1
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Gao Y, Zhang Y, Ma C, Chen Y, Liu C, Wang Y, Wang S, Chen X. Editing the nuclear localization signals of E1 and E1Lb enables the production of tropical soybean in temperate growing regions. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2145-2156. [PMID: 38511622 PMCID: PMC11258983 DOI: 10.1111/pbi.14335] [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: 11/17/2023] [Revised: 02/05/2024] [Accepted: 03/03/2024] [Indexed: 03/22/2024]
Abstract
Soybean is a typical short-day crop, and most commercial soybean cultivars are restricted to a relatively narrow range of latitudes due to photoperiod sensitivity. Photoperiod sensitivity hinders the utilization of soybean germplasms across geographical regions. When grown in temperate regions, tropical soybean responds to prolonged day length by increasing the vegetative growth phase and delaying flowering and maturity, which often pushes the harvest window past the first frost date. In this study, we used CRISPR/LbCas12a to edit a North American subtropical soybean cultivar named 06KG218440 that belongs to maturity group 5.5. By designing one gRNA to edit the nuclear localization signal (NLS) regions of both E1 and E1Lb, we created a series of new germplasms with shortened flowering time and time to maturity and determined their favourable latitudinal zone for cultivation. The novel partial function alleles successfully achieve yield and early maturity trade-offs and exhibit good agronomic traits and high yields in temperate regions. This work offers a straightforward editing strategy to modify subtropical and tropical soybean cultivars for temperate growing regions, a strategy that could be used to enrich genetic diversity in temperate breeding programmes and facilitate the introduction of important crop traits such as disease tolerance or high yield.
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Affiliation(s)
- Yang Gao
- State Key Laboratory of Crop Germplasm Innovation and Molecular BreedingSyngenta Biotechnology (China) Co., LtdBeijingChina
| | - Yuguo Zhang
- State Key Laboratory of Crop Germplasm Innovation and Molecular BreedingSyngenta Biotechnology (China) Co., LtdBeijingChina
| | - Chuanyu Ma
- State Key Laboratory of Crop Germplasm Innovation and Molecular BreedingSyngenta Biotechnology (China) Co., LtdBeijingChina
| | - Yanhui Chen
- State Key Laboratory of Crop Germplasm Innovation and Molecular BreedingSyngenta Biotechnology (China) Co., LtdBeijingChina
| | - Chunxia Liu
- State Key Laboratory of Crop Germplasm Innovation and Molecular BreedingSyngenta Seed Technology China Co., Ltd.YanglingChina
| | - Yanli Wang
- State Key Laboratory of Crop Germplasm Innovation and Molecular BreedingSyngenta Biotechnology (China) Co., LtdBeijingChina
| | - Songyuan Wang
- State Key Laboratory of Crop Germplasm Innovation and Molecular BreedingSyngenta Biotechnology (China) Co., LtdBeijingChina
| | - Xi Chen
- State Key Laboratory of Crop Germplasm Innovation and Molecular BreedingSyngenta Biotechnology (China) Co., LtdBeijingChina
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2
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Fang C, Sun Z, Li S, Su T, Wang L, Dong L, Li H, Li L, Kong L, Yang Z, Lin X, Zatybekov A, Liu B, Kong F, Lu S. Subfunctionalisation and self-repression of duplicated E1 homologues finetunes soybean flowering and adaptation. Nat Commun 2024; 15:6184. [PMID: 39039090 PMCID: PMC11263555 DOI: 10.1038/s41467-024-50623-3] [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: 11/15/2023] [Accepted: 07/17/2024] [Indexed: 07/24/2024] Open
Abstract
Soybean is a photoperiod-sensitive staple crop. Its photoperiodic flowering has major consequences for latitudinal adaptation and grain yield. Here, we identify and characterise a flowering locus named Time of flower 4b (Tof4b), which encodes E1-Like b (E1Lb), a homologue of the key soybean floral repressor E1. Tof4b protein physically associates with the promoters of two FLOWERING LOCUS T (FT) genes to repress their transcription and delay flowering to impart soybean adaptation to high latitudes. Three E1 homologues undergo subfunctionalisation and show differential subcellular localisation. Moreover, they all possess self-repression capability and each suppresses the two homologous counterparts. Subfunctionalisation and the transcriptional regulation of E1 genes collectively finetune flowering time and high-latitude adaptation in soybean. We propose a model for the functional fate of the three E1 genes after the soybean whole-genome duplication events, refine the molecular mechanisms underlying high-latitude adaption, and provide a potential molecular-breeding resource.
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Affiliation(s)
- Chao Fang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhihui Sun
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Shichen Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Tong Su
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Lingshuang Wang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Lidong Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Haiyang Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Lanxin Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Lingping Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Zhiquan Yang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Xiaoya Lin
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Alibek Zatybekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Baohui Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China.
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China.
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China.
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China.
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.
| | - Sijia Lu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China.
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3
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Li J, Li Y, Agyenim-Boateng KG, Shaibu AS, Liu Y, Feng Y, Qi J, Li B, Zhang S, Sun J. Natural variation of domestication-related genes contributed to latitudinal expansion and adaptation in soybean. BMC PLANT BIOLOGY 2024; 24:651. [PMID: 38977969 PMCID: PMC11232268 DOI: 10.1186/s12870-024-05382-0] [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: 05/17/2024] [Accepted: 07/05/2024] [Indexed: 07/10/2024]
Abstract
Soybean is a major source of protein and edible oil worldwide. Originating from the Huang-Huai-Hai region, which has a temperate climate, soybean has adapted to a wide latitudinal gradient across China. However, the genetic mechanisms responsible for the widespread latitudinal adaptation in soybean, as well as the genetic basis, adaptive differentiation, and evolutionary implications of theses natural alleles, are currently lacking in comprehensive understanding. In this study, we examined the genetic variations of fourteen major gene loci controlling flowering and maturity in 103 wild species, 1048 landraces, and 1747 cultivated species. We found that E1, E3, FT2a, J, Tof11, Tof16, and Tof18 were favoured during soybean improvement and selection, which explained 75.5% of the flowering time phenotypic variation. These genetic variation was significantly associated with differences in latitude via the LFMM algorithm. Haplotype network and geographic distribution analysis suggested that gene combinations were associated with flowering time diversity contributed to the expansion of soybean, with more HapA clustering together when soybean moved to latitudes beyond 35°N. The geographical evolution model was developed to accurately predict the suitable planting zone for soybean varieties. Collectively, by integrating knowledge from genomics and haplotype classification, it was revealed that distinct gene combinations improve the adaptation of cultivated soybeans to different latitudes. This study provides insight into the genetic basis underlying the environmental adaptation of soybean accessions, which could contribute to a better understanding of the domestication history of soybean and facilitate soybean climate-smart molecular breeding for various environments.
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Affiliation(s)
- Jing Li
- The State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yecheng Li
- The State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | | | | | - Yitian Liu
- The State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yue Feng
- The State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Jie Qi
- The State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Bin Li
- The State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Shengrui Zhang
- The State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Junming Sun
- The State Key Laboratory of Crop Gene Resources and Breeding, National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China.
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4
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Zhao X, Li H, Wang L, Wang J, Huang Z, Du H, Li Y, Yang J, He M, Cheng Q, Lin X, Liu B, Kong F. A critical suppression feedback loop determines soybean photoperiod sensitivity. Dev Cell 2024; 59:1750-1763.e4. [PMID: 38688276 DOI: 10.1016/j.devcel.2024.04.004] [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: 07/18/2023] [Revised: 02/07/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
Photoperiod sensitivity is crucial for soybean flowering, adaptation, and yield. In soybean, photoperiod sensitivity centers around the evening complex (EC) that regulates the transcriptional level of the core transcription factor E1, thereby regulating flowering. However, little is known about the regulation of the activity of EC. Our study identifies how E2/GIGANTEA (GI) and its homologs modulate photoperiod sensitivity through interactions with the EC. During long days, E2 interacts with the blue-light receptor flavin-binding, kelch repeat, F box 1 (FKF1), leading to the degradation of J/ELF3, an EC component. EC also suppresses E2 expression by binding to its promoter. This interplay forms a photoperiod regulatory loop, maintaining sensitivity to photoperiod. Disruption of this loop leads to losing sensitivity, affecting soybean's adaptability and yield. Understanding this loop's dynamics is vital for molecular breeding to reduce soybean's photoperiod sensitivity and develop cultivars with better adaptability and higher yields, potentially leading to the creation of photoperiod-insensitive varieties for broader agricultural applications.
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Affiliation(s)
- Xiaohui Zhao
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Haiyang Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Lingshuang Wang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Jianhao Wang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China; Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zerong Huang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Haiping Du
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Yaru Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Jiahui Yang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Milan He
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Qun Cheng
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Xiaoya Lin
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
| | - Baohui Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
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5
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Rychel-Bielska S, Książkiewicz M, Kurasiak-Popowska D, Tomkowiak A, Bielski W, Weigt D, Niemann J, Surma A, Kozak B, Nawracała J. Molecular selection of soybean towards adaptation to Central European agroclimatic conditions. J Appl Genet 2024:10.1007/s13353-024-00889-6. [PMID: 38954397 DOI: 10.1007/s13353-024-00889-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/03/2024] [Accepted: 06/20/2024] [Indexed: 07/04/2024]
Abstract
Europe is highly dependent on soybean meal imports and anticipates an increase of domestic plant protein production. Ongoing climate change resulted in northward shift of plant hardiness zones, enabling spring-sowing of freezing-sensitive crops, including soybean. However, it requires efficient reselection of germplasm adapted to relatively short growing season and long-day photoperiod. In the present study, a PCR array has been implemented, targeting early maturity (E1-E4, E7, E9, and E10), pod shattering (qPHD1), and growth determination (Dt1) genes. This array was optimized for routine screening of soybean diversity panel (204 accessions), subjected to the 2018-2020 survey of phenology, morphology, and yield-related traits in a potential cultivation region in Poland. High broad-sense heritability (0.84-0.88) was observed for plant height, thousand grain weight, maturity date, and the first pod height. Significant positive correlations were identified between the number of seeds and pods per plant, between these two traits and seed yield per plant as well as between flowering, maturity, plant height, and first pod height. PCR array genotyping revealed high genetic diversity, yielding 98 allelic combinations. The most remarkable correlations were identified between flowering and E7 or E1, between maturity and E4 or E7 and between plant height and Dt1 or E4. The study demonstrated high applicability of this PCR array for molecular selection of soybean towards adaptation to Central Europe, designating recessive qPHD1 and dominant Dt1, E3, and E4 alleles as major targets to align soybean growth season requirements with the length of the frost-free period, improve plant performance, and increase yield.
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Affiliation(s)
- Sandra Rychel-Bielska
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, 50-363, Wrocław, Poland
| | - Michał Książkiewicz
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznań, Poland.
| | - Danuta Kurasiak-Popowska
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, 60-632, Poznań, Poland
| | - Agnieszka Tomkowiak
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, 60-632, Poznań, Poland
| | - Wojciech Bielski
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznań, Poland
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, 60-632, Poznań, Poland
| | - Dorota Weigt
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, 60-632, Poznań, Poland
| | - Janetta Niemann
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, 60-632, Poznań, Poland
| | - Anna Surma
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznań, Poland
| | - Bartosz Kozak
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, 50-363, Wrocław, Poland
| | - Jerzy Nawracała
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, 60-632, Poznań, Poland
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6
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Rowson M, Jolly M, Dickson S, Gifford ML, Carré I. Timely symbiosis: circadian control of legume-rhizobia symbiosis. Biochem Soc Trans 2024; 52:1419-1430. [PMID: 38779952 DOI: 10.1042/bst20231307] [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: 03/27/2024] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
Legumes house nitrogen-fixing endosymbiotic rhizobia in specialised polyploid cells within root nodules. This results in a mutualistic relationship whereby the plant host receives fixed nitrogen from the bacteria in exchange for dicarboxylic acids. This plant-microbe interaction requires the regulation of multiple metabolic and physiological processes in both the host and symbiont in order to achieve highly efficient symbiosis. Recent studies have showed that the success of symbiosis is influenced by the circadian clock of the plant host. Medicago and soybean plants with altered clock mechanisms showed compromised nodulation and reduced plant growth. Furthermore, transcriptomic analyses revealed that multiple genes with key roles in recruitment of rhizobia to plant roots, infection and nodule development were under circadian control, suggesting that appropriate timing of expression of these genes may be important for nodulation. There is also evidence for rhythmic gene expression of key nitrogen fixation genes in the rhizobium symbiont, and temporal coordination between nitrogen fixation in the bacterial symbiont and nitrogen assimilation in the plant host may be important for successful symbiosis. Understanding of how circadian regulation impacts on nodule establishment and function will identify key plant-rhizobial connections and regulators that could be targeted to increase the efficiency of this relationship.
