Population Structure and Marker-Trait Association in Indigenous Aromatic Rice

Ahmed, 2012, SSR and RAPD analysis of genetic diversity in walnut (Juglans regia L.) genotypes from Jammu and Kashmir, India, Physiol Mol Biol Plants, 18, 149, 10.1007/s12298-012-0104-z Allard, 1992, Predictive methods for germplasm identification, 119 Amarawathi, 2008, Mapping of quantitative trait loci for basmati quality traits in rice (Oryza sativa L.), Mol Breeding, 21, 49, 10.1007/s11032-007-9108-8 Bai, 2010, Genetic dissection of rice grain shape using a recombinant inbred line population derived from two contrasting parents and fine mapping a pleiotropic quantitative trait locus qGL7, BMC Genet, 11, 16, 10.1186/1471-2156-11-16 Besnier, 2013, Parallel structure: A R package to distribute parallel runs of the population genetics program structure on multi-core computers, PLoS One, 8, e70651, 10.1371/journal.pone.0070651 Bian, 2013, Dynamic QTL detection and analysis of tiller number before and after heading in japonica rice, Aust J Crop Sci, 7, 1189 Blair, 1997, Microsatellite and sequenced- tagged site markers diagnostic for the rice bacterial leaf blight resistance gene xa-5, Theor Appl Genet, 95, 174, 10.1007/s001220050545 Bradbury, 2005, A perfect marker for fragrance genotyping in rice, Mol Breeding, 16, 279, 10.1007/s11032-005-0776-y Brondani, 2002, QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice (Oryza sativa) using microsatellite markers, Theor Appl Genet, 104, 1192, 10.1007/s00122-002-0869-5 Das, 2010, Aromatic Joha rice of Assam: A review, Agric Rev, 31, 1 Earl, 2011, Assemblathon 1: A competitive assessment of de novo short read assembly methods, Genome Res, 21, 2224, 10.1101/gr.126599.111 Evanno, 2005, Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study, Mol Ecol, 14, 2611, 10.1111/j.1365-294X.2005.02553.x Falush, 2003, Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies, Genetics, 164, 1567, 10.1093/genetics/164.4.1567 Garris, 2005, Genetic structure and diversity in Oryza sativa L, Genetics, 169, 1631, 10.1534/genetics.104.035642 Grist D. 1983. Rice: Longman. New York, USA. Johanson, 1955, Estimates of genetic and environmental variability in soybean, Agron J, 47, 314, 10.2134/agronj1955.00021962004700070009x Joshi, 2000, Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza, Theor Appl Genet, 100, 1311, 10.1007/s001220051440 Kaw, 1999, Variability and interrelations in rice under cold stress environments, Oryza, 36, 1 Liu, 2008, Genetic analysis of grain yield conditioned on its component traits in rice (Oryza sativa L.), Aust J Agric Res, 59, 189, 10.1071/AR07163 Marri, 2005, Identification and mapping of yield-related QTL from an Indian accession of Oryza rufipogon, BMC Genet, 6, 33, 10.1186/1471-2156-6-33 Moncada, 2001, Quantitative trait loci for yield and yield components in an Oryza sativa × Oryza rufipogon BC2F2 population evaluated in an upland environment, Theor Appl Genet, 102, 41, 10.1007/s001220051616 Nachimuthu, 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, 30, 10.1186/s12284-015-0062-5 Nei, 1973, Analysis of gene diversity in subdivided populations, Proc Natl Acad Sci USA, 70, 3321, 10.1073/pnas.70.12.3321 Ni, 2002, Evaluation of genetic diversity in rice sub-species using microsatellite markers, Crop Sci, 42, 601, 10.2135/cropsci2002.0601 Parikh, 2012, Agro-morphological characterization and assessment of variability in aromatic rice germplasm, Bangl J Agric Res, 37, 1, 10.3329/bjar.v37i1.11168 Plaschke, 1995, Detection of genetic