Genome-Wide Patterns of Runs of Homozygosity in Barka Indigenous Chickens
Kiplangat NGENO 1
1 Moi University, Department of Agriculture, Animal Science and Natural Resources, PO Box 3900, 30100, Eldoret, Kenya
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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 lowinput
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.
Keywords :
Genomic Chicken Breeding Improvement