Comprehensive genotyping of the USA national maize inbred seed bank
Open Access
- 11 June 2013
- journal article
- Published by Springer Science and Business Media LLC in Genome Biology
- Vol. 14 (6), 1-18
- https://doi.org/10.1186/gb-2013-14-6-r55
Abstract
Background Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world. Results The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits. Conclusions The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity.Keywords
This publication has 57 references indexed in Scilit:
- Historical genomics of North American maizeProceedings of the National Academy of Sciences of the United States of America, 2012
- ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maizeProceedings of the National Academy of Sciences of the United States of America, 2012
- Distribution of allele frequencies and effect sizes and their interrelationships for common genetic susceptibility variantsProceedings of the National Academy of Sciences of the United States of America, 2011
- Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativaNature Communications, 2011
- Demographic history and rare allele sharing among human populationsProceedings of the National Academy of Sciences of the United States of America, 2011
- Effect of population structure corrections on the results of association mapping tests in complex maize diversity panelsTheoretical and Applied Genetics, 2011
- Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred linesNature, 2010
- Mixed linear model approach adapted for genome-wide association studiesNature Genetics, 2010
- Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markersTheoretical and Applied Genetics, 2010
- Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maizeProceedings of the National Academy of Sciences of the United States of America, 2007