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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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2
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Hu C, Li X, Zhang M, Jing C, Hai M, Shen J, Xu Q, Dang X, Shi Y, Liu E, Jiang J. Identifying the Quantitative Trait Locus and Candidate Genes of Traits Related to Milling Quality in Rice via a Genome-Wide Association Study. PLANTS (BASEL, SWITZERLAND) 2024; 13:1324. [PMID: 38794395 PMCID: PMC11124788 DOI: 10.3390/plants13101324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024]
Abstract
Milling quality directly affects production efficiency in rice, which is closely related to the brown rice recovery (BRR), the milled rice recovery (MRR) and the head milled rice recovery (HMRR). The present study investigated these three traits in 173 germplasms in two environments, finding abundant phenotypic variation. Three QTLs for BRR, two for MRR, and three for HMRR were identified in a genome-wide association study, five of these were identified in previously reported QTLs and three were newly identified. By combining the linkage disequilibrium (LD) analyses, the candidate gene LOC_Os05g08350 was identified. It had two haplotypes with significant differences and Hap 2 increased the BRR by 4.40%. The results of the qRT-PCR showed that the expression of LOC_Os05g08350 in small-BRR accessions was significantly higher than that in large-BRR accessions at Stages 4-5 of young panicle development, reaching the maximum value at Stage 5. The increase in thickness of the spikelet hulls of the accession carrying LOC_Os05g08350TT occurred due to an increase in the cell width and the cell numbers in cross-sections of spikelet hulls. These results help to further clarify the molecular genetic mechanism of milling-quality-related traits and provide genetic germplasm materials for high-quality breeding in rice.
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Affiliation(s)
- Changmin Hu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xinru Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Mengyuan Zhang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Chunyu Jing
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Mei Hai
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Jiaming Shen
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Qing Xu
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiaojing Dang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Erbao Liu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Jianhua Jiang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
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Chen J, Liu L, Chen G, Wang S, Liu Y, Zhang Z, Li H, Wang L, Zhou Z, Zhao J, Zhang X. CsRAXs negatively regulate leaf size and fruiting ability through auxin glycosylation in cucumber. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1024-1037. [PMID: 38578173 DOI: 10.1111/jipb.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024]
Abstract
Leaves are the main photosynthesis organ that directly determines crop yield and biomass. Dissecting the regulatory mechanism of leaf development is crucial for food security and ecosystem turn-over. Here, we identified the novel function of R2R3-MYB transcription factors CsRAXs in regulating cucumber leaf size and fruiting ability. Csrax5 single mutant exhibited enlarged leaf size and stem diameter, and Csrax1/2/5 triple mutant displayed further enlargement phenotype. Overexpression of CsRAX1 or CsRAX5 gave rise to smaller leaf and thinner stem. The fruiting ability of Csrax1/2/5 plants was significantly enhanced, while that of CsRAX5 overexpression lines was greatly weakened. Similarly, cell number and free auxin level were elevated in mutant plants while decreased in overexpression lines. Biochemical data indicated that CsRAX1/5 directly promoted the expression of auxin glucosyltransferase gene CsUGT74E2. Therefore, our data suggested that CsRAXs function as repressors for leaf size development by promoting auxin glycosylation to decrease free auxin level and cell division in cucumber. Our findings provide new gene targets for cucumber breeding with increased leaf size and crop yield.
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Affiliation(s)
- Jiacai Chen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Liu Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Guangxin Chen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Shaoyun Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Ye Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Zeqin Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Hongfei Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Liming Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhaoyang Zhou
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Jianyu Zhao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaolan Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
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Wang Q, Chen X, Meng Y, Niu M, Jia Y, Huang L, Ma W, Liang C, Li Z, Zhao L, Dang Z. The Potential Role of Genic-SSRs in Driving Ecological Adaptation Diversity in Caragana Plants. Int J Mol Sci 2024; 25:2084. [PMID: 38396759 PMCID: PMC10888960 DOI: 10.3390/ijms25042084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Caragana, a xerophytic shrub genus widely distributed in northern China, exhibits distinctive geographical substitution patterns and ecological adaptation diversity. This study employed transcriptome sequencing technology to investigate 12 Caragana species, aiming to explore genic-SSR variations in the Caragana transcriptome and identify their role as a driving force for environmental adaptation within the genus. A total of 3666 polymorphic genic-SSRs were identified across different species. The impact of these variations on the expression of related genes was analyzed, revealing a significant linear correlation (p < 0.05) between the length variation of 264 polymorphic genic-SSRs and the expression of associated genes. Additionally, 2424 polymorphic genic-SSRs were located in differentially expressed genes among Caragana species. Through weighted gene co-expression network analysis, the expressions of these genes were correlated with 19 climatic factors and 16 plant functional traits in various habitats. This approach facilitated the identification of biological processes associated with habitat adaptations in the studied Caragana species. Fifty-five core genes related to functional traits and climatic factors were identified, including various transcription factors such as MYB, TCP, ARF, and structural proteins like HSP90, elongation factor TS, and HECT. The roles of these genes in the ecological adaptation diversity of Caragana were discussed. Our study identified specific genomic components and genes in Caragana plants responsive to heterogeneous habitats. The results contribute to advancements in the molecular understanding of their ecological adaptation, lay a foundation for the conservation and development of Caragana germplasm resources, and provide a scientific basis for plant adaptation to global climate change.
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Affiliation(s)
- Qinglang Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Xing’er Chen
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Yue Meng
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Miaomiao Niu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Yuanyuan Jia
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Lei Huang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Wenhong Ma
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Cunzhu Liang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Zhiyong Li
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Liqing Zhao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Zhenhua Dang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
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Schneider M, Van Bel M, Inzé D, Baekelandt A. Leaf growth - complex regulation of a seemingly simple process. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1018-1051. [PMID: 38012838 DOI: 10.1111/tpj.16558] [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: 07/19/2023] [Revised: 11/08/2023] [Accepted: 11/11/2023] [Indexed: 11/29/2023]
Abstract
Understanding the underlying mechanisms of plant development is crucial to successfully steer or manipulate plant growth in a targeted manner. Leaves, the primary sites of photosynthesis, are vital organs for many plant species, and leaf growth is controlled by a tight temporal and spatial regulatory network. In this review, we focus on the genetic networks governing leaf cell proliferation, one major contributor to final leaf size. First, we provide an overview of six regulator families of leaf growth in Arabidopsis: DA1, PEAPODs, KLU, GRFs, the SWI/SNF complexes, and DELLAs, together with their surrounding genetic networks. Next, we discuss their evolutionary conservation to highlight similarities and differences among species, because knowledge transfer between species remains a big challenge. Finally, we focus on the increase in knowledge of the interconnectedness between these genetic pathways, the function of the cell cycle machinery as their central convergence point, and other internal and environmental cues.
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Affiliation(s)
- Michele Schneider
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Michiel Van Bel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Alexandra Baekelandt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
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6
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He S, Xu L, Wu W, Zhang J, Hao Z, Lu L, Shi J, Chen J. The Identification and Expression Analysis of the Liriodendron chinense F-Box Gene Family. PLANTS (BASEL, SWITZERLAND) 2024; 13:171. [PMID: 38256726 PMCID: PMC10819036 DOI: 10.3390/plants13020171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/30/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
The F-box gene family is one of the largest gene families in plants, and it plays a crucial role in regulating plant development, reproduction, cellular protein degradation, and response to biotic and abiotic stresses. Despite their significance, a comprehensive analysis of the F-box gene family in Liriodendron chinense and other magnoliaceae species has not been reported. In this study, we report for the first time the identification of 144 full-length F-box genes in L. chinense. Based on specific domains and phylogenetic analyses, these genes were divided into 10 distinct subfamilies. We further analyzed their gene structure, conserved domain and chromosome distribution, genome-wide replication events, and collinearity. Additionally, based on GO analysis, we found that F-box genes exhibit functional specificity, with a significant proportion of them being involved in protein binding (GO:0005515), suggesting that F-box genes may play an important role in gene regulation in L. chinense. Transcriptome data and q-PCR results also showed that F-box genes are involved in the development of multiple tissues in L. chinense, regulate the somatic embryogenesis of Liriodendron hybrids, and play a pivotal role in abiotic stress. Altogether, these findings provide a foundation for understanding the biological function of F-box genes in L. chinense and other plant species.
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Affiliation(s)
- Shichan He
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
| | - Lin Xu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
| | - Weihuang Wu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
| | - Jiaji Zhang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
| | - Zhaodong Hao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
| | - Lu Lu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
| | - Jisen Shi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
| | - Jinhui Chen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
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7
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Lu K, Gong H, Yang D, Ye M, Fang Q, Zhang XY, Wu R. Genome-Wide Network Analysis of Above- and Below-Ground Co-growth in Populus euphratica. PLANT PHENOMICS (WASHINGTON, D.C.) 2024; 6:0131. [PMID: 38188223 PMCID: PMC10769449 DOI: 10.34133/plantphenomics.0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 12/12/2023] [Indexed: 01/09/2024]
Abstract
Tree growth is the consequence of developmental interactions between above- and below-ground compartments. However, a comprehensive view of the genetic architecture of growth as a cohesive whole is poorly understood. We propose a systems biology approach for mapping growth trajectories in genome-wide association studies viewing growth as a complex (phenotypic) system in which above- and below-ground components (or traits) interact with each other to mediate systems behavior. We further assume that trait-trait interactions are controlled by a genetic system composed of many different interactive genes and integrate the Lotka-Volterra predator-prey model to dissect phenotypic and genetic systems into pleiotropic and epistatic interaction components by which the detailed genetic mechanism of above- and below-ground co-growth can be charted. We apply the approach to analyze linkage mapping data of Populus euphratica, which is the only tree species that can grow in the desert, and characterize several loci that govern how above- and below-ground growth is cooperated or competed over development. We reconstruct multilayer and multiplex genetic interactome networks for the developmental trajectories of each trait and their developmental covariation. Many significant loci and epistatic effects detected can be annotated to candidate genes for growth and developmental processes. The results from our model may potentially be useful for marker-assisted selection and genetic editing in applied tree breeding programs. The model provides a general tool to characterize a complete picture of pleiotropic and epistatic genetic architecture in growth traits in forest trees and any other organisms.
