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Davarpanah SJ, Maali-Amiri R, Parastouei K. Effect of low temperature acclimation on developmental regulation of redox responses and phytohormones metabolism in lines of crosses between spring and winter wheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2025; 222:109740. [PMID: 40090075 DOI: 10.1016/j.plaphy.2025.109740] [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: 02/04/2025] [Accepted: 03/03/2025] [Indexed: 03/18/2025]
Abstract
Low temperature (LT) acclimation in winter wheat (Triticum aestivum L.) was related to developmental regulation of transcriptome and metabolome for balancing growth and responses. In this study, six wheat lines from the F8 generation, derived from crosses between spring wheat (Pishtaz) and winter wheat (Claire) with distinct growth habits (based on the Vrn-1 loci) were planted under field conditions. The final leaf number (FLN) and double ridge (DR) formation showed that genotypes without vernalization requirement, including Pishtaz parent, and lines 8041 and 8044 transitioned rapidly into the reproductive stage. They also had lower LT tolerance, antioxidants activity and abscisic acid (ABA) content among genotypes. In these genotypes, cytokinin (CK) and gibberellin (GA3) contents and expression levels of gibberellin 20 oxidase (GA20ox) and gibberellin 3 oxidase (GA3ox) genes, were more active than other genotypes. Facultative lines 8020 and 8025 had higher antioxidants activity and lower hydrogen peroxide (H2O2) and malondialdehyde (MDA) contents compared to spring types. Winter genotypes, including Claire parent, lines 8011 and 8015 had a strong vernalization requirement resulted in prolonged vegetative phase, accompanied by increased LT tolerance, antioxidants activity and expression of ABA biosynthetic genes, confirming that the duration of the vegetative phase plays a key role in determining wheat's winter survival capacity. Higher LT tolerance was effectively related to retarded reproductive phase, minimized redox damages through co-regulating phytohormone-metabolites under developmental periods in winter wheat.
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Affiliation(s)
- Seyed Javad Davarpanah
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Reza Maali-Amiri
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-77871, Iran.
| | - Karim Parastouei
- Health Research Center, Life Style Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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Liu X, Liao N, Tang X, Wang K, Wang W, Khan A, Wang C, Yuan L, Chen G. TMT-label comparative proteomics reveals the vernalization mechanism in Wucai (Brassica campestris L.). J Proteomics 2025; 314:105398. [PMID: 39922279 DOI: 10.1016/j.jprot.2025.105398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Revised: 02/04/2025] [Accepted: 02/04/2025] [Indexed: 02/10/2025]
Abstract
To investigate the molecular basis of vernalization in Wucai [Brassica campestris L. (Syn. Brassica rapa L.) ssp. chinensis var. rosularis Tsen], we performed differential proteomic analysis using a tandem mass tags (TMT)-based approach. Proteins from shoot apices subjected to 0, 15, and 30 days of vernalization (V0, V15, and V30) were analyzed to identify differentially abundant proteins (DAPs). A total of 8066 proteins were obtained, and 507 shared DAPs were involved in both initiation and progression of vernalization. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations revealed functional enrichment in cellular processes, metabolic pathways, and translation-related activities, including photosynthesis, glucosinolate biosynthesis, and flavonoid biosynthesis. Proteomic data showed reduced abundance of photosynthesis-related proteins and upregulation of flavonoid biosynthesis during vernalization. Transcriptional validation of 24 proteins across metabolic and regulatory pathways corroborated proteomic findings, with notable peaks in genes associated with flavonoid biosynthesis at 15 days of vernalization, such as VESR1,CH13, CHS1, FHT, and FLS1. The functions of these genes in vernalization will be further analyzed. SIGNIFICANCE: Wucai is prone to premature bolting and flowering under cold conditions, as vernalization plays a key role in controlling flowering time in Chinese cabbage crops. However, the proteomic basis of vernalization remains poorly understood. In this study, TMT-based proteomic analysis identified DAPs associated with vernalization. Pathway enrichment analysis highlighted key DAPs and their roles in significantly enriched pathways relevant to vernalization. Notably, genes in the flavonoid biosynthesis pathway genes, including VESR1, CH13, CHS1, FHT, and FLS1, respond to vernalization. These findings offer novel insights into the molecular mechanisms underlying flowering time regulation in Wucai.