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Affiliation(s)
- Monique Rowson
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Matthew Jolly
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Suzanna Dickson
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Miriam L Gifford
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, The University of Warwick, Coventry CV4 7AL, U.K
| | - Isabelle Carré
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
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7
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Liu L, Wang W, Lu X, Zhang T, Wu J, Fang Y, Ma L, Pu Y, Yang G, Wang W, Sun W. Methyl-Sensitive Amplification Polymorphism (MSAP) Analysis Provides Insights into the DNA Methylation Changes Underlying Adaptation to Low Temperature of Brassica rapa L. PLANTS (BASEL, SWITZERLAND) 2024; 13:1748. [PMID: 38999588 PMCID: PMC11244143 DOI: 10.3390/plants13131748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/06/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024]
Abstract
BACKGROUND DNA methylation can change rapidly to regulate the expression of stress-responsive genes. Previous studies have shown that there are significant differences in the cold resistance of winter rapeseed (Brassica rapa L.) after being domesticated in different selection environments; however, little is known about the epigenetic regulatory mechanisms of its cold resistance formation. METHODS Four winter rapeseed materials ('CT-2360', 'MXW-1', '2018-FJT', and 'DT-7') domesticated in different environments were selected to analyze the DNA methylation level and pattern changes under low temperature using methylation-sensitive amplified polymorphism technology with 60 primer pairs. RESULTS A total of 18 pairs of primers with good polymorphism were screened, and 1426 clear bands were amplified, with 594 methylation sites, accounting for 41.65% of the total amplified bands. The total methylation ratios of the four materials were reduced after low-temperature treatment, in which the DNA methylation level of 'CT-2360' was higher than that of the other three materials; the analysis of methylation patterns revealed that the degree of demethylation was higher than that of methylation in 'MXW-1', '2018-FJT', and 'DT-7', which were 22.99%, 19.77%, and 24.35%, respectively, and that the methylation events in 'CT-2360' were predominantly dominant at 22.95%. Fifty-three polymorphic methylated DNA fragments were randomly selected and further analyzed, and twenty-nine of the cloned fragments were homologous to genes with known functions. The candidate genes VQ22 and LOC103871127 verified the existence of different expressive patterns before and after low-temperature treatment. CONCLUSIONS Our work implies the critical role of DNA methylation in the formation of cold resistance in winter rapeseed. These results provide a comprehensive insight into the adaptation epigenetic regulatory mechanism of Brassica rapa L. to low temperature, and the identified differentially methylated genes can also be used as important genetic resources for the multilateral breeding of winter-resistant varieties.
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Affiliation(s)
- Lijun Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Wanpeng Wang
- Zhangye Academy of Agricultural Sciences, Zhangye 734000, China
| | - Xiaoming Lu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Tianyu Zhang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Junyan Wu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yan Fang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Li Ma
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuanyuan Pu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Gang Yang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Wangtian Wang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Wancang Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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8
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Sun J, Liu Y, Zheng Y, Xue Y, Fan Y, Ma X, Ji Y, Liu G, Zhang X, Li Y, Wang S, Tian Z, Zhao L. The MADS-box transcription factor GmFULc promotes GmZTL4 gene transcription to modulate maturity in soybean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38869305 DOI: 10.1111/jipb.13682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 04/26/2024] [Accepted: 05/04/2024] [Indexed: 06/14/2024]
Abstract
Flowering time and maturity are crucial agronomic traits that affect the regional adaptability of soybean plants. The development of soybean cultivars with early maturity adapted to longer days and colder climates of high latitudes is very important for ensuring normal ripening before frost begins. FUL belongs to the MADS-box transcription factor family and has several duplicated members in soybeans. In this study, we observed that overexpression of GmFULc in the Dongnong 50 cultivar promoted soybean maturity, while GmFULc knockout mutants exhibited late maturity. Chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) revealed that GmFULc could bind to the CArG, bHLH and homeobox motifs. Further investigation revealed that GmFULc could directly bind to the CArG motif in the promoters of the GmZTL3 and GmZTL4 genes. Overexpression of GmZTL4 promoted soybean maturity, whereas the ztl4 mutants exhibited delayed maturity. Moreover, we found that the cis element box 4 motif of the GmZTL4 promoter, a motif of light response elements, played an important role in controlling the growth period. Deletion of this motif shortened the growth period by increasing the expression levels of GmZTL4. Functional investigations revealed that short-day treatment promoted the binding of GmFULc to the promoter of GmZTL4 and inhibited the expression of E1 and E1Lb, ultimately resulting in the promotion of flowering and early maturation. Taken together, these findings suggest a novel photoperiod regulatory pathway in which GmFULc directly activates GmZTL4 to promote earlier maturity in soybean.
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Affiliation(s)
- Jingzhe Sun
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
- Qingdao Institute of Bioenergy and Bioprocess Technology, The Chinese Academy of Sciences, Qingdao, 266101, China
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuhong Zheng
- Jilin Academy of Agricultural Sciences, China Agricultural Science and Technology Northeast Innovation Center, Changchun, 130033, China
| | - Yongguo Xue
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Yuhuan Fan
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaofei Ma
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Yujia Ji
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Gaoyuan Liu
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaoming Zhang
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Yang Li
- Depatment of Environmental and Plant Biology, Ohio University, Athens, 45701, Ohio, USA
| | - Shuming Wang
- Jilin Academy of Agricultural Sciences, China Agricultural Science and Technology Northeast Innovation Center, Changchun, 130033, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
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9
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Gauley A, Pasquariello M, Yoshikawa GV, Alabdullah AK, Hayta S, Smedley MA, Dixon LE, Boden SA. Photoperiod-1 regulates the wheat inflorescence transcriptome to influence spikelet architecture and flowering time. Curr Biol 2024; 34:2330-2343.e4. [PMID: 38781956 PMCID: PMC11149547 DOI: 10.1016/j.cub.2024.04.029] [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: 11/15/2023] [Revised: 03/08/2024] [Accepted: 04/11/2024] [Indexed: 05/25/2024]
Abstract
Photoperiod insensitivity has been selected by breeders to help adapt crops to diverse environments and farming practices. In wheat, insensitive alleles of Photoperiod-1 (Ppd-1) relieve the requirement of long daylengths to flower by promoting expression of floral promoting genes early in the season; however, these alleles also limit yield by reducing the number and fertility of grain-producing florets through processes that are poorly understood. Here, we performed transcriptome analysis of the developing inflorescence using near-isogenic lines that contain either photoperiod-insensitive or null alleles of Ppd-1, during stages when spikelet number is determined and floret development initiates. We report that Ppd-1 influences the stage-specific expression of genes with roles in auxin signaling, meristem identity, and protein turnover, and analysis of differentially expressed transcripts identified bZIP and ALOG transcription factors, namely PDB1 and ALOG1, which regulate flowering time and spikelet architecture. These findings enhance our understanding of genes that regulate inflorescence development and introduce new targets for improving yield potential.
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Affiliation(s)
- Adam Gauley
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Marianna Pasquariello
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Guilherme V Yoshikawa
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Hartley Grove, Glen Osmond, SA 5064, Australia
| | - Abdul Kader Alabdullah
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Sadiye Hayta
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Mark A Smedley
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Laura E Dixon
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Scott A Boden
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Hartley Grove, Glen Osmond, SA 5064, Australia.
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10
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Wang J, Xu X, Wang P, Zhang L, Liu L, Liu L, Wu T, Song W, Yuan S, Jiang B, Hou W, Wu C, Sun S, Yu L, Han T. Floral-promoting GmFT homologs trigger photoperiodic after-effects: An important mechanism for early-maturing soybean varieties to regulate reproductive development and adapt to high latitudes. PLANT, CELL & ENVIRONMENT 2024; 47:1656-1667. [PMID: 38282250 DOI: 10.1111/pce.14833] [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: 09/05/2023] [Revised: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
Soybean (Glycine max) is a typical short-day plant, but has been widely cultivated in high-latitude long-day (LD) regions because of the development of early-maturing genotypes which are photoperiod-insensitive. However, some early-maturing varieties exhibit significant responses to maturity under different daylengths but not for flowering, depicting an evident photoperiodic after-effect, a poorly understood mechanism. In this study, we investigated the postflowering responses of 11 early-maturing soybean varieties to various preflowering photoperiodic treatments. We confirmed that preflowering SD conditions greatly promoted maturity and other postflowering developmental stages. Soybean homologs of FLOWERING LOCUS T (FT), including GmFT2a, GmFT3a, GmFT3b and GmFT5a, were highly accumulated in leaves under preflowering SD treatment. More importantly, they maintained a high expression level after flowering even under LD conditions. E1 RNAi and GmFT2a overexpression lines showed extremely early maturity regardless of preflowering SD and LD treatments due to constitutively high levels of floral-promoting GmFT homolog expression throughout their life cycle. Collectively, our data indicate that high and stable expression of floral-promoting GmFT homologs play key roles in the maintenance of photoperiodic induction to promote postflowering reproductive development, which confers early-maturing varieties with appropriate vegetative growth and shortened reproductive growth periods for adaptation to high latitudes.
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Affiliation(s)
- Junya Wang
- Key Laboratory of Plant Biology, College of Life Science and Technology, Harbin Normal University, Harbin, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Xu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Peiguo Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixin Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lifeng Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Luping Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tingting Wu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenwen Song
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shan Yuan
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bingjun Jiang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wensheng Hou
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cunxiang Wu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shi Sun
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijie Yu
- Key Laboratory of Plant Biology, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Tianfu Han
- Key Laboratory of Plant Biology, College of Life Science and Technology, Harbin Normal University, Harbin, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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11
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Li Y, Zhang L, Wang J, Wang X, Guo S, Xu Z, Li D, Liu Z, Li Y, Liu B, Qiu L. Flowering time regulator qFT13-3 involved in soybean adaptation to high latitudes. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1164-1176. [PMID: 38070185 PMCID: PMC11022795 DOI: 10.1111/pbi.14254] [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: 07/29/2023] [Revised: 10/22/2023] [Accepted: 11/17/2023] [Indexed: 04/18/2024]
Abstract
Soybean is a short-day plant that typically flowers earlier when exposed to short-day conditions. However, the identification of genes associated with earlier flowering time but without a yield penalty is rare. In this study, we conducted genome-wide association studies (GWAS) using two re-sequencing datasets that included 113 wild soybeans (G. soja) and 1192 cultivated soybeans (G. max), respectively, and simultaneously identified a candidate flowering gene, qFT13-3, which encodes a protein homologous to the pseudo-response regulator (PRR) transcription factor. We identified four major haplotypes of qFT13-3 in the natural population, with haplotype H4 (qFT13-3H4) being lost during domestication, while qFT13-3H1 underwent natural and artificial selection, increasing in proportion from 4.5% in G. soja to 43.8% in landrace and to 81.9% in improve cultivars. Notably, most cultivars harbouring qFT13-3H1 were located in high-latitude regions. Knockout of qFT13-3 accelerated flowering and maturity time under long-day conditions, indicating that qFT13-3 functions as a flowering inhibitor. Our results also showed that qFT13-3 directly downregulates the expression of GmELF3b-2 which is a component of the circadian clock evening complex. Field trials revealed that the qft13-3 mutants shorten the maturity period by 11 days without a concomitant penalty on yield. Collectively, qFT13-3 can be utilized for the breeding of high-yield cultivars with a short maturity time suitable for high latitudes.
