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Bowman JL, Moyroud E. Reflections on the ABC model of flower development. THE PLANT CELL 2024; 36:1334-1357. [PMID: 38345422 PMCID: PMC11062442 DOI: 10.1093/plcell/koae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/07/2024] [Indexed: 05/02/2024]
Abstract
The formulation of the ABC model by a handful of pioneer plant developmental geneticists was a seminal event in the quest to answer a seemingly simple question: how are flowers formed? Fast forward 30 years and this elegant model has generated a vibrant and diverse community, capturing the imagination of developmental and evolutionary biologists, structuralists, biochemists and molecular biologists alike. Together they have managed to solve many floral mysteries, uncovering the regulatory processes that generate the characteristic spatio-temporal expression patterns of floral homeotic genes, elucidating some of the mechanisms allowing ABC genes to specify distinct organ identities, revealing how evolution tinkers with the ABC to generate morphological diversity, and even shining a light on the origins of the floral gene regulatory network itself. Here we retrace the history of the ABC model, from its genesis to its current form, highlighting specific milestones along the way before drawing attention to some of the unsolved riddles still hidden in the floral alphabet.
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Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne, VIC 3800, Australia
| | - Edwige Moyroud
- The Sainsbury Laboratory, Cambridge University, Cambridge CB2 1LR, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EJ, UK
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Zhang G, Yang J, Zhang C, Jiao B, Panero JL, Cai J, Zhang ZR, Gao LM, Gao T, Ma H. Nuclear phylogenomics of Asteraceae with increased sampling provides new insights into convergent morphological and molecular evolution. PLANT COMMUNICATIONS 2024:100851. [PMID: 38409784 DOI: 10.1016/j.xplc.2024.100851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 01/22/2024] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
Convergent morphological evolution is widespread in flowering plants, and understanding this phenomenon relies on well-resolved phylogenies. Nuclear phylogenetic reconstruction using transcriptome datasets has been successful in various angiosperm groups, but it is limited to taxa with available fresh materials. Asteraceae, which are one of the two largest angiosperm families and are important for both ecosystems and human livelihood, show multiple examples of convergent evolution. Nuclear Asteraceae phylogenies have resolved relationships among most subfamilies and many tribes, but many phylogenetic and evolutionary questions regarding subtribes and genera remain, owing to limited sampling. Here, we increased the sampling for Asteraceae phylogenetic reconstruction using transcriptomes and genome-skimming datasets and produced nuclear phylogenetic trees with 706 species representing two-thirds of recognized subtribes. Ancestral character reconstruction supports multiple convergent evolutionary events in Asteraceae, with gains and losses of bilateral floral symmetry correlated with diversification of some subfamilies and smaller groups, respectively. Presence of the calyx-related pappus may have been especially important for the success of some subtribes and genera. Molecular evolutionary analyses support the likely contribution of duplications of MADS-box and TCP floral regulatory genes to innovations in floral morphology, including capitulum inflorescences and bilaterally symmetric flowers, potentially promoting the diversification of Asteraceae. Subsequent divergences and reductions in CYC2 gene expression are related to the gain and loss of zygomorphic flowers. This phylogenomic work with greater taxon sampling through inclusion of genome-skimming datasets reveals the feasibility of expanded evolutionary analyses using DNA samples for understanding convergent evolution.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China; Department of Biology, the Huck Institute of the Life Sciences, the Pennsylvania State University, State College, PA 16801, USA; State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Junbo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Caifei Zhang
- Wuhan Botanical Garden and Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Bohan Jiao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - José L Panero
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Jie Cai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Lijiang National Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan 674100, China.
| | - Tiangang Gao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Hong Ma
- Department of Biology, the Huck Institute of the Life Sciences, the Pennsylvania State University, State College, PA 16801, USA.
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Nardeli SM, Arge LWP, Artico S, de Moura SM, Tschoeke DA, de Freitas Guedes FA, Grossi-de-Sa MF, Martinelli AP, Alves-Ferreira M. Global gene expression profile and functional analysis reveal the conservation of reproduction-associated gene networks in Gossypium hirsutum. PLANT REPRODUCTION 2024:10.1007/s00497-023-00491-6. [PMID: 38183442 DOI: 10.1007/s00497-023-00491-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/29/2023] [Indexed: 01/08/2024]
Abstract
KEY MESSAGE Lastly, the bZIP gene family encompasses genes that have been reported to play a role in flower development, such as bZIP14 (FD). Notably, bZIP14 is essential for Flowering Locus T (FT) initiation of floral development in Arabidopsis (Abe et al. 2005). Cotton (Gossypium hirsutum L.) is the world's most extensively cultivated fiber crop. However, its reproductive development is poorly characterized at the molecular level. Thus, this study presents a detailed transcriptomic analysis of G. hirsutum at three different reproductive stages. We provide evidence that more than 64,000 genes are active in G. hirsutum during flower development, among which 94.33% have been assigned to functional terms and specific pathways. Gene set enrichment analysis (GSEA) revealed that the biological process categories of floral organ development, pollen exine formation, and stamen development were enriched among the genes expressed during the floral development of G. hirsutum. Furthermore, we identified putative Arabidopsis homologs involved in the G. hirsutum gene regulatory network (GRN) of pollen and flower development, including transcription factors such as WUSCHEL (WUS), INNER NO OUTER (INO), AGAMOUS-LIKE 66 (AGL66), SPOROCYTELESS/NOZZLE (SPL/NZZ), DYSFUNCTIONAL TAPETUM 1 (DYT1), ABORTED MICROSPORES (AMS), and ASH1-RELATED 3 (ASHR3), which are known crucial genes for plant reproductive success. The cotton MADS-box protein-protein interaction pattern resembles the previously described patterns for AGAMOUS (AG), SEEDSTICK (STK), SHATTERPROOF (SHP), and SEPALLATA3 (SEP3) homolog proteins from Arabidopsis. In addition to serving as a resource for comparative flower development studies, this work highlights the changes in gene expression profiles and molecular networks underlying stages that are valuable for cotton breeding improvement.
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Affiliation(s)
- Sarah Muniz Nardeli
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Luis Willian Pacheco Arge
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
| | - Sinara Artico
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
| | - Stéfanie Menezes de Moura
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
- Embrapa Genetic Resources and Biotechnology-Embrapa, Brasília, DF, Brazil
| | - Diogo Antonio Tschoeke
- Laboratório de Microbiologia, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
| | - Fernanda Alves de Freitas Guedes
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
| | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology-Embrapa, Brasília, DF, Brazil
- Catholic University of Brasília, Brasília, DF, Brazil
- National Institute of Science and Technology-INCT PlantStress Biotech, Embrapa, Brasília, DF, Brazil
| | | | - Marcio Alves-Ferreira
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil.
- National Institute of Science and Technology-INCT PlantStress Biotech, Embrapa, Brasília, DF, Brazil.
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Zhao X, Li Y, Zhang MM, He X, Ahmad S, Lan S, Liu ZJ. Research advances on the gene regulation of floral development and color in orchids. Gene 2023; 888:147751. [PMID: 37657689 DOI: 10.1016/j.gene.2023.147751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/08/2023] [Accepted: 08/30/2023] [Indexed: 09/03/2023]
Abstract
Orchidaceae is one of the largest monocotyledon families and contributes significantly to worldwide biodiversity, with value in the fields of landscaping, medicine, and ecology. The diverse phenotypes and vibrant colors of orchid floral organs make them excellent research objects for investigating flower development and pigmentation. In recent years, a number of orchid genomes have been published, laying the molecular foundation for revealing flower development and color presentation. In this article, we review transcription factors, the structural genes responsible for the floral pigment synthesis pathways, the molecular mechanisms of flower morphogenesis, and the potential relationship between flower type and flower color. This study provides a theoretical reference for the research on molecular mechanisms related to flower morphogenesis and color presentation, genetic improvement, and new variety creation in orchids.
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Affiliation(s)
- Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meng-Meng Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sagheer Ahmad
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siren Lan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zhong-Jian Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Liu W, Xu X, Wang X. Unique Morphology of Sarcobatus baileyi Male Inflorescence and Its Botanical Implications. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091917. [PMID: 37176975 PMCID: PMC10180837 DOI: 10.3390/plants12091917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
A typical angiosperm flower is usually bisexual, with entomophilous plants having four whorls of organs: the calyx, corolla, stamens, and gynoecium. The flower is usually colorful, and thus, distinct from the dull-colored reproductive organs of gymnosperms; however, this formula is not applicable to all flowers. For example, the male flower of Sarcobatus baileyi is reduced into only a single stamen. Such unusual flowers are largely poorly documented and underappreciated. To fill such a lacuna in our knowledge of the male reproductive organ of S. baileyi, we collected and studied materials of the male inflorescence of S. baileyi (Sarcobataceae). The outcomes of our Micro-CT (micro computed tomography), SEM (scanning electron microscopy), and paraffin sectioning indicate that a male inflorescence of S. baileyi is more comparable with the cone of conifers; its male flowers lack the perianth, are directly attached to a central axis and sheltered by peltate indusium-like shields. To understand the evolutionary logic underlying such a rarely seen male inflorescence, we also studied and compared it with a female cone of Cupressus sempervirens. Although the genera Sarcobatus and Cupressus belong to two distinct major plant groups (angiosperms and gymnosperms), they apply the same propagule-protecting strategy.
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Affiliation(s)
- Wenzhe Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), School of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xiuping Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xin Wang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and CAS Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
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Jia H, Zhao Q, Song J, Zhang X, Yang W, Du Z, Zhu Y, Wang H. Large-scale population structure and genetic architecture of agronomic traits of garlic. HORTICULTURE RESEARCH 2023; 10:uhad034. [PMID: 37799626 PMCID: PMC10548411 DOI: 10.1093/hr/uhad034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/16/2023] [Indexed: 10/07/2023]
Abstract
Garlic, an asexually propagated crop, is the second important bulb crop after the onion and is used as a vegetable and medicinal plant. Abundant and diverse garlic resources have been formed over thousands of years of cultivation. However, genome variation, population structure and genetic architecture of garlic agronomic traits were still not well elucidated. Here, 1 100 258 single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing in 606 garlic accessions collected from 43 countries. Population structure, principal component and phylogenetic analysis showed that these accessions were divided into five subpopulations. Twenty agronomic traits, including above-ground growth traits, bulb-related and bolt-related traits in two consecutive years were implemented in a genome-wide association study. In total, 542 SNPs were associated with these agronomic traits, among which 188 SNPs were repeatedly associated with more than two traits. One SNP (chr6: 1896135972) was repeatedly associated with ten traits. These associated SNPs were located within or near 858 genes, 56 of which were transcription factors. Interestingly, one non-synonymous SNP (Chr4: 166524085) in ribosomal protein S5 was repeatedly associated with above-ground growth and bulb-related traits. Additionally, gene ontology enrichment analysis of candidate genes for genomic selection regions between complete-bolting and non-bolting accessions showed that these genes were significantly enriched in 'vegetative to reproductive phase transition of meristem', 'shoot system development', 'reproductive process', etc. These results provide valuable information for the reliable and efficient selection of candidate genes to achieve garlic genetic improvement and superior varieties.
