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Guo S, Ai J, Zheng N, Hu H, Xu Z, Chen Q, Li L, Liu Y, Zhang H, Li J, Pan Q, Chen F, Yuan L, Fu J, Gu R, Wang J, Du X. A genome-wide association study uncovers a ZmRap2.7-ZCN9/ZCN10 module to regulate ABA signalling and seed vigour in maize. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38761386 DOI: 10.1111/pbi.14362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/20/2024] [Accepted: 03/24/2024] [Indexed: 05/20/2024]
Abstract
Seed vigour, including rapid, uniform germination and robust seedling establishment under various field conditions, is becoming an increasingly essential agronomic trait for achieving high yield in crops. However, little is known about this important seed quality trait. In this study, we performed a genome-wide association study to identify a key transcription factor ZmRap2.7, which regulates seed vigour through transcriptionally repressing expressions of three ABA signalling genes ZmPYL3, ZmPP2C and ZmABI5 and two phosphatidylethanolamine-binding genes ZCN9 and ZCN10. In addition, ZCN9 and ZCN10 proteins could interact with ZmPYL3, ZmPP2C and ZmABI5 proteins, and loss-of-function of ZmRap2.7 and overexpression of ZCN9 and ZCN10 reduced ABA sensitivity and seed vigour, suggesting a complex regulatory network for regulation of ABA signalling mediated seed vigour. Finally, we showed that four SNPs in ZmRap2.7 coding region influenced its transcriptionally binding activity to the downstream gene promoters. Together with previously identified functional variants within and surrounding ZmRap2.7, we concluded that the distinct allelic variations of ZmRap2.7 were obtained independently during maize domestication and improvement, and responded separately for the diversities of seed vigour, flowering time and brace root development. These results provide novel genes, a new regulatory network and an evolutional mechanism for understanding the molecular mechanism of seed vigour.
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Affiliation(s)
- Shasha Guo
- State Key Laboratory of Maize Bio-breeding, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Junmin Ai
- State Key Laboratory of Maize Bio-breeding, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Nannan Zheng
- State Key Laboratory of Maize Bio-breeding, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Hairui Hu
- State Key Laboratory of Maize Bio-breeding, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhuoyi Xu
- State Key Laboratory of Maize Bio-breeding, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Quanquan Chen
- State Key Laboratory of Maize Bio-breeding, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Li Li
- State Key Laboratory of Maize Bio-breeding, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yunjun Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongwei Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jieping Li
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
| | - Qingchun Pan
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
| | - Fanjun Chen
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
| | - Lixing Yuan
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
| | - Junjie Fu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Riliang Gu
- State Key Laboratory of Maize Bio-breeding, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Joint Research Institute of China Agricultural University in Aksu, Aksu, China
| | - Jianhua Wang
- State Key Laboratory of Maize Bio-breeding, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Xuemei Du
- State Key Laboratory of Maize Bio-breeding, Beijing Innovation Center for Crop Seed Technology (MOA), College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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Htwe YM, Shi P, Zhang D, Li Z, Yu Q, Wang Y. GWAS determined genetic loci associated with callus induction in oil palm tissue culture. PLANT CELL REPORTS 2024; 43:128. [PMID: 38652306 DOI: 10.1007/s00299-024-03221-y] [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: 03/01/2024] [Accepted: 04/14/2024] [Indexed: 04/25/2024]
Abstract
KEY MESSAGE GWAS identified six loci at 25 kb downstream of WAK2, a crucial gene for cell wall and callus formation, enabling development of a SNP marker for enhanced callus induction potential. Efficient callus induction is vital for successful oil palm tissue culture, yet identifying genomic loci and markers for early detection of genotypes with high potential of callus induction remains unclear. In this study, immature male inflorescences from 198 oil palm accessions (dura, tenera and pisifera) were used as explants for tissue culture. Callus induction rates were collected at one-, two- and three-months after inoculation (C1, C2 and C3) as phenotypes. Resequencing generated 11,475,258 high quality single nucleotide polymorphisms (SNPs) as genotypes. GWAS was then performed, and correlation analysis revealed a positive association of C1 with both C2 (R = 0.81) and C3 (R = 0.50), indicating that C1 could be used as the major phenotype for callus induction rate. Therefore, only significant SNPs (P ≤ 0.05) in C1 were identified to develop markers for screening individuals with high potential of callus induction. Among 21 significant SNPs in C1, LD block analysis revealed six SNPs on chromosome 12 (Chr12) potentially linked to callus formation. Subsequently, 13 SNP markers were identified from these loci and electrophoresis results showed that marker C-12 at locus Chr12_12704856 can be used effectively to distinguish the GG allele, which showed the highest probability (69%) of callus induction. Furthermore, a rapid SNP variant detection method without electrophoresis was established via qPCR-based melting curve analysis. Our findings facilitated marker-assisted selection for specific palms with high potential of callus induction using immature male inflorescence as explant, aiding ortet palm selection in oil palm tissue culture.
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Affiliation(s)
- Yin Min Htwe
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Peng Shi
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Dapeng Zhang
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Zhiying Li
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Qun Yu
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Yong Wang
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China.
