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Mirzaghaderi G. Genome-wide analysis of MADS-box transcription factor gene family in wild emmer wheat (Triticum turgidum subsp. dicoccoides). PLoS One 2024; 19:e0300159. [PMID: 38451993 PMCID: PMC10919676 DOI: 10.1371/journal.pone.0300159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/19/2024] [Indexed: 03/09/2024] Open
Abstract
The members of MADS-box gene family have important roles in regulating the growth and development of plants. MADS-box genes are highly regarded for their potential to enhance grain yield and quality under shifting global conditions. Wild emmer wheat (Triticum turgidum subsp. dicoccoides) is a progenitor of common wheat and harbors valuable traits for wheat improvement. Here, a total of 117 MADS-box genes were identified in the wild emmer wheat genome and classified to 90 MIKCC, 3 MIKC*, and 24 M-type. Furthermore, a phylogenetic analysis and expression profiling of the emmer wheat MADS-box gene family was presented. Although some MADS-box genes belonging to SOC1, SEP1, AGL17, and FLC groups have been expanded in wild emmer wheat, the number of MIKC-type MADS-box genes per subgenome is similar to that of rice and Arabidopsis. On the other hand, M-type genes of wild emmer wheat is less frequent than that of Arabidopsis. Gene expression patterns over different tissues and developmental stages agreed with the subfamily classification of MADS-box genes and was similar to common wheat and rice, indicating their conserved functionality. Some TdMADS-box genes are also differentially expressed under drought stress. The promoter region of each of the TdMADS-box genes harbored 6 to 48 responsive elements, mainly related to light, however hormone, drought, and low-temperature related cis-acting elements were also present. In conclusion, the results provide detailed information about the MADS-box genes of wild emmer wheat. The present work could be useful in the functional genomics efforts toward breeding for agronomically important traits in T. dicoccoides.
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Affiliation(s)
- Ghader Mirzaghaderi
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
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2
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Jia J, Zhao G, Li D, Wang K, Kong C, Deng P, Yan X, Zhang X, Lu Z, Xu S, Jiao Y, Chong K, Liu X, Cui D, Li G, Zhang Y, Du C, Wu L, Li T, Yan D, Zhan K, Chen F, Wang Z, Zhang L, Kong X, Ru Z, Wang D, Gao L. Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement. MOLECULAR PLANT 2023; 16:1893-1910. [PMID: 37897037 DOI: 10.1016/j.molp.2023.10.015] [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: 08/14/2022] [Revised: 07/12/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023]
Abstract
Despite recent progress in crop genomics studies, the genomic changes brought about by modern breeding selection are still poorly understood, thus hampering genomics-assisted breeding, especially in polyploid crops with compound genomes such as common wheat (Triticum aestivum). In this work, we constructed genome resources for the modern elite common wheat variety Aikang 58 (AK58). Comparative genomics between AK58 and the landrace cultivar Chinese Spring (CS) shed light on genomic changes that occurred through recent varietal improvement. We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study (HGWAS) approach, which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci. A total of 123 major HGWAS loci were detected using a genetic population derived from AK58 and CS. Elite homoeologous haplotypes (HHs), formed by combinations of subgenomic homoeologs of the associated loci, were found in both parents and progeny, and many could substantially improve wheat yield and related traits. We built a website where users can download genome assembly sequence and annotation data for AK58, perform blast analysis, and run JBrowse. Our work enriches genome resources for wheat, provides new insights into genomic changes during modern wheat improvement, and suggests that efficient mining of elite HHs can make a substantial contribution to genomics-assisted breeding in common wheat and other polyploid crops.
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Affiliation(s)
- Jizeng Jia
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China; State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guangyao Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Danping Li
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kai Wang
- Xi'An Shansheng Biosciences Co., Ltd., Xi'an 710000, China
| | - Chuizheng Kong
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Pingchuan Deng
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 612100, China
| | - Xueqing Yan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueyong Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zefu Lu
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shujuan Xu
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kang Chong
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dangqun Cui
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Guangwei Li
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chunguang Du
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Liang Wu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; Hainan Yazhou Bay Seed Laboratory, Hainan Institute of Zhejiang University, Sanya, Hainan 562000, China
| | - Tianbao Li
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China; State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dong Yan
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kehui Zhan
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Feng Chen
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Zhiyong Wang
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuying Kong
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Zhengang Ru
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China.
