Molecular Characterization of Economically Important Penaeid Population in South East Coast of India

P. Rajakumaran<sup>1</sup>; B. Vaseeharan<sup>1</sup>; V. Anita Yeshvadha<sup>2</sup>

Molecular Characterization of Economically Important Penaeid Population in South East Coast of India

P. Rajakumaran¹

, B. Vaseeharan¹

, V. Anita Yeshvadha²

1 Crustacean Molecular Biology and Genomics Laba, Department of Animal Health and Management, Alagappa University, Karaikudi 630003, Tamilnadu, India
2 Department of Zoology and Research Centre, Scott Christian College (Autonomous), Nagercoil 629003, Tamil Nadu, India

Author

Correspondence author
International Journal of Aquaculture, 2013, Vol. 3, No. 19 doi: 10.5376/ija.2013.03.0019
Received: 07 Jun., 2013 Accepted: 27 Jun., 2013 Published: 03 Jul., 2013

This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Preferred citation for this article:

Rajakumaran, 2013, Molecular Characterization of Economically Important Penaeid Population in South East Coast of India, International Journal of Aquaculture, Vol.3, No.19 105-114 (doi: 10.5376/ija.2013. 03.0019)

Abstract

Genetic variation of wild Penaeid populations of South East Coast region in India, using Randomly Amplified Polymorphic DNA (RAPD) analysis as DNA marker has been examined. Important penaeid species like Fenneropenaeus indicus, Penaeus semisulcatus, Penaeus monodon were collected atdifferent geographical location such as Chennai, Nagapattinam, Pudukkottai, Ramanathapuram and Tuticorin, but P. monodon was not obtained from Tuticorin. For RAPD analysis, 15 numbers of primers were used, among which 3, 4, and 6 numbers of primers have worked well for F. indicus, P. semisulcatus and P. monodon respectively. The results of this study, genetic variation (6- 33)% for F. indicus, (16-49)% for P. semisulcatus (16- 53)% for P. monodon. As conclusion, from the pattern of genetic diversity of these three penaeid populations, it could be considered as moderate to high, and maximum three population stocks are within the collected area.

Keywords

Penaeid; RAPD; DNA Marker; Polymorphism; Population stock

Penaeid shrimps constitute one of the most important group of species for aquaculture worldwide, ranking second in overall value in 2006 (FAO, 2007). Sustainable development of this industry could greatly benefit from progress in our basic knowledge of genetics, genomics, and molecular immunology of shrimp. Recently, the application of high throughput molecular tools and approaches has led to significant developments in these fields (Robalino et al., 2012).

In India P. monodon (Fabricius, 1798), F. indicus (H. Milne Edwards, 1837), Fenneropenaeus penicillatus, (Olivier, 1791) P. semisulcatus, (De Haan, 1844), and Fenneropenaeus merguiensis (De Man,1888) are cultured, among which first two are mostly cultivable due to supplying of seed from hatcheries, traditionally which enter along the tidal water also cultured. The estimated brackish water area suitable for undertaking shrimp cultivation in India is around 11.91 lakh ha. spread over 10 states and union territories such as West Bengal, Orissa, Andhra Pradesh, Tamil Nadu, Pondicherry, Kerala, Karnataka, Goa, Maharashtra and Gujarat. Of this only around 1.356 lakh ha are under shrimp farming now. The state with high shrimp culture farms are Andhra Pradesh, Tamil Nadu, and Orissa. In the east coast the Penaeid shrimp culture practices are higher than west coast. Penaeid shrimp aquaculture provides employment opportunities to coastal rural populations and to earn valuable foreign exchange.

