[1] Ali , N.,Farhatullah , N.U.,Khan , M.A.,Rabbani , I. Hussain, S.,Ali , S.A.,Khan and M.Q.,Kakar, 2017.Genetic diversity of Brassica Raps L. indigenous landraces based on cluster and principal component analyses,Pak. J. Bot. 49 1891 -1901
[2] Arai-Kichise , Y.,Y.Shiwa,H.Nagasaki,K.Ebana,H.Yoshikawa,M.Yano,K.Wakasa, 2011.Discovery of genome-wide DNA polymorphisms in a landrace cultivar of japonica rice by whole-genome sequencing,Plant & Cell Physiol 52 274 -282
[3] Caicedo , A.L.,S.H.Williamson,R.D.Hernandez,A.Boyko,A.F.Alon,N.R.Polato,K.M. Olsen , R.,Nielsen and S.R.,McCouch, 2007.Genome-wide patterns of nucleotide polymorphism in domesticated rice,PLoS Genetics 3 e163 -
[4] Cheng , C.,R.Motohashi,S.Tsuchimoto,Y.Fukuta,H.Ohtsubo,E.Ohtsubo,Evol, 2003.Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs,Mol. Biol 20 67 -75
[5] Ebana , K.,J.I.Yonemaru,S.Fukuoka,H.Iwata,H.Kanamori,N.Namiki,H.Nagasaki,M.Yano, 2010.Genetic structure revealed by a whole-genome single-nucleotide polymorphism survey of diverse accessions of cultivated Asian rice (Oryza sativa L.),Breed. Sci. 60 390 -397
[6] Evanno , G., S.,Regnaut and J.,Goudet, 2005.Detecting the number of clusters of individuals using the software structure: a simulation study,Mol. Ecol 14 2611 -2620
[7] Foll , M.,O.Gaggiotti, 2008.A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective,Genetics 180 977 -993
[8] Gabriel , S.,L.Ziaugra,D.Tabbaa, 2009.SNP genotyping using the Sequenom MassARRAYiPLEX platform,Curr. Prot. Human Gen., 2 12 -12
[9] Garris , A.J.,T.H.Tai,J.Coburn,S.Kresovich,S.McCouch, 2005.Genetic structure and diversity in Oryza sativa L, 169 1631 -1638
[10] He , Z.,W.Zhai,H.Wen,T.Tang,Y.Wang,X.Lu,A.J.Greenberg,R.R.Hudson,C.I.Wu,S.Shi, 2011.Two evolutionary histories in the genome of rice: the roles of domestication genes,PLoS Genetics 7 e1002100 -
[11] Huang , P.,J. Molina , J.M.,Flowers , S.,Rubinstein , S.A,Jackson , M.D.,Purugganan and B.A.,Schaal, 2012.Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view,Mol. Ecol 21 4593 -4604
[12] Huang , X.,N.Kurata,X.Wei,Z.X.Wang,A.Wang,Q.Zhao,Y.Zhao,K.Liu,H.Lu,W.Li, 2012.A map of rice genome variation reveals the origin of cultivated rice,Nature 490 497 -501
[13] Huang , X.,X.Wei,T.Sang,Q.Zhao,Q.Feng,Y.Zhao,C.Li,C.Zhu,T.Lu,Z.Zhang, 2010.Genome-wide association studies of 14 agronomic traits in rice landraces,Nature Genetics 42 961 -967
[14] Jeffreys , H., 1961.Theory of probability, -
[15] Li , C.,A.Zhou,T.Sang, 2006.Rice domestication by reducing shattering,Science 311 1936 -1939
[16] Librado , P.,J.Rozas, 2009.DnaSP v5: a software for comprehensive analysis of DNA polymorphism data,Bioinformatics 25 1451 -1452
[17] Londo , J.P.,Y.C.Chiang,K.H.Hung,T.Y.Chiang,B.A.Schaal, 2006.Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa,Proceedings of the National Academy of Sciences of USA 103 9578 -9583
[18] Lu , B.R.,X.Cai,J.Xin, 2009.Efficientindica and japonica rice identification based on the InDel molecular method: Its implication in rice breeding and evolutionary research,Prog. In Nat. Sci 19 1241 -1252
