Đề tài Fish breeding practices and stock improvement strategies in Vietnam in relation to common carp

Fish breeding practices and stock improvement strategies in Vietnam in relation to common carp Christopher M Austin Pham Anh Tuan Thai Thanh Binh Le Quang Hung Nguyen Thi Tan School of Science and Primary Industries Faculty of Health, Education and Science Charles Darwin University, Casuarina Campus, Darwin, Northern Territory 0909, Australia Research Institute for Aquaculture No I (Ministry of Fisheries) Dinh Bang, Tu Son, Bac Ninh Vietnam June 2007 Fish breeding practices and stock improvement strategies in Vietnam in relation to common carp ___________________________________________________________________________ ___________________________________________________________________________ Christopher M Austin, Tuan Anh Pham, Binh Thanh Thai, Hung Quang Le, Tan Thi Nguyen 2 CONTENTS List of Figures..................................................................................................................4 List of Tables ...................................................................................................................6 Summary..........................................................................................................................8 1. Introduction...............................................................................................................11 1.1 Taxonomy and distribution................................................................................11 1.2 Biology of common carp .....................................................................................13 1.3 Common carp culture .........................................................................................14 2. Common carp culture in Vietnam...........................................................................17 2.1 Summary of socio-economic survey of common carp culture in Vietnam ....19 2.1.1 Carp farmer family profile .............................................................................21 2.1.2 Common carp culture.....................................................................................21 2.1.3 Suggestion of fish farmers .............................................................................27 3. Common carp breeding programs in Vietnam. .....................................................28 3.1 Introduction.........................................................................................................28 3.2 Crossbreeding of common carp .........................................................................29 3.3 Mass selection of common carp .........................................................................31 3.4 Family selection of common carp ......................................................................37 3.5 Combination of family and individual selection of common carp..................38 4. Overview molecular genetic studies on common carp in the world .....................42 5. Genetic diversity of common carp in Vietnam using direct sequencing and SSCP analysis of the DNA control region..................................................................45 5.1 Objective ..............................................................................................................47 5.2 Materials and Methods .......................................................................................47 5.2.1 Sample collection...........................................................................................47 5.2.2 DNA extraction and sequencing of control region ........................................49 5.2.3 Single Strand Conformation Polymorphism (SSCP) amplification...............50 5.2.4 Data analysis ..................................................................................................51 5.3 Results ..................................................................................................................52 5.3.1 Control region sequences and SSCP variation...............................................52 5.3.2 Genetic differentiation and relationships among populations........................54 5.4 Discussion.............................................................................................................59 5.4.1 Control region sequence variation and utility of the SSCP techniques .........59 5.4.2 Genetic diversity of common carp in Vietnam ..............................................60 Fish breeding practices and stock improvement strategies in Vietnam in relation to common carp ___________________________________________________________________________ ___________________________________________________________________________ Christopher M Austin, Tuan Anh Pham, Binh Thanh Thai, Hung Quang Le, Tan Thi Nguyen 3 5.4.3 Insights into the dissemination of cultured common carp in Vietnam ..........63 5.4.4 Conservation of wild carp stocks ...................................................................65 5.4.5 Conclusion .....................................................................................................68 6. Genetic diversity of common carp in Vietnam using four microsatellite loci .....69 6.1 Objectives.............................................................................................................72 6.2 Materials and Methods .......................................................................................72 6.2.1 Sample collection and DNA extraction..........................................................72 6.2.2 Data collection ...............................................................................................72 6.2.3 Genetic diversity analysis ..............................................................................73 6.2.4 Genetic differentiation between populations .................................................74 6.3 Results ..................................................................................................................75 6.3.1 Within population variation ...........................................................................75 6.3.2 Genetic differentiation and relationships among populations........................79 6.4 Discussion.............................................................................................................85 6.4.1 Genetic diversity within common carp populations.......................................85 6.4.2 Differentiation between populations ..............................................................88 