Development of genic-SSR markers and genetic diversity of Indian lettuce ( Lactuca indica L.) in South Korea

Abstract

Indian lettuce (Lactuca indica L.) is an undomesticated wild plant with high economic potential. We know little about the plant's genome, such as its DNA markers, making genetic research using this plant difficult. In this study, 100 genic simple sequence repeat (SSR) primers with a 99–250 bp target amplicon were synthesized from L. indica transcriptomic sequences. These primers were examined in 8 diverse L. indica accessions, and 90 polymorphic SSRs were obtained. Twenty-three of the 90 polymorphic SSRs were used to investigate transferability to another two Lactuca species, Lactuca serriola and Lactuca sativa. Genetic diversity was investigated in 77 Lactuca accessions, including 73 L. indica collected from across South Korea, 2 L. serriola, and 2 L. sativa. Our genic-SSR markers were highly polymorphic with a mean polymorphic information content of 0.61 and, on average, 10.83 alleles per locus. The average expected heterozygosity (0.76) was higher than the observed heterozygosity. An analysis of molecular variance revealed that most of the total variance in our population is attributable to genetic variation among accessions, rather than among provinces. STRUCTURE, unweighted neighbor-joining phylogenetic trees, and principal coordinate analyses resulted in three clusters, where northern and central-southern L. indica accessions were grouped into two clusters with some admixture. The L. serriola and L. sativa accessions did not produce a separate cluster due to a small sample size. These results show our SSR markers will be useful in germplasm assessment and genetic studies of L. indica and other Lactuca species.

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