| | - Daowen Wang
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Lifeng Gao
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Xie Z, Zhang L, Zhang Q, Lu Y, Dong C, Li D, Liu X, Xia C, Kong X. A Glu209Lys substitution in DRG1/TaACT7, which disturbs F-actin organization, reduces plant height and grain length in bread wheat. THE NEW PHYTOLOGIST 2023; 240:1913-1929. [PMID: 37668262 DOI: 10.1111/nph.19246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/14/2023] [Indexed: 09/06/2023]
Abstract
Plant height and grain size are two important agronomic traits that are closely related to crop yield. Numerous dwarf and grain-shape mutants have been studied to identify genes that can be used to increase crop yield and improve breeding programs. In this study, we characterized a dominant mutant, dwarf and round grain 1 (drg1-D), in bread wheat (Triticum aestivum L.). drg1-D plants exhibit multiple phenotypic changes, including dwarfism, round grains, and insensitivity to brassinosteroids (BR). Cell structure observation in drg1-D mutant plants showed that the reduced organ size is due to irregular cell shape. Using map-based cloning and verification in transgenic plants, we found that a Glu209Lys substitution in the DRG1 protein is responsible for the irregular cell size and arrangement in the drg1-D mutant. DRG1/TaACT7 encodes an actin family protein that is essential for polymerization stability and microfilament (MF) formation. In addition, the BR response and vesicular transport were altered by the abnormal actin cytoskeleton in drg1-D mutant plants. Our study demonstrates that DRG1/TaACT7 plays an important role in wheat cell shape determination by modulating actin organization and intracellular material transport, which could in the longer term provide tools to better understand the polymerization of actin and its assembly into filaments and arrays.
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Affiliation(s)
- Zhencheng Xie
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiang Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yan Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chunhao Dong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Danping Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chuan Xia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuying Kong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Wang Z, Miao L, Chen Y, Peng H, Ni Z, Sun Q, Guo W. Deciphering the evolution and complexity of wheat germplasm from a genomic perspective. J Genet Genomics 2023; 50:846-860. [PMID: 37611848 DOI: 10.1016/j.jgg.2023.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/29/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023]
Abstract
Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progress in studying on the wheat genome is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research. Here, we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome. New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress, genomic variations at multiple scales contributing to the diversity of wheat germplasm, and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat. Genomics databases and bioinformatics tools meeting the urgent needs of wheat genomics research are also summarized. The ever-increasing omics data, along with advanced tools and well-structured databases, are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.
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Affiliation(s)
- Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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5
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Eragam A, Mohapatra A, Shukla V, Kadumuri RV, George AP, Putta L, Akkareddy S, Chavali S, Vemireddy LR, Ramireddy E. Panicle transcriptome of high-yield mutant indica rice reveals physiological mechanisms and novel candidate regulatory genes for yield under reproductive stage drought stress. BMC PLANT BIOLOGY 2023; 23:493. [PMID: 37833626 PMCID: PMC10571340 DOI: 10.1186/s12870-023-04507-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND Reproductive stage drought stress (RDS) is a major global threat to rice production. Due to climate change, water scarcity is becoming an increasingly common phenomenon in major rice-growing areas worldwide. Understanding RDS mechanisms will allow candidate gene identification to generate novel rice genotypes tolerant to RDS. RESULTS To generate novel rice genotypes that can sustain yield under RDS, we performed gamma-irradiation mediated mutation breeding in the drought stress susceptible mega rice variety, MTU1010. One of the mutant MM11 (MTU1010 derived mutant11) shows consistently increased performance in yield-related traits under field conditions consecutively for four generations. In addition, compared to MTU1010, the yield of MM11 is sustained in prolonged drought imposed during the reproductive stage under field and in pot culture conditions. A comparative emerged panicle transcriptome analysis of the MTU1010 and MM11 suggested metabolic adjustment, enhanced photosynthetic ability, and hormone interplay in regulating yield under drought responses during emerged panicle development. Regulatory network analysis revealed few putative significant transcription factor (TF)-target interactions involved in integrated signalling between panicle development, yield and drought stress. CONCLUSIONS A gamma-irradiate rice mutant MM11 was identified by mutation breeding, and it showed higher potential to sustain yield under reproductive stage drought stress in field and pot culture conditions. Further, a comparative panicle transcriptome revealed significant biological processes and molecular regulators involved in emerged panicle development, yield and drought stress integration. The study extends our understanding of the physiological mechanisms and candidate genes involved in sustaining yield under drought stress.
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Affiliation(s)
- Aparna Eragam
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India
| | - Ankita Mohapatra
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Vishnu Shukla
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Rajashekar Varma Kadumuri
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Abin Panackal George
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Latha Putta
- Regional Agricultural Research Station (RARS), ANGRAU, Tirupati, India
| | | | - Sreenivas Chavali
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Lakshminarayana R Vemireddy
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India.
| | - Eswarayya Ramireddy
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India.
