Comprehensive Comparative Analysis of the JAZ Gene Family in Common Wheat (Triticum aestivum) and Its D-Subgenome Donor Aegilops tauschii
Abstract
:1. Introduction
2. Results
2.1. Identification of JAZ Genes in Common Wheat and Its D-Genome Donor Ae. tauschii
2.2. Expansion of the JAZ Gene Family in Monocots
2.3. Functional Differentiation of JAZ Genes under JA Induction
2.4. JAZ Genes Displayed Imbalanced Subgenome Duplication in Wheat
2.5. JAZ Genes within QTL Intervals May Be Associated with Spike Development
2.6. JAZ Genes Were Preferentially Selected during Wheat Breeding for Yield
3. Discussion
4. Materials and Methods
4.1. Sequence Analysis of JAZ Genes
4.2. Conserved Motif Identification
4.3. Phylogenetic Analysis
4.4. Plant Materials, RNA Extraction, Library Construction, and Illumina Sequencing
4.5. Transcriptome Data Analysis
4.6. Breeding Selection and Haplotype Comparative Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Luo, M.-C.; Gu, Y.Q.; Puiu, D.; Wang, H.; Twardziok, S.O.; Deal, K.R.; Huo, N.; Zhu, T.; Wang, L.; Wang, Y.; et al. Genome sequence of the progenitor of the wheat d genome Aegilops tauschii. Nature 2017, 551, 498–502. [Google Scholar] [CrossRef]
- Zimin, A.V.; Puiu, D.; Luo, M.-C.; Zhu, T.; Koren, S.; Marçais, G.; Yorke, J.A.; Dvořák, J.; Salzberg, S.L. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a Progenitor of Bread Wheat, with the MaSuRCA Mega-Reads Algorithm. Genome Res. 2017, 27, 787–792. [Google Scholar] [CrossRef] [PubMed]
- Kim, J.-S.; Mizoi, J.; Yoshida, T.; Fujita, Y.; Nakajima, J.; Ohori, T.; Todaka, D.; Nakashima, K.; Hirayama, T.; Shinozaki, K.; et al. An ABRE promoter sequence is involved in osmotic stress-responsive expression of the dreb2a gene, which encodes a transcription factor regulating drought-inducible genes in Arabidopsis. Plant Cell Physiol. 2011, 52, 2136–2146. [Google Scholar] [CrossRef] [PubMed]
- Huo, N.; Dong, L.; Zhang, S.; Wang, Y.; Zhu, T.; Mohr, T.; Altenbach, S.; Liu, Z.; Dvorak, J.; Anderson, O.D.; et al. New insights into structural organization and gene duplication in a 1.75-mb genomic region harboring the α-gliadin gene family in Aegilops tauschii, the Source of Wheat D Genome. Plant J. 2017, 92, 571–583. [Google Scholar] [CrossRef]
- Staswick, P.E.; Tiryaki, I. The oxylipin signal jasmonic acid is activated by an enzyme that conjugates it to isoleucine in Arabidopsis [W]. Plant Cell 2004, 16, 2117–2127. [Google Scholar] [CrossRef] [PubMed]
- Sheard, L.B.; Tan, X.; Mao, H.; Withers, J.; Ben-Nissan, G.; Hinds, T.R.; Kobayashi, Y.; Hsu, F.-F.; Sharon, M.; Browse, J.; et al. Jasmonate perception by inositol-phosphate-potentiated COI1–JAZ co-receptor. Nature 2010, 468, 400–405. [Google Scholar] [CrossRef]
- Thines, B.; Katsir, L.; Melotto, M.; Niu, Y.; Mandaokar, A.; Liu, G.; Nomura, K.; He, S.Y.; Howe, G.A.; Browse, J. JAZ repressor proteins are targets of the SCFCOI1 complex during jasmonate signalling. Nature 2007, 448, 661–665. [Google Scholar] [CrossRef]
