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Microsatellite marker information from high-throughput next-generation sequence data of Capsicum annuum varieties Mandarin and Blackcluster

Ahn, Yul-Kyun, Tripathi, Swati, Kim, Jeong-Ho, Cho, Young-Il, Lee, Hye-Eun, Kim, Do-Sun, Woo, Jong-Gyu, Yoon, Moo-Kyoung
Scientia horticulturae 2014 v.170 pp. 123-130
Capsicum annuum, cultivars, databases, genes, genetic markers, marker-assisted selection, microsatellite repeats, nucleotides, pepper, sequence analysis, transcriptomics
Transcriptome profiling of two pepper (Capsicum annuum L., Solanaceae), cultivars, Mandarin and Blackcluster, was performed using 454 GS-FLX pyrosequencing for the identification of microsatellite (SSR) markers for marker-assisted breeding. Sequencing runs yielded 279,221 and 316,357 reads totaling 120.44 and 142.54Mb of sequence data (average read length of 431 and 450 nucleotides), which assembled into 19,388 and 18,057 isotigs, and 22,217 and 13,153 singletons for both, respectively. Reads resulted into 17,525 and 16,341 ‘isogroups’ and were annotated functionally. Assembled sequences were functionally annotated based on homology to genes in multiple public databases and assigned with Gene Ontology (GO) terms. Analysis of sequence variants identified a total of 2067 and 2494 potential SSR motifs located in the transcript regions for both cultivars. Trinucleotide (49%) was the most common repeat unit followed by the di (39.7%), hexa (5.3%), tetra (2.9%) and pentanucleotides (2.8%). AGC/CAG/GCA (17.7%) was the most frequent repeat motif, followed by GGT/GTG/TGG (16%), AAG/AGA/GAA (14.3%), ATC/CAT/TCA (11.9%), and AAC/ACA/CAA (7.5%).