The Transcriptional Regulatory Mechanisms Exploration of Jujube Biological Traits through Multi-Omics Analysis
Abstract
:1. Introduction
2. Progress in Genome Sequencing and Assembly of Jujube Genomes
3. Genomics Improves the Construction of High-Density Genetic Linkage Maps of Jujube
4. Domestication-Related Genes Identified Based on Jujube Genomics
5. Molecular Regulation Identification of Jujube Biology Traits Based on Multi-Omics
5.1. Sugar and Organic Acid Accumulation and Metabolism
5.2. Terpenoid Biosynthesis
5.3. Flavonoid Biosynthesis
5.4. Abiotic Stress Response
6. Conclusions and Perspectives
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Infomation | Dongzao (Fresh Food Cultivar) | Junzao001 (Dry Jujube Cultivar) | Sour Jujube (Wild Ancestor Species of Chinese Jujube) | Dongzao (Fresh Food Cultivar) |
---|---|---|---|---|
Sequencing platform | Illumina | Illumina | PacBio + Illumina | Nanopore + PacBio |
Assembly strategy | WGS + BAC | WGS | Hi-C | HiFi + ONT + Hi-C |
Total length of scaffolds (bp) | 437,645,007 | 351,115,537 | 406,163,984 | 393,332,932 |
Contig N50 length (bp) | 33,948 | 34,020 | 2,144,872 | 32,986,920 |
Sequences anchored to chromosomes (%) | 73.6% | 83.6% | 93.7% | 100% |
BUSCO genes (%) | 89.0% | 93.2% | 95.56% | 98.50% |
Number of protein-coding genes | 27,443 | 31,067 | 25,089 | 29,633 |
Transposable elements (bp) | 136.33 | 204.92 | 215.93 | 220.88 |
Domesticated Traits | Candidate Gene Name | Candidate Gene Name ID | Validated Method | Reference |
---|---|---|---|---|
Sugar- and acid-related metabolism | NADP-dependent malic enzym | Zj.jz006119090 | Expression profiling | [22] |
6-phosphofructokinase | Zj.jz010621015 | |||
Phosphoglucomutase | Zj.jz021807003 | |||
Sugar transporters | Zj.jz042571026 | |||
Zj.jz036789032 | ||||
Zj.jz034227050 | ||||
Zj.jz002249011 | ||||
Zj.jz002249010 | ||||
Pyruvate kinase | Zj.jz006429010 | |||
ERD6-like Sugar transporter | Zj.jz001627070 | |||
Zj.jz007429007 | ||||
Zj.jz007429005 | ||||
Zj.jz007429006 | ||||
sucrose synthase | Zj.jz031941019 | |||
Pyruvate kinase | Zj.jz006429010 | |||
Fruit shape and kernel shape | FS3 | Zj.jz044531027 | GWAS, qPCR, and Transgenic | [31] |
Bearing shoots | NLBS | Zj.jz003639032 | GWAS | |
Prickles on bearing shoots | HDG2 | Zj.jz044447010 | GWAS | |
BLT1 | Zj.jz040945037 | |||
Seed-setting rate | OVA4 | Zj.jz006119092 | GWAS | |
MIK1 | Zj.jz007373151 | |||
RAD51D | Zj.jz001293012 | |||
Fruit softening | Polygalacturonase | Zj.jz044553003 | NO | |
Flowering time | Early flowering 3 | Zj.jz000799141 | NO | [30] |
Seed-setting rate | POD1 | Zj.jz015743041 | GWAS, qPCR | |
Fruit weight | DA3/UBP14 | Zj.jz038707057 | GWAS, qPCR and Transgenic | |
Fruit size | FW2.2/CNR1 | Zj.jz029849045 | NO | |
Environmental adaptation | Histidine kinase 4 | Zijuj10G0113500 | NO | [23] |
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Zhang, S.; Chen, Z.; Feng, L.; Zhi, Z.; Liu, Y.; Zhang, M.; Yue, H.; Zhu, G.-P.; Gao, F. The Transcriptional Regulatory Mechanisms Exploration of Jujube Biological Traits through Multi-Omics Analysis. Forests 2024, 15, 395. https://doi.org/10.3390/f15020395
Zhang S, Chen Z, Feng L, Zhi Z, Liu Y, Zhang M, Yue H, Zhu G-P, Gao F. The Transcriptional Regulatory Mechanisms Exploration of Jujube Biological Traits through Multi-Omics Analysis. Forests. 2024; 15(2):395. https://doi.org/10.3390/f15020395
Chicago/Turabian StyleZhang, Shulin, Zhuo Chen, Luying Feng, Zhaokun Zhi, Yiteng Liu, Mengmeng Zhang, Huafeng Yue, Gao-Pu Zhu, and Fuling Gao. 2024. "The Transcriptional Regulatory Mechanisms Exploration of Jujube Biological Traits through Multi-Omics Analysis" Forests 15, no. 2: 395. https://doi.org/10.3390/f15020395
APA StyleZhang, S., Chen, Z., Feng, L., Zhi, Z., Liu, Y., Zhang, M., Yue, H., Zhu, G.-P., & Gao, F. (2024). The Transcriptional Regulatory Mechanisms Exploration of Jujube Biological Traits through Multi-Omics Analysis. Forests, 15(2), 395. https://doi.org/10.3390/f15020395