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Huang X, Liu H, Wu F, Wei W, Zeng Z, Xu J, Chen C, Hao Y, Xia R, Liu Y. Diversification of FT-like genes in the PEBP family contributes to the variation of flowering traits in Sapindaceae species. MOLECULAR HORTICULTURE 2024; 4:28. [PMID: 39010247 PMCID: PMC11251392 DOI: 10.1186/s43897-024-00104-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/14/2024] [Indexed: 07/17/2024]
Abstract
Many species of Sapindaceae, such as lychee, longan, and rambutan, provide nutritious and delicious fruit. Understanding the molecular genetic mechanisms that underlie the regulation of flowering is essential for securing flower and fruit productivity. Most endogenous and exogenous flowering cues are integrated into the florigen encoded by FLOWERING LOCUS T. However, the regulatory mechanisms of flowering remain poorly understood in Sapindaceae. Here, we identified 60 phosphatidylethanolamine-binding protein-coding genes from six Sapindaceae plants. Gene duplication events led to the emergence of two or more paralogs of the FT gene that have evolved antagonistic functions in Sapindaceae. Among them, the FT1-like genes are functionally conserved and promote flowering, while the FT2-like genes likely serve as repressors that delay flowering. Importantly, we show here that the natural variation at nucleotide position - 1437 of the lychee FT1 promoter determined the binding affinity of the SVP protein (LcSVP9), which was a negative regulator of flowering, resulting in the differential expression of LcFT1, which in turn affected flowering time in lychee. This finding provides a potential molecular marker for breeding lychee. Taken together, our results reveal some crucial aspects of FT gene family genetics that underlie the regulation of flowering in Sapindaceae.
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Affiliation(s)
- Xing Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China
| | - Hongsen Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China
| | - Fengqi Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China
| | - Wanchun Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China
| | - Zaohai Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China
| | - Jing Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China
| | - Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China
| | - Yanwei Hao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China.
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China.
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China.
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China.
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China.
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China.
| | - Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangdong Guangzhou, 510642, China.
- South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangdong Guangzhou, 510642, China.
- South China Agricultural University, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangdong Guangzhou, 510642, China.
- College of Plant Science and Technology, Huazhong Agricultural University, Hubei Wuhan, 430070, China.
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Lee N, Shim JS, Kang MK, Kwon M. Insight from expression profiles of FT orthologs in plants: conserved photoperiodic transcriptional regulatory mechanisms. FRONTIERS IN PLANT SCIENCE 2024; 15:1397714. [PMID: 38887456 PMCID: PMC11180818 DOI: 10.3389/fpls.2024.1397714] [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: 03/08/2024] [Accepted: 05/20/2024] [Indexed: 06/20/2024]
Abstract
Floral transition from the vegetative to the reproductive stages is precisely regulated by both environmental and endogenous signals. Among these signals, photoperiod is one of the most important environmental factors for onset of flowering. A florigen, FLOWERING LOCUS T (FT) in Arabidopsis, has thought to be a major hub in the photoperiod-dependent flowering time regulation. Expression levels of FT likely correlates with potence of flowering. Under long days (LD), FT is mainly synthesized in leaves, and FT protein moves to shoot apical meristem (SAM) where it functions and in turns induces flowering. Recently, it has been reported that Arabidopsis grown under natural LD condition flowers earlier than that grown under laboratory LD condition, in which a red (R)/far-red (FR) ratio of light sources determines FT expression levels. Additionally, FT expression profile changes in response to combinatorial effects of FR light and photoperiod. FT orthologs exist in most of plants and functions are thought to be conserved. Although molecular mechanisms underlying photoperiodic transcriptional regulation of FT orthologs have been studied in several plants, such as rice, however, dynamics in expression profiles of FT orthologs have been less spotlighted. This review aims to revisit previously reported but overlooked expression information of FT orthologs from various plant species and classify these genes depending on the expression profiles. Plants, in general, could be classified into three groups depending on their photoperiodic flowering responses. Thus, we discuss relationship between photoperiodic responsiveness and expression of FT orthologs. Additionally, we also highlight the expression profiles of FT orthologs depending on their activities in flowering. Comparative analyses of diverse plant species will help to gain insight into molecular mechanisms for flowering in nature, and this can be utilized in the future for crop engineering to improve yield by controlling flowering time.
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Affiliation(s)
- Nayoung Lee
- Research Institute of Molecular Alchemy (RIMA), Gyeongsang National University, Jinju, Republic of Korea
| | - Jae Sung Shim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea
| | - Min-Kyoung Kang
- Division of Applied Life Science (BK21 Four), Anti-aging Bio Cell factory Regional Leading Research Center (ABC-RLRC), Gyeongsang National University, Jinju, Republic of Korea
| | - Moonhyuk Kwon
- Division of Applied Life Science (BK21 Four), ABC-RLRC, RIMA, Gyeongsang National University, Jinju, Republic of Korea
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Wang F, Han T, Jeffrey Chen Z. Circadian and photoperiodic regulation of the vegetative to reproductive transition in plants. Commun Biol 2024; 7:579. [PMID: 38755402 PMCID: PMC11098820 DOI: 10.1038/s42003-024-06275-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 05/01/2024] [Indexed: 05/18/2024] Open
Abstract
As sessile organisms, plants must respond constantly to ever-changing environments to complete their life cycle; this includes the transition from vegetative growth to reproductive development. This process is mediated by photoperiodic response to sensing the length of night or day through circadian regulation of light-signaling molecules, such as phytochromes, to measure the length of night to initiate flowering. Flowering time is the most important trait to optimize crop performance in adaptive regions. In this review, we focus on interplays between circadian and light signaling pathways that allow plants to optimize timing for flowering and seed production in Arabidopsis, rice, soybean, and cotton. Many crops are polyploids and domesticated under natural selection and breeding. In response to adaptation and polyploidization, circadian and flowering pathway genes are epigenetically reprogrammed. Understanding the genetic and epigenetic bases for photoperiodic flowering will help improve crop yield and resilience in response to climate change.
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Affiliation(s)
- Fang Wang
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Tongwen Han
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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Lu HC, Huang CW, Mimura T, Sukma D, Chan MT. Temperature-Regulated Flowering Locus T-Like Gene Coordinates the Spike Initiation in Phalaenopsis Orchid. PLANT & CELL PHYSIOLOGY 2024; 65:405-419. [PMID: 38153763 DOI: 10.1093/pcp/pcad166] [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: 10/18/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
Phalaenopsis aphrodite can be induced to initiate spike growth and flowering by exposure to low ambient temperatures. However, the factors and mechanisms responsible for spike initiation in P. aphrodite remain largely unknown. In this study, we show that a repressor Flowing Locus T-like (FTL) gene, FTL, can act as a negative regulator of spike initiation in P. aphrodite. The mRNA transcripts of PaFTL are consistently high during high ambient temperature, thereby preventing premature spike initiation. However, during low ambient temperature, PaFTL expression falls while FT expression increases, allowing for spike initiation. Knock-down of PaFTL expression through virus-inducing gene silencing promoted spike initiation at 30/28°C. Moreover, PaFTL interacts with FLOWERING LOCUS D in a similar manner to FT to regulate downstream flowering initiation genes. Transgenic P. aphrodite plants exhibiting high expression of PaFTL do not undergo spike initiation, even when exposed to low ambient temperatures. These findings shed light on the flowering mechanisms in Phalaenopsis and provide new insights into how perennial plants govern spike initiation in response to temperature cues.
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Affiliation(s)
- Hsiang-Chia Lu
- Academia Sinica Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, No. 100, Sec. 1, Guiren 13th Rd., Guiren Dist., Tainan 741, Taiwan
| | - Chiao-Wen Huang
- Academia Sinica Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, No. 100, Sec. 1, Guiren 13th Rd., Guiren Dist., Tainan 741, Taiwan
| | - Tetsuro Mimura
- Graduate Program of Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, No. 1, Daxue Rd., East Dist., Taiwan 70101, Taiwan
| | - Dewi Sukma
- Department of Agronomy & Horticulture, Faculty of Agriculture, IPB University, Jl. Meranti, Dramaga Campus, Bogor, West Java 16680, Indonesia
| | - Ming-Tsair Chan
- Academia Sinica Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, No. 100, Sec. 1, Guiren 13th Rd., Guiren Dist., Tainan 741, Taiwan
- Graduate Program of Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, No. 1, Daxue Rd., East Dist., Taiwan 70101, Taiwan
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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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Nie M, Li L, He C, Lu J, Guo H, Li X, Jiang M, Zhan R, Sun W, Yin J, Wu Q. Genome-wide identification, subcellular localization, and expression analysis of the phosphatidyl ethanolamine-binding protein family reveals the candidates involved in flowering and yield regulation of Tartary buckwheat ( Fagopyrum tataricum). PeerJ 2024; 12:e17183. [PMID: 38560476 PMCID: PMC10979741 DOI: 10.7717/peerj.17183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Background PEBP (phosphatidyl ethanolamine-binding protein) is widely found in eukaryotes including plants, animals and microorganisms. In plants, the PEBP family plays vital roles in regulating flowering time and morphogenesis and is highly associated to agronomic traits and yields of crops, which has been identified and characterized in many plant species but not well studied in Tartary buckwheat (Fagopyrum tataricum Gaertn.), an important coarse food grain with medicinal value. Methods Genome-wide analysis of FtPEBP gene family members in Tartary buckwheat was performed using bioinformatic tools. Subcellular localization analysis was performed by confocal microscopy. The expression levels of these genes in leaf and inflorescence samples were analyzed using qRT-PCR. Results Fourteen Fagopyrum tataricum PEBP (FtPEBP) genes were identified and divided into three sub-clades according to their phylogenetic relationships. Subcellular localization analysis of the FtPEBP proteins in tobacco leaves indicated that FT- and TFL-GFP fusion proteins were localized in both the nucleus and cytoplasm. Gene structure analysis showed that most FtPEBP genes contain four exons and three introns. FtPEBP genes are unevenly distributed in Tartary buckwheat chromosomes. Three tandem repeats were found among FtFT5/FtFT6, FtMFT1/FtMFT2 and FtTFL4/FtTFL5. Five orthologous gene pairs were detected between F. tataricum and F. esculentum. Seven light-responsive, nine hormone-related and four stress-responsive elements were detected in FtPEBPs promoters. We used real-time PCR to investigate the expression levels of FtPEBPs among two flowering-type cultivars at floral transition time. We found FtFT1/FtFT3 were highly expressed in leaf and young inflorescence of early-flowering type, whereas they were expressed at very low levels in late-flowering type cultivars. Thus, we deduced that FtFT1/FtFT3 may be positive regulators for flowering and yield of Tartary buckwheat. These results lay an important foundation for further studies on the functions of FtPEBP genes which may be utilized for yield improvement.
