Species-informative SNP markers for characterising freshwater prawns of genus Macrobrachium in Cameroon

Abstract

Single Nucleotide Polymorphisms (SNPs) are now popular for a myriad of applications in animal and plant species including, ancestry assignment, conservation genetics, breeding, and traceability of animal products. The objective of this study was to develop a customized cost-effective SNP panel for genetic characterisation of Macrobrachium species in Cameroon. The SNPs identified in a previous characterization study were screened as viable candidates for the reduced panel. Starting from a full set of 1,814 SNPs, a total of 72 core SNPs were chosen using conventional approaches: allele frequency differentials, minor allele frequency profiles, and Wright's Fst statistics. The discriminatory power of reduced set of informative SNPs were then tested using the admixture analysis, principal component analysis, and discriminant analysis of principal components. The panel of prioritised SNP markers (i.e., N = 72 SNPs) distinguished Macrobrachium species with 100% accuracy. However, large sample size is needed to identify more informative SNPs for discriminating genetically closely related species, including M. macrobrachion versus M. vollenhovenii and M. sollaudii versus M. dux. Overall, the findings in this study show that we can accurately characterise Macrobrachium using a small set of core SNPs which could be useful for this economically important species in Cameroon. Given the results obtained in this study, a larger independent validation sample set will be needed to confirm the discriminative capacity of this SNP panel for wider commercial and research applications.

Fig 1. Pictures of seven Macrobrachium species in the coastal area of Cameroon identified based on morphological analysis using [10, 31] keys.

Fig 2. An overview of the identification and validation of ’private SNPs’ or informative SNPs.

Step 1: a total of 52,834 SNPs were generated from genotyping by sequencing of Macrobrachium species. Step 2: the SNPs from ‘Step 1’ were screened for quality parameters leaving a total of 1,814 SNPs for further analysis. Step 3: the SNPs from ‘Step 2’ were used to prioritise 178 informative SNPs based on allele frequency estimates. Step 4: a total of 72 high-quality SNPs (‘private SNPs’) were selected from the 178 SNPs in ‘Step 3’ based on repeat resampling approach. Step 5: the SNPs from ‘Step 4’ were “validated” using three methods: a) PCA–principal component analysis; b) Admixture, and c) DAPC–discriminant analysis of principal components. MAF–minor allele frequency.

Fig 3. Distribution of minor allele frequency (MAF) for different Macrobrachium species: M. dux, M. macrobrachion, M. sollaudii, M. vollenhovenii, M. chevalieri; M. felicinum, and M. sp.

Fig 4. Phylogenetic tree obtained using 72 private SNPs for Macrobrachium species: M. dux, M. macrobrachion, M. sollaudii, M. vollenhovenii, M. chevalieri; M. felicinum, and M. sp.

The phylogenetic tree for these Macrobrachium species using a larger set of SNPs (N = 1,814) is provided in [19].

Fig 5. PCA (left plot) and DAPC (right plot) obtained from using a full set of SNPs (N = 1,814).

PCA–principal component analysis; DAPC–discriminant analysis of principal components. M_ch–M. chevalieri;M_dx–M. dux;M_fe–M. felicinum; M_ma–M. macrobrachion; M_so–M. sollaudii; M_sp–M. sp; M_vo–M. vollenhovenii.

Fig 6. PCA (left plot) and DAPC (right plot) obtained from using the reduced set of ‘private SNPs’ (N = 72 SNPs, called ‘private SNPs80’ panel; see Methods).

PCA–principal component analysis; DAPC–discriminant analysis of the principal components. M_ch–M. chevalieri; M_dx–M. dux; M_fe–M. felicinum; M_ma–M. macrobrachion; M_so–M. sollaudii; M_sp–M. sp; M_vo–M. vollenhovenii.

Fig 7. Cluster membership classification of Macrobrachium species and the Bayesian information criterion (BIC) plot obtained from the full set SNPs (N = 1,814) using the Adegenet package assuming four (K = 4) and five (K = 5) populations.

Each bar in the admixture plot (left) represents an individual: M.ch–M. chevalieri; M.dx–M. dux; M.so–M. sollaudii; M.fe–M. felicinum; M.sp–M. sp; M.ma–M. macrobrachion; M.vo–M. vollenhovenii.

Fig 8. Cluster membership classification of Macrobrachium species and the Bayesian information criterion (BIC) plot obtained from a reduced set of informative or ‘private SNPs’ (N = 72 SNPs) using Adegenet package [36] assuming five clusters (K = 5).

Each bar in the admixture plot (left) represents an individual: M.ch–M. chevalieri; M.dx–M. dux; M.so–M. sollaudii; M.fe–M. felicinum; M.sp–M. sp; M.ma–M. macrobrachion; M.vo–M. vollenhovenii.