Biology subjects

Tijjani, A.

Publications and source records attributed to Tijjani, A..

4 recordsLinked to original sources

bioRxiv2026

The genomic basis of heat stress adaptation in indigenous Ethiopian cattle from arid and hot-humid climates

African zebu cattle (Bos indicus) exhibit remarkable adaptation to extreme thermal conditions, yet the genomic bases of this resilience are not fully elucidated. Ethiopia provides a unique natural setting where closely related zebu populations have divergently adapted to hot-arid (DHETZ) and hot-humid (HHETZ) climates. In this study, we performed whole-genome sequencing of 46 Ethiopian zebu cattle from five populations and compared them with Asian zebu, Sudanese zebu, African taurine, and European taurine breeds. By integrating genome-wide SNP analysis, population genetic structure assessment, and multiple selection scans (iHS, Hp, XP-EHH, and XP-CLR), we identified distinct and shared selection signatures between DHETZ and HHETZ cattle. Ethiopian zebu closely clustered with Sudanese zebu but showed clear divergence from Asian zebu and taurine breeds. Although DHETZ and HHETZ cattle exhibited minimal genetic differentiation, reflecting their shared ancestry, each group displayed unique selection signals. DHETZ cattle showed strong selection in genes involved in oxidative stress regulation, protein folding, mitochondrial function, and vascular remodeling (e.g., SESN2, DNAJC8, GRPEL2, ABLIM3, and AFAP1L1). In contrast, HHETZ cattle displayed signatures in genes associated with immune responses, energy metabolism, and angiogenesis inhibition (e.g., MYD88, PRKACA, PRKACB, and WIF1). Several genes, including VEGFC, TNIP3, and DMXL2, were under selection in both groups, suggesting conserved mechanisms of thermotolerance and reproductive adaptation. These findings reveal a dual pattern of genomic adaptation: while core heat-response pathways are shared, population-specific signatures reflect distinct metabolic and vascular strategies for coping with arid versus humid heat stress. This study provides novel insights into the genomic architecture of environmental adaptation in tropical cattle and offers valuable markers for breeding climate-resilient livestock.

genomics↗

bioRxiv2025

Uncovering Functional Sequence Gaps in Human Reference Genomes using African Pan Genome Contig Sequences

Human reference genomes underpin biomedical discovery but remain incomplete and biased toward European populations, constraining interpretation of genetic variation in underrepresented populations. Here we characterize African Pan Genome (APG) contigs totaling 296.5 Mb to define the sequence and functional landscape of genomic regions absent from current references. Most contigs align to the telomere-to-telomere (T2T-CHM13) genome and across 47 haplotype-resolved Human Pangenome Reference Consortium (HPRC) assemblies, with T2T-CHM13 placements enriched in centromeric and satellite repeats and overlapping 373 genes, including disease-associated loci. Mapping across HPRC assemblies revealed ancestry-associated contig enrichment, particularly in African genomes. Notably, 742 contigs remained unmapped under both stringent and relaxed criteria. These sequences are largely nonrepetitive and exhibit strong functional potential, including predicted protein-coding genes, CpG islands and transcriptional activity. Together, these results demonstrate that functionally relevant, ancestry-enriched genomic sequences remain absent from current references, with important implications for disease variant interpretation and precision medicine.

genomics↗

bioRxiv2021

Genomic signatures of desert adaptation at gene-rich regions in zebu cattle from the African drylands

Sudan, the largest country in Africa, acts as a corridor between North and sub-Saharan Africa along the river Niles. It comprises warm arid and semi-arid grazing lands, and it is home to the second-largest African population of indigenous livestock. Indigenous Sudanese cattle are mainly indicine/zebu (humped) type. They thrive in the harshest dryland environments characterised by high temperatures, long seasonal dry periods, nutritional shortages, and vector diseases challenges. We investigated genome diversity in six indigenous African zebu breeds sampled in Sudan (Aryashai, Baggara, Butana, Fulani, Gash, and Kenana). We adopted three genomic scan approaches to identify candidate selective sweeps regions (ZHp, FST, XP-EHH). We identified a set of gene-rich selective sweep regions shared across African and Asian zebu or unique to Sudanese zebu. In particular, African and Asian zebu candidate gene-rich regions are detected on chromosomes 2, 5 and 7. They include genes involved in immune response, body size and conformation, and stress response to heat. In addition, a 250 kb selective sweep on chromosome 16 was detected exclusively in five Sudanese zebu populations. This region spans seven genes, including PLCH2, PEX10, PRKCZ and SKI, which are involved in alternative adaptive metabolic strategies of insulin signalling, glucose homeostasis, and fat metabolism. Together, these genes may contribute to the zebu cattle resilience to heat, nutritional and water shortages. Our results highlight the putative importance of selection at gene-rich genome regions, which might be under a common regulatory genetic control, as an evolutionary mechanism for rapid adaptation to the complexity of environmental challenges.

evolutionary biology↗

bioRxiv2021

A cattle graph genome incorporating global breed diversity

Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts cattle research in other important global cattle breeds. To mitigate this issue, we have generated the first assemblies of African breeds, which have been integrated with genomic data for 294 diverse cattle into the first graph genome that incorporates global cattle diversity. We illustrate how this more representative reference assembly contains an extra 116.1Mb (4.2%) of sequence absent from the current Hereford sequence and consequently inaccessible to current studies. We further demonstrate how using this graph genome increases read mapping rates, reduces allelic biases and improves the agreement of structural variant calling with independent optical mapping data. Consequently, we present an improved, more representative, reference assembly that will improve global cattle research.

genomics↗