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Affiliation(s)
- Huixia Jia
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qing Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiangping Song
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaohui Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenlong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhenzhen Du
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yue Zhu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiping Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Lou H, Song L, Li X, Zi H, Chen W, Gao Y, Zheng S, Fei Z, Sun X, Wu J. The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis. Nat Commun 2023; 14:1315. [PMID: 36898990 PMCID: PMC10006428 DOI: 10.1038/s41467-023-37038-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/28/2023] [Indexed: 03/12/2023] Open
Abstract
Torreya plants produce dry fruits with assorted functions. Here, we report the 19-Gb chromosome-level genome assembly of T. grandis. The genome is shaped by ancient whole-genome duplications and recurrent LTR retrotransposon bursts. Comparative genomic analyses reveal key genes involved in reproductive organ development, cell wall biosynthesis and seed storage. Two genes encoding a C18 Δ9-elongase and a C20 Δ5-desaturase are identified to be responsible for sciadonic acid biosynthesis and both are present in diverse plant lineages except angiosperms. We demonstrate that the histidine-rich boxes of the Δ5-desaturase are crucial for its catalytic activity. Methylome analysis reveals that methylation valleys of the T. grandis seed genome harbor genes associated with important seed activities, including cell wall and lipid biosynthesis. Moreover, seed development is accompanied by DNA methylation changes that possibly fuel energy production. This study provides important genomic resources and elucidates the evolutionary mechanism of sciadonic acid biosynthesis in land plants.
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Affiliation(s)
- Heqiang Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Lili Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Xiaolong Li
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.,Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou, 311300, Zhejiang, China
| | - Hailing Zi
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Weijie Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Yadi Gao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Shan Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA. .,U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China. .,Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou, 311300, Zhejiang, China.
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
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Gene Structural Specificity and Expression of MADS-Box Gene Family in Camellia chekiangoleosa. Int J Mol Sci 2023; 24:ijms24043434. [PMID: 36834845 PMCID: PMC9960327 DOI: 10.3390/ijms24043434] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
MADS-box genes encode transcription factors that affect plant growth and development. Camellia chekiangoleosa is an oil tree species with ornamental value, but there have been few molecular biological studies on the developmental regulation of this species. To explore their possible role in C. chekiangoleosa and lay a foundation for subsequent research, 89 MADS-box genes were identified across the whole genome of C. chekiangoleosa for the first time. These genes were present on all the chromosomes and were found to have expanded by tandem duplication and fragment duplication. Based on the results of a phylogenetic analysis, the 89 MADS-box genes could be divided into either type I (38) or type II (51). Both the number and proportion of the type II genes were significantly greater than those of Camellia sinensis and Arabidopsis thaliana, indicating that C. chekiangoleosa type II genes experienced a higher duplication rate or a lower loss rate. The results of both a sequence alignment and a conserved motif analysis suggest that the type II genes are more conserved, meaning that they may have originated and differentiated earlier than the type I genes did. At the same time, the presence of extra-long amino acid sequences may be an important feature of C. chekiangoleosa. Gene structure analysis revealed the number of introns of MADS-box genes: twenty-one type I genes had no introns, and 13 type I genes contained only 1~2 introns. The type II genes have far more introns and longer introns than the type I genes do. Some MIKCC genes have super large introns (≥15 kb), which are rare in other species. The super large introns of these MIKCC genes may indicate richer gene expression. Moreover, the results of a qPCR expression analysis of the roots, flowers, leaves and seeds of C. chekiangoleosa showed that the MADS-box genes were expressed in all those tissues. Overall, compared with that of the type I genes, the expression of the type II genes was significantly higher. The CchMADS31 and CchMADS58 genes (type II) were highly expressed specifically in the flowers, which may in turn regulate the size of the flower meristem and petals. CchMADS55 was expressed specifically in the seeds, which might affect seed development. This study provides additional information for the functional characterization of the MADS-box gene family and lays an important foundation for in-depth study of related genes, such as those involved in the development of the reproductive organs of C. chekiangoleosa.
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Tello J, Ibáñez J. Review: Status and prospects of association mapping in grapevine. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 327:111539. [PMID: 36410567 DOI: 10.1016/j.plantsci.2022.111539] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
Thanks to current advances in sequencing technologies, novel bioinformatics tools, and efficient modeling solutions, association mapping has become a widely accepted approach to unravel the link between genotype and phenotype diversity in numerous crops. In grapevine, this strategy has been used in the last decades to understand the genetic basis of traits of agronomic interest (fruit quality, crop yield, biotic and abiotic resistance), of special relevance nowadays to improve crop resilience to cope with future climate scenarios. Genome-wide association studies have identified many putative causative loci for different traits, some of them overlapping well-known causal genes identified by conventional quantitative trait loci studies in biparental progenies, and/or validated by functional approaches. In addition, candidate-gene association studies have been useful to pinpoint the causal mutation underlying phenotypic variation for several traits of high interest in breeding programs (like berry color, seedlessness, and muscat flavor), information that has been used to develop highly informative and useful markers already in use in marker-assisted selection processes. Thus, association mapping has proved to represent a valuable step towards high quality and sustainable grape production. This review summarizes current applications of association mapping in grapevine research and discusses future prospects in view of current viticulture challenges.
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Affiliation(s)
- Javier Tello
- Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), Logroño 26007, Spain.
| | - Javier Ibáñez
- Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), Logroño 26007, Spain
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Dreni L. The ABC of Flower Development in Monocots: The Model of Rice Spikelet. Methods Mol Biol 2023; 2686:59-82. [PMID: 37540354 DOI: 10.1007/978-1-0716-3299-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The initial seminal studies of flower developmental genetics were made from observations in several eudicot model species, particularly Arabidopsis and Antirrhinum. However, an increasing amount of research in monocot model and crop species is finally giving the credit that monocots deserve for their position in the evolutionary history of Angiosperms, their astonishing diversification and adaptation, their diversified floral structures, their pivotal function in most ecosystems on Earth and, finally, their importance in agriculture and farming, economy, landscaping and feeding mankind. Rice is a staple crop and the major monocot model to study the reproductive phase and flower evolution. Inspired by this, this chapter reviews a story of highly conserved functions related to the ABC model of flower development. Nevertheless, this model is complicated in rice by cases of gene neofunctionalization, like the recruitment of MADS-box genes for the development of the unique organs known as lemma and palea, subfunctionalization, and rewiring of conserved molecular pathways.
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Affiliation(s)
- Ludovico Dreni
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia, Spain
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Enyew M, Feyissa T, Carlsson AS, Tesfaye K, Hammenhag C, Seyoum A, Geleta M. Genome-wide analyses using multi-locus models revealed marker-trait associations for major agronomic traits in Sorghum bicolor. FRONTIERS IN PLANT SCIENCE 2022; 13:999692. [PMID: 36275578 PMCID: PMC9585286 DOI: 10.3389/fpls.2022.999692] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/14/2022] [Indexed: 06/01/2023]
Abstract
Globally, sorghum is the fifth most important cereal crop, and it is a major crop in Ethiopia, where it has a high genetic diversity. The country's sorghum gene pool contributes significantly to sorghum improvement worldwide. This study aimed to identify genomic regions and candidate genes associated with major agronomic traits in sorghum by using its genetic resources in Ethiopia for a genome-wide association study (GWAS). Phenotypic data of days to flowering (DTF), plant height (PH), panicle length (PALH), panicle width (PAWD), panicle weight (PAWT), and grain yield (GY) were collected from a GWAS panel comprising 324 sorghum accessions grown in three environments. SeqSNP, a targeted genotyping method, was used to genotype the panel using 5,000 gene-based single nucleotide polymorphism (SNP) markers. For marker-trait association (MTA) analyses, fixed and random model circulating probability unification (FarmCPU), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) models were used. In all traits, high phenotypic variation was observed, with broad-sense heritability ranging from 0.32 (for GY) to 0.90 (for PALH). A population structure, principal component analysis, and kinship analysis revealed that the accessions could be divided into two groups. In total, 54 MTAs were identified, 11 of which were detected by both BLINK and farmCPU. MTAs identified for each trait ranged from five (PAWT and GY) to fourteen (PH) representing both novel and previously identified quantitative trait loci (QTLs). Three SNPs were associated with more than one trait, including a SNP within the Sobic.004G189200 gene that was associated with PH and PAWT. Major effect SNP loci, Sbi2393610 (PVE = 23.3%), Sbi10438246 (PVE = 35.2%), Sbi17789352 (PVE = 11.9%) and Sbi30169733 (PVE = 18.9%) on chromosomes 1, 3, 5 and 9 that showed strong association signals for PAWD, DTF, GY and PALH, respectively, were major findings of this study. The SNP markers and candidate genes identified in this study provide insights into the genetic control of grain yield and related agronomic traits, and once validated, the markers could be used in genomics-led breeding.
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Affiliation(s)
- Muluken Enyew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Tileye Feyissa
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Anders S. Carlsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Amare Seyoum
- National Sorghum Research Program, Crop Research Department, Melkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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12
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Sun L, Nie T, Chen Y, Yin Z. From Floral Induction to Blooming: The Molecular Mysteries of Flowering in Woody Plants. Int J Mol Sci 2022; 23:ijms231810959. [PMID: 36142871 PMCID: PMC9500781 DOI: 10.3390/ijms231810959] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 12/04/2022] Open
Abstract
Flowering is a pivotal developmental process in response to the environment and determines the start of a new life cycle in plants. Woody plants usually possess a long juvenile nonflowering phase followed by an adult phase with repeated flowering cycles. The molecular mechanism underlying flowering regulation in woody plants is believed to be much more complex than that in annual herbs. In this review, we briefly describe the successive but distinct flowering processes in perennial trees, namely the vegetative phase change, the floral transition, floral organogenesis, and final blooming, and summarize in detail the most recent advances in understanding how woody plants regulate flowering through dynamic gene expression. Notably, the florigen gene FLOWERING LOCUS T(FT) and its antagonistic gene TERMINAL FLOWER 1 (TFL1) seem to play a central role in various flowering transition events. Flower development in different taxa requires interactions between floral homeotic genes together with AGL6 conferring floral organ identity. Finally, we illustrate the issues and corresponding measures of flowering regulation investigation. It is of great benefit to the future study of flowering in perennial trees.
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Affiliation(s)
- Liyong Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Department of Biology, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Tangjie Nie
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yao Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Zengfang Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: ; Tel.: +86-025-85427316
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13
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Duan K, Fu H, Fang D, Wang K, Zhang W, Liu H, Sahu SK, Chen X. Genome-Wide Analysis of the MADS-Box Gene Family in Holoparasitic Plants ( Balanophora subcupularis and Balanophora fungosa var. globosa). FRONTIERS IN PLANT SCIENCE 2022; 13:846697. [PMID: 35712591 PMCID: PMC9197559 DOI: 10.3389/fpls.2022.846697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
MADS-box is an important transcription factor family that is involved in the regulation of various stages of plant growth and development, especially flowering regulation and flower development. Being a holoparasitic plant, the body structure of Balanophoraceae has changed dramatically over time, and its vegetative and reproductive organs have been extensively modified, with rudimentary flower organs. Meanwhile, extraordinary gene losses have been identified in holoparasitic plants compared with autotrophs. Our study reveals that the MADS-box gene family contracted sharply in Balanophora subcupularis and Balanophora fungosa var. globosa, and some subfamilies were lost, exhibiting reduced redundancy in both. The genes that functioned in the transition from the vegetative to floral production stages suffered a significant loss, but the ABCE model genes remained intact. We further investigated genes related to flowering regulation in B. subcupularis and B. fungosa var. globosa, vernalization and autonomous ways of regulating flowering time remained comparatively integrated, while genes in photoperiod and circadian clock pathways were almost lost. Convergent gene loss in flowering regulation occurred in Balanophora and another holoparasitic plant Sapria himalayana (Rafflesiaceae). The genome-wide analysis of the MADS-box gene family in Balanophora species provides valuable information for understanding the classification, gene loss pattern, and flowering regulation mechanism of MADS-box gene family in parasitic plants.
