Computational protocol: Genetic diversity and phylogenetic relationships in local cattle breeds of Senegal based on autosomal microsatellite markers

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Protocol publication

[…] The genetic variability of microsatellite loci and populations was measured by estimating a set of characteristic parameters of genetic polymorphism. Before the estimation of these measures, the presence of null allele across loci was checked using the program Micro-Checker version 2.2.3 []. Allele frequencies, observed number of alleles per locus (Na), observed heterozygosity (HO), unbiased expected heterozygosity (HE) [], gene diversity of Nei (HS) [], FIS (f) (amount of inbreeding within a population of Weir and Cockerham []) were estimated using Genetix version 4.05.2 [] and Fstat version []. The significance test of values of the fixation index (FIS) was tested using methods of jackknifing and bootstrapping over loci after 1000 ­permutations of alleles within a population. The allelic richness of a breed is the measure of the number of allele’s independent of sample size which is estimated per locus (Rt) and population (Rs) using Fstat version []. The principle of “Rarefaction” of Hurlbert (1971) suggested by El-Mousadik and Petit [] was applied to correct the observed number of alleles according to the sample size. Other parameters such as the number of private alleles (NPA, alleles found in a single breed), effective number of alleles (Ne), Shannon’s information index (I) were determined using GenAlEx version 6.5 []. The polymorphic information content (PIC, a measure of informativeness of a marker, calculated according to Botstein et al. []) was estimated using Cervus 3.0.6, Field Genetics Ltd. []. The significant differences of Shannon’s Information index (I) and PIC between breeds were tested using t-test implemented in STATVIEW version 5.0 [] at a significance level of 5%.Exact tests for deviations from the Hardy-Weinberg equilibrium (HWE) were performed for each locus, in each population and for all populations using a Markov Chain Monte Carlo simulation (20 batches, 1,000,000 iterations per batch and a dememorization number of 10,000) implemented in Genepop 4 version 4.2.2 []. The significance of probabilities for all loci and populations was determined using Fisher’s method.Test of the genotypic linkage disequilibrium was estimated between all pairs of loci using a G statistic (log - likelihood ratio) implemented in Fstat version [] to test the significance of association between genotypes at pairs of loci in each sample. The p-values of genotypic disequilibrium were based on 550,000 permutations. Adjusted p-value for 5%, 1% and 0.1% nominal levels was 0.000091, 0.000018, and 0.000002, respectively. [...] Genetic relationships among breeds were explored by multivariate statistical analysis and phylogenetic reconstruction. Genetic distances of Nei et al. [] DA were calculated through alleles frequencies to determine the genetic relationships among breeds using Genetix version 4.05.2. Moreover, an unbiased standard genetic distance of Nei [] (DS), was calculated using the GenAlEx software version 6.5.To condense the genetic variation revealed for the panel of 11 microsatellites loci, a multivariate analysis of microsatellite allele frequencies principal components analysis (PCA) was performed from the covariance matrix DS using the GenAlEx program version 6.5.Phylogenetic trees were generated using genetic distances that are suitable for numeric data. For this, two dendrograms of populations were constructed first from the distance matrix of Nei et al. [] (DA) using the unweighted pair group method with arithmetic mean (UPGMA) [] and the second from the chord distance (DC) of Cavalli-Sforza and Edwards [] using the Neighbor-Joining (NJ) method of Nei []. We use genotypes of Syncerus caffer (African buffalo) from eight microsatellite data (ETH10, ETH152, ETH225, HEL1, HEL9, INRA037, INRA063, and TGLA53) [] to root population trees. The construction was performed using Populations version 1.2.28 []. Dendrograms were visualized using Fig Tree version 1.4.2 []. […]

Pipeline specifications

Software tools GenAlEx, Cervus, Genepop, GENETIX
Applications Phylogenetics, Population genetic analysis
Organisms Bos taurus, Bos indicus, Nanger dama
Chemicals Taurine