- Coleman-Derr, D.; Desgarennes, D.; Fonseca-Garcia, C.; Gross, S.; Clingenpeel, S.; Woyke, T.; North, G.; Visel, A.; Partida-Martinez, L.P.; Tringe, S.G. Plant compartment and biogeography affect microbiome composition in cultivated and native agave species. New Phytol. 2016, 209, 798–811. [Google Scholar] [CrossRef]
- Chini, A.; Fonseca, S.; Fernández, G.; Adie, B.; Chico, J.M.; Lorenzo, O.; García-Casado, G.; López-Vidriero, I.; Lozano, F.M.; Ponce, M.R.; et al. The JAZ family of repressors is the missing link in jasmonate signalling. Nature 2007, 448, 666–671. [Google Scholar] [CrossRef]
- Howe, G.A.; Major, I.T.; Koo, A.J. Modularity in jasmonate signaling for multistress resilience. Annu. Rev. Plant Biol. 2018, 69, 387–415. [Google Scholar] [CrossRef]
- Yan, Y.; Stolz, S.; Chételat, A.; Reymond, P.; Pagni, M.; Dubugnon, L.; Farmer, E.E. A downstream mediator in the growth repression limb of the jasmonate pathway. Plant Cell 2007, 19, 2470–2483. [Google Scholar] [CrossRef] [PubMed]
- Ye, H.; Du, H.; Tang, N.; Li, X.; Xiong, L. Identification and expression profiling analysis of TIFY family genes involved in stress and phytohormone responses in rice. Plant Mol. Biol. 2009, 71, 291–305. [Google Scholar] [CrossRef] [PubMed]
- Han, Y.; Luthe, D. Identification and evolution analysis of the JAZ gene family in maize. BMC Genom. 2021, 22, 256. [Google Scholar] [CrossRef] [PubMed]
- Shrestha, K.; Huang, Y. Genome-wide characterization of the sorghum JAZ gene family and their responses to phytohormone treatments and aphid infestation. Sci. Rep. 2022, 12, 3238. [Google Scholar] [CrossRef] [PubMed]
- Kazan, K.; Manners, J.M. JAZ repressors and the orchestration of phytohormone crosstalk. Trends Plant Sci. 2012, 17, 22–31. [Google Scholar] [CrossRef] [PubMed]
- Hori, Y.; Kurotani, K.; Toda, Y.; Hattori, T.; Takeda, S. Overexpression of the JAZ factors with mutated jas domains causes pleiotropic defects in rice spikelet development. Plant Signal. Behav. 2014, 9, e970414. [Google Scholar] [CrossRef] [PubMed]
- Demianski, A.J.; Chung, K.M.; Kunkel, B.N. Analysis of Arabidopsis JAZ gene expression during Pseudomonas syringae pathogenesis. Mol. Plant Pathol. 2012, 13, 46–57. [Google Scholar] [CrossRef]
- Wang, Y.; Qiao, L.; Bai, J.; Wang, P.; Duan, W.; Yuan, S.; Yuan, G.; Zhang, F.; Zhang, L.; Zhao, C. Genome-wide characterization of jasmonate-zim domain transcription repressors in wheat (Triticum aestivum L.). BMC Genom. 2017, 18, 152. [Google Scholar] [CrossRef] [PubMed]
- Ebel, C.; BenFeki, A.; Hanin, M.; Solano, R.; Chini, A. Characterization of wheat (Triticum Aestivum) TIFY family and role of Triticum durum TdTIFY11a in salt stress tolerance. PLoS ONE 2018, 13, e0200566. [Google Scholar] [CrossRef] [PubMed]
- Xie, S.; Cui, L.; Lei, X.; Yang, G.; Li, J.; Nie, X.; Ji, W. The TIFY gene family in wheat and its progenitors: Genome-wide identification, evolution and expression analysis. Curr. Genom. 2019, 20, 371–388. [Google Scholar] [CrossRef]
