Single-nucleotide polymorphisms linked to body weight revealed in growth selected Macrobrachium rosenbergii
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Association of type I single nucleotide polymorphic (SNP) markers with quantitative traits can provide an effective method for detecting genes and functions that are responsible for performance variation in domesticated species. In order to discover novel polymorphisms in candidate genes that could be associated with growth, fragments (175 to 668 bp) from 11 housekeeping, regulatory, and immune response genes of Macrobrachium rosenbergii previously reported to contain 83 SNPs were amplified from genomic DNA of 23 growth selected (cumulative genetic gain of 18%) and 23 unselected individuals and sequenced by Sanger’s method. A total of 45 SNPs were identified from eight genes, of which 20 were novel and 18 were found to be growth associated with allele frequencies > 0.65 in the selected group. Eleven of these were located in exonic regions of which 3 present in crustacean lipocalin (LIPC) and heat shock protein 21 (HSP21) were nonsynonymous. In silico prediction indicates that 2 of the non-synonymous alleles may result in higher stability of the proteins. Of the 5 synonymous growth-associated SNPs, 3 present in phosphoenol pyruvate carboxykinase (PEPCK), cytochrome oxidase 1 (COX1), and HSP70 were a switch to the preferred codon. Seven SNPs were located in the 3′UTRs of lectin 3 and 4 (LEC3, LEC4) and anti-lipopolysaccharide factor 1 (ALF1). Only one altered allele was observed at every locus. No SNPs were found in NaK-ATPase, mitochondrial manganese superoxide dismutase, and tachylectin genes. This is the first such marker association study being reported for M. rosenbergii from India and will be of use in selecting future generations.
KeywordsMarker association study Candidate gene approach Genotyping Genetic selection Growth-associated SNPs
The authors thank ICAR for providing post-graduate fellowship to first author. Dr. Gopal Krishna, Director, ICAR-CIFE and Dr. P. Jayasankar, Director, ICAR-CIFA are acknowledged for providing facilities.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interests.
Institutional animal ethics committee guidelines were followed for the care and maintenance of experimental animals.
- Agarwal D, Aich N, Pavan-Kumar A, Kumar S, Sabnis S, Joshi CG, Koringa P, Pandya D, Patel N, Karnik T, Bhingarde R, Gireesh-Babu P, Chaudhari A (2016) SNP mining in transcripts and concomitant estimation of genetic variation in Macrobrachium rosenbergii stocks. Conserv Genet Resour 8:159–168CrossRefGoogle Scholar
- FAO (2014) Fisheries statistical database, global aquaculture production (Fisheries Global Information System, online query)Google Scholar
- Gjedrem T, Robinson N, Rye M (2012). The importance of selective breeding in aquaculture to meet future demands for animal protein: a review. Aquaculture 350:117-129Google Scholar
- Hartl FU, Hayer-Hartl M (2002). Molecular chaperones in the cytosol: from nascent chain to folded protein. Science 295:1852-1858Google Scholar
- Pillai BR, Mahapatra KD, Ponzoni RW, Sahoo L, Lalrinsanga PL, Nguyen NH, Mohanty S, Sahu S, Sahu S, Khaw HL, Patra G (2011) Genetic evaluation of a complete diallel cross involving three populations of freshwater prawn (Macrobrachium rosenbergii) from different geographical regions of India. Aquaculture 319:347–354CrossRefGoogle Scholar
- Shojaei M, Mohammad Abadi M, Asadi Fozi M, Dayani O, Khezri A, Akhondi M (2011) Association of growth trait and leptin gene polymorphism in Kermani sheep. J Cell Mol Res 2:67–73Google Scholar
- Sodsuk PK, Uraiwan S, Sodsuk S (2006) Allozyme marker based comparison on genetic variation among Macrobrachium rosenbergii populations produced from a cross-breeding system of three different stocks in Thailand. SEAFDEC/AQD Institutional repository (Third round table discussion on the development of genetically improved Macrobrachium), 25–29. http://hdl.handle.net/10862/692 Aaccessed 20 April 2014
- Venkatesan C, Hameed SA, Sundarraj N, Rajkumar T, Balasubramanian G (2014) Analysis of immune genes and heat shock protein genes under exposure to white spot syndrome virus (WSSV) and herbal immune stimulant in Litopenaeus vannamei. J Bacteriol Parasitol 5:1Google Scholar