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Title: Comprehensive genotyping of the USA national maize inbred seed bank

Author
item ROMAY, MARIA - Cornell University
item Millard, Mark
item GLAUBITZ, JEFFREY - Cornell University
item PEIFFER, JASON - Cornell University
item SWARTS, KELLY - Cornell University
item CASSTEVENS, TERRY - Cornell University
item ELSHIRE, ROBERT - Cornell University
item ACHARYA, CHARLOTTE - Cornell University
item MITCHELL, SHARON - Cornell University
item Flint-Garcia, Sherry
item McMullen, Michael
item Holland, Jim - Jim
item Buckler, Edward - Ed
item Gardner, Candice

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/29/2013
Publication Date: 6/13/2013
Citation: Romay, M.C., Millard, M.J., Glaubitz, J.C., Peiffer, J.A., Swarts, K.L., Casstevens, T.M., Elshire, R.J., Acharya, C.B., Mitchell, S.E., Flint Garcia, S.A., McMullen, M.D., Holland, J.B., Buckler IV, E.S., Gardner, C.A. 2013. Comprehensive genotyping of the US national maize inbred seed bank. Genome Biology. 14(6):1-18.

Interpretive Summary: The germplasm bank at the USDA-ARS North Central Regional Plant Introduction Station (NCRPIS) in Ames, Iowa, preserves maize inbred lines from breeding programs from all over the world, a substantial amount of maize's natural diversity including some of the key lines from a century of maize breeding efforts. We genotyped 2,815 maize inbred accessions, most from the NCRPIS, using Genotyping-by-Sequencing (GBS), a low cost, high-throughput sequencing technology. This approach identified genetic markers (SNPs, or single nucleotide polymorphism) useful for assessing whether germplasm is identical at various positions in the genome. 681,257 SNP markers were distributed across the entire maize genome, and most alleles were detected as rare with high confidence levels. These data, based on the entire genome, were used to determine relationships between lines and to examine wheter the collection can be used to study the genetic architecture of maize traits. We were able to identify clusters of lines centered around a few key line ancestors, and show that the extent of genetic variation is highly dependent on the origin and background of each germplasm group. For example, tropical inbreds contribute a large percentage of the rare alleles, although most of those alleles have been incorporated into public temperate breeding programs. In contrast, only a modest amount of the available diversity is present in the commercial germplasm tested. The newly available genotypic information described here allows these publicly available lines to be understood and used in new ways by breeders facing the challenges of sustainable agriculture and by researchers focused on the nature of genetic diversity.

Technical Abstract: The germplasm bank at the USDA-ARS North Central Regional Plant Introduction Station (NCRPIS) in Ames, Iowa, preserves maize inbred lines from breeding programs from all over the world, including some of the key lines from the breeding history of maize. We genotyped 2,815 maize inbred accessions, most of them from the NCRPIS, using Genotyping-by-Sequencing (GBS), a low cost, high-throughput sequencing technology. This method produced 681,257 SNP markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. The collection of accessions we evaluated presents (1) a substantial amount of maize's natural diversity (with most of the alleles being rare), (2) population stratification, including a small number of large clusters centered around key lines, and (3) rapid LD decay. The extent of genetic variation is highly dependent on the origin and background of each germplasm group. For example, tropical inbreds contribute a large percentage of the rare alleles, although most of those alleles have been incorporated into public temperate breeding programs. In contrast, only a modest amount of the available diversity is present in the commercial germplasm. The newly available genotypic information described here allows this publicly available panel, representing a century of maize breeding efforts, to be exploited by breeders facing the challenges of sustainable agriculture and by researchers focused on the nature of genetic diversity.