In Silico Mining and Characterization of High-Quality SNP/Indels in Some Agro-Economically Important Species Belonging to the Family Euphorbiaceae

(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(sic)T (transition) was the most dominant nucleotide substitution, while in transversion, A &(sic)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.

Automated summary

This study aimed to assess the genetic makeup of agro-economically important members of Euphorbiaceae by identifying and characterizing high-quality SNP markers and their distribution in exonic and intronic regions using publicly available ESTs. The quality sequences were assembled into contigs using the CAP3 program and SNP mining was performed using QualitySNP. A total of 25,432 potential SNPs and 14,351 high-quality SNPs, including 2276 indels, were detected. The SNP markers detected can be used for various applications such as linkage mapping, marker-assisted breeding, studying genetic diversity, mapping important phenotypic traits, and screening mutations in important genes for disease resistance.