Agrama HA, McClung AM, Yan WG (2012) Using minimum DNA marker loci for accurate population classification in rice (Oryza sativa L.). Mol Breeding 29:413-425 doi:10.1007/s11032-011-9558-x
Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome research 19:1655-1664 doi:10.1101/gr.094052.109
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 3:1745-1756 doi:10.1371/journal.pgen.0030163
Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631-1638 doi:10.1534/genetics.104.035642
Glaszmann JC (1987) Isozymes and classification of Asian rice varieties. TAG Theoretical and applied genetics Theoretische und angewandte Genetik 74:21-30 doi:10.1007/BF00290078
Huang XH, Zhao Y, Wei XH et al. (2012) Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet 44:32-U53 doi:10.1038/ng.1018
Izawa T (2008) The Process of Rice Domestication: A New Model Based on Recent Data. Rice 1:127-134 doi:10.1007/s12284-008-9014-7
Kahler AL, Kahler JL, Thompson SA, Ferriss RS, Jones ES, Nelson BK, Mikel MA, Smith S (2010) North American Study on Essential Derivation in Maize: II. Selection and Evaluation of a Panel of Simple Sequence Repeat Loci. Crop Sci 50:486-503 doi:10.2135/cropsci2009.03.0121
Khush GS (1997) Origin, dispersal, cultivation and variation of rice. Plant Mol Biol 35:25-34 doi:10.1023/A:1005810616885
Letunic I, Bork P (2016) Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 44:W242-W245 doi:10.1093/nar/gkw290
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760 doi:10.1093/bioinformatics/btp324
Lin ZC, Qin P, Zhang XW et al. (2020) Divergent selection and genetic introgression shape the genome landscape of heterosis in hybrid rice. P Natl Acad Sci USA 117:4623-4631 doi:10.1073/pnas.1919086117
Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209-220
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome research 20:1297-1303 doi:10.1101/gr.107524.110
Nelson BK, Kahler AL, Kahler JL, Mikel MA, Thompson SA, Ferriss RS, Smith S, Jones ES (2011) Evaluation of the Numbers of Single Nucleotide Polymorphisms Required to Measure Genetic Distance in Maize (Zea mays L.). Crop Sci 51:1470-1480 doi:10.2135/cropsci2010.07.0401
Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. Plos Genet 2:e190 doi:10.1371/journal.pgen.0020190
Price MN, Dehal PS, Arkin AP (2009) FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix. Mol Biol Evol 26:1641-1650 doi:10.1093/molbev/msp077
Rousselle Y, Jones E, Charcosset A et al. (2015) Study on Essential Derivation in Maize: III. Selection and Evaluation of a Panel of Single Nucleotide Polymorphism Loci for Use in European and North American Germplasm. Crop Sci 55:1170-1180 doi:10.2135/cropsci2014.09.0627
Sang T, Ge S (2007) Genetics and phylogenetics of rice domestication. Current opinion in genetics & development 17:533-538 doi:10.1016/j.gde.2007.09.005
Vaughan DA, Lu BR, Tomooka N (2008) Was Asian Rice (Oryza sativa) Domesticated More Than Once? Rice 1:16-24 doi:10.1007/s12284-008-9000-0
Wang B, Chang RZ, Tao L, Guang RX, Yan L, Zhang MH, Feng ZF, Qiu LJ (2003) Identification of SSR Primer Numbers for Analyzing Genetic Diversity of Chinese Soybean Cultivated Soybean. Molecular Plant Breeding 1:82-88
Wang CH, Zheng XM, Xu Q, Yuan XP, Huang L, Zhou HF, Wei XH, Ge S (2014) Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm. Heredity 112:489-496 doi:10.1038/hdy.2013.130
Wu CL, Li SF, Dong BX, Zhang QQ, Zhang CQ (2010) Determination of the Number of SSR Alleles Necessary for the Analysis of Genetic Relationships Between Maize Inbred Lines. Agr Sci China 9:1713-1725 doi:10.1016/S1671-2927(09)60270-4
Xu Q, Yuan XP, Wang S, Feng Y, Yu HY, Wang YP, Yang YL, Wei XH, Li XM (2016) The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis. BMC Genet 17 doi:10.1186/s12863-016-0361-x
Yang YL, Xu X, Zhang MC, Xu Q, Feng Y, Yuan XP, Yu HY, Wang YP, Wei XH (2020) Genetic Basis Dissection for Eating and Cooking Qualities of Japonica Rice in Northeast China. Agronomy-Basel 10 doi:10.3390/Agronomy10030423
You GX, Zhang XY, Wang LF (2004) An estimation of the minimum number of SSR loci needed to reveal genetic relationships in wheat varieties: Information from 96 random accessions with maximized genetic diversity. Mol Breeding 14:397-406 doi:10.1007/s11032-004-0285-4
Yuan XP, Wang CH, Deng HZ, Xu Q, Feng Y, Yu HY, Wang YP, Wei XH (2015) Minimum of SSR Markers for Analyzing Genetic Variation of Oryza sativa L. Chin J Rice Sci 29:578-586
Zhang QP, Liu WS, Liu S, Wer X, Liu N (2015) An estimation of SSR alleles numbers for analyzing genetic diversity of apricot. Journal of Fruit Science 32:186-191
Zhang XY, Li CW, Wang LF, Wang HM, You GX, Dong YS (2002) An estimation of the minimum number of SSR alleles needed to reveal genetic relationships in wheat varieties. I. Information from large-scale planted varieties and cornerstone breeding parents in Chinese wheat improvement and production. Theoretical and Applied Genetics 106:112-117 doi:10.1007/s00122-002-1016-z
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 doi:10.1371/journal.pone.0010780
Zhao Q, Feng Q, Lu HY et al. (2018) Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice (vol 50, pg 278, 2018) Nat Genet 50:1196-1196 doi:10.1038/s41588-018-0136-6