Asano K, Yamasaki M, Takuno S, Miura K, Katagiri S, Ito T, Doi K, Wu J, Ebana K, Matsumoto T, Innan H, Kitano H, Ashikari M, Matsuoka M (2011) Artificial selection for a green revolution gene during japonica rice domestication. Proc Natl Acad Sci U.S.A 108(27):11034-11039. doi:10.1073/pnas.1019490108.
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 (2007) Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet 3(9):1745-1756. doi:10.1371/journal.pgen.0030163.
Chakhonkaen S, Pitnjam K, Saisuk W, Ukoskit K, Muangprom A (2012) Genetic structure of Thai rice and rice accessions obtained from the International Rice Research Institute. Rice 5(1):19. doi:10.1186/1939-8433-5-19.
Chang TT (1976) The origin, evolution, cultivation, dissemnination, and diversificaiton of Asian and Africa rice. Euphytica 25:425-441.
Chin HS, Wu YP, Hour AL, Hong CY, Lin YR (2016) Genetic and evolutionary analysis of purple leaf sheath in rice. Rice 9(1):8. doi:10.1186/s12284-016-0080-y.
Choi JY, Platts AE, Fuller DQ, Hsing YL, Wing RA, Purugganan MD (2017) The rice paradox: multiple origins but single domestication in Asian rice. Mol Biol Evol 34(4):969-979. doi:10.1093/molbev/msx049.
Choi JY, Purugganan MD (2018) Multiple origin but single domestication led to Oryza sativa. G3 (Bethesda) 8(3):797-803. doi:10.1534/g3.117.300334.
Chou SL (1948) China is the place of origin of rice. J Rice Soc China 7:53-54. (in Chinese)
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 (2013) Genome-wide association mapping of root traits in a japonica rice panel. PLoS One 8(11): e78037. doi:10.1371/journal.pone.0078037.
Cui D, Tang C, Li J, A X, Yu T, Ma X, Zhang E, Wang Y, Cao G, Xu F, Dai L, Han L, Koh H-J (2017) Genetic structure and isolation by altitude in rice landraces of Yunnan, China revealed by nucleotide and microsatellite marker polymorphisms. PLoS One 12(4):e0175731-e0175731. doi:10.1371/journal.pone.0175731.
Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T, Shimatani Z, Yano M, Yoshimura A (2004) Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev 18(8):926-936. doi:10.1101/gad.1189604.
Dwivedi SL, Ceccarelli S, Blair MW, Upadhyaya HD, Are AK, Ortiz R (2016) Landrace germplasm for improving yield and abiotic stress adaptation. Trends Plant Sci 21(1):31-42. doi:10.1016/j.tplants.2015.10.012.
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14(8):2611-2620. doi:10.1111/j.1365-294X.2005.02553.x.
Evenson RE, Gollin D (2003) Assessing the impact of the green revolution, 1960 to 2000. Science 300(5620):758-762. doi:10.1126/science.1078710.
Fuentes RR, Chebotarov D, Duitama J, Smith S, De la Hoz JF, Mohiyuddin M, Wing RA, McNally KL, Tatarinova T, Grigoriev A, Mauleon R, Alexandrov N (2019) Structural variants in 3000 rice genomes. Genome Res 29(5):870-880. doi:10.1101/gr.241240.118.
Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169(3):1631-1638. doi:10.1534/genetics.104.035642.
Goodman MM, Stuber CW (1983) Races of maize: VI. Isozyme variation among races of maize in Bolivia. Maydica 28:169-187.
Gutaker RM, Groen SC, Bellis ES, Choi JY, Pires IS, Bocinsky RK, Slayton ER, Wilkins O, Castillo CC, Negrao S, Oliveira MM, Fuller DQ, Guedes JAD, Lasky JR, Purugganan MD (2020) Genomic history and ecology of the geographic spread of rice. Nat Plants 6(5):492-502. doi:10.1038/s41477-020-0659-6.
Hsieh JS, Hsing YI, Hsu TF, Li JK, Li KT, Tsang CH (2011) Studies on ancient rice—where botanists, agronomists, archeologists, linguists, and ethnologists meet. Rice 4(3-4):178-183. doi:10.1007/s12284-011-9075-x.
Hsu TF, Wang YH, Fang BX, Chen YQ, Tsai YC, Xie ZS, Hsing YI (2019) A comparative study on morphological types of carbonized rice grains in prehistorical Taiwan. Field Archaeology of Taiwan 19:55-86. (Chinese with English abstract)
Hu CW (1993) Historical review of semidwarf rices and breeding of a new plant type for sustainable agriculture. Res. Bull. Taichung Dist. Agric. Improv. Stn. 38:45-63.
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, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang QF, Li J, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42(11):961-967. doi:10.1038/ng.695.
