Harnessing Knowledge from Plant Functional Genomics and Multi-Omics for Genetic Improvement
1. Introduction
2. Genome-Wide Characterization of Gene Families in Plants
3. Functional Studies of Genes Regulating Various Traits in Plants
4. Dissecting Important Agronomic Traits through Population Genetics
5. Multi-Omic Analysis Facilitates Plant Functional Genomic and Genetic Improvement Studies
6. Concluding Remarks
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Liu, H.; Li, N.; Zhao, Y.; Kang, G.Z.; Zhao, Y.H.; Xu, H.W. Serine Hydroxymethyltransferase (SHMT) Gene Family in Wheat (Triticum aestivum L.): Identification, Evolution, and Expression Analysis. Agronomy 2022, 12, 1346. [Google Scholar] [CrossRef]
- Liang, Y.; Xia, J.; Jiang, Y.; Bao, Y.; Chen, H.; Wang, D.; Zhang, D.; Yu, J.; Cang, J. Genome-Wide Identification and Analysis of bZIP Gene Family and Resistance of TaABI5 (TabZIP96) under Freezing Stress in Wheat (Triticum aestivum). Int. J. Mol. Sci. 2022, 23, 2351. [Google Scholar] [CrossRef]
- Zhang, Y.; Zheng, L.; Yun, L.; Ji, L.; Li, G.; Ji, M.; Shi, Y.; Zheng, X. Catalase (CAT) Gene Family in Wheat (Triticum aestivum L.): Evolution, Expression Pattern and Function Analysis. Int. J. Mol. Sci. 2022, 23, 542. [Google Scholar] [CrossRef] [PubMed]
- Feng, X.; Li, C.; He, F.; Xu, Y.; Li, L.; Wang, X.; Chen, Q.; Li, F. Genome-Wide Identification of Expansin Genes in Wild Soybean (Glycine soja) and Functional Characterization of Expansin B1 (GsEXPB1) in Soybean Hair Root. Int. J. Mol. Sci. 2022, 23, 5407. [Google Scholar] [CrossRef]
- Sehrish, S.; Sumbal, W.; Xie, M.; Zhao, C.; Zuo, R.; Gao, F.; Liu, S. Genome-Wide Identification and Characterization of SET Domain Family Genes in Brassica napus L. Int. J. Mol. Sci. 2022, 23, 1936. [Google Scholar] [CrossRef]
- Liu, H.; Ye, H.; Wang, J.; Chen, S.; Li, M.; Wang, G.; Hou, N.; Zhao, P. Genome-Wide Identification and Characterization of YABBY Gene Family in Juglans regia and Juglans mandshurica. Agronomy 2022, 12, 1914. [Google Scholar] [CrossRef]
- Li, B.; Zhang, X.; Duan, R.; Han, C.; Yang, J.; Wang, L.; Wang, S.; Su, Y.; Wang, L.; Dong, Y.; et al. Genomic Analysis of the Glutathione S-Transferase Family in Pear (Pyrus communis) and Functional Identification of PcGST57 in Anthocyanin Accumulation. Int. J. Mol. Sci. 2022, 23, 746. [Google Scholar] [CrossRef] [PubMed]
- Wang, Y.; Ge, H.; Ahmad, N.; Li, J.; Wang, Y.; Liu, X.; Liu, W.; Li, X.; Wang, N.; Wang, F.; et al. Genome-Wide Identification of MADS-Box Family Genes in Safflower (Carthamus tinctorius L.) and Functional Analysis of CtMADS24 during Flowering. Int. J. Mol. Sci. 2023, 24, 1026. [Google Scholar] [CrossRef]
- Hrmova, M.; Stratilová, B.; Stratilová, E. Broad Specific Xyloglucan: Xyloglucosyl Transferases Are Formidable Players in the Re-Modelling of Plant Cell Wall Structures. Int. J. Mol. Sci. 2022, 23, 1656. [Google Scholar] [CrossRef] [PubMed]
