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.

Gyrodactylus malalai sp. nov. (Monogenea, Gyrodactylidae) from Nile tilapia, Oreochromis niloticus (L.) and Redbelly tilapia, Tilapia zillii (Gervais) (Teleostei, Cichlidae) in the Lake Turkana, Kenya

2012 ◽  
Vol 57 (2) ◽  
Author(s):  
Iva Přikrylová ◽  
Blažek Radim ◽  
Milan Gelnar
Keyword(s):  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Sequence Data ◽  
Marginal Hook ◽  
Lake Turkana ◽  
African Countries ◽  
Tilapia Zillii ◽  
Nile Tilapia Oreochromis Niloticus ◽  
Sarotherodon Galilaeus ◽  
Partial 18S

AbstractGyrodactylus malalai sp. nov. is described from the fin surface of cichlid fishes Oreochromis niloticus (L.) and Tilapia zillii (Gervais) caught in Lake Turkana (Kenya). The new species morphologically resembles Gyrodactylus nyanzae Paperna, 1973, but can be readily distinguished by the shape of the marginal hook sickles and the size of its hamuli. The sequence data of rDNA spanning partial 18S, internal transcribe spacer 1 and 2 and the 5.8S gene is unique within GenBank. Genetically, as most similar Gyrodactylus ergensi Přikrylová, Matějusová, Musilová et Gelnar, 2009 was found (97.5%). Moreover, a specimen of G. cichlidarum from O. niloticus, and a specimen G. ergensi from Sarotherodon galilaeus (L.) were collected during sampling in Kenya. Likewise, additional sampling of O. niloticus from the Blue Nile in Sudan revealed the presence of the newly described species. These findings represent the first records of gyrodactylids in both African countries.

scholarly journals EKSISTENSI USAHA PETANI BUDIDAYA IKAN NILA (OREOCHROMIS NILOTICUS) DI DESA WARUKAPAS KABUPATEN MINAHASA UTARA PROVINSI SULAWESI UTARA

2015 ◽  
Vol 3 (6) ◽  
Author(s):  
Farra F. Wullur ◽  
Florence V. Longdong ◽  
Martha P. Wasak
Keyword(s):  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Descriptive Analysis ◽  
Secondary Data ◽  
Primary Data ◽  
General State ◽  
Farmed Fish ◽  
Purposive Sampling ◽  
North Sulawesi ◽  
Freshwater Aquaculture

Abstract Aquaculture in Indonesia is one of the important components in the fisheries sector, one of the nile tilapia farming. North Sulawesi is generally known as a producer of freshwater farmed fish. The purpose of this study to the location to see the general state of research, the general state of tilapia farming, and to determine the existence of farming nile tilapia fish farmers. This study took place in the village Warukapas North Minahasa regency of North Sulawesi province, starting from September 2012 until January of 2013. Existence is a dynamic process, the cultivation can be said to exist if the activities had been developed in terms of both quality and quantity. The method used has research base descriptive case studies, data collection is the purposive sampling method, the data type used is primary data and secondary data. The method used in this study is a descriptive analysis of qualitative and quantitative descriptive. Size of the pool for maintenance between 1500 m2 to 15,000 m2 Seeds was originally purchased from the Institute of Freshwater Aquaculture Tatelu (BBAT) and Surabaya, now the seeds of its own cultivation. Farmers in the Warukapas village most have their own capital, the initial capital used continuously (sustained) farmers have 1 person workforce. Income earned any tilapia farmers depends how many fish are harvested. Spending just to buy food and basic necessities for daily family life - today. The magnitude of the average profit was 35,604,333. Nile tilapia aquaculture farmers in the Warukapas village which can be said to exist is a farmer who has been farming activities ± 2 years, and still exist in the culture business until now. Keyword: nile tilapia (oreochromis niloticus), existence, farmers, farming Abstrak Perikanan budidaya di Indonesia merupakan salah satu komponen yang penting di sektor perikanan, salah satunya budidaya ikan nila. Sulawesi Utara umumnya dikenal sebagai penghasil ikan budidaya air tawar. Tujuan dari penelitian ini untuk untuk melihat keadaan umum lokasi penelitian, keadaan umum usaha budidaya ikan nila, dan untuk mengetahui eksistensi usaha budidaya ikan nila dari petani ikan. Penelitian ini bertempat di desa Warukapas kabupaten Minahasa Utara Provinsi Sulawesi Utara, dimulai dari bulan September 2012 sampai dengan bulan januari 2013. Eksistensi adalah suatu proses yang dinamis, usaha budidaya dapat dikatakan tetap eksis apabila kegiatan tersebut mengalami perkembangan baik dari segi kualitas maupun kuantitasnya. Metode penelitian yang digunakan memiliki dasar penelitian studi kasus yang bersifat deskriptif, pengambilan data adalah metode purposive sampling, Jenis data yang dipakai adalah data primer dan data sekunder. Metode yang digunakan dalam penelitian ini adalah analisis deskriptif kualitatif dan deskriptif kuantitatif. Ukuran kolam untuk pemeliharaan antara 1500 m2 sampai 15.000 m2 Benih pada awalnya dibeli dari Balai Budidaya Air Tawar Tatelu (BBAT) dan Surabaya, sekarang benih dari hasil budidaya sendiri. Petani di desa Warukapas sebagian besar memiliki modal sendiri, modal awal digunakan secara continue (berkelanjutan) pembudidaya mempunyai tenaga kerja 1 orang. Pendapatan yang diperoleh setiap petani ikan nila tergantung berapa banyak jumlah ikan yang dipanen,. Pengeluaran hanya untuk membeli pakan dan kebutuhan pokok untuk kehidupan keluarga sehari – hari. Besarnya keuntungan rata–rata adalah 35.604.333. Petani budidaya ikan nila di desa Warukapas yang dapat dikatakan eksis adalah petani yang sudah melakukan kegiatan usaha budidaya ± 2 tahun, dan masih eksis dalam usaha budidaya tersebut sampai sekarang. Kata kunci : Ikan nila (Oreochromis niloticus), Eksistensi, Petani, Budidaya

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 Expanding the conservation genomics toolbox: incorporating structural variants to enhance functional studies for species of conservation concern

2021 ◽  
Author(s):  
Jana Wold ◽  
Stephanie Galla ◽  
David Eccles ◽  
Carolyn J. Hogg ◽  
Klaus-Peter Koepfli ◽  
...  
Keyword(s):  
Functional Diversity ◽  
Threatened Species ◽  
Conservation Management ◽  
Sequence Data ◽  
Regulation Of Gene Expression ◽  
Whole Genome Sequence ◽  
Structural Variants ◽  
Conservation Genomics ◽  
Genomic Context ◽  
Snp Data

Increased capability in the conservation genomics community, combined with decreased sequencing costs, is providing new opportunities for the application of whole-genome sequence data to enhance species recovery. Indeed, assessments of genome-wide diversity based on SNP data are already informing the conservation management of threatened species around the world. However, SNP data alone may not sufficiently capture all of the information necessary for the effective conservation management of critically endangered species that suffer from severe inbreeding depression. For threatened species that require significant intervention, it is critical that we as conservation genomicists expand our repertoire to include assessments of functional diversity. Structural variants are a likely source of functional diversity, as their frequency and genomic context affect the dosage and regulation of gene expression through mechanisms that alter genome organization and impact fitness. In this future-focused Opinion, we leverage the existing literature - predominantly focused on model and agricultural species - to identify pan-genomic and chromosomic approaches for readily characterizing structural variants and to consider how integrating these into the conservation genomics toolbox will transform the way we manage some of the world’s most threatened species.

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