Estimating microsatellite based genetic diversity in Rhode Island Red chicken

Document Type: Full paper (Original article)


Molecular Genetics Laboratory, Avian Genetics and Breeding Division, Central Avian Research Institute, Izatnagar 243122, Bareilly, Uttar Pradesh, India


This study aimed to estimate microsatellite based genetic diversity in two lines (the selected RIRS and control line RIRC) of Rhode Island Red (RIR) chicken. Genomic DNA of 24 randomly selected birds maintained at Central Avian Research Institute (India) and 24 microsatellite markers were used. Microsatellite alleles were determined on 6% urea-PAGE, recorded using GelDoc system and the samples were genotyped. Nei’s heterozygosity and Botstein’s polymorphic information content (PIC) at each
microsatellite locus were estimated. Wright’s fixation indices and gene flow were estimated using POPGENE software. All the microsatellite loci were polymorphic and the estimated PIC ranged from 0.3648 (MCW0059) to 0.7819 (ADL0267) in RIRS and from 0.2392 (MCW0059) to 0.8620 (ADL0136) in RIRC. Most of the loci were highly informative (PIC>0.50) in the both lines, except for five loci in RIRS and six loci in RIRC line. Nei’s heterozygosity per locus ranged from 0.4800 (MCW0059) to 0.8056 (ADL0267) in RIRS and from 0.2778 (MCW0059) to 0.875 (ADL0136) in RIRC. Out of 24 loci, 15 (62.5%) in RIRS and 14 loci (58.33%) in RIRC revealed moderate to high negative FIS index indicating heterozygote excess for these loci in corresponding lines, but the rest revealed positive FIS indicating heterozygosity deficiency. A mean FIS across the both lines indicated overall 10.77% heterozygosity deficit and a mean FIT indicated 17.19% inbreeding co-efficient favoring homozygosity over the two lines. The mean FST indicated that 10.18% of the microsatellite variation between the two lines was due to their genetic difference.