1
|
Wang P, Wu Y, Zhang J, Si J, Wang X, Jiao Z, Meng X, Zhang L, Meng F, Li Y. TaMIR397-6A and -6B Homoeologs Encode Active miR397 Contributing to the Regulation of Grain Size in Hexaploid Wheat. Int J Mol Sci 2024; 25:7696. [PMID: 39062941 PMCID: PMC11276883 DOI: 10.3390/ijms25147696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/07/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Wheat is one of the most important food crops globally, and understanding the regulation of grain size is crucial for wheat breeding to achieve a higher grain yield. MicroRNAs (miRNAs) play vital roles in plant growth and development. However, the miRNA-mediated mechanism underlying grain size regulation remains largely elusive in wheat. Here, we report the characterization and functional validation of a miRNA, TamiR397a, associated with grain size regulation in wheat. The function of three TaMIR397 homoeologs was determined through histochemical β-glucuronidase-dependent assay. MiRNA expression was detected using quantitative reverse transcription polymerase chain reaction (qRT-PCR), and the function of TamiR397a was validated through its transgenic overexpression and repression in wheat. It was found that TaMIR397-6A and TaMIR397-6B encode active TamiR397a. The expression profiling indicated that TamiR397a was differentially expressed in various tissues and gradually up-regulated during grain filling. The inhibition of TamiR397a perturbed grain development, leading to a decrease in grain size and weight. Conversely, the overexpression of TamiR397a resulted in increased grain size and weight by accelerating the grain filling process. Transcriptome analysis revealed that TamiR397a regulates a set of genes involved in hormone response, desiccation tolerance, regulation of cellular senescence, seed dormancy, and seed maturation biological processes, which are important for grain development. Among the down-regulated genes in the grains of the TamiR397a-overexpressing transgenic plants, 11 putative targets of the miRNA were identified. Taken together, our results demonstrate that TamiR397a is a positive regulator of grain size and weight, offering potential targets for breeding wheat with an increased grain yield.
Collapse
Affiliation(s)
- Putong Wang
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Yujie Wu
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Junhui Zhang
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Jiao Si
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaoteng Wang
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhongfa Jiao
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaodan Meng
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Li Zhang
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Fanrong Meng
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Yongchun Li
- Henan Technology Innovation Center of Wheat, State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| |
Collapse
|
2
|
Ye B, Liu Y, Wang Z, Shen L, Yin C, Shen K, Sun J, Xu X, Sun M, Wu J, He Z, Yu X, Lu F, Hao Y, Guo Z. Genetic basis of geographical differentiation, breeding selection, domestication effects, and breeding application for TaJAZ1 in wheat. J Genet Genomics 2024; 51:665-668. [PMID: 38295875 DOI: 10.1016/j.jgg.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/19/2024] [Accepted: 01/19/2024] [Indexed: 03/08/2024]
Affiliation(s)
- Botao Ye
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangyang Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liping Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; China National Botanical Garden, Beijing 100093, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Kuocheng Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaqiang Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaowan Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mengjing Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; International Maize and Wheat Improvement Center China Office, c/o CAAS, Beijing 100081, China
| | - Xuchang Yu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Lu
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Zifeng Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; China National Botanical Garden, Beijing 100093, China.
| |
Collapse
|
3
|
Leber R, Heuberger M, Widrig V, Jung E, Paux E, Keller B, Sánchez-Martín J. A diverse panel of 755 bread wheat accessions harbors untapped genetic diversity in landraces and reveals novel genetic regions conferring powdery mildew resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:88. [PMID: 38532180 PMCID: PMC10965746 DOI: 10.1007/s00122-024-04582-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
KEY MESSAGE A bread wheat panel reveals rich genetic diversity in Turkish, Pakistani and Iranian landraces and novel resistance loci to diverse powdery mildew isolates via subsetting approaches in association studies. Wheat breeding for disease resistance relies on the availability and use of diverse genetic resources. More than 800,000 wheat accessions are globally conserved in gene banks, but they are mostly uncharacterized for the presence of resistance genes and their potential for agriculture. Based on the selective reduction of previously assembled collections for allele mining for disease resistance, we assembled a trait-customized panel of 755 geographically diverse bread wheat accessions with a focus on landraces, called the LandracePLUS panel. Population structure analysis of this panel based on the TaBW35K SNP array revealed an increased genetic diversity compared to 632 landraces genotyped in an earlier study and 17 high-quality sequenced wheat accessions. The additional genetic diversity found here mostly originated from Turkish, Iranian and Pakistani landraces. We characterized the LandracePLUS panel for resistance to ten diverse isolates of the fungal pathogen powdery mildew. Performing genome-wide association studies and dividing the panel further by a targeted subsetting approach for accessions of distinct geographical origin, we detected several known and already cloned genes, including the Pm2a gene. In addition, we identified 22 putatively novel powdery mildew resistance loci that represent useful sources for resistance breeding and for research on the mildew-wheat pathosystem. Our study shows the value of assembling trait-customized collections and utilizing a diverse range of pathogen races to detect novel loci. It further highlights the importance of integrating landraces of different geographical origins into future diversity studies.