Ikehashi H (2009) Why are there indica type and japonica type in rice? — history of the studies and a view for origin of two types. Rice Science 16:1-13. doi:10.1016/S1672-6308(08)60050-5.
Ishikawa R, Yamanaka S, Fukuta Y, Chitrakon S, Bounphanousay C, Kanyavong K, Tang LH, Nakamura I, Sato T, Sato YI (2006) Genetic erosion from modern varieties into traditional upland rice cultivars (Oryza sativa L.) in northern Thailand. Genet Resour Crop Evol 53: 245–252. doi:10.1007/s10722-004-6132-y.
Iso E (1964) Talks on Horai rice. Amayomikai, Yamakuchi, Japan, p 89. in Japanese.
Jin L, Lu Y, Xiao P, Sun M, Corke H, Bao J (2010) Genetic diversity and population structure of a diverse set of rice germplasm for association mapping. Theor Appl Genet 121(3):475-487. doi:10.1007/s00122-010-1324-7.
Khush GS (1997) Origin, dispersal, cultivation and variation of rice. Plant Mol Biol 35(1-2):25-34.
Kovach MJ, McCouch SR (2008) Leveraging natural diversity: back through the bottleneck. Curr Opin Plant Biol 11(2):193-200. doi:10.1016/j.pbi.2007.12.006.
Kumar A, Dixit S, Ram T, Yadaw RB, Mishra KK, Mandal NP (2014) Breeding high-yielding drought-tolerant rice: genetic variations and conventional and molecular approaches. J Exp Bot 65(21):6265-6278. doi:10.1093/jxb/eru363.
Kuo SM, Chen YR, Yin SY, Ba QX, Tsai YC, Kuo WHJ, Lin YR (2018) Allelic diversification of Waxy in landraces of foxtail millet (Setaria italica) in Taiwan. PLoS One 13(12):e0210025.
Li JY, Wang J, Zeigler RS (2014) The 3,000 rice genomes project: new opportunities and challenges for future rice research. Gigascience 3:8. doi:10.1186/2047-217X-3-8.
Lin HY, Wu YP, Hour AL, Ho SW, Wei FJ, Hsing YC, Lin YR (2012) Genetic diversity of rice germplasm used in Taiwan breeding programs. Bot Stud 53:363-376.
Lin MS (1991) Field uniformity of the japonica rice region of Taiwan as estimated by relative genetic contribution. Theor Appl Genet 83:115-118.
Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21(9):2128-2129. doi:10.1093/bioinformatics/bti282.
Londo JP, Chiang YC, Hung KH, Chiang TY, Schaal BA (2006) Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci U.S.A 103(25):9578-9583. doi:10.1073/pnas.0603152103.
Lu CT, Lu HY (2010) Establishment and application of Taiwan rice information system. J. Taiwan Agric. Res.(59):61-69. (Chinese with English abstract)
McCouch SR, Teytelman L, Xu YB, Lobos KB, Clare K, Walton M, Fu BY, Maghirang R, Li ZK, Xing YZ, Zhang QF, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9(6):199-207. doi:DOI 10.1093/dnares/9.6.199.
McNally KL, Childs KL, Bohnert R, Davidson RM, 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 CR, Leung H, Leach JE (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U.S.A 106(30):12273-12278. doi:10.1073/pnas.0900992106.
Munasinghe M, Price AH (2016) Genetic and root phenotype diversity in Sri Lankan rice landraces may be related to drought resistance. Rice 9(1):24. doi:10.1186/s12284-016-0092-7.
Nachimuthu VV, Muthurajan R, Duraialaguraja S, Sivakami R, Pandian BA, Ponniah G, Gunasekaran K, Swaminathan M, K KS, Sabariappan R (2015) Analysis of population structure and genetic diversity in rice germplasm using SSR markers: an initiative towards association mapping of agronomic traits in Oryza sativa. Rice 8(1):30. doi:10.1186/s12284-015-0062-5.
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-59.
Pusadee T, Jamjod S, Chiang YC, Rerkasem B, Schaal BA (2009) Genetic structure and isolation by distance in a landrace of Thai rice. Proc Natl Acad Sci U.S.A 106(33):13880-13885. doi:10.1073/pnas.0906720106.
Rohlf F (1987) NTSYS-pc: microcomputer programs for numerical taxonomy and multivariate analysis. Am Stat 41:330. doi:10.2307/2684761.
Sang T, Ge S (2013) Understanding rice domestication and implications for cultivar improvement. Curr Opin Plant Biol 16(2):139-146. doi:10.1016/j.pbi.2013.03.003.
Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, Swapan D, Ishiyama K, Saito T, Kobayashi M, Khush GS, Kitano H, Matsuoka M (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416(6882):701-702. doi:10.1038/416701a.