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Affiliation(s)
- Xueqing Liu
- Anhui Provincial Engineering Research Center for Horticultural Crop Breeding, Hefei 230036, China; College of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Na Liao
- Anhui Provincial Engineering Research Center for Horticultural Crop Breeding, Hefei 230036, China
| | - Xiaoyan Tang
- Anhui Provincial Engineering Research Center for Horticultural Crop Breeding, Hefei 230036, China; College of Horticulture, Anhui Agricultural University, Hefei 230036, China.
| | - Kang Wang
- Anhui Provincial Engineering Research Center for Horticultural Crop Breeding, Hefei 230036, China
| | - Wenjie Wang
- Anhui Provincial Engineering Research Center for Horticultural Crop Breeding, Hefei 230036, China.
| | - Afrasyab Khan
- Anhui Provincial Engineering Research Center for Horticultural Crop Breeding, Hefei 230036, China
| | - Chenggang Wang
- Anhui Provincial Engineering Research Center for Horticultural Crop Breeding, Hefei 230036, China; College of Horticulture, Anhui Agricultural University, Hefei 230036, China.
| | - Lingyun Yuan
- Anhui Provincial Engineering Research Center for Horticultural Crop Breeding, Hefei 230036, China.
| | - Guohu Chen
- Anhui Provincial Engineering Research Center for Horticultural Crop Breeding, Hefei 230036, China; College of Horticulture, Anhui Agricultural University, Hefei 230036, China.
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Díaz Suárez L, Inagaki H, Hirata H, Akimoto Y, Sakakibayashi K, Seino H, Ito M, Cao L, Nakabayashi K, Kato K, Onishi K. Fine-tuning of heading time by earliness per se effect due to multi-allelic variants in VRN-B3 locus of hexaploid wheat. PLANTA 2025; 261:97. [PMID: 40153070 DOI: 10.1007/s00425-025-04674-5] [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: 10/15/2024] [Accepted: 03/12/2025] [Indexed: 03/30/2025]
Abstract
MAIN CONCLUSION Wheat VRN-B3 contains multi-allelic variants conferring earliness per se effects and can generate a new allele by recombining multiple alleles, highlighting its importance for the fine-tuning of heading time. Fine-tuning of heading time is required for breeding well-adapted varieties of wheat in regional environments. The VRN-B3 locus, which encodes the FT-B1 gene, is known as a vernalization gene. In this study, we analyzed two alleles in the VRN-B3 region: QHt-7B_Zen of a Japanese variety (Zenkouji-komugi) and QHt-7B_spelt of a spelt wheat strain (st. Rumania). Phenotypic evaluation of near-isogeneic lines (NILs) of 'Chinese Spring' (CS) under long-day (16 h) conditions showed that QHt-7B_Zen and QHt-7B_spelt conferred approximately 3.9 d earlier and 3.0 d later heading time compared with CS, respectively. Differences in heading times among NILs were also observed for fully vernalized plants under long-day conditions, indicating their earliness per se effect. Both QTLs behaved as single genes with incomplete dominant effects, and fine-mapping showed that FT-B1 was responsible for heading time. Droplet digital PCR analysis revealed that QHt-7B_Zen contained three copies of FT-B1, similar to the CS. QHt-7B_spelt had one FT-B1 copy with 14 substitutions, a 15 bp insertion in the 4.8 kb promoter region, and one amino acid substitution in the third exon, which could be designated as a novel allele, Vrn-B3f. Furthermore, a new allele with two FT-B1 copies conferring an intermediate heading time between the parents was created by the recombination of FT-B1 copies of CS and NIL for QHt-7B_spelt. Our findings indicate that fine-tuning heading time is possible through the versatility of the VRN-B3 locus, which can generate multi-allelic variants that have both vernalization and earliness per se effects in wheat.