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McFarland FL, Kaeppler HF. History and current status of embryogenic culture-based tissue culture, transformation and gene editing of maize (Zea mays L.). THE PLANT GENOME 2024:e20451. [PMID: 38600860 DOI: 10.1002/tpg2.20451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/12/2024] [Accepted: 03/20/2024] [Indexed: 04/12/2024]
Abstract
The production of embryogenic callus and somatic embryos is integral to the genetic improvement of crops via genetic transformation and gene editing. Regenerable embryogenic cultures also form the backbone of many micro-propagation processes for crop species. In many species, including maize, the ability to produce embryogenic cultures is highly genotype dependent. While some modern transformation and genome editing methods reduce genotype dependence, these efforts ultimately fall short of producing truly genotype-independent tissue culture methods. Recalcitrant genotypes are still identified in these genotype-flexible processes, and their presence is magnified by the stark contrast with more amenable lines, which may respond more efficiently by orders of magnitude. This review aims to describe the history of research into somatic embryogenesis, embryogenic tissue cultures, and plant transformation, with particular attention paid to maize. Contemporary research into genotype-flexible morphogenic gene-based transformation and genome engineering is also covered in this review. The rapid evolution of plant biotechnology from nascent technologies in the latter half of the 20th century to well-established, work-horse production processes has, and will continue to, fundamentally changed agriculture and plant genetics research.
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Affiliation(s)
- Frank L McFarland
- Department of Plant and Agroecosystem Sciences, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Crop Innovation Center, University of Wisconsin, Middleton, Wisconsin, USA
| | - Heidi F Kaeppler
- Department of Plant and Agroecosystem Sciences, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Crop Innovation Center, University of Wisconsin, Middleton, Wisconsin, USA
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Cho WK, Choi H, Kim SY, Kim E, Paek SH, Kim J, Song J, Heo K, Min J, Jo Y, Lee JH, Moh SH. Transcriptional Changes in Damask Rose Suspension Cell Culture Revealed by RNA Sequencing. PLANTS (BASEL, SWITZERLAND) 2024; 13:602. [PMID: 38475449 DOI: 10.3390/plants13050602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
Damask roses (Rosa x damascena) are widely used in cosmetics and pharmaceutics. Here, we established an in vitro suspension cell culture for calli derived from damask rose petals. We analyzed rose suspension cell transcriptomes obtained at two different time points by RNA sequencing to reveal transcriptional changes during rose suspension cell culture. Of the 580 coding RNAs (1.3%) highly expressed in the suspension rose cells, 68 encoded cell wall-associated proteins. However, most RNAs encoded by the chloroplasts and mitochondria are not expressed. Many highly expressed coding RNAs are involved in translation, catalyzing peptide synthesis in ribosomes. Moreover, the amide metabolic process producing naturally occurring alkaloids was the most abundant metabolic process during the propagation of rose suspension cells. During rose cell propagation, coding RNAs involved in the stress response were upregulated at an early stage, while coding RNAs associated with detoxification and transmembrane transport were upregulated at the late stage. We used transcriptome analyses to reveal important biological processes and molecular mechanisms during rose suspension cell culture. Most non-coding (nc) RNAs were not expressed in the rose suspension cells, but a few ncRNAs with unknown functions were highly expressed. The expression of ncRNAs and their target coding RNAs was highly correlated. Taken together, we revealed significant biological processes and molecular mechanisms occurring during rose suspension cell culture using transcriptome analyses.
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Affiliation(s)
- Won Kyong Cho
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hoseong Choi
- Plant Health Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Soo-Yun Kim
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
| | - Euihyun Kim
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
| | - Seung Hye Paek
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
| | - Jiyeon Kim
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
| | - Jihyeok Song
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
| | - Kyoungyeon Heo
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
| | - Jiae Min
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
| | - Yeonhwa Jo
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jeong Hun Lee
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
| | - Sang Hyun Moh
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
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Zhang W, Zhang H, Zhao G, Wang N, Guo L, Hou X. Molecular mechanism of somatic embryogenesis in paeonia ostii 'Fengdan' based on transcriptome analysis combined histomorphological observation and metabolite determination. BMC Genomics 2023; 24:665. [PMID: 37924006 PMCID: PMC10625268 DOI: 10.1186/s12864-023-09730-6] [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: 01/05/2023] [Accepted: 10/11/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND Tree peony (Paeonia sect. Moutan DC.) is a famous flower native to China with high ornamental, medicinal, and oil value. However, the low regeneration rate of callus is one of the main constraints for the establishment of a genetic transformation system in tree peony. By histomorphological observation, transcriptomic analysis and metabolite determination, we investigated the molecular mechanism of somatic embryogenesis after the establishment of a culture system and the induction of somatic embryo(SE) formation. RESULTS We found that SE formation was successfully induced when cotyledons were used as explants. A total of 3185 differentially expressed genes were screened by comparative transcriptomic analysis of embryogenic callus (EC), SE, and non-embryogenic callus (NEC). Compared to NEC, the auxin synthesis-related genes GH3.6 and PCO2 were up-regulated, whereas cytokinin dehydrogenase (CKX6) and CYP450 family genes were down-regulated in somatic embryogenesis. In SE, the auxin content was significantly higher than the cytokinin content. The methyltransferase-related gene S-adenosylmethionine synthase (SAMS) and the flavonoid biosynthesis-related gene (ANS and F3'5'H) were down-regulated in somatic embryogenesis. The determination of flavonoids showed that rhoifolin and hyperoside had the highest content in SE. The results of transcriptome analysis were consistent with the relative expression of 8 candidate genes by quantitative polymerase chain reaction analysis. CONCLUSION The results revealed that auxin and cytokinin may play a key role in 'Fengdan' somatic embryogenesis. The genes related to somatic embryogenesis were revealed, which has partly elucidated the molecular mechanism of somatic embryogenesis in 'Fengdan'.