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Affiliation(s)
- Yan‐fei Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- Key Lab of Chinese Medicine Resources ConservationState Administration of Traditional Chinese Medicine of the People's Republic of ChinaInstitute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Liya Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jun Wang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co‐construction by Ministry and Province)JingzhouChina
| | - Xing Wang
- Xuzhou Institute of Agricultural Sciences of Xu‐huai Region of JiangsuXuzhouChina
| | - Shiyu Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Ze‐jun Xu
- Xuzhou Institute of Agricultural Sciences of Xu‐huai Region of JiangsuXuzhouChina
| | - Delin Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Zhangxiong Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Ying‐hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- State Key Laboratory of Crop Gene Resources and BreedingInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Bin Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- State Key Laboratory of Crop Gene Resources and BreedingInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Li‐juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- State Key Laboratory of Crop Gene Resources and BreedingInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
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12
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Maple R, Zhu P, Hepworth J, Wang JW, Dean C. Flowering time: From physiology, through genetics to mechanism. PLANT PHYSIOLOGY 2024; 195:190-212. [PMID: 38417841 PMCID: PMC11060688 DOI: 10.1093/plphys/kiae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/12/2024] [Accepted: 02/12/2024] [Indexed: 03/01/2024]
Abstract
Plant species have evolved different requirements for environmental/endogenous cues to induce flowering. Originally, these varying requirements were thought to reflect the action of different molecular mechanisms. Thinking changed when genetic and molecular analysis in Arabidopsis thaliana revealed that a network of environmental and endogenous signaling input pathways converge to regulate a common set of "floral pathway integrators." Variation in the predominance of the different input pathways within a network can generate the diversity of requirements observed in different species. Many genes identified by flowering time mutants were found to encode general developmental and gene regulators, with their targets having a specific flowering function. Studies of natural variation in flowering were more successful at identifying genes acting as nodes in the network central to adaptation and domestication. Attention has now turned to mechanistic dissection of flowering time gene function and how that has changed during adaptation. This will inform breeding strategies for climate-proof crops and help define which genes act as critical flowering nodes in many other species.
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Affiliation(s)
- Robert Maple
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Pan Zhu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jo Hepworth
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- New Cornerstone Science Laboratory, Shanghai 200032, China
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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13
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Zhang L, Wang P, Wang M, Xu X, Jia H, Wu T, Yuan S, Jiang B, Sun S, Han T, Wang L, Chen F. GmTCP40 Promotes Soybean Flowering under Long-Day Conditions by Binding to the GmAP1a Promoter and Upregulating Its Expression. Biomolecules 2024; 14:465. [PMID: 38672481 PMCID: PMC11047976 DOI: 10.3390/biom14040465] [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: 02/27/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Soybean [Glycine max (L.) Merr.] is a short-day (SD) plant that is sensitive to photoperiod, which influences flowering, maturity, and even adaptation. TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors have been shown to regulate photoperiodic flowering. However, the roles of TCPs in SD plants such as soybean, rice, and maize remain largely unknown. In this study, we cloned the GmTCP40 gene from soybean and investigated its expression pattern and function. Compared with wild-type (WT) plants, GmTCP40-overexpression plants flowered earlier under long-day (LD) conditions but not under SD conditions. Consistent with this, the overexpression lines showed upregulation of the flowering-related genes GmFT2a, GmFT2b, GmFT5a, GmFT6, GmAP1a, GmAP1b, GmAP1c, GmSOC1a, GmSOC1b, GmFULa, and GmAG under LD conditions. Further investigation revealed that GmTCP40 binds to the GmAP1a promoter and promotes its expression. Analysis of the GmTCP40 haplotypes and phenotypes of soybean accessions demonstrated that one GmTCP40 haplotype (Hap6) may contribute to delayed flowering at low latitudes. Taken together, our findings provide preliminary insights into the regulation of flowering time by GmTCP40 while laying a foundation for future research on other members of the GmTCP family and for efforts to enhance soybean adaptability.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Liwei Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (L.Z.); (P.W.); (M.W.); (X.X.); (H.J.); (T.W.); (S.Y.); (B.J.); (S.S.); (T.H.)
| | - Fulu Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (L.Z.); (P.W.); (M.W.); (X.X.); (H.J.); (T.W.); (S.Y.); (B.J.); (S.S.); (T.H.)
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14
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Yu H, Bhat JA, Li C, Zhao B, Bu M, Zhang Z, Guo T, Feng X. Identification of superior and rare haplotypes to optimize branch number in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:93. [PMID: 38570354 PMCID: PMC10991007 DOI: 10.1007/s00122-024-04596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
KEY MESSAGE Using the integrated approach in the present study, we identified eleven significant SNPs, seven stable QTLs and 20 candidate genes associated with branch number in soybean. Branch number is a key yield-related quantitative trait that directly affects the number of pods and seeds per soybean plant. In this study, an integrated approach with a genome-wide association study (GWAS) and haplotype and candidate gene analyses was used to determine the detailed genetic basis of branch number across a diverse set of soybean accessions. The GWAS revealed a total of eleven SNPs significantly associated with branch number across three environments using the five GWAS models. Based on the consistency of the SNP detection in multiple GWAS models and environments, seven genomic regions within the physical distance of ± 202.4 kb were delineated as stable QTLs. Of these QTLs, six QTLs were novel, viz., qBN7, qBN13, qBN16, qBN18, qBN19 and qBN20, whereas the remaining one, viz., qBN12, has been previously reported. Moreover, 11 haplotype blocks, viz., Hap4, Hap7, Hap12, Hap13A, Hap13B, Hap16, Hap17, Hap18, Hap19A, Hap19B and Hap20, were identified on nine different chromosomes. Haplotype allele number across the identified haplotype blocks varies from two to five, and different branch number phenotype is regulated by these alleles ranging from the lowest to highest through intermediate branching. Furthermore, 20 genes were identified underlying the genomic region of ± 202.4 kb of the identified SNPs as putative candidates; and six of them showed significant differential expression patterns among the soybean cultivars possessing contrasting branch number, which might be the potential candidates regulating branch number in soybean. The findings of this study can assist the soybean breeding programs for developing cultivars with desirable branch numbers.
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Affiliation(s)
- Hui Yu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Zhejiang Lab, Hangzhou, 310012, China
| | | | - Candong Li
- Jiamusi Branch Academy of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, China
| | - Beifang Zhao
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Moran Bu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Zhirui Zhang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Tai Guo
- Jiamusi Branch Academy of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, China
| | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.
- Zhejiang Lab, Hangzhou, 310012, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China.
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15
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Chawla S, Oster H, Duffield GE, Maronde E, Guido ME, Chabot C, Dkhissi-Benyahya O, Provencio I, Goel N, Youngstedt SD, Zi-Ching Mak N, Caba M, Nikhat A, Chakrabarti S, Wang L, Davis SJ. Reflections on Several Landmark Advances in Circadian Biology. J Circadian Rhythms 2024; 22:1. [PMID: 38617711 PMCID: PMC11011952 DOI: 10.5334/jcr.236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 04/16/2024] Open
Abstract
Circadian Biology intersects with diverse scientific domains, intricately woven into the fabric of organismal physiology and behavior. The rhythmic orchestration of life by the circadian clock serves as a focal point for researchers across disciplines. This retrospective examination delves into several of the scientific milestones that have fundamentally shaped our contemporary understanding of circadian rhythms. From deciphering the complexities of clock genes at a cellular level to exploring the nuances of coupled oscillators in whole organism responses to stimuli. The field has undergone significant evolution lately guided by genetics approaches. Our exploration here considers key moments in the circadian-research landscape, elucidating the trajectory of this discipline with a keen eye on scientific advancements and paradigm shifts.
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Affiliation(s)
| | - Henrik Oster
- Institute of Neurobiology, Center for Brain, Behavior & Metabolism (CBBM), University of Luebeck, 23562 Luebeck, DE
| | - Giles E. Duffield
- Department of Biological Sciences and Eck Institute for Global Health, Galvin Life Science Center, University of Notre Dame, Notre Dame, IN 46556, US
| | - Erik Maronde
- Institut für Anatomie II, Dr. Senckenbergische Anatomie, Goethe-Universität Frankfurt, Theodor-Stern-Kai-7, 60590 Frankfurt, DE
| | - Mario E. Guido
- CIQUIBIC-CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, AR
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, AR
| | - Christopher Chabot
- Department of Biological Sciences, Plymouth State University, Plymouth, NH 03264, US
| | - Ouria Dkhissi-Benyahya
- Inserm, Stem Cell and Brain Research Institute U1208, Univ Lyon, UniversitéClaude Bernard Lyon 1, 18 Avenue du Doyen Lépine, 69500, Bron, FR
| | - Ignacio Provencio
- Department of Biology and Department of Ophthalmology, University of Virginia, Charlottesville, VA, US
| | - Namni Goel
- Biological Rhythms Research Laboratory, Department of Psychiatry and Behavioral Sciences, Rush University Medical Center, Chicago, IL, US
| | - Shawn D. Youngstedt
- Edson College of Nursing and Health Innovation, Arizona State University, Phoenix, AZ, US
- Department of Medicine, University of Arizona, Tucson, AZ, US
| | | | - Mario Caba
- Centro de Investigaciones Biomédicas, Universidad Veracruzana, Xalapa, Ver., MX
| | - Anjoom Nikhat
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bangalore, Karnataka 560065, IN
| | - Shaon Chakrabarti
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bangalore, Karnataka 560065, IN
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, China National Botanical Garden, Beijing 100093, CN
| | - Seth J. Davis
- Department of Biology, University of York, York YO105DD, UK
- State Key Laboratory of Crop Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, CN
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16
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Fang C, Du H, Wang L, Liu B, Kong F. Mechanisms underlying key agronomic traits and implications for molecular breeding in soybean. J Genet Genomics 2024; 51:379-393. [PMID: 37717820 DOI: 10.1016/j.jgg.2023.09.004] [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: 05/01/2023] [Revised: 09/05/2023] [Accepted: 09/05/2023] [Indexed: 09/19/2023]
Abstract
Soybean (Glycine max [L.] Merr.) is an important crop that provides protein and vegetable oil for human consumption. As soybean is a photoperiod-sensitive crop, its cultivation and yield are limited by the photoperiodic conditions in the field. In contrast to other major crops, soybean has a special plant architecture and a special symbiotic nitrogen fixation system, representing two unique breeding directions. Thus, flowering time, plant architecture, and symbiotic nitrogen fixation are three critical or unique yield-determining factors. This review summarizes the progress made in our understanding of these three critical yield-determining factors in soybean. Meanwhile, we propose potential research directions to increase soybean production, discuss the application of genomics and genomic-assisted breeding, and explore research directions to address future challenges, particularly those posed by global climate changes.
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Affiliation(s)
- Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Haiping Du
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Lingshuang Wang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong 510006, China.
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17
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Tadesse D, Yee EF, Wolabu TW, Wang H, Yun J, Grosjean N, Kumaran D, Santiago K, Kong W, Sharma A, Chen J, Paterson AH, Xie M, Tadege M. Sorghum SbGhd7 is a major regulator of floral transition and directly represses genes crucial for flowering activation. THE NEW PHYTOLOGIST 2024; 242:786-796. [PMID: 38451101 DOI: 10.1111/nph.19591] [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: 11/21/2023] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
Molecular genetic understanding of flowering time regulation is crucial for sorghum development. GRAIN NUMBER, PLANT HEIGHT AND HEADING DATE 7 (SbGhd7) is one of the six classical loci conferring photoperiod sensitivity of sorghum flowering. However, its functions remain poorly studied. The molecular functions of SbGhd7 were characterized. The gene regulatory network controlled by SbGhd7 was constructed and validated. The biological roles of SbGhd7 and its major targets were studied. SbGhd7 overexpression (OE) completely prevented sorghum flowering. Additionally, we show that SbGhd7 is a major negative regulator of flowering, binding to the promoter motif TGAATG(A/T)(A/T/C) and repressing transcription of the major florigen FLOWERING LOCUS T 10 (SbFT10) and floral activators EARLY HEADING DATE (SbEhd1), FLAVIN-BINDING, KELCH REPEAT, F-BOX1 (SbFKF1) and EARLY FLOWERING 3 (SbELF3). Reinforcing the direct effect of SbGhd7, SbEhd1 OE activated the promoters of three functional florigens (SbFT1, SbFT8 and SbFT10), dramatically accelerating flowering. Our studies demonstrate that SbGhd7 is a major repressor of sorghum flowering by directly and indirectly targeting genes for flowering activation. The mechanism appears ancient. Our study extends the current model of floral transition regulation in sorghum and provides a framework for a comprehensive understanding of sorghum photoperiod response.