[19] Mao , T.,X.Li,Z.J.Xu,J.Y.Wang,L.Tang,H.Xu,S.K.Jiang,Z.Zhang,Z.Y.Li, 2018.Development of functional markers for quantitative trait locus underlying rice quality components,Pak. J. Bot. 50 645 -653
[20] Molina , J.,M.Sikora,N.Garud,J.M.Flowers,S.Rubinstein,A.Reynolds,P.Huang,S.Jackson,B.A.Schaal,C.D.Bustamante, 2011.Molecular evidence for a single evolutionary origin of domesticated rice,Proceedings of the National Academy of Sciences of USA 108 8351 -8356
[21] Nagasaki , H., K.,Ebana , T.,Shibaya , J.I.,Yonemaru and M.,Yano, 2010.Core single-nucleotide polymorphisms-a tool for genetic analysis of the Japanese rice population,Breed. Sci. 60 648 -655
[22] Oka , H., 1988.Origin of cultivated rice, -
[23] Pritchard , J.K.,M.Stephens,P.Donnelly, 2000.Inference of population structure using multilocus genotype data,Genetics 155 945 -959
[24] Sang , T. and S.,Ge, 2007.Genetics and phylogenetics of rice domestication,Curr. Opin. Gen. & Develop 17 533 -538
[25] Sun , J.,D.Liu,J.Y.Wang,D.R.Ma,H.Gao,Z.J.Xu,W.F.Chen,App, 2012.The contribution of intersubspecific hybridization to the breeding of super-high-yielding japonica rice in northeast China, 125 1149 -1157
[26] Sun , J.,Q.Qian,D.R.Ma,Z.J.Xu,D.Liu,H.B.Du,W.F.Chen, 2013.Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China, 197 290 -299
[27] Sweeney , M.T.,M.J. Thomson , Y.G.,Cho , Y.J.,Park , S.H.,Williamson , C.D.,Bustamante and S.R.,McCouch, 2007.Global dissemination of a single mutation conferring white pericarp in rice,PLoS Genetics 3 e133 -
[28] Tamura , K.,G.Stecher,D.Peterson,A.Filipski,S.Kumar,Mol,Evol, 2013.MEGA6: Molecular Evolutionary Genetics Analysis version 6.0, 30 2725 -2729
[29] Wei , X.,W.H.Qiao,Y.T.Chen,R.S.Wang,L.R.Cao,W.X.Zhang,N.N.Yuan,Z.C.Li,H.L.Zeng,Q.W.Yang, 2012.Domestication and geographic origin of Oryza sativa in China: insights from multilocus analysis of nucleotide variation of O. sativa and O. rufipogon,Mol. Ecol 21 5073 -5087
[30] Xu , X.,X.Liu,S.Ge,J.D.Jensen,F.Hu,X.Li,Y.Dong,R.N.Gutenkunst,L.Fang,L.Huang, 2012.Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes,Nature Biotechnol 30 105 -111
[31] Yamamoto , T.,H.Nagasaki,J. I.Yonemaru,K.Ebana,M.Nakajima,T.Shibaya,M.Yano, 2010.Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms,BMC Genom 11 267 -
[32] Yonemaru , J.I.,T.Yamamoto,K.Ebana,H.Nagasaki,T.Shibaya,M.Yano, 2012.Genome-wide haplotype changes produced by artificial selection during modern rice breeding in Japan,PLoS One 7 e32982 -
[33] Zhang , L.B.,Q.Zhu,Z.Q.Wu,J.Ross‐Ibarra,B. S.Gaut,S.Ge,T.Sang, 2009.Selection on grain shattering genes and rates of rice domestication, 184 708 -720
[34] Zhao , X.,L.Yang,Y.Zheng,Z.Xu,W.Wu,L.). J. Gen. & Genom, 2009.Subspecies-specific intron length polymorphism markers reveal clear genetic differentiation in common wild rice (Oryza rufipogon L.) in relation to the domestication of cultivated rice (O, 36 435 -442
[35] Zhu , B.F.,L.Si,Z.Wang,Y.Zhou,J.Zhu,Y.Shangguan,D.Lu,D.Fan,C.Li,H.Lin,Q.Qian,T.Sang,B.Zhou,Y.Minobe,B.Han, 2011.Genetic control of a transition from black to straw-white seed hull in rice domestication,Plant 155 1301 -1311