- Li, L.; Shi, F.; Wang, G.; Guan, Y.; Zhang, Y.; Chen, M.; Chang, J.; Yang, G.; He, G.; Wang, Y.; et al. Conservation and Divergence of SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Family between Wheat and Rice. Int. J. Mol. Sci. 2022, 23, 2099. [Google Scholar] [CrossRef]
- Wang, C.; Zhang, L.; Xie, Y.; Irshad, A.; Guo, H.; Gu, J.; Zhao, L.; Xiong, H.; Zhao, S.; Wang, C.; et al. Agronomic Trait Analysis and Genetic Mapping of a New Wheat Semidwarf Gene Rht-SN33d. Int. J. Mol. Sci. 2023, 24, 583. [Google Scholar] [CrossRef] [PubMed]
- Li, G.; Zeng, X.; Li, Y.; Li, J.; Huang, X.; Zhao, D. BRITTLE CULM17, a Novel Allele of TAC4, Affects the Mechanical Properties of Rice Plants. Int. J. Mol. Sci. 2022, 23, 5305. [Google Scholar] [CrossRef] [PubMed]
- Ji, X.; Gao, Q.; Chen, F.; Bai, M.; Zhuang, Z.; Peng, Y. Mutant lpa1 Analysis of ZmLPA1 Gene Regulates Maize Leaf-Angle Development through the Auxin Pathway. Int. J. Mol. Sci. 2022, 23, 4886. [Google Scholar] [CrossRef]
- Xue, Y.; Zhang, Y.; Shan, J.; Ji, Y.; Zhang, X.; Li, W.; Li, D.; Zhao, L. Growth Repressor GmRAV Binds to the GmGA3ox Promoter to Negatively Regulate Plant Height Development in Soybean. Int. J. Mol. Sci. 2022, 23, 1721. [Google Scholar] [CrossRef]
- Wu, Q.; Liu, Y.; Huang, J. CRISPR-Cas9 Mediated Mutation in OsPUB43 Improves Grain Length and Weight in Rice by Promoting Cell Proliferation in Spikelet Hull. Int. J. Mol. Sci. 2022, 23, 2347. [Google Scholar] [CrossRef]
- Peng, X.; Yu, W.; Chen, Y.; Jiang, Y.; Ji, Y.; Chen, L.; Cheng, B.; Wu, J. A Maize CBM Domain Containing the Protein ZmCBM48-1 Positively Regulates Starch Synthesis in the Rice Endosperm. Int. J. Mol. Sci. 2022, 23, 6598. [Google Scholar] [CrossRef] [PubMed]
- Yoon, J.; Jeong, H.J.; Baek, G.; Yang, J.; Peng, X.; Tun, W.; Kim, S.T.; An, G.; Cho, L.H. A VIN3-like Protein OsVIL1 Is Involved in Grain Yield and Biomass in Rice. Plants 2022, 11, 83. [Google Scholar] [CrossRef] [PubMed]
- Yang, F.; Liu, G.; Wu, Z.; Zhang, D.; Zhang, Y.; You, M.; Li, B.; Zhang, X.; Liang, R. Cloning and Functional Analysis of TaWRI1Ls, the Key Genes for Grain Fatty Acid Synthesis in Bread Wheat. Int. J. Mol. Sci. 2022, 23, 5293. [Google Scholar] [CrossRef]
- Zou, H.; Han, L.; Yuan, M.; Zhang, M.; Zhou, L.; Wang, Y. Sequence Analysis and Functional Verification of the Effects of Three Key Structural Genes, PdTHC2’GT, PdCHS and PdCHI, on the Isosalipurposide Synthesis Pathway in Paeonia delavayi var. lutea. Int. J. Mol. Sci. 2022, 23, 5696. [Google Scholar] [CrossRef]
- Wang, Y.; Zhou, W.; Wu, J.; Xie, K.; Li, X. LjAMT2;2 Promotes Ammonium Nitrogen Transport during Arbuscular Mycorrhizal Fungi Symbiosis in Lotus japonicus. Int. J. Mol. Sci. 2022, 23, 9522. [Google Scholar] [CrossRef]
- Teng, R.M.; Yang, N.; Li, J.W.; Liu, C.F.; Chen, Y.; Li, T.; Wang, Y.H.; Xiong, A.S.; Zhuang, J. Isolation and Characterization of an LBD Transcription Factor CsLBD39 from Tea Plant (Camellia sinensis) and Its Roles in Modulating Nitrate Content by Regulating Nitrate Metabolism-Related Genes. Int. J. Mol. Sci. 2022, 23, 9294. [Google Scholar] [CrossRef]
