Evidence map›Paper›PMID 42288912›Full record

ArticleJournal of animal science and biotechnology2026

Pan-tissue transcriptomic profiling of dairy cattle.

Jinfeng He, Ruike Jia, Aixia Du, Weijie Zheng, Bo Han, Qi Zhang, Zijiao Guo, Yanan Liu, Yali Hou, Dongxiao Sun

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of animal science and biotechnology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
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1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Jinfeng HeState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
Ruike JiaState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
Aixia DuState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
Weijie ZhengState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
Bo HanState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
Qi ZhangState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
Zijiao GuoState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
Yanan LiuState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
Yali HouState Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. houyali1210@gmail.com.
Dongxiao SunState Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. sundx@cau.edu.cn.

Funding

Inner Mongolia Autonomous Region Science and Technology Program 2021GG0102National Key R&D Program of China 2021YFF1000700, 2022YFF1000103, 2024YFF1000100Shandong Provincial Key Research and Development Program 2024LZGCQY022STI 2030－Major Projects 2023ZD04069the Agricultural Science and Technology Innovation Program ASTIP-IAS-04-2the Program for Changjiang Scholar and Innovation Research Team in University IRT_15R62
6 · The paper itself

Abstract

backgroundMilk production in dairy cattle is a paradigmatic complex trait emerging from coordinated regulatory programs across multiple tissues and molecular layers, while previous transcriptomic studies have largely focused on a limited number of key tissues, most notably the mammary gland and liver. Consequently, how transcriptional regulatory mechanisms underlying milk traits are coordinated across the whole organism remains poorly understood. In particular, the contributions of non-coding RNA, alternative splicing and alternative polyadenylation vary across tissues and contribute to tissue-specific regulatory landscapes has not been comprehensively profiled at a pan-tissue scale. This study aims to systematically characterize tissue-specific transcriptomic and post-transcriptional profiles across multiple tissues in dairy cattle.

resultsWe generated RNA-seq data for 99 tissues from two adult Holstein cows and integrated these with 400 publicly available RNA-seq samples from 182 adult Holstein cows covering 127 tissues, yielding a profiling that spans 166 tissues. Using a one-versus-all framework, we identified the tissue-specific genes thereby revealing distinct tissue metabolic demands and physiological specialization, with highly active tissues (brain, mammary gland and reproductive organs) harboring larger numbers of tissue specific genes. Further, we predicted potential RNA-RNA interactions and found that tissue-specific genes may be associated with coordinated non-coding RNA interaction networks. At the post-transcriptional level, rMATS profiling revealed skipped exons and mutually exclusive exons as the predominant alternative splicing classes across tissues, whereas proximal polyadenylation site usage was widespread, although brain-expressed genes more frequently used distal sites. Cross-species analysis based on 11,547 one-to-one orthologues shared among cattle, humans, and pigs showed that tissues from the same organ or system of cattle, humans and pigs generally clustered together, whereas the oviduct displayed expression patterns more similar to tissues within the hypothalamic-pituitary-gonadal axis.

conclusionsThis study establishes an integrative multi-tissue transcriptomic and post-transcriptional regulatory profile for dairy cattle across a broad range of organs, providing a valuable resource for investigating tissue-specific variation in transcriptional and post-transcriptional regulation.

Indexed as

Alternative polyadenylationAlternative splicingCross-species analysisDairy cattleNon-coding RNAsPan-tissue transcriptomic profile

Identifiers

PMID42288912
PMCPMC13264825

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.