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ARS Home » Plains Area » Stillwater, Oklahoma » Wheat, Peanut, and Other Field Crops Research » Research » Publications at this Location » Publication #344429

Title: Targeted resequencing in peanuts using the fluidigm access array

item KULKARNI, R - Texas Tech University
item Chopra, Ratan
item CHAGOYA, JENNIFER - Texas Agrilife Research
item CROZDANOV, P - Texas Tech University Health Science Center
item HILLHOUSE, A - Mozambique Agronomic Research Institute
item SIMPSON, CHARLES - Texas Agrilife Research
item BARING, MIKE - Texas Agrilife Research
item PUPPALA, NAVEEN - New Mexico State University
item Chamberlin, Kelly
item BUROW, MARK - Texas Agrilife Research

Submitted to: American Peanut Research and Education Society Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 7/13/2017
Publication Date: 3/1/2018
Citation: Kulkarni, R., Chopra, R., Chagoya, J.C., Crozdanov, P., Hillhouse, A., Simpson, C.E., Baring, M.R., Puppala, N., Chamberlin, K.D., Burow, M.D. 2018. Targeted resequencing in peanuts using the fluidigm access array [abstract]. In: Proceedings of the American Peanut Research and Education Society, July 11-13, 2017, Albuquerque, NM. 49:164.

Interpretive Summary:

Technical Abstract: The presence of homoeologous gene copies in allotetraploid peanut makes it challenging to select homologous SNPs differentiating two or more cultivars. An integrated approach of improved bioinformatics and targeted resequencing to select homologous SNPs in tetraploid peanut is needed. Raw transcriptome reads were mapped to a synthetic tetraploid genome reference generated by combining A and B genome scaffolds to identify and separate homologous SNPs from homoeologous SNPs among 10 tetraploid peanut accessions using the GATK pipeline and custom python scripts. SNP-containing sequences obtained from GATK were filtered using SWEEP, which is a sliding window protocol that filters SNPs based on haplotype. SNPs were also identified using the OLin transcriptome as reference; also a few SNPS were selected from the peanut SNP chip. Forty-eight targets of around 400 bp length were selected for validation on a Fluidigm Access Array as a proof of concept, followed by mass sequencing on an Illumina MiSeq. Some of these targets consisted of adjacent SNPs that differentiated both A- and B- genome copies together. Eighty-one percent of the SNP calls derived from the Fluidigm-MiSeq protocol were validated for diploids, and 72% of the SNP calls were validated for tetraploids. This approach will benefit tetraploid breeding programs by reducing the cost of genotyping of QTL mapping populations and contribute to selection of favorable alleles in both genomes.