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Affiliation(s)
- Lesly Díaz Suárez
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Inada-Cho, Nishi 2-11, Obihiro, Hokkaido, 080-8555, Japan
- Centro de Investigaciones Agropecuarias (CIAP), Universidad Central "Marta Abreu" de Las Villas (UCLV), Carretera a Camajuaní Km 5 ½, 54830, Santa Clara, Cuba
| | - Hatsune Inagaki
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Inada-Cho, Nishi 2-11, Obihiro, Hokkaido, 080-8555, Japan
| | - Hiroshi Hirata
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Inada-Cho, Nishi 2-11, Obihiro, Hokkaido, 080-8555, Japan
| | - Yusuke Akimoto
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Inada-Cho, Nishi 2-11, Obihiro, Hokkaido, 080-8555, Japan
| | - Kana Sakakibayashi
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Inada-Cho, Nishi 2-11, Obihiro, Hokkaido, 080-8555, Japan
| | - Honoka Seino
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Inada-Cho, Nishi 2-11, Obihiro, Hokkaido, 080-8555, Japan
| | - Masaki Ito
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Inada-Cho, Nishi 2-11, Obihiro, Hokkaido, 080-8555, Japan
| | - Liangzi Cao
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang, China
| | - Kazumi Nakabayashi
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Inada-Cho, Nishi 2-11, Obihiro, Hokkaido, 080-8555, Japan
| | - Kenji Kato
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Kita-Ku, Okayama, 700-8530, Japan
| | - Kazumitsu Onishi
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Inada-Cho, Nishi 2-11, Obihiro, Hokkaido, 080-8555, Japan.
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Kiss T, Horváth ÁD, Cseh A, Berki Z, Balla K, Karsai I. Molecular genetic regulation of the vegetative-generative transition in wheat from an environmental perspective. ANNALS OF BOTANY 2025; 135:605-628. [PMID: 39364537 PMCID: PMC11904908 DOI: 10.1093/aob/mcae174] [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: 05/29/2024] [Accepted: 09/30/2024] [Indexed: 10/05/2024]
Abstract
The key to the wide geographical distribution of wheat is its high adaptability. One of the most commonly used methods for studying adaptation is investigation of the transition between the vegetative-generative phase and the subsequent intensive stem elongation process. These processes are determined largely by changes in ambient temperature, the diurnal and annual periodicity of daylength, and the composition of the light spectrum. Many genes are involved in the perception of external environmental signals, forming a complex network of interconnections that are then integrated by a few integrator genes. This hierarchical cascade system ensures the precise occurrence of the developmental stages that enable maximum productivity. This review presents the interrelationship of molecular-genetic pathways (Earliness per se, circadian/photoperiod length, vernalization - cold requirement, phytohormonal - gibberellic acid, light perception, ambient temperature perception and ageing - miRNA) responsible for environmental adaptation in wheat. Detailed molecular genetic mapping of wheat adaptability will allow breeders to incorporate new alleles that will create varieties best adapted to local environmental conditions.
