Genomic analysis of 10 years of artificial selection in community-based breeding programs in two Ethiopian indigenous sheep breeds

Summary

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.