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Affiliation(s)
- Mengping Nie
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Li Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Cailin He
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Jing Lu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Huihui Guo
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Xiao'an Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Mi Jiang
- Key Laboratory of Wheat Crop Research in Ganzi Academy of Agricultural Sciences, Ganzi Academy of Agricultural Sciences, Ganzi, Sichuan, China
| | - Ruiling Zhan
- Key Laboratory of Wheat Crop Research in Ganzi Academy of Agricultural Sciences, Ganzi Academy of Agricultural Sciences, Ganzi, Sichuan, China
| | - Wenjun Sun
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Junjie Yin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qi Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
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Escamilla DM, Dietz N, Bilyeu K, Hudson K, Rainey KM. Genome-wide association study reveals GmFulb as candidate gene for maturity time and reproductive length in soybeans (Glycine max). PLoS One 2024; 19:e0294123. [PMID: 38241340 PMCID: PMC10798547 DOI: 10.1371/journal.pone.0294123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/25/2023] [Indexed: 01/21/2024] Open
Abstract
The ability of soybean [Glycine max (L.) Merr.] to adapt to different latitudes is attributed to genetic variation in major E genes and quantitative trait loci (QTLs) determining flowering time (R1), maturity (R8), and reproductive length (RL). Fully revealing the genetic basis of R1, R8, and RL in soybeans is necessary to enhance genetic gains in soybean yield improvement. Here, we performed a genome-wide association analysis (GWA) with 31,689 single nucleotide polymorphisms (SNPs) to detect novel loci for R1, R8, and RL using a soybean panel of 329 accessions with the same genotype for three major E genes (e1-as/E2/E3). The studied accessions were grown in nine environments and observed for R1, R8 and RL in all environments. This study identified two stable peaks on Chr 4, simultaneously controlling R8 and RL. In addition, we identified a third peak on Chr 10 controlling R1. Association peaks overlap with previously reported QTLs for R1, R8, and RL. Considering the alternative alleles, significant SNPs caused RL to be two days shorter, R1 two days later and R8 two days earlier, respectively. We identified association peaks acting independently over R1 and R8, suggesting that trait-specific minor effect loci are also involved in controlling R1 and R8. From the 111 genes highly associated with the three peaks detected in this study, we selected six candidate genes as the most likely cause of R1, R8, and RL variation. High correspondence was observed between a modifying variant SNP at position 04:39294836 in GmFulb and an association peak on Chr 4. Further studies using map-based cloning and fine mapping are necessary to elucidate the role of the candidates we identified for soybean maturity and adaptation to different latitudes and to be effectively used in the marker-assisted breeding of cultivars with optimal yield-related traits.
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Affiliation(s)
- Diana M. Escamilla
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
| | - Nicholas Dietz
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, United States of America
| | - Kristin Bilyeu
- Plant Genetics Research Unit, United States Department of Agriculture (USDA)−Agricultural Research Service (ARS), Columbia, Missouri, United States of America
| | - Karen Hudson
- USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, Indiana, United States of America
| | - Katy Martin Rainey
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
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Kuznetsova K, Efremova E, Dodueva I, Lebedeva M, Lutova L. Functional Modules in the Meristems: "Tinkering" in Action. PLANTS (BASEL, SWITZERLAND) 2023; 12:3661. [PMID: 37896124 PMCID: PMC10610496 DOI: 10.3390/plants12203661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND A feature of higher plants is the modular principle of body organisation. One of these conservative morphological modules that regulate plant growth, histogenesis and organogenesis is meristems-structures that contain pools of stem cells and are generally organised according to a common principle. Basic content: The development of meristems is under the regulation of molecular modules that contain conservative interacting components and modulate the expression of target genes depending on the developmental context. In this review, we focus on two molecular modules that act in different types of meristems. The WOX-CLAVATA module, which includes the peptide ligand, its receptor and the target transcription factor, is responsible for the formation and control of the activity of all meristem types studied, but it has its own peculiarities in different meristems. Another regulatory module is the so-called florigen-activated complex, which is responsible for the phase transition in the shoot vegetative meristem (e.g., from the vegetative shoot apical meristem to the inflorescence meristem). CONCLUSIONS The review considers the composition and functions of these two functional modules in different developmental programmes, as well as their appearance, evolution and use in plant breeding.
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Affiliation(s)
| | | | - Irina Dodueva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya Emb. 7/9, 199034 Saint Petersburg, Russia; (K.K.); (E.E.); (M.L.); (L.L.)
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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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10
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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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11
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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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12
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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: 1] [Impact Index Per Article: 1.0] [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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13
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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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14
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Du H, Fang C, Li Y, Kong F, Liu B. Understandings and future challenges in soybean functional genomics and molecular breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:468-495. [PMID: 36511121 DOI: 10.1111/jipb.13433] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Soybean (Glycine max) is a major source of plant protein and oil. Soybean breeding has benefited from advances in functional genomics. In particular, the release of soybean reference genomes has advanced our understanding of soybean adaptation to soil nutrient deficiencies, the molecular mechanism of symbiotic nitrogen (N) fixation, biotic and abiotic stress tolerance, and the roles of flowering time in regional adaptation, plant architecture, and seed yield and quality. Nevertheless, many challenges remain for soybean functional genomics and molecular breeding, mainly related to improving grain yield through high-density planting, maize-soybean intercropping, taking advantage of wild resources, utilization of heterosis, genomic prediction and selection breeding, and precise breeding through genome editing. This review summarizes the current progress in soybean functional genomics and directs future challenges for molecular breeding of soybean.
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Affiliation(s)
- 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
| | - 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
| | - Yaru Li
- 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
| | - 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
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15
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Wang F, Li S, Kong F, Lin X, Lu S. Altered regulation of flowering expands growth ranges and maximizes yields in major crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1094411. [PMID: 36743503 PMCID: PMC9892950 DOI: 10.3389/fpls.2023.1094411] [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: 11/10/2022] [Accepted: 01/04/2023] [Indexed: 06/14/2023]
Abstract
Flowering time influences reproductive success in plants and has a significant impact on yield in grain crops. Flowering time is regulated by a variety of environmental factors, with daylength often playing an important role. Crops can be categorized into different types according to their photoperiod requirements for flowering. For instance, long-day crops include wheat (Triticum aestivum), barley (Hordeum vulgare), and pea (Pisum sativum), while short-day crops include rice (Oryza sativa), soybean (Glycine max), and maize (Zea mays). Understanding the molecular regulation of flowering and genotypic variation therein is important for molecular breeding and crop improvement. This paper reviews the regulation of flowering in different crop species with a particular focus on how photoperiod-related genes facilitate adaptation to local environments.
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Affiliation(s)
| | | | | | - Xiaoya Lin
- *Correspondence: Xiaoya Lin, ; Sijia Lu,
| | - Sijia Lu
- *Correspondence: Xiaoya Lin, ; Sijia Lu,
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16
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Wan Z, Liu Y, Guo D, Fan R, Liu Y, Xu K, Zhu J, Quan L, Lu W, Bai X, Zhai H. CRISPR/Cas9-mediated targeted mutation of the E1 decreases photoperiod sensitivity, alters stem growth habits, and decreases branch number in soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:1066820. [PMID: 36589055 PMCID: PMC9794841 DOI: 10.3389/fpls.2022.1066820] [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: 10/11/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
The distribution of elite soybean (Glycine max) cultivars is limited due to their highly sensitive to photoperiod, which affects the flowering time and plant architecture. The recent emergence of CRISPR/Cas9 technology has uncovered new opportunities for genetic manipulation of soybean. The major maturity gene E1 of soybean plays a critical role in soybean photoperiod response. Here, we performed CRISPR/Cas9-mediated targeted mutation of E1 gene in soybean cultivar Tianlong1 carrying the dominant E1 to investigate its precise function in photoperiod regulation, especially in plant architecture regulation. Four types of mutations in the E1 coding region were generated. No off-target effects were observed, and homozygous trans-clean mutants without T-DNA were obtained. The photoperiod sensitivity of e1 mutants decreased relative to the wild type plants; however, e1 mutants still responded to photoperiod. Further analysis revealed that the homologs of E1, E1-La, and E1-Lb, were up-regulated in the e1 mutants, indicating a genetic compensation response of E1 and its homologs. The e1 mutants exhibited significant changes in the architecture, including initiation of terminal flowering, formation of determinate stems, and decreased branch numbers. To identify E1-regulated genes related to plant architecture, transcriptome deep sequencing (RNA-seq) was used to compare the gene expression profiles in the stem tip of the wild-type soybean cultivar and the e1 mutants. The expression of shoot identity gene Dt1 was significantly decreased, while Dt2 was significantly upregulated. Also, a set of MADS-box genes was up-regulated in the stem tip of e1 mutants which might contribute to the determinate stem growth habit.
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Affiliation(s)
- Zhao Wan
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yingxiang Liu
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Dandan Guo
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Rong Fan
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Yang Liu
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Kun Xu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Jinlong Zhu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Le Quan
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Wentian Lu
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Xi Bai
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Hong Zhai
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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17
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Xia Z, Zhai H, Zhang Y, Wang Y, Wang L, Xu K, Wu H, Zhu J, Jiao S, Wan Z, Zhu X, Gao Y, Liu Y, Fan R, Wu S, Chen X, Liu J, Yang J, Song Q, Tian Z. QNE1 is a key flowering regulator determining the length of the vegetative period in soybean cultivars. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2472-2490. [PMID: 35802303 DOI: 10.1007/s11427-022-2117-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
The soybean E1 gene is a major regulator that plays an important role in flowering time and maturity. However, it remains unclear how cultivars carrying the dominant E1 allele adapt to the higher latitudinal areas of northern China. We mapped the novel quantitative trait locus QNE1 (QTL near E1) for flowering time to the region proximal to E1 on chromosome 6 in two mapping populations. Positional cloning revealed Glyma.06G204300, encoding a TCP-type transcription factor, as a strong candidate gene for QNE1. Association analysis further confirmed that functional single nucleotide polymorphisms (SNPs) at nucleotides 686 and 1,063 in the coding region of Glyma.06G204300 were significantly associated with flowering time. The protein encoded by the candidate gene is localized primarily to the nucleus. Furthermore, soybean and Brassica napus plants overexpressing Glyma.06G204300 exhibited early flowering. We conclude that despite their similar effects on flowering time, QNE1 and E4 may control flowering time through different regulatory mechanisms, based on expression studies and weighted gene co-expression network analysis of flowering time-related genes. Deciphering the molecular basis of QNE1 control of flowering time enriches our knowledge of flowering gene networks in soybean and will facilitate breeding soybean cultivars with broader latitudinal adaptation.
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Affiliation(s)
- Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China.