- Wang, Y.; Huang, X.; Huang, X.; Su, W.; Hao, Y.; Liu, H.; Chen, R.; Song, S. BcSOC1 Promotes Bolting and Stem Elongation in Flowering Chinese Cabbage. Int. J. Mol. Sci. 2022, 23, 3459. [Google Scholar] [CrossRef] [PubMed]
- Wang, Y.J.; Zhen, X.H.; Zhou, Y.J.; Wang, Y.L.; Hou, J.Y.; Wang, X.; Li, R.M.; Liu, J.; Hu, X.W.; Geng, M.T.; et al. MeNINV1: An Alkaline/Neutral Invertase Gene of Manihot esculenta, Enhanced Sucrose Catabolism and Promoted Plant Vegetative Growth in Transgenic Arabidopsis. Plants 2022, 11, 946. [Google Scholar] [CrossRef] [PubMed]
- Chen, L.; Lv, Q.; Yang, W.; Yang, H.; Chen, Q.; Wang, B.; Lei, Y.; Xie, Y. TaNBR1, a Novel Wheat NBR1-like Domain Gene Negatively Regulates Drought Stress Tolerance in Transgenic Arabidopsis. Int. J. Mol. Sci. 2022, 23, 4519. [Google Scholar] [CrossRef] [PubMed]
- Liu, M.; Jiang, J.; Han, Y.; Shi, M.; Li, X.; Wang, Y.; Dong, Z.; Yang, C. Functional Characterization of the Lysine-Specific Histone Demethylases Family in Soybean. Plants 2022, 11, 1398. [Google Scholar] [CrossRef] [PubMed]
- Zhang, M.; Wang, X.; Yang, J.; Wang, Z.; Chen, B.; Zhang, X.; Zhang, D.; Sun, Z.; Wu, J.; Ke, H.; et al. GhENODL6 Isoforms from the Phytocyanin Gene Family Regulated Verticillium Wilt Resistance in Cotton. Int. J. Mol. Sci. 2022, 23, 2913. [Google Scholar] [CrossRef] [PubMed]
- Zheng, T.; Yu, X.; Sun, Y.; Zhang, Q.; Zhang, X.; Tang, M.; Lin, C.; Shen, Z. Expression of a Cytochrome P450 Gene from Bermuda Grass Cynodon dactylon in Soybean Confers Tolerance to Multiple Herbicides. Plants 2022, 11, 949. [Google Scholar] [CrossRef]
- Cong, C.; Tan, J.; Li, C.; Liu, F.; Yu, Q.; Zhu, L.; Li, Y. Cloning of Maize TED Transposon into Escherichia coli Reveals the Polychromatic Sequence Landscape of Refractorily Propagated Plasmids. Int. J. Mol. Sci. 2022, 23, 11993. [Google Scholar] [CrossRef] [PubMed]
- Hwarari, D.; Guan, Y.; Ahmad, B.; Movahedi, A.; Min, T.; Hao, Z.; Lu, Y.; Chen, J.; Yang, L. ICE-CBF-COR Signaling Cascade and Its Regulation in Plants Responding to Cold Stress. Int. J. Mol. Sci. 2022, 23, 1549. [Google Scholar] [CrossRef]
- Sun, X.; Sun, X.; Pan, X.; Zhang, H.; Wang, Y.; Ren, H.; Wang, F. Identification and Fine Mapping of a Quantitative Trait Locus Controlling the Total Flower and Pod Numbers in Soybean. Agronomy 2022, 12, 790. [Google Scholar] [CrossRef]
- Di, Q.; Piersanti, A.; Zhang, Q.; Miceli, C.; Li, H.; Liu, X. Genome-Wide Association Study Identifies Candidate Genes Related to the Linoleic Acid Content in Soybean Seeds. Int. J. Mol. Sci. 2022, 23, 454. [Google Scholar] [CrossRef] [PubMed]
- Feng, X.; Du, X.; Wang, S.; Deng, P.; Wang, Y.; Shang, L.; Tian, Z.; Wang, C.; Chen, C.; Zhao, J.; et al. Identification and DNA Marker Development for a Wheat-Leymus mollis 2Ns (2D) Disomic Chromosome Substitution. Int. J. Mol. Sci. 2022, 23, 2676. [Google Scholar] [CrossRef]
