Evaluation of Genetic Diversity in Fourth- Generation Selective Breeding Lines of Pacific White Shrimp Using Microsatellites
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Abstract
The Pacific white shrimp (Litopenaeus vannamei) is a vital aquaculture species in Thailand with substantial economic importance. Ensuring genetic diversity is critical for sustaining a robust gene pool in farmed populations, ensuring resilience to diseases, environmental changes, and enhancing overall productivity. In this study, genetic diversity and structure of 35 families of fourth generation selective breeding lines of L. vannamei were monitored using five microsatellite DNA markers. The polymorphism information content (PIC) of all microsatellite loci exhibited high levels of polymorphism, with PICs greater than 0.70, indicating that the DNA markers were highly informative and effective in detecting allele variations in this population. The number of alleles per locus and the number of effective alleles (Ne) ranged from 3 to 6 and 2.809 to 4.598, with averages of 4.4 and 3.734, respectively. These values indicate that the population possessed a moderate level of genetic diversity. The overall mean observed heterozygosity (Ho) ranged from 0.209 to 0.492, which was lower than the expected heterozygosity (He) (0.714-0.784). The mean inbreeding (Fis) coefficient across all loci was 0.336 indicating a moderate level of inbreeding within this population. The population structure analysis showed that the 35 families were divided into two subpopulations (K=2), related to the sources of the base population collected from two private hatcheries. This study provides valuable insights into population genetics and will help guide breeding strategies of Pacific white shrimp.
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References
Sampantamit T, Ho L, Lachat C, Sutummawong N, Sorgeloos P, Goethals P. Aquaculture Production and Its Environmental Sustainability in Thailand: Challenges and Potential Solutions. Sustainability. 2020; 12(5): 2010.
Vaseeharan B, Rajakamaran P, Jayaseelan D, Vincent AY. Molecular markers and their application in genetic diversity of penaeid shrimp. Aquaculture International. 2013; 21(2): 219-41.
Zane L, Bargelloni L, Patarnello T. Strategies for microsatellite isolation: a review. Molecular Ecology. 2002; 11(1): 1-16.
Chen Y, Xu C, Li Q. Genetic diversity in a genetically improved line of the Pacific oyster Crassostrea gigas with orange shell based on microsatellites and mtDNA data. Aquaculture. 2022; 549: 737791.
Wirgin I, Maceda L, Stabile J, Waldman J. Genetic population structure of summer flounder Paralichthys dentatus using microsatellite DNA analysis. Fisheries Research. 2022; 250: 106270.
Diyie RL, Agyarkwa SK, Armah E, Amonoo NA, Owusu-Frimpong I, Osei-Atweneboana MY. Genetic variations among different generations and cultured populations of Nile Tilapia (Oreochromis niloticus) in Ghana: Application of microsatellite markers. Aquaculture. 2021; 544: 737070.
Bierne N, Beuzart I, Vonau V, Bonhomme F, Bédier E. Microsatellite-associated heterosis in hatchery-propagated stocks of the shrimp Penaeus stylirostris. Aquaculture. 2000; 184(3): 203-19.
Xu Z, Primavera JH, de la Pena LD, Pettit P, Belak J, Alcivar-Warren A. Genetic diversity of wild and cultured Black Tiger Shrimp (Penaeus monodon) in the Philippines using microsatellites. Aquaculture. 2001; 199(1): 13-40.
Cruz P, Ibarra AM, Mejia-Ruiz H, Gaffney PM, Pérez-Enríquez R. Genetic variability assessed by microsatellites in a breeding program of Pacific white shrimp (Litopenaeus vannamei). Marine biotechnology. 2004; 6: 157-64.
Ren S, Mather PB, Tang B, Hurwood DA. Levels of genetic diversity and inferred origins of Penaeus vannamei culture resources in China: Implications for the production of a broad synthetic base population for genetic improvement. Aquaculture. 2018; 491: 221-31.
