ARS | Publication request: Development of EST-SSR Markers for the Study of Population Structure in Lettuce (Lacutca sativa L.).

Submitted to: Journal of Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 11, 2008
Publication Date: February 25, 2009
Citation: Simko, I. 2009. Development of EST-SSR Markers for the Study of Population Structure in Lettuce (Lacutca sativa L.). Journal of Heredity 180: 256-262.

Interpretive Summary: The cultivated lettuce (L. sativa) is a major horticultural crop from the family Asteraceae (Compositae). Lettuce cultivars are classified into horticultural types based on head and leaf shape, size, and texture. Several types of markers are regularly used for cultivar fingerprinting, linkage map construction, mapping alleles for desirable traits, marker-assisted selection,and assessment of population structure; microsatellites among them. Though microsatellites are markers of choice in many plant species due to their high reproducibility, co-dominant inheritance, and high information content, only a very limited number of microsatellite markers are publicly available for lettuce. The present work describes 61 microsatellites developed from coding sequences of lettuce. Polymorphism of new markers was tested on a set of 96 accessions representing different horticultural types and three wild species. Though the EST-based markers have reduced polymorphism as compared to anonymous microsatellites, they can be used for assessment of population structure in cultivated lettuce and wild species. All developed markers are publicly available.

Technical Abstract: A set of 61 simple sequence repeat (SSR) markers was developed from the 19,523 L. sativa and L. serriola unigenes. Approximately 4.5% of the unigenes contained a perfect SSR at least 20 bp long, corresponding to roughly one perfect SSR per 14.7 kb. Marker polymorphism was tested on a set comprising 96 accessions representing all major horticultural types and three wild species (L. serriola, L. saligna, L. virosa). Though both the average marker heterozygosity (UHe = 0.32) and the number of different alleles per locus (Na = 3.56) were significantly reduced in EST-SSRs as compared to anonymous SSRs (UHe = 0.59, Na = 5.53), 15 markers had heterozygosity above 0.50. Marker transfer rate to the wild species corresponded to the decreasing sexual compatibility with L. sativa, and was higher for EST-SSRs (L. serriola 100%, L. saligna 87%, L. virosa 75%) than for anonymous SSRs (93%, 66%, and 42%, respectively). Assessment of population structure among 90 L. sativa cultivars with SSRs was in good agreement with classification into the horticultural types. The average marker heterozygosity was smallest in iceberg (0.097), Latin (0.140) and romaine-type (0.151) cultivars while highest in leaf (green-leaf 0.208, red-leaf 0.240) lettuces.