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United States Department of Agriculture

Agricultural Research Service

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Research Project: Genomic Analyses in Carya

Location: Crop Germplasm Research

Project Number: 3091-21000-036-02-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 30, 2012
End Date: Sep 29, 2017

To 1) determine ploidy level and genome size of Carya species and selected geographic populations; 2) validate the utility of selected Single Nucleotide Polymorphic DNA (SNP) markers for use across diverse Carya accessions; and 3) design efficient and cost-effective standard assays for routine genetic profiling of NCGR-Carya accessions.

Diverse germplasm from the National Collection of Genetic Resources for Pecans and Hickories (NCGR-Carya) and from selected Pecan Breeding Program nurseries will be evaluated with flow cytometry to determine ploidy level and genome size. Using sequence information from a variety of sources, single nucleotide polymorphisms (SNPs) will be identified and will be qualified to ensure at least 20 clear base pairs on each side of the targeted variable base to allow unobstructed primer design. SNPs will be chosen to represent known genic regions that are well distributed across chromosomes in homologous species, as well as SNPs representing organelles. Selected sequence data will be used to generate PCR primers for validation of single nucleotide polymorphic DNA (SNPs) markers. Primers will be designed and SNPs validated using techniques of the KBiosciences competitive Allele Specific PCR assay (KASPar), performed in the AgriGenomics Lab at TAMU. SNPs will be validated for information content using a panel representing diverse species of Carya as well as geographically and phenotypically diverse pecan accessions. Validated SNPs will be configured for maximum utility within the diverse plate readers available in the AgriGenomics lab, recognizing that cost efficiency increases with increasing plate size. When the composition of the assay has been confirmed, DNA will be extracted (if necessary) from remaining NCGR accessions to be profiled and profiles determined.

Last Modified: 10/19/2017
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