Evidence map›Paper›PMID 37010631›Full record

ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2023

GWAS across multiple environments and WGCNA suggest the involvement of ZmARF23 in embryonic callus induction from immature maize embryos.

Tianhu Liang, Yu Hu, Na Xi, Minyan Zhang, Chaoying Zou, Fei Ge, Guangsheng Yuan, Shibin Gao, Suzhi Zhang, Guangtang Pan and 3 more

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In one paragraph

Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2023. 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
5.9field-weighted citation impact, top 4% of its field
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, 19 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Genetic dissection of ten photosynthesis-related traits based on InDel- and SNP-GWAS in soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024
    Article
  6. Review
  7. Article
  8. Roles of auxin pathways in maize biology.Journal of experimental botany · 2023
    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

13 authors at 2 institutions in 2 countries.

Tianhu LiangState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
Yu HuState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
Na XiState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
Minyan ZhangState 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.
Fei GeState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
Guangsheng YuanState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
Shibin GaoState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
Suzhi ZhangState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
Guangtang PanState 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.
Thomas LübberstedtDepartment of Agronomy, Iowa State University, Ames, IA, 50011, USA.
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
Sichuan Agricultural University · CNIowa State University · US

Funding

National Nature Science Foundation of China 31871637National Nature Science Foundation of China 32001500National Nature Science Foundation of China 32072073National Nature Science Foundation of China 32101777Sichuan Science and Technology Program 2021JDTD0004Sichuan Science and Technology Program 2021YJ0476
6 · The paper itself

Abstract

key messageCombined GWAS, WGCNA, and gene-based association studies identified the co-expression network and hub genes for maize EC induction. ZmARF23 bound to ZmSAUR15 promoter and regulated its expression, affecting EC induction. Embryonic callus (EC) induction in immature maize embryos shows high genotype dependence, which limits the application of genetic transformation in transgenic breeding and gene function elucidation in maize. Herein, we conducted a genome-wide association mapping (GWAS) for four EC induction-related traits, namely rate of embryonic callus induction (REC), increased callus diameter (ICD), ratio of shoot formation (RSF), and length of shoot (LS) across different environments. A total of 77 SNPs were significantly associated these traits under three environments and using the averages (across environments). Among these significant SNPs, five were simultaneously detected under multiple environments and 11 had respective phenotypic variation explained > 10%. A total of 257 genes were located in the linkage disequilibrium decay of these REC- and ICD-associated SNPs, of which 178 were responsive to EC induction. According to the expression values of the 178 genes, we performed a weighted gene co-expression network analysis (WGCNA) and revealed an EC induction-associated module and five hub genes. Hub gene-based association studies uncovered that the intragenic variations in GRMZM2G105473 and ZmARF23 influenced EC induction efficiency among different maize lines. Dual-luciferase reporter assay indicated that ZmARF23 bound to the promoter of a known causal gene (ZmSAUR15) for EC induction and positively regulated its expression on the transcription level. Our study will deepen the understanding of genetic and molecular mechanisms underlying EC induction and contribute to the use of genetic transformation in maize.

Indexed as

Genome-Wide Association StudyZea maysChromosome MappingPhenotypePlant BreedingPolymorphism, Single Nucleotide

Identifiers

PMID37010631
OpenAlexW4362523991

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.