Genome-Wide Patterns of Runs of Homozygosity in Barka Indigenous Chickens

Runs of homozygosity (ROH) provide insight into population history, inbreeding, and selection. In this study, genome-wide ROH patterns were evaluated in Barka indigenous chicken reared under scavenging systems in arid and semi-arid lands (ASALs), by stratifying segments by length and assessing their chromosomal distribution and gene content. Average ROH length varied across chromosomes, with the longest tracts observed on chromosomes 1, 2, 3 and 4, and shorter segments on chromosomes 11 and 28, indicating a heterogeneous genomic landscape. Gene-level analysis indicated that significant (P<0.05) associations were confined to a small subset of loci within the intermediate ROH category (1-2 Mb), notably LHX8 and YAP1. LHX8 encodes a LIM homeobox transcription factor essential for oocyte differentiation and early folliculogenesis, while YAP1 is a central effector of Hippo signalling pathway regulating cell proliferation, organ size and tissue homeostasis functions potentially linked to reproductive fitness and adaptive resilience under resource-limited ASAL conditions. These findings suggest that ROH patterns in ASAL-adapted Barka indigenous chickens reflect a combination of recent and historical demographic processes shaped by low-input scavenging systems. The limited but functionally relevant gene enrichment supports the role of localized selection on key biological pathways, while the broader genomic background remains largely neutral.