6.4.3 Comparison of microsatellite and mitochondrial DNA data..........................90 7. Expanded genetic analysis of common carp stocks from private hatcheries, farmer ponds and market places .....................................................................93 7.1 Introduction.........................................................................................................93 7.2 Materials and Methods .......................................................................................94 7.2.1 Sample collection and data set .......................................................................94 7.2.2 DNA extraction and Single Strand Conformation Polymorphism (SSCP) amplification ...........................................................................................................95 7.2.3 Data analysis ..................................................................................................95 7.3 Results ..................................................................................................................96 7.3.1 SSCP variation ...............................................................................................96 7.4 Discussion...........................................................................................................104 7.4.1 Additional insights into diversity of common carp in Vietnam...................104 Appendix ......................................................................................................................108 Reference......................................................................................................................112 Fish breeding practices and stock improvement strategies in Vietnam in relation to common carp ___________________________________________________________________________ ___________________________________________________________________________ Christopher M Austin, Tuan Anh Pham, Binh Thanh Thai, Hung Quang Le, Tan Thi Nguyen 4 List of Figures Figure 1.1. Distribution of common carp in the world (FAO 2003)...............................12 Figure 1.2. World production of common carp (FAO 2003)..........................................15 Figure 2.1. Varieties of common cap in Vietnam (A: Bang Giang River, B&F:Dak Lak, C: Son River red, D: Bac Kan) ...........................................................................18 Figure 2.2. Types of common carp culture in Vietnam (A: Pond culture, B: Rice-fish culture, C: Integrated aquaculture)......................................................................19 Figure 2.3. The locations at which stakeholders were interviewed for the socio- economic survey..................................................................................................20 Figure 2.4. Type of common carp culture in Vietnam....................................................22 Figure 2.5. Percent fish species stocked into household ponds in Vietnam ...................23 Figure 2.6. Water source used for common carp culture ................................................23 Figure 2.7. Common carp sources in the farms in Vietnam............................................24 Figure 2.8. Farmer evaluation quality of seed.................................................................26 Figure 2.9. Demand for common carp in Vietnam .........................................................26 Figure 3.1. Mass selection of three blood common carp (Thien and Thang, 1992) .......33 Figure 5.1. Collection localities for Cyprinus carpio L. samples in Vietnam.................49 Figure 5.2. Silver stained polyacrylamide gel showing the eight SSCP variants detected in common carp populations in Vietnam (a). Neighbour-joining tree reconstruction derived from CR sequences, using HKY+I+G model of evolution. Bootstrap values are based on 1,000 replicates. Bootstrap value is given for nodes with at least 50% or more support (b).......................................................66 Figure 5.3. Relationships among common carp from wild and hatchery population in Vietnam using the unbiased genetic distance of Roger (1972) and UPGMA joining method. A, B, and C are SSCP haplotypes which predominate in each cluster. .................................................................................................................67 Figure 5.4. MDS plot of pairwise Fst value among hatchery and wild populations of common carp in Vietnam. Population codes are given in Table 5.1...................68 Figure 6.1.Allele number and distribution of allele frequencies for Hungarian, Indonesian and Vietnamese experiemtal common carp populations at each microsatellite locus. ............................................................................................80 Figure 6.2. UPGMA dendrogram of common carp populations in Vietnam based on matrixes of genetic distance (Nei et al., 1983)....................................................84 Fish breeding practices and stock improvement strategies in Vietnam in relation to common carp ___________________________________________________________________________ ___________________________________________________________________________ Christopher M Austin, Tuan Anh Pham, Binh Thanh Thai, Hung Quang Le, Tan Thi Nguyen 5 Figure 6.3. MDS plot of paiwise Fst value among experimental, hatchery and wild populations of common carp in Vietnam, (a) based on microsatellite data, (b) mitochondrial DNA data. Population codes are given in Table 5.1. ..................86 Figure 7.1. Collection localities for Cyprinus carpio L. samples in Vietnam. Population code are given in Table 7.1. ................................................................................98 Figure 7.2. Haplotype diversity of Common carp groups in Vietnam base on SSCP analyses. ............................................................................................................101 Figure 7.3. Relationships among common carp from experimental, provincial hatchery, private hatchery, private pond, market, wild populations in Vietnam using the unbiased genetic distance of Rogers (1972) and UPGMA joining methods. A, B, C are SSCP haplotypes which predominate in each cluster. Population codes are given in Table 7.1..............................................................................................102 Figure 7.4. Multidimension scaling (MDS) plot of pairwise Fst values among common carp from experimental, provincial hatchery, private hatchery, private