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Fan Y, Li M, Wu Y, Wang X, Wang P, Zhang L, Meng X, Meng F, Li Y. Characterization of thioredoxin gene TaTrxh9 associated with heading-time regulation in wheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107903. [PMID: 37499575 DOI: 10.1016/j.plaphy.2023.107903] [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: 02/28/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 07/29/2023]
Abstract
Thioredoxins (Trxs) are thiol-disulfide oxidoreductase proteins that play important roles in a spectrum of processes linking redox regulation and signaling in plants. However, little is known about Trxs and their biological functions in wheat, one of the most important food crops worldwide. This study reports the identification and functional characterization of an h-type Trx gene, TaTrxh9, in wheat. Three homoeologs of TaTrxh9 were identified and the sequences in the coding region were highly consistent among the homoeologs. Protein characterization showed that a conserved Trx_family domain, as well as a typical active site with a dithiol signature (WCGPC), was included in TaTrxh9. Structural modeling demonstrated that TaTrxh9 could fold into a canonical thioredoxin structure consisting of five-stranded antiparallel beta sheets sandwiched between four alpha helices. The insulin disulfide reduction assay demonstrated that TaTrxh9 was catalytically active in vitro. TaTrxh9 overexpression in the Arabidopsis mutant trxh9 complemented the abnormal growth phenotypes of the mutant, suggesting is functionality in vivo. The transcription level of TaTrxh9 was higher in leaf tissues and it was differentially expressed during the development of wheat plants. Interestingly, barley stripe mosaic virus-mediated suppression of TaTrxh9 shortened the seedling-heading period of wheat. Furthermore, CRISPR-Cas9 mediated gene knockout confirmed that the TaTrxh9 mutation resulted in early heading of wheat. To our knowledge, this study is the first to report that Trxh is associated with heading-time regulation, which lays a foundation for further exploring the biological function of TaTrxh9 and provides new ideas for molecular breeding focusing on early heading in wheat.
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Affiliation(s)
- Yadong Fan
- Henan Technology Innovation Center of Wheat, Henan Agricultural University, Zhengzhou, 450046, China; College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China; State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Mengyuan Li
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China; College of Life Sciences, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yujie Wu
- Henan Technology Innovation Center of Wheat, Henan Agricultural University, Zhengzhou, 450046, China; College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China; State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiaoteng Wang
- Henan Technology Innovation Center of Wheat, Henan Agricultural University, Zhengzhou, 450046, China; College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China; State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Putong Wang
- Henan Technology Innovation Center of Wheat, Henan Agricultural University, Zhengzhou, 450046, China; College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China; State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Li Zhang
- Henan Technology Innovation Center of Wheat, Henan Agricultural University, Zhengzhou, 450046, China; College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiaodan Meng
- Henan Technology Innovation Center of Wheat, Henan Agricultural University, Zhengzhou, 450046, China; College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Fanrong Meng
- State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China; College of Life Sciences, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Yongchun Li
- Henan Technology Innovation Center of Wheat, Henan Agricultural University, Zhengzhou, 450046, China; College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China; State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China.
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7
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Hu G, Li J, Wang X, Kang Y, Li Y, Niu J, Yin J. Molecular Evolution and Genetic Variation of G2-Like Transcription Factor Genes in Wheat ( Triticum aestivum L.). Genes (Basel) 2023; 14:1341. [PMID: 37510246 PMCID: PMC10379295 DOI: 10.3390/genes14071341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/16/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
The GOLDEN2-LIKE (G2-like) gene family members provide significant contributions to the growth and development of plants. In this study, a total of 76 wheat G2-like gene family members (TaG1-TaG76) were detected in the wheat genome and were categorized into three groups (including six subgroups) based on the gene structure and protein motif analyses. These genes were unevenly distributed in 19 of 21 wheat chromosomes. A total of 63 segmental duplication pairs of TaG2-like genes were identified in the wheat genome. The expression levels of all the TaG2-like genes indicated that TaG2-like genes showed different expression patterns in various organs and tissues. Moreover, the transcriptions of TaG2-like genes were significantly affected under abiotic stress (cold, ABA, NaCl, and PEG). This study offered valuable insights into the functional characterization of TaG2-like genes in wheat.
