Department of Zoology, Mariani College, Mariani 785634, India.
Department of Biochemistry and Agricultural Chemistry, Assam Agricultural University, Jorhat 785013, India.
Genes (Basel). 2023 Jan 27;14(2):332. doi: 10.3390/genes14020332.
(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.
(1) 背景：为了评估经济上重要的大戟科成员的遗传构成，本研究旨在从公开的表达序列标签 (EST) 中鉴定和表征高质量的单核苷酸多态性 (SNP) 标记及其在编码区和非编码区的比较分布。
(2) 方法：通过 EG 组装器进行预处理后获得的高质量序列，使用 CAP3 程序在 95%的同一性下组装成 contigs；通过 QualitySNP 进行 SNP 挖掘；使用 GENSCAN（独立）检测 SNP 在编码区和非编码区的分布。
(3) 结果：从 260479 个 EST 序列中检测到了 25432 个潜在 SNP（pSNP）和 14351 个高质量 SNP（qSNP），包括 2276 个插入缺失。质量 SNP 与潜在 SNP 的比例从 0.22 到 0.75 不等。在编码区比非编码区观察到更多的转换和颠换，而插入缺失在非编码区更常见。C↔T（转换）是最主要的核苷酸取代，而在颠换中，A↔T 是主要的核苷酸取代，在插入缺失中，A/-是主要的。
(4) 结论：检测到的 SNP 标记可用于连锁作图、标记辅助育种、遗传多样性研究、重要表型性状（如适应或产油）的作图、或针对重要基因进行突变筛选以提高疾病抗性。
