Evidence map›Paper›PMID 40322841›Full record

ArticlePlant biotechnology journal2025

Genome assembly and population genomic analysis reveal the genetic basis of popcorn evolution.

Xiaojian Fang, Hangqin Liu, Jiacheng Liu, Yang Song, Min Xu, Xing Jian, Li Dong, Qianwen Zhang, Le Xu, Guorui Fan and 7 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 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. 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

17 authors.

Xiaojian FangState Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Crop Genetics and Breeding, China Agricultural University, Beijing, China.
Hangqin LiuState Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Crop Genetics and Breeding, China Agricultural University, Beijing, China.
Jiacheng LiuState Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Crop Genetics and Breeding, China Agricultural University, Beijing, China.
Yang SongState Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Crop Genetics and Breeding, China Agricultural University, Beijing, China.
Min XuState Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Crop Genetics and Breeding, China Agricultural University, Beijing, China.
Xing JianState Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Crop Genetics and Breeding, China Agricultural University, Beijing, China.
Li DongState Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Crop Genetics and Breeding, China Agricultural University, Beijing, China.
Qianwen ZhangState Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Crop Genetics and Breeding, China Agricultural University, Beijing, China.
Le XuState Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Crop Genetics and Breeding, China Agricultural University, Beijing, China.
Guorui FanState Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Crop Genetics and Breeding, China Agricultural University, Beijing, China.
Zhaoying WangState Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Crop Genetics and Breeding, China Agricultural University, Beijing, China.
Yiwen YouState Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Crop Genetics and Breeding, China Agricultural University, Beijing, China.
Tianyu FengState Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Crop Genetics and Breeding, China Agricultural University, Beijing, China.
Wenyu LiState Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China.
Yuling LiState Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China.
Rentao SongState Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Crop Genetics and Breeding, China Agricultural University, Beijing, China.
Zhongwei LinState Key Laboratory of Maize Bio-Breeding, National Maize Improvement Center, Department of Crop Genetics and Breeding, China Agricultural University, Beijing, China.ORCID https://orcid.org/0000-0002-3161-1221

Funding

National Key Research and Development Program of China 2022YFF1003400
6 · The paper itself

Abstract

Popcorn, one of the world's most popular snack foods, represents the most ancient type of maize domesticated by humans. However, the genetic basis underlying popcorn evolution and kernel-popping traits remains largely unknown. In this study, we assembled a high-quality genome sequence of the popcorn landrace Strawberry Popcorn (SP) and conducted extensive population genomic analyses. The SP genome spans 2.3 Gb and harbours a large inversion on chromosome 8, along with millions of genetic variants that enable the discovery of beneficial alleles. Translocations and substantial duplications of the Ga1 gene occurred in the locus associated with unilateral cross-incompatibility on chromosome 4. Tandemly duplicated Ga1 genes underwent pseudogenisation and truncation with complete loss of gene function. The P1 gene experienced gene expansion and regulatory modifications, leading to downregulation of transcription and subsequent loss of pericarp colour during maize domestication and improvement. Population genomic analysis further identified a subset of 12 marker genes from over 2494 genes under human selection, which were reshaped to enhance kernel-popping traits during domestication. These marker genes include Pl1 and Dek1 for pericarp and aleurone layer thickness; THP9, Sh2, SUS1, Smk10, KW1, O7, and NKD1 for protein and starch biosynthesis; and VP5, CCD7, and Crti3 for carotene biosynthesis, which all influence endosperm vitreousness, a key factor determining kernel hardness for popping. Among these genes, KW1 and O7 stand out as pivotal genes with a significant impact on kernel-popping performance. These results provide a wealth of gene targets to greatly accelerate the molecular breeding of improved popcorn varieties.

Indexed as

Genome, PlantZea maysDomesticationEvolution, MolecularGenes, Plantdomesticationgenome sequencingkernel popingpopcorn

Identifiers

PMID40322841
PMCPMC12205860

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.