FAOSTAT (http://faostat3.fao.org/home/E; accessed 01/08/2013)
Rice Almanac. IRRI, Los Baños 2002.
Fukuoka S, Alpatyeva NV, Ebana K, Luu NT, Nagamine T: Analysis of Vietnamese rice germplasm provides an insight into japonica rice differentiation. Plant Breed. 2003, 122: 497-502. 10.1111/j.1439-0523.2003.00908.x.
Article
CAS
Google Scholar
Sen PT, Tinh LN: Vietnam Second Country Report on the State of the Nation's Plant Genetic Resources for Food and Agriculture. Food and Agriculture Organization, Rome 2009.
Google Scholar
Courtois B, Hong NH, Pham VH, Huong VTT, Carandang C, Xuan VT: Genetic diversity of traditional varieties of upland rice from Vietnam and prospects offered by improved varieties. Agric Dév (in French). 1997, 15: 163-167.
Google Scholar
Khush GS, Brar D, Virk PS, Tang SX, Malik SS, Busto GA, Lee YT, McNally R, Trinh LN, Jiang Y, Shat MAM: Classifying rice germplasm by isozyme polymorphism and origin of cultivated rice. IRRI Discuss Pap. 2003, 46: 279-
Google Scholar
Nguyen TTT, Nguyen NMT, Hoang LH, Furya N, Tuschiya K: Genetic diversity in Vietnamese upland rice germplasm revealed by SSR markers. J Fac Agr Kyushu Univ. 2012, 57 (Suppl): 383-391.
Google Scholar
Tanksley SD, McCouch SR: Seed banks and molecular maps: unlocking genetic potential from the wild. Science. 1997, 277 (Suppl 5329): 1063-1066. 10.1126/science.277.5329.1063.
Article
CAS
PubMed
Google Scholar
Zhu C, Gore M, Buckler ES, Yu J: Status and prospect of association mapping in plants. Plant Genome. 2008, 1: 5-20. 10.3835/plantgenome2008.02.0089.
Article
CAS
Google Scholar
Bailey-Serres J, Fukao T, Ronald P, Ismail A, Heuer S, Mackill D: Submergence tolerant rice: SUB1’s journey from landrace to modern cultivar. Rice. 2010, 3: 138-147. 10.1007/s12284-010-9048-5.
Article
Google Scholar
Gamuyao R, Chin JH, Pariasca-Tanaka J, Pesaresi P, Catausan S, Dalid C, Slamet-Loedin I, Tecson-Mendoza EM, Wissuwa M, Heuer S: The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature. 2012, 488: 535-539. 10.1038/nature11346.
Article
CAS
PubMed
Google Scholar
Nordborg M, Weigel D: Next-generation genetics in plants. Nature. 2008, 456: 720-723. 10.1038/nature07629.
Article
CAS
PubMed
Google Scholar
Flint-Garcia SA, Thornsberry JM, Buckler ES: Structure of linkage disequilibrium in plants. Annu Rev Plant Biol. 2003, 53: 357-374. 10.1146/annurev.arplant.54.031902.134907.
Article
Google Scholar
Mather KA, Caicedo AL, Polato NR, Olsen KM, McCouch S, Purugganan MD: The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics. 2007, 177: 2223-2232. 10.1534/genetics.107.079616.
Article
PubMed Central
CAS
PubMed
Google Scholar
Buckler ES, Thornsberry JM: Plant molecular diversity and applications to genomics. Curr Opin Plant Biol. 2002, 5: 107-111. 10.1016/S1369-5266(02)00238-8.
Article
CAS
PubMed
Google Scholar
Yu J, Pressoir G, Briggs WH, Vroh BI, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES: A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet. 2006, 38: 203-208. 10.1038/ng1702.
Article
CAS
PubMed
Google Scholar
Vitte C, Ishii T, Lamy F, Brar D, Panaud O: Genomic paleontology provides evidence for two distinct origins of Asian rice. Mol Gen Genomics. 2004, 272: 504-511. 10.1007/s00438-004-1069-6.
Article
CAS
Google Scholar
Ma J, Bennetzen JL: Rapid recent growth and divergence of rice nuclear genomes. PNAS. 2004, 101 (Suppl 34): 12404-12410. 10.1073/pnas.0403715101.
Article
PubMed Central
CAS
PubMed
Google Scholar
Glaszmann J-C: Isozymes and classification of Asian rice varieties. Theor Appl Genet. 1987, 74: 21-30. 10.1007/BF00290078.
Article
CAS
PubMed
Google Scholar
Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S: Genetic structure and diversity of O. sativa . Genetics. 2005, 169: 1631-1638. 10.1534/genetics.104.035642.