The over exploitation of shrimps from Indian coastal waters and the ever increasing demand for shrimps in the world market has resulted in the wide gap between the demand and supply. This has necessitated the need for exploring newer avenues for increasing shrimp production. Tamilnadu situated on the south east of Peninsular India is about 130 000 Sq.km. The length of its Coastline is about 1 050 km with its significant portion on the east coast bordering Bay of Bengal. Tamil Nadu is having the second longest coastline in the country with rich natural resources in coastal areas for coastal aqua farming. The total estimated brackish water area of Tamil Nadu is about 56 000 ha. The total area under shrimp farming is 4 455 ha. out of which 3 178 ha. are creek based and 1 277 ha. are sea based. The present culture is 4 455 ha. Which is only 30 per cent of the estimated potential area of 14 880 ha. readily available for shrimp farm development. Hence there is a wide scope for land based costal aquaculture development in Tamil Nadu.

Population genetic have proven valuable for estimating stock boundaries and genetic variability of wild shrimp population for fisheries (Benzie, 2000). Genetic distances between any pair of individuals of same group are smaller than those between pair of specimen any two geographical region (Aubert and Lightner, 2000). Species are often composed of discrete breeding units (population or stock) which are not reproductively isolated from each other, may have limited opportunity to exchange genetic material because of geographic distance, barrier to migration or spawning asynchrony. Low level of gene flow stocks may result, over time, in their genetic divergence and species that are subdivided into morphological and genetically distinct stock are said to be structured. This information will help to the development of selective breeding programs applying quantitative genetic to better the performance of domesticated shrimp stock in aquaculture. Shrimp forming industry in south east Asia, two fundamental problems have risen leading to great economic loss, those are viral diseases, that affect shrimp health resulting in large economic losses in affected countries and effects of domestication on genetic diversity levels in cultured lines. Genetic diversity likely impacted during the domestication process, besides, as result of culture stock they were exposed to repeated bottlenecks as they were developed in culture. This has led to an increasing in consanguinity over time. Since the existence of natural population subdivision may imply adaption to local conditions, genetic assessment of the degree of population structuring and gene flow among natural population are practical ways of helping to preserve existing biodiversity and maintaining valuable adaptive population.

The genetic diversity in the east coast appears to be more than the west coast of India. This could be due to a large fluctuation in the physic- chemical parameters in the east coast because of several river drainage in the east coast (Kumar et al., 2007).Metapenaeus dobsoni (Miers, 1878)populations from the west coast of India state Kerala and Maharashtra clustered together, but Tamil Nadu formed a separate group as east coast of India (Lakra et al., 2010). Distribution of zoeae larvae of these Penaeid species are generally very coastal, as spawning occur in 5 m-90 m depth, The life cycle of this species can be completed in captivity, diminishing the dependence on wild caught broodstock of these species and allowing to commercially breed juveniles to sustain production or to develop selective breeding programs. Before attempting such commercial operation, it is important to obtain data on genetic diversity of wild stocks for successful broodstock and genetic resources management since viable shrimp hatcheries coexist in many of the shrimp farming regions of the south east coast of Indian where collection of larvae and breeding stocks from the wild. It is susceptible to fluctuations in the availability of wild resources as any capture fishery activity. Therefore knowledge about genetic diversity and population differentiation is imperative to assess genetic variability in the wild population for proper conservation.

Nuclear DNA markers have allowed rapid progress in aquaculture investigations of genetic variability and inbreeding, parentage assignments, and species and strain identification and in the construction of high-resolution genetic linkage maps for aquaculture species (Liu and Cordes, 2004). Nuclear DNA markers main attractiveness is abundance in the genome, Mendalian inheritances, and potential to detect high polymorphism. The deleterious effects of inbreeding are to be avoided; crossing organism from genetically different strains is of critical importance. This can be done most effectively if knowledge about genetic similarity or differences between strains is available, especially when pedigree information is lacking (Ferguson, 1994). The limitation of mitochondrial DNA studies is that the genes are linked and act as a single locus and nuclear gene could serve as additional non linked genetic marker of population genetic studies. These nuclear markers would differ from mitochondrial marker in their rates of evolution and biparental mode of inheritance (France et al., 1999).

