Exploiting the genomic diversity of rice (Oryza sativa L.): SNP-typing in 11 early-backcross introgression-breeding populations

Abstract

© 2018 Ali, Aslam, Tariq, Murugaiyan, Schnable, Li, Marfori-Nazarea, Hernandez, Arif, Xu and Li. This study demonstrates genotyping-by-sequencing-based single-nucleotide polymorphism (SNP)-typing in 11 early-backcross introgression populations of rice (at BC1 F5 ), 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 patterns in ILs were characteristic with variable introgression frequency in different genomic regions, attributed mainly to stringent selection under abiotic stress and (b) considerably lower heterozygosity was observed in ILs. Functional annotation revealed 426 non-synonymous deleterious SNPs present in 102 loci with a range of 1–4 SNPs per locus and 120 novel SNPs. SNP-typing this diversity panel will further assist in the development of markers supporting genomic applications in molecular breeding programs.

Source or Periodical Title

Frontiers in Plant Science

Document Type

Article

Subject

Conventional genotyping by sequencing (cGBS), Introgression breeding, Marker-assisted breeding, Non-synonymous SNPs, SNP-typing, Tunable genotyping by sequencing (tGBS)

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