Evidence map›Paper›PMID 27534964›Full record

ArticlePlanta2016

Association mapping of seed and disease resistance traits in Theobroma cacao L.

Lambert A Motilal, Dapeng Zhang, Sue Mischke, Lyndel W Meinhardt, Michel Boccara, Olivier Fouet, Claire Lanaud, Pathmanathan Umaharan

Abstract read
PubMed Publisher
In one paragraph

Article in Planta, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed, 1 pooled it
–field-weighted citation impact
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

10 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Review
  8. Prediction of Cacao (Frontiers in plant science · 2018
    Article
  9. A Larger Chocolate Chip-Development of a 15KFrontiers in plant science · 2017
    Article
  10. 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

8 authors.

Lambert A MotilalCocoa Research Centre, The University of the West Indies, Sir Frank Stockdale Bldg., St. Augustine, Trinidad, 330912, Trinidad and Tobago. lambert.motilal@sta.uwi.edu.
Dapeng ZhangUSDA/ARS, Beltsville Agricultural Research Center, PSI, SPCL, 10300 Baltimore Avenue, Bldg. 001, Rm. 223, BARC-W, Beltsville, MD, 20705, USA.
Sue MischkeUSDA/ARS, Beltsville Agricultural Research Center, PSI, SPCL, 10300 Baltimore Avenue, Bldg. 001, Rm. 223, BARC-W, Beltsville, MD, 20705, USA.
Lyndel W MeinhardtUSDA/ARS, Beltsville Agricultural Research Center, PSI, SPCL, 10300 Baltimore Avenue, Bldg. 001, Rm. 223, BARC-W, Beltsville, MD, 20705, USA.
Michel BoccaraCocoa Research Centre, The University of the West Indies, Sir Frank Stockdale Bldg., St. Augustine, Trinidad, 330912, Trinidad and Tobago.
Olivier FouetCIRAD-UMR AGAP (Centre de coopération internationale en recherche agronomique pour le développement), Montpellier Cedex 5, France.
Claire LanaudCIRAD-UMR AGAP (Centre de coopération internationale en recherche agronomique pour le développement), Montpellier Cedex 5, France.
Pathmanathan UmaharanCocoa Research Centre, The University of the West Indies, Sir Frank Stockdale Bldg., St. Augustine, Trinidad, 330912, Trinidad and Tobago.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

MAIN

conclusionMicrosatellite and single nucleotide polymorphism markers that could be used in marker assisted breeding of cacao were identified for number of filled seeds, black pod resistance and witches' broom disease resistance. An association mapping approach was employed to identify markers for seed number and resistance to black pod and witches' broom disease (WBD) in cacao (Theobroma cacao L.). Ninety-five microsatellites (SSRs) and 775 single nucleotide polymorphisms (SNPs) were assessed on 483 unique trees in the International Cocoa Genebank Trinidad (ICGT). Linkage disequilibrium (LD) and association mapping studies were conducted to identify markers to tag the phenotypic traits. Decay of LD occurred over an average 9.3 cM for chromosomes 1-9 and 2.5 cM for chromosome 10. Marker/trait associations were generally identified based on general linear models (GLMs) that incorporated principal components from molecular information on relatedness factor. Seven markers (mTcCIR 8, 66, 126, 212; TcSNP368, 697, 1370) on chromosomes 1 and 9 were identified for number of filled seeds (NSEED). A single marker was found for black pod resistance (mTcCIR280) on chromosome 3, whereas six markers on chromosomes 4, 5, 6, 8, and 10 were detected for WBD (mTcCIR91, 183; TcSNP375, 720, 1230 and 1374). It is expected that this association mapping study in cacao would contribute to the knowledge of the genetic determinism of cocoa traits and that the markers identified herein would prove useful in marker assisted breeding of cacao.

Indexed as

CacaoChromosome MappingGenetic MarkersGenome-Wide Association StudyLinkage DisequilibriumMicrosatellite RepeatsPlant BreedingPlant ImmunityPolymorphism, Single NucleotideQuantitative Trait, HeritableSeedsGenetic MarkersBlack pod diseaseCocoa seedsLinkage disequilibriumMicrosatellite markersSingle nucleotide polymorphismWitches’ broom disease

Identifiers

PMID27534964

What OpenQuestion holds

Textmetadata
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.