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Sun CF, Zhang XH, Dong JJ, You XX, Tian YY, Gao FY, Zhang HT, Shi Q, Ye X, Shi Q, Ye X. Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass ( Micropterus salmoides). Zool Res 2023; 44:78-89. [PMID: 36349358 PMCID: PMC9841193 DOI: 10.24272/j.issn.2095-8137.2022.274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Largemouth bass ( Micropterus salmoides) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study, we sequenced 149 largemouth bass fish, including protospecies (imported from the US) and improved breeds (four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection, including several associated with growth (p sst1 and grb10), early development ( klf9, sp4, and sp8), and immune traits ( pkn2, sept2, bcl6, and ripk2). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.
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Affiliation(s)
- Cheng-Fei Sun
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Xin-Hui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun-Jian Dong
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Xin-Xin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan-Yuan Tian
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Feng-Ying Gao
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - He-Tong Zhang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China,E-mail:
| | - Xing Ye
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China,
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Wang Y, Sha H, Li X, Zhou T, Luo X, Zou G, Chai Y, Liang H. Microsatellite Characteristics of Silver Carp ( Hypophthalmichthysmolitrix) Genome and Genetic Diversity Analysis in Four Cultured Populations. Genes (Basel) 2022; 13:genes13071267. [PMID: 35886050 PMCID: PMC9320178 DOI: 10.3390/genes13071267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 02/04/2023] Open
Abstract
Hypophthalmichthys molitrix is one of the four most important fish in China and has high breeding potential. However, simple sequence repeat (SSR) markers developed on H. molitrix genome level for genetic diversity analysis are limited. In this study, the distribution characteristics of SSRs in the assembled H. molitrix genome were analyzed, and new markers were developed to preliminarily evaluate the genetic diversity of the four breeding populations. A total of 368,572 SSRs were identified from the H. molitrix genome. The total length of SSRs was 6,492,076 bp, accounting for 0.77% of the total length of the genome sequence. The total frequency and total density were 437.73 loci/Mb and 7713.16 bp/Mb, respectively. Among the 2–6 different nucleotide repeat types, SSRs were dominated by di-nucleotide repeats (204,873, 55.59%), and AC/GT was the most abundant motif. The number of SSRs on each chromosome was positively correlated with the length. The 13 pairs of markers developed were used to analyze the genetic diversity of four cultivated populations in Hubei Province. The results showed that the genetic diversity of the four populations was low, and the ranges of alleles (Na), effective alleles (Ne), observed heterozygosity (Ho), and Shannon’s index information (I) were 3.538–4.462, 2.045–2.461, 0.392–0.450, and 0.879–0.954, respectively. Genetic variation occurs mainly among individuals within populations (95.35%). UPGMA tree and Bayesian analysis showed that four populations could be divided into two different branches. Therefore, the genome-wide SSRs were effectively in genetic diversity analysis on H. molitrix.
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Affiliation(s)
- Yajun Wang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, College of Agriculture, College of Animal Science, Yangtze University, Jingzhou 434025, China;
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (H.S.); (X.L.); (T.Z.); (X.L.); (G.Z.)
| | - Hang Sha
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (H.S.); (X.L.); (T.Z.); (X.L.); (G.Z.)
| | - Xiaohui Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (H.S.); (X.L.); (T.Z.); (X.L.); (G.Z.)
| | - Tong Zhou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (H.S.); (X.L.); (T.Z.); (X.L.); (G.Z.)
| | - Xiangzhong Luo
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (H.S.); (X.L.); (T.Z.); (X.L.); (G.Z.)
| | - Guiwei Zou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (H.S.); (X.L.); (T.Z.); (X.L.); (G.Z.)
| | - Yi Chai
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, College of Agriculture, College of Animal Science, Yangtze University, Jingzhou 434025, China;
- Correspondence: (Y.C.); (H.L.)
| | - Hongwei Liang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (H.S.); (X.L.); (T.Z.); (X.L.); (G.Z.)
- Correspondence: (Y.C.); (H.L.)
