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United States Department of Agriculture

Agricultural Research Service

Research Project: Nonchemical Pest Control and Enhanced Sugar Beet Germplasm Via Traditional and Molecular Technologies Title: High-throughput RAD-SNP genotyping for characterization of sugar beet genotypes

Authors
item Stevanto, Piergiorgio -
item Broccanello, Chiara -
item Biscarini, Filippo -
item Del Corvo, Marcello -
item Sablok, Gaurav -
item Panella, Leonard
item Stella, Allessandra -
item Cohcheri, Guiseppe -

Submitted to: Plant Molecular Biology Reporter
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 27, 2013
Publication Date: June 1, 2014
Citation: Stevanto, P., Broccanello, C., Biscarini, F., Del Corvo, M., Sablok, G., Panella, L.W., Stella, A., Cohcheri, G. 2014. High-throughput RAD-SNP genotyping for characterization of sugar beet genotypes. Plant Molecular Biology Reporter. 32:691-699. DOI: 10.1007/s11105-013-0685-x.

Interpretive Summary: A rapid way of developing a useful set of markers for separating different species genetically is using small differences in their DNA sequence (SNP). In this research, we demonstrate a set of 192 SNP markers can genetically identify sugar beet lines using high-throughput technology called QuantStudio 12K Flex system coupled with Taqman OpenArray technology, Life Technologies, Carlsbad, CA. The selected SNP markers were tested by evaluating the genetic diversity among 15 sugar beet lines from three groups, which include 5 female lines, 5 pollinators and 5 commercial varieties. We demonstrated that the 192 SNP markers effectively could differentiate genetically these lines. The female lines were more diverse when compared to the pollinator lines or varieties. Further Analysis revealed that female lines, pollinator lines and varieties each were subdivided into two distinct groups. On the basis of the observed results, we have shown these technologies are useful for highthroughput SNP marker differentiation in sugar beet.

Technical Abstract: High-throughput SNP genotyping provides a rapid way of developing resourceful set of markers for delineating the genetic architecture and for effective species discrimination. In the presented research, we demonstrate a set of 192 SNPs for effective genotyping in sugar beet using high-throughput marker array technology QuantStudio 12K Flex system coupled with Taqman OpenArray technology, Life Technologies, Carlsbad, CA. The selected SNPs were further assessed for evaluation of genetic diversity among 15 sugar beet accessions from three groups, which include 5 cytoplasmic male sterile lines, 5 pollinators and 5 commercial varieties respectively. We demonstrate that the panel of proposed 192 SNPs was effectively able to differentiate the studied genotypes and a higher degree of polymorphism was observed among the cytoplasmic male sterile lines as compared to the pollinator lines or varieties. Structure analysis revealed that cytoplasmic male sterile lines, pollinator lines and varieties each were clustered into two distinct sub-populations. On the basis of the observed results, we postulate TaqMan OpenArray technology coupled with the proposed panel of 192 SNPs will be useful for highthroughput SNP genotyping in sugar beet.

Last Modified: 11/26/2014
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