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Affiliation(s)
- Wanqing Zhang
- Agricultural college, Henan University of Science and Technology, 471023, Luoyang, Henan, China
| | - Hongxiao Zhang
- Agricultural college, Henan University of Science and Technology, 471023, Luoyang, Henan, China
| | - Guodong Zhao
- National Peony Gene Bank, 471011, Luoyang, Henan, China
| | - Na Wang
- Agricultural college, Henan University of Science and Technology, 471023, Luoyang, Henan, China
| | - Lili Guo
- Agricultural college, Henan University of Science and Technology, 471023, Luoyang, Henan, China
| | - Xiaogai Hou
- Agricultural college, Henan University of Science and Technology, 471023, Luoyang, Henan, China.
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Park JS, Choi Y, Jeong MG, Jeong YI, Han JH, Choi HK. Uncovering transcriptional reprogramming during callus development in soybean: insights and implications. FRONTIERS IN PLANT SCIENCE 2023; 14:1239917. [PMID: 37600197 PMCID: PMC10436568 DOI: 10.3389/fpls.2023.1239917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/21/2023] [Indexed: 08/22/2023]
Abstract
Callus, a valuable tool in plant genetic engineering, originates from dedifferentiated cells. While transcriptional reprogramming during callus formation has been extensively studied in Arabidopsis thaliana, our knowledge of this process in other species, such as Glycine max, remains limited. To bridge this gap, our study focused on conducting a time-series transcriptome analysis of soybean callus cultured for various durations (0, 1, 7, 14, 28, and 42 days) on a callus induction medium following wounding with the attempt of identifying genes that play key roles during callus formation. As the result, we detected a total of 27,639 alterations in gene expression during callus formation, which could be categorized into eight distinct clusters. Gene ontology analysis revealed that genes associated with hormones, cell wall modification, and cell cycle underwent transcriptional reprogramming throughout callus formation. Furthermore, by scrutinizing the expression patterns of genes related to hormones, cell cycle, cell wall, and transcription factors, we discovered that auxin, cytokinin, and brassinosteroid signaling pathways activate genes involved in both root and shoot meristem development during callus formation. In summary, our transcriptome analysis provides significant insights into the molecular mechanisms governing callus formation in soybean. The information obtained from this study contributes to a deeper understanding of this intricate process and paves the way for further investigation in the field.
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Affiliation(s)
- Joo-Seok Park
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Yoram Choi
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Min-Gyun Jeong
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Yeong-Il Jeong
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Ji-Hyun Han
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Hong-Kyu Choi
- Department of Molecular Genetics, Dong-A University, Busan, Republic of Korea
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Bravo-Vázquez LA, Angulo-Bejarano PI, Bandyopadhyay A, Sharma A, Paul S. Regulatory roles of noncoding RNAs in callus induction and plant cell dedifferentiation. PLANT CELL REPORTS 2023; 42:689-705. [PMID: 36753041 DOI: 10.1007/s00299-023-02992-0] [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: 11/11/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Plant regulatory noncoding RNAs (ncRNAs) have emerged as key modulators of gene expression during callus induction. Their further study may promote the design of innovative plant tissue culture protocols. The use of plants by humans has recently taken on a new and expanding insight due to the advent of genetic engineering technologies. In this context, callus cultures have shown remarkable potential for synthesizing valuable biomolecules, crop improvement, plant micropropagation, and biodiversity preservation. A crucial stage in callus production is the conversion of somatic cells into totipotent cells; compelling evidence indicates that stress factors, transcriptional regulators, and plant hormones can trigger this biological event. Besides, posttranscriptional regulators of gene expression might be essential participants in callus induction. However, research related to the analysis of noncoding RNAs (ncRNAs) that modulate callogenesis and plant cell dedifferentiation in vitro is still at an early stage. During the last decade, some relevant studies have enlightened the fact that different classes of ncRNAs, such as microRNAs (miRNAs), small interfering RNAs (siRNAs), and long noncoding RNAs (lncRNAs) are implicated in plant cell dedifferentiation through regulating the expression levels of diverse gene targets. Hence, understanding the molecular relevance of these ncRNAs in the aforesaid biological processes might represent a promising source of new biotechnological approaches for callus culture and plant improvement. In this current work, we review the experimental evidence regarding the prospective roles of ncRNAs in callus induction and plant cell dedifferentiation to promote this field of study.
