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Updated: Mar 14, 2026
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Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
Published on: January 20, 2023
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The jujube pan-TE map identifies transposable element insertions associated with domestication and pericarp
Xingnuo Li1,2, Aidi Zhang3, Muqaddas Bano1,2
1Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430000, China.
Horticulture Research
|March 13, 2026
Summary
Transposable elements (TEs) significantly impact jujube genome size and gene expression, influencing key agronomic traits. These elements provide valuable genetic markers for improving fruit quality and stress resilience in jujube breeding programs.
Area of Science:
- Genomics
- Plant Biology
- Evolutionary Biology
Background:
- Jujube (Ziziphus jujuba) is an economically important fruit crop with significant phenotypic diversity.
- Understanding the genetic basis of jujube's agronomic traits is crucial for crop improvement.
- The role of genetic variants, particularly transposable elements (TEs), in shaping jujube's genome and traits remains underexplored.
Purpose of the Study:
- To construct a comprehensive transposable element (TE) map in jujube using high-quality genome data.
- To investigate the impact of TEs on jujube genome evolution and the formation of agronomic traits.
- To identify transposable element insertion polymorphisms (TIPs) associated with domestication and trait variation.
Main Methods:
- Comparative genomics analysis of seven high-quality jujube genomes.
- Construction of a pan-transposable element (TE) map.
- Population-scale analysis of 1041 jujube accessions.
- Correlation analysis between TE content and genome size.
- Gene expression analysis of TE-impacted genes.
Main Results:
- TEs constitute approximately 30% of the jujube genome, primarily long terminal repeat (LTR) retrotransposons.
- TE content positively correlates with genome size, indicating their role in genomic expansion.
- TE insertions within genes significantly reduce expression, affecting cell wall biosynthesis and glucose metabolism.
- 4176 transposable element insertion polymorphisms (TIPs) were identified, differentiating wild and cultivated jujubes.
- Wild jujubes show stress-related TIPs, while cultivated varieties exhibit TIPs linked to fruit development.
- Specific TE insertions near key genes (ZjCESA4, ZjAGL18) correlate with altered fruit traits and gene expression.
Conclusions:
- Transposable elements are major drivers of genome evolution and genetic variation in jujube.
- Transposable element insertion polymorphisms (TIPs) serve as valuable molecular markers for jujube breeding.
- Targeted manipulation of TIPs can facilitate the development of jujube varieties with improved fruit quality and stress resilience.
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