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M. Shirali

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Open access Aug 2026

Genome-wide cis-expression Quantitative Trait Loci (eQTL) and transcriptomic signals reveal distinct molecular regulation across correlated feed efficiency traits

Feed efficiency (FE) is a complex trait which determines livestock production profitability, yet the molecular mechanisms behind it remain unclear. This study investigated the blood transcriptomic profile of lambs, alongside genotype data with the aim to uncover the genetic basis of FE traits such as absolute dry matter intake (DMI absolute ), DMI adjusted for body size (DMI adjusted ), average daily live weight gain (ADG), and residual feed intake (RFI). Bulk RNA-Seq and genotype data were analysed using three complementary approaches: differential gene expression (DGE) analysis, weighted gene co-expression network analysis (WGCNA), and cis-expression Quantitative Trait Loci (cis-eQTL) mapping. These methods were used independently to identify genes and regulatory networks associated with FE traits and to investigate evidence supporting multi-trait candidate gene selection. DGE analysis revealed 2, 24, 85 and 4 differentially expressed genes for DMI absolute , DMI adjusted , ADG, and RFI ( P adjusted < 0.05), functionally enriched in sensory perception, ATP-dependent chromatin remodeling, Notch signaling and immune response pathways. 9 gene modules significantly associated with the FE traits ( P ≤ 0.05) with correlations ranging from r = -0.56 to 0.49, were identified using WGCNA. Single nucleotide polymorphism (SNP)-level cis-eQTL analysis identified 93 eSNPs associated with 74 genes (false discovery rate (FDR) < 0.05), while permutation-derived gene level analysis identified 280 eGenes (FDR < 0.2, empirical P < 0.03). Across the three analyses, applying thresholds of DGE ( P adjusted < 0.05), WGCNA (correlation, P ≤ 0.05), and cis-eQTL gene-level significance (empirical P < 0.05), multiple overlapping genes were identified including DNMT3A, KANSL1, NCOR1 for DMI adjusted , ACOX2, FANCF, CIMIP2B, LOC101115106, ARMH2, LOC132657496 for ADG, and LOC114114576 for RFI representing regulators of variations in FE. The integration of DGE, WGCNA, and cis-eQTL analyses identified key genes and regulatory mechanisms associated with variation in FE traits. These results highlight that integrated multi-trait candidate gene identification approaches can reveal key genes that lower feed intake while maintaining animal growth, supporting breeding strategies aimed at improving efficiency and long-term economic sustainability in sheep.

S. C. Chacko Kaitholil, Mark H. Mooney, O. Cristóbal-Carballo et al. · Frontiers in Genetics · 0 citations

Open access Jul 2026

Genome-wide comparison of traditional and commercial Mehraban sheep populations reveals differences in genetic structure, linkage disequilibrium, and inbreeding patterns.

Understanding the genetic architecture of sheep under different breeding systems is crucial for enhancing productivity and maintaining adaptive capacity. We analyzed 145 Mehraban sheep from commercial (n = 97) and traditional (n = 48) populations utilizing the OvineSNP50 BeadChip array. The analysis revealed that the linkage disequilibrium (LD) was numerically higher on average in the traditional population at both short and long distances (mean r² = 0.249 at < 10 kb; 0.037 at 5 Mb) in comparison to the commercial population (mean r² = 0.220 and 0.027, respectively), suggesting a smaller historical effective population size (Ne). Principal component and admixture analyses validated strong genetic difference, with the commercial population showing moderate admixture from traditional lines. Principal component and admixture analysis confirmed significant genetic difference, with the commercial population exhibiting considerable admixture from traditional lines. Analysis of runs of homozygosity (ROH) revealed more numerous and longer ROH segments in commercial animals (total ROH ~ 43,768 Mb, FROH = 0.183 ± 0.052) compared to traditional population (11,741 Mb, FROH = 0.139 ± 0.066), potentially indicating a potential increase in inbreeding and prolonged artificial selection. ROH islands contained 1,586 genes in commercial population and 797 genes in traditional population, with quantitative trait loci (QTL) for muscle development, carcass yield, and milk production enriched in commercial population, whereas traditional population harbored QTL for fertility, immune response, and wool characteristics. Functional analysis further identified Hippo signaling, TCA cycle, and growth-related pathways in commercial population, as well as immune (IL-17, TNF), reproductive, and DNA repair pathways in traditional population. These findings demonstrate how breeding systems shape genome-wide diversity, inbreeding, and functionally relevant loci, highlighting the importance of traditional populations as reservoirs of adaptive alleles for sustainable improvement of commercial flocks.

Leyla Eskandari, A. Ahmadi, Reza Talebi et al. · BMC Genomics · 1 citation