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Affiliation(s)
- Luis Alberto Bravo-Vázquez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130, Queretaro, Mexico
| | - Paola Isabel Angulo-Bejarano
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130, Queretaro, Mexico
| | - Anindya Bandyopadhyay
- International Rice Research Institute, 4031, Manila, Philippines
- Reliance Industries Ltd., Navi Mumbai, 400701, India
| | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130, Queretaro, Mexico.
| | - Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, 76130, Queretaro, Mexico.
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Deng J, Sun W, Zhang B, Sun S, Xia L, Miao Y, He L, Lindsey K, Yang X, Zhang X. GhTCE1-GhTCEE1 dimers regulate transcriptional reprogramming during wound-induced callus formation in cotton. THE PLANT CELL 2022; 34:4554-4568. [PMID: 35972347 PMCID: PMC9614502 DOI: 10.1093/plcell/koac252] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Wounded plant cells can form callus to seal the wound site. Alternatively, wounding can cause adventitious organogenesis or somatic embryogenesis. These distinct developmental pathways require specific cell fate decisions. Here, we identify GhTCE1, a basic helix-loop-helix family transcription factor, and its interacting partners as a central regulatory module of early cell fate transition during in vitro dedifferentiation of cotton (Gossypium hirsutum). RNAi- or CRISPR/Cas9-mediated loss of GhTCE1 function resulted in excessive accumulation of reactive oxygen species (ROS), arrested callus cell elongation, and increased adventitious organogenesis. In contrast, GhTCE1-overexpressing tissues underwent callus cell growth, but organogenesis was repressed. Transcriptome analysis revealed that several pathways depend on proper regulation of GhTCE1 expression, including lipid transfer pathway components, ROS homeostasis, and cell expansion. GhTCE1 bound to the promoters of the target genes GhLTP2 and GhLTP3, activating their expression synergistically, and the heterodimer TCE1-TCEE1 enhances this activity. GhLTP2- and GhLTP3-deficient tissues accumulated ROS and had arrested callus cell elongation, which was restored by ROS scavengers. These results reveal a unique regulatory network involving ROS and lipid transfer proteins, which act as potential ROS scavengers. This network acts as a switch between unorganized callus growth and organized development during in vitro dedifferentiation of cotton cells.
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Affiliation(s)
| | | | - Boyang Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Simin Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Linjie Xia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuhuan Miao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Liangrong He
- Authors for correspondence: (X.Y.), (L.K.), (L.H.)
| | | | - Xiyan Yang
- Authors for correspondence: (X.Y.), (L.K.), (L.H.)
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Combined QTL Mapping across Multiple Environments and Co-Expression Network Analysis Identified Key Genes for Embryogenic Callus Induction from Immature Maize Embryos. Int J Mol Sci 2022; 23:ijms23158786. [PMID: 35955919 PMCID: PMC9368897 DOI: 10.3390/ijms23158786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 11/26/2022] Open
Abstract
The ability of immature embryos to induce embryogenic callus (EC) is crucial for genetic transformation in maize, which is highly genotype-dependent. To dissect the genetic basis of maize EC induction, we conducted QTL mapping for four EC induction-related traits, the rate of embryogenic callus induction (REC), rate of shoot formation (RSF), length of shoot (LS), and diameter of callus (DC) under three environments by using an IBM Syn10 DH population derived from a cross of B73 and Mo17. These EC induction traits showed high broad-sense heritability (>80%), and significantly negative correlations were observed between REC and each of the other traits across multiple environments. A total of 41 QTLs for EC induction were identified, among which 13, 12, 10, and 6 QTLs were responsible for DC, RSF, LS, and REC, respectively. Among them, three major QTLs accounted for >10% of the phenotypic variation, including qLS1-1 (11.54%), qLS1-3 (10.68%), and qREC4-1 (11.45%). Based on the expression data of the 215 candidate genes located in these QTL intervals, we performed a weighted gene co-expression network analysis (WGCNA). A combined use of KEGG pathway enrichment and eigengene-based connectivity (KME) values identified the EC induction-associated module and four hub genes (Zm00001d028477, Zm00001d047896, Zm00001d034388, and Zm00001d022542). Gene-based association analyses validated that the variations in Zm00001d028477 and Zm00001d034388, which were involved in tryptophan biosynthesis and metabolism, respectively, significantly affected EC induction ability among different inbred lines. Our study brings novel insights into the genetic and molecular mechanisms of EC induction and helps to promote marker-assisted selection of high-REC varieties in maize.
