The chromosome-level annotated reference genome MakAnk1.0 reveals a putative signature of selection for long horns and provides insights into the demographic history of Ankole cattle.

Summary

This study presents MakAnk1.0, a high-quality haplotype-aware, chromosome-resolved reference genome for Ankole cattle assembled from long-read and proximity-ligation sequencing data. Genome-wide selection analysis identified 421 candidate regions under selection, including the HLCS gene implicated in horn development and genes associated with economically important traits such as tick resistance. The work provides a valuable genomic resource for understanding Ankole cattle's adaptation to harsh tropical environments and supporting breed conservation and improvement.

Regional applicability

Whilst the Ankole breed originates in East Africa, this genomic resource may have indirect relevance to United Kingdom livestock breeding and conservation programmes, particularly regarding understanding disease and parasite tolerance traits that could inform genetic improvement of tropical-adapted breeds. The findings on selection signatures and conservation genetics provide methodology transferable to similar indigenous breeds in temperate regions.

Key measures

Genome assembly metrics (scaffold N50, BUSCO completeness), SNP and INDEL discovery (27.5 million SNPs, 3.6 million INDELs), RAiSD selection scan results (421 candidate regions, 256 annotated genes), effective population size trajectory

Outcomes reported

The study assembled a high-quality chromosome-resolved reference genome (MakAnk1.0) for Ankole cattle and identified 421 genomic regions under selection, including genes associated with long horn development and tick resistance. Population genetic analysis revealed recent population contraction with contemporary effective population sizes between 228 and 278.

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