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The First Genome Survey and De Novo Assembly of the Short Mackerel (Rastrelliger brachysoma) and Indian Mackerel (Rastrelliger kanagurta). Animals (Basel) 2022; 12:ani12141769. [PMID: 35883316 PMCID: PMC9312166 DOI: 10.3390/ani12141769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/29/2022] [Accepted: 07/08/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Mackerel species are commercially important marine species in Southeast Asia, especially short mackerel and Indian mackerel. However, genomic information about them is still limited. Genome survey of these two mackerel species was reported in this study. Next-generation sequencing and comprehensive bioinformatics were performed to obtain the genetic information. The estimated genome size of both species is around 680 Mbp. The heterozygosity of these species was very similar, while the repeat content for Indian mackerel was slightly higher than for short mackerel. Functional annotation also was reported in this study. This is the first reported genome survey and assembly of species in the genus Rastrelliger and could be useful for future comparative genomic studies. Abstract Rastrelliger brachysoma (short mackerel) and Rastrelliger kanagurta (Indian mackerel) are commercially important marine species in Southeast Asia. In recent years, numbers of these two species have been decreasing in the wild, and genomic information about them is still limited. We conducted a genome survey of these two mackerel species to acquire essential genomic information using next-generation sequencing data. To obtain this genetic information, comprehensive bioinformatics analyses were performed, including de novo assembly, gene prediction, functional annotation, and phylogenetic analysis. The estimated genome sizes were around 680.14 Mbp (R. brachysoma) and 688.82 Mbp (R. kanagurta). The heterozygosity of these species was very similar (≈0.81), while the repeat content for R. kanagurta (9.30%) was slightly higher than for R. brachysoma (8.30%). Functional annotation indicated that most of the genes predicted in these two species shared very close average amino acid identities (94.06%). The phylogenetic analysis revealed close phylogenetic relationships between these two species and other scombrids. This is the first reported genome survey and assembly of species in the genus Rastrelliger and could be useful for future comparative genomic studies.
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Agudelo JFG, Mastrochirico‐Filho VA, de Souza Borges CH, Ariede RB, Lira LVG, de Oliveira Neto RR, de Freitas MV, Sucerquia GAL, Vera M, Berrocal MHM, Hashimoto DT. Genomic selection signatures in farmed Colossoma macropomum from tropical and subtropical regions in South America. Evol Appl 2022; 15:679-693. [PMID: 35505878 PMCID: PMC9046916 DOI: 10.1111/eva.13351] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 12/21/2021] [Accepted: 01/21/2022] [Indexed: 11/26/2022] Open
Abstract
Tambaqui or cachama (Colossoma macropomum) is one of the most important neotropical freshwater fish used for aquaculture in South America, and its production is concentrated at low latitudes (close to the Equator, 0°), where the water temperature is warm. Therefore, understanding how selection shapes genetic variations and structure in farmed populations is of paramount importance in evolutionary biology. High‐throughput sequencing to generate genome‐wide data for fish species allows for elucidating the genomic basis of adaptation to local or farmed conditions and uncovering genes that control the phenotypes of interest. The present study aimed to detect genomic selection signatures and analyze the genetic variability in farmed populations of tambaqui in South America using single‐nucleotide polymorphism (SNP) markers obtained with double‐digest restriction site‐associated DNA sequencing. Initially, 199 samples of tambaqui farmed populations from different locations (located in Brazil, Colombia, and Peru), a wild population (Amazon River, Brazil), and the base population of a breeding program (Aquaculture Center, CAUNESP, Jaboticabal, SP, Brazil) were genotyped. Observed and expected heterozygosity was 0.231–0.350 and 0.288–0.360, respectively. Significant genetic differentiation was observed using global FST analyses of SNP loci (FST = 0.064, p < 0.050). Farmed populations from Colombia and Peru that differentiated from the Brazilian populations formed distinct groups. Several regions, particularly those harboring the genes of significance to aquaculture, were identified to be under positive selection, suggesting local adaptation to stress under different farming conditions and management practices. Studies aimed at improving the knowledge of genomics of tambaqui farmed populations are essential for aquaculture to gain deeper insights into the evolutionary history of these fish and provide resources for the establishment of breeding programs.