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Chahal LS, Conner JA, Ozias-Akins P. Phylogenetically Distant BABY BOOM Genes From Setaria italica Induce Parthenogenesis in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:863908. [PMID: 35909735 PMCID: PMC9329937 DOI: 10.3389/fpls.2022.863908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/13/2022] [Indexed: 06/02/2023]
Abstract
The combination of apomixis and hybrid production is hailed as the holy grail of agriculture for the ability of apomixis to fix heterosis of F1 hybrids in succeeding generations, thereby eliminating the need for repeated crosses to produce F1 hybrids. Apomixis, asexual reproduction through seed, achieves this feat by circumventing two processes that are fundamental to sexual reproduction (meiosis and fertilization) and replacing them with apomeiosis and parthenogenesis, resulting in seeds that are clonal to the maternal parent. Parthenogenesis, embryo development without fertilization, has been genetically engineered in rice, maize, and pearl millet using PsASGR-BABY BOOM-like (PsASGR-BBML) transgenes and in rice using the OsBABY BOOM1 (OsBBM1) cDNA sequence when expressed under the control of egg cell-specific promoters. A phylogenetic analysis revealed that BABY BOOM (BBM)/BBML genes from monocots cluster within three different clades. The BBM/BBML genes shown to induce parthenogenesis cluster within clade 1 (the ASGR-BBML clade) along with orthologs from other monocot species, such as Setaria italica. For this study, we tested the parthenogenetic potential of three BBM transgenes from S. italica, each a member of a different phylogenetic BBM clade. All transgenes were genomic constructs under the control of the AtDD45 egg cell-specific promoter. All SiBBM transgenes induced various levels of parthenogenetic embryo development, resulting in viable haploid T1 seedlings. Poor seed set and lower haploid seed production were characteristics of multiple transgenic lines. The results presented in this study illustrate that further functional characterization of BBMs in zygote/embryo development is warranted.
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Affiliation(s)
- Lovepreet Singh Chahal
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States
| | - Joann A. Conner
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States
- Department of Horticulture, University of Georgia, Tifton, GA, United States
| | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States
- Department of Horticulture, University of Georgia, Tifton, GA, United States
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11
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Trunjaruen A, Luecha P, Taratima W. Micropropagation of pokeweed ( Phytolacca americana L.) and comparison of phenolic, flavonoid content, and antioxidant activity between pokeweed callus and other parts. PeerJ 2022; 10:e12892. [PMID: 35186483 PMCID: PMC8830332 DOI: 10.7717/peerj.12892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/16/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Pokeweed (Phytolacca americana L.) is regarded as an invasive plant in many parts of the world but possesses therapeutic characteristics used for antitumor and rheumatism treatment. This study investigated the effects of auxins and four explants on pokeweed callus induction. The effects of cytokinins and combinations between cytokinins and NAA on shoot and root induction were also studied. TPC, TFC and antioxidant activity of calli were screened and compared with other pokeweed plant parts. METHODS Four explants were used to induce callus using 2,4-D and IBA at 1, 2, 3 and 4 mg/l for each auxin. Direct shoot organogenesis from nodal explants was investigated using BAP, kinetin and TDZ (1, 2 and 4 mg/l for each cytokinin). Combined effects between cytokinins and NAA at 0.1, 0.2 and 0.3 mg/l were further simultaneously estimated with root induction. Calli derived from the leaves were compared with other plant parts for TPC, TFC and antioxidant activity using the Folin-Ciocalteu, AlCl3 colorimetric assay and DPPH assays, respectively. RESULTS Results showed that MS medium containing 2 mg/l 2,4-D induced callus formation on leaf explants that provided highest fresh and dry weights. Three types of synthetic cytokinins as kinetin, TDZ and BAP were used for direct shoot organogenesis from pokeweed nodes. MS medium containing 2 mg/l kinetin was effective in stimulating normal shoots, with the largest number of shoots and leaves and the longest shoots. The combination between cytokinins and NAA showed no positive effect on shoot and root induction from pokeweed nodal explants. For TPC and TFC determination, pokeweed seeds and leaves possessed the highest phenolic and flavonoid contents, respectively. Highest phenolic content of pokeweed seeds led to lowest IC50 by DPPH assay. Phenolic content was higher than flavonoid content. CONCLUSION Results suggested promising conditions for callus induction. Leaf explants cultured on MS medium with 2 mg/l 2,4-D and nodal explants cultured on MS medium with 2 mg/l kinetin provided the largest number of normal shoots and leaves. NAA did not show positive effects on shoot and root induction when combined with cytokinins. Chemical constituent screening indicated that seeds and leaves provided highest TPC and TFC, respectively, while pokeweed calli contained higher phenolic than flavonoid content. This is the first report describing chemical constituent screening and antioxidant activity of calli and other parts of the pokeweed plant. Results provided significant information to further enhance bioactive compound contents of pokeweed calli using elicitation methods.