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Affiliation(s)
- Kaiyan Lu
- College of Science,
Beijing Forestry University, Beijing 100083, P. R. China
| | - Huiying Gong
- Center for Computational Biology, College of Biological Sciences and Technology,
Beijing Forestry University, Beijing 100083, P. R. China
| | - Dengcheng Yang
- Center for Computational Biology, College of Biological Sciences and Technology,
Beijing Forestry University, Beijing 100083, P. R. China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology,
Beijing Forestry University, Beijing 100083, P. R. China
| | - Qing Fang
- Faculty of Science,
Yamagata University, Yamagata 990, Japan
| | - Xiao-Yu Zhang
- College of Science,
Beijing Forestry University, Beijing 100083, P. R. China
| | - Rongling Wu
- Yanqi Lake BeijingInstitute of Mathematical Sciences and Applications, Beijing 101408, China
- Center for Computational Biology, College of Biological Sciences and Technology,
Beijing Forestry University, Beijing 100083, P. R. China
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8
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Geng Z, Dou H, Liu J, Zhao G, An Z, Liu L, Zhao N, Zhang H, Wang Y. GhFB15 is an F-box protein that modulates the response to salinity by regulating flavonoid biosynthesis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111899. [PMID: 37865208 DOI: 10.1016/j.plantsci.2023.111899] [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: 05/24/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 10/23/2023]
Abstract
An exposure to extremely saline conditions can lead to significant oxidative damage in plants. Flavonoids, which are potent antioxidants, are critical for the scavenging of reactive oxygen species caused by abiotic stress. In the present study, the cotton F-box gene GhFB15 was isolated and characterized. The expression of GhFB15 was rapidly induced by salt as well as by exogenous hormones (ETH, MeJA, ABA, and GA). An analysis of subcellular localization revealed GhFB15 is mainly distributed in nuclei. Overexpression of GhFB15 adversely affected the salt tolerance of transgenic Arabidopsis plants as evidenced by decreased seed germination and seedling growth, whereas the silencing of GhFB15 improved the salt tolerance of cotton plants. Furthermore, we analyzed the gene expression profiles of VIGS-GhFB15 and TRV:00 plants. Many of the differentially expressed genes were associated with the flavonoid biosynthesis pathway. Moreover, lower flavonoid contents and higher levels of H2O2 and O2- were observed in the transgenic Arabidopsis plants. Conversely, the VIGS-GhFB15 cotton plants had relatively higher flavonoid contents, but lower H2O2 and O2- levels. These results suggest that GhFB15 negatively regulates salt tolerance, and silencing GhFB15 results in increased flavonoid accumulation and improved ROS scavenging.
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Affiliation(s)
- Zhao Geng
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, PR China
| | - Haikuan Dou
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, PR China
| | - Jianguang Liu
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, PR China
| | - Guiyuan Zhao
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, PR China
| | - Zetong An
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, PR China
| | - Linlin Liu
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, PR China
| | - Ning Zhao
- College of Food Science and Biology, Hebei University of Science and Technology, PR China
| | - Hanshuang Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, PR China.
| | - Yongqiang Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, PR China.
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Mao Y, Zhou S, Yang J, Wen J, Wang D, Zhou X, Wu X, He L, Liu M, Wu H, Yang L, Zhao B, Tadege M, Liu Y, Liu C, Chen J. The MIO1-MtKIX8 module regulates the organ size in Medicago truncatula. PHYSIOLOGIA PLANTARUM 2023; 175:e14046. [PMID: 37882293 DOI: 10.1111/ppl.14046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/19/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023]
Abstract
Plant organ size is an important agronomic trait tightly related to crop yield. However, the molecular mechanisms underlying organ size regulation remain largely unexplored in legumes. We previously characterized a key regulator F-box protein MINI ORGAN1 (MIO1)/SMALL LEAF AND BUSHY1 (SLB1), which controls plant organ size in the model legume Medicago truncatula. In order to further dissect the molecular mechanism, MIO1 was used as the bait to screen its interacting proteins from a yeast library. Subsequently, a KIX protein, designated MtKIX8, was identified from the candidate list. The interaction between MIO1 and MtKIX8 was confirmed further by Y2H, BiFC, split-luciferase complementation and pull-down assays. Phylogenetic analyses indicated that MtKIX8 is highly homologous to Arabidopsis KIX8, which negatively regulates organ size. Moreover, loss-of-function of MtKIX8 led to enlarged leaves and seeds, while ectopic expression of MtKIX8 in Arabidopsis resulted in decreased cotyledon area and seed weight. Quantitative reverse-transcription PCR and in situ hybridization showed that MtKIX8 is expressed in most developing organs. We also found that MtKIX8 serves as a crucial molecular adaptor, facilitating interactions with BIG SEEDS1 (BS1) and MtTOPLESS (MtTPL) proteins in M. truncatula. Overall, our results suggest that the MIO1-MtKIX8 module plays a significant and conserved role in the regulation of plant organ size. This module could be a good target for molecular breeding in legume crops and forages.
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Affiliation(s)
- Yawen Mao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shaoli Zhou
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Jiangqi Wen
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma, USA
| | - Dongfa Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xuan Zhou
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinyuan Wu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liangliang He
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Mingli Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- Southwest Forestry University, Kunming, China
| | - Huan Wu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Liling Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Baolin Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Million Tadege
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma, USA
| | - Yu Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
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Xia H, Hao Z, Shen Y, Tu Z, Yang L, Zong Y, Li H. Genome-wide association study of multiyear dynamic growth traits in hybrid Liriodendron identifies robust genetic loci associated with growth trajectories. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1544-1563. [PMID: 37272730 DOI: 10.1111/tpj.16337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/30/2023] [Accepted: 05/29/2023] [Indexed: 06/06/2023]
Abstract
The genetic factors underlying growth traits differ over time points or stages. However, most current studies of phenotypes at single time points do not capture all loci or explain the genetic differences underlying growth trajectories. Hybrid Liriodendron exhibits obvious heterosis and is widely cultivated, although its complex genetic mechanism underlying growth traits remains unknown. A genome-wide association study (GWAS) is an effective method for elucidating the genetic architecture by identifying genetic loci underlying complex quantitative traits. In the present study, using a GWAS, we identified robust loci associated with growth trajectories in hybrid Liriodendron populations. We selected 233 hybrid progenies derived from 25 crosses for resequencing, and measured their tree height (H) and diameter at breast height (DBH) for 11 consecutive years; 192 972 high-quality single nucleotide polymorphisms (SNPs) were obtained. The dynamics of the multiyear single-trait GWAS showed that year-specific SNPs predominated, and only five robust SNPs for DBH were identified in at least three different years. Multitrait GWAS analysis with model parameters as latent variables also revealed 62 SNPs for H and 52 for DBH associated with the growth trajectory, displaying different biomass accumulation patterns, among which four SNPs exerted pleiotropic effects. All identified SNPs also exhibited temporal variations in effect sizes and inheritance patterns potentially related to different growth and developmental stages. The haplotypes resulting from these significant SNPs might pyramid favorable loci, benefitting the selection of superior genotypes. The present study provides insights into the genetic architecture of dynamic growth traits and lays a basis for future molecular-assisted breeding.
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Affiliation(s)
- Hui Xia
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Ziyuan Hao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yufang Shen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhonghua Tu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Lichun Yang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yaxian Zong
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Huogen Li
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
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11
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Liu D, Tan W, Wang H, Li W, Fu J, Li J, Zhou Y, Lin M, Xing W. Genetic diversity and genome-wide association study of 13 agronomic traits in 977 Beta vulgaris L. germplasms. BMC Genomics 2023; 24:413. [PMID: 37488485 PMCID: PMC10364417 DOI: 10.1186/s12864-023-09522-y] [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: 03/09/2023] [Accepted: 07/17/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Sugar beet (Beta vulgaris L.) is an economically essential sugar crop worldwide. Its agronomic traits are highly diverse and phenotypically plastic, influencing taproot yield and quality. The National Beet Medium-term Gene Bank in China maintains more than 1700 beet germplasms with diverse countries of origin. However, it lacks detailed genetic background associated with morphological variability and diversity. RESULTS Here, a comprehensive genome-wide association study (GWAS) of 13 agronomic traits was conducted in a panel of 977 sugar beet accessions. Almost all phenotypic traits exhibited wide genetic diversity and high coefficient of variation (CV). A total of 170,750 high-quality single-nucleotide polymorphisms (SNPs) were obtained using the genotyping-by-sequencing (GBS). Neighbour-joining phylogenetic analysis, principal component analysis, population structure and kinship showed no obvious relationships among these genotypes based on subgroups or regional sources. GWAS was carried out using a mixed linear model, and 159 significant associations were detected for these traits. Within the 25 kb linkage disequilibrium decay of the associated markers, NRT1/PTR FAMILY 6.3 (BVRB_5g097760); nudix hydrolase 15 (BVRB_8g182070) and TRANSPORT INHIBITOR RESPONSE 1 (BVRB_8g181550); transcription factor MYB77 (BVRB_2g023500); and ethylene-responsive transcription factor ERF014 (BVRB_1g000090) were predicted to be strongly associated with the taproot traits of root groove depth (RGD); root shape (RS); crown size (CS); and flesh colour (FC), respectively. For the aboveground traits, UDP-glycosyltransferase 79B6 (BVRB_9g223780) and NAC domain-containing protein 7 (BVRB_5g097990); F-box protein At1g10780 (BVRB_6g140760); phosphate transporter PHO1 (BVRB_3g048660); F-box protein CPR1 (BVRB_8g181140); and transcription factor MYB77 (BVRB_2g023500) and alcohol acyltransferase 9 (BVRB_2g023460) might be associated with the hypocotyl colour (HC); plant type (PT); petiole length (PL); cotyledon size (C); and fascicled leaf type (FLT) of sugar beet, respectively. AP-2 complex subunit mu (BVRB_5g106130), trihelix transcription factor ASIL2 (BVRB_2g041790) and late embryogenesis abundant protein 18 (BVRB_5g106150) might be involved in pollen quantity (PQ) variation. The candidate genes extensively participated in hormone response, nitrogen and phosphorus transportation, secondary metabolism, fertilization and embryo maturation. CONCLUSIONS The genetic basis of agronomical traits is complicated in heterozygous diploid sugar beet. The putative valuable genes found in this study will help further elucidate the molecular mechanism of each phenotypic trait for beet breeding.
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Affiliation(s)
- Dali Liu
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Wenbo Tan
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Hao Wang
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Wangsheng Li
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Jingjing Fu
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Jiajia Li
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Yuanhang Zhou
- Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, P. R. China
| | - Ming Lin
- Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, P. R. China
| | - Wang Xing
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China.
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China.
