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United States Department of Agriculture

Agricultural Research Service

Research Project: Evaluation, Enhancement, Genetics and Breeding of Lettuce, Spinach, and Melon

Location: Crop Improvement and Protection Research

Title: Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes

Authors
item Rauscher, Gilda -
item Simko, Ivan

Submitted to: Biomed Central (BMC) Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 8, 2013
Publication Date: January 28, 2013
Citation: Rauscher, G., Simko, I. 2013. Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes. BMC Plant Biology. 13:11.

Interpretive Summary: Several types of biochemical and molecular markers are applied for lettuce genotyping, but only a very limited number of microsattelite-based markers are publicly available because their development is costly and time-consuming. Previously, we have developed a set of EST-SSR markers [8] from approximately twenty thousand unigenes of L. sativa and its close wild relative prickly lettuce (L. serriola L.). In the present work we describe the development of ‘anonymous’ SSR markers from genomic DNA for fingerprinting lettuce cultivars. Distribution of markers in the genome appeared to be random, with the exception of possible cluster on linkage group 6. Any combination of 32 genomic SSRs was able to distinguish genotypes of all 36 accessions. Fourteen of newly developed SSR markers originate from fragments with high sequence similarity to resistance gene candidates (RGCs) and RGC pseudogenes. The newly developed genomic SSR markers were added to the pool of previously developed EST-SSRs markers. These two types of SSR-based markers provide useful tools for lettuce cultivar fingerprinting, development of integrated molecular linkage maps, and mapping genes.

Technical Abstract: Background: Lettuce (Lactuca sativa L.) is the major vegetable from the group of leafy vegetables. Several types of molecular markers were developed that are effictively used in lettuce breeding and genetic studies. However only a very limited number of microsattelite-based markers are publicly available. We have employed the method of enriched microsatellite libraries to develop 97 genomic SSR markers. Results: Testing of newly developed markers on a set of 36 Lactuca accession (33 L. sativa, and one of each L. serriola L., L. saligna L., and L. virosa L.) revealed that both the genetic heterozygosity (UHe = 0.56) and the number of loci per SSR (Na = 5.50) are significantly higher for genomic SSR markers than for previously developed EST-based SSR markers (UHe = 0.32, Na = 3.56). Fifty-four genomic SSR markers were placed on the molecular linkage map of lettuce. Distribution of markers in the genome appeared to be random, with the exception of possible cluster on linkage group 6. Any combination of 32 genomic SSRs was able to distinguish genotypes of all 36 accessions. Fourteen of newly developed SSR markers originate from fragments with high sequence similarity to resistance gene candidates (RGCs) and RGC pseudogenes. Analysis of molecular variance (AMOVA) of L. sativa accessions showed that approximately 3% of genetic diversity was within accessions, 79% among accessions, and 18% among horticultural types. Conclusions: The newly developed genomic SSR markers were added to the pool of previously developed EST-SSRs markers. These two types of SSR-based markers provide useful tools for lettuce cultivar fingerprinting, development of integrated molecular linkage maps, and mapping genes.

Last Modified: 9/10/2014
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