Random amplification of polymorphic DNA is a simple and easy molecular method to estimate genetic diversity in penaeid shrimp, fish and shell fish (Zhuang et al., 2001a, 2001b; Mishra et al., 2009, Lakra et al., 2010). It has been successfully employed to determine genetic diversity in Litopenaeus vannamei, (Boone, 1931) (Garcia and Benzie, 1995), and P. monodon, (Tassannakajon et al., 1998) for population studies of Penaeid species. In Thailand found Banana prawns F. merguiensis and F. indicus are clearly distinguished by RAPD marker (Phongdara et al., 1999). Due to variation in RAPD profile and difficulties with reproducibility, however many genetic researcher were made because RAPD-PCR is a quick and reliable method for identifying genetic diversity and similarity among various organism (Tassanakajon et al., 1997). Mishra et al. (2009) recommended that RAPD technique is very advantageous as a preliminary tool for studying the population structure of Penaeid. RAPD technique designed to detect sequence changes within the priming site as well as differences in length, through insertion or deletion, between them. Mutation at the priming site will affect primer annealing and amplification of particular segment (Caetano-Anolles and Bassam, 1993), whereas deletion or insertion between primering site will alter the length of amplified fragment, both instances will result in changes in the RAPD profile produced by a given primer, and significance of these differences can be used to determine the extent of population structure. RAPD fragment represent a combination of product amplified from coding and non-coding loci, estimator of genetic diversity extracted from them tend to be more informative of the overall genetic variation in the species than those derived from coding loci alone. The population separated by thousands of kilometers can be genetically more similar than others over very short distances and differences between species in level of genetic variation, and genotype distribution might be related to life history types (Mulley and Latter, 1980; De La Rosa-Velea et al., 2000).

Previously many genetic diversity studies using allozyme analysis has been used to determine the levels of variation and degree of genetic subdivision for several shrimp species (Lester and Pante, 1992; De la Rosa-Velez et al., 2000; Gracia-Machado et al., 2001; Gusmao et al., 2005), and mitochondrial DNA restriction fragment length polymorphism (Benzie et al., 1993; Klinbunga et al., 1999, 2001; Gracia-Machado et al., 2001). Genetic diversity and geographic differentiation of the P. monodon mitochondrial COI sequences (Kumar et al., 2007; Khamnamtong et al., 2009). Randomly amplified polymorphic DNAs (Aubert and Lithtner, 2000; Mishra et al., 2009; Lakra, 2010; Rezvani et al., 2011) and microsatellite (Wolfus et al., 1997; Brooker et al., 2000; Supungal et al., 2000; Maggioni et al., 2003; Robainas-Barcia and García-Machado, 2012; Mandal et al., 2012). In all studies, the major Penaeid were L. vannamei, P. monodon, and Masupenaeus japonicus (Bate, 1888), but in the present study, the most available and economically important Penaeid populations were thecandidate species.Previously no report was available on the molecular characterization of Fenneropenaeus indicus, Penaeus semisulcatus, Penaeus monodon of the south east coast region of India, and hence an attempt has been made to reveal the genetic diversity of three Penaeid populations in south east coast of India.

1 Results
Among 15 numbers of primers used for this study, 3, 4, and 6 number of primers, worked well for F. indicus, P. semisulcatus and P. monodon respectively. The primer sequences for this study (Table 1). Among the primer RM 03, 04, 05, 07, 11, 14, 15, 17 used for present study the RM 03, 04, 07 primers amplified the DNA product of three species taken for genetic analysis. DNA bands size produced 1000 to 10000 bp. For this 1000Kbp maker were used as reference and polymorphic profile for F. indicus, P. semisulcatus, and P. monodon shown as Figure 1, Figure 2, and Figure 3 respectively. The total number of bands, number of polymorphic bands, number of monomorphic bands and percentage of polymorphic

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