Abstract
Very low polymorphism in the germplasm typically used by breeding programs poses a significant bottleneck with regards to molecular breeding and the exploitation of breeding materials for quantitative trait analyses. California rice cultivars, 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 cultivars were easily identified. Reduced representation sequencing methods such as RESCAN are a valuable alternative to SNP chip genotyping and low coverage whole genome sequencing.
Highlights
Recent advances in genomics have made single nucleotide polymorphisms (SNPs) the marker of choice for genome-wide genetic analyses
Resequencing of several different accessions representing the five major subpopulations of cultivated Asian rice [3,4] has facilitated the development of SNP microarrays or chips for analyses of both diverse germplasm accessions for genomewide association studies [5,6] and closely related cultivars to facilitate the genetic analyses of and more fully exploit the phenotypic variation that currently exists in elite breeding programs [4]
The results show that the genome-wide distribution of SNPs derived from Restriction Enzyme Site Comparative Analysis (RESCAN) was suitable for defining pedigree haplotypes and genetic relationships in the very closely related California cultivars
Summary
Recent advances in genomics have made single nucleotide polymorphisms (SNPs) the marker of choice for genome-wide genetic analyses. Resequencing of several different accessions representing the five major subpopulations of cultivated Asian rice [3,4] has facilitated the development of SNP microarrays or chips for analyses of both diverse germplasm accessions for genomewide association studies [5,6] and closely related cultivars to facilitate the genetic analyses of and more fully exploit the phenotypic variation that currently exists in elite breeding programs [4]. A number of other powerful, next-generation sequencing-based methods for the simultaneous identification, confirmation, and genotyping of SNPs are being employed in model and nonmodel species [10,11,12]. Reduced complexity or representation in combination with the use of unique DNA barcoded adapters for each genotype allows multiplexing of libraries from several individuals to exploit the enormous capacity of next-generation sequencing platforms
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