Genetic variants associated with reduced body size in indigenous chickens of Eritrea: A genome-wide association study

Indigenous chickens in Eritrea are raised mainly in low-input village systems and show marked variation in body size, including reduced body size phenotype, a trait associated with reduced feed consumption, thermotolerance, disease resistance, and adaptability to resource-limited environments. This study aimed to identify genomic regions associated with reduced body size using a genome-wide association study (GWAS) in Eritrean chicken ecotypes. Blood samples from 384 ICs across 16 ecotypes (21 to 24 birds per ecotype) were genotyped using DArTseq technology. Three putative short-bodied ecotypes, Barentu (BAR), Foro (FORO), and Gogne (GOG), were compared with five heavier control ecotypes: Fshe-Mrara (FM), Adi-Tekeliezan (ADTEK), Emni-Haili (HAYL), Dekemhare (DEKE), and Adikeyh (KEIH). After filtering for individual missingness, marker call rate, and minor allele frequency, 141 birds and 42,356 SNP remained. Population structure was evaluated by principal component analysis and ADMIXTURE. Exploratory case-control GWAS were conducted for each putative reduced-body-size ecotype and for the 3 ecotypes combined. Complementary quantitative-trait GWAS used body weight, body length, back length, and shank length was carried out. Linear mixed models implemented in GEMMA included sex as a fixed effect and genomic kinship as a random effect. The first 2 principal components showed extensive ancestry sharing, although GOG was more differentiated. Ecotype-specific analyses identified significant regions near CDK6, BDNF, FOXP1, TNS3, and LGR4 in FORO; EIF2AK2, NANP, MDH1, UGP2 and FGF13 in GOG; and HMGA2, IGF2, BRSK1 and SUCNR1 in BAR. The combined analysis showed no genome-wide significant variants but revealed suggestive signals near ASAP1, EIF2AK2, and FOXP1, indicating a polygenic and ecotype-specific architecture. Overlapping candidate genes across analyses included TH (common to all) and EIF2AK2 (present in all ecotypes except FORO). Quantitative-trait analyses detected a single significant SNP within CACNB4 for back length, but none for the other traits. Overall, reduced body size in Eritrean IC appears to be a complex trait controlled by multiple loci, involving both conserved growth regulators and genes related to metabolic efficiency and environmental adaptation. These findings provide a genomic basis for future breeding strategies to improve productivity, resilience and sustainability of village poultry production systems in resource-limited regions of Eritrea.