GBS represents a novel application of NGS protocols  for discovering Single Nucleotide Polymorphism (SNP) markers and performing low-cost, high-throughput genotyping studies. This approach reduces genome complexity with restriction enzymes (REs) in high-diversity, large genome species. GBS offers the advantage of obtaining genotypes and markers from various genetic resources or breeding groups by simultaneously sequencing multiple samples at once. The GBS can be effectively utilized in various  genetic studies, including Genome-Wide Association Studies (GWAS) and Quantitative Trait Loci (QTL) mapping.

▶ AMOVA (Analysis of Molecular Variance)

To assess the partitioning of genetic variation within and among populations.

▶ Population-specific FST

To estimate the inbreeding coefficient (population-specific FIS & population-specific FST).

▶ Population structure

To investigate the genetic composition and organization of populations and to identify and quantify the presence of subgroups or distinct clusters within a population.

▶ Phylogenetic tree

 To visually represent the evolutionary relationships and common ancestry among a group of organisms, species, or genes.

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▶ PCA, DAPC

Principal Component Analysis (PCA) and Discriminant Analysis of Principal Components (DAPC) utilize GBS-based SNP markers to generate plots for visualizing genetic structure among groups.

▶ Pairwise Fst

To quantify the genetic differentiation between two populations or groups. Fst stands for "Fixation Index," and it provides insights into the extent of genetic divergence between populations based on genetic variation.

▶ Genetic diversity indices

To quantify the extent of genetic diversity within and among populations using various indices such as Effective Population Size (Ne), Observed Heterozygosity (Ho), Expected Heterozygosity (He) and Fixation Index (FIS). among populations.

▶ Fst outlier analysis 

To identify genetic loci that exhibit unusual patterns of differentiation (outliers) between populations and assess whether these outliers are indicative of natural selection, implying that certain genomic regions may have been subject to the influence of selection forces, leading to genetic differentiation beyond what is expected by neutral evolutionary processes. 

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