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Affiliation(s)
- Kunyu Duan
- Beijing Genomics Institute College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hui Fu
- Beijing Genomics Institute College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, Shenzhen, China
| | - Kaimeng Wang
- Beijing Genomics Institute College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Wen Zhang
- China National GeneBank, Beijing Genomics Institute, Shenzhen, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, Shenzhen, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, Shenzhen, China
| | - Xiaoli Chen
- Beijing Genomics Institute College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, Shenzhen, China
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14
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Du X, Liu H, Zhu Z, Liu S, Song Z, Xia L, Zhao J, Luan F, Liu S. Identification of Candidate Chromosome Region Related to Melon ( Cucumis melo L.) Fruit Surface Groove Trait Through Biparental Genetic Mapping and Genome-Wide Association Study. FRONTIERS IN PLANT SCIENCE 2022; 13:828287. [PMID: 35463445 PMCID: PMC9022103 DOI: 10.3389/fpls.2022.828287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
The melon fruit surface groove (fsg) not only affects peel structure and causes stress-induced fruit cracking but also fits consumers' requirements in different regions. In this study, genetic inheritance analysis of three F2 populations derived from six parental lines revealed that the fsg trait is controlled by a simple recessive inherited gene. Through bulked segregant analysis sequencing (BSA-seq), the Cmfsg locus was detected in an 8.96 Mb interval on chromosome 11 and then initially mapped to a region of approximately 1.15 Mb. Further fine mapping with a large F2 population including 1,200 plants narrowed this region to 207 kb containing 11 genes. A genome-wide association study (GWAS) with 187 melon accessions also produced the same chromosome region for the Cmfsg locus. Due to the rare molecular markers and lack of mutations in the coding and promoter regions of the 11 candidate genes in the fine-mapped interval, we conducted in silico BSA to explore the natural melon panel to predict candidate genes for the Cmfsg locus. A 1.07 kb segment upstream of MELO3C019694.2 (annotated as the AGAMOUS MADS-box transcription factor) exhibited a correlation with the grooved and non-grooved accessions among the F2 individuals, and a natural panel consisted of 17 melon accessions. The expression level of MELO3C019694.2 in the pericarp was higher in grooved lines than in non-grooved lines and was specifically expressed in fruit compared with other tissues (female flower, male flower, root, and leaf). This work provides fundamental information for further research on melon fsg trait formation and molecular markers for melon breeding.
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Affiliation(s)
- Xin Du
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China
- Horticulture and Landscape Architecture College, Northeast Agricultural University, Harbin, China
| | - Hongyu Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China
- Horticulture and Landscape Architecture College, Northeast Agricultural University, Harbin, China
| | - Zicheng Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China
- Horticulture and Landscape Architecture College, Northeast Agricultural University, Harbin, China
| | - Shusen Liu
- Shouguang Sanmu Seeding Co., Ltd., Shandong, China
| | | | - Lianqin Xia
- Shouguang Sanmu Seeding Co., Ltd., Shandong, China
| | - Jingchao Zhao
- Qinggang Ruixue Agriculture Co., Ltd., Heilongjiang, China
| | - Feishi Luan
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China
- Horticulture and Landscape Architecture College, Northeast Agricultural University, Harbin, China
| | - Shi Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China
- Horticulture and Landscape Architecture College, Northeast Agricultural University, Harbin, China
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15
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Time-course transcriptome profiling revealed the specific expression patterns of MADS-box genes associated with the distinct developmental processes between winter and spring wheat. Gene 2022; 809:146030. [PMID: 34673213 DOI: 10.1016/j.gene.2021.146030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 07/02/2021] [Accepted: 10/14/2021] [Indexed: 11/23/2022]
Abstract
The shoot apex is a region where new cells are produced and elongate. The developmental state of the wheat shoot apex under low temperature affects its cold resistance. In this study, the morphology of shoot apex before overwintering was characterized for 24 wheat line with different winter and spring characteristics. Our research showed that the shoot apex of autumn-sown spring wheat lines reached the temperature sensitive double-ridge stage before overwintering, whereas shoot apex of winter wheat lines are found in temperature-insensitive vegetative or elongation stages. In order to explore how gene expression is associated with shoot apex differentiation in winter and spring wheat, we used strand-specific RNA sequencing to profile the gene expression patterns at four time-points between 14 after germination and 45 days after germination in the winter wheat cultivar Dongnongdongmai No. 1 (DM1) and in the spring wheat cultivar China Spring (CS). We identified 11,848 differentially expressed genes between the two cultivars. Most up-regulated genes in CS were involved in energy metabolism and transport during the seedling stage, whereas up-regulated genes in DM1 were involved in protein and DNA synthesis. MADS-box genes affect plant growth and development. In this study, MADS-boxes with differential expression between CS and DM1 were screened and evolutionary tree analysis was conducted. During all sampling periods, CS highly expressed MADS-box genes that induce flowering promotion genes such as VRN1, VRT and AG, while lowly expressed MADS-box genes that induce flowering-inhibiting homologous genes such as SVP. TaVRN1 composition in DM1 and CS was vrn-A1, vrn-B1, and Vrn-D1b. Analysis of the sequence of TaVRN1 (TraesCS5A01G391700) from DM1 and CS revealed 5 SNP differences in the promoter regions and 3 SNP deletions in the intron regions. The expression levels of cold resistant genes in DM1 were significantly higher than those in CS at seedling stage (neither DM1 nor CS experienced cold in this study), including CBF, cold induced protein,acid desaturase and proline rich proteins. Additionally, the expression levels of auxin-related genes were significantly higher in CS than those in DM1 at 45 days after germination. Our study identified candidate genes associated with the process of differentiation of the shoot apex in winter and spring wheat at the seedling stage and also raised an internal stress tolerance model for winter wheat to endogenously anticipate the coming stressful conditions in winter.
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16
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Shen G, Wang WL. Circlize package in R and Analytic Hierarchy Process (AHP): Contribution values of ABCDE and AGL6 genes in the context of floral organ development. PLoS One 2022; 17:e0261232. [PMID: 35061694 PMCID: PMC8782415 DOI: 10.1371/journal.pone.0261232] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 11/24/2021] [Indexed: 11/29/2022] Open
Abstract
The morphological diversity of floral organs can largely be attributed to functional divergence in the MADS-box gene family. Nonetheless, research based on the ABCDE model has yet to conclusively determine whether the AGAMOUS-LIKE 6 (AGL6) subgroup has a direct influence on floral organ development. In the current study, the ABCDE model was used to quantify the contributions of ABCDE and AGL6 genes in the emergence of floral organs. We determined that the flower formation contribution values of the ABCDE and AGL6 genes were as follows: A gene, 0.192; B gene, 0.231; CD gene, 0.192; E gene, 0.385; and AGL6, 0.077. As AGL6 does not directly influence floral structure formation, the contribution value of AGL6 to flower formation was low. Furthermore, the gradient values of the floral organs were as follows: sepals, 0.572; petals, 1.606; stamens, 2.409; and carpels, 2.288. We also performed detailed analysis of the ABCDE and AGL6 genes using the Circlize package in R. Our results suggest that these genes likely emerged in one of two orders: 1) B genes→CD genes→AGL6→E genes→A genes; or 2) B genes→CD genes→AGL6/E genes→A genes. We use the analytic hierarchy process (AHP) to prove the contribution values and gradient values of floral organs. This is the first study to understand the contribution values of ABCDE and AGL6 genes using the AHP and the Circlize package in R.
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Affiliation(s)
- Gangxu Shen
- School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan
| | - Wei-Lung Wang
- Department of Biology, National Changhua University of Education, Changhua, Taiwan
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17
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Kong X, Wang F, Geng S, Guan J, Tao S, Jia M, Sun G, Wang Z, Wang K, Ye X, Ma J, Liu D, Wei Y, Zheng Y, Fu X, Mao L, Lan X, Li A. The wheat AGL6-like MADS-box gene is a master regulator for floral organ identity and a target for spikelet meristem development manipulation. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:75-88. [PMID: 34487615 PMCID: PMC8710900 DOI: 10.1111/pbi.13696] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 08/22/2021] [Indexed: 05/13/2023]
Abstract
The AGAMOUS-LIKE6 (AGL6)-like genes are ancient MADS-box genes and are functionally studied in a few model plants. The knowledge of these genes in wheat remains limited. Here, by studying a 'double homoeolog mutant' of the AGL6 gene in tetraploid wheat, we showed that AGL6 was required for the development of all four whorls of floral organs with dosage-dependent effect on floret fertility. Yeast two-hybrid analyses detected interactions of AGL6 with all classes of MADS-box proteins in the ABCDE model for floral organ development. AGL6 was found to interact with several additional proteins, including the G protein β and γ (DEP1) subunits. Analysis of the DEP1-B mutant showed a significant reduction in spikelet number per spike in tetraploid wheat, while overexpression of AGL6 in common wheat increased the spikelet number per spike and hence the grain number per spike. RNA-seq analysis identified the regulation of several meristem activity genes by AGL6, such as FUL2 and TaMADS55. Our work therefore extensively updated the wheat ABCDE model and proposed an alternative approach to improve wheat grain yield by manipulating the AGL6 gene.
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Affiliation(s)
- Xingchen Kong
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Fang Wang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Shuaifeng Geng
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Jiantao Guan
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Shu Tao
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Meiling Jia
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Guoliang Sun
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Zhenyu Wang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Ke Wang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Xingguo Ye
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Jian Ma
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Dengcai Liu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yuming Wei
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Youliang Zheng
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Xiangdong Fu
- The State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Xiujin Lan
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Aili Li
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
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18
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Chen L, He F, Long R, Zhang F, Li M, Wang Z, Kang J, Yang Q. A global alfalfa diversity panel reveals genomic selection signatures in Chinese varieties and genomic associations with root development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1937-1951. [PMID: 34487430 DOI: 10.1111/jipb.13172] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 09/03/2021] [Indexed: 05/04/2023]
Abstract
Alfalfa (Medicago sativa L.) is an important forage crop worldwide. However, little is known about the effects of breeding status and different geographical populations on alfalfa improvement. Here, we sequenced 220 alfalfa core germplasms and determined that Chinese alfalfa cultivars form an independent group, as evidenced by comparisons of FST values between different subgroups, suggesting that geographical origin plays an important role in group differentiation. By tracing the influence of geographical regions on the genetic diversity of alfalfa varieties in China, we identified 350 common candidate genetic regions and 548 genes under selection. We also defined 165 loci associated with 24 important traits from genome-wide association studies. Of those, 17 genomic regions closely associated with a given phenotype were under selection, with the underlying haplotypes showing significant differences between subgroups of distinct geographical origins. Based on results from expression analysis and association mapping, we propose that 6-phosphogluconolactonase (MsPGL) and a gene encoding a protein with NHL domains (MsNHL) are critical candidate genes for root growth. In conclusion, our results provide valuable information for alfalfa improvement via molecular breeding.
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Affiliation(s)
- Lin Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Fei He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ruicai Long
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Fan Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Mingna Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qingchuan Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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19
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Wu J, Yu C, Huang L, Gan Y. A rice transcription factor, OsMADS57, positively regulates high salinity tolerance in transgenic Arabidopsis thaliana and Oryza sativa plants. PHYSIOLOGIA PLANTARUM 2021; 173:1120-1135. [PMID: 34287928 DOI: 10.1111/ppl.13508] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 05/24/2023]
Abstract
MADS-box transcription factors (TFs) play indispensable roles in various aspects of plant growth, development as well as in response to environmental stresses. Several MADS-box genes have been reported to be involved in the salt tolerance in different plant species. However, the role of the transcription factor OsMADS57 under salinity stress is still unknown. Here, the results of this study showed that OsMADS57 was mainly expressed in roots and leaves of rice plants (Oryza sativa). Gene expression pattern analysis revealed that OsMADS57 was induced by NaCl. Overexpression of OsMADS57 in both Arabidopsis thaliana (A. thaliana) and rice could improve their salt tolerance, which was demonstrated by higher germination rates, longer root length and better growth status of overexpression plants than wild type (WT) under salinity conditions. In contrast, RNA interference (RNAi) lines of rice showed more sensitivity towards salinity. Moreover, less reactive oxygen species (ROS) accumulated in OsMADS57 overexpressing lines when exposed to salt stress, as measured by 3, 3'-diaminobenzidine (DAB) or nitroblue tetrazolium (NBT) staining. Further experiments exhibited that overexpression of OsMADS57 in rice significantly increased the tolerance ability of plants to oxidative damage under salt stress, mainly by increasing the activities of antioxidative enzymes such as superoxide dismutase (SOD) and peroxidase (POD), reducing malonaldehyde (MDA) content and improving the expression of stress-related genes. Taken together, these results demonstrated that OsMADS57 plays a positive role in enhancing salt tolerance by activating the antioxidant system.