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Affiliation(s)
- Ge Hu
- National Engineering Research Centre for Wheat/Henan Technology Innovation Centre of Wheat, Henan Agricultural University, Zhengzhou 450046, China
| | - Junchang Li
- National Engineering Research Centre for Wheat/Henan Technology Innovation Centre of Wheat, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiang Wang
- National Engineering Research Centre for Wheat/Henan Technology Innovation Centre of Wheat, Henan Agricultural University, Zhengzhou 450046, China
| | - Yunfei Kang
- National Engineering Research Centre for Wheat/Henan Technology Innovation Centre of Wheat, Henan Agricultural University, Zhengzhou 450046, China
| | - Yongchun Li
- National Engineering Research Centre for Wheat/Henan Technology Innovation Centre of Wheat, Henan Agricultural University, Zhengzhou 450046, China
| | - Jishan Niu
- National Engineering Research Centre for Wheat/Henan Technology Innovation Centre of Wheat, Henan Agricultural University, Zhengzhou 450046, China
| | - Jun Yin
- National Engineering Research Centre for Wheat/Henan Technology Innovation Centre of Wheat, Henan Agricultural University, Zhengzhou 450046, China
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8
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Yang Y, Cui L, Lu Z, Li G, Yang Z, Zhao G, Kong C, Li D, Chen Y, Xie Z, Chen Z, Zhang L, Xia C, Liu X, Jia J, Kong X. Genome sequencing of Sitopsis species provides insights into their contribution to the B subgenome of bread wheat. PLANT COMMUNICATIONS 2023:100567. [PMID: 36855304 PMCID: PMC10363506 DOI: 10.1016/j.xplc.2023.100567] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 02/14/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Wheat (Triticum aestivum, BBAADD) is an allohexaploid species that originated from two polyploidization events. The progenitors of the A and D subgenomes have been identified as Triticum urartu and Aegilops tauschii, respectively. Current research suggests that Aegilops speltoides is the closest but not the direct ancestor of the B subgenome. However, whether Ae. speltoides has contributed genomically to the wheat B subgenome and which chromosome regions are conserved between Ae. speltoides and the B subgenome remain unclear. Here, we assembled a high-quality reference genome for Ae. speltoides, resequenced 53 accessions from seven species (Aegilops bicornis, Aegilops longissima, Aegilops searsii, Aegilops sharonensis, Ae. speltoides, Aegilops mutica [syn. Amblyopyrum muticum], and Triticum dicoccoides) and revealed their genomic contributions to the wheat B subgenome. Our results showed that centromeric regions were particularly conserved between Aegilops and Triticum and revealed 0.17 Gb of conserved blocks between Ae. speltoides and the B subgenome. We classified five groups of conserved and non-conserved genes between Aegilops and Triticum, revealing their biological characteristics, differentiation in gene expression patterns, and collinear relationships between Ae. speltoides and the wheat B subgenome. We also identified gene families that expanded in Ae. speltoides during its evolution and 789 genes specific to Ae. speltoides. These genes can serve as genetic resources for improvement of adaptability to biotic and abiotic stress. The newly constructed reference genome and large-scale resequencing data for Sitopsis species will provide a valuable genomic resource for wheat genetic improvement and genomic studies.
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Affiliation(s)
- Yuxin Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Licao Cui
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zefu Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Guangyao Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuizheng Kong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Danping Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yaoyu Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhencheng Xie
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhongxu Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuan Xia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jizeng Jia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xiuying Kong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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9
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Wu L, Fredua-Agyeman R, Strelkov SE, Chang KF, Hwang SF. Identification of Novel Genes Associated with Partial Resistance to Aphanomyces Root Rot in Field Pea by BSR-Seq Analysis. Int J Mol Sci 2022; 23:9744. [PMID: 36077139 PMCID: PMC9456226 DOI: 10.3390/ijms23179744] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 12/04/2022] Open
Abstract
Aphanomyces root rot, caused by Aphanomyces euteiches, causes severe yield loss in field pea (Pisum sativum). The identification of a pea germplasm resistant to this disease is an important breeding objective. Polygenetic resistance has been reported in the field pea cultivar '00-2067'. To facilitate marker-assisted selection (MAS), bulked segregant RNA-seq (BSR-seq) analysis was conducted using an F8 RIL population derived from the cross of 'Carman' × '00-2067'. Root rot development was assessed under controlled conditions in replicated experiments. Resistant (R) and susceptible (S) bulks were constructed based on the root rot severity in a greenhouse study. The BSR-seq analysis of the R bulks generated 44,595,510~51,658,688 reads, of which the aligned sequences were linked to 44,757 genes in a reference genome. In total, 2356 differentially expressed genes were identified, of which 44 were used for gene annotation, including defense-related pathways (jasmonate, ethylene and salicylate) and the GO biological process. A total of 344.1 K SNPs were identified between the R and S bulks, of which 395 variants were located in 31 candidate genes. The identification of novel genes associated with partial resistance to Aphanomyces root rot in field pea by BSR-seq may facilitate efforts to improve management of this important disease.
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Affiliation(s)
| | | | | | | | - Sheau-Fang Hwang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
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