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About the Authors:
Sang-Ic Kim
Affiliation: USDA-ARS Crops Pathology and Genetics Research Unit, Department of Plant Sciences, University of California Davis, Davis, California, United States of America
Thomas H. Tai
* E-mail: [email protected]
Affiliation: USDA-ARS Crops Pathology and Genetics Research Unit, Department of Plant Sciences, University of California Davis, Davis, California, United States of America
Introduction
Recent advances in genomics have made single nucleotide polymorphisms (SNPs) the marker of choice for genome-wide genetic analyses. Since SNPs occur at much higher density than other markers such as microsatellites, they are particularly useful in distinguishing closely related individuals. In rice (Oryza sativa L.), the sequencing of the temperate japonica cultivar Nipponbare [1] established a gold standard reference for the identification of SNPs using expressed sequence tags and other genome sequence data (e.g. indica 93-11, [2]). 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 genome-wide 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]. Whole genome sequencing has also been employed directly to genotype rice germplasm for genome-wide association analyses and to dissect the origins of cultivated rice [7]–[9].
A number of other powerful, next-generation sequencing-based methods for the simultaneous identification, confirmation, and genotyping of SNPs are now being employed in model and non-model species [10]–[12]. One general approach developed over a decade ago for use with Sanger sequencing [13] involves construction of sequencing libraries with reduced genomic complexity (i.e. reduced representation sequencing). Several methods coupled with various next-generation sequencing platforms have been developed and successfully employed in recent years [14]–[19]. By reducing the complexity of a sequencing library, the coverage (i.e. number of times a given fragment is sequenced) is increased, thus increasing the confidence with which a putative SNP can be called. 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.
The history of California rice breeding is relatively short (∼100 years) and most of the...