Genomic selection accelerates sustainable long-term genetic gain in Eritrean indigenous Barentu chicken: A MoBPS simulation study

Indigenous chickens dominate Eritrea’s flock but have low productivity, necessitating genetic improvement. This study evaluated the long-term potential of traditional and genomic selection for developing a specialized egg-laying Barentu indigenous chicken ecotype. A stochastic simulation was conducted using Modular Breeding Program Simulator over 20 generations of a closed nucleus breeding programme. Selection was based on a breeding objective combining age at first egg, egg number at 12 weeks and residual feed intake into a total merit index. Seven selection scenarios were evaluated according to the selection method and the proportion of female candidates genotyped. The scenarios were compared based on cumulative genetic gain, accuracy of estimated breeding values, rate of inbreeding and efficiency of genetic gain relative to inbreeding. Genomic selection consistently produced greater genetic improvement than traditional pedigree-based selection, with genetic gain increasing by 29% in males and 26% in females. The highest accuracy of estimated breeding values was achieved when all selection candidates were genotyped, while accuracy was lowest under traditional pedigree-based selection and when only 25% of females were genotyped. Traditional selection resulted in the lowest rate of inbreeding, whereas genotyping only 25% of females produced the highest inbreeding. Genomic selection achieved the greatest genetic gain relative to inbreeding, exceeding traditional selection by 19–23%. Single-step genomic selection achieved up to 90% of the genetic gain obtained through genomic selection. In conclusion, genomic selection, particularly single-step genomic selection, offers considerable potential to accelerate genetic improvement and support the conservation of genetic diversity.