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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #275047
Title: Empirical evaluation of DArT, SNP, and SSR marker-systems for genotyping, clustering, and assigning sugar beet hybrid varieties into populations

Author
item Simko, Ivan
item Eujayl, Imad
item VAN HINTUM, JL, THEO - Wageningen University And Research Center

Submitted to: Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/13/2011
Publication Date: 2/8/2012
Citation: Simko, I., Eujayl, I.A., Van Hintum, Jl, T. 2012. Empirical evaluation of DArT, SNP, and SSR marker-systems for genotyping, clustering, and assigning sugar beet hybrid varieties into populations. Plant Science. 184:54-62.

Interpretive Summary: Detection of population structure, assignment of an individual into a population, and assessment of genetic variation in both domesticated and wild species is frequently used in plant breeding, germplasm classification in genebanks, investigation of evolutionary processes, and other research areas. In the present study we assessed the success-rate of three marker-systems for estimating genotypic diversity, clustering varieties into populations, and assigning a single variety into the expected population. A set of 54 sugar beet (Beta vulgaris L. ssp. vulgaris) varieties from five seed companies was genotyped with 702 Diversity Array-Technology (DArT), 34 Single Nucleotide Polymorphisms (SNP), and 30 Simple Sequence Repeats (SSR) markers. Analysis of the population structure revealed three well-defined populations and clustering of varieties that generally correlates with their seed company origin. Two populations each contained varieties from two different seed companies indicating genetic similarity of this material. The third population was comprised only of varieties from a single seed company. Analysis of the SSR and SNP datasets indicates that some of the hybrid varieties likely have a common (or very closely related) parent. Generally, about 1.4 to 3 × more SNPs, and 4.9 to 13.3 × more DArTs then SSRs were needed to achieve the 100% success-rate. However, using only DArT markers with a high level of polymorphism decreases the number of DArT loci needed for analyses by 38% to 61%. Results from the present work provide a premise to selecting the type(s) and number of markers that are needed for genetic diversity analysis of sugar beet hybrid varieties.

Technical Abstract: Dominant and co-dominant molecular markers are routinely used in plant genetic diversity research. In the present study we assessed the success-rate of three marker-systems for estimating genotypic diversity, clustering varieties into populations, and assigning a single variety into the expected population. A set of 54 sugar beet (Beta vulgaris L. ssp. vulgaris) varieties from five seed companies was genotyped with 702 Diversity Array-Technology (DArT), 34 Single Nucleotide Polymorphisms (SNP), and 30 Simple Sequence Repeats (SSR) markers. Analysis of the population structure revealed three well-defined populations and clustering of varieties that generally correlates with their seed company origin. Two populations each contained varieties from two different seed companies indicating genetic similarity of this material. The third population was comprised only of varieties from a single seed company. Analysis of the SSR and SNP datasets indicates that some of the hybrid varieties likely have a common (or very closely related) parent. Comparison of the three marker-systems revealed substantial differences in the number of loci needed for analyses. Varietal clustering required approximately 1.8 to 2 × more SSR, 3 to 4.5 × more SNP, and 4.8 × more DArT markers than were required for detection of genotypic diversity. When marker-systems were compared across different types of analyses per locus success-rate was the highest for the SSR and the lowest for the DArT markers. Generally, about 1.4 to 3 × more SNPs, and 4.9 to 13.3 × more DArTs then SSRs were needed to achieve the 100% success-rate. However, using only DArT markers with a high level of polymorphism decreased the number of DArT loci needed for analyses by 38% to 61%. Results from the present work provide a premise to selecting the type(s) and number of markers that are needed for genetic diversity analysis of sugar beet hybrid varieties.