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Affiliation(s)
- Junyu Wu
- Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chunyan Yu
- Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ludong University, College of Agriculture, Yantai, China
| | - Linli Huang
- Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yinbo Gan
- Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, Hainan Province, People's Republic of China
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20
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Ma JJ, Chen X, Song YT, Zhang GF, Zhou XQ, Que SP, Mao F, Pervaiz T, Lin JX, Li Y, Li W, Wu HX, Niu SH. MADS-box transcription factors MADS11 and DAL1 interact to mediate the vegetative-to-reproductive transition in pine. PLANT PHYSIOLOGY 2021; 187:247-262. [PMID: 34618133 PMCID: PMC8418398 DOI: 10.1093/plphys/kiab250] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/12/2021] [Indexed: 06/13/2023]
Abstract
The reproductive transition is an important event that is crucial for plant survival and reproduction. Relative to the thorough understanding of the vegetative phase transition in angiosperms, a little is known about this process in perennial conifers. To gain insight into the molecular basis of the regulatory mechanism in conifers, we used temporal dynamic transcriptome analysis with samples from seven different ages of Pinus tabuliformis to identify a gene module substantially associated with aging. The results first demonstrated that the phase change in P. tabuliformis occurred as an unexpectedly rapid transition rather than a slow, gradual progression. The age-related gene module contains 33 transcription factors and was enriched in genes that belong to the MADS (MCMl, AGAMOUS, DEFICIENS, SRF)-box family, including six SOC1-like genes and DAL1 and DAL10. Expression analysis in P. tabuliformis and a late-cone-setting P. bungeana mutant showed a tight association between PtMADS11 and reproductive competence. We then confirmed that MADS11 and DAL1 coordinate the aging pathway through physical interaction. Overexpression of PtMADS11 and PtDAL1 partially rescued the flowering of 35S::miR156A and spl1,2,3,4,5,6 mutants in Arabidopsis (Arabidopsis thaliana), but only PtMADS11 could rescue the flowering of the ft-10 mutant, suggesting PtMADS11 and PtDAL1 play different roles in flowering regulatory networks in Arabidopsis. The PtMADS11 could not alter the flowering phenotype of soc1-1-2, indicating it may function differently from AtSOC1 in Arabidopsis. In this study, we identified the MADS11 gene in pine as a regulatory mediator of the juvenile-to-adult transition with functions differentiated from the angiosperm SOC1.
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Affiliation(s)
- Jing-Jing Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Xi Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Yi-Tong Song
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Gui-Fang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Xian-Qing Zhou
- Qigou State-Owned Forest Farm, Pingquan, Hebei Province 067509, PR China
| | - Shu-Peng Que
- Beijing Ming Tombs Forest Farm, Beijing 102200, PR China, Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå SE-901 83, Sweden
| | - Fei Mao
- Beijing Ming Tombs Forest Farm, Beijing 102200, PR China, Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå SE-901 83, Sweden
| | - Tariq Pervaiz
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Jin-Xing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Yue Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Wei Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Harry X. Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Shi-Hui Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
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21
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Yuan HY, Caron CT, Ramsay L, Fratini R, de la Vega MP, Vandenberg A, Weller JL, Bett KE. Genetic and gene expression analysis of flowering time regulation by light quality in lentil. ANNALS OF BOTANY 2021; 128:481-496. [PMID: 34185828 PMCID: PMC8414921 DOI: 10.1093/aob/mcab083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/28/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Flowering time is important due to its roles in plant adaptation to different environments and subsequent formation of crop yield. Changes in light quality affect a range of developmental processes including flowering time, but little is known about light quality-induced flowering time control in lentil. This study aims to investigate the genetic basis for differences in flowering response to light quality in lentil. METHODS We explored variation in flowering time caused by changes in red/far-red-related light quality environments of a lentil interspecific recombinant inbred line (RIL) population developed from a cross between Lens culinaris cv. Lupa and L. orientalis accession BGE 016880. A genetic linkage map was constructed and then used for identifying quantitative trait loci (QTLs) associated with flowering time regulation under different light quality environments. Differential gene expression analysis through transcriptomic study and RT-qPCR were used to identify potential candidate genes. KEY RESULTS QTL mapping located 13 QTLs controlling flower time under different light quality environments, with phenotypic variance explained ranging from 1.7 to 62.9 %. Transcriptomic profiling and gene expression analysis for both parents of this interspecific RIL population identified flowering-related genes showing environment-specific differential expression (flowering DEGs). One of these, a member of the florigen gene family FTa1 (LcFTa1), was located close to three major QTLs. Furthermore, gene expression results suggested that two other florigen genes (LcFTb1 and LcFTb2), MADS-box transcription factors such as LcAGL6/13d, LcSVPb, LcSOC1b and LcFULb, as well as bHLH transcription factor LcPIF6 and Gibberellin 20 oxidase LcGA20oxC,G may also be involved in the light quality response. CONCLUSIONS Our results show that a major component of flowering time sensitivity to light quality is tightly linked to LcFTa1 and associated with changes in its expression. This work provides a foundation for crop improvement of lentil with better adaptation to variable light environments.
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Affiliation(s)
- Hai Ying Yuan
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Carolyn T Caron
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Larissa Ramsay
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Richard Fratini
- Area de Genética, Departamento de Biología Molecular, Universidad de León, León, Spain
| | | | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - James L Weller
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Kirstin E Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
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22
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Kuijer HNJ, Shirley NJ, Khor SF, Shi J, Schwerdt J, Zhang D, Li G, Burton RA. Transcript Profiling of MIKCc MADS-Box Genes Reveals Conserved and Novel Roles in Barley Inflorescence Development. FRONTIERS IN PLANT SCIENCE 2021; 12:705286. [PMID: 34539699 PMCID: PMC8442994 DOI: 10.3389/fpls.2021.705286] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/04/2021] [Indexed: 05/26/2023]
Abstract
MADS-box genes have a wide range of functions in plant reproductive development and grain production. The ABCDE model of floral organ development shows that MADS-box genes are central players in these events in dicotyledonous plants but the applicability of this model remains largely unknown in many grass crops. Here, we show that transcript analysis of all MIKCc MADS-box genes through barley (Hordeum vulgare L.) inflorescence development reveals co-expression groups that can be linked to developmental events. Thirty-four MIKCc MADS-box genes were identified in the barley genome and single-nucleotide polymorphism (SNP) scanning of 22,626 barley varieties revealed that the natural variation in the coding regions of these genes is low and the sequences have been extremely conserved during barley domestication. More detailed transcript analysis showed that MADS-box genes are generally expressed at key inflorescence developmental phases and across various floral organs in barley, as predicted by the ABCDE model. However, expression patterns of some MADS genes, for example HvMADS58 (AGAMOUS subfamily) and HvMADS34 (SEPALLATA subfamily), clearly deviate from predicted patterns. This places them outside the scope of the classical ABCDE model of floral development and demonstrates that the central tenet of antagonism between A- and C-class gene expression in the ABC model of other plants does not occur in barley. Co-expression across three correlation sets showed that specifically grouped members of the barley MIKCc MADS-box genes are likely to be involved in developmental events driving inflorescence meristem initiation, floral meristem identity and floral organ determination. Based on these observations, we propose a potential floral ABCDE working model in barley, where the classic model is generally upheld, but that also provides new insights into the role of MIKCc MADS-box genes in the developing barley inflorescence.
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Affiliation(s)
- Hendrik N. J. Kuijer
- School of Agriculture Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Neil J. Shirley
- School of Agriculture Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Shi F. Khor
- School of Agriculture Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Julian Schwerdt
- School of Agriculture Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
| | - Dabing Zhang
- School of Agriculture Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Gang Li
- School of Agriculture Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Rachel A. Burton
- School of Agriculture Food and Wine, University of Adelaide, Glen Osmond, SA, Australia
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23
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Song GQ, Han X, Ryner JT, Thompson A, Wang K. Utilizing MIKC-type MADS-box protein SOC1 for yield potential enhancement in maize. PLANT CELL REPORTS 2021; 40:1679-1693. [PMID: 34091722 PMCID: PMC8376726 DOI: 10.1007/s00299-021-02722-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/25/2021] [Indexed: 05/26/2023]
Abstract
Overexpression of Zea mays SOC gene promotes flowering, reduces plant height, and leads to no reduction in grain production per plant, suggesting enhanced yield potential, at least, through increasing planting density. MIKC-type MADS-box gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) is an integrator conserved in the plant flowering pathway. In this study, the maize SOC1 (ZmSOC1) gene was cloned and overexpressed in transgenic maize Hi-II genotype. The T0 plants were backcrossed with nontransgenic inbred B73 to produce first generation backcross (BC1) seeds. Phenotyping of both transgenic and null segregant (NT) BC1 plants was conducted in three independent experiments. The BC1 transgenic plants showed new attributes such as increased vegetative growth, accelerated flowering time, reduced overall plant height, and increased grain weight. Second generation backcross (BC2) plants were evaluated in the field using two planting densities. Compared to BC2 NT plants, BC2 transgenic plants, were 12-18% shorter, flowered 5 days earlier, and showed no reduction in grain production per plant and an increase in fat, starch, and simple sugars in the grain. Transcriptome comparison in young leaves of 56-day-old BC1 plants revealed that the overexpressed ZmSOC1 resulted in 107 differentially expressed genes. The upregulated transcription factor DNA BINDING WITH ONE FINGER 5.4 (DOF5.4) was among the genes responsible for the reduced plant height. Modulating expression of SOC1 opens a new and effective approach to promote flowering and reduce plant height, which may have potential to enhance crop yield and improve grain quality.
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Affiliation(s)
- Guo-Qing Song
- Department of Horticulture, Plant Biotechnology Resource and Outreach Center, Michigan State University, East Lansing, MI, 48824, USA.
| | - Xue Han
- Department of Horticulture, Plant Biotechnology Resource and Outreach Center, Michigan State University, East Lansing, MI, 48824, USA
| | - John T Ryner
- Department of Horticulture, Plant Biotechnology Resource and Outreach Center, Michigan State University, East Lansing, MI, 48824, USA
| | - Addie Thompson
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Kan Wang
- Department of Agronomy, Crop Bioengineering Center, Iowa State University, Ames, IA, 50011-1051, USA
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24
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Hyden B, Carlson CH, Gouker FE, Schmutz J, Barry K, Lipzen A, Sharma A, Sandor L, Tuskan GA, Feng G, Olson MS, DiFazio SP, Smart LB. Integrative genomics reveals paths to sex dimorphism in Salix purpurea L. HORTICULTURE RESEARCH 2021; 8:170. [PMID: 34333534 PMCID: PMC8325687 DOI: 10.1038/s41438-021-00606-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/23/2021] [Accepted: 06/01/2021] [Indexed: 05/16/2023]
Abstract
Sex dimorphism and gene expression were studied in developing catkins in 159 F2 individuals from the bioenergy crop Salix purpurea, and potential mechanisms and pathways for regulating sex development were explored. Differential expression, eQTL, bisulfite sequencing, and network analysis were used to characterize sex dimorphism, detect candidate master regulator genes, and identify pathways through which the sex determination region (SDR) may mediate sex dimorphism. Eleven genes are presented as candidates for master regulators of sex, supported by gene expression and network analyses. These include genes putatively involved in hormone signaling, epigenetic modification, and regulation of transcription. eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region. Furthermore, data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways. These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus. This further demonstrates the dynamic nature of SDRs in plants, which involves a multitude of mechanisms of sex determination and a high rate of turnover.
