Population genetic analysis of aquaculture salmonid populations in China using a 57K rainbow trout SNP array

Zhao, Zixia; Xu, Jian; Xu, Peng; Bai, Qingli; Yang, Shiyong; Jiang, Lin; Chen, Baohua

doi:10.1371/journal.pone.0202582

Cited by 11 publications

(7 citation statements)

References 38 publications

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“…In general, farmed stocks have the tendency to show reduced genetic variability over generations due to artificial selection and a reduced number of breeders in the initial base population [11,46,47,48]. Therefore, it is important to evaluate how the genetic diversity can be maintained when considering the possibility of bottleneck events due to the low effective population size shown in fish farms.…”

Section: Discussionmentioning

confidence: 99%

Assessing Genetic Diversity for a Pre-Breeding Program in Piaractus mesopotamicus by SNPs and SSRs

Mastrochirico-Filho

Pazo

Hata

et al. 2019

Genes

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The pacu (Piaractus mesopotamicus) is a Neotropical fish with remarkable productive performance for aquaculture. Knowledge of genetic resources in Neotropical fish is essential for their applications in breeding programs. The aim of this study was to characterize the genetic diversity of seven farmed populations of pacu which will constitute the basis for a broodstock foundation for coming breeding programs in Brazil. Analysis of one wild population (Paraná River) was used as a reference to compare genetic parameters in the farmed populations. The analyses were performed using 32 single-nucleotide polymorphisms (SNP) and 8 simple sequence repeat (SSR) markers. No significant differences in genetic diversity between populations estimated through the number of alleles and allelic richness, observed heterozygosity, expected heterozygosity, and minimum allele frequency were detected (p > 0.05). Low genetic diversity was observed in all farmed stocks and the wild population. Moreover, we detected low genetic structure when comparing farmed and wild populations for SNPs (FST = 0.07; K = 3) and SSRs (FST = 0.08; K = 2). Analysis of molecular variance (AMOVA) demonstrated that genetic variation was mostly within populations. Kinship analysis showed that most fish farms included related individuals at a proportion of at least 25%. Our results suggest that the basal broodstock for pacu breeding programs should be founded with individuals from different fish farms for higher genetic diversity and to avoid inbreeding risks.

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Section: Discussionmentioning

confidence: 99%

Assessing Genetic Diversity for a Pre-Breeding Program in Piaractus mesopotamicus by SNPs and SSRs

Mastrochirico-Filho

Pazo

Hata

et al. 2019

Genes

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“…The identification of approximately 900 polymorphic sites facilitated studying the genetic structure of wild Mediterranean brown trout populations in Italy and to begin the selection of native broodstocks. Zhang et al [62] used a 57K DNA chip developed for rainbow trout in different salmonid species, and Drywa et al [63] used a SNP array developed for Atlantic salmon to analyze a population of lake brown trout (S. trutta trutta).…”

Section: Next Generation Sequencing (Ngs)mentioning

confidence: 99%

Genetic and Phenotypic Characteristics of the Salmo trutta Complex in Italy

D’Agaro

Gibertoni²,

Marroni

et al. 2022

Applied Sciences

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Salmonid fish have become ecological and research models of study in the field of conservation genetics and genomics. Over the last decade, brown trout have received a high level of interest in research and publications. The term Salmo trutta complex is used to indicate the large number of geographic forms present in the species Salmo trutta. In Europe, the S. trutta complex consists (based on mitochondrial DNA control region analysis) of seven major evolutionary lineages: Atlantic (AT), Mediterranean (ME), Adriatic (AD), Danubian (DA), Marmoratus (MA), Duero (DU) and Tigris (TI). In several nations, the difficulty of identifying some lineages derives from their wide phenotypic and geographic plasticity and the presence of mixed lineages (due to introgressive hybridization with domestic AT populations). In Italy, the S. trutta complex populations living in the Tyrrhenian area and on the main islands (Sicily, Sardinia and Corsica) showed high genetic diversity. Currently, on the Italian Red List, the protected (near threatened) populations are the AD and ME lineages. Recent studies based on traditional (mitochondrial and nuclear markers) and NGS (next-generation sequencing) analyses have clarified some genetic differences between the populations of the Tyrrhenian region, Sicily, Sardinia and Corsica. Native populations in Sardinia belong to the AD lineage, while those living in Corsica are mainly characterized by the AD, MA and ME haplotypes. In Sicily, in the area of the Iblei mountains, an AT lineage (North African) exists. According to some authors, the term Salmo macrostigma should only be used for populations in North Africa. The use of genotyping methods based on mtDNA and nuclear markers and the latest generation sequencing techniques can improve the study of populations and evolutionary lineages in areas where there are overlaps and hybridization phenomena.

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“…Various high-density SNP chips have been developed in recent years for many model species, including commercially important salmonid species, such as rainbow trout and Atlantic salmon [ 38 , 39 , 40 , 41 ]. Despite the limited genomic data resources available for other salmonids, the high sequence similarity between them has indicated that SNP microarrays may be suitable for the study of any member of this fish family, trout included [ 42 , 43 , 44 ].…”

Section: Introductionmentioning

confidence: 99%

Genotyping of Two Mediterranean Trout Populations in Central-Southern Italy for Conservation Purposes Using a Rainbow-Trout-Derived SNP Array

Palombo

Zio

Salvatore

et al. 2021

Animals

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Mediterranean trout is a freshwater fish of particular interest with economic significance for fishery management, aquaculture and conservation biology. Unfortunately, native trout populations’ abundance is significantly threatened by anthropogenic disturbance. The introduction of commercial hatchery strains for recreation activities has compromised the genetic integrity status of native populations. This work assessed the fine-scale genetic structure of Mediterranean trout in the two main rivers of Molise region (Italy) to support conservation actions. In total, 288 specimens were caught in 28 different sites (14 per basins) and genotyped using the Affymetrix 57 K rainbow-trout-derived SNP array. Population differentiation was analyzed using pairwise weighted FST and overall F-statistic estimated by locus-by-locus analysis of molecular variance. Furthermore, an SNP data set was processed through principal coordinates analysis, discriminant analysis of principal components and admixture Bayesian clustering analysis. Firstly, our results demonstrated that rainbow trout SNP array can be successfully used for Mediterranean trout genotyping. In fact, despite an overwhelming number of loci that resulted as monomorphic in our populations, it must be emphasized that the resulted number of polymorphic loci (i.e., ~900 SNPs) has been sufficient to reveal a fine-scale genetic structure in the investigated populations, which is useful in supporting conservation and management actions. In particular, our findings allowed us to select candidate sites for the collection of adults, needed for the production of genetically pure juvenile trout, and sites to carry out the eradication of alien trout and successive re-introduction of native trout.

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Population genetic analysis of aquaculture salmonid populations in China using a 57K rainbow trout SNP array

Cited by 11 publications

References 38 publications

Assessing Genetic Diversity for a Pre-Breeding Program in Piaractus mesopotamicus by SNPs and SSRs

Assessing Genetic Diversity for a Pre-Breeding Program in Piaractus mesopotamicus by SNPs and SSRs

Genetic and Phenotypic Characteristics of the Salmo trutta Complex in Italy

Genotyping of Two Mediterranean Trout Populations in Central-Southern Italy for Conservation Purposes Using a Rainbow-Trout-Derived SNP Array

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