Effects of 10 years of selection in community-based breeding programs (CBBPs) on the genomes of Ethiopian indigenous sheep

Abstract

The genomics revolution has made it possible to investigate genome dynamics arising from natural and artificial phenomena. Community-based breeding programs (CBBPs) have been advocated as the go-to strategy for genetic improvement of local breeds in smallholder farms in developing countries. Since 2009, CBBPs have been implemented for Ethiopian Bonga and Menz sheep to increase growth rates resulting in significant genetic gains in 6-months weight. With the hypothesis that selection could be impacting their genomes, we systematically screened for possible genome changes in the two breeds by analyzing 600K BeadChip genotype data of 151 individuals (with the highest breeding values for 6-month weights) from CBBP flocks against 98 individuals from non-CBBP flocks. We observed no differences in genetic diversity and in trends in the demographic dynamics between CBBP and non-CBBP flocks. However, selection signature analysis employing ROH, LR-GWAS, FST, XP-EHH and iHS revealed 5 (Bonga) and 9 (Menz) overlapping sweeps, co-localizing with QTLs for production (body size/weight, growth, milk yield), meat/milk quality, and health/parasite resistance, suggesting the decade long selection has just started to impact their genomes although genome-wide genetic differentiation between the CBBP and non-CBBP flocks is not yet clearly evident.