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
[Research 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 | ||||||
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Title: | Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing | ||||||
Series Name/Journal: | Ecology and Evolution | ||||||
Year of publishing : | 2020 | ||||||
Volume: | 10 | ||||||
Page range: | 10044-10056 | ||||||
Number of Pages: | 13 | ||||||
ISSN: | 2045-7758 | ||||||
Language: | English | ||||||
Publication Type: | Research 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: |
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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: | 15 Jan 2021 19:44 |
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