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Affiliation(s)
| | | | | | - Raquel Belini Ariede
- São Paulo State University (Unesp) Aquaculture Center of Unesp 14884‐900 Jaboticabal SP Brazil
| | | | | | | | | | - Manuel Vera
- Facultad de Veterinaria Universidad de Santiago de Compostela (USC) ES27002 Lugo Spain
| | | | - Diogo Teruo Hashimoto
- São Paulo State University (Unesp) Aquaculture Center of Unesp 14884‐900 Jaboticabal SP Brazil
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Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus. Sci Rep 2021; 11:19289. [PMID: 34588599 PMCID: PMC8481427 DOI: 10.1038/s41598-021-98885-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
Scarce genomic resources have limited the development of breeding programs for serrasalmid fish Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu), the key native freshwater fish species produced in South America. The main objectives of this study were to design a dense SNP array for this fish group and to validate its performance on farmed populations from several locations in South America. Using multiple approaches based on different populations of tambaqui and pacu, a final list of 29,575 and 29,612 putative SNPs was selected, respectively, to print an Axiom AFFYMETRIX (THERMOFISHER) SerraSNP array. After validation, 74.17% (n = 21,963) and 71.25% (n = 21,072) of SNPs were classified as polymorphic variants in pacu and tambaqui, respectively. Most of the SNPs segregated within each population ranging from 14,199 to 19,856 in pacu; and from 15,075 to 20,380 in tambaqui. Our results indicate high levels of genetic diversity and clustered samples according to their hatchery origin. The developed SerraSNP array represents a valuable genomic tool approaching in-depth genetic studies for these species.
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Weng Z, Yang Y, Wang X, Wu L, Hua S, Zhang H, Meng Z. Parentage Analysis in Giant Grouper ( Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data. Genes (Basel) 2021; 12:genes12071042. [PMID: 34356058 PMCID: PMC8304347 DOI: 10.3390/genes12071042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 12/18/2022] Open
Abstract
Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.
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Affiliation(s)
- Zhuoying Weng
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Yang Yang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Xi Wang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Lina Wu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Sijie Hua
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Hanfei Zhang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Zining Meng
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
- Southern Laboratory of Ocean Science and Engineering, Zhuhai 519000, China
- Correspondence:
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Tian HF, Hu QM, Li Z. Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in swamp eel (Monopterus albus). Sci Prog 2021; 104:368504211035597. [PMID: 34375541 PMCID: PMC10358632 DOI: 10.1177/00368504211035597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Swamp eel is one model species for sexual reversion and an aquaculture fish in China. One local strain with deep yellow and big spots of Monopterus albus has been selected for consecutive selective breeding. The objectives of this study were characterizing the Simple Sequence Repeats (SSRs) of M. albus in the assembled genome obtained recently, and developing polymorphic SSRs for future breeding programs. METHODS The genome wide SSRs were mined by using MISA software, and their types and genomic distribution patterns were investigated. Based on the available flanking sequences, primer pairs were batched developed, and Polymorphic SSRs were identified by using Polymorphic SSR Retrieval tool. The obtained polymorphic SSRs were validated by using e-PCR and capillary electrophoresis, then they were used to investigate genetic diversity of one breeding population. RESULTS A total of 364,802 SSRs were identified in assembled M. albus genome. The total length, density and frequency of SSRs were 8,204,641 bp, 10,259 bp/Mb, and 456.16 loci/Mb, respectively. Mononucleotide repeats were predominant among SSRs (33.33%), and AC and AAT repeats were the most abundant di- and tri-nucleotide repeats motifs. A total of 287,189 primer pairs were designed, and a high-density physical map was constructed (359.11 markers per Mb). A total of 871 polymorphic SSRs were identified, and 38 SSRs of 101 randomly selected ones were validated by using e-PCR and capillary electrophoresis. Using these 38 polymorphic SSRs, 201 alleles were detected and genetic diversity level (Na, PIC, HO, and He) was evaluated. CONCLUSIONS The genome-wide SSRs and newly developed SSR markers will provide a useful tool for genetic mapping, diversity analysis studies in swamp eel in the future. The high level of genetic diversity (Na = 5.29, PIC = 0.5068, HO = 0.4665, He = 0.5525) but excess of homozygotes (FIS = 0.155) in one breeding population provide baseline information for future breeding program.