Collapse
Affiliation(s)
- Rebecca Leber
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Matthias Heuberger
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Victoria Widrig
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, 37007, Salamanca, Spain
| | - Esther Jung
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Etienne Paux
- Université Clermont Auvergne, INRAE, GDEC, 63000, Clermont-Ferrand, France
- VetAgro Sup Campus Agronomique, 63370, Lempdes, France
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
| | - Javier Sánchez-Martín
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, 37007, Salamanca, Spain.
| |
Collapse
|
4
|
Dai K, Wang X, Liu H, Qiao P, Wang J, Shi W, Guo J, Diao X. Efficient identification of QTL for agronomic traits in foxtail millet (Setaria italica) using RTM- and MLM-GWAS. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:18. [PMID: 38206376 DOI: 10.1007/s00122-023-04522-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/07/2023] [Indexed: 01/12/2024]
Abstract
KEY MESSAGE Eleven QTLs for agronomic traits were identified by RTM- and MLM-GWAS, putative candidate genes were predicted and two markers for grain weight were developed and validated. Foxtail millet (Setaria italica), the second most cultivated millet crop after pearl millet, is an important grain crop in arid regions. Seven agronomic traits of 408 diverse foxtail millet accessions from 15 provinces in China were evaluated in three environments. They were clustered into two divergent groups based on genotypic data using ADMIXTURE, which was highly consistent with their geographical distribution. Two models for genome-wide association studies (GWAS), namely restricted two-stage multi-locus multi-allele (RTM)-GWAS and mixed linear model (MLM)-GWAS, were used to dissect the genetic architecture of the agronomic traits based on 13,723 SNPs. Eleven quantitative trait loci (QTLs) for seven traits were identified using two models (RTM- and MLM-GWAS). Among them, five were considered stable QTLs that were identified in at least two environments using MLM-GWAS. One putative candidate gene (SETIT_006045mg, Chr4: 744,701-746,852) that can enhance grain weight per panicle was identified based on homologous gene comparison and gene expression analysis and was validated by haplotype analysis of 330 accessions with high-depth (10×) resequencing data (unpublished). In addition, homologous gene comparison and haplotype analysis identified one putative foxtail millet ortholog (SETIT_032906mg, Chr2: 5,020,600-5,029,771) with rice affecting the target traits. Two markers (cGWP6045 and kTGW2906) were developed and validated and can be used for marker-assisted selection of foxtail millet with high grain weight. The results provide a fundamental resource for foxtail millet genetic research and breeding and demonstrate the power of integrating RTM- and MLM-GWAS approaches as a complementary strategy for investigating complex traits in foxtail millet.
Collapse
Affiliation(s)
- Keli Dai
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xin Wang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Hanxiao Liu
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Pengfei Qiao
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Jiaxue Wang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Weiping Shi
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Jie Guo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
5
|
Lindsay P, Swentowsky KW, Jackson D. Cultivating potential: Harnessing plant stem cells for agricultural crop improvement. MOLECULAR PLANT 2024; 17:50-74. [PMID: 38130059 DOI: 10.1016/j.molp.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Meristems are stem cell-containing structures that produce all plant organs and are therefore important targets for crop improvement. Developmental regulators control the balance and rate of cell divisions within the meristem. Altering these regulators impacts meristem architecture and, as a consequence, plant form. In this review, we discuss genes involved in regulating the shoot apical meristem, inflorescence meristem, axillary meristem, root apical meristem, and vascular cambium in plants. We highlight several examples showing how crop breeders have manipulated developmental regulators to modify meristem growth and alter crop traits such as inflorescence size and branching patterns. Plant transformation techniques are another innovation related to plant meristem research because they make crop genome engineering possible. We discuss recent advances on plant transformation made possible by studying genes controlling meristem development. Finally, we conclude with discussions about how meristem research can contribute to crop improvement in the coming decades.
Collapse
Affiliation(s)
- Penelope Lindsay
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| |
Collapse
|