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Yanfeng Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100, China
| | - Yaying Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Lu Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Kun Xu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Hongyan Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Jinglong Zhu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Shuang Jiao
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Zhao Wan
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Xiaobin Zhu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Yi Gao
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Yingxiang Liu
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Rong Fan
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Shihao Wu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jinyu Liu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Jiayin Yang
- Huaiyin Institute of Agricultural Science of Xuhuai Region, Jiangsu Academy of Agricultural Sciences, Huai'an, 223001, China
| | - Qijian Song
- USDA ARS, Soybean Genome & Improvement Lab, Beltsville, 20705, USA
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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18
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Zhong C, Li Z, Cheng Y, Zhang H, Liu Y, Wang X, Jiang C, Zhao X, Zhao S, Wang J, Zhang H, Liu X, Yu H. Comparative Genomic and Expression Analysis Insight into Evolutionary Characteristics of PEBP Genes in Cultivated Peanuts and Their Roles in Floral Induction. Int J Mol Sci 2022; 23:ijms232012429. [PMID: 36293287 PMCID: PMC9604132 DOI: 10.3390/ijms232012429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/20/2022] Open
Abstract
Phosphatidyl ethanolamine-binding proteins (PEBPs) are involved in regulating flowering time and various developmental processes. Functions and expression patterns in cultivated peanuts (Arachis hypogaea L.) remain unknown. In this study, 33 PEBP genes in cultivated peanuts were identified and divided into four subgroups: FT, TFL, MFT and FT-like. Gene structure analysis showed that orthologs from A and B genomes in cultivated peanuts had highly similar structures, but some orthologous genes have subgenomic dominance. Gene collinearity and phylogenetic analysis explain that some PEBP genes play key roles in evolution. Cis-element analysis revealed that PEBP genes are mainly regulated by hormones, light signals and stress-related pathways. Multiple PEPB genes had different expression patterns between early and late-flowering genotypes. Further detection of its response to temperature and photoperiod revealed that PEBPs ArahyM2THPA, ArahyEM6VH3, Arahy4GAQ4U, ArahyIZ8FG5, ArahyG6F3P2, ArahyLUT2QN, ArahyDYRS20 and ArahyBBG51B were the key genes controlling the flowering response to different flowering time genotypes, photoperiods and temperature. This study laid the foundation for the functional study of the PEBP gene in cultivated peanuts and the adaptation of peanuts to different environments.
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19
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Duan Z, Zhang M, Zhang Z, Liang S, Fan L, Yang X, Yuan Y, Pan Y, Zhou G, Liu S, Tian Z. Natural allelic variation of GmST05 controlling seed size and quality in soybean. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1807-1818. [PMID: 35642379 PMCID: PMC9398382 DOI: 10.1111/pbi.13865] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 05/26/2023]
Abstract
Seed size is one of the most important agronomic traits determining the yield of crops. Cloning the key genes controlling seed size and pyramiding their elite alleles will facilitate yield improvement. To date, few genes controlling seed size have been identified in soybean, a major crop that provides half of the plant oil and one quarter of the plant protein globally. Here, through a genome-wide association study of over 1800 soybean accessions, we determined that natural allelic variation at GmST05 (Seed Thickness 05) predominantly controlled seed thickness and size in soybean germplasm. Further analyses suggested that the two major haplotypes of GmST05 differed significantly at the transcriptional level. Transgenic experiments demonstrated that GmST05 positively regulated seed size and influenced oil and protein contents, possibly by regulating the transcription of GmSWEET10a. Population genetic diversity analysis suggested that allelic variations of GmST05 were selected during geographical differentiation but have not been fixed. In summary, natural variation in GmST05 determines transcription levels and influences seed size and quality in soybean, making it an important gene resource for soybean molecular breeding.
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Affiliation(s)
- Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Zhifang Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Shan Liang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lei Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Xia Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaqin Yuan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yi Pan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Guoan Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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20
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Yuan S, Wang Y, Wang J, Zhang C, Zhang L, Jiang B, Wu T, Chen L, Xu X, Cai Y, Sun S, Chen F, Song W, Wu C, Hou W, Yu L, Han T. GmFT3a fine-tunes flowering time and improves adaptation of soybean to higher latitudes. FRONTIERS IN PLANT SCIENCE 2022; 13:929747. [PMID: 35958200 PMCID: PMC9358591 DOI: 10.3389/fpls.2022.929747] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/04/2022] [Indexed: 05/30/2023]
Abstract
Onset of flowering of plants is precisely controlled by extensive environmental factors and internal molecular networks, in which FLOWERING LOCUS T (FT) is a key flowering integrator. In soybean, a typical short-day plant, 11 FT homologues are found in its genome, of which several homologues are functionally diversified in flowering pathways and the others including GmFT3a are yet unknown. In the current study, we characterized GmFT3a, which is located on the same chromosome as the flowering promoters GmFT2a and GmFT5a. Overexpression of GmFT3a significantly promoted flowering of Arabidopsis under the inductive long-day (LD) photoperiod. GmFT3a over-expressed soybean also flowered earlier than the control under LD, but they were not significantly different under inductive short-day (SD) conditions, indicating that GmFT3a acts as a flowering promoter in the non-inductive photoperiod in soybean. Compared with other GmFT homologues, GmFT3a exhibited a slighter effect in flowering promotion than GmFT2a, GmFT5a and GmFT2b under LD conditions. GmFT3a promoted flowering by regulating the expression of downstream flowering-related genes and also affected the expression of other GmFTs. According to the re-sequencing data, the regional distributions of two major haplotypes in 176 soybean varieties were analyzed. The varieties with GmFT3a-Hap2 haplotype matured relatively early, and relative higher expression of GmFT3a was detected in early maturing varieties, implying that Hap2 variation may contribute to the adaptation of soybean to higher latitude regions by increasing expression level of genes in metabolism and signaling pathways. The early flowering germplasm generated by overexpression of GmFT3a has potential to be planted at higher latitudes where non-inductive long day is dominant in the growing season, and GmFT3a can be used to fine-tune soybean flowering and maturity time and improve the geographical adaptation.
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Affiliation(s)
- Shan Yuan
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yining Wang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Junya Wang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Chunlei Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Lixin Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bingjun Jiang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tingting Wu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Chen
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Xu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yupeng Cai
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shi Sun
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fulu Chen
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenwen Song
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cunxiang Wu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wensheng Hou
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijie Yu
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Tianfu Han
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Science and Technology, Harbin Normal University, Harbin, China
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21
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Dong W, Li D, Zhang L, Yin B, Zhang Y. Transcriptome Analysis of Short-Day Photoperiod Inducement in Adzuki Bean ( Vigna angularis L.) Based on RNA-Seq. FRONTIERS IN PLANT SCIENCE 2022; 13:893245. [PMID: 35845693 PMCID: PMC9280645 DOI: 10.3389/fpls.2022.893245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
The flowering characteristics of adzuki bean are influenced by several environmental factors. Light is an important ecological factor that induces flowering in adzuki bean, but to date, there have been few reports on the transcriptomic features of photoperiodic regulation of adzuki bean flowering. This study is based on RNA sequencing (RNA-seq) techniques to elucidate the expression of light-related regulatory genes under short-day photoperiod inducement of adzuki bean flowering, providing an important theoretical basis for its accelerated breeding. Short-day photoperiod inducement of 10 h was conducted for 5 day, 10 day, and 15 day periods on "Tang shan hong xiao dou" varieties, which are more sensitive to short-day photoperiod conditions than the other varieties. Plants grown under natural light (14.5 h) for 5 days, 10 days, and 15 days were used as controls to compare the progress of flower bud differentiation and flowering characteristics. The topmost unfolded functional leaves were selected for transcriptome sequencing and bioinformatics analysis. The short-day photoperiod inducement promoted flower bud differentiation and advanced flowering time in adzuki bean. Transcriptomic analysis revealed 5,608 differentially expressed genes (DEGs) for the combination of CK-5d vs. SD-5d, CK-10d vs. SD-10d, and CK-15d vs. SD-15d. The three groups of the DEGs were analyzed using the Gene Ontology (GO) and the Kyoto Encyclopedia of Genomes and Genomes (KEGG) databases; the DEGs were associated with flowering, photosystem, and the circadian rhythm and were mainly concentrated in the hormone signaling and metabolism, circadian rhythm, and antenna protein pathways; So, 13 light-related genes across the three pathways were screened for differential and expression characteristics. Through the functional annotations of orthologs, these genes were related to flowering, which were supposed to be good candidate genes in adzuki bean. The findings provide a deep understanding of the molecular mechanisms of adzuki bean flowering in response to short-day photoperiod inducement, which laid a foundation for the functional verification of genes in the next step, and provide an important reference for the molecular breeding of adzuki bean.
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Affiliation(s)
- Weixin Dong
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
- Hebei Open University, Shijiazhuang, China
| | - Dongxiao Li
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Lei Zhang
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Baozhong Yin
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Yuechen Zhang
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
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22
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Zhai H, Wan Z, Jiao S, Zhou J, Xu K, Nan H, Liu Y, Xiong S, Fan R, Zhu J, Jiang W, Pang T, Luo X, Wu H, Yang G, Bai X, Kong F, Xia Z. GmMDE genes bridge the maturity gene E1 and florigens in photoperiodic regulation of flowering in soybean. PLANT PHYSIOLOGY 2022; 189:1021-1036. [PMID: 35234946 PMCID: PMC9157081 DOI: 10.1093/plphys/kiac092] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/19/2022] [Indexed: 05/30/2023]
Abstract
Soybean (Glycine max) is highly sensitive to photoperiod, which affects flowering time and plant architecture and thus limits the distribution range of elite soybean cultivars. The major maturity gene E1 confers the most prominent effect on photoperiod sensitivity, but its downstream signaling pathway remains largely unknown. Here, we confirm that the encoded E1 protein is a transcriptional repressor. The expression of seven GmMDE genes (Glycine max MADS-box genes downregulated by E1) was suppressed when E1 was overexpressed and promoted when E1 was knocked out through clustered regularly-interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9)-mediated mutagenesis. These GmMDEs exhibited similar tissue specificity and expression patterns, including in response to photoperiod, E1 expression, and E1 genotype. E1 repressed GmMDE promoter activity. Results for two GmMDEs showed that E1 epigenetically silences their expression by directly binding to their promoters to increase H3K27me3 levels. The overexpression of GmMDE06 promoted flowering and post-flowering termination of stem growth. The late flowering phenotype of E1-overexpressing soybean lines was reversed by the overexpression of GmMDE06, placing GmMDE06 downstream of E1. The overexpression of GmMDE06 increased the expression of the soybean FLOWERING LOCUS T orthologs GmFT2a and GmFT5a, leading to feedback upregulation of GmMDE, indicating that GmMDE and GmFT2a/GmFT5a form a positive regulatory feedback loop promoting flowering. GmMDE06 also promoted post-flowering termination of stem growth by repressing the expression of the shoot identity gene Dt1. The E1-GmMDEs-GmFT2a/5a-Dt1 signaling pathway illustrates how soybean responds to photoperiod by modulating flowering time and post-flowering stem termination.