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Affiliation(s)
- Dimiru Tadesse
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
| | - Estella F Yee
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
- National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Tezera W Wolabu
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
| | - Hui Wang
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jianfei Yun
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
| | - Nicolas Grosjean
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Kassandra Santiago
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Wenqian Kong
- Department of Soil and Crop Science, University of Georgia, Athens, GA, 30602, USA
| | - Ankush Sharma
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Jianghua Chen
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Meng Xie
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
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18
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Li X, Chen Z, Li H, Yue L, Tan C, Liu H, Hu Y, Yang Y, Yao X, Kong L, Huang X, Yu B, Zhang C, Guan Y, Liu B, Kong F, Hou X. Dt1 inhibits SWEET-mediated sucrose transport to regulate photoperiod-dependent seed weight in soybean. MOLECULAR PLANT 2024; 17:496-508. [PMID: 38341616 DOI: 10.1016/j.molp.2024.02.007] [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: 04/19/2023] [Revised: 09/25/2023] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Soybean is a photoperiod-sensitive short-day crop whose reproductive period and yield are markedly affected by day-length changes. Seed weight is one of the key traits determining the soybean yield; however, the prominent genes that control the final seed weight of soybean and the mechanisms underlying the photoperiod's effect on this trait remain poorly understood. In this study, we identify SW19 as a major locus controlling soybean seed weight by QTL mapping and determine Dt1, an orthologous gene of Arabidopsis TFL1 that is known to govern the soybean growth habit, as the causal gene of the SW19 locus. We showed that Dt1 is highly expressed in developing seeds and regulates photoperiod-dependent seed weight in soybean. Further analyses revealed that the Dt1 protein physically interacts with the sucrose transporter GmSWEET10a to negatively regulate the import of sucrose from seed coat to the embryo, thus modulating seed weight under long days. However, Dt1 does not function in seed development under short days due to its very low expression. Importantly, we discovered a novel natural allelic variant of Dt1 (H4 haplotype) that decouples its pleiotropic effects on seed size and growth habit; i.e., this variant remains functional in seed development but fails to regulate the stem growth habit of soybean. Collectively, our findings provide new insights into how soybean seed development responds to photoperiod at different latitudes, offering an ideal genetic component for improving soybean's yield by manipulating its seed weight and growth habit.
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Affiliation(s)
- Xiaoming Li
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhonghui Chen
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyang Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Lin Yue
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Cuirong Tan
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongjie Liu
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yilong Hu
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yuhua Yang
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xiani Yao
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lingping Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Xiang Huang
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Bin Yu
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunyu Zhang
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yuefeng Guan
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Baohui Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China; College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| | - Xingliang Hou
- Guangdong Provincial Key Laboratory of Applied Botany & State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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19
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Chen B, Shi Y, Sun Y, Lu L, Wang L, Liu Z, Cheng S. Innovations in functional genomics and molecular breeding of pea: exploring advances and opportunities. ABIOTECH 2024; 5:71-93. [PMID: 38576433 PMCID: PMC10987475 DOI: 10.1007/s42994-023-00129-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/05/2023] [Indexed: 04/06/2024]
Abstract
The garden pea (Pisum sativum L.) is a significant cool-season legume, serving as crucial food sources, animal feed, and industrial raw materials. The advancement of functional genomics over the past two decades has provided substantial theoretical foundations and progress to pea breeding. Notably, the release of the pea reference genome has enhanced our understanding of plant architecture, symbiotic nitrogen fixation (SNF), flowering time, floral organ development, seed development, and stress resistance. However, a considerable gap remains between pea functional genomics and molecular breeding. This review summarizes the current advancements in pea functional genomics and breeding while highlighting the future challenges in pea molecular breeding.
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Affiliation(s)
- Baizhi Chen
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Yan Shi
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Yuchen Sun
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Lu Lu
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Luyao Wang
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Zijian Liu
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Shifeng Cheng
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
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20
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Wang C, Li X, Zhuang Y, Sun W, Cao H, Xu R, Kong F, Zhang D. A novel miR160a-GmARF16-GmMYC2 module determines soybean salt tolerance and adaptation. THE NEW PHYTOLOGIST 2024; 241:2176-2192. [PMID: 38135657 DOI: 10.1111/nph.19503] [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: 10/30/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023]
Abstract
Salt stress is a major challenge that has a negative impact on soybean growth and productivity. Therefore, it is important to understand the regulatory mechanism of salt response to ensure soybean yield under such conditions. In this study, we identified and characterized a miR160a-GmARF16-GmMYC2 module and its regulation during the salt-stress response in soybean. miR160a promotes salt tolerance by cleaving GmARF16 transcripts, members of the Auxin Response Factor (ARF) family, which negatively regulates salt tolerance. In turn, GmARF16 activates GmMYC2, encoding a bHLH transcription factor that reduces salinity tolerance by down-regulating proline biosynthesis. Genomic analysis among wild and cultivated soybean accessions identified four distinct GmARF16 haplotypes. Among them, the GmARF16H3 haplotype is preferentially enriched in localities with relatively saline soils, suggesting GmARF16H3 was artificially selected to improve salt tolerance. Our findings therefore provide insights into the molecular mechanisms underlying salt response in soybean and provide valuable genetic targets for the molecular breeding of salt tolerance.
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Affiliation(s)
- Chaofan Wang
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xiaoming Li
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yongbin Zhuang
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Wancai Sun
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Hongxiang Cao
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Ran Xu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, 250131, China
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Dajian Zhang
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
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21
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Wang L, Niu F, Wang J, Zhang H, Zhang D, Hu Z. Genome-Wide Association Studies Prioritize Genes Controlling Seed Size and Reproductive Period Length in Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:615. [PMID: 38475461 DOI: 10.3390/plants13050615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
Hundred-seed weight (HSW) and reproductive period length (RPL) are two major agronomic traits critical for soybean production and adaptation. However, both traits are quantitatively controlled by multiple genes that have yet to be comprehensively elucidated due to the lack of major genes; thereby, the genetic basis is largely unknown. In the present study, we conducted comprehensive genome-wide association analyses (GWAS) of HSW and RPL with multiple sets of accessions that were phenotyped across different environments. The large-scale analysis led to the identification of sixty-one and seventy-four significant QTLs for HSW and RPL, respectively. An ortholog-based search analysis prioritized the most promising candidate genes for the QTLs, including nine genes (TTG2, BZR1, BRI1, ANT, KLU, EOD1/BB, GPA1, ABA2, and ABI5) for HSW QTLs and nine genes (such as AGL8, AGL9, TOC1, and COL4) and six known soybean flowering time genes (E2, E3, E4, Tof11, Tof12, and FT2b) for RPL QTLs. We also demonstrated that some QTLs were targeted during domestication to drive the artificial selection of both traits towards human-favored traits. Local adaptation likely contributes to the increased genomic diversity of the QTLs underlying RPL. The results provide additional insight into the genetic basis of HSW and RPL and prioritize a valuable resource of candidate genes that merits further investigation to reveal the complex molecular mechanism and facilitate soybean improvement.
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Affiliation(s)
- Le Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Fu'an Niu
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jinshe Wang
- National Innovation Centre for Bio-Breeding Industry, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Hengyou Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhenbin Hu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
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22
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Wei Y, Xu Y, Khan A, Jiang C, Li H, Wu Y, Zhang C, Wang M, Chen J, Zeng L, Zhang M. Analysis of Photosynthetic Characteristics and Screening High Light-Efficiency Germplasm in Sugarcane. PLANTS (BASEL, SWITZERLAND) 2024; 13:587. [PMID: 38475434 DOI: 10.3390/plants13050587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/09/2024] [Accepted: 01/17/2024] [Indexed: 03/14/2024]
Abstract
Sugarcane is a globally significant crop for sugar and energy production, and developing high light-efficiency sugarcane varieties is crucial for enhancing yield and quality. However, limited research is available on the screening of sugarcane germplasm with high photosynthetic efficiency, especially with different leaf positions. The present study, conducted in Guangxi, China, aimed to analyze the photosynthetic characteristics of 258 sugarcane varieties at different leaf positions over three consecutive years in field experiments. The results showed significant differences in photosynthetic characteristics among genotypes, years, and leaf positions. Heritability estimates for various photosynthetic parameters ranged from 0.76 to 0.88. Principal component analysis revealed that the first three principal components accounted for over 99% of the cumulative variance. The first component represented photosynthetic efficiency and light utilization, the second focused on electron transfer and reaction center status, and the third was associated with chlorophyll content. Cluster and discriminant analysis classified sugarcane genotypes into three categories: high photosynthetic efficiency (HPE) with 86 genotypes, medium photosynthetic efficiency (MPE) with 60 genotypes, and low photosynthetic efficiency (LPE) with 112 genotypes. Multi-year trials confirmed that HPE sugarcane genotypes had higher single-stem weight and sucrose content. This study provides valuable insights into the photosynthetic physiological characteristics of different sugarcane varieties, which can contribute to further research regarding high yields and sugar breeding.
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Affiliation(s)
- Yibin Wei
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Yuzhi Xu
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Abdullah Khan
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Chunxiu Jiang
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Huojian Li
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Yuling Wu
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Chi Zhang
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Maoyao Wang
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Jun Chen
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Lifang Zeng
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Muqing Zhang
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
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23
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Biová J, Kaňovská I, Chan YO, Immadi MS, Joshi T, Bilyeu K, Škrabišová M. Natural and artificial selection of multiple alleles revealed through genomic analyses. Front Genet 2024; 14:1320652. [PMID: 38259621 PMCID: PMC10801239 DOI: 10.3389/fgene.2023.1320652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/17/2023] [Indexed: 01/24/2024] Open
Abstract
Genome-to-phenome research in agriculture aims to improve crops through in silico predictions. Genome-wide association study (GWAS) is potent in identifying genomic loci that underlie important traits. As a statistical method, increasing the sample quantity, data quality, or diversity of the GWAS dataset positively impacts GWAS power. For more precise breeding, concrete candidate genes with exact functional variants must be discovered. Many post-GWAS methods have been developed to narrow down the associated genomic regions and, ideally, to predict candidate genes and causative mutations (CMs). Historical natural selection and breeding-related artificial selection both act to change the frequencies of different alleles of genes that control phenotypes. With higher diversity and more extensive GWAS datasets, there is an increased chance of multiple alleles with independent CMs in a single causal gene. This can be caused by the presence of samples from geographically isolated regions that arose during natural or artificial selection. This simple fact is a complicating factor in GWAS-driven discoveries. Currently, none of the existing association methods address this issue and need to identify multiple alleles and, more specifically, the actual CMs. Therefore, we developed a tool that computes a score for a combination of variant positions in a single candidate gene and, based on the highest score, identifies the best number and combination of CMs. The tool is publicly available as a Python package on GitHub, and we further created a web-based Multiple Alleles discovery (MADis) tool that supports soybean and is hosted in SoyKB (https://soykb.org/SoybeanMADisTool/). We tested and validated the algorithm and presented the utilization of MADis in a pod pigmentation L1 gene case study with multiple CMs from natural or artificial selection. Finally, we identified a candidate gene for the pod color L2 locus and predicted the existence of multiple alleles that potentially cause loss of pod pigmentation. In this work, we show how a genomic analysis can be employed to explore the natural and artificial selection of multiple alleles and, thus, improve and accelerate crop breeding in agriculture.
