Evidence map›Paper›PMID 34876002›Full record

ArticleBMC plant biology2021

Comparative transcriptome analysis reveals compatible and recalcitrant genotypic response of barley microspore-derived embryogenic callus toward Agrobacterium infection.

Yingbo Li, Guimei Guo, Hongwei Xu, Ting He, Yingjie Zong, Shuwei Zhang, Muhammad Faheem, Ruiju Lu, Longhua Zhou, Chenghong Liu

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

Article in BMC plant biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.2field-weighted citation impact, top 50% 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

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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

2 citing papers in PubMed, 5 citations in OpenAlex.

  1. Establishment of an efficientFrontiers in plant science · 2026
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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

10 authors at 2 institutions in 2 countries.

Yingbo Li *Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China.
Guimei Guo *Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China.
Hongwei XuBiotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China.
Ting HeBiotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China.
Yingjie ZongBiotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China.
Shuwei ZhangBiotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China.
Muhammad FaheemNuclear Institute of Agriculture, Tando jam, Pakistan.
Ruiju LuBiotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China.
Longhua ZhouBiotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China. zhoulonghua@saas.sh.cn.
Chenghong LiuBiotech Research Institute, Shanghai Academy of Agricultural Sciences/Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China. liuchenghong@saas.sh.cn.
Shanghai Academy of Agricultural Sciences · CNNuclear Institute for Agriculture and Biology · PK

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThe Agrobacterium mediated transformation has been routinely used in lots of plant species as a powerful tool to deliver genes of interest into a host plant. However, the transformation of elite and commercially valuable cultivar is still limited by the genotype-dependency, and the efficiency of Agrobacterium infection efficiency is crucial for the success of transformation.

resultsIn this study, the microspore-derived embryogenic calli (MDEC) of barley elite cultivars and breeding lines were employed as unique subjects to characterize the genotypic response during Agrobacterium infection process. Our results identified compatible barley genotypes (GanPi 6 and L07, assigned as GP6-L07 group) and one recalcitrant genotype (Hong 99, assigned as H99) for the Agrobacterium strain LBA4404 infection using GUS assay. The accumulation trend of reactive oxygen species (ROS) was similar among genotypes across the time course. The results of RNA-seq depicted that the average expressional intensity of whole genomic genes was similar among barley genotypes during Agrobacterium infection. However, the numbers of differentially expressed genes (DEGs) exhibited significant expressional variation between GP6-L07 and H99 groups from 6 to 12 h post-inoculation (hpi). Gene ontology (GO) enrichment analysis revealed different regulation patterns for the predicted biological processes between the early (up-regulated DEGs overrepresented at 2 hpi) and late stages (down-regulated DEGs overrepresented from 6 to 24 hpi) of infection. KEGG analysis predicted 12 pathways during Agrobacterium infection. Among which one pathway related to pyruvate metabolism was enriched in GP6 and L07 at 6 hpi. Two pathways related to plant hormone signal transduction and DNA replication showed expressional variation between GP6-L07 and H99 at 24 hpi. It was further validated by qRT-PCR assay for seven candidate genes (Aldehyde dehydrogenase, SAUR, SAUR50, ARG7, Replication protein A, DNA helicase and DNA replication licensing factor) involved in the three pathways, which are all up-regulated in compatible while down-regulated in recalcitrant genotypes, suggesting the potential compatibility achieved at later stage for the growth of Agrobacterium infected cells.

conclusionsOur findings demonstrated the similarity and difference between compatible and recalcitrant genotypes of barley MDEC upon Agrobacterium infection. Seven candidate genes involved in pyruvate metabolism, hormonal signal transduction and DNA replication were identified, which advocates the genotypic dependency during Agrobacterium infection process.

Indexed as

Transformation, GeneticAgrobacteriumDisease ResistanceGene Expression ProfilingGene OntologyGenes, PlantGenotypeHordeumPlant DiseasesReactive Oxygen SpeciesSequence Analysis, RNAReactive Oxygen SpeciesAgrobacteriumBarleyGenotypeMicrospore-derived embryogenic callusTranscriptome analysisTransformation

Identifiers

PMID34876002
PMCPMC8650547
OpenAlexW4200048357

What OpenQuestion holds

Textmetadata
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.