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Affiliation(s)
- Tibor Kiss
- HUN-REN Centre for Agricultural Research, Agricultural Institute, H-2462 Martonvásár, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, H-3300 Eger, Hungary
| | - Ádám D Horváth
- HUN-REN Centre for Agricultural Research, Agricultural Institute, H-2462 Martonvásár, Hungary
| | - András Cseh
- HUN-REN Centre for Agricultural Research, Agricultural Institute, H-2462 Martonvásár, Hungary
| | - Zita Berki
- HUN-REN Centre for Agricultural Research, Agricultural Institute, H-2462 Martonvásár, Hungary
| | - Krisztina Balla
- HUN-REN Centre for Agricultural Research, Agricultural Institute, H-2462 Martonvásár, Hungary
| | - Ildikó Karsai
- HUN-REN Centre for Agricultural Research, Agricultural Institute, H-2462 Martonvásár, Hungary
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5
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Janeczko A, Oklestkova J, Jurczyk B, Drygaś B. Pregnane derivatives in wheat (Triticum aestivum) and their potential role in generative development. JOURNAL OF PLANT RESEARCH 2025; 138:377-388. [PMID: 39903397 DOI: 10.1007/s10265-024-01614-4] [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: 08/01/2024] [Accepted: 12/26/2024] [Indexed: 02/06/2025]
Abstract
Pregnane derivatives such as pregnenolone or progesterone and many other metabolites are important in mammals where many of them act as hormones including sexual hormones. Much less is known about the presence and functions of pregnane derivatives in plants. The main objectives of this work were (1) to determine the presence of pregnane derivatives in winter wheat (2) verify if there are changes of concentration of pregnane derivatives during wheat growth/development with special attention to vernalisation process (3) to answer the question of whether selected pregnane derivatives are stimulators of wheat development and whether the potential stimulation of this development is accompanied by the expression of the Vrn1 (Vernalisation1) gene. To the best of our knowledge, this is the first report that demonstrates the presence of pregnenolone and 5α-dihydroprogesterone in the leaves and intact crowns of winter wheat. The levels of some of the pregnane derivatives changed during plant growth/development, it was demonstrated that pregnenolone, pregnanolone and 17α-hydroxypregnenolone stimulated wheat development. The changes in the Vrn1 expression are discussed in light of the stimulation of generative development by the pregnane derivatives.
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Affiliation(s)
- Anna Janeczko
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, Kraków, 30-239, Poland.
| | - Jana Oklestkova
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences & Palacký University, Šlechtitelů 27, Olomouc, CZ - 77900, Czech Republic
| | - Barbara Jurczyk
- Department of Plant Breeding, Physiology, and Seed Science, University of Agriculture in Kraków, Podłużna 3, Kraków, 30-239, Poland
| | - Barbara Drygaś
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, College of Natural Science, Rzeszów University, Ćwiklińskiej 2D, Rzeszów, 35-601, Poland
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6
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Verrico B, Preston JC. Historic rewiring of grass flowering time pathways and implications for crop improvement under climate change. THE NEW PHYTOLOGIST 2025; 245:1864-1878. [PMID: 39722593 PMCID: PMC11798905 DOI: 10.1111/nph.20375] [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: 10/01/2024] [Accepted: 12/09/2024] [Indexed: 12/28/2024]
Abstract
Grasses are fundamental to human survival, providing a large percentage of our calories, fuel, and fodder for livestock, and an enormous global carbon sink. A particularly important part of the grass plant is the grain-producing inflorescence that develops in response to both internal and external signals that converge at the shoot tip to influence meristem behavior. Abiotic signals that trigger reproductive development vary across the grass family, mostly due to the unique ecological and phylogenetic histories of each clade. The time it takes a grass to flower has implications for its ability to escape harsh environments, while also indirectly affecting abiotic stress tolerance, inflorescence architecture, and grain yield. Here, we synthesize recent insights into the evolution of grass flowering time in response to past climate change, particularly focusing on genetic convergence in underlying traits. We then discuss how and why the rewiring of a shared ancestral flowering pathway affects grass yields, and outline ways in which researchers are using this and other information to breed higher yielding, climate-proof cereal crops.
