Evaluation of selection response in indigenous Kedu chickens using phenotype-genotype integrated under low-resource breeding systems

Abstract

Background: Genetic improvement of indigenous chickens in low- and middle-income countries are commonly constrained by limited population size, incomplete pedigree records, and restricted access to advanced genomic tools. Under such conditions, integrating phenotypic selection with targeted genotypic validation may provide a practical approach for genetic improvement. Aim: This study aimed to evaluate selection response in a closed population of Kedu chickens across 3 generations (G0–G2) by integrating phenotypic and genotypic data evaluation. Methods: This study integrated phenotypic and genetic evaluations to assess selection response across 3 generations of Kedu chickens, namely the base generation (G0), first generation (G1), and second generation (G2). Selection was conducted using a truncation selection scheme based on body weight (BW) measured at 30 days of age. To identify growth related candidate genes, a systematic literature review was first performed. Three candidate genes associated with growth regulation, namely growth hormone (GH), insulin-like growth factor 1 (IGF1), and insulin-like growth factor 2 (IGF2), were selected for genotypic variation analysis using polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) method. Changes in phenotypic performance were assessed together with shifts in allele and genotype frequencies across generations. Results: The results demonstrated an increase in BW traits from G0 to G2, indicating the positive response to selection. These phenotypic improvements were also accompanied by changes in allele and genotype frequencies, particularly at GH and IGF1, where directional shifts in growth-associated alleles were observed. In contrast, IGF2 loci exhibited a more balanced pattern with sustained heterozygosity, suggesting a more complex or complementary role in growth regulation. The combined evidence indicates that phenotypic selection is associated with underlying genetic changes, although the response reflects a polygenic architecture involving multiple genes. Conclusion: This study provides empirical evidence that integrating phenotypic and genotypic information is an effective method for evaluating genetic progress in small, closed populations under resource-limited conditions.