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Development and characterization of genic SSR markers from low depth genome sequence of Clarias batrachus (magur)

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Title Development and characterization of genic SSR markers from low depth genome sequence of Clarias batrachus (magur)
Not Available
 
Creator SHREYA SRIVASTAVA
BASDEO KUSHWAHA
JYOTI PRAKASH
RAVINDRA KUMAR
N. S. NAGPURE
SUYASH AGARWAL
MANMOHAN PANDEY
P.DAS
C.G. JOSHI
J. K. JENA
 
Subject microsatellites
next generation sequencing
genic region
Clarias batrachus (magur)
 
Description Not Available
Indian magur (Clarias batrachus) is an important freshwater catfish, which is listed as endangered under A3cde+4acde ver.3.1 categories by the IUCN (2015) due to decreasing population trend. Micro-satellites or short sequence repeats (SSRs) tagged to genes have been utilized as gene marker. In the present study, 31,814 SSRs of C. batrachus (magur) were identified using microsatellite identification tool programme from the next generation sequencing data generated on Roche 454 and Ion Torrent platforms. A bioinformatics pipeline, with stringent criteria resulted in selection of 1672 microsatellite loci falling in the genic region. Initially, a total of 30 loci were selected for primer development; and of these 14 were successfully amplified and five were found to be polymorphic in 30 individuals of C. batrachus (magur). The observed as well as expected heterozygosity ranged from 0.038 to 0.526 and 0.434 to 0.784, respectively, and the number of observed alleles ranged from three to five.The study reported the application of next generation sequencing technologies for rapid development of microsatellite loci in Indian catfish species,C. batrachus (magur).
The financial support provided by Department of Biotechnology, Government of India vide sanction grant no. BT/PR3688/AAQ/3/571/2011 for present work is duly acknowledged
 
Date 2021-07-23T06:43:21Z
2021-07-23T06:43:21Z
2016-09
 
Type Research Paper
 
Identifier Srivastava S., Kushwaha B., Prakash J., Kumar R., Nagpure N. S., Agarwal S., Pandey M., Das P., Joshi C. G. and Jena J. K. 2016. Development and characterization of genic SSR markers from low depth genome sequence of Clarias batrachus (magur). J. Genet.95, 603–609
0022-1333 (print)
0973-7731 (online)
http://krishi.icar.gov.in/jspui/handle/123456789/49476
 
Language English
 
Relation Not Available;
 
Publisher Indian Academy of Sciences