About RiceSzWtBase Rice (Oryza sativa) is one of the most important cereal crops for human nutrition all over the world. Proper seed development is the crucial step for grain size/weight determination and productivity. This site provides extensive information and analysis of genetic variations discovered in four different rice genotypes including two long grain genotypes (LGR, PB 1121) and two short grain genotypes (Sonasal and Bindli) with contrasting seed size/weight trait. SNP and InDel genotyping was called against reference genome Os-Nipponbare-Reference-IRGSP-1.0. Further, combined genomic and phylogenetic analysis with 3000 rice accessions provide the global insight of sequence variations which can be used by researchers involved in understanding the genetic basis of variation in traits of rice genotypes and breeders involved in improvement of rice varieties. A contiguous ~ 6 Mb long low diversity region (LDR) carrying a major grain weight QTL (harbouring OsTOR gene) was identified on chromosome 5. This LDR was identified as an evolutionary important site with significant positive selection and multiple selection sweeps, and showed association with many domestication-related traits including grain size/weight. The aus population retained more allelic variations in the LDR than japonica and indica populations, suggesting it to be one of the divergence loci. This dataset supplements the study entitled "Genome-wide analysis of polymorphisms identified domestication-associated long low diversity region carrying important rice grain size/weight QTL". Kumar, A., Daware, A., Kumar, A., Kumar, V., Gopala Krishnan, S., , Patra, BC., Singh, AK., Tyagi, AK., Parida, SK., and Thakur, JK. (2020) Genome-wide analysis of polymorphisms identified domestication-associated long low diversity region carrying important rice grain size/weight QTL. The Plant Journal. https://doi.org/10.1111/tpj.14845.
	Rice genotype Raw reads High Quality reads (>= Q30) Coverage (%) Sequencing Depth (X) LGR (long grain) 24,34,60,282 21,24,43,442 (87.2%) 91.4 59.4 PB 1121 (long grain) 24,51,48,640 21,57,30,803 (88.1%) 91.9 57.6 Sonasal (short grain) 18,27,13,442 16,33,45,817 (89.4%) 93.4 43.9 Bindli (short grain) 25,70,78,610 22,80,28,727 (88.7%) 94.3 64.9
	For Queries & Suggetions: Dr. Jitendra K. Thakur jthakur@nipgr.ac.in National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi - 110067