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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Publications at this Location » Publication #348739

Title: STARP: A user-friendly and broadly applicable technique for SNP genotyping in wheat and other crops

item LONG, YUNMING - North Dakota State University
item Qi, Lili
item CAI, XIWEN - North Dakota State University
item Faris, Justin
item Xu, Steven

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/8/2017
Publication Date: 1/13/2018
Citation: Long, Y., Qi, L., Cai, X., Faris, J.D., Xu, S.S. 2018. STARP: A user-friendly and broadly applicable technique for SNP genotyping in wheat and other crops. Plant and Animal Genome Conference. Available:

Interpretive Summary:

Technical Abstract: Single nucleotide polymorphisms (SNPs) are widely distributed in the genome of every organism. Recent advances in DNA sequencing technology have accelerated the discovery of variations in DNA sequences. Multiplex chip-based technology for genome-scale SNP genotyping has made great progress in the past two decades. However, PCR-based genotyping of individual SNPs remains a challenge task. Here, we report a novel SNP genotyping method designated semi-thermal asymmetric reverse PCR (STARP), which combines all of the advantages in accuracy, throughput, simplicity, and operational costs as well as compatibility with multiple platforms. STARP assays employ two universal priming element-adjustable primers (PEA-primers) and one group of three locus-specific primers: two asymmetrically modified allele-specific primers (AMAS-primers) and their common reverse primer. The two AMAS-primers are used to specifically amplify target alleles and generate PEA-primer binding sites. The two PEA-primers are common for all genotyping assays to stringently target AMAS-primer amplicons with similar PCR efficiencies and for flexible detection using either gel-free fluorescence signals or gel-based size separation. STARP is a broadly applicable and more user-friendly alternative to KASP. We developed numerous STARP markers associated with important agronomic genes for low cadmium accumulation and resistance to Hessian fly, Fusarium head blight, and stem rust in wheat. These STARP markers are being employed in wheat breeding. In addition, the STARP technique has been successfully extended to analyze the differential expression of homologous genes and specifically amplify target DNA fragments in highly repetitive regions. STARP will facilitate genomic research in wheat and other species with large and complex genomes.