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Affiliation(s)
- Brittany Verrico
- Department of Plant BiologyUniversity of Vermont63 Carrigan DriveBurlingtonVT05405USA
| | - Jill C. Preston
- Department of Plant BiologyUniversity of Vermont63 Carrigan DriveBurlingtonVT05405USA
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7
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Kosová K, Nešporová T, Vítámvás P, Vítámvás J, Klíma M, Ovesná J, Prášil IT. How to survive mild winters: Cold acclimation, deacclimation, and reacclimation in winter wheat and barley. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2025; 220:109541. [PMID: 39862458 DOI: 10.1016/j.plaphy.2025.109541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 01/09/2025] [Accepted: 01/21/2025] [Indexed: 01/27/2025]
Abstract
Cold acclimation and vernalization represent the major evolutionary adaptive responses to ensure winter survival of temperate plants. Due to climate change, mild winters can paradoxically worsen plant winter survival due to cold deacclimation induced by warm periods during winter. It seems that the ability of cold reacclimation in overwintering Triticeae cereals is limited, especially in vernalized plants. In the present review, the major factors determining cold acclimation (CA), deacclimation (DA) and reacclimation (RA) processes in winter-type Triticeae, namely wheat and barley, are discussed. Recent knowledge on cold sensing and signaling is briefly summarized. The impacts of chilling temperatures, photoperiod and light spectrum quality as the major environmental factors, and the roles of soluble proteins and sugars (carbohydrates) as well as cold stress memory molecular mechanisms as the major plant-based factors determining CA, DA, and RA processes are discussed. The roles of plant stress memory mechanisms and development processes, namely vernalization, in winter Triticeae reacclimation are elucidated. Recent findings about the role of O-glucose N-acetylation of target proteins during vernalization and their impacts on the expression of VRN1 gene and other target proteins resulting in cold-responsive modules reprogramming are presented.
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Affiliation(s)
- Klára Kosová
- Laboratory of Plant Stress Biology and Biotechnology, Department of Plant Genetics and Crop Breeding, Czech Agrifood Research Center, Drnovská 507, 161 06, Prague 6, Ruzyně, Czech Republic.
| | - Tereza Nešporová
- Laboratory of Plant Stress Biology and Biotechnology, Department of Plant Genetics and Crop Breeding, Czech Agrifood Research Center, Drnovská 507, 161 06, Prague 6, Ruzyně, Czech Republic; Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Pavel Vítámvás
- Laboratory of Plant Stress Biology and Biotechnology, Department of Plant Genetics and Crop Breeding, Czech Agrifood Research Center, Drnovská 507, 161 06, Prague 6, Ruzyně, Czech Republic
| | - Jan Vítámvás
- Laboratory of Plant Stress Biology and Biotechnology, Department of Plant Genetics and Crop Breeding, Czech Agrifood Research Center, Drnovská 507, 161 06, Prague 6, Ruzyně, Czech Republic; Faculty of Forestry and Wood Science, Czech University of Life Sciences, Prague, Czech Republic
| | - Miroslav Klíma
- Laboratory of Plant Stress Biology and Biotechnology, Department of Plant Genetics and Crop Breeding, Czech Agrifood Research Center, Drnovská 507, 161 06, Prague 6, Ruzyně, Czech Republic
| | - Jaroslava Ovesná
- Laboratory of Plant Stress Biology and Biotechnology, Department of Plant Genetics and Crop Breeding, Czech Agrifood Research Center, Drnovská 507, 161 06, Prague 6, Ruzyně, Czech Republic
| | - Ilja Tom Prášil
- Laboratory of Plant Stress Biology and Biotechnology, Department of Plant Genetics and Crop Breeding, Czech Agrifood Research Center, Drnovská 507, 161 06, Prague 6, Ruzyně, Czech Republic
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8
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Zhao Q. Thermodynamic for biological development: A hypothesis. Biosystems 2025; 249:105413. [PMID: 39929432 DOI: 10.1016/j.biosystems.2025.105413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 02/04/2025] [Accepted: 02/07/2025] [Indexed: 02/17/2025]
Abstract
This paper proposes a thermodynamic model of biological development. Several key thoughts are presented: 1) in view of thermodynamics, biological development processes irreversibly; 2) in view of thermodynamics and molecular biology, positive autoregulation, or self-regulation, of transcription factors is the only way to ensure irreversibility of a thermodynamic process of biology; 3) change in the autoregulation of transcription factors can irreversibly result in alterations in the physiological state) a physiological state is a system of signaling networks; 5) a cell and its physiological state can be identified by the pattern of its transcription factors. 6) from points aforementioned, we can analyze some thermodynamic properties of biological development by knowledge of molecular biology and biochemistry. The possible mechanisms of plant vernalization are also proposed.
