Evidence map›Paper›PMID 38360697›Full record

ArticleBMC biology2024

A combination of conserved and diverged responses underlies Theobroma cacao's defense response to Phytophthora palmivora.

Noah P Winters, Eric K Wafula, Benjamin J Knollenberg, Tuomas Hämälä, Prakash R Timilsena, Melanie Perryman, Dapeng Zhang, Lena L Sheaffer, Craig A Praul, Paula E Ralph and 9 more

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

Article in BMC biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
28.5field-weighted citation impact, top 1% 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

5 citing papers in PubMed, 19 citations in OpenAlex.

  1. Article
  2. Perspectives of Gene Editing for the Conservation of Plant Genetic Resources.Methods in molecular biology (Clifton, N.J.) · 2026
    Review
  3. Article
  4. Article
  5. Article
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

19 authors at 5 institutions in 4 countries.

Noah P Winters *IGDP Ecology, The Pennsylvania State University, 422 Huck Life Sciences Building, University Park, PA, 16803, USA.
Eric K Wafula *Department of Biology, The Pennsylvania State University, University Park, PA, USA.
Benjamin J KnollenbergIGDP Plant Biology, The Pennsylvania State University, University Park, PA, USA.
Tuomas HämäläDepartment of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA.
Prakash R TimilsenaDepartment of Biology, The Pennsylvania State University, University Park, PA, USA.
Melanie PerrymanDepartment of Plant Science, The Pennsylvania State University, University Park, PA, USA.
Dapeng ZhangSustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, USA.
Lena L SheafferDepartment of Plant Science, The Pennsylvania State University, University Park, PA, USA.
Craig A PraulHuck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
Paula E RalphDepartment of Biology, The Pennsylvania State University, University Park, PA, USA.
Sarah PrewittDepartment of Plant Science, The Pennsylvania State University, University Park, PA, USA.
Mariela E Leandro-MuñozCATIE, Tropical Agricultural Research and Higher Education Center, Turrialba, Costa Rica.
Diego A Delgadillo-DuranColombian Corporation for Agricultural Research (AGROSAVIA), Mosquera, Colombia.
Naomi S AltmanDepartment of Statistics, The Pennsylvania State University, University Park, PA, USA.
Peter TiffinDepartment of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA.
Siela N MaximovaHuck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
Claude W dePamphilisHuck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
James H MardenHuck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
Mark J GuiltinanHuck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA. Mjg9@psu.edu.ORCID 0000-0003-0018-9846
Pennsylvania State University · USUniversity of Minnesota · USAgricultural Research Service · USCentro Agronomico Tropical de Investigacion y Ensenanza Catie · CRColombian Corporation for Agricultural Research - AGROSAVIA · CO

Funding

Division of Integrative Organismal Systems IOS-1546863National Institute of Food and Agriculture 2018-07789National Institute of Food and Agriculture PEN04569 accession 1003147
6 · The paper itself

Abstract

backgroundPlants have complex and dynamic immune systems that have evolved to resist pathogens. Humans have worked to enhance these defenses in crops through breeding. However, many crops harbor only a fraction of the genetic diversity present in wild relatives. Increased utilization of diverse germplasm to search for desirable traits, such as disease resistance, is therefore a valuable step towards breeding crops that are adapted to both current and emerging threats. Here, we examine diversity of defense responses across four populations of the long-generation tree crop Theobroma cacao L., as well as four non-cacao Theobroma species, with the goal of identifying genetic elements essential for protection against the oomycete pathogen Phytophthora palmivora.

resultsWe began by creating a new, highly contiguous genome assembly for the P. palmivora-resistant genotype SCA 6 (Additional file 1: Tables S1-S5), deposited in GenBank under accessions CP139290-CP139299. We then used this high-quality assembly to combine RNA and whole-genome sequencing data to discover several genes and pathways associated with resistance. Many of these are unique, i.e., differentially regulated in only one of the four populations (diverged 40 k-900 k generations). Among the pathways shared across all populations is phenylpropanoid biosynthesis, a metabolic pathway with well-documented roles in plant defense. One gene in this pathway, caffeoyl shikimate esterase (CSE), was upregulated across all four populations following pathogen treatment, indicating its broad importance for cacao's defense response. Further experimental evidence suggests this gene hydrolyzes caffeoyl shikimate to create caffeic acid, an antimicrobial compound and known inhibitor of Phytophthora spp.

conclusionsOur results indicate most expression variation associated with resistance is unique to populations. Moreover, our findings demonstrate the value of using a broad sample of evolutionarily diverged populations for revealing the genetic bases of cacao resistance to P. palmivora. This approach has promise for further revealing and harnessing valuable genetic resources in this and other long-generation plants.

Indexed as

CacaoPhytophthoraHumansPlant BreedingPlant DiseasesShikimic AcidshikimateShikimic AcidCacaoEvolutionGenomicsPhytophthoraPlant-defenseRNA-seq

Identifiers

PMID38360697
PMCPMC10870529
OpenAlexW4391880354

What Socratic 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 Socratic graph.