pond, market, wild populations in Vietnam. Population codes are given in Table 7.1. A, B, C are main groups.........................................................................................103 Fish breeding practices and stock improvement strategies in Vietnam in relation to common carp ___________________________________________________________________________ ___________________________________________________________________________ Christopher M Austin, Tuan Anh Pham, Binh Thanh Thai, Hung Quang Le, Tan Thi Nguyen 6 List of Tables Table 2.1. Number of fish farms surveyed......................................................................21 Table 2.2. Frequency changed common carp broodstocks in hatcheries are changed....25 Table 3.1. Survival rate (%) for fry and fingerling of Vietnamese common carp (V), Hungarian common carp and their reciprocal hybrids (VH, HV) (Thien and Thang, 1992) .......................................................................................................30 Table 3.2 Morphology and morphometrics of common carp varieties and their hybrids (H: Hungarian; Y: Indonesian Yellow; V: Vietnamese White) (Nguyen et al., 2005) ...................................................................................................................31 Table 3.3. Adjusted average body weight of the common carp in an experiment on determination of realized heritability in 1988 (Thien and Thang, 1992)............32 Table 3.4. Summary data of the mass individual selection of the hybrid stocks of common carp (V: Vietnamese, H: Hungarian and Y: Indonesian yellow common carp) (Tran and Nguyen, 1992)...........................................................................34 Table 3.5. Heritability (h2) of the body weight of hybrid common carp Hungarian x (Vietnamese x Yellow) (Tran and Nguyen, 1992)..............................................35 Table 3.6. Growth rate of common carp of the F3 and F5 selected generations in a grow- out pond; Stocks [Hungarian x (Vietnamese x Yellow)] in Communal stocking in 1995 (Nguyen, 2005). .....................................................................................36 Table 3.7. Body weight of common carp in pure stocks and their hybrids reared in the same pond, 1995 (Thien and Thang, 1992). .......................................................37 Table 3.8. Current crossbreeding between carp lines to produce 86 families (Nguyen, 2005) ...................................................................................................................40 Table 5.1. Location, code and number of samples sequenced and analysed by the SSCP technique. ............................................................................................................48 Table 5.2. Number of haplotypes and haplotype diversity in each common carp population. Population code given in Table 5.1..................................................57 Table 5.3. Pair-wise estimate of variance of haplotype frequencies (Fst) among of samples. Population codes given in Table 5.1. ...................................................58 Table 5.4. AMOVA results for three groups (experimental, hatchery, wild) of 20 common carp populations base on SSCP data. (Intra = intrapopulation, Inter = interpopulation, values are %).............................................................................59 Table 6.1. Characteristics of Cyprinus carpio microsatellite loci tested.........................73 Fish breeding practices and stock improvement strategies in Vietnam in relation to common carp ___________________________________________________________________________ ___________________________________________________________________________ Christopher M Austin, Tuan Anh Pham, Binh Thanh Thai, Hung Quang Le, Tan Thi Nguyen 7 Table 6.2. Genetic variability of four microsatellite loci in 20 populations for common carp in Vietnam. Population codes given in Table 5.1. ......................................77 Table 6.3. Number of private alleles at four microsatellite loci in 20 common carp populations and group. The population codes are given in Table 5.1.................78 Table 6.4. Pairwise Fst values between 20 common carp populations in Vietnam based on four microsatellite loci. Population codes given Table 5.1............................81 Table 6.5.Results of assignment test (self-classification) of common carp individuals based on four microsatellite loci. Population code are given in Table 5.1. ........82 Table 6.6. Genetic diversity of experimental, hatchery and wild common carp groups in Vietnam based on variation at four microsatellite loci (Intra = intrapopulation, Inter = interpopulation, values are %).................................................................85 Table 7.1. Location, code and number of common carp sample fro Vietnam analysed by the SSCP technique.............................................................................................97 Table 7.2. Number of haplotype (N) and haplotype diversity (Hd) in each common carp population in Vietnam.........................................................................................99 Table 7.3. Number of population (N), haplotype (n) and haplotype diversity (Hd) of six common carp groups in Vietnam. .....................................................................100 Table 7.4. AMOVA results for six groups (experimental, provincial hatchery, private hatchery, private pond, market and wild) of common carp population in Vietnam base on SSCP data. (N = number of population was analysed, Intra = intrapopulation, Inter = interpopulation, value are %)......................................104 Fish breeding practices and stock improvement strategies in Vietnam in relation to common carp ___________________________________________________________________________ ___________________________________________________________________________ Christopher M Austin, Tuan Anh Pham, Binh Thanh Thai, Hung Quang Le, Tan Thi Nguyen 8 Summary This document brings together, for the first time, information from diverse sources relating to common carp breeding and genetic improvement strategies in Vietnam. These sources include the results of a survey of common carp farmers and hatchery operators, published and unpublished reports in Vietnamese on fish breeding and genetic improvement programs and experiments and the results of a comprehensive molecular genetic analysis of common carp stocks throughout Vietnam. The survey of common carp farmers an