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Li M, Li J, Nie P, Li G, Liu W, Gong Q, Dong X, Gao X, Chen W, Zhang A. A high-quality assembled genome of a representative peach landrace, 'Feichenghongli', and analysis of distinct late florescence and narrow leaf traits. BMC PLANT BIOLOGY 2023; 23:230. [PMID: 37120546 PMCID: PMC10148998 DOI: 10.1186/s12870-023-04242-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 04/22/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Peach (Prunus persica L. Batsch) is one of the most popular fruits worldwide. Although the reference genome of 'Lovell' peach has been released, the diversity of genome-level variations cannot be explored with one genome. To detect these variations, it is necessary to assemble more genomes. RESULTS We sequenced and de novo assembled the genome of 'Feichenghongli' (FCHL), a representative landrace with strict self-pollination, which maintained the homozygosity of the genome as much as possible. The chromosome-level genome of FCHL was 239.06 Mb in size with a contig N50 of 26.93 Mb and only 4 gaps at the scaffold level. The alignment of the FCHL genome with the reference 'Lovell' genome enabled the identification of 432535 SNPs, 101244 insertions and deletions, and 7299 structural variants. Gene family analysis showed that the expanded genes in FCHL were enriched in sesquiterpenoids and triterpenoid biosynthesis. RNA-seq analyses were carried out to investigate the two distinct traits of late florescence and narrow leaves. Two key genes, PpDAM4 and PpAGL31, were identified candidates for the control of flower bud dormancy, and an F-box gene, PpFBX92, was identified as a good candidate gene in the regulation of leaf size. CONCLUSIONS The assembled high-quality genome could deepen our understanding of variations among diverse genomes and provide valuable information for identifying functional genes and improving the molecular breeding process.
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Affiliation(s)
- Miao Li
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
| | - Jian Li
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
| | - Peixian Nie
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
| | - Guixiang Li
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
| | - Wei Liu
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
| | - Qingtao Gong
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
| | - Xiaomin Dong
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
| | - Xiaolan Gao
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
| | - Wenyu Chen
- Feicheng peach Industry Development Center, Feicheng City, 271600 Shandong Province China
| | - Anning Zhang
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
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Niu J, Si Y, Tian S, Liu X, Shi X, Ma S, Yu Z, Ling HQ, Zheng S. A Wheat 660 K SNP array-based high-density genetic map facilitates QTL mapping of flag leaf-related traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:51. [PMID: 36913011 DOI: 10.1007/s00122-023-04248-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 11/26/2022] [Indexed: 06/18/2023]
Abstract
A high-density genetic map containing 122,620 SNP markers was constructed, which facilitated the identification of eight major flag leaf-related QTL in relatively narrow intervals. The flag leaf plays an important role in photosynthetic capacity and yield potential in wheat. In this study, we used a recombinant inbred line population containing 188 lines derived from a cross between 'Lankao86' (LK86) and 'Ermangmai' to construct a genetic map using the Wheat 660 K single-nucleotide polymorphism (SNP) array. The high-density genetic map contains 122,620 SNP markers spanning 5185.06 cM. It shows good collinearity with the physical map of Chinese Spring and anchors multiple sequences of previously unplaced scaffolds onto chromosomes. Based on the high-density genetic map, we identified seven, twelve, and eight quantitative trait loci (QTL) for flag leaf length (FLL), width (FLW), and area (FLA) across eight environments, respectively. Among them, three, one, and four QTL for FLL, FLW, and FLA are major and stably express in more than four environments. The physical distance between the flanking markers for QFll.igdb-3B/QFlw.igdb-3B/QFla.igdb-3B is only 444 kb containing eight high confidence genes. These results suggested that we could directly map the candidate genes in a relatively small region by the high-density genetic map constructed with the Wheat 660 K array. Furthermore, the identification of environmentally stable QTL for flag leaf morphology laid a foundation for the following gene cloning and flag leaf morphology improvement.
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Affiliation(s)
- Jianqing Niu
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yaoqi Si
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shuiquan Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shengwei Ma
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zhongqing Yu
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Hong-Qing Ling
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
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14
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Johnson SE, Tittes S, Franks SJ. Rapid, nonparallel genomic evolution of Brassica rapa (field mustard) under experimental drought. J Evol Biol 2023; 36:550-562. [PMID: 36721268 DOI: 10.1111/jeb.14152] [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: 04/20/2022] [Revised: 09/22/2022] [Accepted: 12/08/2022] [Indexed: 02/02/2023]
Abstract
While we know that climate change can potentially cause rapid phenotypic evolution, our understanding of the genetic basis and degree of genetic parallelism of rapid evolutionary responses to climate change is limited. In this study, we combined the resurrection approach with an evolve-and-resequence design to examine genome-wide evolutionary changes following drought. We exposed genetically similar replicate populations of the annual plant Brassica rapa derived from a field population in southern California to four generations of experimental drought or watered conditions in a greenhouse. Genome-wide sequencing of ancestral and descendant population pools identified hundreds of SNPs that showed evidence of rapidly evolving in response to drought. Several of these were in stress response genes, and two were identified in a prior study of drought response in this species. However, almost all genetic changes were unique among experimental populations, indicating that the evolutionary changes were largely nonparallel, despite the fact that genetically similar replicates of the same founder population had experienced controlled and consistent selection regimes. This nonparallelism of evolution at the genetic level is potentially because of polygenetic adaptation allowing for multiple different genetic routes to similar phenotypic outcomes. Our findings help to elucidate the relationship between rapid phenotypic and genomic evolution and shed light on the degree of parallelism and predictability of genomic evolution to environmental change.
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Affiliation(s)
- Stephen E Johnson
- Department of Biological Sciences and Louis Calder Center, Fordham University, Bronx, New York, USA
| | - Silas Tittes
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Steven J Franks
- Department of Biological Sciences and Louis Calder Center, Fordham University, Bronx, New York, USA
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15
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Compton S, Stackpole C, Dixit A, Sekhwal MK, Kolb T, De la Torre AR. Differences in heat tolerance, water use efficiency and growth among Douglas-fir families and varieties evidenced by GWAS and common garden studies. AOB PLANTS 2023; 15:plad008. [PMID: 37007611 PMCID: PMC10052383 DOI: 10.1093/aobpla/plad008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Severe and frequent heat and drought events challenge the survival and development of long-generation trees. In this study, we investigated the genomic basis of heat tolerance, water use efficiency and growth by performing genome-wide association studies in coastal Douglas-fir (Pseudotsuga menziesii) and intervarietal (menziesii × glauca) hybrid seedlings. GWAS results identified 32 candidate genes involved in primary and secondary metabolism, abiotic stress and signaling, among other functions. Water use efficiency (inferred from carbon isotope discrimination), photosynthetic capacity (inferred from %N), height and heat tolerance (inferred from electrolyte leakage in a heat stress experiment) were significantly different among Douglas-fir families and varieties. High-elevation seed sources had increased water use efficiency, which could be a result of higher photosynthetic capacity. Similarly, families with greater heat tolerance also had higher water use efficiency and slower growth, suggesting a conservative growth strategy. Intervarietal hybrids showed increased heat tolerance (lower electrolyte leakage at 50 and 55 °C) and higher water use efficiency compared with coastal families, suggesting that hybridization might be a source of pre-adapted alleles to warming climates and should be considered for large-scale reforestation projects under increasingly arid conditions.
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Affiliation(s)
| | | | - Aalap Dixit
- Department of Forestry, New Mexico Highlands University, Las Vegas, NM 87701, USA
| | - Manoj K Sekhwal
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, AZ 86011, USA
| | - Thomas Kolb
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, AZ 86011, USA
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Kong B, Ma J, Zhang P, Chen T, Liu Y, Che Z, Shahinnia F, Yang D. Deciphering key genomic regions controlling flag leaf size in wheat via integration of meta-QTL and in silico transcriptome assessment. BMC Genomics 2023; 24:33. [PMID: 36658498 PMCID: PMC9854125 DOI: 10.1186/s12864-023-09119-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Grain yield is a complex and polygenic trait influenced by the photosynthetic source-sink relationship in wheat. The top three leaves, especially the flag leaf, are considered the major sources of photo-assimilates accumulated in the grain. Determination of significant genomic regions and candidate genes affecting flag leaf size can be used in breeding for grain yield improvement. RESULTS With the final purpose of understanding key genomic regions for flag leaf size, a meta-analysis of 521 initial quantitative trait loci (QTLs) from 31 independent QTL mapping studies over the past decades was performed, where 333 loci eventually were refined into 64 meta-QTLs (MQTLs). The average confidence interval (CI) of these MQTLs was 5.28 times less than that of the initial QTLs. Thirty-three MQTLs overlapped the marker trait associations (MTAs) previously reported in genome-wide association studies (GWAS) for flag leaf traits in wheat. A total of 2262 candidate genes for flag leaf size, which were involved in the peroxisome, basal transcription factor, and tyrosine metabolism pathways were identified in MQTL regions by the in silico transcriptome assessment. Of these, the expression analysis of the available genes revealed that 134 genes with > 2 transcripts per million (TPM) were highly and specifically expressed in the leaf. These candidate genes could be critical to affect flag leaf size in wheat. CONCLUSIONS The findings will make further insight into the genetic determinants of flag leaf size and provide some reliable MQTLs and putative candidate genes for the genetic improvement of flag leaf size in wheat.
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Affiliation(s)
- Binxue Kong
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jingfu Ma
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Peipei Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
| | - Tao Chen
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuan Liu
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhuo Che
- Plant Seed Master Station of Gansu Province, Lanzhou, 730000, China
| | - Fahimeh Shahinnia
- Bavarian State Research Centre for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
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17
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Curci PL, Zhang J, Mähler N, Seyfferth C, Mannapperuma C, Diels T, Van Hautegem T, Jonsen D, Street N, Hvidsten TR, Hertzberg M, Nilsson O, Inzé D, Nelissen H, Vandepoele K. Identification of growth regulators using cross-species network analysis in plants. PLANT PHYSIOLOGY 2022; 190:2350-2365. [PMID: 35984294 PMCID: PMC9706488 DOI: 10.1093/plphys/kiac374] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/05/2022] [Indexed: 05/11/2023]
Abstract
With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.
