A genome-wide scan for signatures of selection in two indigenous Sicilian chicken breeds

Natural and artificial selection can leave distinctive genomic signatures that provide insights into the evolutionary history of populations. In this study, we used high-density SNP arrays to investigate genomic signatures of selection in two indigenous Sicilian chicken breeds: the Siciliana, also known as Coronata (SIC), and the recently recognized Cornuta di Caltanissetta, also known as Cornuta di Sicilia (COR). We combined two extended haplotype homozygosity (EHH)-based methods, iHS and Rsb, with a complementary site frequency spectrum (SFS)-based analysis using SweeD software, to identify genomic regions potentially affected by selection. Several candidate regions were identified in COR, with regions on chicken chromosomes (GGA) 1, 8, and 21. On GGA1 strong iHS signals coincided with elevated composite likelihood ratio (CLR) values from SweeD, whereas regions on GGA8 and GGA21 showed overlapping iHS and Rsb signals, supported by additional exploratory evidence from SweeD. These regions contain several genes associated with nervous system development and function, including PCDH9 on GGA1; ASTN1, TNR, and BRINP2 on GGA8; and CLSTN1, NMNAT1, UBE4B, and KIF1B on GGA21. Additional candidate genes identified within regions showing differential selection signals on GGA3, including TTBK1, SLC8A1, TTL, and VSX1, also have reported roles in neural processes. Collectively, these genes highlight potential links between the identified genomic signals and neural processes that may contribute to phenotypic differentiation between the two breeds, although their involvement in breed-specific traits remains to be established. Beyond these candidates, we identified selection signatures encompassing genes associated with gene regulation, including transcriptional co-regulation and alternative splicing. Several highly significant variants were also located within long non-coding RNA (lncRNA) regions, pointing to a possible contribution of regulatory variation to the observed genomic patterns. Overall, our results identify candidate genomic regions containing genes involved in neural function and gene regulatory processes, providing a basis for future investigations into the evolutionary history and phenotypic differentiation of these indigenous Sicilian chicken breeds.