Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.02.22.707281

Genome-Wide Linkage Disequilibrium, Haplotype Block Structure, and Population Diversity in Nili-Ravi Buffalo (Bubalus bubalis)

Ahmad, A.·mustafa, h.·Khan, W. A.·Manan, A.·Anwer, I.·Akram, W.
View original source ↗Export metadata ↓

Abstract

Linkage disequilibrium (LD) and haplotype block structure govern the resolution and utility of genomic selection, marker-assisted selection, and genome-wide association studies (GWAS) in livestock. We performed a comprehensive genome-wide characterization of LD decay, haplotype block architecture, and population diversity across all 24 autosomes in Nili-Ravi buffalo (Bubalus bubalis; n = 85), using 43,543 post-quality-control SNPs. Mean genome-wide r2 was 0.124 (median 0.074) and mean D was 0.540 (median 0.481), with LD half-decay at {approx}70 kb. A total of 133 haplotype blocks encompassing 721 SNPs were identified (Gabriel et al., 2002). Haploview analysis of nine chromosomes harbouring bTB resistance candidate genes revealed contrasting selection signatures: directional selection at innate immune loci (IFNG, TLR1; H < 0.55) versus balancing selection at adaptive immune loci (BoLA-DRB3, SP110; H > 1.0). Critically, BBU15 Block 3 (28.6 kb; OR52E5/NCR1 locus, 47.16 Mb) showed a genome-wide significant integrated haplotype score (iHS; -log1 0 p = 5.408), directly co-localising with the published bTB susceptibility QTL (Bermingham et al., 2014). The TAA haplotype (frequency 53.3%) at this block represents a candidate resistance-associated haplotype for marker-assisted selection. These findings provide essential parameters for SNP panel design and bTB resistance breeding in South Asian buffalo.

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Ahmad, A., mustafa, h., Khan, W. A., Manan, A., Anwer, I., Akram, W.. 2026-02-23. Genome-Wide Linkage Disequilibrium, Haplotype Block Structure, and Population Diversity in Nili-Ravi Buffalo (Bubalus bubalis). https://doi.org/10.64898/2026.02.22.707281

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Integrative Nanopore and Illumina sequencing reveals age-associated tRNA modification and CCA-tail dynamics in yeast

Aging is characterized by a progressive loss of proteostasis. Transfer RNAs (tRNAs) are essential regulators of translation, yet their dynamics during aging remain poorly understood due to challenges in sequencing highly modified RNAs. Here we present a benchmarked Nanopore direct RNA sequencing (RNA004 chemistry) resource that profiles the Saccharomyces cerevisiae tRNAome during replicative aging at single-molecule resolution. Using in vitro transcribed tRNA controls, we establish modification detection thresholds and validate key findings with orthogonal Illumina sequencing. While overall tRNA abundance remains largely stable, our resource reveals age-associated terminal A cleavage at the 3' CCA tail of mature tRNAs, targeted T-loop and anticodon modification changes, and single-molecule evidence of modification co-occurrence. This dataset provides a resource for exploring tRNA regulation, translation fidelity, and longevity.

genomics↗
bioRxiv2026

A hydrogen-producing mitochondrion in an anaerobic eukaryotrophic rhizarian

Diverse eukaryotes thrive under low oxygen conditions, in part through highly modified mitochondrion-related organelles (MROs) that use alternate metabolic pathways to support ATP production and cofactor recycling. Anaerobic lifestyles have evolved repeatedly across the eukaryotic tree of life, each providing an independent opportunity to understand how eukaryotes adapt to life in low oxygen conditions. Here, we use single-cell transcriptomics to reconstruct the MRO metabolism of PCE SSF, a benthic eukaryotrophic flagellate and the first cultivated representative of Novel Clade 12 (NC12; Rhizaria), an independently anaerobic rhizarian lineage. PCE SSF possesses an anaerobic hydrogen-producing mitochondrion capable of hydrogenosome-type substrate-level phosphorylation. It also retains a nearly complete but likely branched tricarboxylic acid pathway that lacks citrate synthase and malate dehydrogenase. The function of citrate synthase may instead be fulfilled by the typically cytosolic ATP citrate lyase, previously reported in this context only in the anaerobic cercozoan, Brevimastigomonas motovehiculus. Unlike B. motovehiculus, however, PCE SSF retains only Complex II and the NuoE/NuoF subunits of the electron transport chain and lacks a mitochondrial genome. Together, these features indicate an atypical and reduced mitochondrial metabolism, highlighting the diversity of evolutionary solutions to anaerobic energy metabolism in eukaryotes.

genomics↗
bioRxiv2026

Targeted CRISPRi screening reveals unexpected resilience across the RNA polymerase III transcriptome

Increased RNA polymerase III (Pol III) activity and tRNA abundance are widely linked to cancer cell growth, yet the functional requirement for individual Pol III genes and core components remains unclear, in part due to the difficulty of achieving gene-specific perturbation of highly conserved loci. Here, we developed an inducible CRISPR interference platform and a custom single-guide RNA (sgRNA) library enabling gene-specific targeting of Pol III-transcribed genes and Pol III machinery. Genome-wide screening identified several Pol III dependencies in diploid fibroblasts and HEK293T cells, including multiple initiator methionine tRNA genes among the strongest fitness dependencies. Unexpectedly, glioblastoma models remained largely insensitive to repression of both individual Pol III genes and core Pol III components, despite efficient target repression. These findings establish a general strategy for gene-specific interrogation of conserved Pol III genes and indicate that glioblastoma models tolerate extensive perturbation of Pol III genes and machinery.

genomics↗