Evidence map›Paper›PMID 40192301›Full record

ArticlePlant biotechnology journal2025

A large-scale gene regulatory network for rice endosperm starch biosynthesis and its application in genetic improvement of rice quality.

Kunyong Huang, Feifei Lu, Pengfei Chen, Guiai Jiao, Haiyan Lin, Jian Zhang, Shaolu Zhao, Ruijie Cao, Gaoneng Shao, Zhonghua Sheng and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Plant biotechnology journal, 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. Article
  4. Article
  5. Review
  6. Article
  7. Polyploidization-Driven Functional Innovation of AGPase Small Subunit GeneInternational journal of molecular sciences · 2026
    Article
  8. Review
  9. 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

14 authors.

Kunyong Huang *State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.
Feifei Lu *State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.
Pengfei Chen *State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.
Guiai JiaoState Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.
Haiyan LinZeuda Technology Co., Ltd, Hangzhou, China.
Jian ZhangState Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.ORCID https://orcid.org/0000-0003-2804-0162
Shaolu ZhaoState Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.
Ruijie CaoState Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.
Gaoneng ShaoState Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.
Zhonghua ShengState Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.ORCID https://orcid.org/0000-0002-5960-8307
Shikai HuState Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.
Shaoqing TangState Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.
Peisong HuState Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.ORCID https://orcid.org/0000-0002-8568-5621
Xiangjin WeiState Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.ORCID https://orcid.org/0000-0002-1190-5222

Funding

Innovation Program of Chinese Academy of Agricultural Sciences CAAS-CSCB-202402National Agricultural Science and Technology project of China NK2022050102National Natural Science Foundation of China 32172080National Natural Science Foundation of China 32372099
6 · The paper itself

Abstract

Rice (Oryza sativa L.) is one of the most important food crops. Starch is the main substance of rice endosperm and largely determines the grain quality and yield. Starch biosynthesis in endosperm is very complex, requiring a series of enzymes which are also regulated by many transcription factors (TFs). But until now, the large-scale regulatory network for rice endosperm starch biosynthesis has not been established. Here, we constructed a rice endosperm starch biosynthesis regulatory network comprised of 277 TFs and 15 starch synthesis enzyme-encoding genes (SSEGs) using DNA affinity chromatography/pull-down combined with liquid chromatography-mass spectrometry (DNA pull-down and LC-MS). In this regulatory network, each SSEG is directly regulated by 7-46 TFs. Based on this network, we found a new pathway 'ABA-OsABI5-OsERF44-SSEGs' that regulates rice endosperm starch biosynthesis. We also knocked out five TFs targeting the key amylose synthesis enzyme gene OsGBSSI in japonica rice 'Nipponbare' background and found that all mutants had moderately decreased amylose content (AC) in endosperm and improved eating and cooking quality (ECQ). Notably, the knockout of OsSPL7 and OsB3 improves the ECQ without compromising the rice appearance quality, which was further validated in the indica rice 'Zhongjiazao17' background. In summary, this gene regulatory network for rice endosperm starch biosynthesis established here will provide important theoretical and practical guidance for the genetic improvement of rice quality.

Indexed as

EndospermGene Regulatory NetworksOryzaStarchAmyloseGene Expression Regulation, PlantPlant ProteinsTranscription FactorsAmylosePlant ProteinsStarchTranscription FactorsDNA pull‐downeating and cooking qualityricestarch biosynthesistranscriptional regulatory network

Identifiers

PMID40192301
PMCPMC12205878

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

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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.