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Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing

Nyinondi, Christer Simon and Mtolera, Matern S. P. and Mmochi, Aviti J. and Lopes Pinto, Fernando A and Houston, Ross D. and De Koning, Dirk-Jan and Palaiokostas, Christos (2020). Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing. Ecology and Evolution. 10 , 10044-10056
[Journal article]

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Abstract

Rufiji tilapia (Oreochromis urolepis urolepis) is an endemic cichlid in Tanzania. In addition to its importance for biodiversity conservation, Rufiji tilapia is also attractive for farming due to its high growth rate, salinity tolerance, and the production of all-male hybrids when crossed with Nile tilapia (Oreochromis niloticus). The aim of the current study was to assess the genetic diversity and population structure of both wild and farmed Rufiji tilapia populations in order to inform conservation and aquaculture practices. Double-digest restriction-site-associated DNA (ddRAD) libraries were constructed from 195 animals originating from eight wild (Nyamisati, Utete, Mansi, Mindu, Wami, Ruaha, Kibasira, and Kilola) and two farmed (Bwawani and Chemchem) populations. The identified single nucleotide polymorphisms (SNPs;n = 2,182) were used to investigate the genetic variation within and among the studied populations. Genetic distance estimates (F-st) were low among populations from neighboring locations, with the exception of Utete and Chemchem populations (F-st = 0.34). Isolation-by-distance (IBD) analysis among the wild populations did not detect any significant correlation signal (r = .05;p-value = .4) between the genetic distance and the sampling (Euclidean distance) locations. Population structure and putative ancestry were further investigated using both Bayesian (Structure) and multivariate approaches (discriminant analysis of principal components). Both analysis indicated the existence of three distinct genetic clusters. Two cross-validation scenarios were conducted in order to test the efficiency of the SNP dataset for discriminating between farmed and wild animals or predicting the population of origin. Approximately 95% of the test dataset was correctly classified in the first scenario, while in the case of predicting for the population of origin 68% of the test dataset was correctly classified. Overall, our results provide novel insights regarding the population structure of Rufiji tilapia and a new database of informative SNP markers for both conservation management and aquaculture activities.

Authors/Creators:Nyinondi, Christer Simon and Mtolera, Matern S. P. and Mmochi, Aviti J. and Lopes Pinto, Fernando A and Houston, Ross D. and De Koning, Dirk-Jan and Palaiokostas, Christos
Title:Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing
Year of publishing :2020
Volume:10
Page range:10044-10056
Number of Pages:13
ISSN:2045-7758
Language:English
Publication Type:Journal article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
Keywords:ddRAD-seq, genetic diversity, Rufiji tilapia
URN:NBN:urn:nbn:se:slu:epsilon-p-107731
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-107731
Additional ID:
Type of IDID
DOI10.1002/ece3.6664
Web of Science (WoS)000560354200001
ID Code:17947
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: SLUpub Connector
Deposited On:27 Oct 2020 11:11
Metadata Last Modified:27 Oct 2020 11:21

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