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http://dx.doi.org/10.7235/hort.2013.13055

Identification of Lettuce Germplasms and Commercial Cultivars Using SSR Markers Developed from EST  

Hong, Jee-Hwa (Variety Testing Division, Korea Seed & Variety Service, Ministry of Agriculture, Food and Rural Affairs)
Kwon, Yong-Sham (Variety Testing Division, Korea Seed & Variety Service, Ministry of Agriculture, Food and Rural Affairs)
Choi, Keun-Jin (Variety Testing Division, Korea Seed & Variety Service, Ministry of Agriculture, Food and Rural Affairs)
Mishra, Raghvendra Kumar (Department of Molecular Biotechnology, Konkuk University)
Kim, Doo Hwan (Department of Molecular Biotechnology, Konkuk University)
Publication Information
Horticultural Science & Technology / v.31, no.6, 2013 , pp. 772-781 More about this Journal
Abstract
The objective of this study was to develop simple sequence repeat (SSR) markers from expressed sequence tags (EST) of lettuce (Lactuca sativa) and identify 9 germplasms from 3 wild species of lettuce and 61 commercial cultivars using the developed EST-SSR markers. A total of 81,330 lettuce ESTs from NCBI databases were used to search for SSR and 4,229 SSR loci were identified. The highest proportion (59.12%, 2500) was represented by trinucleotide, followed by dinucleotide (29.70%, 1256) and hexanucleotide (6.62%, 280) among SSR repeat motifs. Totally 474 EST-SSR primers were developed from EST and a random set of 267 primers was used to assess the genetic diversity among 9 germplasms and 61 cultivars. Out of 267 primers, 47 EST-SSR markers showed polymorphism between 7 cultivars. Twenty-six EST-SSR markers among 47 EST-SSR markers showed high polymorphism, reproducibility, and band clearance. The relationship between 26 markers genotypes and 70 accessions was analyzed. Totally 127 polymorphic amplified fragments were obtained by 26 EST-SSR markers and two to nine SSR alleles were detected for each locus with an average of 4.88 alleles per locus. Average polymorphism information content was 0.542, ranging from 0.269 to 0.768. Genetic distance of clusters ranged from 0.05 to 0.94 between 70 accessions and dendrogram at a similarity of 0.34 gave 7 main clusters. Analysis of genetic diversity revealed by these 26 EST-SSR markers showed that the 9 germplasms and 61 commercial cultivars were discriminated by marker genotypes. These newly developed EST-SSR markers will be useful for cultivar identification and distinctness, uniformity and stability test of lettuce.
Keywords
genetic diversity; genetic relationship; molecular marker; plant variety protection;
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