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Affiliation(s)
- Brennan Hyden
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Fred E Gouker
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
- Floral and Nursery Plants Research Unit, US National Arboretum, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
| | - Jeremy Schmutz
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kerrie Barry
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | - Anna Lipzen
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | - Aditi Sharma
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | - Laura Sandor
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | - Gerald A Tuskan
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Guanqiao Feng
- Department of Biology, Texas Tech University, Lubbock, TX, USA
| | - Matthew S Olson
- Department of Biology, Texas Tech University, Lubbock, TX, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA.
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25
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Song GQ, Han X. K-Domain Technology: Constitutive Expression of a Blueberry Keratin-Like Domain Mimics Expression of Multiple MADS-Box Genes in Enhancing Maize Grain Yield. FRONTIERS IN PLANT SCIENCE 2021; 12:664983. [PMID: 34025703 PMCID: PMC8137907 DOI: 10.3389/fpls.2021.664983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/15/2021] [Indexed: 06/02/2023]
Abstract
MADS-box genes are considered as the foundation of all agronomic traits because they play essential roles in almost every aspect of plant reproductive development. Keratin-like (K) domain is a conserved protein domain of tens of MIKC-type MADS-box genes in plants. K-domain technology constitutively expresses a K-domain to mimic expression of the K-domains of other MADS-box genes simultaneously and thus to generate new opportunities for yield enhancement, because the increased K-domains can likely prevent MADS-domain proteins from binding to target DNA. In this study, we evaluated utilizing the K-domain technology to increase maize yield. The K-domain of a blueberry's SUPPRESSOR of CONSTITUTIVE EXPRESSION OF CONSTANS 1 (VcSOC1K) has similarities to five MADS-box genes in maize. Transgenic maize plants expressing the VcSOC1K showed 13-100% of more grain per plant than the nontransgenic plants in all five experiments conducted under different experimental conditions. Transcriptome comparisons revealed 982 differentially expressed genes (DEGs) in the leaves from 83-day old plants, supporting that the K-domain technology were powerful and multiple functional. The results demonstrated that constitutive expression of the VcSOC1K was very effective to enhance maize grain production. With the potential of mimicking the K-domains of multiple MADS-box genes, the K-domain technology opens a new approach to increase crop yield.
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26
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Zinelabidine LH, Torres-Pérez R, Grimplet J, Baroja E, Ibáñez S, Carbonell-Bejerano P, Martínez-Zapater JM, Ibáñez J, Tello J. Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 306:110875. [PMID: 33775372 DOI: 10.1016/j.plantsci.2021.110875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/02/2021] [Accepted: 03/06/2021] [Indexed: 06/12/2023]
Abstract
Grapevine is one of the most valuable fruit crops in the world. Adverse environmental conditions reduce fruit quality and crop yield, so understanding the genetic and molecular mechanisms determining crop yield components is essential to optimize grape production. The analysis of a diverse collection of grapevine cultivars allowed us to evaluate the relationship between fruit set-related components of yield, including the incidence of reproductive disorders such as coulure and millerandage. The collection displayed a great phenotypic variation that we surveyed in a genetics association study using 15,309 single nucleotide polymorphisms (SNPs) detected in the sequence of 289 candidate genes scattered across the 19 grapevine linkage groups. After correcting statistical models for population structure and linkage disequilibrium effects, 164 SNPs from 34 of these genes were found to associate with fruit set-related traits, supporting a complex polygenic determinism. Many of them were found in the sequence of different putative MADS-box transcription factors, a gene family related with plant reproductive development control. In addition, we observed an additive effect of some of the associated SNPs on the phenotype, suggesting that advantageous alleles from different loci could be pyramided to generate superior cultivars with optimized fruit production.
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Affiliation(s)
- Lalla Hasna Zinelabidine
- Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), Logroño, 26007, Spain; Laboratory of Biotechnology and Valorisation of Plant Genetic Resources, Faculty of Sciences and Techniques, University of Sultan Moulay Slimane, Beni Mellal, 23000, Morocco
| | - Rafael Torres-Pérez
- Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), Logroño, 26007, Spain; Servicio de Bioinformática para Genómica y Proteómica (BioinfoGP), Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
| | - Jérôme Grimplet
- Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), Logroño, 26007, Spain; Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, 50059, Spain; Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), Zaragoza, 50059, Spain
| | - Elisa Baroja
- Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), Logroño, 26007, Spain
| | - Sergio Ibáñez
- Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), Logroño, 26007, Spain
| | - Pablo Carbonell-Bejerano
- Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), Logroño, 26007, Spain; Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tuebingen, Germany
| | | | - Javier Ibáñez
- Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), Logroño, 26007, Spain
| | - Javier Tello
- Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), Logroño, 26007, Spain.
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27
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Gupta SK, Barg R, Arazi T. Tomato agamous-like6 parthenocarpy is facilitated by ovule integument reprogramming involving the growth regulator KLUH. PLANT PHYSIOLOGY 2021; 185:969-984. [PMID: 33793903 PMCID: PMC8133625 DOI: 10.1093/plphys/kiaa078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/02/2020] [Indexed: 05/07/2023]
Abstract
Fruit set is established during and soon after fertilization of the ovules inside the quiescent ovary, but the signaling pathways involved remain obscure. The tomato (Solanum lycopersicum) CRISPR loss-of-function mutant of the transcription factor gene AGAMOUS-like6 (SlAGL6; slagl6CR-sg1) is capable of fertilization-independent setting of normal, yet seedless (parthenocarpic), fruit. To gain insight into the mechanism of fleshy fruit set, in this study, we investigated how slagl6CR-sg1 uncouples fruit set from fertilization. We found that mutant ovules were enlarged due to integument over-proliferation and failed to differentiate an endothelium, the integument's innermost layer, upon maturation. A causal relationship between slagl6 loss-of-function and these abnormal phenotypes is inferred from the observation that SlAGL6 is predominantly expressed in the immature ovule integument, and upon ovule maturation, its expression shifts to the endothelium. The transcriptome of unfertilized mutant ovules profoundly differs from that of wild-type and exhibits substantial overlap with the transcriptomes of fertilized ovules sporophytic tissues. One prominent upregulated gene was the fertilization-induced cytochrome P450 cell proliferation regulator SlKLUH. Indeed, ectopic overexpression of SlKLUH stimulated both integument growth in unfertilized ovules and parthenocarpy, suggesting that its suppression by SlAGL6 is paramount for preventing fertilization-independent fruit set. Taken together, our study informs on the transcriptional programs that are regulated by SlAGL6 and demonstrates that it acts from within the ovule integument to inhibit ovary growth beyond anthesis. That by suppressing components of the fertilization-induced ovule reprogramming underlying fruit set.
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Affiliation(s)
- Suresh Kumar Gupta
- ARO, Volcani Center, Institute of Plant Sciences, HaMaccabbim Road 68, Rishon LeZion 7505101, Israel
| | - Rivka Barg
- ARO, Volcani Center, Institute of Plant Sciences, HaMaccabbim Road 68, Rishon LeZion 7505101, Israel
| | - Tzahi Arazi
- ARO, Volcani Center, Institute of Plant Sciences, HaMaccabbim Road 68, Rishon LeZion 7505101, Israel
- Author for communication:
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28
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Hu Y, Wang L, Jia R, Liang W, Zhang X, Xu J, Chen X, Lu D, Chen M, Luo Z, Xie J, Cao L, Xu B, Yu Y, Persson S, Zhang D, Yuan Z. Rice transcription factor MADS32 regulates floral patterning through interactions with multiple floral homeotic genes. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2434-2449. [PMID: 33337484 DOI: 10.1093/jxb/eraa588] [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: 09/01/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
Floral patterning is regulated by intricate networks of floral identity genes. The peculiar MADS32 subfamily genes, absent in eudicots but prevalent in monocots, control floral organ identity. However, how the MADS32 family genes interact with other floral homeotic genes during flower development is mostly unknown. We show here that the rice homeotic transcription factor OsMADS32 regulates floral patterning by interacting synergistically with E class protein OsMADS6 in a dosage-dependent manner. Furthermore, our results indicate important roles for OsMADS32 in defining stamen, pistil, and ovule development through physical and genetic interactions with OsMADS1, OsMADS58, and OsMADS13, and in specifying floral meristem identity with OsMADS6, OsMADS3, and OsMADS58, respectively. Our findings suggest that OsMADS32 is an important factor for floral meristem identity maintenance and that it integrates the action of other MADS-box homeotic proteins to sustain floral organ specification and development in rice. Given that OsMADS32 is an orphan gene and absent in eudicots, our data substantially expand our understanding of flower development in plants.
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Affiliation(s)
- Yun Hu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Li Wang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ru Jia
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuelian Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Xu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaofei Chen
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dan Lu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mingjiao Chen
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhijing Luo
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiayang Xie
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Liming Cao
- Crop Breeding & Cultivation Research Institute, Shanghai Academy of Agriculture Sciences, Shanghai, China
| | - Ben Xu
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Yu Yu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Staffan Persson
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Biosciences, University of Melbourne, Parkville VIC, Melbourne, Australia
- Department for Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, Frederiksberg C, Denmark
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia, Australia
| | - Zheng Yuan
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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29
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Genome-wide identification and expression analysis of the MADS-box transcription factor family in Camellia sinensis. J Appl Genet 2021; 62:249-264. [PMID: 33598859 DOI: 10.1007/s13353-021-00621-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 02/06/2021] [Accepted: 02/11/2021] [Indexed: 10/22/2022]
Abstract
The MADS-box genes are an important class of transcription factors and play critical roles in flower development. However, the functions of these genes in the economically important drinking plant, Camellia sinensis, are still not reported. Here, an evolutionary analysis of tea MADS-box genes was performed at whole genome level. A total of 83 MADS-box genes were identified in tea, and their gene structures and expression patterns were further analyzed. The tea MADS-box genes were classified into Mα (26), Mβ (12), Mγ (9), MIKC* (7), and MIKCC (29) clade according to their phylogenetic relationship with Arabidopsis thaliana. Several cis-elements were identified in the promoter regions of the CsMADS genes that are important in regulating growth, development, light responses, and the response to several stresses. Most CsMADS genes display clear different expression patterns in different organs and different species of tea plant. The expression of CsMADS genes can be regulated by abiotic stresses and phytohormone treatment. Our results lay the foundation for future research on the function of CsMADS genes and beneficial for improving tea agricultural traits in the future.
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Hsu HF, Chen WH, Shen YH, Hsu WH, Mao WT, Yang CH. Multifunctional evolution of B and AGL6 MADS box genes in orchids. Nat Commun 2021; 12:902. [PMID: 33568671 PMCID: PMC7876132 DOI: 10.1038/s41467-021-21229-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 01/13/2021] [Indexed: 01/30/2023] Open
Abstract
We previously found that B and AGL6 proteins form L (OAP3-2/OAGL6-2/OPI) and SP (OAP3-1/OAGL6-1/OPI) complexes to determine lip/sepal/petal identities in orchids. Here, we show that the functional L' (OAP3-1/OAGL6-2/OPI) and SP' (OAP3-2/OAGL6-1/OPI) complexes likely exist and AP3/PI/AGL6 genes have acquired additional functions during evolution. We demonstrate that the presumed L' complex changes the structure of the lower lateral sepals and helps the lips fit properly in the center of the flower. In addition, we find that OAP3-1/OAGL6-1/OPI in SP along with presumed SP' complexes regulate anthocyanin accumulation and pigmentation, whereas presumed L' along with OAP3-2/OAGL6-2/OPI in L complexes promotes red spot formation in the perianth. Furthermore, the B functional proteins OAP3-1/OPI and OAGL6-1 in the SP complex could function separately to suppress sepal/petal senescence and promote pedicel abscission, respectively. These findings expand the current knowledge behind the multifunctional evolution of the B and AGL6 genes in plants.
