Overview of the HITSNP framework. (A) The functionality of the “feature SNP screening” module. This module takes genotype data and corresponding breed information of the samples as input. It outputs the selected feature SNPs and provides evaluation results of breed diversity based on the feature SNPs. (B) The “ancestry estimation” module estimates the number of ancestral breeds and the specific ancestral breeds of the hybrid population. Input*: The purebred and classifier I are derived from the “feature SNP screening” output. Simulated hybrids are generated based on the inputs of “feature SNP screening” (purebred data). HITSNP extracts feature SNP information from the genotype data of purebreds and simulated hybrids, which are then used as input for classifier I. (C) The “minimum subset selection” module selects the smallest possible feature SNPs set with the capability of breed discrimination. Input**: HITSNP extracts the feature SNPs identified in “feature SNP screening” from the initial input, which are then used as input for the sequential forward selection (SFS) method.