Thomson MJ, Polato NR, Prasetiyono J, Trijatmiko KR, Silitonga TS, McCouch SR (2009) Genetic diversity of isolated populations of indonesian landraces of rice (Oryza sativa L.) collected in east Kalimantan on the island of Borneo. Rice 2(1):80-92. doi:10.1007/s12284-009-9023-1.
Thomson MJ, Septiningsih EM, Suwardjo F, Santoso TJ, Silitonga TS, McCouch SR (2007) Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theor Appl Genet 114(3):559-568. doi:10.1007/s00122-006-0457-1.
Tsang CH (2012) Issues relating to the ancient rice and millet grains unearthed from the archaeological sites in Tainan Science Park. Journal of Chinese Dietary Culture 8:1-14. (Chinese with English abtract)
Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M, Zheng T, Fuentes RR, Zhang F, Mansueto L, Copetti D, Sanciangco M, Palis KC, Xu J, Sun C, Fu B, Zhang H, Gao Y, Zhao X, Shen F, Cui X, Yu H, Li Z, Chen M, Detras J, Zhou Y, Zhang X, Zhao Y, Kudrna D, Wang C, Li R, Jia B, Lu J, He X, Dong Z, Xu J, Li Y, Wang M, Shi J, Li J, Zhang D, Lee S, Hu W, Poliakov A, Dubchak I, Ulat VJ, Borja FN, Mendoza JR, Ali J, Li J, Gao Q, Niu Y, Yue Z, Naredo MEB, Talag J, Wang X, Li J, Fang X, Yin Y, Glaszmann JC, Zhang J, Li J, Hamilton RS, Wing RA, Ruan J, Zhang G, Wei C, Alexandrov N, McNally KL, Li Z, Leung H (2018) Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature 557(7703):43-49. doi:10.1038/s41586-018-0063-9.
Wang YH (2007) The preliminary notes on the ancient rice grains excavated in Taiwan. Master thesis. Department of Agronomy, National Taiwan University, Taipei, Taiwan. (Chinese with English abstract)
Wei FJ, Tsai YC, Wu HP, Huang LT, Chen YC, Chen YF, Wu CC, Tseng YT, Hsing YC (2016) Both Hd1 and Ehd1 are important for artificial selection of flowering time in cultivated rice. Plant Sci 242:187-194. doi:10.1016/j.plantsci.2015.09.005.
Wu YP, Ko PY, Lee WC, Wei FJ, Kuo SC, Ho SW, Hour AL, Hsing YI, Lin YR (2010) Comparative analyses of linkage maps and segregation distortion of two F2 populations derived from japonica crossed with indica rice. Hereditas 147(5):225-236. doi:10.1111/j.1601-5223.2010.02120.x.
Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the arabidopsis flowering time gene CONSTANS. Plant Cell 12(12):2473-2483. doi:10.1105/tpc.12.12.2473.
Yap R, Hsu YC, Wu YP, Lin YR, Kuo CW (2016) Multiplex PCR genotyping for five bacterial blight resistance genes applied to marker-assisted selection in rice (Oryza sativa). Plant Breed 135:309-317.
Yin SY, Kuo SM, Chen YR, Tsai YC, Wu YP, Lin YR (2019) Genetic variation of physicochemical properties and digestibility of foxtail millet (Setaria italica) landraces of Taiwan. Molecules 24(23): 4323. doi:ARTN 432310.3390/molecules24234323.
Zhang D, Zhang H, Wang M, Sun J, Qi Y, Wang F, Wei X, Han L, Wang X, Li Z (2009) Genetic structure and differentiation of Oryza sativa L. in China revealed by microsatellites. Theor Appl Genet 119(6):1105-1117. doi:10.1007/s00122-009-1112-4.
Zhang H, Sun J, Wang M, Liao D, Zeng Y, Shen S, Yu P, Mu P, Wang X, Li Z (2007) Genetic structure and phylogeography of rice landraces in Yunnan, China, revealed by SSR. Genome 50(1):72-83. doi:10.1139/g06-130.
Zhao KY, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A, Bustamante CD, McCouch SR (2010) Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS One 5(5): e10780.
Zhao Q, Feng Q, Lu H, Li Y, Wang A, Tian Q, Zhan Q, Lu Y, Zhang L, Huang T, Wang Y, Fan D, Zhao Y, Wang Z, Zhou C, Chen J, Zhu C, Li W, Weng Q, Xu Q, Wang ZX, Wei X, Han B, Huang X (2018) Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nat Genet 50(2):278-284. doi:10.1038/s41588-018-0041-z.
Zhu Q, Zheng X, Luo J, Gaut BS, Ge S (2007) Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol 24(3): 875-888. doi:10.1093/molbev/msm005.