geneHapR

geneHapR performs identification, statistical analysis, and visualization of gene haplotypes to support functional gene dissection and marker-assisted selection.

Key Features:

• Integration of genotype, genomic annotation, and phenotypic variation: Integrates genotype data with genomic annotation and phenotypic variation to link genetic variants to phenotypes and evolutionary relationships.
• Variants visualization and network construction: Provides variants visualization and network construction to represent haplotype relationships and variant patterns.
• Linkage disequilibrium analysis: Implements linkage disequilibrium block analysis to identify non-random associations of alleles across loci.
• Geographical distribution visualization: Visualizes geographical distribution of haplotypes to assess population structure and spatial evolutionary patterns.
• Phenotypic comparison among haplotypes: Performs phenotypic comparisons among haplotypes to associate haplotypes with observable traits and identify superior alleles.

Scientific Applications:

• Marker-Assisted Selection: Clarifies functional-gene haplotypes to aid selection of superior alleles in crop and livestock breeding programs.
• Genetic Research: Enables dissection of gene function and genotype–phenotype relationships through comprehensive haplotype analysis.
• Population Genetics: Supports study of haplotype distribution and evolution across geographical regions to inform population structure and migration analyses.

Methodology:

Integration of genotype, genomic annotation, and phenotypic variation data; statistical assessment of linkage disequilibrium blocks; and visualization of variants, haplotype networks, and geographical haplotype distributions.