Nyinondi Christer S, Mtolera Matern S P, Mmochi Aviti J, Lopes Pinto Fernando A, Houston Ross D, de Koning Dirk J, Palaiokostas Christos
Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden.
Institute of Marine Sciences University of Dar es Salaam Zanzibar Tanzania.
Ecol Evol. 2020 Aug 18;10(18):10044-10056. doi: 10.1002/ece3.6664. eCollection 2020 Sep.
Rufiji tilapia () 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 (). 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; = 2,182) were used to investigate the genetic variation within and among the studied populations. Genetic distance estimates ( ) were low among populations from neighboring locations, with the exception of Utete and Chemchem populations ( = 0.34). Isolation-by-distance (IBD) analysis among the wild populations did not detect any significant correlation signal ( = .05; -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.
鲁菲吉罗非鱼（）是坦桑尼亚特有的丽鱼科鱼类。除了对生物多样性保护具有重要意义外，鲁菲吉罗非鱼因其生长速度快、耐盐性强以及与尼罗罗非鱼（）杂交时能产生全雄杂种而对养殖也具有吸引力。本研究的目的是评估野生和养殖的鲁菲吉罗非鱼种群的遗传多样性和种群结构，以便为保护和水产养殖实践提供信息。从来自8个野生种群（尼亚米萨蒂、乌泰特、曼西、明杜、瓦米、鲁阿哈、基巴西拉和基洛拉）和2个养殖种群（布瓦瓦尼和切姆切姆）的195只动物构建了双酶切限制性位点关联DNA（ddRAD）文库。所鉴定的单核苷酸多态性（SNP； = 2182）用于研究研究种群内和种群间的遗传变异。相邻地点种群之间的遗传距离估计值（）较低，但乌泰特和切姆切姆种群除外（ = 0.34）。野生种群之间的距离隔离（IBD）分析未检测到遗传距离与采样（欧几里得距离）地点之间有任何显著的相关信号（ = 0.05；-值 = 0.4）。使用贝叶斯方法（Structure）和多变量方法（主成分判别分析）进一步研究了种群结构和假定祖先。两种分析均表明存在三个不同的遗传簇。进行了两种交叉验证方案，以测试SNP数据集区分养殖和野生动物或预测来源种群的效率。在第一种方案中，约95%的测试数据集被正确分类，而在预测来源种群的情况下，68%的测试数据集被正确分类。总体而言，我们的结果为鲁菲吉罗非鱼的种群结构提供了新的见解，并为保护管理和水产养殖活动提供了一个新的信息丰富的SNP标记数据库。
