Comprehensive genotyping of the USA national maize inbred seed bank

Genome Biology

Candice A Gardner⁶  Edward S Buckler⁵  James B Holland⁴  Michael D McMullen¹  Sherry A Flint-Garcia¹  Sharon E Mitchell³  Charlotte B Acharya³  Robert J Elshire³  Terry M Casstevens³  Kelly L Swarts⁵  Jason A Peiffer²  Jeffrey C Glaubitz³  Mark J Millard⁶  Maria C Romay³ 

[1] Division of Plant Sciences, Curtis Hall, University of Missouri, Columbia, MO, 65211,USA;Bioinformatics Research Center, Thomas Hall, North Carolina State University, Raleigh, NC, 27606, USA;Institute for Genomic Diversity, Biotechnology bldg., Cornell University, Ithaca, NY, 14853, USA;Department of Crop Science, Williams Hall, North Carolina State University, Raleigh, NC, 27695, USA;Department of Plant Breeding and Genetics, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA;North Central Regional Plant Introduction Station, Agronomy bldg., Department of Agronomy, Iowa State University, Ames, IA, 50001, USA

关键词: Public;    Maize;    Germplasm;    Genotyping by sequencing;    Diversity;   

Others  :  1135336
DOI  :  10.1186/gb-2013-14-6-r55

 received in 2013-02-26, accepted in 2013-06-11,  发布年份 2013

【 摘 要 】

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.

【 授权许可】

   
2013 Romay et al.; licensee BioMed Central Ltd.

【 图 表 】

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