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Affiliation(s)
- Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding (2013DP173244), Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhao Wan
- Key Laboratory of Soybean Molecular Design Breeding (2013DP173244), Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuang Jiao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Jingwen Zhou
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Kun Xu
- Key Laboratory of Soybean Molecular Design Breeding (2013DP173244), Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
| | - Haiyang Nan
- Key Laboratory of Soybean Molecular Design Breeding (2013DP173244), Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
| | - Yingxiang Liu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Shangshang Xiong
- Key Laboratory of Soybean Molecular Design Breeding (2013DP173244), Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Fan
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Jinlong Zhu
- Key Laboratory of Soybean Molecular Design Breeding (2013DP173244), Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
| | - Wenting Jiang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Tian Pang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xiao Luo
- Institute of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Hongyan Wu
- Key Laboratory of Soybean Molecular Design Breeding (2013DP173244), Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
| | - Guang Yang
- Cultivation and Crop Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xi Bai
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding (2013DP173244), Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
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23
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Moraes TS, Immink RGH, Martinelli AP, Angenent GC, van Esse W, Dornelas MC. Passiflora organensis FT/TFL1 gene family and their putative roles in phase transition and floral initiation. PLANT REPRODUCTION 2022; 35:105-126. [PMID: 34748087 DOI: 10.1007/s00497-021-00431-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Comprehensive analysis of the FT/TFL1 gene family in Passiflora organensis results in understanding how these genes might be involved in the regulation of the typical plant architecture presented by Passiflora species. Passion fruit (Passiflora spp) is an economic tropical fruit crop, but there is hardly any knowledge available about the molecular control of phase transition and flower initiation in this species. The florigen agent FLOWERING LOCUS T (FT) interacts with the bZIP protein FLOWERING LOCUS D (FD) to induce flowering in the model species Arabidopsis thaliana. Current models based on research in rice suggest that this interaction is bridged by 14-3-3 proteins. We identified eight FT/TFL1 family members in Passiflora organensis and characterized them by analyzing their phylogeny, gene structure, expression patterns, protein interactions and putative biological roles by heterologous expression in Arabidopsis. PoFT was highest expressed during the adult vegetative phase and it is supposed to have an important role in flowering induction. In contrast, its paralogs PoTSFs were highest expressed in the reproductive phase. While ectopic expression of PoFT in transgenic Arabidopsis plants induced early flowering and inflorescence determinacy, the ectopic expression of PoTSFa caused a delay in flowering. PoTFL1-like genes were highest expressed during the juvenile phase and their ectopic expression caused delayed flowering in Arabidopsis. Our protein-protein interaction studies indicate that the flowering activation complexes in Passiflora might deviate from the hexameric complex found in the model system rice. Our results provide insights into the potential functions of FT/TFL1 gene family members during floral initiation and their implications in the special plant architecture of Passiflora species, contributing to more detailed studies on the regulation of passion fruit reproduction.
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Affiliation(s)
- Tatiana S Moraes
- Plant Biotechnology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil.
| | - Richard G H Immink
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, The Netherlands
- Bioscience, Wageningen University & Research, Wageningen, The Netherlands
| | - Adriana P Martinelli
- Plant Biotechnology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Gerco C Angenent
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, The Netherlands
- Bioscience, Wageningen University & Research, Wageningen, The Netherlands
| | - Wilma van Esse
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Marcelo C Dornelas
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
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24
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Imoto Y, Yoshikawa S, Horiuchi Y, Iida T, Oka T, Matsuda S, Tokuji Y, Mori M, Kato K. Flowering Date1, a major photoperiod sensitivity gene in adzuki bean, is a soybean floral repressor E1 ortholog. BREEDING SCIENCE 2022; 72:132-140. [PMID: 36275936 PMCID: PMC9522530 DOI: 10.1270/jsbbs.21051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/27/2021] [Indexed: 06/16/2023]
Abstract
Adzuki bean is an important legume crop originating in temperate regions, with photoperiod in sensitivity being a key factor in its latitudinal adaptation. The Flowering Date1 (FD1) gene has a large effect on the photoperiodic response of flowering time, but the molecular basis for the effect of this locus is undetermined. The present study delimited the FD1 locus to a 17.1 kb sequence, containing a single gene, an E1 ortholog (VaE1). A comparison between Vigna angularis 'Shumari' (photoperiod insensitive) and 'Acc2265' (photoperiod sensitive) identified 29 insertions/deletions and 178 SNPs upstream of VaE1 in the FD1 locus. VaE1 expression in 'Acc2265' was greater under long-day than short-day conditions, whereas VaE1 expression in 'Shumari' was lower regardless of day length. These findings suggested that responsible gene of FD1 is a VaE1, which acts as a floral repressor by being upregulated in response to long-day conditions. The inability to upregulate VaE1 under long-day conditions was linked to its ability to flower under these conditions. These results provide greater understanding of the molecular control of a flowering date and clues enabling the breeding of adzuki bean at higher latitudes.
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Affiliation(s)
- Yusuke Imoto
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Shoko Yoshikawa
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Yuki Horiuchi
- Tokachi Agricultural Experiment Station, Agricultural Research Department, Hokkaido Research Organization, Memuro, Hokkaido 082-0081, Japan
| | - Takumi Iida
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Taisei Oka
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Shuichi Matsuda
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Yoshihiko Tokuji
- Department of Human Sciences, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Masahiko Mori
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Kiyoaki Kato
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan
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25
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Su Q, Chen L, Cai Y, Chen Y, Yuan S, Li M, Zhang J, Sun S, Han T, Hou W. Functional Redundancy of FLOWERING LOCUS T 3b in Soybean Flowering Time Regulation. Int J Mol Sci 2022; 23:2497. [PMID: 35269637 PMCID: PMC8910378 DOI: 10.3390/ijms23052497] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 12/17/2022] Open
Abstract
Photoperiodic flowering is an important agronomic trait that determines adaptability and yield in soybean and is strongly influenced by FLOWERING LOCUS T (FT) genes. Due to the presence of multiple FT homologs in the genome, their functions in soybean are not fully understood. Here, we show that GmFT3b exhibits functional redundancy in regulating soybean photoperiodic flowering. Bioinformatic analysis revealed that GmFT3b is a typical floral inducer FT homolog and that the protein is localized to the nucleus. Moreover, GmFT3b expression was induced by photoperiod and circadian rhythm and was more responsive to long-day (LD) conditions. We generated a homozygous ft3b knockout and three GmFT3b-overexpressing soybean lines for evaluation under different photoperiods. There were no significant differences in flowering time between the wild-type, the GmFT3b overexpressors, and the ft3b knockouts under natural long-day, short-day, or LD conditions. Although the downstream flowering-related genes GmFUL1 (a, b), GmAP1d, and GmLFY1 were slightly down-regulated in ft3b plants, the floral inducers GmFT5a and GmFT5b were highly expressed, indicating potential compensation for the loss of GmFT3b. We suggest that GmFT3b acts redundantly in flowering time regulation and may be compensated by other FT homologs in soybean.
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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 100081, China; (Q.S.); (L.C.); (Y.C.); (Y.C.); (J.Z.)
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.Y.); (M.L.); (S.S.); (T.H.)
| | - Li Chen
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Q.S.); (L.C.); (Y.C.); (Y.C.); (J.Z.)
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.Y.); (M.L.); (S.S.); (T.H.)
| | - Yupeng Cai
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Q.S.); (L.C.); (Y.C.); (Y.C.); (J.Z.)
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.Y.); (M.L.); (S.S.); (T.H.)
| | - Yingying Chen
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Q.S.); (L.C.); (Y.C.); (Y.C.); (J.Z.)
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.Y.); (M.L.); (S.S.); (T.H.)
| | - Shan Yuan
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.Y.); (M.L.); (S.S.); (T.H.)
| | - Min Li
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.Y.); (M.L.); (S.S.); (T.H.)
| | - Jialing Zhang
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Q.S.); (L.C.); (Y.C.); (Y.C.); (J.Z.)
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.Y.); (M.L.); (S.S.); (T.H.)
| | - Shi Sun
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.Y.); (M.L.); (S.S.); (T.H.)
| | - Tianfu Han
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.Y.); (M.L.); (S.S.); (T.H.)
| | - Wensheng Hou
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Q.S.); (L.C.); (Y.C.); (Y.C.); (J.Z.)
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.Y.); (M.L.); (S.S.); (T.H.)
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26
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Zhang M, Liu S, Wang Z, Yuan Y, Zhang Z, Liang Q, Yang X, Duan Z, Liu Y, Kong F, Liu B, Ren B, Tian Z. Progress in soybean functional genomics over the past decade. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:256-282. [PMID: 34388296 PMCID: PMC8753368 DOI: 10.1111/pbi.13682] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 05/24/2023]
Abstract
Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.
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Affiliation(s)
- Min Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Zhao Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaqin Yuan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhifang Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qianjin Liang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xia Yang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Baohui Liu
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Bo Ren
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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27
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A Point Mutation in Phytochromobilin synthase Alters the Circadian Clock and Photoperiodic Flowering of Medicago truncatula. PLANTS 2022; 11:plants11030239. [PMID: 35161220 PMCID: PMC8839385 DOI: 10.3390/plants11030239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 11/17/2022]
Abstract
Plants use seasonal cues to initiate flowering at an appropriate time of year to ensure optimal reproductive success. The circadian clock integrates these daily and seasonal cues with internal cues to initiate flowering. The molecular pathways that control the sensitivity of flowering to photoperiods (daylengths) are well described in the model plant Arabidopsis. However, much less is known for crop species, such as legumes. Here, we performed a flowering time screen of a TILLING population of Medicago truncatula and found a line with late-flowering and altered light-sensing phenotypes. Using RNA sequencing, we identified a nonsense mutation in the Phytochromobilin synthase (MtPΦBS) gene, which encodes an enzyme that carries out the final step in the biosynthesis of the chromophore required for phytochrome (phy) activity. The analysis of the circadian clock in the MtpΦbs mutant revealed a shorter circadian period, which was shared with the MtphyA mutant. The MtpΦbs and MtphyA mutants showed downregulation of the FT floral regulators MtFTa1 and MtFTb1/b2 and a change in phase for morning and night core clock genes. Our findings show that phyA is necessary to synchronize the circadian clock and integration of light signalling to precisely control the timing of flowering.
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28
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Jiang L, Jiang X, Li Y, Gao Y, Wang S, Ma Y, Wang G. FT-like paralogs are repressed by an SVP protein during the floral transition in Phalaenopsis orchid. PLANT CELL REPORTS 2022; 41:233-248. [PMID: 34713321 DOI: 10.1007/s00299-021-02805-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
An SVP protein, PhSVP, bound to the CArG-boxes in the promoter regions of FT-like paralogs and repressed their expression, thus affecting the floral transition in Phalaenopsis orchid. Phalaenopsis is an important ornamental flower native to tropical rain forests. It usually reaches vegetative maturity after 4-5 leaves and, after a juvenile stage, forms a flower spike (inflorescence) from the axillary buds. The PEBP gene family encodes a phosphatidyl-ethanolamine-binding protein (PEBP) domain involved in regulating flowering and other aspects of plant development. Here, we identified eight PEBP family genes in Phalaenopsis and detected the expression patterns of seven of them in various organs. Among them, PhFT1 (Phalaenopsis hybrid FLOWERING LOCUS T1), PhFT3, PhFT5, and PhMFT (Phalaenopsis hybrid MOTHER OF FT AND TFL1) promoted flowering in transgenic Arabidopsis, while PhFT6 inhibited flowering. PhSVP (Phalaenopsis hybrid SHORT VEGETATIVE PHASE), an SVP protein that repressed flowering in Arabidopsis, bound to the CArG-boxes in the promoter regions of PhFT3, PhFT6, and PhMFT in a yeast one-hybrid assay. Additionally, dual-luciferase and transient expression assays showed that PhSVP significantly inhibits the expression of both PhFT3 and PhFT6. Together, our work provides a comprehensive understanding of the PhFT-like genes that can promote or repress flowering, and it suggests strategies for regulating the floral transition in Phalaenopsis that exploit the evolutionary versatility of PhFTs to respond to various signals stimuli.
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Affiliation(s)
- Li Jiang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoxiao Jiang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanna Li
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yongxia Gao
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shiyao Wang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuehua Ma
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangdong Wang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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29
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Luo X, Yin M, He Y. Molecular Genetic Understanding of Photoperiodic Regulation of Flowering Time in Arabidopsis and Soybean. Int J Mol Sci 2021; 23:466. [PMID: 35008892 PMCID: PMC8745532 DOI: 10.3390/ijms23010466] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/25/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022] Open
Abstract
The developmental switch from a vegetative phase to reproduction (flowering) is essential for reproduction success in flowering plants, and the timing of the floral transition is regulated by various environmental factors, among which seasonal day-length changes play a critical role to induce flowering at a season favorable for seed production. The photoperiod pathways are well known to regulate flowering time in diverse plants. Here, we summarize recent progresses on molecular mechanisms underlying the photoperiod control of flowering in the long-day plant Arabidopsis as well as the short-day plant soybean; furthermore, the conservation and diversification of photoperiodic regulation of flowering in these two species are discussed.
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Affiliation(s)
- Xiao Luo
- Peking University Institute of Advanced Agricultural Sciences, Weifang 261325, China
| | - Mengnan Yin
- Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai 201602, China;
| | - Yuehui He
- Peking University Institute of Advanced Agricultural Sciences, Weifang 261325, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences, Peking University, Beijing 100871, China
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30
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Perfil'ev RN, Shcherban AB, Salina EA. Development of a marker panel for genotyping of domestic soybean cultivars for genes controlling the duration of vegetation and response to photoperiod. Vavilovskii Zhurnal Genet Selektsii 2021; 25:761-769. [PMID: 34964019 PMCID: PMC8654678 DOI: 10.18699/vj21.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 11/19/2022] Open
Abstract
Soybean, Glycine max L., is one of the most important agricultural crops grown in a wide range of latitude. In this regard, in soybean breeding, it is necessary to pay attention to the set of genes that control the transition to the f lowering stage, which will make it possible to adapt genotypes to local growing conditions as accurately as possible. The possibilities of soybean breeding for this trait have now signif icantly expanded due to identif ication of the main genes (E1–E4, GmFT2a, GmFT5a) that control the processes of f lowering and maturation in soybean, depending on the day length. The aim of this work was to develop a panel of markers for these genes, which could be used for a rapid and eff icient genotyping of domestic soybean cultivars and selection of plant material based on sensitivity to photoperiod and the duration of vegetation. Combinations of 10 primers, both previously developed and our own, were tested to identify different alleles of the E1–E4, GmFT2a, and GmFT5a genes using 10 soybean cultivars from different maturity groups. As a result, 5 combinations of dominant and recessive alleles for the E1–E4 genes were identif ied: (1) e1-nl(e1-as)/
e2-ns/e3-tr(e3-fs)/e4; (2) e1-as/e2-ns/e3-tr/E4; (3) e1-as/e2-ns/E3-Ha/e4; (4) E1/e2-ns/e3-tr/E4; (5) e1-nl/e2-ns/E3-Ha/E4. The studied cultivars contained the most common alleles of the GmFT2a and GmFT5a genes, with the exception of the ‘Cassidi’ cultivar having a rare dominant allele GmFT5a-H4. The degree of earliness of cultivars positively correlated with the number of recessive genes E1–E4, which is consistent with the data of foreign authors on different sets of cultivars from Japan and North China. Thus, the developed panel of markers can be successfully used in the selection
of soybean for earliness and sensitivity to photoperiod.
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Affiliation(s)
- R N Perfil'ev
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A B Shcherban
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E A Salina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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31
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Molinari MDC, Fuganti-Pagliarini R, Barbosa DDA, Marin SRR, Marin DR, Rech EL, Mertz-Henning LM, Nepomuceno AL. Flowering process in soybean under water deficit conditions: A review on genetic aspects. Genet Mol Biol 2021; 45:e20210016. [PMID: 34919115 PMCID: PMC8679260 DOI: 10.1590/1678-4685-gmb-2021-0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 09/30/2021] [Indexed: 11/22/2022] Open
Abstract
Soybean is a key crop in many countries, being used from human food to the animal industry due to its nutritional properties. Financially, the grain chain moves large sums of money into the economy of producing countries. However, like other agricultural commodities around the world, it can have its final yield seriously compromised by abiotic environmental stressors, like drought. As flowers imply in pods and in grains inside it to minimize damages caused by water restriction, researchers have focused on understanding flowering-process related genes and their interactions. Here a review dedicated to the soybean flowering process and gene network involved in it is presented, describing gene interactions and how genes act in this complex mechanism, also ruled by environmental triggers such as day-light and circadian cycle. The objective was to gather information and insights on the soybean flowering process, aiming to provide knowledge useful to assist in the development of drought-tolerant soybean lines, minimizing losses due to delays or anticipation of flowering and, consequently, restraining financial and productivity losses.
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Affiliation(s)
- Mayla Daiane Correa Molinari
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil.,Embrapa Soja, Londrina, PR, Brazil
| | | | - Daniel de Amorim Barbosa
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil.,Embrapa Soja, Londrina, PR, Brazil
| | | | | | - Elíbio Leopoldo Rech
- Embrapa Recursos Genéticos e Biotecnologia, Instituto Nacional de Ciência e Tecnologia em Biologia Sintética, Brasília, DF, Brazil
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Hu B, Li Y, Wu H, Zhai H, Xu K, Gao Y, Zhu J, Li Y, Xia Z. Identification of quantitative trait loci underlying five major agronomic traits of soybean in three biparental populations by specific length amplified fragment sequencing (SLAF-seq). PeerJ 2021; 9:e12416. [PMID: 34993010 PMCID: PMC8679901 DOI: 10.7717/peerj.12416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/10/2021] [Indexed: 11/20/2022] Open
Abstract
Flowering time, plant height, branch number, node numbers of main stem and pods per plant are important agronomic traits related to photoperiodic sensitivity, plant type and yield of soybean, which are controlled by multiple genes or quantitative trait loci (QTL). The main purpose of this study is to identify new QTL for five major agronomic traits, especially for flowering time. Three biparental populations were developed by crossing cultivars from northern and central China. Specific loci amplified fragment sequencing (SLAF-seq) was used to construct linkage map and QTL mapping was carried out. A total of 10 QTL for flowering time were identified in three populations, some of which were related to E1 and E2 genes or the other reported QTL listed in Soybase. In the Y159 population (Xudou No.9 × Kenfeng No.16), QTL for flowering time on chromosome 4, qFT4_1 and qFT4_2 were new. Compared with the QTL reported in Soybase, 1 QTL for plant height (PH), 3 QTL for branch number (BR), 5 QTL for node numbers of main stem, and 3 QTL for pods per plant were new QTL. Major E genes were frequently detected in different populations indicating that major the E loci had a great effect on flowering time and adaptation of soybean. Therefore, in order to further clone minor genes or QTL, it may be of great significance to carefully select the genotypes of known loci. These results may lay a foundation for fine mapping and clone of QTL/genes related to plant-type, provided a basis for high yield breeding of soybean.
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Affiliation(s)
- Bo Hu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuqiu Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Hongyan Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Kun Xu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Yi Gao
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinlong Zhu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Yuzhuo Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
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33
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Zimmer G, Miller MJ, Steketee CJ, Jackson SA, de Tunes LVM, Li Z. Genetic control and allele variation among soybean maturity groups 000 through IX. THE PLANT GENOME 2021; 14:e20146. [PMID: 34514734 DOI: 10.1002/tpg2.20146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Soybean [Glycinemax (L.) Merr.] maturity determines the growing region of a given soybean variety and is a primary factor in yield and other agronomic traits. The objectives of this research were to identify the quantitative trait loci (QTL) associated with maturity groups (MGs) and determine the genetic control of soybean maturity in each MG. Using data from 16,879 soybean accessions, genome-wide association (GWA) analyses were conducted for each paired MG and across MGs 000 through IX. Genome-wide association analyses were also performed using 184 genotypes (MGs V-IX) with days to flowering (DTF) and maturity (DTM) collected in the field. A total of 58 QTL were identified to be significantly associated with MGs in individual GWAs, which included 12 reported maturity loci and two stem termination genes. Genome-wide associations across MGs 000-IX detected a total of 103 QTL and confirmed 54 QTL identified in the individual GWAs. Of significant loci identified, qMG-5.2 had effects on the highest number (9) of MGs, followed by E2, E3, Dt2, qMG-15.5, E1, qMG-13.1, qMG-7.1, and qMG-16.1, which affected five to seven MGs. A high number of genetic loci (8-25) that affected MGs 0-V were observed. Stem termination genes Dt1 and Dt2 mainly had significant allele variation in MGs II-V. Genome-wide associations for DTF, DTM, and reproductive period (RP) in the diversity panel confirmed 15 QTL, of which seven were observed in MGs V-IX. The results generated can help soybean breeders manipulate the maturity loci for genetic improvement of soybean yield.
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Affiliation(s)
- Gustavo Zimmer
- Institute of Plant Breeding, Genetics, and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Crop Production, Federal University of Pelotas, Capão do Leão, RS, 96160-000, Brazil
| | - Mark J Miller
- Institute of Plant Breeding, Genetics, and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Clinton J Steketee
- Institute of Plant Breeding, Genetics, and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Scott A Jackson
- Institute of Plant Breeding, Genetics, and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | | | - Zenglu Li
- Institute of Plant Breeding, Genetics, and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
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34
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Rani A, Kumar V, Shukla S, Manjaya JG. Molecular characterization of a novel mutation in the E1 flowering gene induced by gamma irradiation in soybean. Genome 2021; 64:915-925. [PMID: 33683922 DOI: 10.1139/gen-2020-0137] [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] [Indexed: 11/22/2022]
Abstract
Soybean is a typical short-day (SD) plant. It undergoes reproductive growth only when the day length becomes shorter than a critical length. Fourteen major genes/loci affecting soybean flowering and maturity period have been mapped to date. These are E1 and E7 on chr6, E1La, E1Lb, E6, E8, and J on chr4, E2 on chr10, E3 on chr19, E4 on chr20, E9 on chr6, E10 on chr8, Dt1 on chr19, and GmAGL1 on chr14. The functional allele of all these genes, except E6, E9, J, and GmAGL1, delay flowering, while the non-functional counterpart accelerates flowering and maturity. The contribution of the E1 gene in delaying flowering is highest. Four non-functional/dysfunctional allelic variants of the E1 gene are already known, which accelerates the flowering by 20-25 days and are being used in development of early maturing soybean varieties in many parts of the world. In this study, seeds of the late maturing Indian variety NRC 37 were irradiated with gamma rays to develop an early maturing variety. One early maturing variant was obtained. Molecular characterization of the gene responsible for early flowering proved it to be a non-functional variant of the E1 gene with major deletion.
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Affiliation(s)
- Anita Rani
- ICAR-Indian Institute of Soybean Research, Indore, India
| | - Vineet Kumar
- ICAR-Indian Institute of Soybean Research, Indore, India
| | - Shruti Shukla
- ICAR-Indian Institute of Soybean Research, Indore, India
| | - J G Manjaya
- Bhabha Atomic Research Centre (BARC), Mumbai, India
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35
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Li X, Fang C, Yang Y, Lv T, Su T, Chen L, Nan H, Li S, Zhao X, Lu S, Dong L, Cheng Q, Tang Y, Xu M, Abe J, Hou X, Weller JL, Kong F, Liu B. Overcoming the genetic compensation response of soybean florigens to improve adaptation and yield at low latitudes. Curr Biol 2021; 31:3755-3767.e4. [PMID: 34270946 DOI: 10.1016/j.cub.2021.06.037] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/30/2021] [Accepted: 06/11/2021] [Indexed: 10/20/2022]
Abstract
The classical soybean (Glycine max) trait long juvenile (LJ) is essentially a reduction in sensitivity to short-day (SD) conditions for induction and completion of flowering, and has been introduced into soybean cultivars to improve yield in tropical environments. However, only one locus, J, is known to confer LJ in low-latitude varieties. Here, we defined two quantitative trait loci contributing to the LJ trait, LJ16.1 and LJ16.2, and identified them as the florigen (FT) homologs FT2a and FT5a, respectively. The two selected florigen variations both delay flowering time under SD conditions by repressing the floral meristem identity gene GmAPETALA1. Single mutants have a relatively subtle effect on flowering time and displayed a substantial genetic compensation response, but this was absent in ft2a ft5a double mutants, which showed an enhanced LJ phenotype that translated to higher yields under SD conditions. A survey of sequence diversity suggests that FT2a and FT5a variants have diverse origins and have played distinct roles as soybean spread to lower latitudes. Our results show that integration of variants in the florigen genes offers a strategy for customizing flowering time to adjust adaptation and improve crop productivity in tropical regions.
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Affiliation(s)
- Xiaoming Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Chao Fang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Yongqing Yang
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tianxiao Lv
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Tong Su
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China; University of Chinese Academy of Sciences, Beijing, China
| | - Liyu Chen
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Haiyang Nan
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Shichen Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohui Zhao
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Sijia Lu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Lidong Dong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Qun Cheng
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Yang Tang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Meilan Xu
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo 060-0811, Japan
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Xingliang Hou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou 510650, China
| | - James L Weller
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, TAS 7001, Australia
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China; Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China.
| | - Baohui Liu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China; Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China.
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36
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Wang Y, Xu C, Sun J, Dong L, Li M, Liu Y, Wang J, Zhang X, Li D, Sun J, Zhang Y, Shan J, Li W, Zhao L. GmRAV confers ecological adaptation through photoperiod control of flowering time and maturity in soybean. PLANT PHYSIOLOGY 2021; 187:361-377. [PMID: 34618136 PMCID: PMC8418415 DOI: 10.1093/plphys/kiab255] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/12/2021] [Indexed: 05/31/2023]
Abstract
Photoperiod strictly controls vegetative and reproductive growth stages in soybean (Glycine max). A soybean GmRAV (Related to ABI3/VP1) transcription factor containing both AP2 and B3 domains was shown to be a key component of this process. We identified six polymorphisms in the GmRAV promoter that showed significant association with flowering time and maturity of soybean in one or multiple environments. Soybean varieties with minor polymorphism exhibited a longer growth period contributing to soybean adaptation to lower latitudes. The cis-acting element GT1CONSENSUS motif of the GmRAV promoter controlled the growth period, and the major allele in this motif shortened duration of late reproductive stages by reducing GmRAV expression levels. Three GmRAV-overexpressing (GmRAV-ox) transgenic lines displayed later flowering time and maturity, shorter height and fewer numbers of leaves compared with control plants, whereas transgenic inhibition of GmRAV expression resulted in earlier flowering time and maturity and increased plant height. Combining DNA affinity purification sequencing and RNA sequencing analyses revealed 154 putative target genes directly bound and transcriptionally regulated by GmRAV. Two GmRAV binding motifs [C(A/G)AACAA(G/T)A(C/T)A(G/T)] and [C(T/A)A(C)C(T/G)CTG] were identified, and acting downstream of E3E4, GmRAV repressed GmFT5a transcriptional activity through binding a CAACA motif, thereby delaying soybean growth and extending both vegetative and reproductive phases.
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Affiliation(s)
- Yuhe Wang
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Chongjing Xu
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Jiafan Sun
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Lidong Dong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Minmin Li
- 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
| | - Jianhui Wang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xiaoming Zhang
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Dongmei Li
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Jingzhe Sun
- 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
| | - Jinming Shan
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Wenbin 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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Yue Y, Jiang Z, Sapey E, Wu T, Sun S, Cao M, Han T, Li T, Nian H, Jiang B. Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars. BMC Genomics 2021; 22:529. [PMID: 34246232 PMCID: PMC8272290 DOI: 10.1186/s12864-021-07869-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 07/01/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND In soybean, some circadian clock genes have been identified as loci for maturity traits. However, the effects of these genes on soybean circadian rhythmicity and their impacts on maturity are unclear. RESULTS We used two geographically, phenotypically and genetically distinct cultivars, conventional juvenile Zhonghuang 24 (with functional J/GmELF3a, a homolog of the circadian clock indispensable component EARLY FLOWERING 3) and long juvenile Huaxia 3 (with dysfunctional j/Gmelf3a) to dissect the soybean circadian clock with time-series transcriptomal RNA-Seq analysis of unifoliate leaves on a day scale. The results showed that several known circadian clock components, including RVE1, GI, LUX and TOC1, phase differently in soybean than in Arabidopsis, demonstrating that the soybean circadian clock is obviously different from the canonical model in Arabidopsis. In contrast to the observation that ELF3 dysfunction results in clock arrhythmia in Arabidopsis, the circadian clock is conserved in soybean regardless of the functional status of J/GmELF3a. Soybean exhibits a circadian rhythmicity in both gene expression and alternative splicing. Genes can be grouped into six clusters, C1-C6, with different expression profiles. Many more genes are grouped into the night clusters (C4-C6) than in the day cluster (C2), showing that night is essential for gene expression and regulation. Moreover, soybean chromosomes are activated with a circadian rhythmicity, indicating that high-order chromosome structure might impact circadian rhythmicity. Interestingly, night time points were clustered in one group, while day time points were separated into two groups, morning and afternoon, demonstrating that morning and afternoon are representative of different environments for soybean growth and development. However, no genes were consistently differentially expressed over different time-points, indicating that it is necessary to perform a circadian rhythmicity analysis to more thoroughly dissect the function of a gene. Moreover, the analysis of the circadian rhythmicity of the GmFT family showed that GmELF3a might phase- and amplitude-modulate the GmFT family to regulate the juvenility and maturity traits of soybean. CONCLUSIONS These results and the resultant RNA-seq data should be helpful in understanding the soybean circadian clock and elucidating the connection between the circadian clock and soybean maturity.
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Affiliation(s)
- Yanlei Yue
- College of Life Sciences, Henan Agricultural University, 450002, Zhengzhou, China
| | - Ze Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Enoch Sapey
- MARA Key Lab of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Tingting Wu
- MARA Key Lab of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Shi Sun
- MARA Key Lab of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Mengxue Cao
- College of Life Sciences, Henan Agricultural University, 450002, Zhengzhou, China
| | - Tianfu Han
- MARA Key Lab of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Tao Li
- College of Life Sciences, Henan Agricultural University, 450002, Zhengzhou, China.
| | - Hai Nian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China.
| | - Bingjun Jiang
- MARA Key Lab of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
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Lin X, Liu B, Weller JL, Abe J, Kong F. Molecular mechanisms for the photoperiodic regulation of flowering in soybean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:981-994. [PMID: 33090664 DOI: 10.1111/jipb.13021] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 09/27/2020] [Indexed: 06/11/2023]
Abstract
Photoperiodic flowering is one of the most important factors affecting regional adaptation and yield in soybean (Glycine max). Plant adaptation to long-day conditions at higher latitudes requires early flowering and a reduction or loss of photoperiod sensitivity; adaptation to short-day conditions at lower latitudes involves delayed flowering, which prolongs vegetative growth for maximum yield potential. Due to the influence of numerous major loci and quantitative trait loci (QTLs), soybean has broad adaptability across latitudes. Forward genetic approaches have uncovered the molecular basis for several of these major maturity genes and QTLs. Moreover, the molecular characterization of orthologs of Arabidopsis thaliana flowering genes has enriched our understanding of the photoperiodic flowering pathway in soybean. Building on early insights into the importance of the photoreceptor phytochrome A, several circadian clock components have been integrated into the genetic network controlling flowering in soybean: E1, a repressor of FLOWERING LOCUS T orthologs, plays a central role in this network. Here, we provide an overview of recent progress in elucidating photoperiodic flowering in soybean, how it contributes to our fundamental understanding of flowering time control, and how this information could be used for molecular design and breeding of high-yielding soybean cultivars.
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Affiliation(s)
- Xiaoya Lin
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510642, China
| | - Baohui Liu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510642, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - James L Weller
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, 7001, Australia
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510642, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
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Xia Z, Zhai H, Wu H, Xu K, Watanabe S, Harada K. The Synchronized Efforts to Decipher the Molecular Basis for Soybean Maturity Loci E1, E2, and E3 That Regulate Flowering and Maturity. FRONTIERS IN PLANT SCIENCE 2021; 12:632754. [PMID: 33995435 PMCID: PMC8113421 DOI: 10.3389/fpls.2021.632754] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
The general concept of photoperiodism, i.e., the photoperiodic induction of flowering, was established by Garner and Allard (1920). The genetic factor controlling flowering time, maturity, or photoperiodic responses was observed in soybean soon after the discovery of the photoperiodism. E1, E2, and E3 were named in 1971 and, thereafter, genetically characterized. At the centennial celebration of the discovery of photoperiodism in soybean, we recount our endeavors to successfully decipher the molecular bases for the major maturity loci E1, E2, and E3 in soybean. Through systematic efforts, we successfully cloned the E3 gene in 2009, the E2 gene in 2011, and the E1 gene in 2012. Recently, successful identification of several circadian-related genes such as PRR3a, LUX, and J has enriched the known major E1-FTs pathway. Further research progresses on the identification of new flowering and maturity-related genes as well as coordinated regulation between flowering genes will enable us to understand profoundly flowering gene network and determinants of latitudinal adaptation in soybean.
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Affiliation(s)
- Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Hongyan Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Kun Xu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | | | - Kyuya Harada
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
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Lee SH, Choi CW, Park KM, Jung WH, Chun HJ, Baek D, Cho HM, Jin BJ, Park MS, No DH, Lim LH, Shim SI, Chung JI, Kim MC. Diversification in Functions and Expressions of Soybean FLOWERING LOCUS T Genes Fine-Tunes Seasonal Flowering. FRONTIERS IN PLANT SCIENCE 2021; 12:613675. [PMID: 33981322 PMCID: PMC8107440 DOI: 10.3389/fpls.2021.613675] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 04/08/2021] [Indexed: 06/01/2023]
Abstract
The proper timing of flowering in response to environmental changes is critical for ensuring crop yields. FLOWERING LOCUS T (FT) homologs of the phosphatidylethanolamine-binding protein family play important roles as floral integrators in many crops. In soybean, we identified 17 genes of this family, and characterized biological functions in flowering for ten FT homologs. Overexpression of GmFT homologs in Arabidopsis revealed that a set of GmFT homologs, including GmFT2a/2b, GmFT3a/3b, and GmFT5a/5b, promoted flowering similar to FT; in contrast, GmFT1a/1b, GmFT4, and GmFT6 delayed flowering. Consistently, expressions of GmFT2a, GmFT2b, and GmFT5a were induced in soybean leaves in response to floral inductive short days, whereas expressions of GmFT1a and GmFT4 were induced in response to long days. Exon swapping analysis between floral activator GmFT2a and floral repressor GmFT4 revealed that the segment B region in the fourth exon is critical for their antagonistic functions. Finally, expression analysis of GmFT2a, GmFT5a, and GmFT4 in soybean accessions exhibiting various flowering times indicated that the mRNA levels of GmFT2a and GmFT5a were higher in early flowering accessions than in late-flowering accessions, while GmFT4 showed the opposite pattern. Moreover, the relative mRNA levels between GmFT2a/GmFT5a and GmFT4 was important in determining day length-dependent flowering in soybean accessions. Taken together, our results suggest that the functions of GmFT homologs have diversified into floral activators and floral repressors during soybean evolution, and the timing of flowering in response to changing day length is determined by modulating the activities of antagonistic GmFT homologs.
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Affiliation(s)
- Su Hyeon Lee
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Cheol Woo Choi
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Kyoung Mi Park
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Wook-Hun Jung
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Hyun Jin Chun
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, South Korea
| | - Dongwon Baek
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Hyun Min Cho
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Byung Jun Jin
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Mi Suk Park
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Dong Hyeon No
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Lack Hyeon Lim
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Sang In Shim
- Department of Agronomy, Gyeongsang National University, Jinju, South Korea
| | - Jong Il Chung
- Department of Agronomy, Gyeongsang National University, Jinju, South Korea
| | - Min Chul Kim
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, South Korea
- Department of Agronomy, Gyeongsang National University, Jinju, South Korea
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41
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McClung CR. Circadian Clock Components Offer Targets for Crop Domestication and Improvement. Genes (Basel) 2021; 12:genes12030374. [PMID: 33800720 PMCID: PMC7999361 DOI: 10.3390/genes12030374] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/31/2022] Open
Abstract
During plant domestication and improvement, farmers select for alleles present in wild species that improve performance in new selective environments associated with cultivation and use. The selected alleles become enriched and other alleles depleted in elite cultivars. One important aspect of crop improvement is expansion of the geographic area suitable for cultivation; this frequently includes growth at higher or lower latitudes, requiring the plant to adapt to novel photoperiodic environments. Many crops exhibit photoperiodic control of flowering and altered photoperiodic sensitivity is commonly required for optimal performance at novel latitudes. Alleles of a number of circadian clock genes have been selected for their effects on photoperiodic flowering in multiple crops. The circadian clock coordinates many additional aspects of plant growth, metabolism and physiology, including responses to abiotic and biotic stresses. Many of these clock-regulated processes contribute to plant performance. Examples of selection for altered clock function in tomato demonstrate that with domestication, the phasing of the clock is delayed with respect to the light–dark cycle and the period is lengthened; this modified clock is associated with increased chlorophyll content in long days. These and other data suggest the circadian clock is an attractive target during breeding for crop improvement.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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42
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Bu T, Lu S, Wang K, Dong L, Li S, Xie Q, Xu X, Cheng Q, Chen L, Fang C, Li H, Liu B, Weller JL, Kong F. A critical role of the soybean evening complex in the control of photoperiod sensitivity and adaptation. Proc Natl Acad Sci U S A 2021; 118:e2010241118. [PMID: 33558416 PMCID: PMC7923351 DOI: 10.1073/pnas.2010241118] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Photoperiod sensitivity is a key factor in plant adaptation and crop production. In the short-day plant soybean, adaptation to low latitude environments is provided by mutations at the J locus, which confer extended flowering phase and thereby improve yield. The identity of J as an ortholog of Arabidopsis ELF3, a component of the circadian evening complex (EC), implies that orthologs of other EC components may have similar roles. Here we show that the two soybean homeologs of LUX ARRYTHMO interact with J to form a soybean EC. Characterization of mutants reveals that these genes are highly redundant in function but together are critical for flowering under short day, where the lux1 lux2 double mutant shows extremely late flowering and a massively extended flowering phase. This phenotype exceeds that of any soybean flowering mutant reported to date, and is strongly reminiscent of the "Maryland Mammoth" tobacco mutant that featured in the seminal 1920 study of plant photoperiodism by Garner and Allard [W. W. Garner, H. A. Allard, J. Agric. Res. 18, 553-606 (1920)]. We further demonstrate that the J-LUX complex suppresses transcription of the key flowering repressor E1 and its two homologs via LUX binding sites in their promoters. These results indicate that the EC-E1 interaction has a central role in soybean photoperiod sensitivity, a phenomenon also first described by Garner and Allard. EC and E1 family genes may therefore constitute key targets for customized breeding of soybean varieties with precise flowering time adaptation, either by introgression of natural variation or generation of new mutants by gene editing.
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Affiliation(s)
- Tiantian Bu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Sijia Lu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Kai Wang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Lidong Dong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Shilin Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
| | - Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
| | - Qun Cheng
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Liyu Chen
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Chao Fang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Haiyang Li
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Baohui Liu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 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, 150081 Harbin, China
| | - James L Weller
- School of Natural Sciences, University of Tasmania, Hobart, 7001 TAS, Australia
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 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, 150081 Harbin, China
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Zhang S, Singh MB, Bhalla PL. Molecular characterization of a soybean FT homologue, GmFT7. Sci Rep 2021; 11:3651. [PMID: 33574496 PMCID: PMC7878754 DOI: 10.1038/s41598-021-83305-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/29/2021] [Indexed: 11/16/2022] Open
Abstract
Soybean (Glycine max) is a vital oilseed legume crop that provides protein and oil for humans and feedstock for animals. Flowering is a prerequisite for seed production. Floral transition, from vegetative to reproductive stage, in a plant, is regulated by environmental (light, temperature) and endogenous factors. In Arabidopsis, Flowering Locus T (FT) protein is shown to be a mobile signal that moves from leaf to shoot apical meristem to induce flowering. However, FTs role in soybean is not fully resolved due to the presence of multiple (ten) homologs in the genome. Two of the ten FT homologs (GmFT2a and GmFT5a) have a role in the floral transition while GmFT1a and GmFT4 suppress soybean flowering. Recent deep sequencing data revealed that six FT homologs are expressed in shoot apical meristem and leaves during floral transition. One FT homolog, GmFT7 showed strong expression during soybean floral transition. Though bioinformatic analyses revealed that GmFT7 had high similarity with GmFT2a, ectopic GmFT7 expression in Arabidopsis could not promote flowering or rescue the late-flowering phenotype of Arabidopsis ft-10 mutant.
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Affiliation(s)
- Senhao Zhang
- Plant Molecular Biology and Biotechnology Laboratory, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
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Kang X, Hajek B, Hanzawa Y. From graph topology to ODE models for gene regulatory networks. PLoS One 2020; 15:e0235070. [PMID: 32603340 PMCID: PMC7326199 DOI: 10.1371/journal.pone.0235070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/08/2020] [Indexed: 11/28/2022] Open
Abstract
A gene regulatory network can be described at a high level by a directed graph with signed edges, and at a more detailed level by a system of ordinary differential equations (ODEs). The former qualitatively models the causal regulatory interactions between ordered pairs of genes, while the latter quantitatively models the time-varying concentrations of mRNA and proteins. This paper clarifies the connection between the two types of models. We propose a property, called the constant sign property, for a general class of ODE models. The constant sign property characterizes the set of conditions (system parameters, external signals, or internal states) under which an ODE model is consistent with a signed, directed graph. If the constant sign property for an ODE model holds globally for all conditions, then the ODE model has a single signed, directed graph. If the constant sign property for an ODE model only holds locally, which may be more typical, then the ODE model corresponds to different graphs under different sets of conditions. In addition, two versions of constant sign property are given and a relationship between them is proved. As an example, the ODE models that capture the effect of cis-regulatory elements involving protein complex binding, based on the model in the GeneNetWeaver source code, are described in detail and shown to satisfy the global constant sign property with a unique consistent gene regulatory graph. Even a single gene regulatory graph is shown to have many ODE models of GeneNetWeaver type consistent with it due to combinatorial complexity and continuous parameters. Finally the question of how closely data generated by one ODE model can be fit by another ODE model is explored. It is observed that the fit is better if the two models come from the same graph.
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Affiliation(s)
- Xiaohan Kang
- Department of Electrical and Computer Engineering, and Coordinated Science Laboratory, University of Illinois at Urbana–Champaign, Urbana, Illinois, United States of America
| | - Bruce Hajek
- Department of Electrical and Computer Engineering, and Coordinated Science Laboratory, University of Illinois at Urbana–Champaign, Urbana, Illinois, United States of America
| | - Yoshie Hanzawa
- Department of Biology, California State University, Northridge, Northridge, California, United States of America
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GmNMHC5, A Neoteric Positive Transcription Factor of Flowering and Maturity in Soybean. PLANTS 2020; 9:plants9060792. [PMID: 32630379 PMCID: PMC7356762 DOI: 10.3390/plants9060792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 01/02/2023]
Abstract
The soybean (Glycine max (L.) Merr.) is an important oil and food crop. Its growth and development is regulated by complex genetic networks, and there are still many genes with unknown functions in regulation pathways. In this study, GmNMHC5, a member of the MADS-box protein family, was found to promote flowering and maturity in the soybean. Gene expression profiling in transgenic plants confirmed that the 35S:GmNMHC5 T3 generation had early flowering and precocity. We used CRISPR-Cas9 to edit GmNMHC5 and found that late flowering and maturity occurred in Gmnmhc5 lines with stable inheritance. Remarkably, in the 35S:GmNMHC5 plants, the expression of flowering inhibitors GmFT1a and GmFT4 was inhibited. In addition, overexpression of GmNMHC5 in ft-10 (a late flowering Arabidopsis thaliana mutant lacking Flowering Locus T (FT) function) rescued the extremely late-flowering phenotype of the mutant A. thaliana. These results suggest that GmNMHC5 is a positive transcription factor of flowering and maturity in the soybean, which has a close relationship with FT homologs in the flowering regulation pathway. This discovery provides new ideas for the improvement of the flowering regulation network, and can also provide guidance for future breeding work.
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46
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Evolution and functional diversification of FLOWERING LOCUS T/TERMINAL FLOWER 1 family genes in plants. Semin Cell Dev Biol 2020; 109:20-30. [PMID: 32507412 DOI: 10.1016/j.semcdb.2020.05.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/11/2020] [Accepted: 05/11/2020] [Indexed: 01/01/2023]
Abstract
Plant growth and development, particularly the induction of flowering, are tightly controlled by key regulators in response to endogenous and environmental cues. The FLOWERING LOCUS T (FT)/TERMINAL FLOWER 1 (TFL1) family of phosphatidylethanolamine-binding protein (PEBP) genes is central to plant development, especially the regulation of flowering time and plant architecture. FT, the long-sought florigen, promotes flowering and TFL1 represses flowering. The balance between FT and TFL1 modulates plant architecture by switching the meristem from indeterminate to determinate growth, or vice versa. Recent studies in a broad range of plant species demonstrated that, in addition to their roles in flowering time and plant architecture, FT/TFL1 family genes participate in diverse aspects of plant development, such as bamboo seed germination and potato tuber formation. In this review, we briefly summarize the evolution of the FT/TFL1 family and highlight recent findings on their conserved and divergent functions in different species.
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47
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Lorenzo CD, García‐Gagliardi P, Antonietti MS, Sánchez‐Lamas M, Mancini E, Dezar CA, Vazquez M, Watson G, Yanovsky MJ, Cerdán PD. Improvement of alfalfa forage quality and management through the down-regulation of MsFTa1. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:944-954. [PMID: 31536663 PMCID: PMC7061867 DOI: 10.1111/pbi.13258] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 09/06/2019] [Accepted: 09/16/2019] [Indexed: 05/02/2023]
Abstract
Alfalfa (Medicago sativa L.) is one of the most important forage crops worldwide. As a perennial, alfalfa is cut several times each year. Farmers face a dilemma: if cut earlier, forage nutritive value is much higher but regrowth is affected and the longevity of the stand is severely compromised. On the other hand, if alfalfa is cut later at full flower, stands persist longer and more biomass may be harvested, but the nutritive value diminishes. Alfalfa is a strict long-day plant. We reasoned that by manipulating the response to photoperiod, we could delay flowering to improve forage quality and widen each harvesting window, facilitating management. With this aim, we functionally characterized the FLOWERING LOCUS T family of genes, represented by five members: MsFTa1, MsFTa2, MsFTb1, MsFTb2 and MsFTc. The expression of MsFTa1 correlated with photoperiodic flowering and its down-regulation led to severe delayed flowering. Altogether, with late flowering, low expression of MsFTa1 led to changes in plant architecture resulting in increased leaf to stem biomass ratios and forage digestibility. By manipulating photoperiodic flowering, we were able to improve the quality of alfalfa forage and management, which may allow farmers to cut alfalfa of high nutritive value without compromising stand persistence.
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Affiliation(s)
| | | | | | | | | | - Carlos A. Dezar
- Instituto de Agrobiotecnología de Rosario (INDEAR)CONICETRosarioArgentina
| | - Martin Vazquez
- Instituto de Agrobiotecnología de Rosario (INDEAR)CONICETRosarioArgentina
| | - Gerónimo Watson
- Instituto de Agrobiotecnología de Rosario (INDEAR)CONICETRosarioArgentina
| | | | - Pablo D. Cerdán
- Fundación Instituto LeloirIIBBA‐CONICETBuenos AiresArgentina
- Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresBuenos AiresArgentina
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48
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Chen L, Cai Y, Qu M, Wang L, Sun H, Jiang B, Wu T, Liu L, Sun S, Wu C, Yao W, Yuan S, Han T, Hou W. Soybean adaption to high-latitude regions is associated with natural variations of GmFT2b, an ortholog of FLOWERING LOCUS T. PLANT, CELL & ENVIRONMENT 2020; 43:934-944. [PMID: 31981430 PMCID: PMC7154755 DOI: 10.1111/pce.13695] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/25/2019] [Accepted: 12/01/2019] [Indexed: 05/03/2023]
Abstract
Day length has an important influence on flowering and growth habit in many plant species. In crops such as soybean, photoperiod sensitivity determines the geographical range over which a given cultivar can grow and flower. The soybean genome contains ~10 genes homologous to FT, a central regulator of flowering from Arabidopsis thaliana. However, the precise roles of these soybean FTs are not clearly. Here we show that one such gene, GmFT2b, promotes flowering under long-days (LDs). Overexpression of GmFT2b upregulates expression of flowering-related genes which are important in regulating flowering time. We propose a 'weight' model for soybean flowering under short-day (SD) and LD conditions. Furthermore, we examine GmFT2b sequences in 195 soybean cultivars, as well as flowering phenotypes, geographical distributions and maturity groups. We found that Hap3, a major GmFT2b haplotype, is associated with significantly earlier flowering at higher latitudes. We anticipate our assay to provide important resources for the genetic improvement of soybean, including new germplasm for soybean breeding, and also increase our understanding of functional diversity in the soybean FT gene family.
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Affiliation(s)
- Li Chen
- National Center for Transgenic Research in PlantsInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing)Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Yupeng Cai
- National Center for Transgenic Research in PlantsInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing)Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Mengnan Qu
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing)Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Liwei Wang
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing)Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Hongbo Sun
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing)Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Bingjun Jiang
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing)Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Tingting Wu
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing)Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Luping Liu
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing)Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Shi Sun
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing)Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Cunxiang Wu
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing)Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Weiwei Yao
- National Center for Transgenic Research in PlantsInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing)Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Shan Yuan
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing)Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Tianfu Han
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing)Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Wensheng Hou
- National Center for Transgenic Research in PlantsInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing)Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
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49
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Lyu J, Cai Z, Li Y, Suo H, Yi R, Zhang S, Nian H. The Floral Repressor GmFLC-like Is Involved in Regulating Flowering Time Mediated by Low Temperature in Soybean. Int J Mol Sci 2020; 21:E1322. [PMID: 32075331 PMCID: PMC7072909 DOI: 10.3390/ijms21041322] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/04/2020] [Accepted: 02/13/2020] [Indexed: 01/09/2023] Open
Abstract
Soybean is an important crop that is grown worldwide. Flowering time is a critical agricultural trait determining successful reproduction and yields. For plants, light and temperature are important environmental factors that regulate flowering time. Soybean is a typical short-day (SD) plant, and many studies have elucidated the fine-scale mechanisms of how soybean responds to photoperiod. Low temperature can delay the flowering time of soybean, but little is known about the detailed mechanism of how temperature affects soybean flowering. In this study, we isolated GmFLC-like from soybean, which belongs to the FLOWERING LOCUS C clade of the MADS-box family and is intensely expressed in soybean leaves. Heterologous expression of GmFLC-like results in a delayed-flowering phenotype in Arabidopsis. Additional experiments revealed that GmFLC-like is involved in long-term low temperature-triggered late flowering by inhibiting FT gene expression. In addition, yeast one-hybrid, dual-luciferase reporter assay, and electrophoretic mobility shift assay revealed that the GmFLC-like protein could directly repress the expression of FT2a by physically interacting with its promoter region. Taken together, our results revealed that GmFLC-like functions as a floral repressor involved in flowering time during treatments with various low temperature durations. As the only the FLC gene in soybean, GmFLC-like was meaningfully retained in the soybean genome over the course of evolution, and this gene may play an important role in delaying flowering time and providing protective mechanisms against sporadic and extremely low temperatures.
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Affiliation(s)
- Jing Lyu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (J.L.); (Z.C.); (R.Y.)
| | - Zhandong Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (J.L.); (Z.C.); (R.Y.)
| | - Yonghong Li
- School of Applied Chemistry and Biological Technology, Postdoctoral Innovation Practice Base, Shenzhen Polytechnic, Shenzhen 518055, China;
| | - Haicui Suo
- Crop Research Institute, Guangdong Academy of Agriculture, Guangzhou 510642, China;
| | - Rong Yi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (J.L.); (Z.C.); (R.Y.)
- Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Shuai Zhang
- School of Applied Chemistry and Biological Technology, Postdoctoral Innovation Practice Base, Shenzhen Polytechnic, Shenzhen 518055, China;
| | - Hai Nian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (J.L.); (Z.C.); (R.Y.)
- Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
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50
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Kim KH, Kim JY, Lim WJ, Jeong S, Lee HY, Cho Y, Moon JK, Kim N. Genome-wide association and epistatic interactions of flowering time in soybean cultivar. PLoS One 2020; 15:e0228114. [PMID: 31968016 PMCID: PMC6975553 DOI: 10.1371/journal.pone.0228114] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/07/2020] [Indexed: 12/02/2022] Open
Abstract
Genome-wide association studies (GWAS) have enabled the discovery of candidate markers that play significant roles in various complex traits in plants. Recently, with increased interest in the search for candidate markers, studies on epistatic interactions between single nucleotide polymorphism (SNP) markers have also increased, thus enabling the identification of more candidate markers along with GWAS on single-variant-additive-effect. Here, we focused on the identification of candidate markers associated with flowering time in soybean (Glycine max). A large population of 2,662 cultivated soybean accessions was genotyped using the 180k Axiom® SoyaSNP array, and the genomic architecture of these accessions was investigated to confirm the population structure. Then, GWAS was conducted to evaluate the association between SNP markers and flowering time. A total of 93 significant SNP markers were detected within 59 significant genes, including E1 and E3, which are the main determinants of flowering time. Based on the GWAS results, multilocus epistatic interactions were examined between the significant and non-significant SNP markers. Two significant and 16 non-significant SNP markers were discovered as candidate markers affecting flowering time via interactions with each other. These 18 candidate SNP markers mapped to 18 candidate genes including E1 and E3, and the 18 candidate genes were involved in six major flowering pathways. Although further biological validation is needed, our results provide additional information on the existing flowering time markers and present another option to marker-assisted breeding programs for regulating flowering time of soybean.
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Affiliation(s)
- Kyoung Hyoun Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Jae-Yoon Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Seongmun Jeong
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Ho-Yeon Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Youngbum Cho
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Jung-Kyung Moon
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
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