Abstract
Macrobrachium rosenbergii is an aquaculture species of global importance whose production has sharply declined since 2005. Single nucleotide polymorphisms (SNPs) in transcribed sequences are likely to have high association with economic traits and are important for marker assisted selection. SNPs were mined in 34 reported transcripts from 4 wild M. rosenbergii stocks of India using the amplicon approach and high-throughput sequencing platforms. Out of 320 SNPs detected, 134 were common to all stocks while 3 were diagnostic. Pair-wise Nei’s genetic distances (0.304–0.469) showed phylogeny consistent with geographical distribution. AMOVA analysis revealed estimated variance of 21.5 among populations. The transition to transversion ratio was 2.20. Changes in amino acid classes and peptide stability were recorded for 80 non-synonymous SNPs while change in codon preference was noted for 138 synonymous ones. Four pathogen defence genes were highly polymorphic, of which lectin 3 had the highest SNP rate (6 SNPs/100 bp). This approach for mining SNPs and using them for population differentiation in a single step is reported for the first time.
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References
Andreassen R, Lunner S, Hoyheim B (2010) Targeted SNP discovery in Atlantic salmon (Salmo salar) genes using a 3′UTR-primed SNP detection approach. BMC Genom 11:706. doi:10.1186/1471-2164-11-706
Brouillette JA, Andrew JR, Venta PJ (2000) Estimate of nucleotide diversity in dogs with a pool-and-sequence method. Mamm Genome 11:1079–1086. doi:10.1007/s003350010220
Bruyn MD, Mather PB (2007) Molecular signatures of Pleistocene sea-level changes that affected connectivity among freshwater shrimp in Indo-Australian waters. Mol Ecol 16:4295–4307. doi:10.1111/j.1365-294X.2007.03481.x
Bruyn MD, Wilson JC, Mather PB (2004) Huxley’s line demarcates extensive genetic divergence between eastern and western forms of the giant freshwater prawn, Macrobrachium rosenbergii. Mol Phylogenet Evol 30:251–257
Chand V, Bruyn MD, Mather PM (2005) Microsatellite loci in the eastern form of the giant freshwater prawn (Macrobrachium rosenbergii). Mol Ecol Notes 5:308–310. doi:10.1111/j.1471-8286.2005.00910.x
Chareontawee K, Poompuang S, Na-Nakorn U (2006) Isolation and characterization of microsatellites in giant freshwater prawn Macrobrachium rosenbergii. Mol Ecol Notes 6:823–825. doi:10.1111/j.1471-8286.2006.01358.x
Ciobanu DC, Bastiaansen JWM, Magrin J, Jiang DH, Yu N, Geiger B (2010) A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei). Anim Genet 41:39–47. doi:10.1111/j.1365-2052.2009.01961.x
Divu D, Khushiramani R, Malathi S, Karunasagar I, Karunasagar I (2008) Isolation, characterization and evaluation of microsatellite DNA markers in the giant freshwater prawn, Macrobrachium rosenbergii, from South India. Aquaculture 284:281–284. doi:10.1016/j.aquaculture.2008.07.023
FAO (2014) FAO Global Aquaculture Production Volume and Value Statistics Database Updated to 2012. Fisheries and Aquaculture Department, FAO. http://www.fao.org/fishery/statistics/global-aquaculture-production/query/en. Accessed 25 April 2014
Fridjonsson O, Olafsson K, Tompsett S, Bjornsdottir S, Consuegra S, Knox D, Leaniz CGD, Magnusdottir S, Olafsdottir G, Verspoor E, Hjorleifsdottir S (2011) Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing. BMC Genom 12:179. doi:10.1186/1471-2164-12-179
Hora SL (1949) Satpura hypothesis of the distribution of the Malayan fauna and flora to Peninsular India. Proc Natl Inst Sci India 15:309–313
Hora SL (1950) Satpura hypothesis as aspect of Indian biogeography. Curr Sci 19:364–370
Hooshmand S. (2009). Microsatellite development and cross-phylum amplification for characterization of the giant freshwater prawn (Macrobrachium rosenbergii). Dissertation, Universiti Putra, Malaysia
Hurwood DA, Dammannagoda S, Krosch MN, Jung H, Salin KR, Youssef MA-BH, de Bruyn M, Mather PB (2014) Impacts of climatic factors on evolution of molecular diversity and the natural distribution of wild stocks of the giant freshwater prawn (Macrobrachium rosenbergii). Freshw Sci 33(1):217–231
Jung H, Russell LE, Dinh H, David HA, Sean MW, Mather PB (2011) Transcriptomics of a giant freshwater prawn M. rosenbergii: denovo assembly annotation and marker discovery. PLoS One 6:e27938. doi:10.1371/journal.pone.0027938
Jung H, Lyons RE, Li Y, Thanh NM, Dinh H, Hurwood DA, Salin KR, Mather PB (2014) A candidate gene association study for growth performance in an improved giant freshwater prawn (Macrobrachium rosenbergii) culture line. Mar Biotechnol 16:161–180. doi:10.1007/s10126-013-9555-7
Khan SR, Akter H, Sultana N, Khan MGQ, Wahab MA, Alamet MS (2014) Genetic diversity in three river populations of the giant freshwater prawn, Macrobrachium rosenbergii in Bangladesh assessed by microsatellite DNA markers. Int J Agric Biol 13:195–200
Lynch M (2007) The origins of genome architecture. J Hered 98:633–634. doi:10.1093/jhered/esm073