Article
PubMed Central
CAS
PubMed
Google Scholar
Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Hiuang T, Zhou T, Jing Y, Li W, Lin Z, Buckler E, Qian Q, Zhang QF, Li J, Han B: Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet. 2010, 42: 961-967. 10.1038/ng.695.
Article
CAS
PubMed
Google Scholar
Zhao K, Tung C-W, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam R, Reynolds A, Mezey J, McClung AM, Bustamante CD, McCouch SR: Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa . Nat Commun. 2011, 2: 467-10.1038/ncomms1467.
Article
PubMed Central
PubMed
Google Scholar
Ayling S, Rogers C, Trung KH, Ham LH, Oldroyd G, Caccamo M: Vietnamese rice varieties resequenced. Poster 0143 Plant and Animal Genome XXI, January 12–16 2013, San Diego, CA (https://pag.confex.com/pag/xxi/webprogram/Paper6997.html).
Jaccoud D, Peng K, Feinstein D, Kilian A: Diversity arrays: a solid-state technology for sequence information independent genotyping. Nucleic Acids Res. 2001, 29: e25-10.1093/nar/29.4.e25.
Article
PubMed Central
CAS
PubMed
Google Scholar
Xie Y, McNally K, Li CY, Leung H, Zhu YY: A high throughput genomic tool: diversity array technology complementary for rice genotyping. J Integr Plant Biol. 2006, 48 (Suppl 9): 1069-1076. 10.1111/j.1744-7909.2006.00298.x.
Article
CAS
Google Scholar
Yu LX, Lorenz A, Rutkoski J, Singh RP, Bhavani S, Huerta-Espino J, Sorrells ME: Association mapping and gene-gene interaction for stem rust resistance in CIMMYT spring wheat germplasm. Theor Appl Genet. 2011, 123: 1257-1268. 10.1007/s00122-011-1664-y.
Article
CAS
PubMed
Google Scholar
Xia L, Peng K, Yang S, Wenzl P, de Vicente C, Fregene M, Kilian A: DArT for high throughput genotyping of cassava (Manihot esculenta) and its wild relatives. Theor Appl Genet. 2005, 110: 1092-1098. 10.1007/s00122-005-1937-4.
Article
CAS
PubMed
Google Scholar
Risterucci AM, Hippolyte I, Perrier X, Xia L, Caig V, Evers M, Huttner E, Kilian A, Glaszmann JC: Development and assessment of Diversity Arrays Technology for high-throughput DNA analyses in Musa . Theor Appl Genet. 2009, 119 (6): 1093-1103. 10.1007/s00122-009-1111-5.
Article
CAS
PubMed
Google Scholar
Wenzl P, Li H, Carling J, Zhou M, Raman H, Paul E, Hearnden P, Maier C, Xia L, Caig V, Ovesna J, Cakir M, Poulsen D, Wang J, Raman R, Smith KP, Muehlbauer GJ, Chalmers KJ, Kleinhofs A, Huttner E, Kilian A: A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and phenotypic traits. BMC Genomics. 2006, 7: 206-10.1186/1471-2164-7-206.
Article
PubMed Central
PubMed
Google Scholar
Feltus AF, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AP: An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res. 2004, 14: 1812-1819. 10.1101/gr.2479404.
Article
PubMed Central
CAS
PubMed
Google Scholar
McNally KL, Childs KL, Bonhert R, Davidson R, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer KA, Cox DR, Padhukasahasram B, Bustamante CD, Weigel D, Mackill DJ, Bruskiewich RM, Ratsch G, Buell RC, Leung H, Leach JE: Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A. 2009, 106 (Suppl): 12273-12278. 10.1073/pnas.0900992106.
Article
PubMed Central
CAS
PubMed
Google Scholar
Poland JA, Rife TW: Genotyping-by-sequencing for plant breeding and genetics. Plant Genome. 2012, 5 (3): 92-102. 10.3835/plantgenome2012.05.0005.
Article
CAS
Google Scholar
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler E, Mitchell SE: A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 2011, 6: e19379-10.1371/journal.pone.0019379.
Article
PubMed Central
CAS
PubMed
Google Scholar
Spindel J, Wright M, Chen C, Cobb J, Gage J, Harrington S, Lorieux M, Ahmadi N, McCouch S: Bridging the genotype gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Theor Appl Genet. 2013, 126: 2699-2716. 10.1007/s00122-013-2166-x.