diversity in closely related bread wheat using microsatellite markers, Theor Appl Genet, 91, 1001, 10.1007/BF00223912 Pritchard, 2000, Inference of population structure using multilocus genotype data, Genetics, 155, 945, 10.1093/genetics/155.2.945 Rabiei, 2004, Identification of QTLs for rice grain size and shape of Iranian cultivars using SSR markers, Euphytica, 137, 325, 10.1023/B:EUPH.0000040452.76276.76 Ram, 2007, Genetic diversity among cultivars, landraces and wild relatives of rice as revealed by microsatellite markers, J Appl Genet, 48, 337, 10.1007/BF03195230 Rathi, 2010, Variability in grain quality characters of upland rice of Assam, India. Rice Sci, 17, 330, 10.1016/S1672-6308(09)60035-4 Rathi, 2014, Genetic diversity in upland rice of Assam detected by SSR markers, Ind J Genet, 74, 238, 10.5958/0975-6906.2014.00161.8 Rohlf, 1998 Roy, 2015, Genetic diversity and population structure in aromatic and quality rice (Oryza sativa L.) landraces from North-Eastern India, PLoS One, 10, e0129607, 10.1371/journal.pone.0129607 Sakthivel, 2009, Genetic and molecular basis of fragrance in rice, Biotechn Adv, 27, 468, 10.1016/j.biotechadv.2009.04.001 Samal, 2014, Study of genetic divergence of indigenous aromatic rice (Oryza sativa L.): Potentials and consequences of on farm management in traditional farming, Int J Agric Sci, 4, 176 Sandhu, 2013, Genetic variation, linkage mapping of QTL and correlation studies for yield, root, and agronomic traits for aerobic adaptation, BMC Genet, 14, 4, 10.1186/1471-2156-14-104 Shenoy V V, Kalagudi G M. 2004. Amplified fragment length polymorphism in select specialty rice of India. New directions for a diverse planet. Proceedings of the 4th International Crop Science Congress, Brisbane, Australia. Sneath, 1973 Sood, 1978, A rapid technique for scent determination in rice, Ind J Genet Plant Breeding, 38, 268 Sun, 2008, Genetic analysis and gene fine mapping of aroma in rice (Oryza sativa L. Cyperales, Poaceae), Genet Mol Biol, 31, 532, 10.1590/S1415-47572008000300021 Temnykh, 2000, Mapping and genome organization of microsatellites in rice (Oryza sativa L.), Theor Appl Genet, 100, 697, 10.1007/s001220051342 Temnykh, 2001, Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Fequency, length variation, transposon associations, and genetic marker potential, Genome Res, 11, 1441, 10.1101/gr.184001 Thomson, 2003, Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson, Theor Appl Genet, 107, 479, 10.1007/s00122-003-1270-8 Travis, 2015, Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal, Rice, 8, 35, 10.1186/s12284-015-0068-z Tuwar, 2013, Appraisal of genetic variability for yield and its component characters in rice (Oryza sativa L.), Biolofe, 1, 84 Vhora, 2013, Molecular studies of aromatic and non aromatic rice (Oryza sativa L.) genotypes for quality traits using microsatellite markers, Biosacn, 8, 359 Virk, 1995, Use of RAPD for the study of diversity within plant germplasm collections, Heredity, 74, 170, 10.1038/hdy.1995.25 Yoon, 2006, Mapping quantitative trait loci for yield components and morphological traits in an advanced backcross population between Oryza grandiglumis and the O. sativa japonica cultivar Hwaseongbyeo, Theor Appl Genet, 112, 1052, 10.1007/s00122-006-0207-4 Yu, 2006, A unified mixed-model method for association mapping that accounts for multiple levels of relatedness, Nat Genet, 38, 203, 10.1038/ng1702 Zhao, 2010, Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome, PLoS One, 5, e10780, 10.1371/journal.pone.0010780