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

Abstract

Long-horned Ankole cattle belong to the Sanga group of cattle, which is widely distributed throughout sub-Saharan Africa. They are valued for disease, vector, and parasite tolerance, adaptation to harsh tropical environments, in addition to their unique cultural significance. In this study, a haplotype-aware, chromosome-resolved genome of Ankole cattle (MakAnk1.0) spanning 2.84 Gb, with a scaffold N50 of 110.9 Mb was assembled from PacBio HiFi and Omni-C data. The primary assembly attained 99.5% BUSCO completeness, while haplotypes 1 and 2 had lengths of 2.69 and 2.62 Gb, scaffold N50 of 106.41 and 106.48 Mb, and BUSCO scores of 98.9% and 96.7%, respectively. Gene prediction for the primary assembly yielded 19,406 genes, with a BUSCO completeness score of 88.7%. Repeat sequences accounted for 56.41% of the primary assembly, whereas haplotypes 1 and 2 contained 54.71% and 54.86%, respectively. Using the assembled genome, 27.5 million SNPs and 3.6 million INDELs were discovered, while genome-wide RAiSD analysis identified 421 candidate genomic regions under selection, from which 256 genes were subsequently annotated. These included the HLCS gene, which plays a role in biotinylation and keratinization, potentially supporting development of the long horns in Ankole cattle. Moreover, the annotated genes under selection overlapped with economically significant QTLs in tropical cattle, including tick resistance. Furthermore, the estimated recent effective population size (Ne) trajectory revealed a population contraction, with contemporary Ne estimates ranging from 228 to 278. Collectively, this study provides a valuable genomic resource for advancing research, breed improvement, and conservation of the transboundary Ankole cattle.