- The International Wheat Genome Sequencing Consortium (IWGSC); Appels, R.; Eversole, K.; Stein, N.; Feuillet, C.; Keller, B.; Rogers, J.; Pozniak, C.J.; Choulet, F.; Distelfeld, A.; et al. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 2018, 361, eaar7191. [Google Scholar] [CrossRef]
- Ferrante, A.; Savin, R.; Slafer, G.A. Floret development and grain setting differences between modern durum wheats under contrasting nitrogen availability. J. Exp. Bot. 2013, 64, 169–184. [Google Scholar] [CrossRef] [PubMed]
- Li, A.; Hao, C.; Wang, Z.; Geng, S.; Jia, M.; Wang, F.; Han, X.; Kong, X.; Yin, L.; Tao, S.; et al. Wheat breeding history reveals synergistic selection of pleiotropic genomic sites for plant architecture and grain yield. Mol. Plant 2022, 15, 504–519. [Google Scholar] [CrossRef] [PubMed]
- Hao, C.; Jiao, C.; Hou, J.; Li, T.; Liu, H.; Wang, Y.; Zheng, J.; Liu, H.; Bi, Z.; Xu, F.; et al. Resequencing of 145 landmark cultivars reveals asymmetric sub-genome selection and strong founder genotype effects on wheat breeding in China. Mol. Plant 2020, 13, 1733–1751. [Google Scholar] [CrossRef] [PubMed]
- Lin, X.; Xu, Y.; Wang, D.; Yang, Y.; Zhang, X.; Bie, X.; Gui, L.; Chen, Z.; Ding, Y.; Mao, L.; et al. Systemic identification of wheat spike development regulators by integrated multi-omics, transcriptional network, gwas and genetic analyses. Mol. Plant 2024, 17, 438–459. [Google Scholar] [CrossRef]
- Gabay, G.; Wang, H.; Zhang, J.; Moriconi, J.I.; Burguener, G.F.; Gualano, L.D.; Howell, T.; Lukaszewski, A.; Staskawicz, B.; Cho, M.-J.; et al. Dosage differences in 12-oxophytodienoate reductase genes modulate wheat root growth. Nat. Commun. 2023, 14, 539. [Google Scholar] [CrossRef]
- Chen, C.; Chen, H.; Zhang, Y.; Thomas, H.R.; Frank, M.H.; He, Y.; Xia, R. TBtools: An integrative toolkit developed for interactive analyses of big biological data. Mol. Plant 2020, 13, 1194–1202. [Google Scholar] [CrossRef] [PubMed]
- Duvaud, S.; Gabella, C.; Lisacek, F.; Stockinger, H.; Ioannidis, V.; Durinx, C. Expasy, the Swiss bioinformatics resource portal, as designed by its users. Nucleic Acids Res. 2021, 49, W216–W227. [Google Scholar] [CrossRef]
- Sperschneider, J.; Catanzariti, A.-M.; DeBoer, K.; Petre, B.; Gardiner, D.M.; Singh, K.B.; Dodds, P.N.; Taylor, J.M. LOCALIZER: Subcellular localization prediction of both plant and effector proteins in the plant cell. Sci. Rep. 2017, 7, 44598. [Google Scholar] [CrossRef]
- Anand, L.; Rodriguez Lopez, C.M. ChromoMap: An R package for interactive visualization of multi-omics data and annotation of chromosomes. BMC Bioinform. 2022, 23, 33. [Google Scholar] [CrossRef]
- Bailey, T.L.; Johnson, J.; Grant, C.E.; Noble, W.S. The MEME suite. Nucleic Acids Res. 2015, 43, W39–W49. [Google Scholar] [CrossRef]
- Filipski, A.; Murillo, O.; Freydenzon, A.; Tamura, K.; Kumar, S. Prospects for building large timetrees using molecular data with incomplete gene coverage among species. Mol. Biol. Evol. 2014, 31, 2542–2550. [Google Scholar] [CrossRef]