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Affiliation(s)
- Qinyi Zhao
- Medical Institute, CRRC, Beijing, PR China.
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9
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Liu Y, Wang D, Yuan Y, Liu Y, Lv B, Lv H. Transcriptome Profiling Reveals Key Regulatory Networks for Age-Dependent Vernalization in Welsh Onion ( Allium fistulosum L.). Int J Mol Sci 2024; 25:13159. [PMID: 39684870 DOI: 10.3390/ijms252313159] [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: 08/27/2024] [Revised: 12/02/2024] [Accepted: 12/04/2024] [Indexed: 12/18/2024] Open
Abstract
Plants exhibit diverse pathways to regulate the timing of flowering. Some plant species require a vegetative phase before being able to perceive cold stimuli for the acceleration of flowering through vernalization. This research confirms the correlation between the vernalization process and seedling age in Welsh onions. Findings from two vernalization experiments conducted at different time intervals demonstrate that seedlings must reach a vegetative phase of at least 8 weeks to consistently respond to vernalization. Notably, 8-week-old seedlings subjected to 6 weeks of vernalization displayed the shortest time to bolting, with an average duration of 138.1 days. Transcriptome analysis led to the identification of genes homologous to those in Arabidopsis thaliana that regulate flowering. Specifically, AfisC7G05578 (CO), AfisC2G05881 (AP1), AfisC1G07745 (FT), AfisC1G06473 (RAP2.7), and AfisC2G01843 (VIM1) were identified and suggested to have potential significance in age-dependent vernalization in Welsh onions. This study not only presents a rapid vernalization method for Welsh onions but also provides a molecular foundation for understanding the interplay between seedling age and vernalization.
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Affiliation(s)
- Yin Liu
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China
| | - Dan Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Yu Yuan
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Yue Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Bingsheng Lv
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Haiyan Lv
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China
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10
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Mateos B, Preedy K, Milne L, Morris J, Hedley PE, Simpson C, Hancock RD, Graham J. Altered expression of a raspberry homologue of VRN1 is associated with disruption of dormancy induction and misregulation of subsets of dormancy-associated genes. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:6167-6181. [PMID: 39243357 PMCID: PMC11480652 DOI: 10.1093/jxb/erae371] [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: 02/26/2024] [Accepted: 09/06/2024] [Indexed: 09/09/2024]
Abstract
Winter dormancy is a key process in the phenology of temperate perennials. Climate change is severely impacting its course leading to economic losses in agriculture. A better understanding of the underlying mechanisms, as well as the genetic basis of the different responses, is necessary for the development of climate-resilient cultivars. This study aims to provide an insight into winter dormancy in red raspberry (Rubus idaeus L). We report the transcriptomic profiles during dormancy in two raspberry cultivars with contrasting responses. The cultivar 'Glen Ample' showed a typical perennial phenology, whereas 'Glen Dee' registered consistent dormancy dysregulation, exhibiting active growth and flowering out of season. RNA-seq combined with weighted gene co-expression network analysis identified gene clusters in both genotypes that exhibited time-dependent expression profiles. Functional analysis of 'Glen Ample' gene clusters highlighted the significance of the cell and structural development prior to dormancy entry as well the role of genetic and epigenetic processes such as RNAi and DNA methylation in regulating gene expression. Dormancy release in 'Glen Ample' was associated with up-regulation of transcripts associated with the resumption of metabolism, nucleic acid biogenesis, and processing signal response pathways. Many of the processes occurring in 'Glen Ample' were dysregulated in 'Glen Dee' and 28 transcripts exhibiting time-dependent expression in 'Glen Ample' that also had an Arabidopsis homologue were not found in 'Glen Dee'. These included a gene with homology to Arabidopsis VRN1 (RiVRN1.1) that exhibited a sharp decline in expression following dormancy induction in 'Glen Ample'. Characterization of the gene region in the 'Glen Dee' genome revealed two large insertions upstream of the ATG start codon. We propose that expression below detection level of a specific VRN1 homologue in 'Glen Dee' causes dormancy misregulation as a result of inappropriate expression of a subset of genes that are directly or indirectly regulated by RiVRN1.1.
