scholarly journals Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus)

2019 ◽  
Author(s):  
María I. Cádiz ◽  
María E. López ◽  
Diego Díaz-Domínguez ◽  
Giovanna Cáceres ◽  
Grazyella M. Yoshida ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Illumina Hiseq ◽  
Extended Haplotype ◽  
Commercial Interest ◽  
Snp Data ◽  
Improvement Programs ◽  
Signatures Of Selection ◽  
Log Ratio

AbstractNile tilapia (Oreochromis niloticus Linnaeus, 1758) belong to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs in this species began in the late 1980s to enhance some traits of commercial interest. The resulting domestication process of Nile tilapia may have modified the genome through selective pressure, leaving signals that can be detected at the molecular level. In this work, signatures of selection were identified using genome-wide SNP data, using two complementary methods based in extended haplotype homozygosity (EHH)._Whole-genome sequencing of 326 individuals from three strains (A, B and C) of farmed tilapia from two countries (Brazil and Costa Rica) was carried out using Illumina HiSeq 2500 technology. After applying conventional SNP-calling and quality-control pipelines, a total of ~1.3M high-quality SNPs were inferred and used as input for the Integrated Haplotype Score (|iHS|) and standardized log-ratio of integrated EHH between pairs of populations (Rsb) methods. We detected 16, 174 and 96 candidate genes subjected to selection in strain A, B, and C, respectively. These candidate genes represent putative genomic landmarks that could contain functions of biological and commercial interest.

scholarly journals Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
María I. Cádiz ◽  
María E. López ◽  
Diego Díaz-Domínguez ◽  
Giovanna Cáceres ◽  
Grazyella M. Yoshida ◽  
...  
Keyword(s):  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Whole Genome ◽  
Nile Tilapia Oreochromis Niloticus ◽  
Signatures Of Selection

scholarly journals Development and Validation of an Open Access SNP Array for Nile Tilapia (Oreochromis niloticus)

2020 ◽  
Vol 10 (8) ◽  
pp. 2777-2785 ◽  
Author(s):  
Carolina Peñaloza ◽  
Diego Robledo ◽  
Agustin Barría ◽  
Trọng Quốc Trịnh ◽  
Mahirah Mahmuddin ◽  
...  
Keyword(s):  
Open Access ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Sequence Data ◽  
Snp Array ◽  
Whole Genome Sequence ◽  
Farmed Fish ◽  
Snp Data ◽  
Genetically Improved ◽  
Development And Validation

Tilapia are among the most important farmed fish species worldwide, and are fundamental for the food security of many developing countries. Several genetically improved Nile tilapia (Oreochromis niloticus) strains exist, such as the iconic Genetically Improved Farmed Tilapia (GIFT), and breeding programs typically follow classical pedigree-based selection. The use of genome-wide single-nucleotide polymorphism (SNP) data can enable an understanding of the genetic architecture of economically important traits and the acceleration of genetic gain via genomic selection. Due to the global importance and diversity of Nile tilapia, an open access SNP array would be beneficial for aquaculture research and production. In the current study, a ∼65K SNP array was designed based on SNPs discovered from whole-genome sequence data from a GIFT breeding nucleus population and the overlap with SNP datasets from wild fish populations and several other farmed Nile tilapia strains. The SNP array was applied to clearly distinguish between different tilapia populations across Asia and Africa, with at least ∼30,000 SNPs segregating in each of the diverse population samples tested. It is anticipated that this SNP array will be an enabling tool for population genetics and tilapia breeding research, facilitating consistency and comparison of results across studies.

scholarly journals High-throughput single nucleotide polymorphism (SNP) discovery and validation through whole-genome resequencing of hundreds of individuals in Nile tilapia (Oreochromis niloticus)

2019 ◽  
Author(s):  
J.M. Yáñez ◽  
G. Yoshida ◽  
A. Barria ◽  
R. Palma-Véjares ◽  
D. Travisany ◽  
...  
Keyword(s):  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Site Quality ◽  
Whole Genome ◽  
Snp Discovery ◽  
Genome Resequencing ◽  
Genome Wide ◽  
The World ◽  
Improvement Programs ◽  
Whole Genome Resequencing

ABSTRACTNile Tilapia (Oreochromis niloticus) is the second most important farmed fish in the world and a sustainable source of protein for human consumption. Several genetic improvement programs have been established for this species in the world and so far, they are mainly based on conventional selection using genealogical and phenotypic information to estimate the genetic merit of breeders and make selection decisions. Genome-wide information can be exploited to efficiently incorporate traits that are difficult to measure in the breeding goal. Thus, SNPs are required to investigate phenotype–genotype associations and determine the genomic basis of economically important traits. We performed de novo SNP discovery in three different populations of farmed tilapias. A total of 29.9 million non-redundant SNPs were identified through Illumina (HiSeq 2500) whole-genome resequencing of 326 individual samples. After applying several filtering steps including removing SNP based on genotype and site quality, presence of Mendelian errors, and non unique position in the genome, a total of high quality 50,000 SNP were selected for validation purposes. These SNPs were highly informative in the three populations analyzed showing between 43,869 (94%) and 46,139 (99%) SNP in HWE; 37,843 (76%) and 45,171(90%) SNP with a MAF higher than 0.05 and; 43,450 (87%) and 46,570 (93%) SNPs with a MAF higher than 0.01. The final list of 50K SNPs will be very useful for the dissection of economically relevant traits, enhancing breeding programs through genomic selection as well as supporting genetic studies in farmed populations Nile tilapia using dense genome-wide information.

