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Title: Identification of SNPs in closely-related temperate japonica rice cultivars using restriction enzyme-phased sequencing

item KIM, SANG-IC - University Of California
item Tai, Thomas

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/25/2013
Publication Date: 3/26/2013
Citation: Kim, S., Tai, T. 2013. Identification of SNPs in closely-related temperate japonica rice cultivars using restriction enzyme-phased sequencing. PLoS One. 8(3): e60176. doi:10.1371/journal.pone.0060176.

Interpretive Summary: Rice breeding programs typically use old varieties to breed newer varieties. This results in very closely related genetic materials that are hard to distinguish at the DNA level using the commonly applied methods. This makes it very difficult to use modern molecular breeding tools such as DNA marker-assisted selection and to conduct genetic studies using lines that are relevant to breeders. We have employed a relatively new method of DNA fingerprinting based on cutting edge DNA sequencing. This approach shows great promise for enabling very closely related rice lines to be distinguished, thus overcoming a significant hurdle for molecular breeding and genetic analysis of agriculturally important traits in rice.

Technical Abstract: Very low polymorphism in the germplasm typically used by breeding programs poses a significant bottleneck with regarding to molecular breeding and the exploitation of breeding materials for quantitative trait analyses. California rice varieties, derived from a very small base of temperate japonica germplasm and having a relatively brief breeding history, are a good example. In this study, we employed a reduced representation sequencing approach called Restriction Enzyme Site Comparative Analysis (RESCAN) to simultaneously identify and genotype single nucleotide polymorphisms (SNPs) in forty-five rice cultivars representing the majority of the 100 year-old breeding history in California. Over 20,000 putative SNPs were detected relative to the Nipponbare reference genome which enabled the identification and analysis of inheritance of pedigree haplotypes. Haplotype blocks distinguishing modern California cultivars from each other and from the ancestral short grain temperate japonica varieties were easily identified. Reduced representation sequencing methods such as RESCAN are a valuable alternative to SNP chip genotyping and low coverage whole genome sequencing.