scholarly journals Genome-Wide Patterns of Population Structure and Linkage Disequilibrium in Farmed Nile Tilapia (Oreochromis niloticus)

2019 ◽  
Vol 10 ◽  
Author(s):  
Grazyella M. Yoshida ◽  
Agustín Barria ◽  
Katharina Correa ◽  
Giovanna Cáceres ◽  
Ana Jedlicki ◽  
...  
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Genome Wide ◽  
Nile Tilapia Oreochromis Niloticus

scholarly journals Genome-wide patterns of population structure and linkage disequilibrium in farmed Nile tilapia (Oreochromis niloticus)

2019 ◽  
Author(s):  
Grazyella M. Yoshida ◽  
Agustín Barria ◽  
Katharina Correa ◽  
Giovanna Cáceres ◽  
Ana Jedlicki ◽  
...  
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Genomic Selection ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Population Genomics ◽  
Association Studies ◽  
Demographic History ◽  
Genome Wide Association Studies ◽  
Genome Wide

AbstractNile tilapia (Oreochromis niloticus) is one of the most produced farmed fish in the world and represents an important source of protein for human consumption. Farmed Nile tilapia populations are increasingly based on genetically improved stocks, which have been established from admixed populations. To date, there is scarce information about the population genomics of farmed Nile tilapia, assessed by dense single nucleotide polymorphism (SNP) panels. The patterns of linkage disequilibrium (LD) may affect the success of genome-wide association studies (GWAS) and genomic selection and can also provide key information about demographic history of farmed Nile tilapia populations. The objectives of this study were to provide further knowledge about the population structure and LD patterns, as well as, estimate the effective population size (Ne) for three farmed Nile tilapia populations, one from Brazil (POP A) and two from Costa Rica (POP B and POP C). A total of 55, 56 and 57 individuals from POP A, POP B and POP C, respectively, were genotyped using a 50K SNP panel selected from a whole-genome sequencing (WGS) experiment. Two principal components explained about 20% of the total variation and clearly discriminated between the three populations. Population genetic structure analysis showed evidence of admixture, especially for POP C. The contemporary Ne values calculated based to LD values, ranged from 71 to 141. No differences were observed in the LD decay among populations, with a rapid decrease of r2 when increasing inter-marker distance. Average r2 between adjacent SNP pairs ranged from 0.03 to 0.18, 0.03 to 0.17 and 0.03 to 0.16 for POP A, POP B and POP C, respectively. Based on the number of independent chromosome segments in the Nile tilapia genome, at least 4.2 K SNP are required for the implementation of GWAS and genomic selection in farmed Nile tilapia populations.

scholarly journals Population Structure and Genetic Diversity of Nile Tilapia (Oreochromis niloticus) Strains Cultured in Tanzania

2019 ◽  
Vol 10 ◽  
Author(s):  
Redempta A. Kajungiro ◽  
Christos Palaiokostas ◽  
Fernando A. Lopes Pinto ◽  
Aviti J. Mmochi ◽  
Marten Mtolera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Nile Tilapia Oreochromis Niloticus

Genetic structure of wild and farmed Nile tilapia (Oreochromis niloticus) populations in Benin based on genome wide SNP technology

Aquaculture ◽  
2021 ◽  
Vol 535 ◽  
pp. 736432
Author(s):  
Mohammed Nambyl A. Fagbémi ◽  
Lise-Marie Pigneur ◽  
Adrien André ◽  
Nathalie Smitz ◽  
Vincent Gennotte ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Genome Wide ◽  
Nile Tilapia Oreochromis Niloticus
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