Construction of EST-SSR Databases for Effective Cultivar Identification and Their Applicability to Complement for Lettuce (Lactuca sativa L.) Distinctness Test

Abstract

The objectives of this study were to construct a database of expressed sequence tag (EST)-simple sequence repeat (SSR) markers to identify lettuce cultivars. A set of 370 EST-SSR primer pairs were applied for fingerprinting the lettuce cultivars. Fifty-eight EST-SSR markers showed hyper-variability and were able to differentiate 92 cultivars. A total of 176 polymorphic amplified fragments were obtained by the 58 markers, and two to eight SSR alleles were detected for each l˚Cus with an average of three alleles per locus. Average polymorphism information content (PIC) was 0.425, ranging from 0.022 to 0.743. Cluster analysis was based on Jaccard's distance coefficients using the method of unweighted pair group. In this method we used arithmetical averages (UPGMA) algorithm categorized 4 major groups, which were in accordance to morphological traits. The eight cultivars of three groups with 100% genetic similarity through SSR analysis were investigated by phenotypic traits. These cultivars including these pairs are very similar in 27 morphological characteristics. Therefore, these EST-SSR markers could be used to select similar cultivars through management of reference collection to complement distinctiveness test of lettuce cultivars.

Development and Identification of SSR Markers Associated with Starch Properties and β-Carotene Content in the Storage Root of Sweet Potato (Ipomoea batatas L.)

“…Simple sequence repeats (SSRs; also called microsatellites) are useful genetic markers in many organisms. Due to their co-dominant and highly polymorphic nature, their even distribution throughout the genome, and their relative ease of development from enriched genomic libraries and expressed sequence tag (EST) collections (Collard and MacKill, 2008 ; Miah et al, 2013 ), SSRs are the marker of choice in linkage and genetic map construction (Varshney et al, 2009 ; Bindler et al, 2011 ; El-Rodeny et al, 2014 ), genetic diversity and population structure analysis (Barkley et al, 2006 ; Zhang et al, 2011 ; Chen et al, 2012 ; Xiao et al, 2012 ; Yoon et al, 2012 ), germplasm identification (Hong et al, 2015 ), and QTL mapping (Collard and MacKill, 2008 ; Varshney et al, 2009 ).…”

In silico identification of putative expressed sequence tag (EST)-simple sequence repeats (SSRs) markers of resistance to Meloidogyne spp. in common bean

“…In expressed plant sequences, the prevalence of these repetitions has been widely reported (Gupta et al, 2010;Wang et al, 2014;Hong et al, 2015;Boccacci et al, 2015). The regions of ESTs are transcriptional targets rich in dimers in the untranslated regions (UTR) and in the predominance of trimers in the open reading frame (ORF) (Ellegren, 2004).…”

Development of a core set of KASP markers for assaying genetic diversity in Brassica rapa subsp. chinensis Makino

“…For plant geneticists and breeders seeking to understand genomic architecture and devise crop improvement strategies, molecular detection and exploitation of genetic variation in crop genomes is one of the most important tasks. Various DNA marker technologies, such as random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and simple sequence repeats (SSRs), have been applied in recent decades to detect the genetic diversity of major crop plant species (Fernández, Figueiras, & Benito, ; Hong, Kwon, Mishra, & Kim, ; Mujaju, Sehic, & Nybom, ). Several polymorphic DNA markers have already been used to analyse cultivated non‐heading Chinese cabbage (Han et al, ; Song, Ge, Li, & Hou, ); however, the different datasets are not comparable because of the absence of a common core set of reference genotypes and the use of different marker systems.…”