Estimating microsatellite based genetic diversity in Rhode Island Red chicken

Area of Science:

• Animal Genetics
• Poultry Science
• Molecular Ecology

Background:

• Rhode Island Red (RIR) chickens are a globally important breed.
• Understanding genetic diversity is crucial for effective conservation and breeding programs.
• Microsatellite markers offer a powerful tool for assessing genetic variation within and between populations.

Purpose of the Study:

• To estimate microsatellite-based genetic diversity in selected (RIR(S)) and control (RIR(C)) lines of RIR chickens.
• To assess genetic variation using polymorphic information content (PIC) and heterozygosity.
• To evaluate population genetic parameters including fixation indices (FIS, FIT, FST) and gene flow.

Main Methods:

• Genomic DNA extraction from 48 RIR chickens (24 RIR(S), 24 RIR(C)).
• Genotyping using 24 polymorphic microsatellite markers analyzed via 6% urea-PAGE.
• Estimation of genetic diversity parameters using Nei's heterozygosity, PIC, and Wright's fixation indices via POPGENE software.

Main Results:

• All microsatellite loci were polymorphic, with PIC values ranging from 0.2392 to 0.8620.
• Nei's heterozygosity per locus varied from 0.2778 to 0.875 across both lines.
• A significant heterozygote excess was observed at most loci (FIS < 0), indicating heterozygosity deficit overall (mean FIS = 10.77%) and inbreeding (mean FIT = 17.19%).
• Genetic differentiation between the two lines (FST) accounted for 10.18% of the microsatellite variation.

Conclusions:

• Both RIR chicken lines exhibit substantial genetic diversity, with most loci being highly informative.
• The observed heterozygote excess suggests potential balancing selection or other evolutionary forces.
• A moderate level of inbreeding and genetic differentiation exists between the selected and control lines, warranting consideration in breeding strategies.