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Affiliation(s)
- Pasquale Luca Curci
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
- Institute of Biosciences and Bioresources, National Research Council (CNR), Via Amendola 165/A, 70126 Bari, Italy
| | - Jie Zhang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Niklas Mähler
- Department of Plant Physiology, Umea Plant Science Centre (UPSC), Umeå University, 90187 Umeå, Sweden
| | - Carolin Seyfferth
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
- Department of Plant Physiology, Umea Plant Science Centre (UPSC), Umeå University, 90187 Umeå, Sweden
| | - Chanaka Mannapperuma
- Department of Plant Physiology, Umea Plant Science Centre (UPSC), Umeå University, 90187 Umeå, Sweden
| | - Tim Diels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Tom Van Hautegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - David Jonsen
- SweTree Technologies AB, Skogsmarksgränd 7, SE-907 36 Umeå, Sweden
| | - Nathaniel Street
- Department of Plant Physiology, Umea Plant Science Centre (UPSC), Umeå University, 90187 Umeå, Sweden
| | - Torgeir R Hvidsten
- Department of Plant Physiology, Umea Plant Science Centre (UPSC), Umeå University, 90187 Umeå, Sweden
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Magnus Hertzberg
- SweTree Technologies AB, Skogsmarksgränd 7, SE-907 36 Umeå, Sweden
| | - Ove Nilsson
- Department of Forest Genetics and Plant Physiology, Umea Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
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18
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Cheng M, Meng F, Mo F, Qi H, Wang P, Chen X, Liu J, Ghanizadeh H, Zhang H, Wang A. Slym1 control the color etiolation of leaves by facilitating the decomposition of chlorophyll in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111457. [PMID: 36089196 DOI: 10.1016/j.plantsci.2022.111457] [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: 06/13/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Photosynthesis, as an important biological process of plants, produces organic substances for plant growth and development. Although the molecular mechanisms of photosynthesis had been well investigated, the relationship between chlorophyll synthesis and photosynthesis remains largely unknown. The leaf-color mutant was an ideal material for studying photosynthesis and chlorophyll synthesis, which had been seldom investigated in tomato. Here, we obtained a yellow leaf tomato mutant ym (The mutant plants from the line of zs4) in field. Transmission electron microscopy (TEM) and photosynthetic parameters results demonstrated that chloroplast's structure was obviously destroyed and photosynthetic capacity gets weak. The mutant was hybridized with the control to construct the F2 segregation population for sequencing. Slym1 gene, controlling yellow mutant trait, was identified using Bulked Segregation Analysis. Slym1 was up-regulated in the mutant and Slym1 was located in the nucleus. The genes associated with photosynthesis and chlorophyll synthesis were down-regulated in Slym1-OE transgenic tomato plants. The results suggested that Slym1 negatively regulate photosynthesis. Photosynthetic pigment synthesis related genes HEMA, HEMB1, CHLG and CAO were up-regulated in Slym1 silencing plants. The redundant Slym1 binding the intermediate proteins MP resulting in hindering the interaction between MP and HY5 due to the Slym1 with a high expression level in ym mutant, lead to lots of the HY5 with unbound state accumulates in cells, that could accelerate the decomposition of chlorophyll. Therefore, the yellow leaf-color mutant ym could be used as an ideal material for further exploring the relationship between leaf color mutant and photosynthesis and the specific mechanism.
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Affiliation(s)
- Mozhen Cheng
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China.
| | - Fanyue Meng
- College of Life Sciences, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China.
| | - Fulei Mo
- College of Life Sciences, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China.
| | - Haonan Qi
- College of Life Sciences, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China.
| | - Peiwen Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China.
| | - Xiuling Chen
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China.
| | - Jiayin Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China; College of Arts and Sciences, Northeast Agricultural University, Harbin, China.
| | - Hossein Ghanizadeh
- School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand.
| | - He Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China.
| | - Aoxue Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China; College of Life Sciences, Northeast Agricultural University, Harbin, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China.
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19
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Zheng H, Hou L, Xie J, Cao F, Wei R, Yang M, Qi Z, Zhu R, Zhang Z, Xin D, Li C, Liu C, Jiang H, Chen Q. Construction of Chromosome Segment Substitution Lines and Inheritance of Seed-Pod Characteristics in Wild Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:869455. [PMID: 35783974 PMCID: PMC9247457 DOI: 10.3389/fpls.2022.869455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Genetic populations provide the basis for genetic and genomic research, and chromosome segment substitution lines (CSSLs) are a powerful tool for the fine mapping of quantitative traits, new gene mining, and marker-assisted breeding. In this study, 213 CSSLs were obtained by self-crossing, backcrossing, and marker-assisted selection between cultivated soybean (Glycine max [L.] Merr.) variety Suinong14 (SN14) and wild soybean (Glycine soja Sieb. et Zucc.) ZYD00006. The genomes of these 213 CSSLs were resequenced and 580,524 single-nucleotide polymorphism markers were obtained, which were divided into 3,780 bin markers. The seed-pod-related traits were analyzed by quantitative trait locus (QTL) mapping using CSSLs. A total of 170 QTLs were detected, and 32 QTLs were detected stably for more than 2 years. Through epistasis analysis, 955 pairs of epistasis QTLs related to seed-pod traits were obtained. Furthermore, the hundred-seed weight QTL was finely mapped to the region of 64.4 Kb on chromosome 12, and Glyma.12G088900 was identified as a candidate gene. Taken together, a set of wild soybean CSSLs was constructed and upgraded by a resequencing technique. The seed-pod-related traits were studied by bin markers, and a candidate gene for the hundred-seed weight was finely mapped. Our results have revealed the CSSLs can be an effective tool for QTL mapping, epistatic effect analysis, and gene cloning.
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Affiliation(s)
| | - Lilong Hou
- Northeast Agricultural University, Harbin, China
| | - Jianguo Xie
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun, China
| | - Fubin Cao
- Northeast Agricultural University, Harbin, China
| | - Ruru Wei
- Northeast Agricultural University, Harbin, China
| | | | - Zhaoming Qi
- Northeast Agricultural University, Harbin, China
| | | | | | - Dawei Xin
- Northeast Agricultural University, Harbin, China
| | - Candong Li
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Chunyan Liu
- Northeast Agricultural University, Harbin, China
| | - Hongwei Jiang
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun, China
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20
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Metabolome and Transcriptome Profiling Unveil the Mechanisms of Polyphenol Synthesis in the Developing Endopleura of Walnut ( Juglans regia L.). Int J Mol Sci 2022; 23:ijms23126623. [PMID: 35743068 PMCID: PMC9224426 DOI: 10.3390/ijms23126623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/01/2022] [Accepted: 06/13/2022] [Indexed: 12/04/2022] Open
Abstract
Walnut (Juglans regia L.) is an important woody nut tree species, and its endopleura (the inner coating of a seed) is rich in many polyphenols. Thus far, the pathways and essential genes involved in polyphenol biosynthesis in developing walnut endopleura remain largely unclear. We compared metabolite differences between endopleura and embryo in mature walnuts, and analyzed the changes of metabolites in endopleura at 35, 63, 91, 119, and 147 days after pollination (DAP). A total of 760 metabolites were detected in the metabolome, and the polyphenol contents in endopleura were higher than those in embryos. A total of 15 types of procyanidins, 10 types of kaempferol glycosides, and 21 types of quercetin glycosides that accumulated during endopleura development were identified. The analysis of the phenylpropane metabolic pathway showed that phenylalanine was gradually transformed into proanthocyanidins and other secondary metabolites with the development of endopleura. A total of 49 unigenes related to polyphenol synthesis were identified by transcriptome analysis of endopleura. The expression patterns of PAL, C4H, 4CL, CHS, CHI, F3H, LDOX, and ANR were similar, and their expression levels were highest in endopleura at maturity. Transcriptome and metabolome analysis showed that endopleura rapidly synthesized and accumulated polyphenols during maturation. Moreover, the transcription factor MYB111 played an important role in synthesizing polyphenols in endopleura, and its expression pattern was positively correlated with the accumulation pattern of quercetin, kaempferol, and proanthocyanidins. MYB111 was co-expressed with NAP, NAC, ATR1, and other genes related to cell senescence and abiotic stress response. Our study analyzed the composition and molecular synthesis mechanism of polyphenols in walnut endopleura, and provided new perspectives and insights regarding the nutritional research of walnut nuts.
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21
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Smalley S, Hellmann H. Review: Exploring possible approaches using ubiquitylation and sumoylation pathways in modifying plant stress tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 319:111275. [PMID: 35487671 DOI: 10.1016/j.plantsci.2022.111275] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Ubiquitin and similar proteins, such as SUMO, are utilized by plants to modify target proteins to rapidly change their stability and activity in cells. This review will provide an overview of these crucial protein interactions with a focus on ubiquitylation and sumoylation in plants and how they contribute to stress tolerance. The work will also explore possibilities to use these highly conserved pathways for novel approaches to generate more robust crop plants better fit to cope with abiotic and biotic stress situations.
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Affiliation(s)
- Samuel Smalley
- Washington State University, Pullman, WA 99164, United States
| | - Hanjo Hellmann
- Washington State University, Pullman, WA 99164, United States.
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22
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Bai X, Wang X, Wang Y, Wei Y, Fu Y, Rao J, Ma Y, Zeng Z, Li F, Wang M, Zhu S. Genome-Wide Association Study of Six Forage Traits in Ramie ( Boehmeria nivea L. Gaud). PLANTS (BASEL, SWITZERLAND) 2022; 11:1443. [PMID: 35684216 PMCID: PMC9182863 DOI: 10.3390/plants11111443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Genome-wide association study (GWAS) of six forage traits using whole-genome sequencing data generated from 301 ramie accessions found that traits were continuously distributed; the maximum variant coefficient was fresh weight per clump (FWPC) (2019) and individual plant height (IPH) (2019) minimum. Correlation analysis demonstrated that 2019 and 2020 results were similar; all traits were correlated. GWAS analysis demonstrated that six traits exhibited consistent and precise association signals. Of the latter, 104 were significant and detected in 43 genomic regions. By screening forage trait-associated single nucleotide polymorphisms and combining Manhattan map with genome annotation, signals were categorized according to functional annotations. One loci associated with fresh weight per plant (FWP) (chromosome 5; Bnt05G007759), two associated with FWPC (chromosome 13; Bnt13G018582, and Bnt13G018583), and two associated with leaf dry weight per plant (LDWP) and dry weight per plant (DWP) (chromosome 4; Bnt04G005779 and Bnt04G005780), were identified. We describe forage trait candidate genes that are highly correlated with FWP and FWPC; Bnt05G007759 may be involved in nitrogen metabolism, while Bnt13G018582 and Bnt13G018583 may encode TEOSINTE branch 1/CYCLOIDEA/proliferating cytokine 1 (TCP) domains. Bnt04G005779 and Bnt04G005780, which may regulate growth and development, are highly related to LDWP and DWP. These genomic resources will provide a basis for breeding varieties.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Siyuan Zhu
- Correspondence: ; Tel.: +86-138-7580-0740
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23
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Amoanimaa-Dede H, Shao Z, Su C, Yeboah A, Zhu H. Genome-wide identification and characterization of F-box family proteins in sweet potato and its expression analysis under abiotic stress. Gene 2022; 817:146191. [PMID: 35026290 DOI: 10.1016/j.gene.2022.146191] [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: 05/05/2021] [Revised: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 11/04/2022]
Abstract
In this study, genome-wide characterization of F-box proteins in sweet potato yielded 243 IbFBX genes, unevenly distributed on the 15 chromosomes of sweet potato. Gene duplication analysis suggested segmental duplication as the principal factor influencing the expansive evolution of IbFBX genes in sweet potato. Phylogenetic analysis clustered F-box proteins in sweet potato, Arabidopsis, and rice into six clades (I-VI). Gene structure analysis of the IbFBX genes revealed that most of the genes within the same clade were highly conserved. Expression profiles of IbFBX family genes in 9 different tissues and under stress conditions revealed that the IbFBXs were highly upregulated or downregulated in response to salt and drought stress, suggesting their significant roles in abiotic stress response and adaptation. Knowledge of the diverse functions and expression patterns of IbFBXs presents a solid theoretical basis for annotating the functions of IbFBXs and further facilitate the molecular breeding of sweet potato.