Article
CAS
PubMed
Google Scholar
Courtois B, Audebert A, Dardou A, Roques S, Ghneim-Herrera T, Droc G, Frouin J, Rouan L, Gozé E, Kilian A, Ahmadi N, Dingkuhn M: Genome-wide association mapping of root traits in a japonica rice panel. PLoS ONE. 2013, 8 (Suppl 11): e78037-10.1371/journal.pone.0078037.
Article
PubMed Central
CAS
PubMed
Google Scholar
Grenier C, Cao TV, Ospina Y, Tohme J, Courtois B, Ahmadi N: Accuracy of genomic selection in a rice synthetic population developed for recurrent selection (abstract). In Rice Genetics 7: 4–8 November 2013; Manila Philippines. ,
Google Scholar
Glaszmann J-C, Mew T, Hibino H, Kim CK, Mew TI, Vera Cruz CH, Notteghem J-L, Bonman JM: Molecular variation as a diverse source of disease resistance in cultivated rice. In Rice Genetics 3. Edited by Los Baños, Philippines: IRRI. 1995: 460–466.
Google Scholar
Murray MG, Thompson WF: Rapid isolation of high molecular weight plant DNA. Nucleic Acid Res. 1980, 8 (Suppl 19): 4321-4325. 10.1093/nar/8.19.4321.
Article
PubMed Central
CAS
PubMed
Google Scholar
Perrier X, Jacquemoud-Collet J: DARwin software. CIRAD, Montpellier 2006.
Google Scholar
Pritchard JK, Stephens M, Donnelly P: Inference of population structure using multilocus genotype data. Genetics. 2000, 155: 945-959.
PubMed Central
CAS
PubMed
Google Scholar
Earl DA, vonHoldt BM: STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour. 2012, 4 (Suppl 2): 359-361. 10.1007/s12686-011-9548-7.
Article
Google Scholar
Evanno G, Regnaut S, Goudet J: Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 2005, 14: 2611-2620. 10.1111/j.1365-294X.2005.02553.x.
Article
CAS
PubMed
Google Scholar
Jombart T, Devillard S, Balloux F: Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet. 2010, 11: 94-10.1186/1471-2156-11-94.
Article
PubMed Central
PubMed
Google Scholar
Jombart T: Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics. 2008, 24: 1403-1405. 10.1093/bioinformatics/btn129.
Article
CAS
PubMed
Google Scholar
Wright S: Evolution and the Genetics of Populations. Variability within and among Natural Populations. University of Chicago Press, Chicago 1978.
Google Scholar
Excoffier L, Laval G, Schneider S: Arlequin v3.1. An integrated Software for Population Genetic Data Analysis. University of Bern, Switzerland 2006.
Google Scholar
Sokal RR, Michener CD: A statistical method for evaluating systematic relationships. Univ Kansas Sci Bull. 1958, 28: 1409-1438.
Google Scholar
Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler E: TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 2007, 23: 2633-2635. 10.1093/bioinformatics/btm308.
Article
CAS
PubMed
Google Scholar
Schneider CA, Rasband WS, Eliceiri KW: NIH Image to ImageJ: 25 years of image analysis. Nat Methods. 2012, 9: 671-675. 10.1038/nmeth.2089.
Article
CAS
PubMed
Google Scholar
Juliano BO, Villareal CP: Grain Quality Evaluation of World Rices. IRRI, Los Baños 1993.
Google Scholar
Browning SR, Browning BL: Rapid and accurate haploytpe phasing and missing data inference for whole genome association studies by use of localized haplotype clustering. Am J Human Genet. 2007, 81: 1084-1097. 10.1086/521987.
Article
CAS
Google Scholar
Rincent R, Moreau L, Monod H, Kuhn E, Melchinger AE, Malvar RA, Moreno-Gonzalez J, Nicolas S, Madur D, Combes V, Dumas F, Altmann T, Brunel D, Ouzunova M, Flament P, Dubreuil P, Charcosset A, Mary-Huard T: Recovering power in association mapping panels with variable levels of linkage disequilibrium. Genetics. 2014, 197: 375-387. 10.1534/genetics.113.159731.
Article
PubMed Central
PubMed
Google Scholar
Glaubitz JC, Casstevens TM, Lu F, Harriman J, Eshire RJ, Sun Q, Buckler E: TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS ONE. 2014, 9 (Suppl 2): e90346-10.1371/journal.pone.0090346.
Article
PubMed Central
PubMed
Google Scholar
Marchini J, Howie B: Genotype imputation for genome-wide association studies. Nat Rev Genet. 2010, 11: 499-511. 10.1038/nrg2796.
Article
CAS
PubMed
Google Scholar
Wang CH, Zheng XM, Xu Q, Yuan XP, Huang L, Zhou HF, Wei ZH, Ge S: Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm. Heredity. 2014, 112: 489-496. 10.1038/hdy.2013.130.