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Affiliation(s)
- Hai-feng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, China
| | - Qiao-mu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, China
| | - Zhong Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, China
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Freitas MVD, Ariede RB, Hata ME, Mastrochirico-Filho VA, Pazo FD, Villanova GV, Mendonça FF, Porto-Foresti F, Hashimoto DT. Haplotypes traceability and genetic variability of the breeding population of pacu (Piaractus mesopotamicus) revealed by mitochondrial DNA. Genet Mol Biol 2021; 44:e20200249. [PMID: 33721013 PMCID: PMC7958636 DOI: 10.1590/1678-4685-gmb-2020-0249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/20/2021] [Indexed: 11/22/2022] Open
Abstract
The main objective of this study was to estimate the genetic diversity levels and haplotype traceability in pacu Piaractus mesopotamicus from the breeding program located in Brazil by analyses of the mitochondrial DNA control region (mtDNA). Moreover, broodstocks from eight commercial fish farms were used for comparative evaluation, four from Brazil (Br1-Br4) and four from Argentina (Ar1-Ar4). The descriptive results revealed 47 polymorphic sites and 51 mutations, which evidenced 34 haplotypes. Ten haplotypes were shared among fish farms and 24 were exclusive. The nucleotide diversity (π) ranged from 0.00031 to 0.01462 and haplotype diversity (Hd) from 0.125 to 0.868. The analysis of molecular variance (AMOVA) indicated high structure present in the analyzed stocks (FST = 0.13356 and ФST = 0.52707). The genetic diversity was high in most of the commercial broodstocks, especially those from Brazil. We observed seven haplotypes in the genetic breeding population, of which four were exclusive and three shared among the commercial fish farms. The genetic diversity was moderate (π = 0.00265 and Hd = 0.424) and considered appropriated for this breeding population of pacu. Our results provide support for the genetic diversity maintenance and mtDNA traceability of pacu commercial broodstocks.
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Affiliation(s)
- Milena V de Freitas
- Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Centro de Aquicultura, Jaboticabal, SP, Brazil
| | - Raquel B Ariede
- Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Centro de Aquicultura, Jaboticabal, SP, Brazil
| | - Milene E Hata
- Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Centro de Aquicultura, Jaboticabal, SP, Brazil
| | - Vito A Mastrochirico-Filho
- Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Centro de Aquicultura, Jaboticabal, SP, Brazil
| | - Felipe Del Pazo
- Universidad Nacional de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas - Ministerio de Ciencia, Tecnología e Innovación productiva de Santa Fe, Centro Científico y Tecnológico Acuario del Río Paraná, Rosario, Santa Fe, Argentina
| | - Gabriela V Villanova
- Universidad Nacional de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas - Ministerio de Ciencia, Tecnología e Innovación productiva de Santa Fe, Centro Científico y Tecnológico Acuario del Río Paraná, Rosario, Santa Fe, Argentina
| | - Fernando F Mendonça
- Universidade Federal de São Paulo (UNIFESP), Instituto do Mar, Santos, SP, Brazil
| | - Fábio Porto-Foresti
- Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Faculdade de Ciências, Bauru, SP, Brazil
| | - Diogo T Hashimoto
- Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Centro de Aquicultura, Jaboticabal, SP, Brazil
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Anggraeni A, Thalib C, Ardhati Rani Hapsari A. Polymorphism Exploration of Growth Family (GH, GHRH and PIT-1) Genes Polymorphisms of Local Swamp Buffalo for Productivity Improvement in North Tapanuli Regency, North Sumatra. BIO WEB OF CONFERENCES 2021. [DOI: 10.1051/bioconf/20213302005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genetic improvement of livestock productivity can be done through molecular selection on the genes controlling growth traits. Genetic polymorphism of the growth family (GH, GHRH, and PIT1) genes were studied in local swamp buffalo (106 hds.) from a government buffalo breeding station (46 heads) and smallholders (60 heads) in North Tapanuli District, North Sumatra Province. Genotype variants of the three genes were identified by PCR-RFLP method using restriction enzymes of MspI (GH gene), HaeIII (GHRH gene) and HinfI (PIT -1 gene). Genotyping on individual GH_g.1547T>C, GHRH_g.4666G>C, and PIT -1_g.1256G >A loci resulted only one type genotype, respectively TT, CC, an d AA, with one type of allele, respectively T, C, and A. Heterozygosity observation (Ho) and expectation (He) values values and the PIC value for each locus was 0.00. It could be suggested to increase genotype frequenciest of the three growth genes that are positively associated with the growth traits and economic traits of the buffalo.
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