- Bolger, A.M.; Lohse, M.; Usadel, B. Trimmomatic: A flexible trimmer for illumina sequence data. Bioinformatics 2014, 30, 2114–2120. [Google Scholar] [CrossRef]
- Peng, L.; Wang, L.; Yang, Y.-F.; Zou, M.-M.; He, W.-Y.; Wang, Y.; Wang, Q.; Vasseur, L.; You, M.-S. Transcriptome profiling of the Plutella xyloastella (Lepidoptera: Plutellidae) ovary reveals genes involved in oogenesis. Gene 2017, 637, 90–99. [Google Scholar] [CrossRef]
- Kim, D.; Paggi, J.M.; Park, C.; Bennett, C.; Salzberg, S.L. Graph-based genome alignment and genotyping with hisat2 and hisat-genotype. Nat. Biotechnol. 2019, 37, 907–915. [Google Scholar] [CrossRef]
- Anders, S.; Pyl, P.T.; Huber, W. HTSeq—A Python framework to work with high-throughput sequencing data. Bioinformatics 2015, 31, 166–169. [Google Scholar] [CrossRef]
- Love, M.I.; Huber, W.; Anders, S. Moderated estimation of fold change and dispersion for rna-seq data with deseq2. Genome Biol. 2014, 15, 550. [Google Scholar] [CrossRef]
- Zhang, R.; Jia, G.; Diao, X. geneHapR: An R package for gene haplotypic statistics and visualization. BMC Bioinform. 2023, 24, 199. [Google Scholar] [CrossRef]
Names | ID | Window | Method | Value |
---|---|---|---|---|
TaJAZ4-A | TraesCS4A01G007800 | Chr4A:4832295-4837294 | Pi | 0.341 |
TaJAZ5-A | TraesCS4A01G007900 | Chr4A:4700001-4900000 | Pi | 0.341 |
TaJAZ6-A | TraesCS4A01G008000 | Chr4A:4700001-4900000 | Pi | 0.341 |
TaJAZ7-A | TraesCS5A01G204900 | Chr5A:414700001-415000000 | Pi | 0.330 |
TaJAZ10-B | TraesCS5B01G211000 | Chr7A:381600001-382800000 | Fst | 5.06 |
TaJAZ12-A | TraesCS7A01G201100 | Chr7A:162300001-164900000 | Fst | 10.12 |
TaJAZ13-A | TraesCS7A01G201200 | Chr7A:162300001-164900000 | Fst | 10.12 |
TaJAZ14-A | TraesCS7A01G201300 | Chr7A:162300001-164900000 | Fst | 10.12 |
TaJAZ15-A | TraesCS7A01G201400 | Chr7A:162300001-164900000 | Fst | 10.12 |
TaJAZ16-A | TraesCS7A01G201500 | Chr7A:162300001-164900000 | Fst | 10.12 |
TaJAZ17-A | TraesCS7A01G201600 | Chr7A:162300001-164900000 | Fst | 10.12 |
TaJAZ12-B | TraesCS7B01G107700 | Chr7B:124127813-124132812 | XPCLR | 6.55 |
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Zhai, Z.; Che, Y.; Geng, S.; Liu, S.; Zhang, S.; Cui, D.; Deng, Z.; Fu, M.; Li, Y.; Zou, X.; et al. Comprehensive Comparative Analysis of the JAZ Gene Family in Common Wheat (Triticum aestivum) and Its D-Subgenome Donor Aegilops tauschii. Plants 2024, 13, 1259. https://doi.org/10.3390/plants13091259
Zhai Z, Che Y, Geng S, Liu S, Zhang S, Cui D, Deng Z, Fu M, Li Y, Zou X, et al. Comprehensive Comparative Analysis of the JAZ Gene Family in Common Wheat (Triticum aestivum) and Its D-Subgenome Donor Aegilops tauschii. Plants. 2024; 13(9):1259. https://doi.org/10.3390/plants13091259
Chicago/Turabian StyleZhai, Zhiwen, Yuqing Che, Shuaifeng Geng, Shaoshuai Liu, Shuqin Zhang, Dada Cui, Zhongyin Deng, Mingxue Fu, Yang Li, Xinyu Zou, and et al. 2024. "Comprehensive Comparative Analysis of the JAZ Gene Family in Common Wheat (Triticum aestivum) and Its D-Subgenome Donor Aegilops tauschii" Plants 13, no. 9: 1259. https://doi.org/10.3390/plants13091259