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Affiliation(s)
- Hanna Amoanimaa-Dede
- Department of Biotechnology, College of Coastal Agricultural Sciences, Guangdong Ocean University, No. 1 Haida Road, Mazhang District, Zhanjiang 524088, Guangdong, PR China
| | - Zhengwei Shao
- Department of Biotechnology, College of Coastal Agricultural Sciences, Guangdong Ocean University, No. 1 Haida Road, Mazhang District, Zhanjiang 524088, Guangdong, PR China
| | - Chuntao Su
- Department of Biotechnology, College of Coastal Agricultural Sciences, Guangdong Ocean University, No. 1 Haida Road, Mazhang District, Zhanjiang 524088, Guangdong, PR China
| | - Akwasi Yeboah
- Department of Biotechnology, College of Coastal Agricultural Sciences, Guangdong Ocean University, No. 1 Haida Road, Mazhang District, Zhanjiang 524088, Guangdong, PR China
| | - Hongbo Zhu
- Department of Biotechnology, College of Coastal Agricultural Sciences, Guangdong Ocean University, No. 1 Haida Road, Mazhang District, Zhanjiang 524088, Guangdong, PR China.
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24
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Iantcheva A, Zhiponova M, Revalska M, Heyman J, Dincheva I, Badjakov I, De Geyter N, Boycheva I, Goormachtig S, De Veylder L. A common F-box gene regulates the leucine homeostasis of Medicago truncatula and Arabidopsis thaliana. PROTOPLASMA 2022; 259:277-290. [PMID: 33973099 DOI: 10.1007/s00709-021-01662-w] [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: 11/04/2020] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
The F-box domain is a conserved structural protein motif that most frequently interacts with the SKP1 protein, the core of the SCFs (SKP1-CULLIN-F-box protein ligase) E3 ubiquitin protein ligases. As part of the SCF complexes, the various F-box proteins recruit substrates for degradation through ubiquitination. In this study, we functionally characterized an F-box gene (MtF-box) identified earlier in a population of Tnt1 retrotransposon-tagged mutants of Medicago truncatula and its Arabidopsis thaliana homolog (AtF-box) using gain- and loss-of-function plants. We highlighted the importance of MtF-box in leaf development of M. truncatula. Protein-protein interaction analyses revealed the 2-isopropylmalate synthase (IPMS) protein as a common interactor partner of MtF-box and AtF-box, being a key enzyme in the biosynthesis pathway of the branched-chain amino acid leucine. For further detailed analysis, we focused on AtF-box and its role during the cell division cycle. Based on this work, we suggest a mechanism for the role of the studied F-box gene in regulation of leucine homeostasis, which is important for growth.
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Affiliation(s)
- Anelia Iantcheva
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164, Sofia, Bulgaria.
| | - Miroslava Zhiponova
- Department of Plant Physiology, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tsankov blvd., 1164, Sofia, Bulgaria
| | - Miglena Revalska
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164, Sofia, Bulgaria
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Ivayla Dincheva
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164, Sofia, Bulgaria
| | - Ilian Badjakov
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tsankov 8, 1164, Sofia, Bulgaria
| | - Nathan De Geyter
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Irina Boycheva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bl. 21, 1113, Sofia, Bulgaria
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
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25
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Li BW, Gao S, Yang ZM, Song JB. The F-box E3 ubiquitin ligase AtSDR is involved in salt and drought stress responses in Arabidopsis. Gene 2022; 809:146011. [PMID: 34655724 DOI: 10.1016/j.gene.2021.146011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/24/2021] [Accepted: 10/11/2021] [Indexed: 11/04/2022]
Abstract
F-box protein genes have been shown to play vital roles in plant development and stress respones. In Arabidopsis, there are more than 600 F-box proteins, and most of their functions are unclear. The present study shows that the F-box (SKP1-Cullin/CDC53-F-box) gene At5g15710 (Salt and Drought Responsiveness, SDR) is involved in abiotic stress responses in Arabidopsis. SDR is expressed in all tissues of Arabidopsis and is upregulated by salt and heat stresses and ABA treatment but downregulated by drought stress. Subcellular localization analysis shows that the SDR protein colocalizes with the nucleus. 35S:AntiSDR plants are hypersensitive to salt stress, but 35S:SDR plants display a salt-tolerant phenotype. Furthermore, 35S:SDR plants are hypersensitive to drought stress, while 35S:AntiSDR plants are significantly more drought tolerant. Overall, our results suggest that SDR is involved in salt and drought stress responses in Arabidopsis.
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Affiliation(s)
- Bo Wen Li
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China; Department of Neurosurgery, The First People's Hospital of Changzhou, Changzhou 213003 , PR China
| | - Shuai Gao
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas, College of Horticulture Science, Zhejiang A&F University, Hangzhou, Zhejiang 311300, PR China
| | - Zhi Min Yang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jian Bo Song
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang 330045, PR China.
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QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea. Heredity (Edinb) 2022; 128:411-419. [PMID: 35022582 PMCID: PMC9177671 DOI: 10.1038/s41437-021-00486-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 12/20/2022] Open
Abstract
To identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F2) derived from the cross combination- ICP 5529 × ICP 11605. A total of 126.63 million paired-end (PE) whole-genome resequencing data were generated for five samples, including one parent ICP 5529 (obcordate leaf and late-flowering plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTL-seq identified two significant genomic regions, one on CcLG03 (1.58 Mb region spanned from 19.22 to 20.80 Mb interval) for days to flowering (LF and EF pools) and another on CcLG08 (2.19 Mb region spanned from 6.69 to 8.88 Mb interval) for OLF and LLF pools, respectively. Analysis of genomic regions associated SNPs with days to flowering and leaf shape revealed 5 genic SNPs present in the unique regions. The identified genomic regions for days to flowering were also validated with the genotyping-by-sequencing based classical QTL mapping method. A comparative analysis of the identified seven genes associated with days to flowering on 12 Fabaceae genomes, showed synteny with 9 genomes. A total of 153 genes were identified through the synteny analysis ranging from 13 to 36. This study demonstrates the usefulness of QTL-seq approach in precise identification of candidate gene(s) for days to flowering and leaf shape which can be deployed for pigeonpea improvement. QTL-seq approach was utilized for mapping of genomic regions/genes associated with days to flowering and leaf shape in pigeonpea. Analysis of genomic regions and associated SNPs with days to flowering and leaf shape revealed 1 and 4 non-synonymous SNPs, respectively. The study demonstrated sequencing-based trait mapping approach can accelerate trait mapping of the targeted traits.
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Lu L, Chen H, Wang X, Zhao Y, Yao X, Xiong B, Deng Y, Zhao D. Genome-level diversification of eight ancient tea populations in the Guizhou and Yunnan regions identifies candidate genes for core agronomic traits. HORTICULTURE RESEARCH 2021; 8:190. [PMID: 34376642 PMCID: PMC8355299 DOI: 10.1038/s41438-021-00617-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 05/18/2023]
Abstract
The ancient tea plant, as a precious natural resource and source of tea plant genetic diversity, is of great value for studying the evolutionary mechanism, diversification, and domestication of plants. The overall genetic diversity among ancient tea plants and the genetic changes that occurred during natural selection remain poorly understood. Here, we report the genome resequencing of eight different groups consisting of 120 ancient tea plants: six groups from Guizhou Province and two groups from Yunnan Province. Based on the 8,082,370 identified high-quality SNPs, we constructed phylogenetic relationships, assessed population structure, and performed genome-wide association studies (GWAS). Our phylogenetic analysis showed that the 120 ancient tea plants were mainly clustered into three groups and five single branches, which is consistent with the results of principal component analysis (PCA). Ancient tea plants were further divided into seven subpopulations based on genetic structure analysis. Moreover, it was found that the variation in ancient tea plants was not reduced by pressure from the external natural environment or artificial breeding (nonsynonymous/synonymous = 1.05). By integrating GWAS, selection signals, and gene function prediction, four candidate genes were significantly associated with three leaf traits, and two candidate genes were significantly associated with plant type. These candidate genes can be used for further functional characterization and genetic improvement of tea plants.
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Affiliation(s)
- Litang Lu
- College of Tea Science, Guizhou University, Guiyang, 550025, People's Republic of China
- College of Life Sciences and The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in the Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Hufang Chen
- College of Tea Science, Guizhou University, Guiyang, 550025, People's Republic of China
- College of Life Sciences and The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in the Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Xiaojing Wang
- College of Tea Science, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Yichen Zhao
- College of Tea Science, Guizhou University, Guiyang, 550025, People's Republic of China
- College of Life Sciences and The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in the Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Xinzhuan Yao
- College of Tea Science, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Biao Xiong
- College of Tea Science, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Yanli Deng
- College of Tea Science, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Degang Zhao
- College of Life Sciences and The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in the Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, People's Republic of China.
- Guizhou Academy of Agricultural Sciences, Guiyang, 550025, People's Republic of China.