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Affiliation(s)
- Hsing-Fun Hsu
- grid.260542.70000 0004 0532 3749Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan 40227 ROC
| | - Wei-Han Chen
- grid.260542.70000 0004 0532 3749Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan 40227 ROC
| | - Yi-Hsuan Shen
- grid.260542.70000 0004 0532 3749Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan 40227 ROC
| | - Wei-Han Hsu
- grid.260542.70000 0004 0532 3749Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan 40227 ROC
| | - Wan-Ting Mao
- grid.260542.70000 0004 0532 3749Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan 40227 ROC
| | - Chang-Hsien Yang
- grid.260542.70000 0004 0532 3749Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan 40227 ROC ,grid.260542.70000 0004 0532 3749Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan 40227 ROC
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Shen G. Campbell biology (edited by Lisa Urry, Michael Cain, Steven Wasserman, Peter Minorsky and Jane Reece). JOURNAL OF BIOLOGICAL RESEARCH-THESSALONIKI 2020; 27:19. [PMID: 33298185 PMCID: PMC7727124 DOI: 10.1186/s40709-020-00127-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/28/2020] [Indexed: 11/10/2022]
Abstract
AbstractCampbell Biology is divided into eight units and 56 chapters. The organization and size of this book are appropriate and easy for first-year university students and help them to learn and digest the content. Campbell Biology is currently among the best biology books and it is listed with the best shelling textbooks. Campbell Biology is mainly for first-year university students, but it is also an important book for postgraduate medical examinations. Moreover, some high school students may use it as an essential reference book. In its current edition, the latest information in various fields has been added, such as the basal body, which was previously called the 9*3 type microtube arrangement but now has been renamed as the 9 + 0 type in Chapter 6. The updates in molecular biology are closer to the current situation, such as the addition of information on next-generation sequencing and CRISPR/Cas9 in Chapter 20. This content can enable readers to acquire the latest knowledge. Reading this book and understanding the information presented in its pages is very helpful for the future life science professionals. Thus, Campbell Biology is very valuable textbook in the field of biology.
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Lin Z, Cao D, Damaris RN, Yang P. Genome-wide identification of MADS-box gene family in sacred lotus (Nelumbo nucifera) identifies a SEPALLATA homolog gene involved in floral development. BMC PLANT BIOLOGY 2020; 20:497. [PMID: 33121437 PMCID: PMC7599106 DOI: 10.1186/s12870-020-02712-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Sacred lotus (Nelumbo nucifera) is a vital perennial aquatic ornamental plant. Its flower shape determines the horticultural and ornamental values. However, the mechanisms underlying lotus flower development are still elusive. MADS-box transcription factors are crucial in various features of plant development, especially in floral organogenesis and specification. It is still unknown how the MADS-box transcription factors regulate the floral organogenesis in lotus. RESULTS To obtain a comprehensive insight into the functions of MADS-box genes in sacred lotus flower development, we systematically characterized members of this gene family based on the available genome information. A total of 44 MADS-box genes were identified, of which 16 type I and 28 type II genes were categorized based on the phylogenetic analysis. Furthermore, the structure of MADS-box genes and their expressional patterns were also systematically analyzed. Additionally, subcellular localization analysis showed that they are mainly localized in the nucleus, of which a SEPALLATA3 (SEP3) homolog NnMADS14 was proven to be involved in the floral organogenesis. CONCLUSION These results provide some fundamental information about the MADS-box gene family and their functions, which might be helpful in not only understanding the mechanisms of floral organogenesis but also breeding of high ornamental value cultivars in lotus.
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Affiliation(s)
- Zhongyuan Lin
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
- Institute of Oceanography, Minjiang University, Fuzhou, 350108 China
| | - Dingding Cao
- Institute of Oceanography, Minjiang University, Fuzhou, 350108 China
| | - Rebecca Njeri Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062 China
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Li C, Chen L, Fan X, Qi W, Ma J, Tian T, Zhou T, Ma L, Chen F. MawuAP1 promotes flowering and fruit development in the basal angiosperm Magnolia wufengensis (Magnoliaceae). TREE PHYSIOLOGY 2020; 40:1247-1259. [PMID: 32348527 DOI: 10.1093/treephys/tpaa057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 04/06/2020] [Accepted: 04/24/2020] [Indexed: 06/11/2023]
Abstract
The APETALA1/SQUAMOSA (AP1/SQUA)-like genes of flowering plants play crucial roles in the development processes of floral meristems, sepals, petals and fruits. Although many of the AP1/SQUA-like genes have been characterized in angiosperms, few have been identified in basal angiosperm taxa. Therefore, the functional evolution of the AP1/SQUA subfamily is still unclear. We characterized an AP1 homolog, MawuAP1, from Magnolia wufengensis that is an ornamental woody plant belonging to the basal angiosperms. Gene sequence and phylogenetic analyses suggested that MawuAP1 was clustered with the FUL-like homologous genes of basal angiosperms and had FUL motif and paleoAP1 motif domain, but it did not have the euAP1 motif domain of core eudicots. Expression pattern analysis showed that MawuAP1 was highly expressed in vegetative and floral organs, particularly in the early stage of flower bud development and pre-anthesis. Protein-protein interaction pattern analysis revealed that MawuAP1 has interaction with an A-class gene (MawuAP1), C-class gene (MawuAG-1) and E-class gene (MawuAGL9) of the MADS-box family genes. Ectopic expression in Arabidopsis thaliana indicated that MawuAP1 could significantly promote flowering and fruit development, but it could not restore the sepal and petal formation of ap1 mutants. These results demonstrated that there are functional differences in the specification of sepal and petal floral organs and development of fruits among the AP1/SQUA-like genes, and functional conservation in the regulation of floral meristem. These findings provide strong evidence for the important functions of MawuAP1 in floral meristem determination, promoting flowering and fruit development, and further highlight the importance of AP1/SQUA subfamily in biological evolution and diversity.
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Affiliation(s)
- Cunjie Li
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang 443000, P.R. China
| | - Liyuan Chen
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing 100083, P.R. China
| | - Xiaoning Fan
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang 443000, P.R. China
| | - Wenjuan Qi
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang 443000, P.R. China
| | - Jiang Ma
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing 100083, P.R. China
| | - Tian Tian
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang 443000, P.R. China
| | - Tao Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang 443000, P.R. China
| | - Luyi Ma
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing 100083, P.R. China
| | - Faju Chen
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang 443000, P.R. China
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Ding L, Song A, Zhang X, Li S, Su J, Xia W, Zhao K, Zhao W, Guan Y, Fang W, Chen S, Jiang J, Chen F. The core regulatory networks and hub genes regulating flower development in Chrysanthemum morifolium. PLANT MOLECULAR BIOLOGY 2020; 103:669-688. [PMID: 32472481 DOI: 10.1007/s11103-020-01017-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/24/2020] [Indexed: 05/17/2023]
Abstract
The study has facilitated important insights into the regulatory networks involved in flower development in chrysanthemum (Asteraceae), and is informative with respect to the mechanism of flower shape determination. Chrysanthemum morifolium, valued as an ornamental species given the diversity of its inflorescence form, is viewed as a model for understanding flower development in the Asteraceae. Yet, the underlying regulatory networks remain largely unexplored. Here, a transcriptomic survey of the Chrysanthemum morifolium variety 'Jinba' was undertaken to uncover the global gene expression profiles and identify the modules of co-transcribed genes associated with flower development. The weighted gene coexpression network analysis revealed important networks and hub genes including ray floret petals-specific coexpression network, disc floret petals-specific network, B and E class genes involved network and CYC2 genes network. Three ray floret petal-specific hub genes were also strongly transcribed in the ray florets of a selection of six diverse varieties and especially so in those which form ligulate ray floret petals. CmCYC2c was strongly transcribed in the distal and lateral regions of the ray floret petals, and also, along with CmCYC2d, in the tubular ray florets. Furthermore, CmOFP, belonging to the family of ovate proteins, was identified in the CYC2 genes network. CmOFP can interact with CmCYC2d that physically interact with CmCYC2c. This work provides important insights into the regulatory networks involved in flower development in chrysanthemum, and is informative with respect to the mechanistic basis of the regulation of flower shape.
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Affiliation(s)
- Lian Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Aiping Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xue Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Song Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiangshuo Su
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weikang Xia
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kunkun Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenqian Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunxiao Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weimin Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Liu Z, Ma H, Jung S, Main D, Guo L. Developmental Mechanisms of Fleshy Fruit Diversity in Rosaceae. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:547-573. [PMID: 32442388 DOI: 10.1146/annurev-arplant-111119-021700] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Rosaceae (the rose family) is an economically important family that includes species prized for high-value fruits and ornamentals. The family also exhibits diverse fruit types, including drupe (peach), pome (apple), drupetum (raspberry), and achenetum (strawberry). Phylogenetic analysis and ancestral fruit-type reconstruction suggest independent evolutionary paths of multiple fleshy fruit types from dry fruits. A recent whole genome duplication in the Maleae/Pyreae tribe (with apple, pear, hawthorn, and close relatives; referred to as Maleae here) may have contributed to the evolution of pome fruit. MADS-box genes, known to regulate floral organ identity, are emerging as important regulators of fruit development. The differential competence of floral organs to respond to fertilization signals may explain the different abilities of floral organs to form fleshy fruit. Future comparative genomics and functional studies in closely related Rosaceae species with distinct fruit types will test hypotheses and provide insights into mechanisms of fleshy fruit diversity. These efforts will be facilitated by the wealth of genome data and resources in Rosaceae.
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Affiliation(s)
- Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA; ,
| | - Hong Ma
- Department of Biology, Eberly College of Science, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, Washington 99164, USA; ,
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, Washington 99164, USA; ,
| | - Lei Guo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA; ,
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Ma J, Deng S, Jia Z, Sang Z, Zhu Z, Zhou C, Ma L, Chen F. Conservation and divergence of ancestral AGAMOUS/SEEDSTICK subfamily genes from the basal angiosperm Magnolia wufengensis. TREE PHYSIOLOGY 2020; 40:90-107. [PMID: 31553477 DOI: 10.1093/treephys/tpz091] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/14/2019] [Indexed: 06/10/2023]
Abstract
AGAMOUS/SEEDSTICK (AG/STK) subfamily genes play crucial roles in the reproductive development of plants. However, most of our current knowledge of AG/STK subfamily genes is restricted to core eudicots and grasses, and the knowledge of ancestral exon-intron structures, expression patterns, protein-protein interaction patterns and functions of AG/STK subfamily genes remains unclear. To determine these, we isolated AG/STK subfamily genes (MawuAG1, MawuAG2 and MawuSTK) from a woody basal angiosperm Magnolia wufengensis (Magnoliaceae). MawuSTK arose from the gene duplication event occurring before the diversification of extant angiosperms, and MawuAG1 and MawuAG2 may result from a gene duplication event occurring before the divergence of Magnoliaceae and Lauraceae. Gene duplication led to apparent diversification in their expression and interaction patterns. It revealed that expression in both stamens and carpels likely represents the ancestral expression profiles of AG lineage genes, and expression of STK-like genes in stamens may have been lost soon after the appearance of the STK lineage. Moreover, AG/STK subfamily proteins may have immediately established interactions with the SEPALLATA (SEP) subfamily proteins following the emergence of the SEP subfamily; however, their interactions with the APETALA1/FRUITFULL subfamily proteins or themselves differ from those found in monocots and basal and core eudicots. MawuAG1 plays highly conserved roles in the determinacy of stamen, carpel and ovule identity, while gene duplication contributed to the functional diversification of MawuAG2 and MawuSTK. In addition, we investigated the evolutionary history of exon-intron structural changes of the AG/STK subfamily, and a novel splice-acceptor mode (GUU-AU) and the convergent evolution of N-terminal extension in the euAG and PLE subclades were revealed for the first time. These results further advance our understanding of ancestral AG/STK subfamily genes in terms of phylogeny, exon-intron structures, expression and interaction patterns, and functions, and provide strong evidence for the significance of gene duplication in the expansion and evolution of the AG/STK subfamily.