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Affiliation(s)
- Brezo Mateos
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
- Biomathematics and Statistics Scotland, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Katharine Preedy
- Biomathematics and Statistics Scotland, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Linda Milne
- Informational and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jenny Morris
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Pete E Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Craig Simpson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Robert D Hancock
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Julie Graham
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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Abdelrahman M, Gorafi YSA, Sulieman S, Jogaiah S, Gupta A, Tsujimoto H, Nguyen HT, Herrera-Estrella L, Tran LSP. Wild grass-derived alleles represent a genetic architecture for the resilience of modern common wheat to stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1685-1702. [PMID: 38935838 DOI: 10.1111/tpj.16887] [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: 12/15/2023] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024]
Abstract
This review explores the integration of wild grass-derived alleles into modern bread wheat breeding to tackle the challenges of climate change and increasing food demand. With a focus on synthetic hexaploid wheat, this review highlights the potential of genetic variability in wheat wild relatives, particularly Aegilops tauschii, for improving resilience to multifactorial stresses like drought, heat, and salinity. The evolutionary journey of wheat (Triticum spp.) from diploid to hexaploid species is examined, revealing significant genetic contributions from wild grasses. We also emphasize the importance of understanding incomplete lineage sorting in the genomic evolution of wheat. Grasping this information is crucial as it can guide breeders in selecting the appropriate alleles from the gene pool of wild relatives to incorporate into modern wheat varieties. This approach improves the precision of phylogenetic relationships and increases the overall effectiveness of breeding strategies. This review also addresses the challenges in utilizing the wheat wild genetic resources, such as the linkage drag and cross-compatibility issues. Finally, we culminate the review with future perspectives, advocating for a combined approach of high-throughput phenotyping tools and advanced genomic techniques to comprehensively understand the genetic and regulatory architectures of wheat under stress conditions, paving the way for more precise and efficient breeding strategies.
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Affiliation(s)
- Mostafa Abdelrahman
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, 79409, Texas, USA
| | - Yasir Serag Alnor Gorafi
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kitashirakawa, 606-8502, Kyoto, Japan
| | - Saad Sulieman
- Department of Agronomy, Faculty of Agriculture, University of Khartoum, Khartoum North, 13314, Sudan
| | - Sudisha Jogaiah
- Department of Environmental Science, Central University of Kerala, Periye, Kasaragod, 671316, Kerala, India
| | - Aarti Gupta
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, 79409, Texas, USA
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan
| | - Henry T Nguyen
- Division of Plant Sciences and Technology, University of Missouri, Columbia, 65211, Missouri, USA
| | - Luis Herrera-Estrella
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, 79409, Texas, USA
- Unidad de Genomica Avanzada, Centro de Investigación y de Estudios Avanzados del Intituto Politécnico Nacional, Irapuato, 36821, Mexico
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, 79409, Texas, USA
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Afshari-Behbahanizadeh S, Puglisi D, Esposito S, De Vita P. Allelic Variations in Vernalization ( Vrn) Genes in Triticum spp. Genes (Basel) 2024; 15:251. [PMID: 38397240 PMCID: PMC10887697 DOI: 10.3390/genes15020251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Rapid climate changes, with higher warming rates during winter and spring seasons, dramatically affect the vernalization requirements, one of the most critical processes for the induction of wheat reproductive growth, with severe consequences on flowering time, grain filling, and grain yield. Specifically, the Vrn genes play a major role in the transition from vegetative to reproductive growth in wheat. Recent advances in wheat genomics have significantly improved the understanding of the molecular mechanisms of Vrn genes (Vrn-1, Vrn-2, Vrn-3, and Vrn-4), unveiling a diverse array of natural allelic variations. In this review, we have examined the current knowledge of Vrn genes from a functional and structural point of view, considering the studies conducted on Vrn alleles at different ploidy levels (diploid, tetraploid, and hexaploid). The molecular characterization of Vrn-1 alleles has been a focal point, revealing a diverse array of allelic forms with implications for flowering time. We have highlighted the structural complexity of the different allelic forms and the problems linked to the different nomenclature of some Vrn alleles. Addressing these issues will be crucial for harmonizing research efforts and enhancing our understanding of Vrn gene function and evolution. The increasing availability of genome and transcriptome sequences, along with the improvements in bioinformatics and computational biology, offers a versatile range of possibilities for enriching genomic regions surrounding the target sites of Vrn genes, paving the way for innovative approaches to manipulate flowering time and improve wheat productivity.