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28
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Parida AP, Srivastava A, Mathur S, Sharma AK, Kumar R. Identification, evolutionary profiling, and expression analysis of F-box superfamily genes under phosphate deficiency in tomato. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:349-362. [PMID: 33730620 DOI: 10.1016/j.plaphy.2021.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/02/2021] [Indexed: 05/26/2023]
Abstract
F-box genes are an integral component of the Skp1-cullin-F-box (SCF) complex in eukaryotes. These genes are primarily involved in determining substrate specificities during cellular proteolysis. Here we report that 410 members constitute the F-box superfamily in tomato. Based on the incidence of C-terminal domains, these genes fell into ten subfamilies, leucine-rich repeat domain-containing F-box members constituting the largest subfamily. The F-box genes are present on all 12 chromosomes with varying gene densities. Both segmental and tandem duplication events contribute significantly to their expansion in the tomato genome. The syntenic analysis revealed close relationships among F-box homologs within Solanaceae species genomes. Transcript profiling of F-box members identified several ripening-associated genes with altered expression in the ripening mutants. RNA-sequencing data analysis showed that phosphate (Pi) deficiency affected 55 F-box transcripts in the Pi-deficient seedlings compared to their control seedlings. The persistent up-regulation of eight members, including two phloem protein 2B (PP2-B) genes, PP2-B15, and MATERNAL EFFECT EMBRYO ARREST 66 (MEE66) homologs, at multiple time-points in the roots, shoot, and seedling, point towards their pivotal roles in Pi starvation response in tomato. The attenuation of such upregulation in sucrose absence revealed the necessity of this metabolite for robust activation of these genes in the Pi-deficient seedlings. Altogether, this study identifies novel F-box genes with potential roles in fruit ripening and Pi starvation response and unlocks new avenues for functional characterization of candidate genes in tomato and other related species.
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Affiliation(s)
- Adwaita Prasad Parida
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Alok Srivastava
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Amity Education Valley, Gurgaon, India; Institute of Bioinformatics and Computational Biology, Visakhapatnam, Andhra Pradesh, India
| | - Saloni Mathur
- National Institute of Plant Genome Research, New Delhi, India
| | - Arun Kumar Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Rahul Kumar
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India.
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29
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Zhou S, Yang T, Mao Y, Liu Y, Guo S, Wang R, Fangyue G, He L, Zhao B, Bai Q, Li Y, Zhang X, Wang D, Wang C, Wu Q, Yang Y, Liu Y, Tadege M, Chen J. The F-box protein MIO1/SLB1 regulates organ size and leaf movement in Medicago truncatula. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2995-3011. [PMID: 33506247 PMCID: PMC8023213 DOI: 10.1093/jxb/erab033] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
The size of leaf and seed organs, determined by the interplay of cell proliferation and expansion, is closely related to the final yield and quality of forage and crops. Yet the cellular and molecular mechanisms underlying organ size modulation remain poorly understood, especially in legumes. Here, MINI ORGAN1 (MIO1), which encodes an F-box protein SMALL LEAF AND BUSHY1 (SLB1) recently reported to control lateral branching in Medicago truncatula, was identified as a key regulator of organ size. We show that loss-of-function of MIO1/SLB1 severely reduced organ size. Conversely, plants overexpressing MIO1/SLB1 had enlarged organs. Cellular analysis revealed that MIO1/SLB1 controlled organ size mainly by modulating primary cell proliferation during the early stages of leaf development. Biochemical analysis revealed that MIO1/SLB1 could form part of SKP1/Cullin/F-box (SCF) E3 ubiquitin ligase complex, to target BIG SEEDS1 (BS1), a repressor of primary cell division, for degradation. Interestingly, we found that MIO1/SLB1 also played a key role in pulvinus development and leaf movement by modulating cell proliferation of the pulvinus as leaves developed. Our study not only demonstrates a conserved role of MIO1/SLB1 in the control of organ size in legumes, but also sheds light on the novel function of MIO1/SLB1 in leaf movement.
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Affiliation(s)
- Shaoli Zhou
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tianquan Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yawen Mao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ye Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Shiqi Guo
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruoruo Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Genwang Fangyue
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liangliang He
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Baolin Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Quanzi Bai
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Youhan Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiaojia Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dongfa Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Chaoqun Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qing Wu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuanfan Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, China
| | - Yu Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK, USA
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, China
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30
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Hüther P, Schandry N, Jandrasits K, Bezrukov I, Becker C. ARADEEPOPSIS, an Automated Workflow for Top-View Plant Phenomics using Semantic Segmentation of Leaf States. THE PLANT CELL 2020; 32:3674-3688. [PMID: 33037149 PMCID: PMC7721323 DOI: 10.1105/tpc.20.00318] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/28/2020] [Accepted: 10/07/2020] [Indexed: 06/03/2023]
Abstract
Linking plant phenotype to genotype is a common goal to both plant breeders and geneticists. However, collecting phenotypic data for large numbers of plants remain a bottleneck. Plant phenotyping is mostly image based and therefore requires rapid and robust extraction of phenotypic measurements from image data. However, because segmentation tools usually rely on color information, they are sensitive to background or plant color deviations. We have developed a versatile, fully open-source pipeline to extract phenotypic measurements from plant images in an unsupervised manner. ARADEEPOPSIS (https://github.com/Gregor-Mendel-Institute/aradeepopsis) uses semantic segmentation of top-view images to classify leaf tissue into three categories: healthy, anthocyanin rich, and senescent. This makes it particularly powerful at quantitative phenotyping of different developmental stages, mutants with aberrant leaf color and/or phenotype, and plants growing in stressful conditions. On a panel of 210 natural Arabidopsis (Arabidopsis thaliana) accessions, we were able to not only accurately segment images of phenotypically diverse genotypes but also to identify known loci related to anthocyanin production and early necrosis in genome-wide association analyses. Our pipeline accurately processed images of diverse origin, quality, and background composition, and of a distantly related Brassicaceae. ARADEEPOPSIS is deployable on most operating systems and high-performance computing environments and can be used independently of bioinformatics expertise and resources.
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Affiliation(s)
- Patrick Hüther
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Niklas Schandry
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
- Genetics, Faculty of Biology, Ludwig-Maximilians-University München, 82152 Martinsried, Germany
| | - Katharina Jandrasits
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Ilja Bezrukov
- Department of Molecular Biology, Max Planck Institute of Developmental Biology, 72076 Tübingen, Germany
| | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
- Genetics, Faculty of Biology, Ludwig-Maximilians-University München, 82152 Martinsried, Germany
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31
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Madritsch S, Bomers S, Posekany A, Burg A, Birke R, Emerstorfer F, Turetschek R, Otte S, Eigner H, Sehr EM. Integrative transcriptomics reveals genotypic impact on sugar beet storability. PLANT MOLECULAR BIOLOGY 2020; 104:359-378. [PMID: 32754876 PMCID: PMC7593311 DOI: 10.1007/s11103-020-01041-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/25/2020] [Indexed: 06/11/2023]
Abstract
An integrative comparative transcriptomic approach on six sugar beet varieties showing different amount of sucrose loss during storage revealed genotype-specific main driver genes and pathways characterizing storability. Sugar beet is next to sugar cane one of the most important sugar crops accounting for about 15% of the sucrose produced worldwide. Since its processing is increasingly centralized, storage of beet roots over an extended time has become necessary. Sucrose loss during storage is a major concern for the sugar industry because the accumulation of invert sugar and byproducts severely affect sucrose manufacturing. This loss is mainly due to ongoing respiration, but changes in cell wall composition and pathogen infestation also contribute. While some varieties can cope better during storage, the underlying molecular mechanisms are currently undiscovered. We applied integrative transcriptomics on six varieties exhibiting different levels of sucrose loss during storage. Already prior to storage, well storable varieties were characterized by a higher number of parenchyma cells, a smaller cell area, and a thinner periderm. Supporting these findings, transcriptomics identified changes in genes involved in cell wall modifications. After 13 weeks of storage, over 900 differentially expressed genes were detected between well and badly storable varieties, mainly in the category of defense response but also in carbohydrate metabolism and the phenylpropanoid pathway. These findings were confirmed by gene co-expression network analysis where hub genes were identified as main drivers of invert sugar accumulation and sucrose loss. Our data provide insight into transcriptional changes in sugar beet roots during storage resulting in the characterization of key pathways and hub genes that might be further used as markers to improve pathogen resistance and storage properties.
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Affiliation(s)
- Silvia Madritsch
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Tulln, Austria
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Medical University of Vienna, Vienna, Austria
| | - Svenja Bomers
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Tulln, Austria
| | - Alexandra Posekany
- University of Technology Vienna, Research Unit of Computational Statistics, Vienna, Austria
| | - Agnes Burg
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Tulln, Austria
| | - Rebekka Birke
- AGRANA Research & Innovation Center GmbH, Tulln, Austria
| | | | | | - Sandra Otte
- Strube Research GmbH & Co. KG, Söllingen, Germany
| | - Herbert Eigner
- AGRANA Research & Innovation Center GmbH, Tulln, Austria
| | - Eva M Sehr
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Tulln, Austria.
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32
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Hong MJ, Kim JB, Seo YW, Kim DY. F-Box Genes in the Wheat Genome and Expression Profiling in Wheat at Different Developmental Stages. Genes (Basel) 2020; 11:genes11101154. [PMID: 33007852 PMCID: PMC7650748 DOI: 10.3390/genes11101154] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 11/16/2022] Open
Abstract
Genes of the F-box family play specific roles in protein degradation by post-translational modification in several biological processes, including flowering, the regulation of circadian rhythms, photomorphogenesis, seed development, leaf senescence, and hormone signaling. F-box genes have not been previously investigated on a genome-wide scale; however, the establishment of the wheat (Triticum aestivum L.) reference genome sequence enabled a genome-based examination of the F-box genes to be conducted in the present study. In total, 1796 F-box genes were detected in the wheat genome and classified into various subgroups based on their functional C-terminal domain. The F-box genes were distributed among 21 chromosomes and most showed high sequence homology with F-box genes located on the homoeologous chromosomes because of allohexaploidy in the wheat genome. Additionally, a synteny analysis of wheat F-box genes was conducted in rice and Brachypodium distachyon. Transcriptome analysis during various wheat developmental stages and expression analysis by quantitative real-time PCR revealed that some F-box genes were specifically expressed in the vegetative and/or seed developmental stages. A genome-based examination and classification of F-box genes provide an opportunity to elucidate the biological functions of F-box genes in wheat.
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Affiliation(s)
- Min Jeong Hong
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu, Jeongeup 56212, Korea; (M.J.H.); (J.-B.K.)
