Vol. 7, Issue 2 (2019)
Development and validation of simple sequence repeat markers from genome of dill (Anethum graveolens L.)
Author(s): Shiwani, MK Mandavia and RS Tomar
Abstract: Dill (Anethum graveolens L.) is one of the important spice crops. Dill is an important medicinal and industrial plant. Considering the importance of this herbal spice plant various biochemical studies has been carried out and which are still going on including traditional and modern approaches. In present study, Ion Torrent Genome Sequencing (Ion S5) technology was used to generate dill draft genome using genotype Gujarat Dill 1. Gujarat Dill-1 genotype was sequenced using next generation sequencing platform Ion S5 which yielded 10.44 Gb of raw data. After quality check and its control total of 3.2 Gb of data was remained in the data set. In order to maintain the quality of assembled data contigs were filtered, after filter 32 contigs were remained with 5000 bp of minimum, 42,775 bp of maximum and 9,568 bp of average contig length. After Blast2Go analysis approximately 542 putative functions were found from 32 input sequences, which were contributing for 498 GO terms (biological processes (206), cellular components (157) and molecular processes (135). Out of 32 sequences, all most all sequences showed positive InterPro result while 5 sequences did not showed any InterPro results and 15 sequences were scanned with GOs. 47 IPS IDs were identified, among them 30 were IPS domains, 14 were IPS family and 4 were IPS active sites. SSR primers from assembled data were designed in silico using batchprimer3 v1.0 online program. Total 80 primers were identified from 32 contig data, in which most of them were tetranucleotide repeats (40%) followed by dinucleotide repeats (22.5%), pentanucleotide repeats (20%) and trinucleotide repeats (7.5%). For validation of SSR primers, among identified 80 primers only 25 primers were used which were having melting temperature more than 55 ºC. Primers were validated using five Dill genotype (Ajmer Dill1, Ajmer Dill2, Gujarat Dill1, Gujarat Dill2, Gujarat Dill3). Among 25 primers, 19 primers amplified the DNA. From 19 primers, three primers were found polymorphic among five genotypes of Dill. These primer were related to those sequence which were having putative function for cytochrome c oxidase. The polymorphic primer can be used in genetic diversity analysis of Dill and its relatives.
Pages: 1070-1076 | 320 Views 69 Downloads
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How to cite this article:
Shiwani, MK Mandavia, RS Tomar. Development and validation of simple sequence repeat markers from genome of dill (Anethum graveolens L.). Int J Chem Stud 2019;7(2):1070-1076.