The effect of vaccination in controling bacterial disease caused by Aeromonas hydrophila in nile tilapia (Oreochromis niloticus)

2014 ◽  
pp. 27
Author(s):  
Arne A Ratulangi ◽  
Reiny Tumbol ◽  
Hengky Manoppo ◽  
Henneke Pangkey
Keyword(s):  
Survival Rate ◽  
Aeromonas Hydrophila ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Bacterial Disease ◽  
Immersion Method ◽  
Nile Tilapia Oreochromis Niloticus ◽  
Different Ages ◽  
Motile Aeromonas Septicaemia

This study aims to apply vaccination against bacterial disease. The purpose of vaccination is to trigger the immune respone both non-specific and specific of fish against bacteria Motile Aeromonas Septicaemia (MAS) caused by Aeromonas hydrophila. The vaccination for fish with different ages: 2-3 weeks and 5 weeks were done using immersion method. The fish were re-vaccinated (booster) after two weeks of the first vaccination. The survival rate was < 50 % for juveniles 2-3 weeks and > 50% for juveniles 5 weeks. Survival rate for juveniles 5 weeks was higher than juveniles of 2-3 weeks. This shows that organs of juveniles of 5 weeks were more complete than the 2-3 weeks juveniles. The age of fish is one of the important factors for successfully vaccination. Penelitian ini bertujuan untuk melakukan penerapan vaksinasi terhadap penyakit bakterial. Vaksinasi ditujukan untuk merangsang respon kekebalan non- spesifik dan spesifik pada tubuh ikan terhadap penyakit Motile Aeromonas Septicaemia (MAS) yang disebabkan oleh bakteri Aeromonas hydrophila. Vaksin diberikan pada benih ikan nila yang berbeda umur yaitu 2-3 minggu dan 5 minggu dengan menggunakan metode perendaman. Ikan divaksinasi ulang (booster) setelah 2 (dua) minggu dari vaksinasi yang pertama. Prosentase kelangsungan hidup < 50 % untuk benih umur 2-3 minggu dan > 50% untuk benih umur 5 minggu. Jumlah kematian benih umur 2-3 minggu lebih tinggi dari 5 minggu. Hal ini menunjukkan bahwa fungsi organ benih umur 5 minggu telah lebih lengkap dari pada benih umur 2-3 minggu. Umur ikan merupakan salah satu faktor penting penentu keberhasilan suatu kegiatan vaksinasi.

Incidence and molecular characterization of fungi and yeast isolated from cultured catfish and Nile tilapia

2020 ◽  
Vol 21 (3) ◽  
pp. 61-66
Author(s):  
Ola Hashem ◽  
Viola Zaki ◽  
Rawia Adawy
Keyword(s):  
Molecular Characterization ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Clarias Gariepinus ◽  
Fungal Species ◽  
High Rate ◽  
Fish Farms ◽  
Isolation And Identification ◽  
Penicillium Spp

Objective: To study the incidence and seasonal dynamics of different fungi affected freshwater fishes in Lake Manzala with molecular identification of the isolated fungi. Animals: 300 Nile tilapia (Oreochromis niloticus) and 300 catfish (Clarias gariepinus). Design: Descriptive study. Procedures: Random samples of Oreochromis niloticus (O. niloticus) and Clarias gariepinus (C. gariepinus) were collected from Manzala fish farms. Clinical and postmortem examination of fish was applied. Isolation and identification of different fungi were performed by conventional methods. Furthermore, the molecular characterization of isolated fungi was carried out. Results: C. gariepinus had a higher rate of infection with different fungal species than O. niloticus. Aspergillus spp. (Aspergillus niger and Aspergillus flavus) were the most fungal isolated from the examined fishes, followed by Penicillium spp. and Candida albicans. Aspergillus spp were detected in all seasons with a higher rate in summer and spring. A. flavus, A. niger, Penicillium spp. and C.albicans isolates were amplified from both C. gariepinus and O. niloticus at the specified molecular weight using PCR. Conclusion and clinical relevance: Fungal infection affected the fish showing different external and internal lesions, all species of Aspergillus were found in all seasons with a high rate in, hot seasons, summer and spring. The Prevalence of Penicillium and C. albicans were also reported. All fungal isolates were identified on the phenotypic and molecular bases.

Effect of low temperature on genomic DNA methylation in Nile tilapia (Oreochromis niloticus)

2013 ◽  
Vol 37 (10) ◽  
pp. 1460 ◽  
Author(s):  
Huaping ZHU ◽  
Maixin LU ◽  
Zhanghan HUANG ◽  
Fengying GAO ◽  
Xiaoli KE ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Low Temperature ◽  
Oreochromis Niloticus ◽  
Genomic Dna ◽  
Nile Tilapia ◽  
Nile Tilapia Oreochromis Niloticus
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