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu, Jeongeup 56212, Korea; (M.J.H.); (J.-B.K.)
| | - Yong Weon Seo
- Division of Biotechnology, Korea University, 145 Anam-ro, Seongbuk-Gu, Seoul 02841, Korea;
| | - Dae Yeon Kim
- Institute of Animal Molecular Biotechnology, Korea University, 145 Anam-ro, Seongbuk-Gu, Seoul 02841, Korea
- Correspondence:
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33
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Vercruysse J, Baekelandt A, Gonzalez N, Inzé D. Molecular networks regulating cell division during Arabidopsis leaf growth. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2365-2378. [PMID: 31748815 PMCID: PMC7178401 DOI: 10.1093/jxb/erz522] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/21/2019] [Indexed: 05/02/2023]
Abstract
Leaves are the primary organs for photosynthesis, and as such have a pivotal role for plant growth and development. Leaf development is a multifactorial and dynamic process involving many genes that regulate size, shape, and differentiation. The processes that mainly drive leaf development are cell proliferation and cell expansion, and numerous genes have been identified that, when ectopically expressed or down-regulated, increase cell number and/or cell size during leaf growth. Many of the genes regulating cell proliferation are functionally interconnected and can be grouped into regulatory modules. Here, we review our current understanding of six important gene regulatory modules affecting cell proliferation during Arabidopsis leaf growth: ubiquitin receptor DA1-ENHANCER OF DA1 (EOD1), GROWTH REGULATING FACTOR (GRF)-GRF-INTERACTING FACTOR (GIF), SWITCH/SUCROSE NON-FERMENTING (SWI/SNF), gibberellin (GA)-DELLA, KLU, and PEAPOD (PPD). Furthermore, we discuss how post-mitotic cell expansion and these six modules regulating cell proliferation make up the final leaf size.
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Affiliation(s)
- Jasmien Vercruysse
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Alexandra Baekelandt
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Nathalie Gonzalez
- INRAE, Université de Bordeaux, UMR1332 Biologie du fruit et Pathologie, INRA Bordeaux Aquitaine, Villenave d’Ornon cedex, France
| | - Dirk Inzé
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Correspondence:
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34
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Abd-Hamid NA, Ahmad-Fauzi MI, Zainal Z, Ismail I. Diverse and dynamic roles of F-box proteins in plant biology. PLANTA 2020; 251:68. [PMID: 32072251 DOI: 10.1007/s00425-020-03356-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 02/05/2020] [Indexed: 05/23/2023]
Abstract
The SCF complex is a widely studied multi-subunit ring E3 ubiquitin ligase that tags targeted proteins with ubiquitin for protein degradation by the ubiquitin 26S-proteasome system (UPS). The UPS is an important system that generally keeps cellular events tightly regulated by purging misfolded or damaged proteins and selectively degrading important regulatory proteins. The specificity of this post-translational regulation is controlled by F-box proteins (FBPs) via selective recognition of a protein-protein interaction motif at the C-terminal domain. Hence, FBPs are pivotal proteins in determining the plant response in multiple scenarios. It is not surprising that the FBP family is one of the largest protein families in the plant kingdom. In this review, the roles of FBPs, specifically in plants, are compiled to provide insights into their involvement in secondary metabolites, plant stresses, phytohormone signalling, plant developmental processes and miRNA biogenesis.
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Affiliation(s)
- Nur-Athirah Abd-Hamid
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Muhammad-Izzat Ahmad-Fauzi
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Zamri Zainal
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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35
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Zhang S, Tian Z, Li H, Guo Y, Zhang Y, Roberts JA, Zhang X, Miao Y. Genome-wide analysis and characterization of F-box gene family in Gossypium hirsutum L. BMC Genomics 2019; 20:993. [PMID: 31856713 PMCID: PMC6921459 DOI: 10.1186/s12864-019-6280-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 11/13/2019] [Indexed: 11/18/2022] Open
Abstract
Background F-box proteins are substrate-recognition components of the Skp1-Rbx1-Cul1-F-box protein (SCF) ubiquitin ligases. By selectively targeting the key regulatory proteins or enzymes for ubiquitination and 26S proteasome mediated degradation, F-box proteins play diverse roles in plant growth/development and in the responses of plants to both environmental and endogenous signals. Studies of F-box proteins from the model plant Arabidopsis and from many additional plant species have demonstrated that they belong to a super gene family, and function across almost all aspects of the plant life cycle. However, systematic exploration of F-box family genes in the important fiber crop cotton (Gossypium hirsutum) has not been previously performed. The genome-wide analysis of the cotton F-box gene family is now possible thanks to the completion of several cotton genome sequencing projects. Results In current study, we first conducted a genome-wide investigation of cotton F-box family genes by reference to the published F-box protein sequences from other plant species. 592 F-box protein encoding genes were identified in the Gossypium hirsutume acc.TM-1 genome and, subsequently, we were able to present their gene structures, chromosomal locations, syntenic relationships with their parent species. In addition, duplication modes analysis showed that cotton F-box genes were distributed to 26 chromosomes, with the maximum number of genes being detected on chromosome 5. Although the WGD (whole-genome duplication) mode seems play a dominant role during cotton F-box gene expansion process, other duplication modes including TD (tandem duplication), PD (proximal duplication), and TRD (transposed duplication) also contribute significantly to the evolutionary expansion of cotton F-box genes. Collectively, these bioinformatic analysis suggest possible evolutionary forces underlying F-box gene diversification. Additionally, we also conducted analyses of gene ontology, and expression profiles in silico, allowing identification of F-box gene members potentially involved in hormone signal transduction. Conclusion The results of this study provide first insights into the Gossypium hirsutum F-box gene family, which lays the foundation for future studies of functionality, particularly those involving F-box protein family members that play a role in hormone signal transduction.
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Affiliation(s)
- Shulin Zhang
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China.,College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, China
| | - Zailong Tian
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China
| | - Haipeng Li
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China
| | - Yutao Guo
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China
| | - Yanqi Zhang
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China
| | - Jeremy A Roberts
- Faculty of Science and Engineering, School of Biological & Marine Sciences, University of Plymouth, Devon, UK
| | - Xuebin Zhang
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China.
| | - Yuchen Miao
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China.
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Dong MY, Fan XW, Pang XY, Li YZ. Decrypting tubby-like protein gene family of multiple functions in starch root crop cassava. AOB PLANTS 2019; 11:plz075. [PMID: 31871614 PMCID: PMC6920310 DOI: 10.1093/aobpla/plz075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/24/2019] [Indexed: 05/23/2023]
Abstract
Tubby-like proteins (TLPs) are ubiquitous in eukaryotes and function in abiotic stress tolerance of some plants. Cassava (Manihot esculenta Crantz) is a high-yield starch root crop and has a high tolerance to poor soil conditions and abiotic stress. However, little is known about TLP gene characteristics and their expression in cassava. We identified cassava TLP genes, MeTLPs, and further analysed structure, duplication, chromosome localization and collinearity, cis-acting elements in the promoter regions and expression patterns of MeTLPs, and three-dimensional structure of the encoded proteins MeTLPs. In conclusion, there is a MeTLP family containing 13 members, which are grouped into A and C subfamilies. There are 11 pairs of MeTLPs that show the duplication which took place between 10.11 and 126.69 million years ago. Two MeTLPs 6 and 9 likely originate from one gene in an ancestral species, may be common ancestors for other MeTLPs and would most likely not be eligible for ubiquitin-related protein degradation because their corresponding proteins (MeTLPs 6 and 9) have no the F-box domain in the N-terminus. MeTLPs feature differences in the number from TLPs in wheat, apple, Arabidopsis, poplar and maize, and are highlighted by segmental duplication but more importantly by the chromosomal collinearity with potato StTLPs. MeTLPs are at least related to abiotic stress tolerance in cassava. However, the subtle differences in function among MeTLPs are predictable partly because of their differential expression profiles, which are coupled with various cis‑acting elements existing in the promoter regions depending on genes.
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Affiliation(s)
- Ming-You Dong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Xian-Wei Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Xiang-Yu Pang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - You-Zhi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
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Villajuana-Bonequi M, Matei A, Ernst C, Hallab A, Usadel B, Doehlemann G. Cell type specific transcriptional reprogramming of maize leaves during Ustilago maydis induced tumor formation. Sci Rep 2019; 9:10227. [PMID: 31308451 PMCID: PMC6629649 DOI: 10.1038/s41598-019-46734-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 07/04/2019] [Indexed: 02/05/2023] Open
Abstract
Ustilago maydis is a biotrophic pathogen and well-established genetic model to understand the molecular basis of biotrophic interactions. U. maydis suppresses plant defense and induces tumors on all aerial parts of its host plant maize. In a previous study we found that U. maydis induced leaf tumor formation builds on two major processes: the induction of hypertrophy in the mesophyll and the induction of cell division (hyperplasia) in the bundle sheath. In this study we analyzed the cell-type specific transcriptome of maize leaves 4 days post infection. This analysis allowed identification of key features underlying the hypertrophic and hyperplasic cell identities derived from mesophyll and bundle sheath cells, respectively. We examined the differentially expressed (DE) genes with particular focus on maize cell cycle genes and found that three A-type cyclins, one B-, D- and T-type are upregulated in the hyperplasic tumorous cells, in which the U. maydis effector protein See1 promotes cell division. Additionally, most of the proteins involved in the formation of the pre-replication complex (pre-RC, that assure that each daughter cell receives identic DNA copies), the transcription factors E2F and DPa as well as several D-type cyclins are deregulated in the hypertrophic cells.
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Affiliation(s)
- Mitzi Villajuana-Bonequi
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), BioCenter, University of Cologne, Zülpicher Str. 47a, Cologne, 50674, Germany
| | - Alexandra Matei
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), BioCenter, University of Cologne, Zülpicher Str. 47a, Cologne, 50674, Germany
| | - Corinna Ernst
- Center for Familial Breast and Ovarian Cancer, Medical Faculty, University Hospital Cologne, University of Cologne, Cologne, 50931, Germany
| | - Asis Hallab
- BioSC, IBG-2, Institute of Botany, RWTH Aachen, Worringer Weg 3, Aachen, 52074, Germany
| | - Björn Usadel
- BioSC, IBG-2, Institute of Botany, RWTH Aachen, Worringer Weg 3, Aachen, 52074, Germany
| | - Gunther Doehlemann
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), BioCenter, University of Cologne, Zülpicher Str. 47a, Cologne, 50674, Germany.
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Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Peanut. Genes (Basel) 2019; 10:genes10070536. [PMID: 31311183 PMCID: PMC6679159 DOI: 10.3390/genes10070536] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/29/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in various regulatory processes although they do not encode protein. Presently, there is little information regarding the identification of lncRNAs in peanut (Arachis hypogaea Linn.). In this study, 50,873 lncRNAs of peanut were identified from large-scale published RNA sequencing data that belonged to 124 samples involving 15 different tissues. The average lengths of lncRNA and mRNA were 4335 bp and 954 bp, respectively. Compared to the mRNAs, the lncRNAs were shorter, with fewer exons and lower expression levels. The 4713 co-expression lncRNAs (expressed in all samples) were used to construct co-expression networks by using the weighted correlation network analysis (WGCNA). LncRNAs correlating with the growth and development of different peanut tissues were obtained, and target genes for 386 hub lncRNAs of all lncRNAs co-expressions were predicted. Taken together, these findings can provide a comprehensive identification of lncRNAs in peanut.