Wong LL, Chun LC, Deris ZM, Zainudin AA, Ikhwanuddin M, Iehata S, et al. Genetic diversity and population structure of wild and domesticated black tiger shrimp (Penaeus monodon) broodstocks in the Indo-Pacific regions using consolidated mtDNA and microsatellite markers. Gene Reports. 2021; 23: 101047.
Sambrook Joseph, Russell DW. Molecular Cloning: A Laboratory Manual. 3rd Edition ed. Cold Spring Harbor Laboratory Press: New York; 2001.
Meehan D, Xu Z, Zuniga G, Alcivar-Warren A. High frequency and large number of polymorphic microsatellites in cultured shrimp, Penaeus (Litopenaeus) vannamei [Crustacea:Decapoda]. Mar Biotechnol (NY). 2003; 5(4): 311-30.
Pérez F, Ortiz J, Zhinaula M, Gonzabay C, Calderón J, Volckaert FA. Development of EST-SSR markers by data mining in three species of shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy. Mar Biotechnol (NY). 2005; 7(5): 554-69.
Marques C, Santos C, Galetti Jr P, Freitas P. Informative microsatellites for freshwater and marine shrimp species. International Journal of Biodiversity and Conservation. 2013; 5: 599-603.
Yeh F, Yang RC, Boyle T, Ye Z, Mao J, editors. POPGENE, version 1.32: the user friendly software for population genetic analysis 1999.
Liu K, Muse SV. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics. 2005; 21(9): 2128-9.
Rohlf F. NTSYS-pc-Numerical Taxonomy and Multivariate Analysis System. Applied Biostatistics Inc New York. 1988; 2.1.
Pritchard JK, Stephens M, Donnelly P. Inference of Population Structure Using Multilocus Genotype Data. Genetics. 2000; 155(2): 945-59.
Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software structure: a simulation study.
Molecular Ecology. 2005; 14(8): 2611-20.
Excoffier L, Lischer HE. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 2010; 10(3): 564-7.
Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 1980; 32(3): 314-31.
Zhang Z, Lu C, Lin K, You W, Yang Z. Genetic Diversity and Genetic Structure among Four Selected Strains of Whiteleg Shrimp (Litopenaeus vannamei) Using SSR Markers. Fishes. 2023; 8(11): 544.
Valles-Jimenez R, Cruz P, Perez-Enriquez R. Population genetic structure of Pacific white shrimp (Litopenaeus vannamei) from Mexico to Panama: microsatellite DNA variation. Mar Biotechnol (NY). 2004; 6(5): 475-84.
Klongklaew N, Songsangjinda P, editors. Genetic Diversity Evaluation of Pacific White Shrimp Populations (Litopenaeus vannamei Boone, 1931) Using Microsatellite DNA Marker. Proceedings of 55th Kasetsart University Annual Conference: Plants, Animals, Veterinary
Medicine, Fisheries, Agricultural Extension and Home Economics; 2016.
Wolfus GM, Garcia DK, Alcivar-Warren A. Application of the microsatellite technique for analyzing genetic diversity in shrimp breeding programs. Aquaculture. 1997; 152(1): 35-47.
Huang X, Xu Y, Hu X, Xu W, Su H, Wen G, et al. Genetic diversity analysis of first filial generation of seven introduced Litopenaeus vannamei populations using microsatellite DNA markers. South China Fisheries Science. 2019; 15(1): 54-62.
Chareontawee K, Poompuang S, Na-Nakorn U, Kamonrat W. Genetic diversity of hatchery stocks of giant freshwater prawn (Macrobrachium rosenbergii) in Thailand. Aquaculture. 2007; 271(1): 121-9.
Lima A, Silva S, Oliveira K, Maggioni R, Coimbra M. Genetics of two marine shrimp hatcheries of the Pacific white shrimp Litopenaeus vannamei (Boone, 1931) in Pernambuco, Brazil. Ciencia Rural - CIENC RURAL. 2010; 40.