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ARS Home » Plains Area » El Reno, Oklahoma » Oklahoma and Central Plains Agricultural Research Center » Peanut and Small Grains Research Unit » Research » Publications at this Location » Publication #370325
Research Project: Genetic Improvement of Peanut for Production in the Southwest United States Region

Location: Peanut and Small Grains Research Unit

Title: Use of targeted amplicon sequencing in peanut to generate allele information on allotetraploid sub-genomes

Author
item KULKARNI, ROSHAN - TEXAS TECH UNIVERSITY
item CHOPRA, RATAN
item CHAGOYA, JENNIFER - TEXAS A&M AGRILIFE
item SIMPSON, CHARLES - TEXAS A&M AGRILIFE
item BARING, MICHAEL - TEXAS A&M AGRILIFE
item HILLHOUSE, ANDREW - TEXAS A&M UNIVERSITY
item PUPPALA, NAVEEN - NEW MEXICO STATE UNIVERSITY
item Chamberlin, Kelly
item BUROW, MARK - TEXAS A&M AGRILIFE

Submitted to: Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/14/2020
Publication Date: 10/18/2020
Citation: Kulkarni, R., Chopra, R., Chagoya, J., Simpson, C.E., Baring, M.R., Hillhouse, A., Puppala, N., Chamberlin, K., Burow, M.D. 2020. Use of targeted amplicon sequencing in peanut to generate allele information on allotetraploid sub-genomes. Genes. 11(10). Article 1220. https://doi.org/10.3390/genes11101220.
DOI: https://doi.org/10.3390/genes11101220

Interpretive Summary: Use of molecular markers in plant breeding has become a routine practice but the cost per accession can be a hinderance to routine use of QTL identification in breeding progarms. In this study, we demonstrate the use of targeted re-sequencing as a proof of concept of a cost-effective approach to retrieve highly informative genetic information, and develop a bioinformatics strategy to capture the genome-specific information of a polyploid species. Single nucleotide polymorphism (SNP) information obtained using the targeted re-sequencing approach was validated using allele-specific genotyping, and it was found that 81% of the SNP calls in diploids and 68% of the SNP calls in tetraploids were confirmed, respectively. Targeted re-sequencing of markers allowed for validating the existing information and provided new information in regions of interest. Such markers will benefit polyploid breeding programs such as peanut due to reduced costs per accession.

Technical Abstract: Use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of targeted re-sequencing as a proof of concept of a cost-effective approach to retrieve highly informative allele information, as well as develop a bioinformatics strategy to capture the genome-specific information of a polyploid species. SNPs were identified from alignment of raw transcriptome reads (2 x 50 bp) to a synthetic tetraploid genome using BWA followed by a GATK pipeline. Regions containing high polymorphic SNPs in both A genome and B genomes were selected as targets for the resequencing study. Targets were amplified using multiplex PCR followed by sequencing on an Illumina HiSeq. Eighty-one percent of the SNP calls in diploids and 68% of the SNP calls in tetraploids were confirmed. These results were also confirmed by KASP validation. Based on this study, we find that targeted resequencing technologies have potential for obtaining maximum allele information in allopolyploids at reduced cost.