Chand Subodh Kumar, Nanda Satyabrata, Rout Ellojita, Joshi Raj Kumar
Functional Genomics laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India.
Bioinformation. 2015 Mar 31;11(3):145-50. doi: 10.6026/97320630011145. eCollection 2015.
Expressed Sequence Tags (ESTs) with comprehensive transcript information are valuable resources for development of molecular markers as they are derived from conserved genic regions. The present study highlights the mining of EST database to deduce the class I hyper variable SSRs in A. sativum. From 21694 garlic EST sequences, 642 non-redundant SSRs were identified with an average frequency of 1 per 14.9 kb of garlic transcriptome. The most abundant SSR motifs were the mononucleotides (32.86%) followed by trinucleotides (28.50%) and dinucleotides (13.39%). Among the individual SSRs, (A/T)n accounted for the highest number (137; 21.33%) followed by (G/C)n (74; 11.52%) and (AAG)n (63;9.81%). Primers designed from a robust set of 7 AsESTSSRs resulted in the amplification of 63 polymorphic alleles in 14 accessions of garlic. The resolving power of the markers varied from 4.286 (AsSSR7) to 18.143 (AsSSR13) while the average marker index (MI) was 5.087. These EST-SSRs markers for garlic could be useful for the improvement of garlic linkage map and could be used for evaluating genetic variation and comparative genomics studies in Allium species.
具有全面转录信息的表达序列标签（EST）是开发分子标记的宝贵资源，因为它们源自保守的基因区域。本研究着重挖掘EST数据库，以推断大蒜中的I类高变SSR。从21694条大蒜EST序列中，鉴定出642个非冗余SSR，大蒜转录组中平均每14.9 kb出现1个。最丰富的SSR基序是单核苷酸（32.86%），其次是三核苷酸（28.50%）和二核苷酸（13.39%）。在单个SSR中，（A/T）n数量最多（137个；21.33%），其次是（G/C）n（74个；11.52%）和（AAG）n（63个；9.81%）。从一组可靠的7个大蒜EST-SSR设计的引物，在14份大蒜材料中扩增出63个多态性等位基因。这些标记的分辨能力从4.
