Evidence map›Paper›PMID 41148340›Full record

ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2025

GWAS and gene co-expression network analysis reveal the genetic control of seed germination under salt stress in maize.

Minyan Zhang, Yinchao Zhang, Zhike Deng, Tao Liu, Yuru Liang, Qinglin Li, Chaoying Zou, Zhong Chen, Langlang Ma, Yaou Shen

Abstract read
PubMed Publisher
In one paragraph

Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Article
  2. Article
  3. Genome-wide and co-expression network dissection ofFrontiers in plant science · 2026
    Article
  4. Article
  5. 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

10 authors.

Minyan Zhang *State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
Yinchao Zhang *Industrial Crop Research Institute of Sichuan Academy of Agricultural Sciences, Chengdu, 610300, China.
Zhike DengState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
Tao LiuState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
Yuru LiangState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
Qinglin LiState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
Chaoying ZouState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
Zhong ChenState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
Langlang MaState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China. sxyljxml@163.com.
Yaou ShenState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China. shenyaou@sicau.edu.cn.ORCID http://orcid.org/0000-0001-7603-0108

Funding

Biological Breeding Project of National Key Laboratory SKL-ZD202211National Natural Science Foundation of China 32372203Sichuan Science and Technology Program 2024NSFSC0313
6 · The paper itself

Abstract

key messageGWAS and WGCNA uncovered ZmKCH5 involved in seed germination under salt stress. Role of ZmKCH5 in modulating salt-germination ability was validated via overexpression in Arabidopsis and knockout in maize. Seed germination ability in salinized soil is a crucial factor affecting maize productivity. Herein, genome-wide association study (GWAS) and weighted gene co-expression network analysis (WGCNA) were combined to elucidate the genetic control of seed germination ability under salt stress in maize. A total of 50 single nucleotide polymorphisms (SNPs) and 537 candidate genes were associated with seed germination traits under salt stress using GWAS. Meanwhile, transcriptome libraries at five salt-germination stages were constructed using two inbred lines with contrasting salt tolerances. We uncovered 19,929 differentially expressed genes (DEG) that were differentially responsive to salt stress during seed germination. The 221 overlaps between the 537 candidate genes and 19,929 DEGs were subjected to WGCNA based the gene expression values, detecting a salt stress-related module and four hub genes. Zm00001d011473, one of the hub genes, encodes the potassium channel protein 5 (ZmKCH5). Gene-based association analysis indicated that the variants in ZmKCH5 affected post-germinated root growth and salt tolerance, with "GA" being the favorable haplotype. Overexpression in Arabidopsis and knockout in maize indicated that ZmKCH5 positively mediated seed germination rate and primary root growth under salt stress. These findings will contribute to understanding the genetic and molecular mechanisms underlying maize seed germination under salt stress.

Indexed as

Gene Expression Regulation, PlantGene Regulatory NetworksGerminationPlant ProteinsSalt StressSeedsZea maysArabidopsisGenome-Wide Association StudyPhenotypePolymorphism, Single NucleotideSalt TolerancePlant Proteins

Identifiers

PMID41148340

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.