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Affiliation(s)
- Attachai Trunjaruen
- Salt-Tolerant Rice Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Prathan Luecha
- Department of Pharmacognosy and Toxicology, Faculty of Pharmaceutical Science, Khon Kaen University, Khon Kaen, Thailand
| | - Worasitikulya Taratima
- Salt-Tolerant Rice Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
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12
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Chen J, Tomes S, Gleave AP, Hall W, Luo Z, Xu J, Yao JL. Significant improvement of apple (Malus domestica Borkh.) transgenic plant production by pre-transformation with a Baby boom transcription factor. HORTICULTURE RESEARCH 2022; 9:uhab014. [PMID: 35039859 PMCID: PMC8795818 DOI: 10.1093/hr/uhab014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/18/2022] [Accepted: 10/16/2021] [Indexed: 05/24/2023]
Abstract
BABY BOOM (BBM) is a member of the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) family and its expression has been shown to improve herbaceous plant transformation and regeneration. However, this improvement has not been shown clearly for tree species. This study demonstrated that the efficiency of transgenic apple (Malus domestica Borkh.) plant production was dramatically increased by ectopic expression of the MdBBM1 gene. "Royal Gala" apple plants were first transformed with a CaMV35S-MdBBM1 construct (MBM) under kanamycin selection. These MBM transgenic plants exhibited enhanced shoot regeneration from leaf explants on tissue culture media, with most plants displaying a close-to-normal phenotype compared with CaMV35S-GUS transgenic plants when grown under greenhouse conditions, the exception being that some plants had slightly curly leaves. Thin leaf sections revealed the MBM plants produced more cells than the GUS plants, indicating that ectopic-expression of MdBBM1 enhanced cell division. Transcriptome analysis showed that mRNA levels for cell division activators and repressors linked to hormone (auxin, cytokinin and brassinosteroid) signalling pathways were enhanced and reduced, respectively, in the MBM plants compared with the GUS plants. Plants of eight independent MBM lines were compared with the GUS plants by re-transforming them with an herbicide-resistant gene construct. The number of transgenic plants produced per 100 leaf explants was 0-3% for the GUS plants, 3-8% for five MBM lines, and 20-30% for three MBM lines. Our results provided a solution for overcoming the barriers to transgenic plant production in apple, and possibly in other trees.
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Affiliation(s)
- Jiajing Chen
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, 430070, China
| | - Sumathi Tomes
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Andrew P Gleave
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Wendy Hall
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Zhiwei Luo
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Juan Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, 430070, China
| | - Jia-Long Yao
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, 32 Gangwan Road
Zhengzhou 450009, China
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13
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Zhang Y, Jiao F, Li J, Pei Y, Zhao M, Song X, Guo X. Transcriptomic analysis of the maize inbred line Chang7-2 and a large-grain mutant tc19. BMC Genomics 2022; 23:4. [PMID: 34983391 PMCID: PMC8725412 DOI: 10.1186/s12864-021-08230-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/10/2021] [Indexed: 11/10/2022] Open
Abstract
Backgrounds Grain size is a key factor in crop yield that gradually develops after pollination. However, few studies have reported gene expression patterns in maize grain development using large-grain mutants. To investigate the developmental mechanisms of grain size, we analyzed a large-grain mutant, named tc19, at the morphological and transcriptome level at five stages corresponding to days after pollination (DAP). Results After maturation, the grain length, width, and thickness in tc19 were greater than that in Chang7-2 (control) and increased by 3.57, 8.80, and 3.88%, respectively. Further analysis showed that grain width and 100-kernel weight in tc19 was lower than in Chang7-2 at 14 and 21 DAP, but greater than that in Chang7-2 at 28 DAP, indicating that 21 to 28 DAP was the critical stage for kernel width and weight development. For all five stages, the concentrations of auxin and brassinosteroids were significantly higher in tc19 than in Chang7-2. Gibberellin was higher at 7, 14, and 21 DAP, and cytokinin was higher at 21 and 35 DAP, in tc19 than in Chang7-2. Through transcriptome analysis at 14, 21, and 28 DAP, we identified 2987, 2647 and 3209 differentially expressed genes (DEGs) between tc19 and Chang7-2. By using KEGG analysis, 556, 500 and 633 DEGs at 14, 21 and 28 DAP were pathway annotated, respectively, 77 of them are related to plant hormone signal transduction pathway. ARF3, AO2, DWF4 and XTH are higher expressed in tc19 than that in Chang7-2. Conclusions We found some DEGs in maize grain development by using Chang7-2 and a large-grain mutant tc19. These DEGs have potential application value in improving maize performance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08230-9.
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Affiliation(s)
- Yanrong Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China.,Key Laboratory of Major Crop Germplasm Innovation and Application in Qingdao, Qingdao, 266109, Shandong, China
| | - Fuchao Jiao
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China.,Key Laboratory of Major Crop Germplasm Innovation and Application in Qingdao, Qingdao, 266109, Shandong, China
| | - Jun Li
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China.,Key Laboratory of Major Crop Germplasm Innovation and Application in Qingdao, Qingdao, 266109, Shandong, China
| | - Yuhe Pei
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China.,Key Laboratory of Major Crop Germplasm Innovation and Application in Qingdao, Qingdao, 266109, Shandong, China
| | - Meiai Zhao
- Key Laboratory of Major Crop Germplasm Innovation and Application in Qingdao, Qingdao, 266109, Shandong, China.,College of Life Science, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xiyun Song
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China. .,Key Laboratory of Major Crop Germplasm Innovation and Application in Qingdao, Qingdao, 266109, Shandong, China.
| | - Xinmei Guo
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China. .,Key Laboratory of Major Crop Germplasm Innovation and Application in Qingdao, Qingdao, 266109, Shandong, China.