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Affiliation(s)
- Sanaz Afshari-Behbahanizadeh
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, SS 673 Meters 25 200, 71122 Foggia, Italy; (S.A.-B.); (D.P.)
- Department of Agriculture, Food, Natural Science, Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Damiano Puglisi
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, SS 673 Meters 25 200, 71122 Foggia, Italy; (S.A.-B.); (D.P.)
| | - Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, SS 673 Meters 25 200, 71122 Foggia, Italy; (S.A.-B.); (D.P.)
- National Research Council of Italy, Institute of Biosciences and BioResources, Research Division Portici (CNR-IBBR), 80055 Portici, Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, SS 673 Meters 25 200, 71122 Foggia, Italy; (S.A.-B.); (D.P.)
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Amalova A, Yermekbayev K, Griffiths S, Winfield MO, Morgounov A, Abugalieva S, Turuspekov Y. Population Structure of Modern Winter Wheat Accessions from Central Asia. PLANTS (BASEL, SWITZERLAND) 2023; 12:2233. [PMID: 37375859 DOI: 10.3390/plants12122233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
Despite the importance of winter wheat in Central Asian countries, there are limited reports describing their diversity within this region. In this study, the population structures of 115 modern winter wheat cultivars from four Central Asian countries were compared to germplasms from six other geographic origins using 10,746 polymorphic single-nucleotide polymorphism (SNP) markers. After applying the STRUCTURE package, we found that in terms of the most optimal K steps, samples from Kazakhstan and Kyrgyzstan were grouped together with samples from Russia, while samples from Tajikistan and Uzbekistan were grouped with samples from Afghanistan. The mean value of Nei's genetic diversity index for the germplasm from four groups from Central Asia was 0.261, which is comparable to that of the six other groups studied: Europe, Australia, the USA, Afghanistan, Turkey, and Russia. The Principal Coordinate Analysis (PCoA) showed that samples from Kyrgyzstan, Tajikistan, and Uzbekistan were close to samples from Turkey, while Kazakh accessions were located near samples from Russia. The evaluation of 10,746 SNPs in Central Asian wheat suggested that 1006 markers had opposing allele frequencies. Further assessment of the physical positions of these 1006 SNPs in the Wheat Ensembl database indicated that most of these markers are constituents of genes associated with plant stress tolerance and adaptability. Therefore, the SNP markers identified can be effectively used in regional winter wheat breeding projects for facilitating plant adaptation and stress resistance.
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Affiliation(s)
- Akerke Amalova
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
| | - Kanat Yermekbayev
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
- Crop Genetics Department, John Innes Centre, Norwich NR4 7UH, UK
| | - Simon Griffiths
- Crop Genetics Department, John Innes Centre, Norwich NR4 7UH, UK
| | | | - Alexey Morgounov
- Science Department, S. Seifullin Kazakh Agrotechnical University, Astana 010011, Kazakhstan
| | - Saule Abugalieva
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Yerlan Turuspekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
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