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Affiliation(s)
- Jana Biová
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Olomouc, Czechia
| | - Ivana Kaňovská
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Olomouc, Czechia
| | - Yen On Chan
- MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, United States
| | - Manish Sridhar Immadi
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, United States
| | - Trupti Joshi
- MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, United States
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, United States
- Department of Biomedical Informatics, Biostatistics and Medical Epidemiology, University of Missouri-Columbia, Columbia, MO, United States
| | - Kristin Bilyeu
- United States Department of Agriculture-Agricultural Research Service, Plant Genetics Research Unit, Columbia, MO, United States
| | - Mária Škrabišová
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Olomouc, Czechia
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24
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Xie Y, Zhao Y, Chen L, Wang Y, Xue W, Kong D, Li C, Zhou L, Li H, Zhao Y, Wang B, Xu M, Zhao B, Bilska-Kos A, Wang H. ZmELF3.1 integrates the RA2-TSH4 module to repress maize tassel branching. THE NEW PHYTOLOGIST 2024; 241:490-503. [PMID: 37858961 DOI: 10.1111/nph.19329] [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: 03/24/2023] [Accepted: 09/08/2023] [Indexed: 10/21/2023]
Abstract
Tassel branch number (TBN) is a key agronomic trait for adapting to high-density planting and grain yield in maize. However, the molecular regulatory mechanisms underlying tassel branching are still largely unknown. Here, we used molecular and genetic studies together to show that ZmELF3.1 plays a critical role in regulating TBN in maize. Previous studies showed that ZmELF3.1 forms the evening complex through interacting with ZmELF4 and ZmLUX to regulate flowering in maize and that RA2 and TSH4 (ZmSBP2) suppresses and promotes TBN in maize, respectively. In this study, we show that loss-of-function mutants of ZmELF3.1 exhibit a significant increase of TBN. We also show that RA2 directly binds to the promoter of TSH4 and represses its expression, thus leading to reduced TBN. We further demonstrate that ZmELF3.1 directly interacts with both RA2 and ZmELF4.2 to form tri-protein complexes that further enhance the binding of RA2 to the promoter of TSH4, leading to suppressed TSH4 expression and consequently decreased TBN. Our combined results establish a novel functional link between the ELF3-ELF4-RA2 complex and miR156-SPL regulatory module in regulating tassel branching and provide a valuable target for genetic improvement of tassel branching in maize.
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Affiliation(s)
- Yurong Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Yongping Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lihong Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yanli Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Weicong Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Dexin Kong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Changyu Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Linyu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huiru Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanfeng Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Miaoyun Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Binbin Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Anna Bilska-Kos
- Plant Breeding and Acclimatization Institute-National Research Institute, Department of Biochemistry and Biotechnology, Radzików, 05-870, Błonie, Poland
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
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25
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Su Q, Chen L, Cai Y, Wang L, Chen Y, Zhang J, Liu L, Zhang Y, Yuan S, Gao Y, Sun S, Han T, Hou W. The FLOWERING LOCUS T 5b positively regulates photoperiodic flowering and improves the geographical adaptation of soybean. PLANT, CELL & ENVIRONMENT 2024; 47:246-258. [PMID: 37830787 DOI: 10.1111/pce.14739] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/25/2023] [Accepted: 10/05/2023] [Indexed: 10/14/2023]
Abstract
Plants can sense the photoperiod to flower at the right time. As a sensitive short-day crop, soybean (Glycine max) flowering varies greatly depending on photoperiods, affecting yields. Adaptive changes in soybeans rely on variable genetic loci such as E1 and FLOWERING LOCUS T orthologs. However, the precise coordination and control of these molecular components remain largely unknown. In this study, we demonstrate that GmFT5b functions as a crucial factor for soybean flowering. Overexpressed or mutated GmFT5b resulted in significantly early or later flowering, altering expression profiles for several downstream flowering-related genes under a long-day photoperiod. GmFT5b interacts with the transcription factor GmFDL15, suggesting transcriptional tuning of flowering time regulatory genes via the GmFT5b/GmFDL15 complex. Notably, GmFT5a partially compensated for GmFT5b function, as ft5a ft5b double mutants exhibited an enhanced late-flowering phenotype. Association mapping revealed that GmFT5b was associated with flowering time, maturity, and geographical distribution of soybean accessions, all associated with the E1 locus. Therefore, GmFT5b is a valuable target for enhancing regional adaptability. Natural variants or multiple mutants in this region can be utilized to generate optimized soybean varieties with precise flowering times.
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Affiliation(s)
- Qiang Su
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Chen
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yupeng Cai
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liwei Wang
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingying Chen
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jialing Zhang
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Luping Liu
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Zhang
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shan Yuan
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Gao
- Syngenta Biotechnology (China) Co., Ltd, Beijing, China
| | - Shi Sun
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianfu Han
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wensheng Hou
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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26
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Zhang Y, Ma Y, Zhang H, Xu J, Gao X, Zhang T, Liu X, Guo L, Zhao D. Environmental F actors coordinate circadian clock function and rhythm to regulate plant development. PLANT SIGNALING & BEHAVIOR 2023; 18:2231202. [PMID: 37481743 PMCID: PMC10364662 DOI: 10.1080/15592324.2023.2231202] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 07/25/2023]
Abstract
Changes in the external environment necessitate plant growth plasticity, with environmental signals such as light, temperature, and humidity regulating growth and development. The plant circadian clock is a biological time keeper that can be "reset" to adjust internal time to changes in the external environment. Exploring the regulatory mechanisms behind plant acclimation to environmental factors is important for understanding how plant growth and development are shaped and for boosting agricultural production. In this review, we summarize recent insights into the coordinated regulation of plant growth and development by environmental signals and the circadian clock, further discussing the potential of this knowledge.
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Affiliation(s)
- Ying Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Yuru Ma
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Hao Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Jiahui Xu
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Xiaokuan Gao
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
| | - Tengteng Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Xigang Liu
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Lin Guo
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Dan Zhao
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
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27
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Wang Z, Xing S, Li M, Zhang Q, Yang Q, Xu P, Song B, Shang P, Yang M, Du C, Chen J, Liu S, Zhang S. Soybean WRINKLED1 protein GmWRI1a promotes flowering under long-day conditions via regulating expressions of flowering-related genes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 337:111865. [PMID: 37696474 DOI: 10.1016/j.plantsci.2023.111865] [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: 05/19/2023] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
Flowering time is an important agronomic character that influences the adaptability and yield of soybean [Glycine max (L.) Merrill]. WRINKLED 1 (WRI1) plays an important regulatory role in plant growth and development. In this study, we found that the expression of GmWIR1a could be induced by long days. Compared with the wild type, transgenic soybean overexpressing GmWRI1a showed earlier flowering and maturity under long days but no significant changes under short days. Overexpression of GmWRI1a led to up-regulated expression of genes involved in the regulation of flowering time. The GmWRI1a protein was able to directly bind to the promoter regions of GmAP1, GmFUL1a, GmFUL2 and up-regulated their expression. GmCOL3 was identified by yeast one-hybrid library screening using the GmWRI1a promoter as bait. GmCOL3 was revealed to be a nucleus-localized protein that represses the transcription of GmWRI1a. Expression of GmCOL3 was induced by short days. Taken together, the results show that overexpression of GmWRI1a promotes flowering under long days by promoting the transcriptional activity of flowering-related genes in soybean, and that GmCOL3 binds to the GmWRI1a promoter and directly down-regulates its transcription. This discovery reveals a new function for GmWRI1a, which regulates flowering and maturity in soybean.
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Affiliation(s)
- Zhikun Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Siqi Xing
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Meng Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Qingyan Zhang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Qiang Yang
- Center for Agricultural Technology, Northeast Institute of Geography and Agroecology, CAS, Harbin, China
| | - Pengfei Xu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Bo Song
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Ping Shang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Mingming Yang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Changhuan Du
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Jihan Chen
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Shanshan Liu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China.
| | - Shuzhen Zhang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China.
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28
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Liu S, He M, Lin X, Kong F. Epigenetic regulation of photoperiodic flowering in plants. THE PLANT GENOME 2023; 16:e20320. [PMID: 37013370 DOI: 10.1002/tpg2.20320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/12/2023] [Accepted: 01/30/2023] [Indexed: 06/19/2023]
Abstract
In response to changeable season, plants precisely control the initiation of flowering in appropriate time of the year to ensure reproductive success. Day length (photoperiod) acts as the most important external cue to determine flowering time. Epigenetics regulates many major developmental stages in plant life, and emerging molecular genetics and genomics researches reveal their essential roles in floral transition. Here, we summarize the recent advances in epigenetic regulation of photoperiod-mediated flowering in Arabidopsis and rice, and discuss the potential of epigenetic regulation in crops improvement, and give the brief prospect for future study trends.
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Affiliation(s)
- Shuangrong Liu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Milan He
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xiaoya Lin
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
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29
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Hu Y, Liu Y, Wei JJ, Zhang WK, Chen SY, Zhang JS. Regulation of seed traits in soybean. ABIOTECH 2023; 4:372-385. [PMID: 38106437 PMCID: PMC10721594 DOI: 10.1007/s42994-023-00122-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/18/2023] [Indexed: 12/19/2023]
Abstract
Soybean (Glycine max) is an essential economic crop that provides vegetative oil and protein for humans, worldwide. Increasing soybean yield as well as improving seed quality is of great importance. Seed weight/size, oil and protein content are the three major traits determining seed quality, and seed weight also influences soybean yield. In recent years, the availability of soybean omics data and the development of related techniques have paved the way for better research on soybean functional genomics, providing a comprehensive understanding of gene functions. This review summarizes the regulatory genes that influence seed size/weight, oil content and protein content in soybean. We also provided a general overview of the pleiotropic effect for the genes in controlling seed traits and environmental stresses. Ultimately, it is expected that this review will be beneficial in breeding improved traits in soybean.
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Affiliation(s)
- Yang Hu
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yue Liu
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jun-Jie Wei
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wan-Ke Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Shou-Yi Chen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jin-Song Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
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30
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Zhang Y, Xu P, Xue W, Zhu W, Yu X. Diurnal gene oscillations modulated by RNA metabolism in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:728-743. [PMID: 37492018 DOI: 10.1111/tpj.16400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/16/2023] [Accepted: 07/13/2023] [Indexed: 07/27/2023]
Abstract
Diurnal rhythms are known to regulate the expression of a large number of genes, coordinating plant growth and development with diel changes in light and temperature. However, the impact of RNA metabolism on rhythmic gene oscillations in plant is not yet fully understood. To address this question, we performed transcriptome and degradome profiling on tomato leaves at 6 time points during one 24 h cycle, using RNA-seq and genome-wide mapping of uncapped and cleavage transcripts (GMUCT). Time-series profiling of RNA-seq revealed 9342 diurnal-oscillated genes, which were enriched in various metabolic processes. To quantify the general level of RNA degradation for each gene, we utilized the Proportion Uncapped (PU) metric, which represents the GMUCT/RNA-seq ratio. Oscillated PU analysis revealed that 3885 genes were regulated by rhythmic RNA degradation. The RNA decay of these diurnal genes was highly coordinated with mRNA downregulation during oscillation, highlighting the critical role of internal transcription-degradation balance in rhythmic gene oscillation. Furthermore, we identified 2190 genes undergoing co-translational RNA decay (CTRD) with 5' phosphate read ends enriched at the boundary of ribosomes stalling at translational termination sites. Interestingly, diurnal-changed mRNAs with large amplitudes tended to be co-translationally decay, suggesting that CTRD contributed to the rapid turnover of diurnal mRNAs. Finally, we also identified several genes, whose miRNA cleavage efficiency oscillated in a diurnal manner. Taken together, these findings uncovered the vital functions of RNA metabolism, including rhythmic RNA degradation, CTRD, and miRNA cleavage, in modulating the diurnal mRNA oscillations during diel change at post-transcriptional level in tomato.
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Affiliation(s)
- Yingying Zhang
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Pengfei Xu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wanxin Xue
- Shanghai Yuanyi Seedling Co. Ltd, Shanghai, 201318, China
| | - Weimin Zhu
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Xiang Yu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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31
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Xu H, Zuo Y, Wei J, Wang L. The Circadian Clock Coordinates the Tradeoff between Adaptation to Abiotic Stresses and Yield in Crops. BIOLOGY 2023; 12:1364. [PMID: 37997963 PMCID: PMC10669628 DOI: 10.3390/biology12111364] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 11/25/2023]
Abstract
Plants have evolved a circadian clock to adapt to ever-changing diel and seasonal environmental conditions. The circadian clock is generally considered an internal system that has evolved to adapt to cyclic environmental cues, especially diel light and temperature changes, which is essential for higher plants as they are sessile organisms. This system receives environmental signals as input pathways which are integrated by circadian core oscillators to synchronize numerous output pathways, such as photosynthesis, the abiotic stress response, metabolism, and development. Extreme temperatures, salinity, and drought stresses cause huge crop losses worldwide, imposing severe pressure on areas of agricultural land. In crop production, the circadian system plays a significant role in determining flowering time and responding to external abiotic stresses. Extensive studies over the last two decades have revealed that the circadian clock can help balance the tradeoff between crop yield-related agronomic traits and adaptation to stress. Herein, we focus on summarizing how the circadian clock coordinates abiotic stress responses and crop yield. We also propose that there might be an urgent need to better utilize circadian biology in the future design of crop breeding to achieve high yields under stress conditions.