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14
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Yassitepe JEDCT, da Silva VCH, Hernandes-Lopes J, Dante RA, Gerhardt IR, Fernandes FR, da Silva PA, Vieira LR, Bonatti V, Arruda P. Maize Transformation: From Plant Material to the Release of Genetically Modified and Edited Varieties. FRONTIERS IN PLANT SCIENCE 2021; 12:766702. [PMID: 34721493 PMCID: PMC8553389 DOI: 10.3389/fpls.2021.766702] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 09/15/2021] [Indexed: 05/17/2023]
Abstract
Over the past decades, advances in plant biotechnology have allowed the development of genetically modified maize varieties that have significantly impacted agricultural management and improved the grain yield worldwide. To date, genetically modified varieties represent 30% of the world's maize cultivated area and incorporate traits such as herbicide, insect and disease resistance, abiotic stress tolerance, high yield, and improved nutritional quality. Maize transformation, which is a prerequisite for genetically modified maize development, is no longer a major bottleneck. Protocols using morphogenic regulators have evolved significantly towards increasing transformation frequency and genotype independence. Emerging technologies using either stable or transient expression and tissue culture-independent methods, such as direct genome editing using RNA-guided endonuclease system as an in vivo desired-target mutator, simultaneous double haploid production and editing/haploid-inducer-mediated genome editing, and pollen transformation, are expected to lead significant progress in maize biotechnology. This review summarises the significant advances in maize transformation protocols, technologies, and applications and discusses the current status, including a pipeline for trait development and regulatory issues related to current and future genetically modified and genetically edited maize varieties.
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Affiliation(s)
- Juliana Erika de Carvalho Teixeira Yassitepe
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Viviane Cristina Heinzen da Silva
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - José Hernandes-Lopes
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Ricardo Augusto Dante
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Isabel Rodrigues Gerhardt
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Fernanda Rausch Fernandes
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Priscila Alves da Silva
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Leticia Rios Vieira
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Vanessa Bonatti
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Paulo Arruda
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
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15
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Kausch AP, Wang K, Kaeppler HF, Gordon-Kamm W. Maize transformation: history, progress, and perspectives. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:38. [PMID: 37309443 PMCID: PMC10236110 DOI: 10.1007/s11032-021-01225-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/14/2021] [Indexed: 06/14/2023]
Abstract
Maize functional genomics research and genetic improvement strategies have been greatly accelerated and refined through the development and utilization of genetic transformation systems. Maize transformation is a composite technology based on decades' efforts in optimizing multiple factors involving microbiology and physical/biochemical DNA delivery, as well as cellular and molecular biology. This review provides a historical reflection on the development of maize transformation technology including the early failures and successful milestones. It also provides a current perspective on the understanding of tissue culture responses and their impact on plant regeneration, the pros and cons of different DNA delivery methods, the identification of a palette of selectable/screenable markers, and most recently the development of growth-stimulating or morphogenic genes to improve efficiencies and extend the range of transformable genotypes. Steady research progress in these interdependent components has been punctuated by benchmark reports celebrating the progress in maize transformation, which invariably relied on a large volume of supporting research that contributed to each step and to the current state of the art. The recent explosive use of CRISPR/Cas9-mediated genome editing has heightened the demand for higher transformation efficiencies, especially for important inbreds, to support increasingly sophisticated and complicated genomic modifications, in a manner that is widely accessible. These trends place an urgent demand on taking maize transformation to the next level, presaging a new generation of improvements on the horizon. Once realized, we anticipate a near-future where readily accessible, genotype-independent maize transformation, together with advanced genomics, genome editing, and accelerated breeding, will contribute to world agriculture and global food security.
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Affiliation(s)
- Albert P. Kausch
- Department of Cell and Molecular Biology, University of Rhode Island, South Kingstown, RI 02892 USA
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Heidi F. Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA
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16
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MicroRNA Zma-miR528 Versatile Regulation on Target mRNAs during Maize Somatic Embryogenesis. Int J Mol Sci 2021; 22:ijms22105310. [PMID: 34069987 PMCID: PMC8157881 DOI: 10.3390/ijms22105310] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate the accumulation and translation of their target mRNAs through sequence complementarity. miRNAs have emerged as crucial regulators during maize somatic embryogenesis (SE) and plant regeneration. A monocot-specific miRNA, mainly accumulated during maize SE, is zma-miR528. While several targets have been described for this miRNA, the regulation has not been experimentally confirmed for the SE process. Here, we explored the accumulation of zma-miR528 and several predicted targets during embryogenic callus induction, proliferation, and plantlet regeneration using the maize cultivar VS-535. We confirmed the cleavage site for all tested zma-miR528 targets; however, PLC1 showed very low levels of processing. The abundance of zma-miR528 slightly decreased in one month-induced callus compared to the immature embryo (IE) explant tissue. However, it displayed a significant increase in four-month sub-cultured callus, coincident with proliferation establishment. In callus-regenerated plantlets, zma-miR528 greatly decreased to levels below those observed in the initial explant. Three of the target transcripts (MATE, bHLH, and SOD1a) showed an inverse correlation with the miRNA abundance in total RNA samples at all stages. Using polysome fractionation, zma-miR528 was detected in the polysome fraction and exhibited an inverse distribution with the PLC1 target, which was not observed at total RNA. Accordingly, we conclude that zma-miR528 regulates multiple target mRNAs during the SE process by promoting their degradation, translation inhibition or both.
