Evidence map›Paper›PMID 39994510›Full record

ArticleBMC genomics2025

Time-course RNA-seq analysis of upland cotton (Gossypium hirsutum L.) responses to Southern root-knot nematode (Meloidogyne incognita) during compatible and incompatible interactions.

Sameer Khanal, Pawan Kumar, Mychele B da Silva, Rippy Singh, Nelson Suassuna, Don C Jones, Richard F Davis, Peng W Chee

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2025. 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
–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

2 citing papers in PubMed.

  1. Article
  2. Combating Root-Knot Nematodes (Plants (Basel, Switzerland) · 2025
    Review
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.

Sameer KhanalDepartment of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, 2356 Rainwater Road, Tifton, GA, 31793, USA. sameer@uga.edu.
Pawan KumarDepartment of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, 2356 Rainwater Road, Tifton, GA, 31793, USA.
Mychele B da SilvaDepartment of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, 2356 Rainwater Road, Tifton, GA, 31793, USA.
Rippy SinghDepartment of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, 2356 Rainwater Road, Tifton, GA, 31793, USA.
Nelson SuassunaDepartment of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, 2356 Rainwater Road, Tifton, GA, 31793, USA.
Don C JonesCotton Incorporated, 6399 Weston Parkway, Cary, NC, 27513, USA.
Richard F DavisU.S. Department of Agriculture - Agricultural Research Service, 115 Coastal Way, Tifton, GA, 31793, USA.
Peng W CheeDepartment of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, 2356 Rainwater Road, Tifton, GA, 31793, USA. pwchee@uga.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThe Southern root-knot nematode (Meloidogyne incognita) poses a substantial threat to cotton (Gossypium hirsutum L.) by causing significant agricultural losses. Host plant resistance is the most plausible approach for minimizing these losses. QTL mapping and early transcriptomic studies have identified candidate genes within the QTL regions on chromosome 11 (qMi-C11) and chromosome 14 (qMi-C14). Although these QTL regions have been fine-mapped and candidate genes identified, expression profiling of Meloidogyne-Gossypium interactions across different stages of infection could further refine the list of candidate genes. This study advances our understanding of the molecular mechanisms underlying the resistance conferred by qMi-C11 and qMi-C14 against Southern root-knot nematode.

resultsUsing time-course RNA-seq analyses across nematode developmental phases, we uncovered transcriptomic events-both genome-wide and within QTL intervals-underlying defense responses during compatible interactions (with Cocker 201, a susceptible line) and incompatible interactions (with M-120 RNR, a resistant line). Basal defense responses were observed in both compatible and incompatible interactions, with stronger expression in the incompatible interaction. Nematode-responsive genes associated with defense pathways showed distinct dynamics, characterized by repression during compatible interactions and early induction, greater diversity, and heightened upregulation during incompatible interactions. This study uncovers a broad repertoire of disease resistance and putative resistance genes, as well as pathogenesis-related genes, ligands, and receptors, that are differentially expressed in response to nematode parasitism. Mapping of these genes across the cotton genome identified promising candidates, including Gh_A11G3090 (PUB21) and Gh_A11G2836 (RPPL1) within the chromosome 11 QTL region, andGh_D02G0257 (RLP12) and Gh_D02G0259 (RLP12) within the chromosome 14 QTL region.

conclusionsThe findings of this study deepen our understanding of host-nematode interactions, identify candidate genes for downstream applications, and contribute to advancements in resistance breeding and sustainable nematode management strategies.

Indexed as

GossypiumHost-Parasite InteractionsPlant DiseasesTylenchoideaAnimalsDisease ResistanceGene Expression ProfilingGene Expression Regulation, PlantPlant RootsQuantitative Trait LociRNA-SeqTranscriptomeComparative transcriptomicsCotton molecular breedingDifferentially expressed genes and pathwaysHost-parasite interactionHost plant resistance

Identifiers

PMID39994510
PMCPMC11849305

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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.