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United States Department of Agriculture

Agricultural Research Service

Title: Robust and Highly Informative Microsatellite-Based Genetic Identity Kit for Potato

Authors
item Ghislain, M - INTL POTATO CNTR PERU
item Nunez, J - INTL POTATO CNTR PERU
item Del Rosario Herrera, M - INTL POTATO CNTR PERU
item Pignataro, J - INTL POTATO CNTR PERU
item Guzman, F - INTL POTATO CNTR PERU
item Spooner, David

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 15, 2008
Publication Date: February 28, 2009
Citation: Ghislain, M., Nunez, J., Del Rosario Herrera, M., Pignataro, J., Guzman, F., Spooner, D.M. 2009. Robust and Highly Informative Microsatellite-Based Genetic Identity Kit for Potato. Molecular Breeding. 23:377-388.

Interpretive Summary: Microsatellites, also known as simple sequence repeats (SSRs) refer to a particular type of molecular marker tool that is extremely useful for a variety of purposes. These purposes range from their ability to investigate relationships among plants, to figuring out where certain genes are located on chromosomes (molecular mapping), to their use in identifying individual plants (fingerprinting). Once SSRs have been identified in a group of plants they have many advantages that often make them better than any other molecular marker, but it takes considerable time and expense to identify them. This paper explains how SSRs were identified in cultivated potato, explains in a statistical way how good they are, shows how they are better than a previous set of SSRs, and shows examples of how they have been used in potato, and outlines their possible future uses.

Technical Abstract: The fingerprinting of 742 potato landraces with 51 simple sequence repeat (SSR, microsatellite) markers resulted in improving a previously constructed potato genetic identity (PGI) kit. In addition, we mapped 27 new SSR markers on at least one of three potato genetic linkage maps. All SSR marker loci were assayed with a collection of highly diverse landraces of all four cultivated potato species (S. tuberosum Group Andigenum and Group Chilotanum, S. ajanhuiri, S. curtilobum, and S. juzepczukii) with ploidies ranging from diploid to pentaploid. Loci number, amplification reproducibility, and polymorphic information content (PIC) were recorded. These results permitted the selection of a new PGI kit based of 24 SSRs based on the following three criteria: two SSR markers per chromosome separated by at least 10 cM, high polymorphic information content, and high quality of amplicons as determined by clarity and reproducibility. The new PGI kit consists of nine SSR markers from a prior PGI kit and 15 new ones. The comparison of a similarity matrix of 742 landraces obtained with the 24 SSR markers of the new kit and with the entire dataset of 51 SSR markers resulted with a high correlation (r = 0.93) by Mantel test and even higher correlations regarding topological comparisons of major branches of a neighbor joining tree. This new PGI kit is able to discriminate 96.99% of the 531 landraces compared to 99.06% with 51 SSR markers. In addition, we made a marker-specific set of allele size standards that conveniently and unambiguously can be used to provide accurate sizing of all SSR alleles across laboratories and platforms. The new PGI kit will be of particular utility to standardize the choice and allele sizing of microsatellites in potato and aid in collaborative projects.

Last Modified: 8/30/2014
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