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Affiliation(s)
- Hang Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (H.X.); (Y.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (H.X.); (Y.Z.)
| | - Jian Wei
- Center of Soybean, Jilin Agricultural University, Changchun 130117, China;
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (H.X.); (Y.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Academician Workstation of Agricultural High-Tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying 257300, China
- China National Botanical Garden, Beijing 100093, China
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32
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Alcantara M, Iftikhar H, Kagan K, Dzheyranyan D, Abbasi P, Alamilla A, Ayala N, Baca T, Benoit V, Clausen N, Coto C, Guerrero C, Hernandez Catalan E, Hurtado S, Lopez A, Lopez J, Majarian N, Mesfin N, Mishegyan A, Mkrtchyan G, Ordonez A, Pachanyan A, Pelayo T, Rosas A, Rowsey K, Sharma E, Sharma S, Van Grinsven S, Hanzawa Y. Clarifying the Temporal Dynamics of the Circadian Clock and Flowering Gene Network Using Overexpression and Targeted Mutagenesis of Soybean EARLY FLOWERING 3-1 ( GmELF3-1 ). MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000935. [PMID: 37908495 PMCID: PMC10613878 DOI: 10.17912/micropub.biology.000935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/20/2023] [Accepted: 10/11/2023] [Indexed: 11/02/2023]
Abstract
With progressing climate fluctuations, an understanding of the molecular mechanisms of crop plants that regulate their flowering responses to environments is crucial. To achieve this goal, we aimed at clarifying the gene regulatory networks among the circadian clock and flowering genes in soybean ( Glycine max ). Based on our network inference approach , we hypothesize that GmELF3-1 , one of the Evening Complex (EC) gene homologs in soybean's circadian clock, may have an integrative role in transcriptional regulation of the circadian clock and flowering gene network. In this study, we verify GmELF3-1 ' s regulatory roles in its potential downstream genes by modulating the activity of GmELF3-1 using overexpression and CRISPR-Cas9 in soybean protoplasts. Our results indicate that GmELF3-1 may control the expression of the PRR genes in the circadian clock and the flowering gene GmCOL1a .
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Affiliation(s)
| | - Hira Iftikhar
- Department of Biology, California State University Northridge
| | - Kimberly Kagan
- Department of Biology, California State University Northridge
| | | | - Pedram Abbasi
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Alejandra Alamilla
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Nicole Ayala
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Trixy Baca
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Vanessa Benoit
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Natalia Clausen
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Caroline Coto
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Celia Guerrero
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Erik Hernandez Catalan
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Sierra Hurtado
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Angela Lopez
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Jacqueline Lopez
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Nicholas Majarian
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Noah Mesfin
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Avetis Mishegyan
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Goharik Mkrtchyan
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Amy Ordonez
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Arthur Pachanyan
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Tanya Pelayo
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Alondra Rosas
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Kylee Rowsey
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Elina Sharma
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Sanjiti Sharma
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Shauna Van Grinsven
- Department of Biology, BIOL 481L Plant Physiology, California State University Northridge
| | - Yoshie Hanzawa
- Department of Biology, California State University Northridge
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33
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Zhao H, Huang X, Yang Z, Li F, Ge X. Synergistic optimization of crops by combining early maturation with other agronomic traits. TRENDS IN PLANT SCIENCE 2023; 28:1178-1191. [PMID: 37208203 DOI: 10.1016/j.tplants.2023.04.011] [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: 11/21/2022] [Revised: 04/16/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023]
Abstract
Many newly created early maturing varieties exhibit poor stress resistance and low yield, whereas stress-resistant varieties are typically late maturing. For this reason, the polymerization of early maturity and other desired agronomic qualities requires overcoming the negative connection between early maturity, multi-resistance, and yield, which presents a formidable challenge in current breeding techniques. We review the most salient constraints of early maturity breeding in current crop planting practices and the molecular mechanisms of different maturation timeframes in diverse crops from their origin center to production areas. We explore current breeding tactics and the future direction of crop breeding and the issues that must be resolved to accomplish the polymerization of desirable traits in light of the current obstacles and limitations.
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Affiliation(s)
- Hang Zhao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; College of Life Sciences, Qufu Normal University, Qufu, 273165, China
| | - Xianzhong Huang
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou, China
| | - Zhaoen Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100 Xinjiang, China; Hainan Yazhou Bay Seed Lab, Sanya 572000, Hainan, China.
| | - Xiaoyang Ge
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100 Xinjiang, China; Hainan Yazhou Bay Seed Lab, Sanya 572000, Hainan, China.
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Wang X, Hu Y, Wang W. Comparative Analysis of Circadian Transcriptomes Reveals Circadian Characteristics between Arabidopsis and Soybean. PLANTS (BASEL, SWITZERLAND) 2023; 12:3344. [PMID: 37836084 PMCID: PMC10574400 DOI: 10.3390/plants12193344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 10/15/2023]
Abstract
The circadian clock, an endogenous timing system, exists in nearly all organisms on Earth. The plant circadian clock has been found to be intricately linked with various essential biological activities. Extensive studies of the plant circadian clock have yielded valuable applications. However, the distinctions of circadian clocks in two important plant species, Arabidopsis thaliana and Glycine max (soybean), remain largely unexplored. This study endeavors to address this gap by conducting a comprehensive comparison of the circadian transcriptome profiles of Arabidopsis and soybean to uncover their distinct circadian characteristics. Utilizing non-linear regression fitting (COS) integrated with weights, we identified circadian rhythmic genes within both organisms. Through an in-depth exploration of circadian parameters, we unveiled notable differences between Arabidopsis and soybean. Furthermore, our analysis of core circadian clock genes shed light on the distinctions in central oscillators between these two species. Additionally, we observed that the homologous genes of Arabidopsis circadian clock genes in soybean exert a significant influence on the regulation of flowering and maturity of soybean. This phenomenon appears to stem from shifts in circadian parameters within soybean genes. These findings highlight contrasting biological activities under circadian regulation in Arabidopsis and soybean. This study not only underscores the distinctive attributes of these species, but also offers valuable insights for further scrutiny into the soybean circadian clock and its potential applications.
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Affiliation(s)
- Xingwei Wang
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (X.W.); (Y.H.)
- Center for Life Sciences, Beijing 100871, China
| | - Yanfei Hu
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (X.W.); (Y.H.)
- Center for Life Sciences, Beijing 100871, China
| | - Wei Wang
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (X.W.); (Y.H.)
- Center for Life Sciences, Beijing 100871, China
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Sun J, Zheng Y, Guo J, Zhang Y, Liu Y, Tao Y, Wang M, Liu T, Liu Y, Li X, Zhang X, Zhao L. GmGAMYB-BINDING PROTEIN 1 promotes small auxin-up RNA gene transcription to modulate soybean maturity and height. PLANT PHYSIOLOGY 2023; 193:775-791. [PMID: 37204820 DOI: 10.1093/plphys/kiad293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/13/2023] [Accepted: 04/26/2023] [Indexed: 05/20/2023]
Abstract
Flowering time, maturity, and plant height are crucial agronomic traits controlled by photoperiod that affect soybean (Glycine max [L.] Merr.) yield and regional adaptability. It is important to cultivate soybean cultivars of earlier maturity that adapt to high latitudes. GAMYB-binding protein 1 (GmGBP1), a member of the SNW/SKIP family of transcriptional coregulators in soybean, is induced by short days and interacts with transcription factor GAMYB (GmGAMYB) during photoperiod control of flowering time and maturity. In the present study, GmGBP1:GmGBP1 soybean showed the phenotypes of earlier maturity and higher plant height. Chromatin immunoprecipitation sequencing (ChIP-seq) assays of GmGBP1-binding sites and RNA sequencing (RNA-seq) of differentially expressed transcripts in GmGBP1:GmGBP1 further identified potential targets of GmGBP1, including small auxin-up RNA (GmSAUR). GmSAUR:GmSAUR soybean also showed earlier maturity and higher plant height. GmGBP1 interacted with GmGAMYB, bound to the promoter of GmSAUR and promoted the expression of FLOWER LOCUS T homologs 2a (GmFT2a) and FLOWERING LOCUS D LIKE 19 (GmFDL19). Flowering repressors such as GmFT4 were negatively regulated, resulting in earlier flowering and maturity. Furthermore, the interaction of GmGBP1 with GmGAMYB increased the gibberellin (GA) signal to promote height and hypocotyl elongation by activating GmSAUR and GmSAUR bound to the promoter of the GA-positive activating regulator gibberellic acid-stimulated Arabidopsis 32 (GmGASA32). These results suggested a photoperiod regulatory pathway in which the interaction of GmGBP1 with GmGAMYB directly activated GmSAUR to promote earlier maturity and plant height in soybean.
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Affiliation(s)
- Jingzhe Sun
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Yuhong Zheng
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Jinpeng Guo
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Yuntong Zhang
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Ying Liu
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Yahan Tao
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Mengyuan Wang
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Tianmeng Liu
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Yangyang Liu
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Xin Li
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | | | - Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
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Wu T, Lu S, Cai Y, Xu X, Zhang L, Chen F, Jiang B, Zhang H, Sun S, Zhai H, Zhao L, Xia Z, Hou W, Kong F, Han T. Molecular breeding for improvement of photothermal adaptability in soybean. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:60. [PMID: 37496825 PMCID: PMC10366068 DOI: 10.1007/s11032-023-01406-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/08/2023] [Indexed: 07/28/2023]
Abstract
Soybean (Glycine max (L.) Merr.) is a typical short-day and temperate crop that is sensitive to photoperiod and temperature. Responses of soybean to photothermal conditions determine plant growth and development, which affect its architecture, yield formation, and capacity for geographic adaptation. Flowering time, maturity, and other traits associated with photothermal adaptability are controlled by multiple major-effect and minor-effect genes and genotype-by-environment interactions. Genetic studies have identified at least 11 loci (E1-E4, E6-E11, and J) that participate in photoperiodic regulation of flowering time and maturity in soybean. Molecular cloning and characterization of major-effect flowering genes have clarified the photoperiod-dependent flowering pathway, in which the photoreceptor gene phytochrome A, circadian evening complex (EC) components, central flowering repressor E1, and FLOWERING LOCUS T family genes play key roles in regulation of flowering time, maturity, and adaptability to photothermal conditions. Here, we provide an overview of recent progress in genetic and molecular analysis of traits associated with photothermal adaptability, summarizing advances in molecular breeding practices and tools for improving these traits. Furthermore, we discuss methods for breeding soybean varieties with better adaptability to specific ecological regions, with emphasis on a novel strategy, the Potalaization model, which allows breeding of widely adapted soybean varieties through the use of multiple molecular tools in existing elite widely adapted varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01406-z.
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Affiliation(s)
- Tingting Wu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Sijia Lu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Yupeng Cai
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xin Xu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lixin Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Fulu Chen
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Bingjun Jiang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Honglei Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shi Sun
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
| | - Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education of China, Northeast Agricultural University, Harbin, 150030 China
| | - Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
| | - Wensheng Hou
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Tianfu Han
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Steel L, Welling M, Ristevski N, Johnson K, Gendall A. Comparative genomics of flowering behavior in Cannabis sativa. FRONTIERS IN PLANT SCIENCE 2023; 14:1227898. [PMID: 37575928 PMCID: PMC10421669 DOI: 10.3389/fpls.2023.1227898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/03/2023] [Indexed: 08/15/2023]
Abstract
Cannabis sativa L. is a phenotypically diverse and multi-use plant used in the production of fiber, seed, oils, and a class of specialized metabolites known as phytocannabinoids. The last decade has seen a rapid increase in the licit cultivation and processing of C. sativa for medical end-use. Medical morphotypes produce highly branched compact inflorescences which support a high density of glandular trichomes, specialized epidermal hair-like structures that are the site of phytocannabinoid biosynthesis and accumulation. While there is a focus on the regulation of phytocannabinoid pathways, the genetic determinants that govern flowering time and inflorescence structure in C. sativa are less well-defined but equally important. Understanding the molecular mechanisms that underly flowering behavior is key to maximizing phytocannabinoid production. The genetic basis of flowering regulation in C. sativa has been examined using genome-wide association studies, quantitative trait loci mapping and selection analysis, although the lack of a consistent reference genome has confounded attempts to directly compare candidate loci. Here we review the existing knowledge of flowering time control in C. sativa, and, using a common reference genome, we generate an integrated map. The co-location of known and putative flowering time loci within this resource will be essential to improve the understanding of C. sativa phenology.
