Open AccessLarge‐Scale Discovery of Gene‐Enriched SNPs
Author(s) -
Gore Michael A.,
Wright Mark H.,
Ersoz Elhan S.,
Bouffard Pascal,
Szekeres Edward S.,
Jarvie Thomas P.,
Hurwitz Bonnie L.,
Narechania Apurva,
Harkins Timothy T.,
Grills George S.,
Ware Doreen H.,
Buckler Edward S.
Publication year - 2009
Publication title -
the plant genome
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 41
ISSN - 1940-3372
DOI - 10.3835/plantgenome2009.01.0002
Subject(s) - biology , molecular inversion probe , snp genotyping , single nucleotide polymorphism , genome , tag snp , computational biology , genetics , sanger sequencing , genotyping , snp , pyrosequencing , snp array , false discovery rate , locus (genetics) , reference genome , dna sequencing , gene , genotype
Whole‐genome association studies of complex traits in higher eukaryotes require a high density of single nucleotide polymorphism (SNP) markers at genome‐wide coverage. To design high‐throughput, multiplexed SNP genotyping assays, researchers must first discover large numbers of SNPs by extensively resequencing multiple individuals or lines. For SNP discovery approaches using short read‐lengths that next‐generation DNA sequencing technologies offer, the highly repetitive and duplicated nature of large plant genomes presents additional challenges. Here, we describe a genomic library construction procedure that facilitates pyrosequencing of genic and low‐copy regions in plant genomes, and a customized computational pipeline to analyze and assemble short reads (100–200 bp), identify allelic reference sequence comparisons, and call SNPs with a high degree of accuracy. With maize ( Zea mays L.) as the test organism in a pilot experiment, the implementation of these methods resulted in the identification of 126,683 putative SNPs between two maize inbred lines at an estimated false discovery rate (FDR) of 15.1%. We estimated rates of false SNP discovery using an internal control, and we validated these FDR rates with an external SNP dataset that was generated using locus‐specific PCR amplification and Sanger sequencing. These results show that this approach has wide applicability for efficiently and accurately detecting gene‐enriched SNPs in large, complex plant genomes.