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We are analyzing https://www.biorxiv.org/content/10.1101/2025.06.23.661035v1.

Title:
An atlas of cell type specific regulatory effects in cattle | bioRxiv
Description:
Understanding the genetic and molecular architecture of complex traits and artificial selection is crucial for advancing sustainable precision breeding in cattle and other livestock. Yet, how genetic variation affects cellular gene expression remains elusive in cattle. Here, by integrating 8,866 bulk RNA-seq samples and 999,192 single cells of 81 cell types in 22 bovine tissues, we presented a comprehensive atlas of regulatory variants at the cell type resolution in cattle. By colocalizing with bulk-tissue expression quantitative trait loci (beQTL), we detected 57,043 novel cell-type stratified eQTL and cell-type/state interaction eQTL in 18,153 genes, which also exhibited a stronger tissue/cell-type specificity than beQTL. By examining genome-wide associations (GWAS) of 44 complex traits, these cell-resolved eQTL were colocalized with 505 (24%) additional GWAS loci compared to beQTL. Through integrating this resource with selection signatures between dairy and beef cattle, we provided tissue/cell-specific regulatory insights into cattle breeding. Overall, the current atlas of cell-type-specific regulatory variants will serve as an invaluable resource for cattle genomics and selective breeding. ### Competing Interest Statement The authors have declared no competing interest. All raw data analyzed in this study are publicly available for download without restrictions from SRA (<https://www.ncbi.nlm.nih.gov/sra/>). The ARS-UCD1.2 (v.110) cattle reference genome is available at Ensembl (<https://www.ensembl.org>). Details of RNA-Seq samples, eQTL summary results, selection analysis results, and ATAC peaks can be found in Supplementary Tables, respectively. All processed data and the full summary statistics of eQTL mapping and genotype imputation reference panel are available at <https://cattlecellgtex.farmgtex.org/>.
Website Age:
12 years and 2 months (reg. 2013-04-08).

Matching Content Categories {📚}

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Content Management System {📝}

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Website use Drupal 7 (http://drupal.org).

Traffic Estimate {📈}

What is the average monthly size of biorxiv.org audience?

💥 Very Strong Traffic: 200k - 500k visitors per month


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How Does Biorxiv.org Make Money? {💸}

We can't see how the site brings in money.

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Keywords {🔍}

cattle, biology, view, orcid, profile, wang, eqtl, results, cell, regulatory, medrxiv, subject, reviews, clinical, preprint, atlas, zhu, selection, breeding, beqtl, data, biorxiv, university, genetics, trials, epidemiology, search, type, zhang, liu, yang, jiang, sun, pdf, genetic, molecular, complex, traits, expression, integrating, rnaseq, samples, variants, loci, gwas, resource, genomics, competing, interest, authors,

Topics {✒️}

stronger tissue/cell-type specificity cell-type/state interaction eqtl cell-type-specific regulatory variants epidemiology subject categories clinical trials cell-type stratified eqtl molecular architecture cattle genomics examining genome-wide associations genetics cell type resolution microbiology biorxiv subject category cell-resolved eqtl epidemiology papers raw data analyzed reviews rna-seq samples author/funder keyword advanced search health-related information full summary statistics generous financial support chan zuckerberg initiative imperial college london vrije universiteit amsterdam articles animal behavior eqtl summary results cattle reference genome jing-sheng lu 81 cell types ya-nan wang ming-shan wang lingzhao fang doi regulatory variants competing interest statement download context cattle houcheng li selection analysis results data availability processed data ying ma yu jiang eqtl mapping congjun li bingjie li competing interest selective breeding cattle breeding

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Emails and Hosting {✉️}

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CDN Services {📦}

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