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Xu C, Ge Y, Wang J. Molecular basis underlying the successful invasion of hexaploid cytotypes of Solidago canadensis L.: Insights from integrated gene and miRNA expression profiling. Ecol Evol 2019; 9:4820-4852. [PMID: 31031947 PMCID: PMC6476842 DOI: 10.1002/ece3.5084] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 02/20/2019] [Accepted: 03/01/2019] [Indexed: 12/04/2022] Open
Abstract
Dissecting complex connections between cytogenetic traits (ploidy levels) and plant invasiveness has emerged as a popular research subject in the field of invasion biology. Although recent work suggests that polyploids are more likely to be invasive than their corresponding diploids, the molecular basis underlying the successful invasion of polyploids remains largely unexplored. To this end, we adopted an RNA-seq and sRNA-seq approach to describe how polyploids mediate invasiveness differences in two contrasting cytotypes of Solidago canadensis L., a widespread wild hexaploid invader with localized cultivated diploid populations. Our analysis of the leaf transcriptome revealed 116,801 unigenes, of which 12,897 unigenes displayed significant differences in expression levels. A substantial number of these differentially expressed unigenes (DEUs) were significantly associated with the biosynthesis of secondary metabolites, carbohydrate metabolism, lipid metabolism, and environmental adaptation pathways. Gene Ontology term enrichment-based categorization of DEU-functions was consistent with this observation, as terms related to single-organism, cellular, and metabolic processes including catalytic, binding, transporter, and enzyme regulator activity were over-represented. Concomitantly, 186 miRNAs belonging to 44 miRNA families were identified in the same leaf tissues, with 59 miRNAs being differentially expressed. Furthermore, we discovered 83 miRNA-target interacting pairs that were oppositely regulated, and a meticulous study of these targets depicted that several unigenes encoding transcription factors, DNA methyltransferase, and leucine-rich repeat receptor-like kinases involved in the stress response were greatly influenced. Collectively, these transcriptional and epigenetic data provide new insights into miRNA-mediated gene expression regulatory mechanisms that may operate in hexaploid cytotypes to favor successful invasion.
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Affiliation(s)
- Chanchan Xu
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Yimeng Ge
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
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Genome-Wide Identification and Transcriptional Expression Profiles of the F-box Gene Family in Common Walnut (Juglans regia L.). FORESTS 2019. [DOI: 10.3390/f10030275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The common walnut (or Persian walnut), Juglans regia L., is an economically important temperate tree species valued for both its edible nut and high-quality wood. F-box gene family members are involved in plant development, which includes regulating plant development, reproduction, cellular protein degradation, response to biotic and abiotic stresses, and flowering. However, in common walnut (J. regia), there are no reports about the F-box gene family. Here, we report a genome-wide identification of J. regia F-box genes and analyze their phylogeny, duplication, microRNA, pathway, and transcriptional expression profile. In this study, 74 F-box genes were identified and clustered into three groups based on phylogenetic analysis and eight subfamilies based on special domains in common walnut. These common walnut F-box genes are distributed on 31 different pseudo-chromosomes. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and microRNA profiles showed that the F-box gene family might play a critical role in the flowering of common walnut. The expressions were significantly higher in female flowers and male flowers compared with leaf and hull tissues at a transcriptome level. The results revealed that the expressions of the F-box gene in female flowers were positively correlated with male flowers, but there was no correlation between any other tissue combinations in common walnut. Our results provided insight into the general characteristics of the F-box genes in common walnut.
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Yang L, Liu H, Zhao J, Pan Y, Cheng S, Lietzow CD, Wen C, Zhang X, Weng Y. LITTLELEAF (LL) encodes a WD40 repeat domain-containing protein associated with organ size variation in cucumber. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:834-847. [PMID: 29901823 DOI: 10.1111/tpj.13991] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 05/03/2023]
Abstract
Plants employ tight genetic control to integrate intrinsic growth signals and environmental cues to enable organs to grow to a defined size. Many genes contributing to cell proliferation and/or cell expansion, and consequently organ size control, have been identified, but the regulatory pathways are poorly understood. Here we have characterized a cucumber littleleaf (ll) mutant which exhibits smaller organ sizes but more lateral branches than the wild type. The small organ size in ll was due to a reduction of both cell number and cell size. Quantitative trait locus (QTL) analyses revealed co-localization of major-effect QTLs for fruit size, fruit and seed weight, as well as number of lateral branches, with the LL locus indicating pleiotropic effects of the ll mutation. We demonstrate that LL is an ortholog of Arabidopsis STERILE APETALA (SAP) encoding a WD40 repeat domain-containing protein; the mutant protein differed from the wild type by a single amino acid substitution (W264G) in the second WD40 repeat. W264 was conserved in 34 vascular plant genomes examined. Phylogenetic analysis suggested that LL originated before the emergence of flowering plants but was lost in the grass genome lineage. The function of LL in organ size control was confirmed by its overexpression in transgenic cucumbers and ectopic expression in Arabidopsis. Transcriptome profiling in LL and ll bulks revealed a complex regulatory network for LL-mediated organ size variation that involves several known organ size regulators and associated pathways. The data support LL as an important player in organ size control and lateral branch development in cucumber.
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Affiliation(s)
- Luming Yang
- Horticulture Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hanqiang Liu
- Horticulture Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jianyu Zhao
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, 100193, China
| | - Yupeng Pan
- Horticulture Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Siyuan Cheng
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
| | - Calvin D Lietzow
- Horticulture Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Changlong Wen
- Horticulture Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | - Xiaolan Zhang
- Department of Vegetable Sciences, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, 100193, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
- USDA-ARS, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, WI, 53706, USA
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Li J, Wang Y, Wei J, Pan Y, Su C, Zhang X. A tomato proline-, lysine-, and glutamic-rich type gene SpPKE1 positively regulates drought stress tolerance. Biochem Biophys Res Commun 2018; 499:777-782. [PMID: 29608895 DOI: 10.1016/j.bbrc.2018.03.222] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 03/30/2018] [Indexed: 11/29/2022]
Abstract
Plant abiotic resistance in cultivated species features limited variability. Using genes of wild species serves as a valid approach for improving abiotic resistance of cultivated plants. In this study, we uncovered a previously uncharacterized proline-, lysine-, and glutamic-rich protein gene (SpPKE1), which was isolated from drought-resistant wild tomato species Solanum pennellii (LA0716). When M82, which is a drought-sensitive tomato cultivar, was engineered to overexpress SpPKE1, its tolerance under drought stress was significantly improved by the accumulation of more chlorophyll, proline, and limited malondialdehyde compared with that in RNA interference (RNAi)-suppression lines, which were more sensitive than the wild-type plants. Several ion transporter genes, abiotic-related transcriptional factors, and reactive oxygen species-scavenging genes were upregulated in PKE1 overexpression (OE) lines but downregulated in RNAi plants. OE of SpPKE1 enhanced drought tolerance in tobacco. Screening results of yeast two-hybrid protein-protein interaction revealed that SpPKE1 can bind to an F-box protein that plays an important role in plant drought resistance. We posited that PKE1 enhanced drought tolerance by modulating the expressions of stress-responsive genes and interacting with the F-box protein.
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Affiliation(s)
- Jinhua Li
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architechture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Yaling Wang
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architechture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Juanjuan Wei
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architechture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Yu Pan
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architechture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Chenggang Su
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architechture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Xingguo Zhang
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architechture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing, 400715, China.
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Suzuki M, Shinozuka N, Hirakata T, Nakata MT, Demura T, Tsukaya H, Horiguchi G. OLIGOCELLULA1/ HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES15 Promotes Cell Proliferation With HISTONE DEACETYLASE9 and POWERDRESS During Leaf Development in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:580. [PMID: 29774040 PMCID: PMC5943563 DOI: 10.3389/fpls.2018.00580] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/13/2018] [Indexed: 05/18/2023]
Abstract
Organ size regulation is dependent on the precise spatial and temporal regulation of cell proliferation and cell expansion. A number of transcription factors have been identified that play a key role in the determination of aerial lateral organ size, but their functional relationship to various chromatin modifiers has not been well understood. To understand how leaf size is regulated, we previously isolated the oligocellula1 (oli1) mutant of Arabidopsis thaliana that develops smaller first leaves than the wild type (WT) mainly due to a reduction in the cell number. In this study, we further characterized oli1 leaf phenotypes and identified the OLI1 gene as well as interaction partners of OLI1. Detailed characterizations of leaf development suggested that the cell proliferation rate in oli1 leaf primordia is lower than that in the WT. In addition, oli1 was associated with a slight delay of the progression from the juvenile to adult phases of leaf traits. A classical map-based approach demonstrated that OLI1 is identical to HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES15 (HOS15). HOS15/OLI1 encodes a homolog of human transducin β-like protein1 (TBL1). TBL1 forms a transcriptional repression complex with the histone deacetylase (HDAC) HDAC3 and either nuclear receptor co-repressor (N-CoR) or silencing mediator for retinoic acid and thyroid receptor (SMRT). We found that mutations in HISTONE DEACETYLASE9 (HDA9) and a switching-defective protein 3, adaptor 2, N-CoR, and transcription factor IIIB-domain protein gene, POWERDRESS (PWR), showed a small-leaf phenotype similar to oli1. In addition, hda9 and pwr did not further enhance the oli1 small-leaf phenotype, suggesting that these three genes act in the same pathway. Yeast two-hybrid assays suggested physical interactions, wherein PWR probably bridges HOS15/OLI1 and HDA9. Earlier studies suggested the roles of HOS15, HDA9, and PWR in transcriptional repression. Consistently, transcriptome analyses showed several genes commonly upregulated in the three mutants. From these findings, we propose a possibility that HOS15/OLI1, PWR, and HDA9 form an evolutionary conserved transcription repression complex that plays a positive role in the regulation of final leaf size.
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Affiliation(s)
- Marina Suzuki
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Nanae Shinozuka
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Tomohiro Hirakata
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Miyuki T. Nakata
- Research Center for Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Hirokazu Tsukaya
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Okazaki Institute for Integrative Bioscience, Okazaki, Japan
| | - Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
- Research Center for Life Science, College of Science, Rikkyo University, Tokyo, Japan
- *Correspondence: Gorou Horiguchi,
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