Evidence map›Paper›PMID 40226955›Full record

ReviewJournal of integrative plant biology2025

Fast-forwarding plant breeding with deep learning-based genomic prediction.

Shang Gao, Tingxi Yu, Awais Rasheed, Jiankang Wang, Jose Crossa, Sarah Hearne, Huihui Li

Abstract readReview
In one paragraph

Review in Journal of integrative plant biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing 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

9 citing papers in PubMed.

  1. Review
  2. Review
  3. Harnessing artificial intelligence in plant breeding: innovations in digital phenotyping and breeding methodologies.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026
    Review
  4. Article
  5. Article
  6. Article
  7. Omics landscapes in molecular mechanisms withFood chemistry. Molecular sciences · 2025
    Review
  8. Review
  9. 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

7 authors.

Shang GaoState Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, CIMMYT-China office, Beijing, 100081, China.ORCID http://orcid.org/0000-0002-2176-6553
Tingxi YuState Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, CIMMYT-China office, Beijing, 100081, China.ORCID http://orcid.org/0000-0002-1844-3956
Awais RasheedDepartment of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.ORCID http://orcid.org/0000-0003-2528-708X
Jiankang WangState Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, CIMMYT-China office, Beijing, 100081, China.ORCID http://orcid.org/0000-0002-8069-5329
Jose CrossaInternational Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Texcoco, D.F. 06600, Mexico.ORCID http://orcid.org/0000-0001-9429-5855
Sarah HearneInternational Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Texcoco, D.F. 06600, Mexico.ORCID http://orcid.org/0000-0003-2015-2450
Huihui LiState Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, CIMMYT-China office, Beijing, 100081, China.ORCID http://orcid.org/0000-0002-9117-5011

Funding

Hainan Provincial Natural Science Foundation of China 624MS119Innovation Program of Chinese Academy of Agricultural Sciences CAAS-CSIAF-202303National Natural Science Foundation of China 32361143514
6 · The paper itself

Abstract

Deep learning-based genomic prediction (DL-based GP) has shown promising performance compared to traditional GP methods in plant breeding, particularly in handling large, complex multi-omics data sets. However, the effective development and widespread adoption of DL-based GP still face substantial challenges, including the need for large, high-quality data sets, inconsistencies in performance benchmarking, and the integration of environmental factors. Here, we summarize the key obstacles impeding the development of DL-based GP models and propose future developing directions, such as modular approaches, data augmentation, and advanced attention mechanisms.

Indexed as

Deep LearningGenome, PlantGenomicsPlant Breedingartificial intelligencedeep learninggenomic predictionplant breeding

Identifiers

PMID40226955
PMCPMC12225013

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.