Miller AD, Murphy NP, Burridge CP, Austin CM (2005) Complete mitochondrial DNA sequences of the decapod crustaceans Pseudocarcinus gigas (Menippidae) and Macrobrachium rosenbergii (Palaemonidae). Mar Biotechnol 7:339–349. doi:10.1007/s10126-004-4077-8
Morin PA, Luikart G, Wayne RK, Allendorf FW, Aquadro CF, Axelsson T, Beaumont M, Chambers K, Durstewitz G, Mitchell-Olds T, Palsbøll PJ, Poinar H, Przeworski M, Taylor B, Wakeley J (2004) SNPs in ecology, evolution and conservation. Trends Genet 19:208–216. doi:10.1016/j.tree.2004.01.009
New MB, Nair CM (2012) Global scale of freshwater prawn farming. Aquac Res 43:960–969. doi:10.1111/j.1365-2109.2011.03008.x
Ngernsoungnern P, Ngernsoungnern A, Weerachatyanukul W, Meeratana P, Hanna PJ (2009) Abalone egg-laying hormone induces rapid ovarian maturation and early spawning of giant freshwater prawn, Macrobrachium rosenbergii. Aquaculture 296:143–149. doi:10.1016/j.aquaculture.2009.08.011
Pariset L, Cappuccio I, Joost S, D’Andrea M, Marletta D, Marsan AP, Valentini A (2006) Characterization of single nucleotide polymorphisms in sheep and their variation as evidence of selection. Anim Genet 37:290–292. doi:10.1111/j.1365-2052.2006.01441.x
Quilang J, Wang S, Li P, Abernathy J, Peatman E, Wang Y, Wang L, Shi Y, Wallace R, Guo X, Liu Z (2007) Generation and analysis of ESTs from the eastern oyster Crassostrea virginica Gmelin and identification of microsatellite and SNP markers. BMC Genom 8:157–167. doi:10.1186/1471-2164-8-157
Ra’anan Z, Cohen D (1984) Characterization of size distribution development in the fresh water prawn Macrobrachium rosenbergii (De Man) juvenile populations. Crustaceana 46:271–282
Raj Kumar A, Gopalakrishnan PR, Divya VS, Basheer, Rajeev KS, Vindya M, Kuldeep KL, Jena JK (2016) Population genetic structure of Macrobrachium rosenbergii (Palaemonidae) from Indian waters using mitochondrial ATPase 6/8 gene, Mitochondrial DNA Part A. http://dx.doi.org/10.3109/24701394.2016.1149829
Sauvage C, Bierne N, Lapegue S, Boudry P (2007) Single Nucleotide polymorphisms and their relationship to codon usage bias in the Pacific oyster Crassostrea gigas. Gene 406:13–22. doi:10.1016/j.gene.2007.05.011
See LM, Hassan R, Tan SG, Bhassu S (2008) Genetic characterization of wild stock of Prawn M. rosenbergii using Random amplified polymorphic DNA marker. J Biotechnol 7:338–342. doi:10.3923/biotech.2008.338.342
See LM, Tan SG, Hassan R, Siraj SS, Bhassu S (2009) Development of microsatellite markers from an enriched genomic library for the genetic analysis of the Malaysian giant freshwater prawn, Macrobrachium rosenbergii. Biochem Genet 47:722–726. doi:10.1007/s10528-009-9270-2
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. Accessed 20 April 2014
Sun Y, Yu X, Tong J (2012) Polymorphisms in myostatin gene and associations with growth traits in the common carp (Cyprinus carpio L.). Int J Mol Sci 13(11):14956–14961. doi:10.3390/ijms131114956
Sung HH, Yang CW, Lin YH, Chang PT (2009) The effect of two CpG oligodeoxynucleotides with different sequences on haemocytic immune responses of giant freshwater prawn, Macrobrachium rosenbergii. Fish and Shellfish Immunol 26:256–263. doi:10.1016/j.fsi.2008.11.017
Suresh E, Reddy AK, Krishna G, Sharma R, Chaudhari A, Sankar M, Sekar M, Kathirvelpandian A (2014) Microsatellite DNA analysis of giant freshwater prawn (Macrobrachium rosenbergii) from India. Israeli J Aquac—Bamidgeh 67:1–7
Suwansa-ard S, Thongbuakaew T, Wang T, Zhao M, Elizur A, Hanna PJ, Sretarugsa P, Cummins SF, Sobhon P (2015) In silico neuropeptidome of female Macrobrachium rosenbergii based on transcriptome and peptide mining of eyestalk, central nervous system and ovary. PLoS One 10(5):e0123848. doi:10.1371/journal.pone.0123848
Thanh NM, Barnes AC, Mather PB, Yutao L, Lyons RE (2010) Single nucleotide polymorphisms in the actin and crustacean hyperglycemic hormone genes and their correlation with individual growth performance in giant freshwater prawn Macrobrachium rosenbergii. Aquac 301:7–15. doi:10.1016/j.aquaculture.2010.02
Tiwari KK (1955) Distribution of Indo Burmese fresh water prawns of the genus Palaemon (Fabr) and its bearing on the Satpura hypothesis. Bull Natn Inst Sci India 7:230–239
Vignal A, Milan D, San Cristobal M, Eggen A (2002) A review on SNP and other molecular markers and their use in animal genetics. Genet Sel Evol 34:275–305. doi:10.1186/1297-9686-34-3-275
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The authors thank ICAR for providing post-graduate fellowship to first two authors. Dr. W. S. Lakra, Director, ICAR-CIFE and Dr. N. C. Patel, Vice Chancellor, Anand Agricultural University are acknowledged for providing facilities.
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Deepak Agarwal and Nilav Aich have contributed equally to this work.
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Agarwal, D., Aich, N., Pavan-Kumar, A. et al. SNP mining in transcripts and concomitant estimation of genetic variation in Macrobrachium rosenbergii stocks. Conservation Genet Resour 8, 159–168 (2016). https://doi.org/10.1007/s12686-016-0528-9
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DOI: https://doi.org/10.1007/s12686-016-0528-9