cedex 2, France
| | - Baboucarr Manneh
- />Africa Rice Center, AfricaRice Sahel Regional Station, B.P. 96, St Louis, Senegal
| | - Xiaorong Mo
- />State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058 China
| | | | | | - Adam Price
- />University of Aberdeen, Aberdeen, AB24 3UU UK
| | | | - Hervé Sentenac
- />Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/386 INRA/Montpellier SupAgro/Université Montpellier 2, F-34060 Montpellier Cedex 2, France
| | - Bassirou Sine
- />Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air - BP 1386, CP 18524 Dakar, Sénégal
- />ISRA, CERAAS, Thiès, Senegal
| | - Yusaku Uga
- />National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, 305-8602 Ibaraki, Japan
| | - Anne Aliénor Véry
- />Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/386 INRA/Montpellier SupAgro/Université Montpellier 2, F-34060 Montpellier Cedex 2, France
| | - Matthias Wissuwa
- />Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, 305-8686 Japan
| | - Ping Wu
- />State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058 China
| | - Jian Xu
- />Department of Biological Sciences and NUS Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore 117543 Singapore
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258
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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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259
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Kollmar M, Kollmar L, Hammesfahr B, Simm D. diArk--the database for eukaryotic genome and transcriptome assemblies in 2014. Nucleic Acids Res 2014; 43:D1107-12. [PMID: 25378341 PMCID: PMC4384042 DOI: 10.1093/nar/gku990] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic genomes are the basis for understanding the complexity of life from populations to the molecular level. Recent technological innovations have revolutionized the speed of data generation enabling the sequencing of eukaryotic genomes and transcriptomes within days. The database diArk (http://www.diark.org) has been developed with the aim to provide access to all available assembled genomes and transcriptomes. In September 2014, diArk contains about 2600 eukaryotes with 6000 genome and transcriptome assemblies, of which 22% are not available via NCBI/ENA/DDBJ. Several indicators for the quality of the assemblies are provided to facilitate their comparison for selecting the most appropriate dataset for further studies. diArk has a user-friendly web interface with extensive options for filtering and browsing the sequenced eukaryotes. In this new version of the database we have also integrated species, for which transcriptome assemblies are available, and we provide more analyses of assemblies.
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Affiliation(s)
- Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, 37085, Germany
| | - Lotte Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, 37085, Germany
| | - Björn Hammesfahr
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, 37085, Germany
| | - Dominic Simm
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, 37085, Germany
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261
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Ristova D, Busch W. Natural variation of root traits: from development to nutrient uptake. PLANT PHYSIOLOGY 2014; 166:518-27. [PMID: 25104725 PMCID: PMC4213084 DOI: 10.1104/pp.114.244749] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/06/2014] [Indexed: 05/17/2023]
Abstract
The root system has a crucial role for plant growth and productivity. Due to the challenges of heterogeneous soil environments, diverse environmental signals are integrated into root developmental decisions. While root growth and growth responses are genetically determined, there is substantial natural variation for these traits. Studying the genetic basis of the natural variation of root growth traits can not only shed light on their evolution and ecological relevance but also can be used to map the genes and their alleles responsible for the regulation of these traits. Analysis of root phenotypes has revealed growth strategies and root growth responses to a variety of environmental stimuli, as well as the extent of natural variation of a variety of root traits including ion content, cellular properties, and root system architectures. Linkage and association mapping approaches have uncovered causal genes underlying the variation of these traits.
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Affiliation(s)
- Daniela Ristova
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Bicenter, 1030 Vienna, Austria
| | - Wolfgang Busch
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Bicenter, 1030 Vienna, Austria
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Zhao H, Yao W, Ouyang Y, Yang W, Wang G, Lian X, Xing Y, Chen L, Xie W. RiceVarMap: a comprehensive database of rice genomic variations. Nucleic Acids Res 2014; 43:D1018-22. [PMID: 25274737 PMCID: PMC4384008 DOI: 10.1093/nar/gku894] [Citation(s) in RCA: 174] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Rice Variation Map (RiceVarMap, http:/ricevarmap.ncpgr.cn) is a database of rice genomic variations. The database provides comprehensive information of 6 551 358 single nucleotide polymorphisms (SNPs) and 1 214 627 insertions/deletions (INDELs) identified from sequencing data of 1479 rice accessions. The SNP genotypes of all accessions were imputed and evaluated, resulting in an overall missing data rate of 0.42% and an estimated accuracy greater than 99%. The SNP/INDEL genotypes of all accessions are available for online query and download. Users can search SNPs/INDELs by identifiers of the SNPs/INDELs, genomic regions, gene identifiers and keywords of gene annotation. Allele frequencies within various subpopulations and the effects of the variation that may alter the protein sequence of a gene are also listed for each SNP/INDEL. The database also provides geographical details and phenotype images for various rice accessions. In particular, the database provides tools to construct haplotype networks and design PCR-primers by taking into account surrounding known genomic variations. These data and tools are highly useful for exploring genetic variations and evolution studies of rice and other species.
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Affiliation(s)
- Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Wen Yao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Lingling Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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263
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Affiliation(s)
- Dani Zamir
- Institute of Plant Sciences and Genetics, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel.
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264
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Li JY, Wang J, Zeigler RS. The 3,000 rice genomes project: new opportunities and challenges for future rice research. Gigascience 2014; 3:8. [PMID: 24872878 PMCID: PMC4035671 DOI: 10.1186/2047-217x-3-8] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 05/12/2014] [Indexed: 12/19/2023] Open
Abstract
Rice is the world's most important staple grown by millions of small-holder farmers. Sustaining rice production relies on the intelligent use of rice diversity. The 3,000 Rice Genomes Project is a giga-dataset of publically available genome sequences (averaging 14× depth of coverage) derived from 3,000 accessions of rice with global representation of genetic and functional diversity. The seed of these accessions is available from the International Rice Genebank Collection. Together, they are an unprecedented resource for advancing rice science and breeding technology. Our immediate challenge now is to comprehensively and systematically mine this dataset to link genotypic variation to functional variation with the ultimate goal of creating new and sustainable rice varieties that can support a future world population that will approach 9.6 billion by 2050.
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Affiliation(s)
- Jia-Yang Li
- Chinese Academy of Agricultural Sciences, 12 S. Zhong-Guan-Cun St, Beijing 100081, China
| | - Jun Wang
- BGI, Bei Shan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Robert S Zeigler
- International Rice Research Institute, DAPO 7777, Metro Manila 1301, Philippines
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