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Affiliation(s)
- Jiang Ma
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing 100083, PR China
| | - Shixin Deng
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing 100083, PR China
| | - Zhongkui Jia
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing 100083, PR China
| | - Ziyang Sang
- Forestry Bureau of Wufeng County, Yichang, 443002, Hubei Province, PR China
| | - Zhonglong Zhu
- Wufeng Bo Ling Magnolia Wufengensis Technology Development Co., Ltd, Yichang, 443002, Hubei Province, PR China
| | - Chao Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang 443002, PR China
| | - Lvyi Ma
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing 100083, PR China
| | - Faju Chen
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang 443002, PR China
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Wang T, Wei L, Wang J, Xie L, Li YY, Ran S, Ren L, Lu K, Li J, Timko MP, Liu L. Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed ( Brassica napus L.). BIOTECHNOLOGY FOR BIOFUELS 2020; 13:134. [PMID: 32774455 PMCID: PMC7397576 DOI: 10.1186/s13068-020-01774-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/24/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Brassica napus is one of the most important oilseed crops, and also an important biofuel plant due to its low air pollution and renewability. Growth period are important traits that affect yield and are crucial for its adaptation to different environments in B. napus. RESULTS To elucidate the genetic basis of growth period traits, genome-wide association analysis (GWAS) and linkage mapping were employed to detect the quantitative trait loci (QTL) for days to initial flowering (DIF), days to final flowering (DFF), flowering period (FP), maturity time (MT), and whole growth period (GP). A total of 146 SNPs were identified by association mapping, and 83 QTLs were identified by linkage mapping using the RIL population. Among these QTLs, 19 were pleiotropic SNPs related to multiple traits, and six (q18DFF.A03-2, q18MT.A03-2, q17DFF.A05-1, q18FP.C04, q17DIF.C05 and q17GP.C09) were consistently detected using both mapping methods. Additionally, we performed RNA sequencing to analyze the differential expression of gene (DEG) transcripts between early- and late-flowering lines selected from the RIL population, and the DEGs were integrated with association mapping and linkage analysis to confirm their roles in the growth period. Consequently, 12 candidate genes associated with growth period traits were identified in B. napus. Among these genes, seven have polymorphic sites in the coding sequence and the upstream 2-kb sequence based on the resequencing data. The haplotype BnaSOC1.A05-Haplb and BnaLNK2.C06-Hapla showed more favorable phenotypic traits. CONCLUSIONS The candidate genes identified in this study will contribute to our genetic understanding of growth period traits and can be used as targets for target mutations or marker-assisted breeding for rapeseed adapted to different environments.
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Affiliation(s)
- Tengyue Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Lijuan Wei
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Jia Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Ling Xie
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Yang Yang Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Shuyao Ran
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Lanyang Ren
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
| | - Michael P. Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904 USA
| | - Liezhao Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715 China
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Yang C, Liu X, Li D, Zhu X, Wei Z, Feng Z, Zhang L, He J, Mou C, Jiang L, Wan J. OsLUGL is involved in the regulating auxin level and OsARFs expression in rice (Oryza sativa L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110239. [PMID: 31521225 DOI: 10.1016/j.plantsci.2019.110239] [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: 05/06/2019] [Revised: 07/27/2019] [Accepted: 08/25/2019] [Indexed: 06/10/2023]
Abstract
Specification of floral organ identity is critical for floral morphology and inflorescence architecture. Floral organ identity in plants is controlled by floral homeotic A/B/C/D/E-class genes. Although multiple genes regulate floral organogenesis, our understanding of the regulatory network remains fragmentary. Here, we characterized a rice floral organ gene KAIKOUXIAO (KKX), mutation of which produces an uncharacteristic open hull, abnormal seed and semi-sterility. KKX encodes a putative LEUNIG-like (LUGL) transcriptional regulator OsLUGL. OsLUGL is preferentially expressed in young panicles and its protein can interact with OsSEU, which functions were reported as an adaptor for LEUNIG. OsLUGL-OsSEU functions together as a transcriptional co-regulatory complex to control organ identity. SEP3 (such as OsMADS8) and AP1 (such as OsMADS18) serve as the DNA-binding partner of OsLUGL-OsSEU complex. Further studies indicated that OsMADS8 and OsMADS18 could bind to the promoter of OsGH3-8. The altered expression of OsGH3-8 might cause the increased auxin level and the decreased expression of OsARFs. Overall, our results demonstrate a possible pathway whereby OsLUGL-OsSEU-OsAP1-OsSEP3 complex as a transcriptional co-regulator by targeting the promoter of OsGH3-8, then affecting auxin level, OsARFs expression and thereby influencing floral development. These findings provide a valuable insight into the molecular functions of OsLUGL in rice floral development.
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Affiliation(s)
- Chunyan Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dianli Li
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xingjie Zhu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ziyao Wei
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhiming Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Long Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun He
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Changling Mou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China; National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Su Y, Liu J, Liang W, Dou Y, Fu R, Li W, Feng C, Gao C, Zhang D, Kang Z, Li H. Wheat AGAMOUS LIKE 6 transcription factors function in stamen development by regulating the expression of Ta APETALA3. Development 2019; 146:dev.177527. [PMID: 31540915 DOI: 10.1242/dev.177527] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 09/11/2019] [Indexed: 11/20/2022]
Abstract
Previous studies have revealed the functions of rice and maize AGAMOUS LIKE 6 (AGL6) genes OsMADS6 and ZAG3, respectively, in floral development; however, the functions of three wheat (Triticum aestivum) AGL6 genes are still unclear. Here, we report the main functions of wheat AGL6 homoeologous genes in stamen development. In RNAi plants, stamens showed abnormality in number and morphology, and a tendency to transform into carpels. Consistently, the expression of the B-class gene TaAPETALA3 (AP3) and the auxin-responsive gene TaMGH3 was downregulated, whereas the wheat ortholog of the rice carpel identity gene DROOPING LEAF was ectopically expressed in RNAi stamens. TaAGL6 proteins bind to the promoter of TaAP3 directly. Yeast one-hybrid and transient expression assays further showed that TaAGL6 positively regulates the expression of TaAP3 in vivo. Wheat AGL6 transcription factors interact with TaAP3, TaAGAMOUS and TaMADS13. Our findings indicate that TaAGL6 transcription factors play an essential role in stamen development through transcriptional regulation of TaAP3 and other related genes. We propose a model to illustrate the function and probable mechanism of this regulation. This study extends our understanding of AGL6 genes.
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Affiliation(s)
- Yali Su
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Jinxing Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wanqi Liang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanhua Dou
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Ruifeng Fu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenqiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Cuizhu Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Caixia Gao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dabing Zhang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haifeng Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, China
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Zhao HB, Jia HM, Wang Y, Wang GY, Zhou CC, Jia HJ, Gao ZS. Genome-wide identification and analysis of the MADS-box gene family and its potential role in fruit development and ripening in red bayberry (Morella rubra). Gene 2019; 717:144045. [PMID: 31425741 DOI: 10.1016/j.gene.2019.144045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 02/08/2023]
Abstract
The MADS-box gene family encodes transcription factors and plays an important role in plant growth and the development of flower and fruit. A perennial dioecious plant, the red bayberry genome has been published recently, providing the opportunity to analyze the MADS-box gene family and its role in fruit development and ripening. Here, we identified 54 MADS-box genes in the red bayberry genome, and classified them into two types based on phylogenetic analysis. Thirteen Type I MADS-box genes were subdivided into three subfamilies and 41 Type II MADS-box genes into 13 subfamilies. A total of 46 MADS-box genes were distributed across eight red bayberry chromosomes, and the other eight genes were located on the unmapped scaffolds. Transcriptome analysis suggested that the expression of most Type II genes was higher than Type I in five female tissues. Moreover, 26 MADS-box genes were expressed during red bayberry fruit development and ten of them showed high expression. qRT-PCR showed that the expression of MrMADS01 (SEP, MIKCC), with differences between the pale pink and red varieties, increased significantly at the final ripening stage, suggesting it may participate in ripening as positive regulator and related to anthocyanin biosynthesis. These results provide some clues for future study of MADS-box genes in red bayberry, especially in ripening process.
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Affiliation(s)
- Hai-Bo Zhao
- Institute of Fruit Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hui-Min Jia
- Institute of Fruit Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; current address: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, 201602, China.
| | - Yan Wang
- Institute of Fruit Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Guo-Yun Wang
- Agriculture Extensions and Services Station, Bureau of Agriculture and Rural Affairs, Yuyao, Ningbo 315400, China
| | - Chao-Chao Zhou
- Agriculture Extensions and Services Station, Bureau of Agriculture and Rural Affairs, Yuyao, Ningbo 315400, China
| | - Hui-Juan Jia
- Institute of Fruit Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhong-Shan Gao
- Institute of Fruit Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
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Ma J, Deng S, Chen L, Jia Z, Sang Z, Zhu Z, Ma L, Chen F. Gene duplication led to divergence of expression patterns, protein-protein interaction patterns and floral development functions of AGL6-like genes in the basal angiosperm Magnolia wufengensis (Magnoliaceae). TREE PHYSIOLOGY 2019; 39:861-876. [PMID: 31034013 DOI: 10.1093/treephys/tpz010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/07/2019] [Accepted: 01/31/2019] [Indexed: 06/09/2023]
Abstract
The MADS-box family genes play critical roles in the regulation of growth and development of flowering plants. AGAMOUS-LIKE 6 (AGL6)-like genes are one of the most enigmatic subfamilies of the MADS-box family because of highly variable expression patterns and ambiguous functions, which have long puzzled researchers. A lot of AGL6 homologs have been identified from gymnosperms and angiosperms. However, only a few have been characterized, especially for basal angiosperm taxa. Magnolia wufengensis is a woody basal angiosperm from the family Magnoliaceae. In the current study, the phylogenesis, expression and protein-protein interaction (PPI) patterns, and functions of two AGL6 homologs from M. wufengensis, MawuAGL6-1 and MawuAGL6-2, were analyzed. Phylogenetic analysis indicated that the two AGL6 duplicates may have arisen by gene duplication before the divergence of Magnoliaceae and Lauraceae, with the diversification of their expression and PPI patterns after gene duplication. Functional analysis revealed that, in addition to common functions in accelerating flowering, MawuAGL6-1 might be responsible for flower meristem determinacy, while MawuAGL6-2 is preferentially recruited to regulate tepal morphogenesis. These findings further advance our understanding of the evolution of phylogenesis, expression, interaction and functions of AGL6 lineage genes from basal angiosperms, as well as the entire AGL6 lineage genes, and the significance of AGL6 lineage genes in the evolution and biological diversity.