- Yao, D.; Ijaz, W.; Liu, Y.; Hu, J.; Peng, W.; Zhang, B.; Wen, X.; Wang, J.; Qiu, D.; Li, H.; et al. Identification of a Pm4 Allele as a Powdery Mildew Resistance Gene in Wheat Line Xiaomaomai. Int. J. Mol. Sci. 2022, 23, 1194. [Google Scholar] [CrossRef] [PubMed]
- Guan, H.; Chen, X.; Wang, K.; Liu, X.; Zhang, D.; Li, Y.; Song, Y.; Shi, Y.; Wang, T.; Li, C.; et al. Genetic Variation in ZmPAT7 Contributes to Tassel Branch Number in Maize. Int. J. Mol. Sci. 2022, 23, 2586. [Google Scholar] [CrossRef] [PubMed]
- Xu, J.; Qin, X.; Ni, Z.; Chen, F.; Fu, X.; Yu, F. Identification of Zinc Effificiency-Associated Loci (ZEALs) and Candidate Genes for Zn Deficiency Tolerance of Two Recombination Inbred Line Populations in Maize. Int. J. Mol. Sci. 2022, 23, 4852. [Google Scholar] [CrossRef]
- Lu, H.; Wu, H.; Zhu, G.; Yin, C.; Zhao, L.; Wen, J.; Yi, B.; Ma, C.; Tu, J.; Fu, T.; et al. Identification and Fine Mapping of the Candidate Gene Controlling Multi-Inflorescence in Brassica napus. Int. J. Mol. Sci. 2022, 23, 7244. [Google Scholar] [CrossRef] [PubMed]
- Sodedji, F.A.K.; Ryu, D.; Choi, J.; Agbahoungba, S.; Assogbadjo, A.E.; N’Guetta, S.P.A.; Jung, J.H.; Nho, C.W.; Kim, H.Y. Genetic Diversity and Association Analysis for Carotenoid Content among Sprouts of Cowpea (Vigna unguiculata L. Walp). Int. J. Mol. Sci. 2022, 23, 3696. [Google Scholar] [CrossRef] [PubMed]
- Zhou, G.; Chen, C.; Liu, X.; Yang, K.; Wang, C.; Lu, X.; Tian, Y.; Chen, H. The Formation of Hollow Trait in Cucumber (Cucumis sativus L.) Fruit Is Controlled by CsALMT2. Int. J. Mol. Sci. 2022, 23, 6173. [Google Scholar] [CrossRef] [PubMed]
- Huang, X.; Huang, X.; Guo, L.; He, L.; Xiao, D.; Zhan, J.; Wang, A.; Liang, R. Comparative Transcriptome Analysis Provides Insights into the Resistance in Pueraria [Pueraria lobata (Willd.) Ohwi] in Response to Pseudo-Rust Disease. Int. J. Mol. Sci. 2022, 23, 5223. [Google Scholar] [CrossRef] [PubMed]
- Jiang, Y.; Liu, S.; Li, L.; Zang, K.; Wang, Y.; Zhao, M.; Wang, K.; Zhu, L.; Chen, P.; Lei, J.; et al. Transcriptome and Phenotype Integrated Analysis Identifies Genes Controlling Ginsenoside Rb1 Biosynthesis and Reveals Their Interactions in the Process in Panax ginseng. Int. J. Mol. Sci. 2022, 23, 14016. [Google Scholar] [CrossRef]
- Li, M.; Zhao, L.; Zhou, Q.; Fang, L.; Luo, D.; Liu, W.; Searle, I.R.; Liu, Z. Transcriptome and Coexpression Network Analyses Provide In-Sights into the Molecular Mechanisms of Hydrogen Cyanide Synthesis during Seed Development in Common Vetch (Vicia sativa L.). Int. J. Mol. Sci. 2022, 23, 2275. [Google Scholar] [CrossRef] [PubMed]
- Sun, Y.; Zhang, D.; Zheng, H.; Wu, Y.; Mei, J.; Ke, L.; Yu, D.; Sun, Y. Biochemical and Expression Analyses Revealed the Involvement of Proanthocyanidins and/or Their Derivatives in Fiber Pigmentation of Gossypium stocksii. Int. J. Mol. Sci. 2022, 23, 1008. [Google Scholar] [CrossRef]
- Yang, J.; Li, L.; Zhang, X.; Wu, S.; Han, X.; Li, X.; Xu, J. Comparative Transcriptomics Analysis of Roots and Leaves under Cd Stress in Calotropis gigantea L. Int. J. Mol. Sci. 2022, 23, 3329. [Google Scholar] [CrossRef] [PubMed]
