Content area
Full text
About the Authors:
Qijian Song
Affiliation: Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
David L. Hyten
Current address: Pioneer Hi-Bred International Inc, Johnston, Iowa, United States of America
Affiliation: Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
Gaofeng Jia
Affiliation: Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
Charles V. Quigley
Affiliation: Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
Edward W. Fickus
Affiliation: Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
Randall L. Nelson
Affiliation: Pathology and Genetics Research Unit and Department of Crop Sciences, Soybean/Maize Germplasm, Agricultural Research Service, United States Department of Agriculture, University of Illinois, Urbana, Illinois, United States of America
Perry B. Cregan
* E-mail: [email protected]
Affiliation: Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
Introduction
Even with the extensive linkage disequilibrium (LD) in the soybean [Glycine max (L). Merr.] genome, a large number of molecular markers are required to cover the genome for the purpose of genome-wide genetic analysis. Single nucleotide polymorphisms (SNPs) are the most abundant form of DNA polymorphism in eukaryotic genomes [1], and are suitable for the development of high-throughput, easy-to-automate genotyping methods because most SNPs have only two alleles, thereby simplifying genotyping approaches and analysis [2]–[6]. Previous procedures of SNP discovery in plants involved primer selection, PCR amplification and sequencing of amplicons from a small set of diverse genotypes [7]–[9]. This approach is time-consuming and expensive. With the advent of second generation sequencing technology, large amounts of DNA sequence data can be generated in a short period of time. Coupled with the availability of the soybean whole genome sequence [10], large numbers of sequence variants can be efficiently identified via the alignment of the short sequence reads from diverse genotypes to the whole genome sequence [11]–[13]. High throughput SNP discovery is a necessity in light of the availability of high throughput SNP assay systems such as the Infinium...