Article
PubMed Central
CAS
PubMed
Google Scholar
Myint KK, Courtois B, Risterucci A-M, Frouin J, Soe K, Maung Thet K, Vanavichit A, Glaszmann J-C: Specific patterns of genetic diversity among aromatic rice varieties in Myanmar. Rice. 2012, 5: 20-33. 10.1186/1939-8433-5-20.
Article
Google Scholar
Radanielina T, Ramanantsoanirina A, Raboin LM, Frouin J, Perrier X, Brabant P, Ahmadi N: The original features of rice genetic diversity and the importance of within variety diversity in the highlands of Madagascar build a strong case for in situ conservation. Genet Resour Crop Evol. 2013, 60: 311-323. 10.1007/s10722-012-9837-3.
Article
Google Scholar
Appa Rao S, Schiller JM, Bounphanousay C, Jackson MT: Diversity within the traditional rice varieties of Laos. Rice in Laos. Edited by: Schiller JM, Chanphengxay MB, Linquist B, Appa Rao S. 2006, IRRI, Los Banos, Philippines, 123-139.
Google Scholar
Zhang H, Sun J, Wang M, Liao D, Zeng Y, Shen S, Yu P, Mu P, Wang X, Li Z: Genetic structure and phylogeography of rice landraces in Yunnan, China, revealed by SSR. Genome. 2007, 50: 72-83. 10.1139/g06-130.
Article
CAS
PubMed
Google Scholar
Ishii T, Hiraoka T, Kanzaki T, Akimoto M, Shishido R, Ishikawa R: Evaluation of genetic variation among wild populations and local varieties of rice. Rice. 2011, 4: 170-177. 10.1007/s12284-011-9067-x.
Article
Google Scholar
Bong BB: Bridging the rice yield gap in Vietnam. Bridging the Rice Yield Gap in the Asia Pacific Region. Edited by: Papademetriou MK, Dent FJ, Herath EM. 2000, Food and Agricultural Organization, Bangkok, Thailand, 157-163.
Google Scholar
Van Keer K, Trebuil G, Courtois B, Vejpat C: On-farm characterization of upland rice varieties in North Thailand. Int Rice Res Notes. 1998, 23 (Suppl3): 21-22.
Google Scholar
Schiller JM, Appa Rao S, Inthapanya P: Hastadong: Glutinous rice in Laos . Rice in Laos. Edited by: Schiller JM, Chanphengxay MB, Linquist B, Appa Rao S. 2006, IRRI, Los Baños, Philippines, 197-214.
Google Scholar
Olsen KM, Purugganan MD: Molecular evidence on the origin and evolution of glutinous rice. Genetics. 2002, 162: 941-950.
PubMed Central
CAS
PubMed
Google Scholar
Londo JP, Chiang YC, Hung KH, Chiang TY, Schaal BA: Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci U S A. 2006, 103: 9578-9583. 10.1073/pnas.0603152103.
Article
PubMed Central
CAS
PubMed
Google Scholar
Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S, Rynolds A, Huang P, Jackson SA, Schaal BA, Bustanante CD, Boyko AR, Purugganan MD: Molecular evidence for a single evolutionary origin of domesticated rice. Proc Natl Acad Sci U S A. 2011, 108: 8351-8356. 10.1073/pnas.1104686108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Huang X, Kurata N, Wei X, Wang Z-X, Wang A, Zhao Q, Zhun Y, Liu K, Lu H, Li W, Guo Y, Lu Y, Zhou C, Fan D, Weng Q, Zhu C, Huang T, Zhang L, Wang Y, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan X, Xu Q, Dong G, Zhan Q, Li C, Fujiyama A, Toyoda A, Lu T, Feng Q, Qian Q, Li J, Han B: A map of rice genome variation reveals the origin of cultivated rice. Nature. 2012, 490: 497-501. 10.1038/nature11532.
Article
CAS
PubMed
Google Scholar
Olsen KM, Caicedo AL, Polato N, McClung A, McCouch S, Purugganan MD: Selection under domestication: evidence for a sweep in the rice waxy genomic region. Genetics. 2006, 173: 975-983. 10.1534/genetics.106.056473.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wu C, You C, Li C, Long T, Che G, Byrne ME, Zhang Q: RID1, encoding a Cys2/His2-type zinc finger transcription factor, acts as a master switch from vegetative to floral development in rice. Proc Natl Acad Sci U S A. 2008, 105: 12915-12920. 10.1073/pnas.0806019105.
Article
PubMed Central
CAS
PubMed
Google Scholar