- Zhang, D.; Tang, J.; Wei, K.; Jia, S.; Jiang, Y.; Cai, H.; Mao, P.; Li, M. Physiological and Molecular Responses of Zoysia japonica to Rust Infection. Int. J. Mol. Sci. 2022, 23, 4185. [Google Scholar] [CrossRef] [PubMed]
- Mei, J.; Wu, Y.; Niu, Q.; Miao, M.; Zhang, D.; Zhao, Y.; Cai, F.; Yu, D.; Ke, L.; Feng, H.; et al. Integrative Analysis of Expression Profiles of mRNA and MicroRNA Provides Insights of Cotton Response to Verticillium dahliae. Int. J. Mol. Sci. 2022, 23, 4702. [Google Scholar] [CrossRef]
- Cai, J.; Lv, L.; Zeng, X.; Zhang, F.; Chen, Y.; Tian, W.; Li, J.; Li, X.; Li, Y. Integrative Analysis of Metabolomics and Transcriptomics Reveals Molecular Mechanisms of Anthocyanin Metabolism in the Zikui Tea Plant (Camellia sinensis cv. Zikui). Int. J. Mol. Sci. 2022, 23, 4780. [Google Scholar] [CrossRef]
- Cheng, H.; Zha, S.; Luo, Y.; Li, L.; Wang, S.; Wu, S.; Cheng, S.; Li, L. JAZ1-3 and MYC2-1 Synergistically Regulate the Transformation from Completely Mixed Flower Buds to Female Flower Buds in Castanea mollisima. Int. J. Mol. Sci. 2022, 23, 6452. [Google Scholar] [CrossRef] [PubMed]
- Zhang, L.; Miao, L.; He, J.; Li, H.; Li, M. The Transcriptome and Metabolome Reveal the Potential Mechanism of Lodging Resistance in Intergeneric Hybrids between Brassica napus and Capsella bursa-pastoris. Int. J. Mol. Sci. 2022, 23, 4481. [Google Scholar] [CrossRef] [PubMed]
- Li, H.; Tahir ul Qamar, M.; Yang, L.; Liang, J.; You, J.; Wang, L. Current Progress, Applications and Challenges of Multi-Omics Approaches in Sesame Genetic Improvement. Int. J. Mol. Sci. 2023, 24, 3105. [Google Scholar] [CrossRef] [PubMed]
- Kirov, I.; Polkhovskaya, E.; Dudnikov, M.; Merkulov, P.; Vlasova, A.; Karlov, G.; Soloviev, A. Searching for a Needle in a Haystack: Cas9-Targeted Nanopore Sequencing and DNA Methylation Profiling of Full-Length Glutenin Genes in a Big Cereal Genome. Plants 2022, 11, 5. [Google Scholar] [CrossRef]
- Qin, G.; Wu, S.; Zhang, L.; Li, Y.; Liu, C.; Yu, J.; Deng, L.; Xiao, G.; Zhang, Z. An Efficient Modular Gateway Recombinase-Based Gene Stacking System for Generating Multi-Trait Transgenic Plants. Plants 2022, 11, 488. [Google Scholar] [CrossRef] [PubMed]
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Wang, Y.; Zeng, J.; Yang, G.; Wan, Y.; Li, Y. Harnessing Knowledge from Plant Functional Genomics and Multi-Omics for Genetic Improvement. Int. J. Mol. Sci. 2023, 24, 10347. https://doi.org/10.3390/ijms241210347
Wang Y, Zeng J, Yang G, Wan Y, Li Y. Harnessing Knowledge from Plant Functional Genomics and Multi-Omics for Genetic Improvement. International Journal of Molecular Sciences. 2023; 24(12):10347. https://doi.org/10.3390/ijms241210347
Chicago/Turabian StyleWang, Yaqiong, Jian Zeng, Guangxiao Yang, Yongfang Wan, and Yin Li. 2023. "Harnessing Knowledge from Plant Functional Genomics and Multi-Omics for Genetic Improvement" International Journal of Molecular Sciences 24, no. 12: 10347. https://doi.org/10.3390/ijms241210347