Exploiting the Genomic Diversity of Rice (Oryza sativa L.): SNP-Typing in 11 Early-Backcross Introgression-Breeding Populations.

ABSTRACT: This study demonstrates genotyping-by-sequencing-based single-nucleotide polymorphism (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 b

SUBMITTER: Ali J 

PROVIDER: S-EPMC6024854 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature