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Sun J, Liu Y, Zheng Y, Xue Y, Fan Y, Ma X, Ji Y, Liu G, Zhang X, Li Y, Wang S, Tian Z, Zhao L. The MADS-box transcription factor GmFULc promotes GmZTL4 gene transcription to modulate maturity in soybean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1603-1619. [PMID: 38869305 DOI: 10.1111/jipb.13682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 04/26/2024] [Accepted: 05/04/2024] [Indexed: 06/14/2024]
Abstract
Flowering time and maturity are crucial agronomic traits that affect the regional adaptability of soybean plants. The development of soybean cultivars with early maturity adapted to longer days and colder climates of high latitudes is very important for ensuring normal ripening before frost begins. FUL belongs to the MADS-box transcription factor family and has several duplicated members in soybeans. In this study, we observed that overexpression of GmFULc in the Dongnong 50 cultivar promoted soybean maturity, while GmFULc knockout mutants exhibited late maturity. Chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) revealed that GmFULc could bind to the CArG, bHLH and homeobox motifs. Further investigation revealed that GmFULc could directly bind to the CArG motif in the promoters of the GmZTL3 and GmZTL4 genes. Overexpression of GmZTL4 promoted soybean maturity, whereas the ztl4 mutants exhibited delayed maturity. Moreover, we found that the cis element box 4 motif of the GmZTL4 promoter, a motif of light response elements, played an important role in controlling the growth period. Deletion of this motif shortened the growth period by increasing the expression levels of GmZTL4. Functional investigations revealed that short-day treatment promoted the binding of GmFULc to the promoter of GmZTL4 and inhibited the expression of E1 and E1Lb, ultimately resulting in the promotion of flowering and early maturation. Taken together, these findings suggest a novel photoperiod regulatory pathway in which GmFULc directly activates GmZTL4 to promote earlier maturity in soybean.
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Affiliation(s)
- Jingzhe Sun
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
- Qingdao Institute of Bioenergy and Bioprocess Technology, The Chinese Academy of Sciences, Qingdao, 266101, China
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuhong Zheng
- Jilin Academy of Agricultural Sciences, China Agricultural Science and Technology Northeast Innovation Center, Changchun, 130033, China
| | - Yongguo Xue
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Yuhuan Fan
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaofei Ma
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Yujia Ji
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Gaoyuan Liu
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaoming Zhang
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
| | - Yang Li
- Depatment of Environmental and Plant Biology, Ohio University, Athens, 45701, Ohio, USA
| | - Shuming Wang
- Jilin Academy of Agricultural Sciences, China Agricultural Science and Technology Northeast Innovation Center, Changchun, 130033, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, The Chinese Academy of Sciences, Beijing, 100101, China
| | - Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, 150030, China
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2
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Fang C, Sun Z, Li S, Su T, Wang L, Dong L, Li H, Li L, Kong L, Yang Z, Lin X, Zatybekov A, Liu B, Kong F, Lu S. Subfunctionalisation and self-repression of duplicated E1 homologues finetunes soybean flowering and adaptation. Nat Commun 2024; 15:6184. [PMID: 39039090 PMCID: PMC11263555 DOI: 10.1038/s41467-024-50623-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 07/17/2024] [Indexed: 07/24/2024] Open
Abstract
Soybean is a photoperiod-sensitive staple crop. Its photoperiodic flowering has major consequences for latitudinal adaptation and grain yield. Here, we identify and characterise a flowering locus named Time of flower 4b (Tof4b), which encodes E1-Like b (E1Lb), a homologue of the key soybean floral repressor E1. Tof4b protein physically associates with the promoters of two FLOWERING LOCUS T (FT) genes to repress their transcription and delay flowering to impart soybean adaptation to high latitudes. Three E1 homologues undergo subfunctionalisation and show differential subcellular localisation. Moreover, they all possess self-repression capability and each suppresses the two homologous counterparts. Subfunctionalisation and the transcriptional regulation of E1 genes collectively finetune flowering time and high-latitude adaptation in soybean. We propose a model for the functional fate of the three E1 genes after the soybean whole-genome duplication events, refine the molecular mechanisms underlying high-latitude adaption, and provide a potential molecular-breeding resource.
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Affiliation(s)
- Chao Fang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhihui Sun
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Shichen Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Tong Su
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Lingshuang Wang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Lidong Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Haiyang Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Lanxin Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Lingping Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Zhiquan Yang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Xiaoya Lin
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Alibek Zatybekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Baohui Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China.
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China.
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China.
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China.
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.
| | - Sijia Lu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China.
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3
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Zhao X, Li H, Wang L, Wang J, Huang Z, Du H, Li Y, Yang J, He M, Cheng Q, Lin X, Liu B, Kong F. A critical suppression feedback loop determines soybean photoperiod sensitivity. Dev Cell 2024; 59:1750-1763.e4. [PMID: 38688276 DOI: 10.1016/j.devcel.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 02/07/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
Photoperiod sensitivity is crucial for soybean flowering, adaptation, and yield. In soybean, photoperiod sensitivity centers around the evening complex (EC) that regulates the transcriptional level of the core transcription factor E1, thereby regulating flowering. However, little is known about the regulation of the activity of EC. Our study identifies how E2/GIGANTEA (GI) and its homologs modulate photoperiod sensitivity through interactions with the EC. During long days, E2 interacts with the blue-light receptor flavin-binding, kelch repeat, F box 1 (FKF1), leading to the degradation of J/ELF3, an EC component. EC also suppresses E2 expression by binding to its promoter. This interplay forms a photoperiod regulatory loop, maintaining sensitivity to photoperiod. Disruption of this loop leads to losing sensitivity, affecting soybean's adaptability and yield. Understanding this loop's dynamics is vital for molecular breeding to reduce soybean's photoperiod sensitivity and develop cultivars with better adaptability and higher yields, potentially leading to the creation of photoperiod-insensitive varieties for broader agricultural applications.
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Affiliation(s)
- Xiaohui Zhao
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Haiyang Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Lingshuang Wang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Jianhao Wang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China; Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zerong Huang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Haiping Du
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Yaru Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Jiahui Yang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Milan He
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Qun Cheng
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Xiaoya Lin
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
| | - Baohui Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
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4
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Rychel-Bielska S, Książkiewicz M, Kurasiak-Popowska D, Tomkowiak A, Bielski W, Weigt D, Niemann J, Surma A, Kozak B, Nawracała J. Molecular selection of soybean towards adaptation to Central European agroclimatic conditions. J Appl Genet 2024:10.1007/s13353-024-00889-6. [PMID: 38954397 DOI: 10.1007/s13353-024-00889-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/03/2024] [Accepted: 06/20/2024] [Indexed: 07/04/2024]
Abstract
Europe is highly dependent on soybean meal imports and anticipates an increase of domestic plant protein production. Ongoing climate change resulted in northward shift of plant hardiness zones, enabling spring-sowing of freezing-sensitive crops, including soybean. However, it requires efficient reselection of germplasm adapted to relatively short growing season and long-day photoperiod. In the present study, a PCR array has been implemented, targeting early maturity (E1-E4, E7, E9, and E10), pod shattering (qPHD1), and growth determination (Dt1) genes. This array was optimized for routine screening of soybean diversity panel (204 accessions), subjected to the 2018-2020 survey of phenology, morphology, and yield-related traits in a potential cultivation region in Poland. High broad-sense heritability (0.84-0.88) was observed for plant height, thousand grain weight, maturity date, and the first pod height. Significant positive correlations were identified between the number of seeds and pods per plant, between these two traits and seed yield per plant as well as between flowering, maturity, plant height, and first pod height. PCR array genotyping revealed high genetic diversity, yielding 98 allelic combinations. The most remarkable correlations were identified between flowering and E7 or E1, between maturity and E4 or E7 and between plant height and Dt1 or E4. The study demonstrated high applicability of this PCR array for molecular selection of soybean towards adaptation to Central Europe, designating recessive qPHD1 and dominant Dt1, E3, and E4 alleles as major targets to align soybean growth season requirements with the length of the frost-free period, improve plant performance, and increase yield.
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Affiliation(s)
- Sandra Rychel-Bielska
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, 50-363, Wrocław, Poland
| | - Michał Książkiewicz
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznań, Poland.
| | - Danuta Kurasiak-Popowska
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, 60-632, Poznań, Poland
| | - Agnieszka Tomkowiak
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, 60-632, Poznań, Poland
| | - Wojciech Bielski
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznań, Poland
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, 60-632, Poznań, Poland
| | - Dorota Weigt
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, 60-632, Poznań, Poland
| | - Janetta Niemann
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, 60-632, Poznań, Poland
| | - Anna Surma
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznań, Poland
| | - Bartosz Kozak
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, 50-363, Wrocław, Poland
| | - Jerzy Nawracała
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, 60-632, Poznań, Poland
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5
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Shi K, Dong H, Du H, Li Y, Zhou L, Liang C, Şakiroğlu M, Wang Z. The chromosome-level assembly of the wild diploid alfalfa genome provides insights into the full landscape of genomic variations between cultivated and wild alfalfa. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1757-1772. [PMID: 38288521 PMCID: PMC11123407 DOI: 10.1111/pbi.14300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 11/22/2023] [Accepted: 01/15/2024] [Indexed: 05/25/2024]
Abstract
Alfalfa (Medicago sativa L.) is one of the most important forage legumes in the world, including autotetraploid (M. sativa ssp. sativa) and diploid alfalfa (M. sativa ssp. caerulea, progenitor of autotetraploid alfalfa). Here, we reported a high-quality genome of ZW0012 (diploid alfalfa, 769 Mb, contig N50 = 5.5 Mb), which was grouped into the Northern group in population structure analysis, suggesting that our genome assembly filled a major gap among the members of M. sativa complex. During polyploidization, large phenotypic differences occurred between diploids and tetraploids, and the genetic information underlying its massive phenotypic variations remains largely unexplored. Extensive structural variations (SVs) were identified between ZW0012 and XinJiangDaYe (an autotetraploid alfalfa with released genome). We identified 71 ZW0012-specific PAV genes and 1296 XinJiangDaYe-specific PAV genes, mainly involved in defence response, cell growth, and photosynthesis. We have verified the positive roles of MsNCR1 (a XinJiangDaYe-specific PAV gene) in nodulation using an Agrobacterium rhizobia-mediated transgenic method. We also demonstrated that MsSKIP23_1 and MsFBL23_1 (two XinJiangDaYe-specific PAV genes) regulated leaf size by transient overexpression and virus-induced gene silencing analysis. Our study provides a high-quality reference genome of an important diploid alfalfa germplasm and a valuable resource of variation landscape between diploid and autotetraploid, which will facilitate the functional gene discovery and molecular-based breeding for the cultivars in the future.
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Affiliation(s)
- Kun Shi
- College of Grassland Science and TechnologycChina Agricultural UniversityBeijingChina
| | - Hongbin Dong
- College of Grassland Science and TechnologycChina Agricultural UniversityBeijingChina
| | - Huilong Du
- School of Life Sciences, Institute of Life Sciences and Green DevelopmentHebei UniversityBaodingChina
| | - Yuxian Li
- School of Life SciencesNorth China University of Science and TechnologyTangshanChina
| | - Le Zhou
- College of Grassland Science and TechnologycChina Agricultural UniversityBeijingChina
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Muhammet Şakiroğlu
- Department of BioengineeringAdana AlparslanTürkeş Science and Technology UniversityAdanaTurkey
| | - Zan Wang
- College of Grassland Science and TechnologycChina Agricultural UniversityBeijingChina
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6
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Lin X, Yin J, Wang Y, Yao J, Li QQ, Latzel V, Bossdorf O, Zhang YY. Environment-induced heritable variations are common in Arabidopsis thaliana. Nat Commun 2024; 15:4615. [PMID: 38816460 PMCID: PMC11139905 DOI: 10.1038/s41467-024-49024-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
Parental or ancestral environments can induce heritable phenotypic changes, but whether such environment-induced heritable changes are a common phenomenon remains unexplored. Here, we subject 14 genotypes of Arabidopsis thaliana to 10 different environmental treatments and observe phenotypic and genome-wide gene expression changes over four successive generations. We find that all treatments caused heritable phenotypic and gene expression changes, with a substantial proportion stably transmitted over all observed generations. Intriguingly, the susceptibility of a genotype to environmental inductions could be predicted based on the transposon abundance in the genome. Our study thus challenges the classic view that the environment only participates in the selection of heritable variation and suggests that the environment can play a significant role in generating of heritable variations.
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Affiliation(s)
- Xiaohe Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Junjie Yin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Yifan Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Jing Yao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA, USA
| | - Vit Latzel
- Institute of Botany of the CAS, Zamek 1, 252 43, Pruhonice, Czech Republic
| | - Oliver Bossdorf
- Institute of Evolution & Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China.
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7
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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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8
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Wang J, Xu X, Wang P, Zhang L, Liu L, Liu L, Wu T, Song W, Yuan S, Jiang B, Hou W, Wu C, Sun S, Yu L, Han T. Floral-promoting GmFT homologs trigger photoperiodic after-effects: An important mechanism for early-maturing soybean varieties to regulate reproductive development and adapt to high latitudes. PLANT, CELL & ENVIRONMENT 2024; 47:1656-1667. [PMID: 38282250 DOI: 10.1111/pce.14833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
Soybean (Glycine max) is a typical short-day plant, but has been widely cultivated in high-latitude long-day (LD) regions because of the development of early-maturing genotypes which are photoperiod-insensitive. However, some early-maturing varieties exhibit significant responses to maturity under different daylengths but not for flowering, depicting an evident photoperiodic after-effect, a poorly understood mechanism. In this study, we investigated the postflowering responses of 11 early-maturing soybean varieties to various preflowering photoperiodic treatments. We confirmed that preflowering SD conditions greatly promoted maturity and other postflowering developmental stages. Soybean homologs of FLOWERING LOCUS T (FT), including GmFT2a, GmFT3a, GmFT3b and GmFT5a, were highly accumulated in leaves under preflowering SD treatment. More importantly, they maintained a high expression level after flowering even under LD conditions. E1 RNAi and GmFT2a overexpression lines showed extremely early maturity regardless of preflowering SD and LD treatments due to constitutively high levels of floral-promoting GmFT homolog expression throughout their life cycle. Collectively, our data indicate that high and stable expression of floral-promoting GmFT homologs play key roles in the maintenance of photoperiodic induction to promote postflowering reproductive development, which confers early-maturing varieties with appropriate vegetative growth and shortened reproductive growth periods for adaptation to high latitudes.
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Affiliation(s)
- Junya Wang
- Key Laboratory of Plant Biology, College of Life Science and Technology, Harbin Normal University, Harbin, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Xu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Peiguo Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixin Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lifeng Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Luping Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tingting Wu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenwen Song
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shan Yuan
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bingjun Jiang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wensheng Hou
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cunxiang Wu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shi Sun
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijie Yu
- Key Laboratory of Plant Biology, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Tianfu Han
- Key Laboratory of Plant Biology, College of Life Science and Technology, Harbin Normal University, Harbin, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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9
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Fang C, Du H, Wang L, Liu B, Kong F. Mechanisms underlying key agronomic traits and implications for molecular breeding in soybean. J Genet Genomics 2024; 51:379-393. [PMID: 37717820 DOI: 10.1016/j.jgg.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/05/2023] [Accepted: 09/05/2023] [Indexed: 09/19/2023]
Abstract
Soybean (Glycine max [L.] Merr.) is an important crop that provides protein and vegetable oil for human consumption. As soybean is a photoperiod-sensitive crop, its cultivation and yield are limited by the photoperiodic conditions in the field. In contrast to other major crops, soybean has a special plant architecture and a special symbiotic nitrogen fixation system, representing two unique breeding directions. Thus, flowering time, plant architecture, and symbiotic nitrogen fixation are three critical or unique yield-determining factors. This review summarizes the progress made in our understanding of these three critical yield-determining factors in soybean. Meanwhile, we propose potential research directions to increase soybean production, discuss the application of genomics and genomic-assisted breeding, and explore research directions to address future challenges, particularly those posed by global climate changes.
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Affiliation(s)
- Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Haiping Du
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Lingshuang Wang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong 510006, China.
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10
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Gélinas Bélanger J, Copley TR, Hoyos-Villegas V, O'Donoughue L. Dissection of the E8 locus in two early maturing Canadian soybean populations. FRONTIERS IN PLANT SCIENCE 2024; 15:1329065. [PMID: 38390301 PMCID: PMC10881665 DOI: 10.3389/fpls.2024.1329065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/15/2024] [Indexed: 02/24/2024]
Abstract
Soybean [Glycine max (L.) Merr.] is a short-day crop for which breeders want to expand the cultivation range to more northern agro-environments by introgressing alleles involved in early reproductive traits. To do so, we investigated quantitative trait loci (QTL) and expression quantitative trait loci (eQTL) regions comprised within the E8 locus, a large undeciphered region (~7.0 Mbp to 44.5 Mbp) associated with early maturity located on chromosome GM04. We used a combination of two mapping algorithms, (i) inclusive composite interval mapping (ICIM) and (ii) genome-wide composite interval mapping (GCIM), to identify major and minor regions in two soybean populations (QS15524F2:F3 and QS15544RIL) having fixed E1, E2, E3, and E4 alleles. Using this approach, we identified three main QTL regions with high logarithm of the odds (LODs), phenotypic variation explained (PVE), and additive effects for maturity and pod-filling within the E8 region: GM04:16,974,874-17,152,230 (E8-r1); GM04:35,168,111-37,664,017 (E8-r2); and GM04:41,808,599-42,376,237 (E8-r3). Using a five-step variant analysis pipeline, we identified Protein far-red elongated hypocotyl 3 (Glyma.04G124300; E8-r1), E1-like-a (Glyma.04G156400; E8-r2), Light-harvesting chlorophyll-protein complex I subunit A4 (Glyma.04G167900; E8-r3), and Cycling dof factor 3 (Glyma.04G168300; E8-r3) as the most promising candidate genes for these regions. A combinatorial eQTL mapping approach identified significant regulatory interactions for 13 expression traits (e-traits), including Glyma.04G050200 (Early flowering 3/E6 locus), with the E8-r3 region. Four other important QTL regions close to or encompassing major flowering genes were also detected on chromosomes GM07, GM08, and GM16. In GM07:5,256,305-5,404,971, a missense polymorphism was detected in the candidate gene Glyma.07G058200 (Protein suppressor of PHYA-105). These findings demonstrate that the locus known as E8 is regulated by at least three distinct genomic regions, all of which comprise major flowering genes.
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Affiliation(s)
- Jérôme Gélinas Bélanger
- Centre de recherche sur les grains (CÉROM) Inc., St-Mathieu-de-Beloeil, QC, Canada
- Department of Plant Science, McGill University, Montréal, QC, Canada
| | - Tanya Rose Copley
- Centre de recherche sur les grains (CÉROM) Inc., St-Mathieu-de-Beloeil, QC, Canada
| | | | - Louise O'Donoughue
- Centre de recherche sur les grains (CÉROM) Inc., St-Mathieu-de-Beloeil, QC, Canada
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11
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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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12
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Nakashima K, Yuhazu M, Mikuriya S, Kasai M, Abe J, Taneda A, Kanazawa A. Frequency of cytosine methylation in the adjacent regions of soybean retrotransposon SORE-1 depends on chromosomal location. Genome 2024; 67:1-12. [PMID: 37746933 DOI: 10.1139/gen-2023-0044] [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: 09/26/2023]
Abstract
Mobilization of transposable elements (TEs) is suppressed by epigenetic mechanisms involving cytosine methylation. However, few studies have focused on clarifying relationships between epigenetic influences of TEs on the adjacent DNA regions and time after insertion of TEs into the genome and/or their chromosomal location. Here we addressed these issues using soybean retrotransposon SORE-1. We analyzed SORE-1, inserted in exon 1 of the GmphyA2 gene, one of the newest insertions in this family so far identified. Cytosine methylation was detected in this element but was barely present in the adjacent regions. These results were correlated, respectively, with the presence and absence of the production of short interfering RNAs. Cytosine methylation profiles of 74 SORE-1 elements in the Williams 82 reference genome indicated that methylation frequency in the adjacent regions of SORE-1 was profoundly higher in pericentromeric regions than in euchromatic chromosome arms and was only weakly correlated with the length of time after insertion into the genome. Notably, the higher level of methylation in the 5' adjacent regions of SORE-1 coincided with the presence of repetitive elements in pericentromeric regions. Together, these results suggest that epigenetic influence of SORE-1 on the adjacent regions is influenced by its location on the chromosome.
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Affiliation(s)
- Kenta Nakashima
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Mashiro Yuhazu
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Shun Mikuriya
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Megumi Kasai
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Akito Taneda
- Graduate School of Science and Technology, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Akira Kanazawa
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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13
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Su Q, Chen L, Cai Y, Wang L, Chen Y, Zhang J, Liu L, Zhang Y, Yuan S, Gao Y, Sun S, Han T, Hou W. The FLOWERING LOCUS T 5b positively regulates photoperiodic flowering and improves the geographical adaptation of soybean. PLANT, CELL & ENVIRONMENT 2024; 47:246-258. [PMID: 37830787 DOI: 10.1111/pce.14739] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/25/2023] [Accepted: 10/05/2023] [Indexed: 10/14/2023]
Abstract
Plants can sense the photoperiod to flower at the right time. As a sensitive short-day crop, soybean (Glycine max) flowering varies greatly depending on photoperiods, affecting yields. Adaptive changes in soybeans rely on variable genetic loci such as E1 and FLOWERING LOCUS T orthologs. However, the precise coordination and control of these molecular components remain largely unknown. In this study, we demonstrate that GmFT5b functions as a crucial factor for soybean flowering. Overexpressed or mutated GmFT5b resulted in significantly early or later flowering, altering expression profiles for several downstream flowering-related genes under a long-day photoperiod. GmFT5b interacts with the transcription factor GmFDL15, suggesting transcriptional tuning of flowering time regulatory genes via the GmFT5b/GmFDL15 complex. Notably, GmFT5a partially compensated for GmFT5b function, as ft5a ft5b double mutants exhibited an enhanced late-flowering phenotype. Association mapping revealed that GmFT5b was associated with flowering time, maturity, and geographical distribution of soybean accessions, all associated with the E1 locus. Therefore, GmFT5b is a valuable target for enhancing regional adaptability. Natural variants or multiple mutants in this region can be utilized to generate optimized soybean varieties with precise flowering times.
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Affiliation(s)
- Qiang Su
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Chen
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yupeng Cai
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liwei Wang
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingying Chen
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jialing Zhang
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Luping Liu
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Zhang
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shan Yuan
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Gao
- Syngenta Biotechnology (China) Co., Ltd, Beijing, China
| | - Shi Sun
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianfu Han
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wensheng Hou
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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14
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Souza R, Rouf Mian MA, Vaughn JN, Li Z. Introgression of a Danbaekkong high-protein allele across different genetic backgrounds in soybean. FRONTIERS IN PLANT SCIENCE 2023; 14:1308731. [PMID: 38173927 PMCID: PMC10761420 DOI: 10.3389/fpls.2023.1308731] [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: 10/07/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024]
Abstract
Soybean meal is a major component of livestock feed due to its high content and quality of protein. Understanding the genetic control of protein is essential to develop new cultivars with improved meal protein. Previously, a genomic region on chromosome 20 significantly associated with elevated protein content was identified in the cultivar Danbaekkong. The present research aimed to introgress the Danbaekkong high-protein allele into elite lines with different genetic backgrounds by developing and deploying robust DNA markers. A multiparent population consisting of 10 F5-derived populations with a total of 1,115 recombinant inbred lines (RILs) was developed using "Benning HP" as the donor parent of the Danbaekkong high-protein allele. A new functional marker targeting the 321-bp insertion in the gene Glyma.20g085100 was developed and used to track the Danbaekkong high-protein allele across the different populations and enable assessment of its effect and stability. Across all populations, the high-protein allele consistently increased the content, with an increase of 3.3% in seed protein. A total of 103 RILs were selected from the multiparent population for yield testing in five environments to assess the impact of the high-protein allele on yield and to enable the selection of new breeding lines with high protein and high yield. The results indicated that the high-protein allele impacts yield negatively in general; however, it is possible to select high-yielding lines with high protein content. An analysis of inheritance of the Chr 20 high-protein allele in Danbaekkong indicated that it originated from a Glycine soja line (PI 163453) and is the same as other G. soja lines studied. A survey of the distribution of the allele across 79 G. soja accessions and 35 Glycine max ancestors of North American soybean cultivars showed that the high-protein allele is present in all G. soja lines evaluated but not in any of the 35 North American soybean ancestors. These results demonstrate that G. soja accessions are a valuable source of favorable alleles for improvement of protein composition.
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Affiliation(s)
- Renan Souza
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - M. A. Rouf Mian
- Soybean and Nitrogen Fixation Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Raleigh, NC, United States
| | - Justin N. Vaughn
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
- Genomics and Bioinformatics Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Athens, GA, United States
| | - Zenglu Li
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
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15
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Wang Z, Xing S, Li M, Zhang Q, Yang Q, Xu P, Song B, Shang P, Yang M, Du C, Chen J, Liu S, Zhang S. Soybean WRINKLED1 protein GmWRI1a promotes flowering under long-day conditions via regulating expressions of flowering-related genes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 337:111865. [PMID: 37696474 DOI: 10.1016/j.plantsci.2023.111865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
Flowering time is an important agronomic character that influences the adaptability and yield of soybean [Glycine max (L.) Merrill]. WRINKLED 1 (WRI1) plays an important regulatory role in plant growth and development. In this study, we found that the expression of GmWIR1a could be induced by long days. Compared with the wild type, transgenic soybean overexpressing GmWRI1a showed earlier flowering and maturity under long days but no significant changes under short days. Overexpression of GmWRI1a led to up-regulated expression of genes involved in the regulation of flowering time. The GmWRI1a protein was able to directly bind to the promoter regions of GmAP1, GmFUL1a, GmFUL2 and up-regulated their expression. GmCOL3 was identified by yeast one-hybrid library screening using the GmWRI1a promoter as bait. GmCOL3 was revealed to be a nucleus-localized protein that represses the transcription of GmWRI1a. Expression of GmCOL3 was induced by short days. Taken together, the results show that overexpression of GmWRI1a promotes flowering under long days by promoting the transcriptional activity of flowering-related genes in soybean, and that GmCOL3 binds to the GmWRI1a promoter and directly down-regulates its transcription. This discovery reveals a new function for GmWRI1a, which regulates flowering and maturity in soybean.
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Affiliation(s)
- Zhikun Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Siqi Xing
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Meng Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Qingyan Zhang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Qiang Yang
- Center for Agricultural Technology, Northeast Institute of Geography and Agroecology, CAS, Harbin, China
| | - Pengfei Xu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Bo Song
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Ping Shang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Mingming Yang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Changhuan Du
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Jihan Chen
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China
| | - Shanshan Liu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China.
| | - Shuzhen Zhang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education/Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture, Soybean Science Research Institute, Northeast Agricultural University, Harbin, China.
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16
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Qin C, Li YH, Li D, Zhang X, Kong L, Zhou Y, Lyu X, Ji R, Wei X, Cheng Q, Jia Z, Li X, Wang Q, Wang Y, Huang W, Yang C, Liu L, Wang X, Xing G, Hu G, Shan Z, Wang R, Li H, Li H, Zhao T, Liu J, Lu Y, Hu X, Kong F, Qiu LJ, Liu B. PH13 improves soybean shade traits and enhances yield for high-density planting at high latitudes. Nat Commun 2023; 14:6813. [PMID: 37884530 PMCID: PMC10603158 DOI: 10.1038/s41467-023-42608-5] [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: 03/24/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
Shading in combination with extended photoperiods can cause exaggerated stem elongation (ESE) in soybean, leading to lodging and reduced yields when planted at high-density in high-latitude regions. However, the genetic basis of plant height in adaptation to these regions remains unclear. Here, through a genome-wide association study, we identify a plant height regulating gene on chromosome 13 (PH13) encoding a WD40 protein with three main haplotypes in natural populations. We find that an insertion of a Ty1/Copia-like retrotransposon in the haplotype 3 leads to a truncated PH13H3 with reduced interaction with GmCOP1s, resulting in accumulation of STF1/2, and reduced plant height. In addition, PH13H3 allele has been strongly selected for genetic improvement at high latitudes. Deletion of both PH13 and its paralogue PHP can prevent shade-induced ESE and allow high-density planting. This study provides insights into the mechanism of shade-resistance and offers potential solutions for breeding high-yielding soybean cultivar for high-latitude regions.
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Affiliation(s)
- Chao Qin
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ying-Hui Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Delin Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xueru Zhang
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Lingping Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Yonggang Zhou
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, China
| | - Xiangguang Lyu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ronghuan Ji
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuzhi Wei
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qican Cheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiwei Jia
- Longping Biotechnology (Hainan) Co., Ltd, Yazhou-Bay Science and Technology City, Sanya, Hainan, 572025, China
| | - Xiaojiao Li
- Longping Biotechnology (Hainan) Co., Ltd, Yazhou-Bay Science and Technology City, Sanya, Hainan, 572025, China
| | - Qiang Wang
- Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, 150086, China
| | - Yueqiang Wang
- Jilin Academy of Agricultural Sciences, Changchun, Jilin, 130033, China
| | - Wen Huang
- Tonghua Academy of Agricultural Sciences, Tonghua, Jilin, 135007, China
| | - Chunyan Yang
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, 050035, China
| | - Like Liu
- Liaocheng University, Liaocheng, Shandong, 252000, China
| | - Xing Wang
- Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou, Jiangsu, 221131, China
| | - Guangnan Xing
- Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Guoyu Hu
- Anhui Academy of Agricultural Sciences, Hefei, Anhui, 230041, China
| | - Zhihui Shan
- Oil Crops Research Institute, Chinese Academy of Agriculture Sciences, Wuhan, Hubei, 430062, China
| | - Ruizhen Wang
- Crops Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, 330200, China
| | - Haiyan Li
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, China
| | - Hongyu Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tao Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jun Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuping Lu
- Longping Biotechnology (Hainan) Co., Ltd, Yazhou-Bay Science and Technology City, Sanya, Hainan, 572025, China
| | - Xiping Hu
- Beidahuang KenFeng Seed Co., Ltd, Binxi Economic Development Zone, Harbin, Heilongjiang, 150090, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong, 510006, China.
| | - Li-Juan Qiu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Bin Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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17
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Kiseleva AA, Leonova IN, Ageeva EV, Likhenko IE, Salina EA. Identification of genetic loci for early maturity in spring bread wheat using the association analysis and gene dissection. PeerJ 2023; 11:e16109. [PMID: 37842052 PMCID: PMC10569184 DOI: 10.7717/peerj.16109] [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: 05/31/2023] [Accepted: 08/25/2023] [Indexed: 10/17/2023] Open
Abstract
Background Early maturity in spring bread wheat is highly desirable in the regions where it enables the plants to evade high temperatures and plant pathogens at the end of the growing season. Methods To reveal the genetic loci responsible for the maturity time association analysis was carried out based on phenotyping for an 11-year period and high-throughput SNP genotyping of a panel of the varieties contrasting for this trait. The expression of candidate genes was verified using qPCR. The association between the SNP markers and the trait was validated using the biparental F2:3 population. Results Our data showed that under long-day conditions, the period from seedling to maturity is mostly influenced by the time from heading to maturity, rather than the heading time. The QTLs associated with the trait were located on 2A, 3B, 4A, 5B, 7A and 7B chromosomes with the 7BL locus being the most significant and promising for its SNPs accelerated the maturity time by about 9 days. Gene dissection in this locus detected a number of candidates, the best being TraesCS7B02G391800 (bZIP9) and TraesCS7B02G412200 (photosystem II reaction center). The two genes are predominantly expressed in the flag leaf while flowering. The effect of the SNPs was verified in F2:3 population and confirmed the association of the 4A, 5B and 7BL loci with the maturity time.
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Affiliation(s)
- Antonina A. Kiseleva
- Laboratory of Plant Molecular Genetics and Cytogenetics, The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Irina N. Leonova
- Laboratory of Plant Molecular Genetics and Cytogenetics, The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena V. Ageeva
- Laboratory of Field Crop Breeding and Seed Industry, Siberian Research Institute of Plant Production and Breeding, Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Ivan E. Likhenko
- Laboratory of Field Crop Breeding and Seed Industry, Siberian Research Institute of Plant Production and Breeding, Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena A. Salina
- Laboratory of Plant Molecular Genetics and Cytogenetics, The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
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18
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Wang X, Hu Y, Wang W. Comparative Analysis of Circadian Transcriptomes Reveals Circadian Characteristics between Arabidopsis and Soybean. PLANTS (BASEL, SWITZERLAND) 2023; 12:3344. [PMID: 37836084 PMCID: PMC10574400 DOI: 10.3390/plants12193344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 10/15/2023]
Abstract
The circadian clock, an endogenous timing system, exists in nearly all organisms on Earth. The plant circadian clock has been found to be intricately linked with various essential biological activities. Extensive studies of the plant circadian clock have yielded valuable applications. However, the distinctions of circadian clocks in two important plant species, Arabidopsis thaliana and Glycine max (soybean), remain largely unexplored. This study endeavors to address this gap by conducting a comprehensive comparison of the circadian transcriptome profiles of Arabidopsis and soybean to uncover their distinct circadian characteristics. Utilizing non-linear regression fitting (COS) integrated with weights, we identified circadian rhythmic genes within both organisms. Through an in-depth exploration of circadian parameters, we unveiled notable differences between Arabidopsis and soybean. Furthermore, our analysis of core circadian clock genes shed light on the distinctions in central oscillators between these two species. Additionally, we observed that the homologous genes of Arabidopsis circadian clock genes in soybean exert a significant influence on the regulation of flowering and maturity of soybean. This phenomenon appears to stem from shifts in circadian parameters within soybean genes. These findings highlight contrasting biological activities under circadian regulation in Arabidopsis and soybean. This study not only underscores the distinctive attributes of these species, but also offers valuable insights for further scrutiny into the soybean circadian clock and its potential applications.
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Affiliation(s)
- Xingwei Wang
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (X.W.); (Y.H.)
- Center for Life Sciences, Beijing 100871, China
| | - Yanfei Hu
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (X.W.); (Y.H.)
- Center for Life Sciences, Beijing 100871, China
| | - Wei Wang
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (X.W.); (Y.H.)
- Center for Life Sciences, Beijing 100871, China
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19
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Zheng N, Guo Y, Wang S, Zhang H, Wang L, Gao Y, Xu M, Wang W, Liu W, Yang W. Identification of E1-E4 allele combinations and ecological adaptability of soybean varieties from different geographical origins in China. FRONTIERS IN PLANT SCIENCE 2023; 14:1222755. [PMID: 37731975 PMCID: PMC10507326 DOI: 10.3389/fpls.2023.1222755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/17/2023] [Indexed: 09/22/2023]
Abstract
The duration of soybean growth and development is regulated by E1-E4 allele genes, which form the basis for ecological adaptation related to biomass accumulation, flowering and pod formation, maturation, and yield. To elucidate the effects of different combinations of E1-E4 allele genes on soybean ecological adaptation, this study conducted competitive allele-specific PCR (KASP) analysis and photoperiod gene typing on 101 main soybean cultivars from different latitudes in China. The ecological adaptation of these cultivars in Sichuan was also investigated. The results showed that within a certain range (60-95 days), soybean varieties with a genotype combination of E1/e2-ns/E3/E4 exhibited a longer growth period and demonstrated higher biomass and yield, displaying overall better performance. These varieties showed strong ecological adaptation in the Chengdu Plain region and are suitable for introduction in similar low to mid-latitude areas like the Chengdu Plain (30°N~32°N). Conversely, soybean varieties carrying a higher number of recessive alleles of E1-E4 are not suitable for introduction in this region.
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Affiliation(s)
- Naiwen Zheng
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Yukai Guo
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Siyu Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Han Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Li Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Yang Gao
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Mei Xu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Wenyan Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Weiguo Liu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Chengdu, China
| | - Wenyu Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China, Ministry of Agriculture, Chengdu, China
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20
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Li B, Gschwend AR. Vitis labrusca genome assembly reveals diversification between wild and cultivated grapevine genomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1234130. [PMID: 37719220 PMCID: PMC10501149 DOI: 10.3389/fpls.2023.1234130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
Wild grapevines are important genetic resources in breeding programs to confer adaptive fitness traits and unique fruit characteristics, but the genetics underlying these traits, and their evolutionary origins, are largely unknown. To determine the factors that contributed to grapevine genome diversification, we performed comprehensive intragenomic and intergenomic analyses with three cultivated European (including the PN40024 reference genome) and two wild North American grapevine genomes, including our newly released Vitis labrusca genome. We found the heterozygosity of the cultivated grapevine genomes was twice as high as the wild grapevine genomes studied. Approximately 30% of V. labrusca and 48% of V. vinifera Chardonnay genes were heterozygous or hemizygous and a considerable number of collinear genes between Chardonnay and V. labrusca had different gene zygosity. Our study revealed evidence that supports gene gain-loss events in parental genomes resulted in the inheritance of hemizygous genes in the Chardonnay genome. Thousands of segmental duplications supplied source material for genome-specific genes, further driving diversification of the genomes studied. We found an enrichment of recently duplicated, adaptive genes in similar functional pathways, but differential retention of environment-specific adaptive genes within each genome. For example, large expansions of NLR genes were discovered in the two wild grapevine genomes studied. Our findings support variation in transposable elements contributed to unique traits in grapevines. Our work revealed gene zygosity, segmental duplications, gene gain-and-loss variations, and transposable element polymorphisms can be key driving forces for grapevine genome diversification.
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Affiliation(s)
| | - Andrea R. Gschwend
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
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21
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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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22
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Yerzhebayeva R, Didorenko S, Amangeldiyeva A, Daniyarova A, Mazkirat S, Zinchenko A, Shavrukov Y. Marker-Assisted Selection for Early Maturing E Loci in Soybean Yielded Prospective Breeding Lines for High Latitudes of Northern Kazakhstan. Biomolecules 2023; 13:1146. [PMID: 37509181 PMCID: PMC10377072 DOI: 10.3390/biom13071146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The photoperiodic sensitivity of soybean (Glycine max L.) is one of the limiting factors affecting plant growth and yield. At higher latitudes, early flowering and maturity with neutral reaction to photoperiods are required for adaptation of soybean plants to long-day conditions. Currently, the production and distribution of new varieties of soybeans adapted to widespread agricultural regions in northern Kazakhstan is in strong demand. Eleven soybean hybrid populations were obtained from crosses between 17 parents with four maturity groups, MG 000, 00, 0, and I. Marker-assisted selection (MAS) was assessed for suitable SSR markers and successfully applied for genes E1, E3, E4, and E7, targeting homozygous genotypes with recessive alleles. The identified and selected genotypes were propagated and tested in the conditions of 53° N latitude in the Kostanay region of northern Kazakhstan. Finally, 20 early maturing F4 breeding lines were identified and developed with genotypes e1 e3 E4 e7, e1 E3 E4 e7, and e1 E3 e4 e7, all completing their growth period within 92-102 days. These breeding lines were developed by MAS and should provide very prospective superior varieties of soybean for northern Kazakhstan through a strategy that may be very helpful to other countries with high latitudes.
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Affiliation(s)
- Raushan Yerzhebayeva
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan
| | - Svetlana Didorenko
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan
| | - Aigul Amangeldiyeva
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan
| | - Aliya Daniyarova
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan
| | - Shynar Mazkirat
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan
| | - Alyona Zinchenko
- Breeding Station 'Zarechnoe', Kostanay District, Zarechnoe 111108, Kazakhstan
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia
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23
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Lukanda MM, Dramadri IO, Adjei EA, Badji A, Arusei P, Gitonga HW, Wasswa P, Edema R, Ochwo-Ssemakula M, Tukamuhabwa P, Muthuri HM, Tusiime G. Genome-Wide Association Analysis for Resistance to Coniothyrium glycines Causing Red Leaf Blotch Disease in Soybean. Genes (Basel) 2023; 14:1271. [PMID: 37372451 DOI: 10.3390/genes14061271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Soybean is a high oil and protein-rich legume with several production constraints. Globally, several fungi, viruses, nematodes, and bacteria cause significant yield losses in soybean. Coniothyrium glycines (CG), the causal pathogen for red leaf blotch disease, is the least researched and causes severe damage to soybean. The identification of resistant soybean genotypes and mapping of genomic regions associated with resistance to CG is critical for developing improved cultivars for sustainable soybean production. This study used single nucleotide polymorphism (SNP) markers generated from a Diversity Arrays Technology (DArT) platform to conduct a genome-wide association (GWAS) analysis of resistance to CG using 279 soybean genotypes grown in three environments. A total of 6395 SNPs was used to perform the GWAS applying a multilocus model Fixed and random model Circulating Probability Unification (FarmCPU) with correction of the population structure and a statistical test p-value threshold of 5%. A total of 19 significant marker-trait associations for resistance to CG were identified on chromosomes 1, 5, 6, 9, 10, 12, 13, 15, 16, 17, 19, and 20. Approximately 113 putative genes associated with significant markers for resistance to red leaf blotch disease were identified across soybean genome. Positional candidate genes associated with significant SNP loci-encoding proteins involved in plant defense responses and that could be associated with soybean defenses against CG infection were identified. The results of this study provide valuable insight for further dissection of the genetic architecture of resistance to CG in soybean. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving resistance traits in soybean.
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Affiliation(s)
- Musondolya Mathe Lukanda
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
- Faculté des Sciences Agronomiques, Université Catholique du Graben, Butembo P.O. Box 29, Democratic Republic of the Congo
| | - Isaac Onziga Dramadri
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Emmanuel Amponsah Adjei
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
- Council for Scientific and Industrial Research-Savanna Agricultural Research Institute, Tamale P.O. Box TL 52, Ghana
| | - Arfang Badji
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Perpetua Arusei
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
- Department of Biological Sciences, Moi University, Eldoret P.O. Box 3900-30100, Kenya
| | - Hellen Wairimu Gitonga
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Peter Wasswa
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Richard Edema
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Mildred Ochwo-Ssemakula
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Phinehas Tukamuhabwa
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Harun Murithi Muthuri
- Agricultural Research Service Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN 37831, USA
- International Institute of Tropical Agriculture (IITA), ILRI, Nairobi P.O. Box 30709-00100, Kenya
| | - Geoffrey Tusiime
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
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Wang C, Hao X, Liu X, Su Y, Pan Y, Zong C, Wang W, Xing G, He J, Gai J. An Improved Genome-Wide Association Procedure Explores Gene-Allele Constitutions and Evolutionary Drives of Growth Period Traits in the Global Soybean Germplasm Population. Int J Mol Sci 2023; 24:ijms24119570. [PMID: 37298521 DOI: 10.3390/ijms24119570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
In soybeans (Glycine max (L.) Merr.), their growth periods, DSF (days of sowing-to-flowering), and DFM (days of flowering-to-maturity) are determined by their required accumulative day-length (ADL) and active temperature (AAT). A sample of 354 soybean varieties from five world eco-regions was tested in four seasons in Nanjing, China. The ADL and AAT of DSF and DFM were calculated from daily day-lengths and temperatures provided by the Nanjing Meteorological Bureau. The improved restricted two-stage multi-locus genome-wide association study using gene-allele sequences as markers (coded GASM-RTM-GWAS) was performed. (i) For DSF and its related ADLDSF and AATDSF, 130-141 genes with 384-406 alleles were explored, and for DFM and its related ADLDFM and AATDFM, 124-135 genes with 362-384 alleles were explored, in a total of six gene-allele systems. DSF shared more ADL and AAT contributions than DFM. (ii) Comparisons between the eco-region gene-allele submatrices indicated that the genetic adaptation from the origin to the geographic sub-regions was characterized by allele emergence (mutation), while genetic expansion from primary maturity group (MG)-sets to early/late MG-sets featured allele exclusion (selection) without allele emergence in addition to inheritance (migration). (iii) Optimal crosses with transgressive segregations in both directions were predicted and recommended for breeding purposes, indicating that allele recombination in soybean is an important evolutionary drive. (iv) Genes of the six traits were mostly trait-specific involved in four categories of 10 groups of biological functions. GASM-RTM-GWAS showed potential in detecting directly causal genes with their alleles, identifying differential trait evolutionary drives, predicting recombination breeding potentials, and revealing population gene networks.
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Affiliation(s)
- Can Wang
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoshuai Hao
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Xueqin Liu
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanzhu Su
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongpeng Pan
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunmei Zong
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Wubin Wang
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Guangnan Xing
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianbo He
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Junyi Gai
- Soybean Research Institute, MARA National Center for Soybean Improvement, MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
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25
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Jiang L, Wang P, Jia H, Wu T, Yuan S, Jiang B, Sun S, Zhang Y, Wang L, Han T. Haplotype Analysis of GmSGF14 Gene Family Reveals Its Roles in Photoperiodic Flowering and Regional Adaptation of Soybean. Int J Mol Sci 2023; 24:ijms24119436. [PMID: 37298387 DOI: 10.3390/ijms24119436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Flowering time and photoperiod sensitivity are fundamental traits that determine soybean adaptation to a given region or a wide range of geographic environments. The General Regulatory Factors (GRFs), also known as 14-3-3 family, are involved in protein-protein interactions in a phosphorylation-dependent manner, thus regulating ubiquitous biological processes, such as photoperiodic flowering, plant immunity and stress response. In this study, 20 soybean GmSGF14 genes were identified and divided into two categories according to phylogenetic relationships and structural characteristics. Real-time quantitative PCR analysis revealed that GmSGF14g, GmSGF14i, GmSGF14j, GmSGF14k, GmSGF14m and GmSGF14s were highly expressed in all tissues compared to other GmSGF14 genes. In addition, we found that the transcript levels of GmSGF14 family genes in leaves varied significantly under different photoperiodic conditions, indicating that their expression responds to photoperiod. To explore the role of GmSGF14 in the regulation of soybean flowering, the geographical distribution of major haplotypes and their association with flowering time in six environments among 207 soybean germplasms were studied. Haplotype analysis confirmed that the GmSGF14mH4 harboring a frameshift mutation in the 14-3-3 domain was associated with later flowering. Geographical distribution analysis demonstrated that the haplotypes related to early flowering were frequently found in high-latitude regions, while the haplotypes associated with late flowering were mostly distributed in low-latitude regions of China. Taken together, our results reveal that the GmSGF14 family genes play essential roles in photoperiodic flowering and geographical adaptation of soybean, providing theoretical support for further exploring the function of specific genes in this family and varietal improvement for wide adaptability.
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Affiliation(s)
- Liwei Jiang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163316, China
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Peiguo Wang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Hongchang Jia
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- Heihe Branch, Heilongjiang Academy of Agricultural Sciences, Heihe 164399, China
| | - Tingting Wu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Shan Yuan
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Bingjun Jiang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Shi Sun
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Yuxian Zhang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163316, China
| | - Liwei Wang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Tianfu Han
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163316, China
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
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26
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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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27
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Tang Y, Lu S, Fang C, Liu H, Dong L, Li H, Su T, Li S, Wang L, Cheng Q, Liu B, Lin X, Kong F. Diverse flowering responses subjecting to ambient high temperature in soybean under short-day conditions. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:782-791. [PMID: 36578141 PMCID: PMC10037154 DOI: 10.1111/pbi.13996] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/06/2022] [Accepted: 12/17/2022] [Indexed: 06/14/2023]
Abstract
Flowering time is one of important agronomic traits determining the crop yield and affected by high temperature. When facing high ambient temperature, plants often initiate early flowering as an adaptive strategy to escape the stress and ensure successful reproduction. However, here we find opposing ways in the short-day crop soybean to respond to different levels of high temperatures, in which flowering accelerates when temperature changes from 25 to 30 °C, but delays when temperature reaches 35 °C under short day. phyA-E1, possibly photoperiodic pathway, is crucial for 35 °C-mediated late flowering, however, does not contribute to promoting flowering at 30 °C. 30 °C-induced up-regulation of FT2a and FT5a leads to early flowering, independent of E1. Therefore, distinct responsive mechanisms are adopted by soybean when facing different levels of high temperatures for successful flowering and reproduction.
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Affiliation(s)
- Yang Tang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Sijia Lu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Chao Fang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Huan Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Lidong Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Haiyang Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Tong Su
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Shichen Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Lingshuang Wang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Qun Cheng
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Baohui Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and Agroecology, Chinese Academy of SciencesHarbinChina
| | - Xiaoya Lin
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and Agroecology, Chinese Academy of SciencesHarbinChina
- College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
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28
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Lyu X, Mu R, Liu B. Shade avoidance syndrome in soybean and ideotype toward shade tolerance. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:31. [PMID: 37313527 PMCID: PMC10248688 DOI: 10.1007/s11032-023-01375-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/27/2023] [Indexed: 06/15/2023]
Abstract
The shade avoidance syndrome (SAS) in soybean can have destructive effects on yield, as essential carbon resources reserved for yield are diverted to the petiole and stem for exaggerated elongation, resulting in lodging and susceptibility to disease. Despite numerous attempts to reduce the unfavorable impacts of SAS for the development of cultivars suitable for high-density planting or intercropping, the genetic bases and fundamental mechanisms of SAS remain largely unclear. The extensive research conducted in the model plant Arabidopsis provides a framework for understanding the SAS in soybean. Nevertheless, recent investigations suggest that the knowledge obtained from model Arabidopsis may not be applicable to all processes in soybean. Consequently, further efforts are required to identify the genetic regulators of SAS in soybean for molecular breeding of high-yield cultivars suitable for density farming. In this review, we present an overview of the recent developments in SAS studies in soybean and suggest an ideal planting architecture for shade-tolerant soybean intended for high-yield breeding.
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Affiliation(s)
- Xiangguang Lyu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Ruolan Mu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Bin Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
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29
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Jo H, Ha BK, Park SK, Jeong SC, Lee JD, Moon JK. Genetic Diversity of Korean Wild Soybean Core Collections and Genome-Wide Association Study for Days to Flowering. PLANTS (BASEL, SWITZERLAND) 2023; 12:1305. [PMID: 36986992 PMCID: PMC10058364 DOI: 10.3390/plants12061305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
The utilization of wild soybean germplasms in breeding programs increases genetic diversity, and they contain the rare alleles of traits of interest. Understanding the genetic diversity of wild germplasms is essential for determining effective strategies that can improve the economic traits of soybeans. Undesirable traits make it challenging to cultivate wild soybeans. This study aimed to construct a core subset of 1467 wild soybean accessions of the total population and analyze their genetic diversity to understand their genetic variations. Genome-wild association studies were conducted to detect the genetic loci underlying the time to flowering for a core subset collection, and they revealed the allelic variation in E genes for predicting maturity using the available resequencing data of wild soybean. Based on principal component and cluster analyses, 408 wild soybean accessions in the core collection covered the total population and were explained by 3 clusters representing the collection regions, namely, Korea, China, and Japan. Most of the wild soybean collections in this study had the E1e2E3 genotype according to association mapping and a resequencing analysis. Korean wild soybean core collections can provide helpful genetic resources to identify new flowering and maturity genes near the E gene loci and genetic materials for developing new cultivars, facilitating the introgression of genes of interest from wild soybean.
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Affiliation(s)
- Hyun Jo
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Upland-Field Machinery Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Soo-Kwon Park
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Jeong-Dong Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jung-Kyung Moon
- Agricultural Genome Center, National Academy of Agricultural Sciences, Rural Development Administration, Jeonju 55365, Republic of Korea
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30
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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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31
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Genome-wide signatures of the geographic expansion and breeding of soybean. SCIENCE CHINA. LIFE SCIENCES 2023; 66:350-365. [PMID: 35997916 DOI: 10.1007/s11427-022-2158-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/30/2022] [Indexed: 10/15/2022]
Abstract
Soybean is a leguminous crop that provides oil and protein. Exploring the genomic signatures of soybean evolution is crucial for breeding varieties with improved adaptability to environmental extremes. We analyzed the genome sequences of 2,214 soybeans and proposed a soybean evolutionary route, i.e., the expansion of annual wild soybean (Glycine soja Sieb. & Zucc.) from southern China and its domestication in central China, followed by the expansion and local breeding selection of its landraces (G. max (L.) Merr.). We observed that the genetic introgression in soybean landraces was mostly derived from sympatric rather than allopatric wild populations during the geographic expansion. Soybean expansion and breeding were accompanied by the positive selection of flowering time genes, including GmSPA3c. Our study sheds light on the evolutionary history of soybean and provides valuable genetic resources for its future breeding.
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32
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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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33
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Zhang C, Xu X, Chen F, Yuan S, Wu T, Jiang B, Sapey E, Wu C, Sun S, Guo C, Han T. Establishment of a novel experimental system for studying the photoperiodic response of short-day dicots using soybean 'cotyledon-only plant' as material. FRONTIERS IN PLANT SCIENCE 2023; 13:1101715. [PMID: 36684791 PMCID: PMC9853180 DOI: 10.3389/fpls.2022.1101715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Soybean is an important model crop for photoperiodic response studies in plants and contributes significantly to the study of plant development and physiology in the past century. Because soybean plant is much bigger in size and longer in life cycle than Arabidopsis, it needs much more space for growth and time for investigation, which significantly hamper the efficiency of research. In the current study, we tested the photoperiodic response of a distinctive artificially-made cotyledon-only plant (COP) using a photoperiod-sensitive soybean variety Zigongdongdou (ZGDD) and other varieties with diverse sensitivity to photoperiod. ZGDD COPs flowered 39.4 ± 2.5 d after emergence under short-day conditions but maintained vegetative growth under long-day and night break conditions, which is similar to the case in the intact ZGDD plants. The COPs of early-maturing and medium-maturing soybean varieties also grew and flowered normally under natural day-length conditions. At the molecular level, the key genes in the photoperiodic pathway such as E1, GmFT1a, GmFT2a, and GmFT5a in the COPs also showed the same photoperiod sensitivity as in the intact plants. In addition, a simpler material of COP with only one cotyledon and root was generated and found to be sensitive to photoperiod as well. Notably, the COPs are only one-fifth the height of intact plants and one-third the maximum diameter of the intact plants grown in chambers 30 d after emergence. Based on COPs, we established a novel experimental system characterized by an entire photoperiodic response and longer longevity of cotyledons in addition to small plant size, ensuring the consistency, reliability, and stability of plant materials. COPs have the potential to be a novel model material for studies of the developmental biology of soybean and other dicots.
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Affiliation(s)
- Chunlei Zhang
- College of Life Science and Technology, Harbin Normal University, Harbin, China
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Xu
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fulu Chen
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shan Yuan
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tingting Wu
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bingjun Jiang
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Enoch Sapey
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
- Council for Scientific and Industrial Research (CSIR)-Oil Palm Research Institute, Kade, Ghana
| | - Cunxiang Wu
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shi Sun
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changhong Guo
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Tianfu Han
- College of Life Science and Technology, Harbin Normal University, Harbin, China
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
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34
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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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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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36
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Wang Z, Huang C, Niu Y, Yung WS, Xiao Z, Wong FL, Huang M, Wang X, Man CK, Sze CC, Liu A, Wang Q, Chen Y, Liu S, Wu C, Liu L, Hou W, Han T, Li MW, Lam HM. QTL analyses of soybean root system architecture revealed genetic relationships with shoot-related traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4507-4522. [PMID: 36422673 DOI: 10.1007/s00122-022-04235-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
The genetic basis of soybean root system architecture (RSA) and the genetic relationship between shoot and RSA were revealed by integrating data from recombinant inbred population grafting and QTL mapping. Variations in root system architecture (RSA) affect the functions of roots and thus play vital roles in plant adaptations and agricultural productivity. The aim of this study was to unravel the genetic relationship between RSA traits and shoot-related traits in soybean. This study characterized RSA variability at seedling stage in a recombinant inbred population, derived from a cross between cultivated soybean C08 and wild soybean W05, and performed high-resolution quantitative trait locus (QTL) mapping. In total, 34 and 41 QTLs were detected for RSA-related and shoot-related traits, respectively, constituting eight QTL clusters. Significant QTL correspondence was found between shoot biomass and RSA-related traits, consistent with significant correlations between these phenotypes. RSA-related QTLs also overlapped with selection regions in the genome, suggesting the cultivar RSA could be a partial consequence of domestication. Using reciprocal grafting, we confirmed that shoot-derived signals affected root development and the effects were controlled by multiple loci. Meanwhile, RSA-related QTLs were found to co-localize with four soybean flowering-time loci. Consistent with the phenotypes of the parental lines of our RI population, diminishing the function of flowering controlling E1 family through RNA interference (RNAi) led to reduced root growth. This implies that the flowering time-related genes within the RSA-related QTLs are actually contributing to RSA. To conclude, this study identified the QTLs that determine RSA through controlling root growth indirectly via regulating shoot functions, and discovered superior alleles from wild soybean that could be used to improve the root structure in existing soybean cultivars.
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Affiliation(s)
- Zhili Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Cheng Huang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Yongchao Niu
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wai-Shing Yung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Zhixia Xiao
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Fuk-Ling Wong
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Mingkun Huang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China
| | - Xin Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Chun-Kuen Man
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ching-Ching Sze
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ailin Liu
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Qianwen Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yinglong Chen
- The UWA Institute of Agriculture, & School of Agriculture and Environment, The University of Western Australia, Perth, WA6001, Australia
- State Key Laboratory of Soil Erosion and Dryland Farming On the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shuo Liu
- State Key Laboratory of Soil Erosion and Dryland Farming On the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Cunxiang Wu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Lifeng Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Wensheng Hou
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Tianfu Han
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Man-Wah Li
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
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37
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Lv T, Wang L, Zhang C, Liu S, Wang J, Lu S, Fang C, Kong L, Li Y, Li Y, Hou X, Liu B, Kong F, Li X. Identification of two quantitative genes controlling soybean flowering using bulked-segregant analysis and genetic mapping. FRONTIERS IN PLANT SCIENCE 2022; 13:987073. [PMID: 36531378 PMCID: PMC9749486 DOI: 10.3389/fpls.2022.987073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Photoperiod responsiveness is important to soybean production potential and adaptation to local environments. Varieties from temperate regions generally mature early and exhibit extremely low yield when grown under inductive short-day (SD) conditions. The long-juvenile (LJ) trait is essentially a reduction and has been introduced into soybean cultivars to improve yield in tropical environments. In this study, we used next-generation sequencing (NGS)-based bulked segregant analysis (BSA) to simultaneously map qualitative genes controlling the LJ trait in soybean. We identified two genomic regions on scaffold_32 and chromosome 18 harboring loci LJ32 and LJ18, respectively. Further, we identified LJ32 on the 228.7-kb scaffold_32 as the soybean pseudo-response-regulator gene Tof11 and LJ18 on a 301-kb region of chromosome 18 as a novel PROTEIN FLOWERING LOCUS T-RELATED gene, Glyma.18G298800. Natural variants of both genes contribute to LJ trait regulation in tropical regions. The molecular identification and functional characterization of Tof11 and LJ18 will enhance understanding of the molecular mechanisms underlying the LJ trait and provide useful genetic resources for soybean molecular breeding in tropical regions.
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Affiliation(s)
- Tianxiao Lv
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Lingshuang Wang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Chunyu Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
| | - Shu Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinxing Wang
- Suihua Branch Institute, Heilongjiang Academy of Agricultural Sciences, Suihua, Heilongjiang, China
| | - Sijia Lu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Chao Fang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Lingping Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Yunlong Li
- Suihua Branch Institute, Heilongjiang Academy of Agricultural Sciences, Suihua, Heilongjiang, China
| | - Yuge Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
| | - Xingliang Hou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
| | - Baohui Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Xiaoming Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
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38
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Zhang Z, Yang S, Wang Q, Yu H, Zhao B, Wu T, Tang K, Ma J, Yang X, Feng X. Soybean GmHY2a encodes a phytochromobilin synthase that regulates internode length and flowering time. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6646-6662. [PMID: 35946571 PMCID: PMC9629791 DOI: 10.1093/jxb/erac318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Plant height and flowering time are important agronomic traits that directly affect soybean [Glycine max (L.) Merr.] adaptability and yield. Here, the Glycine max long internode 1 (Gmlin1) mutant was selected from an ethyl methyl sulfonate (EMS)-mutated Williams 82 population due to its long internodes and early flowering. Using bulked segregant analysis (BSA), the Gmlin1 locus was mapped to Glyma.02G304700, a homologue of the Arabidopsis HY2 gene, which encodes a phytochromobilin (PΦB) synthase involved in phytochrome chromophore synthesis. Mutation of GmHY2a results in failure of the de-etiolation response under both red and far-red light. The Gmlin1 mutant exhibits a constitutive shade avoidance response under normal light, and the mutations influence the auxin and gibberellin pathways to promote internode elongation. The Gmlin1 mutant also exhibits decreased photoperiod sensitivity. In addition, the soybean photoperiod repressor gene E1 is down-regulated in the Gmlin1 mutant, resulting in accelerated flowering. The nuclear import of phytochrome A (GmphyA) and GmphyB following light treatment is decreased in Gmlin1 protoplasts, indicating that the weak light response of the Gmlin1 mutant is caused by a decrease in functional phytochrome. Together, these results indicate that GmHY2a plays an important role in soybean phytochrome biosynthesis and provide insights into the adaptability of the soybean plant.
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Affiliation(s)
- Zhirui Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun 130102, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Qiushi Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun 130102, China
| | - Hui Yu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun 130102, China
| | - Beifang Zhao
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun 130102, China
| | - Tao Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun 130102, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuanqiang Tang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun 130102, China
| | - Jingjing Ma
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun 130102, China
| | - Xinjing Yang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun 130102, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun 130102, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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39
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Lin X, Dong L, Tang Y, Li H, Cheng Q, Li H, Zhang T, Ma L, Xiang H, Chen L, Nan H, Fang C, Lu S, Li J, Liu B, Kong F. Novel and multifaceted regulations of photoperiodic flowering by phytochrome A in soybean. Proc Natl Acad Sci U S A 2022; 119:e2208708119. [PMID: 36191205 PMCID: PMC9565047 DOI: 10.1073/pnas.2208708119] [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: 05/20/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Photoperiod is an important environmental cue. Plants can distinguish the seasons and flower at the right time through sensing the photoperiod. Soybean is a sensitive short-day crop, and the timing of flowering varies greatly at different latitudes, thus affecting yields. Soybean cultivars in high latitudes adapt to the long day by the impairment of two phytochrome genes, PHYA3 and PHYA2, and the legume-specific flowering suppressor, E1. However, the regulating mechanism underlying phyA and E1 in soybean remains largely unknown. Here, we classified the regulation of the E1 family by phyA2 and phyA3 at the transcriptional and posttranscriptional levels, revealing that phyA2 and phyA3 regulate E1 by directly binding to LUX proteins, the critical component of the evening complex, to regulate the stability of LUX proteins. In addition, phyA2 and phyA3 can also directly associate with E1 and its homologs to stabilize the E1 proteins. Therefore, phyA homologs control the core flowering suppressor E1 at both the transcriptional and posttranscriptional levels, to double ensure the E1 activity. Thus, our results disclose a photoperiod flowering mechanism in plants by which the phytochrome A regulates LUX and E1 activity.
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Affiliation(s)
- Xiaoya Lin
- 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
| | - Lidong Dong
- 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
| | - Yang Tang
- 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
| | - Haiyang 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
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Qun Cheng
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Hong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Ting Zhang
- 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
| | - Lixin Ma
- 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
| | - Hongli Xiang
- 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
| | - Linnan Chen
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Haiyang Nan
- 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
| | - 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
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, 100193 Beijing, 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
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, 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
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
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40
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Maeda AE, Nakamichi N. Plant clock modifications for adapting flowering time to local environments. PLANT PHYSIOLOGY 2022; 190:952-967. [PMID: 35266545 PMCID: PMC9516756 DOI: 10.1093/plphys/kiac107] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/09/2022] [Indexed: 05/25/2023]
Abstract
During and after the domestication of crops from ancestral wild plants, humans selected cultivars that could change their flowering time in response to seasonal daylength. Continuous selection of this trait eventually allowed the introduction of crops into higher or lower latitudes and different climates from the original regions where domestication initiated. In the past two decades, numerous studies have found the causal genes or alleles that change flowering time and have assisted in adapting crop species such as barley (Hordeum vulgare), wheat (Triticum aestivum L.), rice (Oryza sativa L.), pea (Pisum sativum L.), maize (Zea mays spp. mays), and soybean (Glycine max (L.) Merr.) to new environments. This updated review summarizes the genes or alleles that contributed to crop adaptation in different climatic areas. Many of these genes are putative orthologs of Arabidopsis (Arabidopsis thaliana) core clock genes. We also discuss how knowledge of the clock's molecular functioning can facilitate molecular breeding in the future.
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Affiliation(s)
- Akari E Maeda
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Norihito Nakamichi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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Wang P, Wang L, Zhang L, Wu T, Sun B, Zhang J, Sapey E, Yuan S, Jiang B, Chen F, Wu C, Hou W, Sun S, Bai J, Han T. Genomic Dissection and Diurnal Expression Analysis Reveal the Essential Roles of the PRR Gene Family in Geographical Adaptation of Soybean. Int J Mol Sci 2022; 23:ijms23179970. [PMID: 36077363 PMCID: PMC9456279 DOI: 10.3390/ijms23179970] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Pseudo-response regulator (PRR) family members serve as key components of the core clock of the circadian clock, and play important roles in photoperiodic flowering, stress tolerance, growth, and the development of plants. In this study, 14 soybean PRR genes were identified, and classified into three groups according to phylogenetic analysis and structural characteristics. Real-time quantitative PCR analysis revealed that 13 GmPRRs exhibited obvious rhythmic expression under long-day (LD) and short-day (SD) conditions, and the expression of 12 GmPRRs was higher under LD in leaves. To evaluate the effects of natural variations in GmPRR alleles on soybean adaptation, we examined the sequences of GmPRRs among 207 varieties collected across China and the US, investigated the flowering phenotypes in six environments, and analyzed the geographical distributions of the major haplotypes. The results showed that a majority of non-synonymous mutations in the coding region were associated with flowering time, and we found that the nonsense mutations resulting in deletion of the CCT domain were related to early flowering. Haplotype analysis demonstrated that the haplotypes associated with early flowering were mostly distributed in Northeast China, while the haplotypes associated with late flowering were mostly cultivated in the lower latitudes of China. Our study of PRR family genes in soybean provides not only an important guide for characterizing the circadian clock-controlled flowering pathway but also a theoretical basis and opportunities to breed varieties with adaptation to specific regions and farming systems.
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Affiliation(s)
- Peiguo Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Liwei Wang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Lixin Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Tingting Wu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Baiquan Sun
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Junquan Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Enoch Sapey
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
- Council for Scientific and Industrial Research (CSIR)-Oil Palm Research Institute, Kade P.O. Box 74, Ghana
| | - Shan Yuan
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Bingjun Jiang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Fulu Chen
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Cunxiang Wu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Wensheng Hou
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Shi Sun
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Jiangping Bai
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence: (J.B.); (T.H.)
| | - Tianfu Han
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
- Correspondence: (J.B.); (T.H.)
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Yang A, Xu Q, Hong Z, Wang X, Zeng K, Yan L, Liu Y, Zhu Z, Wang H, Xu Y. Modified photoperiod response of CsFT promotes day neutrality and early flowering in cultivated cucumber. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2735-2746. [PMID: 35710636 DOI: 10.1007/s00122-022-04146-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
Map-based cloning and photoperiod response detection suggested that CsFT is the critical gene for cucumber photoperiod domestication. Photoperiod sensitivity is important for sensing seasonal changes and local adaptation. However, day-length sensitivity limits crop geographical adaptation and it should be modified during domestication. Cucumber was domesticated in southern Asia and is currently cultivated worldwide across a wide range of latitudes, but its photoperiod sensitivity and its change during cucumber domestication are unknown. Here, we confirmed wild cucumber (Hardwickii) was a short-day plant, and its flowering depends on short-day (SD) conditions, while the cultivated cucumber (9930) is a day-neutral plant that flowers independently of day length. A photoperiod sensitivity locus (ps-1) was identified by the 9930 × Hardwickii F2 segregating populations, which span a ~ 970 kb region and contain 60 predicted genes. RNA-seq analysis showed that the critical photoperiod pathway gene FLOWERING LOCUS T (CsFT) within the ps-1 locus exhibits differential expression between 9930 and Hardwickii, which was confirmed by qRT-PCR detection. CsFT in Hardwickii was sensitive to day length and could be significantly induced by SD conditions, whereas CsFT was highly expressed in 9930 and was insensitive to day length. Moreover, the role of CsFT in promoting flowering was verified by overexpression of CsFT in Arabidopsis. We also identified the genetic variations existing in the promoter of CsFT among the different geographic cucumbers and suggest they have possible roles in photoperiod domestication. The results of this study suggest that a variation in photoperiod sensitivity of CsFT is associated with day neutrality and early flowering in cultivated cucumber and could contribute to cucumber cultivation in diverse regions throughout the world.
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Affiliation(s)
- Aiyi Yang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Qinglan Xu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Zezhou Hong
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Xinrui Wang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Kang Zeng
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Ling Yan
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Yuanyuan Liu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China
| | - Zhujun Zhu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China.
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou, 311300, Zhejiang, China.
| | - Huasen Wang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China.
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou, 311300, Zhejiang, China.
| | - Yunmin Xu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, Zhejiang, China.
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou, 311300, Zhejiang, China.
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Development of Ethyl Methanesulfonate Mutant Edamame Soybean (Glycine max (L.) Merr.) Populations and Forward and Reverse Genetic Screening for Early-Flowering Mutants. PLANTS 2022; 11:plants11141839. [PMID: 35890474 PMCID: PMC9315854 DOI: 10.3390/plants11141839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 11/26/2022]
Abstract
Induced mutation is a viable breeding strategy that is widely utilized in the development of elite plant varieties. We aimed to improve a variety of edamame by constructing novel mutant populations using the ethyl methanesulfonate in soybeans (Glycine max (L.) Merr.). In the M2 population, the flowering stage showed a considerable standard deviation compared to the wild type, confirming that the mutant populations had the expected DNA mutations. To identify the DNA mutations in the mutant populations, we used the targeting induced local lesions in genomes (TILLING) method, which is a reverse genetic method, to search for soybean flowering-related gene mutants. A total of 30 mutants from E1, E3, E4, and PhyA1 genes, which are known to be highly effective genes, or their homologous gene for flowering and maturation found in soybean quantitative trait locus analyses were isolated from our TILLING screening. Among these mutants, there were eleven nonsynonymous substitution mutants, one nonsense mutant, and two single nucleotide deletion mutants that could be expected to reduce or eliminate gene function. The e1, e3, and e4 mutants obtained in this study flowered considerably earlier than the wild type. In particular, the e1 mutant with a nonsynonymous substitution flowered approximately 1 month after sowing regardless of the sowing date, and its harvest date was approximately 1 month earlier than that of the wild type. Mutations identified using the TILLING method could not only be used as gel-based DNA markers with the same manipulation method, but the mutations could also be detected as DNA markers by the high-resolution melting method. These results indicate that mutations achieved without chromosome modification by crossbreeding are effective for early and practical improvement of superior varieties and that efficient selection of mutants by reverse genetics is an effective method for the identification of genetic modifications. The edamame mutant populations developed in this study are believed to possess various useful alleles which may be applicable in the search for mutations that lead to improved edamame yield and eating quality beyond the flowering stage.
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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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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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Lu S, Fang C, Abe J, Kong F, Liu B. Current overview on the genetic basis of key genes involved in soybean domestication. ABIOTECH 2022; 3:126-139. [PMID: 36312442 PMCID: PMC9590488 DOI: 10.1007/s42994-022-00074-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 06/11/2022] [Indexed: 11/28/2022]
Abstract
Modern crops were created through the domestication and genetic introgression of wild relatives and adaptive differentiation in new environments. Identifying the domestication-related genes and unveiling their molecular diversity provide clues for understanding how the domesticated variants were selected by ancient people, elucidating how and where these crops were domesticated. Molecular genetics and genomics have explored some domestication-related genes in soybean (Glycine max). Here, we summarize recent studies about the quantitative trait locus (QTL) and genes involved in the domestication traits, introduce the functions of these genes, clarify which alleles of domesticated genes were selected during domestication. A deeper understanding of soybean domestication could help to break the bottleneck of modern breeding by highlighting unused genetic diversity not selected in the original domestication process, as well as highlighting promising new avenues for the identification and research of important agronomic traits among different crop species.
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Affiliation(s)
- Sijia Lu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Crop Gene Editing, Guangzhou University, Guangzhou, 510006 China
| | - Chao Fang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Crop Gene Editing, Guangzhou University, Guangzhou, 510006 China
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-0808 Japan
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Crop Gene Editing, Guangzhou University, Guangzhou, 510006 China
| | - Baohui Liu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Crop Gene Editing, Guangzhou University, Guangzhou, 510006 China
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Zhuang Y, Li X, Hu J, Xu R, Zhang D. Expanding the gene pool for soybean improvement with its wild relatives. ABIOTECH 2022; 3:115-125. [PMID: 36304518 PMCID: PMC9590452 DOI: 10.1007/s42994-022-00072-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/19/2022] [Indexed: 11/29/2022]
Abstract
Genetic diversity is a cornerstone of crop improvement, However, cultivated soybean (Glycine max) has undergone several genetic bottlenecks, including domestication in China, the introduction of landraces to other areas of the world and, latterly, selective breeding, leading to low genetic diversity the poses a major obstacle to soybean improvement. By contrast, there remains a relatively high level of genetic diversity in soybean's wild relatives, especially the perennial soybeans (Glycine subgenus Glycine), which could serve as potential gene pools for improving soybean cultivars. Wild soybeans are phylogenetically diversified and adapted to various habitats, harboring resistance to various biotic and abiotic stresses. Advances in genome and transcriptome sequencing enable alleles associated with desirable traits that were lost during domestication of soybean to be discovered in wild soybean. The collection and conservation of soybean wild relatives and the dissection of their genomic features will accelerate soybean breeding and facilitate sustainable agriculture and food production.
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Affiliation(s)
- Yongbin Zhuang
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, 271018 Shandong China
| | - Xiaoming Li
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, 271018 Shandong China
| | - Junmei Hu
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, 271018 Shandong China
| | - Ran Xu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250131 Shandong China
| | - Dajian Zhang
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, 271018 Shandong China
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Gu X, Su Y, Wang T. 转座元件对植物基因组进化、表观遗传和适应性的作用. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Huang M, Zhang L, Zhou L, Yung WS, Wang Z, Xiao Z, Wang Q, Wang X, Li MW, Lam HM. Identification of the accessible chromatin regions in six tissues in the soybean. Genomics 2022; 114:110364. [PMID: 35421559 DOI: 10.1016/j.ygeno.2022.110364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/25/2022] [Accepted: 04/06/2022] [Indexed: 01/14/2023]
Abstract
Accessible chromatin regions (ACRs) are tightly associated with gene expressions in the genome. Conserved non-coding cis-regulatory elements, such as transcription factor binding motifs, are usually found in ACRs, indicating an essential regulatory role of ACRs in the plant genome architecture. However, there have been few studies on soybean ACRs, especially those focusing on specific tissues. Hence, in this study, with the convenient ATAC-seq, we identified the ACRs in six soybean tissues, including root, leaf bud, flower, flower bud, developing seed, and pod. In total, the ACRs occupied about 3.3% of the entire soybean genome. By integrating the results from RNA-seq and transcription factor (TF) ChIP-seq, ACRs were found to be tightly associated with gene expressions and TF binding capacities in soybean. Together, these data provide a comprehensive understanding of the genomic features of ACRs in soybean. As a collection of essential genomic resources, these processed data are made available at datahub.wildsoydb.org.
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Affiliation(s)
- Mingkun Huang
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China; Lushan Botanical Garden Jiangxi Province and Chinese Academy of Sciences, NO.9 Zhiqing Road, Lushan, Jiujiang, Jiangxi, PR China.
| | - Ling Zhang
- Lushan Botanical Garden Jiangxi Province and Chinese Academy of Sciences, NO.9 Zhiqing Road, Lushan, Jiujiang, Jiangxi, PR China
| | - Limeng Zhou
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China
| | - Wai-Shing Yung
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China
| | - Zhili Wang
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China
| | - Zhixia Xiao
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China
| | - Qianwen Wang
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China
| | - Xin Wang
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China.
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China.
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Dietz N, Chan YO, Scaboo A, Graef G, Hyten D, Happ M, Diers B, Lorenz A, Wang D, Joshi T, Bilyeu K. Candidate Genes Modulating Reproductive Timing in Elite US Soybean Lines Identified in Soybean Alleles of Arabidopsis Flowering Orthologs With Divergent Latitude Distribution. FRONTIERS IN PLANT SCIENCE 2022; 13:889066. [PMID: 35574141 PMCID: PMC9100572 DOI: 10.3389/fpls.2022.889066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/08/2022] [Indexed: 05/30/2023]
Abstract
Adaptation of soybean cultivars to the photoperiod in which they are grown is critical for optimizing plant yield. However, despite its importance, only the major loci conferring variation in flowering time and maturity of US soybean have been isolated. By contrast, over 200 genes contributing to floral induction in the model organism Arabidopsis thaliana have been described. In this work, putative alleles of a library of soybean orthologs of these Arabidopsis flowering genes were tested for their latitudinal distribution among elite US soybean lines developed in the United States. Furthermore, variants comprising the alleles of genes with significant differences in latitudinal distribution were assessed for amino acid conservation across disparate genera to infer their impact on gene function. From these efforts, several candidate genes from various biological pathways were identified that are likely being exploited toward adaptation of US soybean to various maturity groups.
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Affiliation(s)
- Nicholas Dietz
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Yen On Chan
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- MU Data Science and Informatics Institute, University of Missouri, Columbia, MO, United States
| | - Andrew Scaboo
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - George Graef
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - David Hyten
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Mary Happ
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Brian Diers
- Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Aaron Lorenz
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Trupti Joshi
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- MU Data Science and Informatics Institute, University of Missouri, Columbia, MO, United States
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, United States
- Department of Health Management and Informatics, School of Medicine, University of Missouri, Columbia, MO, United States
| | - Kristin Bilyeu
- USDA/ARS Plant Genetics Research Unit, Columbia, MO, United States
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