(1) Background: To assess the genetic makeup among the agro-economically important members of Euphorbiaceae, the present study was conducted to identify and characterize high-quality single-nucleotide polymorphism (SNP) markers and their comparative distribution in exonic and intronic regions from the publicly available expressed sequence tags (ESTs). (2) Methods: Quality sequences obtained after pre-processing by an EG assembler were assembled into contigs using the CAP3 program at 95% identity; the mining of SNP was performed by QualitySNP; GENSCAN (standalone) was used for detecting the distribution of SNPs in the exonic and intronic regions. (3) Results: A total of 25,432 potential SNPs (pSNP) and 14,351 high-quality SNPs (qSNP), including 2276 indels, were detected from 260,479 EST sequences. The ratio of quality SNP to potential SNP ranged from 0.22 to 0.75. A higher frequency of transitions and transversions was observed more in the exonic than the intronic region, while indels were present more in the intronic region. C↔T (transition) was the most dominant nucleotide substitution, while in transversion, A↔T was the dominant nucleotide substitution, and in indel, A/- was dominant. (4) Conclusions: Detected SNP markers may be useful for linkage mapping; marker-assisted breeding; studying genetic diversity; mapping important phenotypic traits, such as adaptation or oil production; or disease resistance by targeting and screening mutations in important genes.

Department of Biochemistry and Agricultural Chemistry Assam Agricultural University Jorhat 785013 India

Department of Life Science and Bioinformatics Assam University Silchar 788011 India

Department of Pharmaceutical Sciences Assam University Silchar 788011 India

Department of Pharmaceutical Technology Division of Pharmacognosy Jadavpur University Kolkata 700032 India

Department of Zoology Mariani College Mariani 785634 India

GyanArras Academy Gothapatna Malipada Bhubaneswar 751003 India

Laboratory of Animal Immunology and Biotechnology Department of Animal Morphology Physiology and Genetics Faculty of AgriSciences Mendel University in Brno 61300 Brno Czech Republic

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