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17
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Zeng D, Teixeira da Silva JA, Zhang M, Yu Z, Si C, Zhao C, Dai G, He C, Duan J. Genome-Wide Identification and Analysis of the APETALA2 (AP2) Transcription Factor in Dendrobium officinale. Int J Mol Sci 2021; 22:5221. [PMID: 34069261 PMCID: PMC8156592 DOI: 10.3390/ijms22105221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 11/17/2022] Open
Abstract
The APETALA2 (AP2) transcription factors (TFs) play crucial roles in regulating development in plants. However, a comprehensive analysis of the AP2 family members in a valuable Chinese herbal orchid, Dendrobium officinale, or in other orchids, is limited. In this study, the 14 DoAP2 TFs that were identified from the D. officinale genome and named DoAP2-1 to DoAP2-14 were divided into three clades: euAP2, euANT, and basalANT. The promoters of all DoAP2 genes contained cis-regulatory elements related to plant development and also responsive to plant hormones and stress. qRT-PCR analysis showed the abundant expression of DoAP2-2, DoAP2-5, DoAP2-7, DoAP2-8 and DoAP2-12 genes in protocorm-like bodies (PLBs), while DoAP2-3, DoAP2-4, DoAP2-6, DoAP2-9, DoAP2-10 and DoAP2-11 expression was strong in plantlets. In addition, the expression of some DoAP2 genes was down-regulated during flower development. These results suggest that DoAP2 genes may play roles in plant regeneration and flower development in D. officinale. Four DoAP2 genes (DoAP2-1 from euAP2, DoAP2-2 from euANT, and DoAP2-6 and DoAP2-11 from basal ANT) were selected for further analyses. The transcriptional activation of DoAP2-1, DoAP2-2, DoAP2-6 and DoAP2-11 proteins, which were localized in the nucleus of Arabidopsis thaliana mesophyll protoplasts, was further analyzed by a dual-luciferase reporter gene system in Nicotiana benthamiana leaves. Our data showed that pBD-DoAP2-1, pBD-DoAP2-2, pBD-DoAP2-6 and pBD-DoAP2-11 significantly repressed the expression of the LUC reporter compared with the negative control (pBD), suggesting that these DoAP2 proteins may act as transcriptional repressors in the nucleus of plant cells. Our findings on AP2 genes in D. officinale shed light on the function of AP2 genes in this orchid and other plant species.
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Affiliation(s)
- Danqi Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
- College of Life Sciences, University of the Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | | | - Mingze Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
- College of Life Sciences, University of the Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Zhenming Yu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
| | - Can Si
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
| | - Conghui Zhao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
- College of Life Sciences, University of the Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Guangyi Dai
- Opening Public Laboratory, Chinese Academy of Sciences, Guangzhou 510650, China;
| | - Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
| | - Juan Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (D.Z.); (M.Z.); (Z.Y.); (C.S.); (C.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
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18
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Du X, Fang T, Liu Y, Wang M, Zang M, Huang L, Zhen S, Zhang J, Shi Z, Wang G, Fu J, Liu Y. Global profiling of N 6 -methyladenosine methylation in maize callus induction. THE PLANT GENOME 2020; 13:e20018. [PMID: 33016611 DOI: 10.1002/tpg2.20018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/24/2020] [Accepted: 03/05/2020] [Indexed: 05/26/2023]
Abstract
Callus induction is a dedifferentiation process that accompanies a cell fate transition, and epigenetic regulation plays a crucial role in the process. N6 -methyladenosine (m6A) methylation is an important mechanism in post-transcriptional epigenetic regulation and functions in cell reprogramming. However, the function of m6A methylation during callus induction is still unknown. Here, we performed transcriptome-wide m6A-seq on immature maize embryos after culturing for 2, 4, or 8 days with or without the auxin analogue 2,4-D. A total of 26,794 unique m6A peaks were detected from 17,456 maize genes; and 2,338 specific, 2,4-D-induced m6A peaks (D-specific m6A) were detected only in embryos cultured with 2,4-D. Furthermore, a positive correlation between m6A methylation and mRNA abundance was discovered in the genes with D-specific m6A deposition, especially at the beginning of callus induction. Key genes involved in callus induction, i.e. BABY BOOM and LBD transcription factors, underwent m6A methylation, increasing their transcript levels, thus improving callus induction. These results revealed the importance of m6A methylation during the early stage of callus induction and provided new insights into the molecular mechanism of callus induction at an epitranscriptomic level.
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Affiliation(s)
- Xuemei Du
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ting Fang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meng Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Maosen Zang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Liying Huang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Sihan Zhen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jie Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zichen Shi
- Beijing No.4 High School International Campus, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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