Survey sequencing and in-silico development and validation of genomic SSR markers in Indian dill seed

Kumar, S and Gandham, P and Palve, A and Rathore, A (2020) Survey sequencing and in-silico development and validation of genomic SSR markers in Indian dill seed. Journal of King Saud University - Science (TSI), 32 (1). pp. 862-866. ISSN 1018-3647

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Abstract

Indian dill seed (Anethum sowa Roxb. ex Fleming) is an important member of family Apiaceae. It is a significant seed spice having many medicinal properties. But, this aromatic herb is still orphan from breeding and crop improvement perspective as no serious attention has been given by breeders. To swift the breeding program, molecular markers play the main role. But due to the paucity of markers, breeding is slower in dill seed. Therefore, an attempt was made to develop the genomic SSR markers in dill seed through next-generation sequencing. A total of 2119.51 Mbp of raw data were generated on the Miseq NGS platform during survey sequencing. In 2,25,956 contigs created by Spades assembler, a total 48,951 repeat motifs were identified. A set of 20,294 primer pairs (dimer to hexamer repeats) were produced. Among detected repeat motifs, 48.89% was mononucleotides. Of 12 primers, 10 (83%) primers could be successfully amplified in dill seed and produced 11 amplicons. During cross-genera amplification of markers, 9 out of 10 primers could be successfully amplified in related genera. Developed markers can also be used to initiate the molecular breeding program, association mapping and to assess the evolutionary relationship among seed spices.

Item Type:	Article
Divisions:	Statistics, Bio-Informatics & Data Management
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Anethum, Seed spices, SSR, Transferability
Subjects:	Others > Oilseeds Others > Seeds/Seed Bank
Depositing User:	Mr Arun S
Date Deposited:	22 Mar 2021 09:10
Last Modified:	22 Mar 2021 09:10
URI:	http://oar.icrisat.org/id/eprint/11755
Official URL:	https://doi.org/10.1016/j.jksus.2019.04.006
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	Authors acknowledge Anand Agricultural University, India for providing all necessary facilities. SK acknowledges the INSA, N. Delhi for providing visiting scientist fellowship at ICRISAT, Hyderabad during the analysis of data.
Links:	Google Scholar

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