Evaluating the Genomic Diversity of Rice (Oryza sativa L.): SNP-typing in 11 Early-Backcross Introgression Breeding Populations
<|begin_of_text|><|start_header_id|>system<|end_header_id|> You are a research archivist expert in dataset metadata. Answer the question truthfully.  <|eot_id|><|start_header_id|>user<|end_header_id|> Here is the Description of a dataset. Description:'This study demonstrates GBS based SNP-typing in 11 early-backcross introgression populations of rice (at BC1F5), comprising a set of 564 diverse introgression lines and 12 parents. Sequencing using 10 Ion Proton runs generated a total of ~943.4 million raw reads, out of which ~881.6 million reads remained after trimming for low-quality bases. After alignment, 794,297 polymorphic SNPs were identified, and filtering resulted in LMD50 SNPs (low missing data, with each SNP, genotyped in at least 50% of the samples) for each sub-population. Every data point was supported by actual sequencing data without any imputation, eliminating imputation-induced errors in SNP-calling. Genotyping substantiated the impacts of novel breeding strategy revealing: (a) the donor introgression pattern in ILs were characteristic with variable introgression frequ' . Please return only a json list of at most 3 Keywords corresponding to the Description:.<|eot_id|><|start_header_id|>assistant<|end_header_id|> {"Answer" : ["genotyping by sequencing","Genotyping-by-Sequencing","introgression","marker-assisted breeding (selection)","non-synonymous SNP","Oryza sativa","single nucleotide polymorphism","SNP-typing","tunable Genotyping-by-Sequencing (tGBS®)"]} <|eot_id|>
 Here is the Description of a dataset. Description:'This study demonstrates GBS based SNP-typing in 11 early-backcross introgression populations of rice (at BC1F5), comprising a set of 564 diverse introgression lines and 12 parents. Sequencing using 10 Ion Proton runs generated a total of ~943.4 million raw reads, out of which ~881.6 million reads remained after trimming for low-quality bases. After alignment, 794,297 polymorphic SNPs were identified, and filtering resulted in LMD50 SNPs (low missing data, with each SNP, genotyped in at least 50% of the samples) for each sub-population. Every data point was supported by actual sequencing data without any imputation, eliminating imputation-induced errors in SNP-calling. Genotyping substantiated the impacts of novel breeding strategy revealing: (a) the donor introgression pattern in ILs were characteristic with variable introgression frequ' . Please return only a json list of at most 3 Keywords corresponding to the Description:.
This study demonstrates GBS based SNP-typing in 11 early-backcross introgression populations of rice (at BC1F5), comprising a set of 564 diverse introgression lines and 12 parents. Sequencing using 10 Ion Proton runs generated a total of ~943.4 million raw reads, out of which ~881.6 million reads remained after trimming for low-quality bases. After alignment, 794,297 polymorphic SNPs were identified, and filtering resulted in LMD50 SNPs (low missing data, with each SNP, genotyped in at least 50% of the samples) for each sub-population. Every data point was supported by actual sequencing data without any imputation, eliminating imputation-induced errors in SNP-calling. Genotyping substantiated the impacts of novel breeding strategy revealing: (a) the donor introgression pattern in ILs were characteristic with variable introgression frequ
genotyping by sequencing; Genotyping-by-Sequencing; introgression; marker-assisted breeding (selection); non-synonymous SNP; Oryza sativa; single nucleotide polymorphism; SNP-typing; tunable Genotyping-by-Sequencing (tGBS®)