Evidence map›Paper›PMID 40297728›Full record

ArticleFrontiers in plant science2025

Uncovering the breeding contribution of transposable elements from landraces to improved varieties through pan-genome-wide analysis in rice.

Xiaoxia Li, Xiaofan Dai, Huiying He, Wu Chen, Qian Qian, Lianguang Shang, Longbiao Guo, Wenchuang He

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Article in Frontiers in plant science, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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

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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

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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

1 citing paper in PubMed.

  1. Structural Variation and Its Roles in Plant Genomes.Plants (Basel, Switzerland) · 2026
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4 · The record

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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.

Xiaoxia Li *Rice Research Institute, Shenyang Agricultural University, Shenyang, China.
Xiaofan Dai *Rice Research Institute, Shenyang Agricultural University, Shenyang, China.
Huiying He *Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Wu ChenShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Qian QianYazhouwan National Laboratory, Sanya, Hainan, China.
Lianguang ShangShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Longbiao GuoState Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, China.
Wenchuang HeShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Introduction: The rice improvement process, driven by modern breeding techniques, represents the second revolutionary advancement in rice agronomic traits, following domestication. Advances in pan-genomes and enhanced capacity for analyzing structural variations have increasingly highlighted their role in rice genetic improvement. Transposable element (TE) variants have been previously reported to influence rice genomic diversity during the domestication, but their contribution to the improvement from landraces to improved varieties remains unclear. Methods: Here, we combined a high-quality pan-TE variation map, transcriptome profiles, and phenotypic data for 100 landraces and 92 improved varieties to investigate the contribution of TE variations to phenotypic improvement in rice. Results: The total number and length of TE variations in improved varieties were significantly greater than those in rice landraces, particularly for Ty3-retrotransposons, LTR Discussion: Collectively, our results highlight the contributions of TE variations to rice improvement in shaping the genetic basis of modern rice varieties and will facilitate the exploration of superior genes and advance molecular breeding efforts in rice.

Indexed as

improvementmolecular breedingricesuper pan-genometransposable element

Identifiers

PMID40297728
PMCPMC12034714

What Socratic holds

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LicenceCC BY
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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 Socratic graph.