Identification of novel microsatellite markers for P. argenteus from Kuwait waters
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MICROSATELLITE LETTERS
Identification of novel microsatellite markers for P. argenteus from Kuwait waters Sabah AlMomin • Vinod Kumar • Sami Al-Amad Mohsen Al-Hussaini • Talal Dashti • Khaznah Al-Enzi • Abrar Akbar
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Received: 29 September 2014 / Accepted: 3 December 2014 Ó Springer Science+Business Media Dordrecht 2014
Abstract Silver pomfret is a coastal fish of economic significance. While its natural populations have dwindled due to various human activities, the genetic information on this species is still limited. We have used the next generation sequencing to identify microsatellites and developed corresponding primers in Arabian Gulf populations. PCR studies were performed on the 48 short-listed loci across multiple individuals from Iranian and Kuwait waters. Twenty-seven polymorphic loci were analyzed and 16 of them showed significant deviations from expected Hardy– Weinberg equilibrium, for the Iranian or Kuwait populations. The developed primers may be highly useful for detailed population genetic studies of silver pomfret from various geographical locations. Keywords Fish genome Genome sequence Microsatellites Next generation sequencing Pampus argenteus Silver pomfret Pampus argenteus (‘Silver pomfret’, or Zobaidy -as locally known in the Gulf region), is a benthopelagic fish from Stromateidae family. It is distributed across Indian Ocean, North sea, China sea and coastal regions of Persian gulf and Oman sea. This is a commercially important fish species in Kuwait, India, and China. Its natural populations
Electronic supplementary material The online version of this article (doi:10.1007/s12686-014-0399-x) contains supplementary material, which is available to authorized users. S. AlMomin V. Kumar (&) S. Al-Amad M. Al-Hussaini T. Dashti K. Al-Enzi A. Akbar Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, PO Box 24885, Safat 13109, Kuwait e-mail: [email protected]
have declined in the Arabian Gulf region due to various anthropogenic factors. Due to high demand, over fishing has been posing great threat to the existence of this species. Population genetic studies are crucial for the management of natural populations as well as for artificial breeding. Here we report for the first time, discovery of larger number of microsatellite markers in silver pomfret, using the next generation sequencing methods, for Kuwaiti and Iranian populations. Total DNA was extracted from one individual of P. argenteus, for use in isolation of microsatellite loci. An Illumina paired-end shotgun library was prepared using Illumina TruSeq DNA Library Kit and a multiplex identifier adaptor index following the standard protocol. Sequencing was conducted on the Illumina HiSeq with 100 bp pairedend reads. Five million of the resulting reads were analyzed with the program PAL_FINDER_v0.02.03 (Castoe et al. 2012) to extract those reads that contained di-, tri-, tetra-, penta- and hexanucleotide microsatellites. The positive reads were batched to a local installation of
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