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Affiliation(s)
| | | | | | | | - Anthony Gendall
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe Institute for Sustainable Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia
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Yerzhebayeva R, Didorenko S, Amangeldiyeva A, Daniyarova A, Mazkirat S, Zinchenko A, Shavrukov Y. Marker-Assisted Selection for Early Maturing E Loci in Soybean Yielded Prospective Breeding Lines for High Latitudes of Northern Kazakhstan. Biomolecules 2023; 13:1146. [PMID: 37509181 PMCID: PMC10377072 DOI: 10.3390/biom13071146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The photoperiodic sensitivity of soybean (Glycine max L.) is one of the limiting factors affecting plant growth and yield. At higher latitudes, early flowering and maturity with neutral reaction to photoperiods are required for adaptation of soybean plants to long-day conditions. Currently, the production and distribution of new varieties of soybeans adapted to widespread agricultural regions in northern Kazakhstan is in strong demand. Eleven soybean hybrid populations were obtained from crosses between 17 parents with four maturity groups, MG 000, 00, 0, and I. Marker-assisted selection (MAS) was assessed for suitable SSR markers and successfully applied for genes E1, E3, E4, and E7, targeting homozygous genotypes with recessive alleles. The identified and selected genotypes were propagated and tested in the conditions of 53° N latitude in the Kostanay region of northern Kazakhstan. Finally, 20 early maturing F4 breeding lines were identified and developed with genotypes e1 e3 E4 e7, e1 E3 E4 e7, and e1 E3 e4 e7, all completing their growth period within 92-102 days. These breeding lines were developed by MAS and should provide very prospective superior varieties of soybean for northern Kazakhstan through a strategy that may be very helpful to other countries with high latitudes.
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Affiliation(s)
- Raushan Yerzhebayeva
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan
| | - Svetlana Didorenko
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan
| | - Aigul Amangeldiyeva
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan
| | - Aliya Daniyarova
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan
| | - Shynar Mazkirat
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan
| | - Alyona Zinchenko
- Breeding Station 'Zarechnoe', Kostanay District, Zarechnoe 111108, Kazakhstan
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia
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Li Y, Wang C, Zheng L, Ma W, Li M, Guo Z, Zhao Q, Zhang K, Liu R, Liu Y, Tian Z, Bai Y, Zhong Y, Liao H. Natural variation of GmRj2/Rfg1 determines symbiont differentiation in soybean. Curr Biol 2023; 33:2478-2490.e5. [PMID: 37301200 DOI: 10.1016/j.cub.2023.05.037] [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: 01/28/2023] [Revised: 04/17/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023]
Abstract
Symbiotic nitrogen fixation (SNF) provides much of the N utilized by leguminous plants throughout growth and development. Legumes may simultaneously establish symbiosis with different taxa of microbial symbionts. Yet, the mechanisms used to steer associations toward symbionts that are most propitious across variations in soil types remain mysterious. Here, we demonstrate that GmRj2/Rfg1 is responsible for regulating symbiosis with multiple taxa of soybean symbionts. In our experiments, the GmRj2/Rfg1SC haplotype favored association with Bradyrhizobia, which is mostly distributed in acid soils, whereas the GmRj2/Rfg1HH haplotype and knockout mutants of GmRj2/Rfg1SC associated equally with Bradyrhizobia and Sinorhizobium. Association between GmRj2/Rfg1 and NopP, furthermore, appeared to be involved in symbiont selection. Furthermore, geographic distribution analysis of 1,821 soybean accessions showed that GmRj2/Rfg1SC haplotypes were enriched in acidic soils where Bradyrhizobia were the dominant symbionts, whereas GmRj2/Rfg1HH haplotypes were most prevalent in alkaline soils dominated by Sinorhizobium, and neutral soils harbored no apparent predilections toward either haplotype. Taken together, our results suggest that GmRj2/Rfg1 regulates symbiosis with different symbionts and is a strong determinant of soybean adaptability across soil regions. As a consequence, the manipulation of the GmRj2/Rfg1 genotype or application of suitable symbionts according to the haplotype at the GmRj2/Rfg1 locus might be suitable strategies to explore for increasing soybean yield through the management of SNF.
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Affiliation(s)
- Yanjun Li
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cunhu Wang
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lei Zheng
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenjing Ma
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mingjia Li
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zilong Guo
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qingsong Zhao
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kefei Zhang
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ran Liu
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongjia Zhong
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Hong Liao
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Wang C, Hao X, Liu X, Su Y, Pan Y, Zong C, Wang W, Xing G, He J, Gai J. An Improved Genome-Wide Association Procedure Explores Gene-Allele Constitutions and Evolutionary Drives of Growth Period Traits in the Global Soybean Germplasm Population. Int J Mol Sci 2023; 24:ijms24119570. [PMID: 37298521 DOI: 10.3390/ijms24119570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
In soybeans (Glycine max (L.) Merr.), their growth periods, DSF (days of sowing-to-flowering), and DFM (days of flowering-to-maturity) are determined by their required accumulative day-length (ADL) and active temperature (AAT). A sample of 354 soybean varieties from five world eco-regions was tested in four seasons in Nanjing, China. The ADL and AAT of DSF and DFM were calculated from daily day-lengths and temperatures provided by the Nanjing Meteorological Bureau. The improved restricted two-stage multi-locus genome-wide association study using gene-allele sequences as markers (coded GASM-RTM-GWAS) was performed. (i) For DSF and its related ADLDSF and AATDSF, 130-141 genes with 384-406 alleles were explored, and for DFM and its related ADLDFM and AATDFM, 124-135 genes with 362-384 alleles were explored, in a total of six gene-allele systems. DSF shared more ADL and AAT contributions than DFM. (ii) Comparisons between the eco-region gene-allele submatrices indicated that the genetic adaptation from the origin to the geographic sub-regions was characterized by allele emergence (mutation), while genetic expansion from primary maturity group (MG)-sets to early/late MG-sets featured allele exclusion (selection) without allele emergence in addition to inheritance (migration). (iii) Optimal crosses with transgressive segregations in both directions were predicted and recommended for breeding purposes, indicating that allele recombination in soybean is an important evolutionary drive. (iv) Genes of the six traits were mostly trait-specific involved in four categories of 10 groups of biological functions. GASM-RTM-GWAS showed potential in detecting directly causal genes with their alleles, identifying differential trait evolutionary drives, predicting recombination breeding potentials, and revealing population gene networks.
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Affiliation(s)
- Can Wang
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoshuai Hao
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Xueqin Liu
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanzhu Su
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongpeng Pan
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunmei Zong
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Wubin Wang
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Guangnan Xing
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianbo He
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Junyi Gai
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
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Wang P, Li Y, Liu Z, Li X, Wang Y, Liu W, Li X, Hu J, Zhu W, Wang C, Li S, Gu T, Xu D, Tang C, Wang Y, Li C, Zhang S, Wu J. Reciprocal regulation of flower induction by ELF3α and ELF3β generated via alternative promoter usage. THE PLANT CELL 2023; 35:2095-2113. [PMID: 36883592 PMCID: PMC10226570 DOI: 10.1093/plcell/koad067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/21/2023] [Accepted: 02/21/2023] [Indexed: 05/30/2023]
Abstract
Flowering is critical for sexual reproduction and fruit production. Several pear (Pyrus sp.) varieties produce few flower buds, but the underlying mechanisms are unknown. The circadian clock regulator EARLY FLOWERING3 (ELF3) serves as a scaffold protein in the evening complex that controls flowering. Here, we report that the absence of a 58-bp sequence in the 2nd intron of PbELF3 is genetically associated with the production of fewer flower buds in pear. From rapid amplification of cDNA ends sequencing results, we identified a short, previously unknown transcript from the PbELF3 locus, which we termed PbELF3β, whose transcript level was significantly lower in pear cultivars that lacked the 58-bp region. The heterologous expression of PbELF3β in Arabidopsis (Arabidopsis thaliana) accelerated flowering, whereas the heterologous expression of the full-length transcript PbELF3α caused late flowering. Notably, ELF3β was functionally conserved in other plants. Deletion of the 2nd intron reduced AtELF3β expression and caused delayed flowering time in Arabidopsis. AtELF3β physically interacted with AtELF3α, disrupting the formation of the evening complex and consequently releasing its repression of flower induction genes such as GIGANTEA (GI). AtELF3β had no effect in the absence of AtELF3α, supporting the idea that AtELF3β promotes flower induction by blocking AtELF3α function. Our findings show that alternative promoter usage at the ELF3 locus allows plants to fine-tune flower induction.
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Affiliation(s)
- Peng Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhe Liu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Department of Pharmacy, Changzhi Medical College, Changzhi 046000, China
| | - Xuhan Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Yicheng Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Weijuan Liu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao Li
- Shijiazhuang Institute of Fruit Trees, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050061, China
| | - Jianjian Hu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenyi Zhu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Changquan Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shan Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Tingting Gu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Dongqing Xu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Tang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Yingtao Wang
- Shijiazhuang Institute of Fruit Trees, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050061, China
| | - Chao Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Juyou Wu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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Vollmann J, Škrabišová M. Going north: adaptation of soybean to long-day environments. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2933-2936. [PMID: 37208832 DOI: 10.1093/jxb/erad105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 05/21/2023]
Abstract
This article comments on:
Zhu X, Leiser WL, Hahn V, Würschum T. 2023. The genetic architecture of soybean photothermal adaptation to high latitudes. Journal of Experimental Botany 74,2987–3002
In plant breeding, understanding genetic variation in the photoperiodic control of flowering time of crop plants such as soybean is a prerequisite for managing adaptation to new environments. Zhu et al. (2023) analyzed a large diversity panel of >1500 early maturity soybean lines to disclose the genetic architecture behind the timing of flowering and maturity. Their findings confirm known maturity loci and reveal new candidate genes and alleles as well as environmental interactions of individual quantitative trait loci (QTLs) for flowering and maturity time. The results shed light on the complexity of the regulatory network which controls the timing of flowering in soybean. This supports the fine-tuning of plant architectures through the combination of stem termination and flowering genes towards a better adaptation of soybean to high latitudes or other stressful environments.
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Affiliation(s)
- Johann Vollmann
- Department of Crop Sciences, University of Natural Resources and Life Sciences Vienna, 3430 Tulln an der Donau, Austria
| | - Mária Škrabišová
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, 78371 Olomouc, Czech Republic
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Zhu X, Leiser WL, Hahn V, Würschum T. The genetic architecture of soybean photothermal adaptation to high latitudes. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2987-3002. [PMID: 36808470 DOI: 10.1093/jxb/erad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/16/2023] [Indexed: 05/21/2023]
Abstract
Soybean is a major plant protein source for both human food and animal feed, but to meet global demands as well as a trend towards regional production, soybean cultivation needs to be expanded to higher latitudes. In this study, we developed a large diversity panel consisting of 1503 early-maturing soybean lines and used genome-wide association mapping to dissect the genetic architecture underlying two crucial adaptation traits, flowering time and maturity. This revealed several known maturity loci, E1, E2, E3, and E4, and the growth habit locus Dt2 as causal candidate loci, and also a novel putative causal locus, GmFRL1, encoding a homolog of the vernalization pathway gene FRIGIDA-like 1. In addition, the scan for quantitative trait locus (QTL)-by-environment interactions identified GmAPETALA1d as a candidate gene for a QTL with environment-dependent reversed allelic effects. The polymorphisms of these candidate genes were identified using whole-genome resequencing data of 338 soybeans, which also revealed a novel E4 variant, e4-par, carried by 11 lines, with nine of them originating from Central Europe. Collectively, our results illustrate how combinations of QTL and their interactions with the environment facilitate the photothermal adaptation of soybean to regions far beyond its center of origin.
