Evidence map›Paper›PMID 32272881›Full record

ArticleBMC genomics2020

Identification of key genes and pathways associated with feed efficiency of native chickens based on transcriptome data via bioinformatics analysis.

Lei Yang, Tingting He, Fengliang Xiong, Xianzhen Chen, Xinfeng Fan, Sihua Jin, Zhaoyu Geng

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.

0numbers the graph read from it
0cells of the map it votes in
28citing papers in PubMed
5.6field-weighted citation impact, top 3% of its field
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

28 citing papers in PubMed, 61 citations in OpenAlex.

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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

7 authors at 1 institution in 1 country.

Lei YangCollege of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei, 230036, China.ORCID https://orcid.org/0000-0002-4954-7205
Tingting HeCollege of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei, 230036, China.
Fengliang XiongCollege of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei, 230036, China.
Xianzhen ChenCollege of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei, 230036, China.
Xinfeng FanCollege of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei, 230036, China.
Sihua JinCollege of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei, 230036, China.
Zhaoyu GengCollege of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei, 230036, China. gzy@ahau.edu.cn.ORCID https://orcid.org/0000-0003-1898-7459
Anhui Agricultural University · CN

Funding

Key Science and Technology Program of Anhui Province 1704a07020091Natural Science Foundation of Anhui Province 1808085QC61Open Fund of Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Biobreeding AKLGRCB2017008
6 · The paper itself

Abstract

backgroundImproving feed efficiency is one of the important breeding targets for poultry industry. The aim of current study was to investigate the breast muscle transcriptome data of native chickens divergent for feed efficiency. Residual feed intake (RFI) value was calculated for 1008 closely related chickens. The 5 most efficient (LRFI) and 5 least efficient (HRFI) birds were selected for further analysis. Transcriptomic data were generated from breast muscle collected post-slaughter.

resultsThe differently expressed genes (DEGs) analysis showed that 24 and 325 known genes were significantly up- and down-regulated in LRFI birds. An enrichment analysis of DEGs showed that the genes and pathways related to inflammatory response and immune response were up-regulated in HRFI chickens. Moreover, Gene Set Enrichment Analysis (GSEA) was also employed, which indicated that LRFI chickens increased expression of genes related to mitochondrial function. Furthermore, protein network interaction and function analyses revealed ND2, ND4, CYTB, RAC2, VCAM1, CTSS and TLR4 were key genes for feed efficiency. And the 'phagosome', 'cell adhesion molecules (CAMs)', 'citrate cycle (TCA cycle)' and 'oxidative phosphorylation' were key pathways contributing to the difference in feed efficiency.

conclusionsIn summary, a series of key genes and pathways were identified via bioinformatics analysis. These key genes may influence feed efficiency through deep involvement in ROS production and inflammatory response. Our results suggested that LRFI chickens may synthesize ATP more efficiently and control reactive oxygen species (ROS) production more strictly by enhancing the mitochondrial function in skeletal muscle compared with HRFI chickens. These findings provide some clues for understanding the molecular mechanism of feed efficiency in birds and will be a useful reference data for native chicken breeding.

Indexed as

EatingGene Regulatory NetworksAnimal FeedAnimalsBreedingChickensGene Expression ProfilingGene Expression RegulationMuscle, SkeletalProtein Interaction MapsSequence Analysis, RNAFeed efficiencyNative chickensResidual feed intakeRNA-seqTranscriptome

Identifiers

PMID32272881
PMCPMC7146967
OpenAlexW3015623397

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LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.