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Affiliation(s)
- Xintian Zhu
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, D-70599 Stuttgart, Germany
- State Plant Breeding Institute, University of Hohenheim, D-70599 Stuttgart, Germany
| | - Willmar L Leiser
- State Plant Breeding Institute, University of Hohenheim, D-70599 Stuttgart, Germany
| | - Volker Hahn
- State Plant Breeding Institute, University of Hohenheim, D-70599 Stuttgart, Germany
| | - Tobias Würschum
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, D-70599 Stuttgart, Germany
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Yuan B, Qi G, Yuan C, Wang Y, Zhao H, Li Y, Wang Y, Dong L, Dong Y, Liu X. Major genetic locus with pleiotropism determined seed-related traits in cultivated and wild soybeans. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:125. [PMID: 37165285 DOI: 10.1007/s00122-023-04358-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/04/2023] [Indexed: 05/12/2023]
Abstract
KEY MESSAGE Here, a novel pleiotropic QTL qSS14 simultaneously regulating four seed size traits and two consistently detected QTLs qSW17 and qSLW02 were identified across multiple years. Seed-related traits were the key agronomic traits that have been artificially selected during the domestication of wild soybean. Identifying the genetic loci and genes that regulate seed size could clarify the genetic variations in seed-related traits and provide novel insights into high-yield soybean breeding. In this study, we used a high-density genetic map constructed by F10 RIL populations from a cross between Glycine max and Glycine soja to detect additive QTLs for seven seed-related traits over the last three years. As a result, we identified one novel pleiotropic QTL, qSS14, that simultaneously controlled four seed size traits (100-seed weight, seed length, seed width, and seed thickness) and two consistently detected QTLs, qSW17, and qSLW02, in multiple years of phenotypic data. Furthermore, we predicted two, two and three candidate genes within these three critical loci based on the parental resequencing data and gene function annotations. And the relative expression of four candidate genes GLYMA_14G155100, GLYMA_17G061000, GLYMA_02G273100, and GLYMA_02G273300 showed significant differences among parents and the extreme materials through qRT-PCR analysis. These findings could facilitate the determination of beneficial genes in wild soybean and contribute to our understanding of the soybean domestication process.
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Affiliation(s)
- Baoqi Yuan
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, China
| | - Guangxun Qi
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Cuiping Yuan
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Yumin Wang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Hongkun Zhao
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Yuqiu Li
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Yingnan Wang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Lingchao Dong
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China
| | - Yingshan Dong
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, Jilin, China.
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, China.
| | - Xiaodong Liu
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, China.
- Crop Germplasm Institute, Jilin Academy of Agricultural Sciences, Changchun, Jilin, China.
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Xu H, Wang X, Wei J, Zuo Y, Wang L. The Regulatory Networks of the Circadian Clock Involved in Plant Adaptation and Crop Yield. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091897. [PMID: 37176955 PMCID: PMC10181312 DOI: 10.3390/plants12091897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
Global climatic change increasingly threatens plant adaptation and crop yields. By synchronizing internal biological processes, including photosynthesis, metabolism, and responses to biotic and abiotic stress, with external environmental cures, such as light and temperature, the circadian clock benefits plant adaptation and crop yield. In this review, we focus on the multiple levels of interaction between the plant circadian clock and environmental factors, and we summarize recent progresses on how the circadian clock affects yield. In addition, we propose potential strategies for better utilizing the current knowledge of circadian biology in crop production in the future.
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Affiliation(s)
- Hang Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiling Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Wei
- College of Life Sciences, Changchun Normal University, Changchun 130032, China
| | - Yi Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Li D, Zhang Z, Gao X, Zhang H, Bai D, Wang Q, Zheng T, Li YH, Qiu LJ. The elite variations in germplasms for soybean breeding. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:37. [PMID: 37312749 PMCID: PMC10248635 DOI: 10.1007/s11032-023-01378-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/03/2023] [Indexed: 06/15/2023]
Abstract
The genetic base of soybean cultivars (Glycine max (L.) Merr.) has been narrowed through selective domestication and specific breeding improvement, similar to other crops. This presents challenges in breeding new cultivars with improved yield and quality, reduced adaptability to climate change, and increased susceptibility to diseases. On the other hand, the vast collection of soybean germplasms offers a potential source of genetic variations to address those challenges, but it has yet to be fully leveraged. In recent decades, rapidly improved high-throughput genotyping technologies have accelerated the harness of elite variations in soybean germplasm and provided the important information for solving the problem of a narrowed genetic base in breeding. In this review, we will overview the situation of maintenance and utilization of soybean germplasms, various solutions provided for different needs in terms of the number of molecular markers, and the omics-based high-throughput strategies that have been used or can be used to identify elite alleles. We will also provide an overall genetic information generated from soybean germplasms in yield, quality traits, and pest resistance for molecular breeding.
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Affiliation(s)
- Delin Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Zhengwei Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xinyue Gao
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hao Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Dong Bai
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Qi Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Tianqing Zheng
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Ying-Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Alvarez MA, Li C, Lin H, Joe A, Padilla M, Woods DP, Dubcovsky J. EARLY FLOWERING 3 interactions with PHYTOCHROME B and PHOTOPERIOD1 are critical for the photoperiodic regulation of wheat heading time. PLoS Genet 2023; 19:e1010655. [PMID: 37163495 PMCID: PMC10171656 DOI: 10.1371/journal.pgen.1010655] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/04/2023] [Indexed: 05/12/2023] Open
Abstract
The photoperiodic response is critical for plants to adjust their reproductive phase to the most favorable season. Wheat heads earlier under long days (LD) than under short days (SD) and this difference is mainly regulated by the PHOTOPERIOD1 (PPD1) gene. Tetraploid wheat plants carrying the Ppd-A1a allele with a large deletion in the promoter head earlier under SD than plants carrying the wildtype Ppd-A1b allele with an intact promoter. Phytochromes PHYB and PHYC are necessary for the light activation of PPD1, and mutations in either of these genes result in the downregulation of PPD1 and very late heading time. We show here that both effects are reverted when the phyB mutant is combined with loss-of-function mutations in EARLY FLOWERING 3 (ELF3), a component of the Evening Complex (EC) in the circadian clock. We also show that the wheat ELF3 protein interacts with PHYB and PHYC, is rapidly modified by light, and binds to the PPD1 promoter in planta (likely as part of the EC). Deletion of the ELF3 binding region in the Ppd-A1a promoter results in PPD1 upregulation at dawn, similar to PPD1 alleles with intact promoters in the elf3 mutant background. The upregulation of PPD1 is correlated with the upregulation of the florigen gene FLOWERING LOCUS T1 (FT1) and early heading time. Loss-of-function mutations in PPD1 result in the downregulation of FT1 and delayed heading, even when combined with the elf3 mutation. Taken together, these results indicate that ELF3 operates downstream of PHYB as a direct transcriptional repressor of PPD1, and that this repression is relaxed both by light and by the deletion of the ELF3 binding region in the Ppd-A1a promoter. In summary, the regulation of the light mediated activation of PPD1 by ELF3 is critical for the photoperiodic regulation of wheat heading time.
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Affiliation(s)
- Maria Alejandra Alvarez
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Chengxia Li
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Huiqiong Lin
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Anna Joe
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Mariana Padilla
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Daniel P Woods
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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Li H, Du H, He M, Wang J, Wang F, Yuan W, Huang Z, Cheng Q, Gou C, Chen Z, Liu B, Kong F, Fang C, Zhao X, Yu D. Natural variation of FKF1 controls flowering and adaptation during soybean domestication and improvement. THE NEW PHYTOLOGIST 2023; 238:1671-1684. [PMID: 36811193 DOI: 10.1111/nph.18826] [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: 11/07/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Soybean (Glycine max) is a major source of protein and edible oil world-wide and is cultivated in a wide range of latitudes. However, it is extremely sensitive to photoperiod, which influences flowering time, maturity, and yield, and severely limits soybean latitude adaptation. In this study, a genome-wide association study (GWAS) identified a novel locus in accessions harboring the E1 allele, called Time of flowering 8 (Tof8), which promotes flowering and enhances adaptation to high latitude in cultivated soybean. Gene functional analyses showed that Tof8 is an ortholog of Arabidopsis FKF1. We identified two FKF1 homologs in the soybean genome. Both FKF1 homologs are genetically dependent on E1 by binding to E1 promoter to activate E1 transcription, thus repressing FLOWERING LOCUS T 2a (FT2a) and FT5a transcription, which modulate flowering and maturity through the E1 pathway. We also demonstrate that the natural allele FKF1bH3 facilitated adaptation of soybean to high-latitude environments and was selected during domestication and improvement, leading to its rapid expansion in cultivated soybean. These findings provide novel insights into the roles of FKF1 in controlling flowering time and maturity in soybean and offer new means to fine-tune adaptation to high latitudes and increase grain yield.
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Affiliation(s)
- Haiyang Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Haiping Du
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Milan He
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Jianhao Wang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Fan Wang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Wenjie Yuan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zerong Huang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Qun Cheng
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Chuanjie Gou
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Zheng Chen
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Xiaohui Zhao
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Deyue Yu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
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Hou Z, Fang C, Liu B, Yang H, Kong F. Origin, variation, and selection of natural alleles controlling flowering and adaptation in wild and cultivated soybean. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:36. [PMID: 37309391 PMCID: PMC10248697 DOI: 10.1007/s11032-023-01382-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/12/2023] [Indexed: 06/14/2023]
Abstract
Soybean (Glycine max) is an economically important crop worldwide, serving as a major source of oil and protein for human consumption and animal feed. Cultivated soybean was domesticated from wild soybean (Glycine soja) which both species are highly sensitive to photoperiod and can grow over a wide geographical range. The extensive ecological adaptation of wild and cultivated soybean has been facilitated by a series of genes represented as quantitative trait loci (QTLs) that control photoperiodic flowering and maturation. Here, we review the molecular and genetic basis underlying the regulation of photoperiodic flowering in soybean. Soybean has experienced both natural and artificial selection during adaptation to different latitudes, resulting in differential molecular and evolutionary mechanisms between wild and cultivated soybean. The in-depth study of natural and artificial selection for the photoperiodic adaptability of wild and cultivated soybean provides an important theoretical and practical basis for enhancing soybean adaptability and yield via molecular breeding. In addition, we discuss the possible origin of wild soybean, current challenges, and future research directions in this important topic.
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Affiliation(s)
- Zhihong Hou
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Hui Yang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
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Zhu Z, Esche F, Babben S, Trenner J, Serfling A, Pillen K, Maurer A, Quint M. An exotic allele of barley EARLY FLOWERING 3 contributes to developmental plasticity at elevated temperatures. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2912-2931. [PMID: 36449391 DOI: 10.1093/jxb/erac470] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/28/2022] [Indexed: 06/06/2023]
Abstract
Increase in ambient temperatures caused by climate change affects various morphological and developmental traits of plants, threatening crop yield stability. In the model plant Arabidopsis thaliana, EARLY FLOWERING 3 (ELF3) plays prominent roles in temperature sensing and thermomorphogenesis signal transduction. However, how crop species respond to elevated temperatures is poorly understood. Here, we show that the barley ortholog of AtELF3 interacts with high temperature to control growth and development. We used heterogeneous inbred family (HIF) pairs generated from a segregating mapping population and systematically studied the role of exotic ELF3 variants in barley temperature responses. An exotic ELF3 allele of Syrian origin promoted elongation growth in barley at elevated temperatures, whereas plant area and estimated biomass were drastically reduced, resulting in an open canopy architecture. The same allele accelerated inflorescence development at high temperature, which correlated with early transcriptional induction of MADS-box floral identity genes BM3 and BM8. Consequently, barley plants carrying the exotic ELF3 allele displayed stable total grain number at elevated temperatures. Our findings therefore demonstrate that exotic ELF3 variants can contribute to phenotypic and developmental acclimation to elevated temperatures, providing a stimulus for breeding of climate-resilient crops.
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Affiliation(s)
- Zihao Zhu
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Finn Esche
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Steve Babben
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Jana Trenner
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin-Baur-Str. 27, D-06484, Quedlinburg, Germany
| | - Klaus Pillen
- Chair of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
| | - Andreas Maurer
- Chair of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research, Halle-Jena-Leipzig, Puschstrasse 4, D-04103, Leipzig, Germany
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