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Affiliation(s)
- Jiang Ma
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing, PR China
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang, PR China
| | - Shixin Deng
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing, PR China
| | - Liyuan Chen
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing, PR China
| | - Zhongkui Jia
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing, PR China
| | - Ziyang Sang
- Forestry Bureau of Wufeng County, Wufeng, Hubei Province, PR China
| | - Zhonglong Zhu
- Wufeng Bo Ling Magnolia Wufengensis Technology Development Co., Ltd, Wufeng, Hubei Province, PR China
| | - Lvyi Ma
- Ministry of Education Key Laboratory of Silviculture and Conservation, Forestry College, Beijing Forestry University, Beijing, PR China
| | - Faju Chen
- Key Laboratory of Three Gorges Regional Plant Genetics & Germplasm Enhancement (CTGU)/Biotechnology Research Center, China Three Gorges University, Yichang, PR China
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Shen G, Yang CH, Shen CY, Huang KS. Origination and selection of ABCDE and AGL6 subfamily MADS-box genes in gymnosperms and angiosperms. Biol Res 2019; 52:25. [PMID: 31018872 PMCID: PMC6480507 DOI: 10.1186/s40659-019-0233-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/18/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The morphological diversity of flower organs is closely related to functional divergence within the MADS-box gene family. Bryophytes and seedless vascular plants have MADS-box genes but do not have ABCDE or AGAMOUS-LIKE6 (AGL6) genes. ABCDE and AGL6 genes belong to the subgroup of MADS-box genes. Previous works suggest that the B gene was the first ABCDE and AGL6 genes to emerge in plant but there are no mentions about the probable origin time of ACDE and AGL6 genes. Here, we collected ABCDE and AGL6 gene 381 protein sequences and 361 coding sequences from gymnosperms and angiosperms and reconstructed a complete Bayesian phylogeny of these genes. In this study, we want to clarify the probable origin time of ABCDE and AGL6 genes is a great help for understanding the role of the formation of the flower, which can decipher the forming order of MADS-box genes in the future. RESULTS These genes appeared to have been under purifying selection and their evolutionary rates are not significantly different from each other. Using the Bayesian evolutionary analysis by sampling trees (BEAST) tool, we estimated that: the mutation rate of the ABCDE and AGL6 genes was 2.617 × 10-3 substitutions/site/million years, and that B genes originated 339 million years ago (MYA), CD genes originated 322 MYA, and A genes shared the most recent common ancestor with E/AGL6 296 MYA, respectively. CONCLUSIONS The phylogeny of ABCDE and AGL6 genes subfamilies differed. The APETALA1 (AP1 or A gene) subfamily clustered into one group. The APETALA3/PISTILLATA (AP3/PI or B genes) subfamily clustered into two groups: the AP3 and PI clades. The AGAMOUS/SHATTERPROOF/SEEDSTICK (AG/SHP/STK or CD genes) subfamily clustered into a single group. The SEPALLATA (SEP or E gene) subfamily in angiosperms clustered into two groups: the SEP1/2/4 and SEP3 clades. The AGL6 subfamily clustered into a single group. Moreover, ABCDE and AGL6 genes appeared in the following order: AP3/PI → AG/SHP/STK → AGL6/SEP/AP1. In this study, we collected candidate sequences from gymnosperms and angiosperms. This study highlights important events in the evolutionary history of the ABCDE and AGL6 gene families and clarifies their evolutionary path.
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Affiliation(s)
- Gangxu Shen
- Department of Electrical Engineering, I-Shou University, Kaohsiung, Taiwan
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan
| | - Chih-Hui Yang
- College of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Chi-Yen Shen
- Department of Electrical Engineering, I-Shou University, Kaohsiung, Taiwan
| | - Keng-Shiang Huang
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan
- College of Medicine, I-Shou University, Kaohsiung, Taiwan
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Chongloi GL, Prakash S, Vijayraghavan U. Regulation of meristem maintenance and organ identity during rice reproductive development. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1719-1736. [PMID: 30753578 DOI: 10.1093/jxb/erz046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Grasses have evolved complex inflorescences, where the primary unit is the specialized short branch called a spikelet. Detailed studies of the cumulative action of the genetic regulators that direct the progressive change in axillary meristem identity and their terminal differentiation are crucial to understanding the complexities of the inflorescence and the development of a determinate floret. Grass florets also pose interesting questions concerning the morphologies and functions of organs as compared to other monocots and eudicots. In this review, we summarize our current knowledge of the regulation of the transitions that occur in grass inflorescence meristems, and of the specification of floret meristems and their determinate development. We primarily use rice as a model, with appropriate comparisons to other crop models and to the extensively studied eudicot Arabidopsis. The role of MADS-domain transcription factors in floral organ patterning is well documented in many eudicots and in grasses. However, there is evidence to suggest that some of these rice floral regulators have evolved distinctive functions and that other grass species-specific factors and regulatory pathways occur - for example the LOFSEP 'E' class genes OsMADS1 and OsMAD34, and ramosa genes. A better understanding of these systems and the epigenetic regulators and hormone signaling pathways that interact with them will provide new insights into the rice inflorescence meristem and the differentiation of its floret organs, and should indicate genetic tools that can be used to control yield-related traits in both rice and other cereal crops.
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Affiliation(s)
- Grace L Chongloi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Sandhan Prakash
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Usha Vijayraghavan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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Schultz JC, Edger PP, Body MJA, Appel HM. A galling insect activates plant reproductive programs during gall development. Sci Rep 2019; 9:1833. [PMID: 30755671 PMCID: PMC6372598 DOI: 10.1038/s41598-018-38475-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/28/2018] [Indexed: 12/02/2022] Open
Abstract
Many insect species have acquired the ability to redirect plant development to form unique organs called galls, which provide these insects with unique, enhanced food and protection from enemies and the elements. Many galls resemble flowers or fruits, suggesting that elements of reproductive development may be involved. We tested this hypothesis using RNA sequencing to quantify the transcriptional responses of wild grapevine (Vitis riparia) leaves to a galling parasite, phylloxera (Daktulosphaira vitifoliae). If development of reproductive structures is part of gall formation, we expected to find significantly elevated expression of genes involved in flower and/or fruit development in developing galls as opposed to ungalled leaves. We found that reproductive gene ontology categories were significantly enriched in developing galls, and that expression of many candidate genes involved in floral development were significantly increased, particularly in later gall stages. The patterns of gene expression found in galls suggest that phylloxera exploits vascular cambium to provide meristematic tissue and redirects leaf development towards formation of carpels. The phylloxera leaf gall appears to be phenotypically and transcriptionally similar to the carpel, due to the parasite hijacking underlying genetic machinery in the host plant.
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Affiliation(s)
- Jack C Schultz
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
- Department of Environmental Sciences, Bowman-Oddy Laboratories, University of Toledo, Toledo, OH, 43606, USA.
| | - Patrick P Edger
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- Department of Horticulture, Michigan State University and Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Mélanie J A Body
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- Department of Environmental Sciences, Bowman-Oddy Laboratories, University of Toledo, Toledo, OH, 43606, USA
| | - Heidi M Appel
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- Department of Environmental Sciences, Bowman-Oddy Laboratories, University of Toledo, Toledo, OH, 43606, USA
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Song GQ, Chen Q. Overexpression of the MADS-box gene K-domain increases the yield potential of blueberry. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 276:22-31. [PMID: 30348321 DOI: 10.1016/j.plantsci.2018.07.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/18/2018] [Accepted: 07/29/2018] [Indexed: 05/27/2023]
Abstract
MADS-box genes play a significant role for plant flowering. Keratin-like (K) domains are involved in protein-to-protein interactions in the formation of the MIKC-type MADS-box domain proteins. In this study, the potential of utilizing the K domain of a Vaccinium corymbosum SOC1-like gene (VcSOC1K) was investigated to modulate expression of other blueberry MADS-box genes for increasing blueberry productivity. Chilled transgenic blueberry plants overexpressing the VcSOC1K showed a significant increase in the number of canes, floral buds, and flower and fruit clusters compared to chilled non-transgenic plants. Additionally, nonchilled transgenic plants flowered whereas nonchilled non-transgenic plants did not. Transgenic plants showed an increase in tolerance to high soil pH. Comparative transcriptome analysis of transgenic and non-transgenic leaves showed differential expression of 17% of the MADS-box genes identified in blueberry. These differentially expressed (DE) MADS-box genes were associated with genes related to plant flowering, phytohormones, and response to various biotic and abiotic stimuli. The phenotypic changes and the DE MADS-box genes caused by the overexpression of VcSOC1K not only reveal that the MADS-box genes are involved in chilling/vernalization-mediated flowering in blueberry but also demonstrated that the overexpression of the K domain can effectively modulate plant reproductive processes.
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Affiliation(s)
- Guo-Qing Song
- Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.
| | - Qiuxia Chen
- Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
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Takisawa R, Nakazaki T, Nunome T, Fukuoka H, Kataoka K, Saito H, Habu T, Kitajima A. The parthenocarpic gene Pat-k is generated by a natural mutation of SlAGL6 affecting fruit development in tomato (Solanum lycopersicum L.). BMC PLANT BIOLOGY 2018; 18:72. [PMID: 29699487 PMCID: PMC5921562 DOI: 10.1186/s12870-018-1285-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 04/10/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Parthenocarpy is a desired trait in tomato because it can overcome problems with fruit setting under unfavorable environmental conditions. A parthenocarpic tomato cultivar, 'MPK-1', with a parthenocarpic gene, Pat-k, exhibits stable parthenocarpy that produces few seeds. Because 'MPK-1' produces few seeds, seedlings are propagated inefficiently via cuttings. It was reported that Pat-k is located on chromosome 1. However, the gene had not been isolated and the relationship between the parthenocarpy and low seed set in 'MPK-1' remained unclear. In this study, we isolated Pat-k to clarify the relationship between parthenocarpy and low seed set in 'MPK-1'. RESULTS Using quantitative trait locus (QTL) analysis for parthenocarpy and seed production, we detected a major QTL for each trait on nearly the same region of the Pat-k locus on chromosome 1. To isolate Pat-k, we performed fine mapping using an F4 population following the cross between a non-parthenocarpic cultivar, 'Micro-Tom' and 'MPK-1'. The results showed that Pat-k was located in the 529 kb interval between two markers, where 60 genes exist. By using data from a whole genome re-sequencing and genome sequence analysis of 'MPK-1', we could identify that the SlAGAMOUS-LIKE 6 (SlAGL6) gene of 'MPK-1' was mutated by a retrotransposon insertion. The transcript level of SlAGL6 was significantly lower in ovaries of 'MPK-1' than a non-parthenocarpic cultivar. From these results, we could conclude that Pat-k is SlAGL6, and its down-regulation in 'MPK-1' causes parthenocarpy and low seed set. In addition, we observed abnormal micropyles only in plants homozygous for the 'MPK-1' allele at the Pat-k/SlAGL6 locus. This result suggests that Pat-k/SlAGL6 is also related to ovule formation and that the low seed set in 'MPK-1' is likely caused by abnormal ovule formation through down-regulation of Pat-k/SlAGL6. CONCLUSIONS Pat-k is identical to SlAGL6, and its down-regulation causes parthenocarpy and low seed set in 'MPK-1'. Moreover, down-regulation of Pat-k/SlAGL6 could cause abnormal ovule formation, leading to a reduction in the number of seeds.
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Affiliation(s)
- Rihito Takisawa
- Graduate School of Agriculture, Kyoto University, Kizugawa, 619-0218 Japan
| | - Tetsuya Nakazaki
- Graduate School of Agriculture, Kyoto University, Kizugawa, 619-0218 Japan
| | - Tsukasa Nunome
- NARO Institute of Vegetable and Floriculture Science, Tsu, 514-2392 Japan
| | - Hiroyuki Fukuoka
- NARO Institute of Vegetable and Tea Science, Tsu, 514-2392 Japan
| | - Keiko Kataoka
- Graduate School of Agriculture, Ehime University, Matsuyama, 790-8566 Japan
| | - Hiroki Saito
- Graduate School of Agriculture, Kyoto University, Kizugawa, 619-0218 Japan
- Present Address: Tropical Agriculture Research Front Japan International Research Center Agricultural Sciences, 1091-1, Kawarabaru, Aza Maezato, Ishigaki, Okinawa 907-0002 Japan
| | - Tsuyoshi Habu
- Graduate School of Agriculture, Ehime University, Matsuyama, 790-8566 Japan
| | - Akira Kitajima
- Graduate School of Agriculture, Kyoto University, Kizugawa, 619-0218 Japan
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Callens C, Tucker MR, Zhang D, Wilson ZA. Dissecting the role of MADS-box genes in monocot floral development and diversity. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2435-2459. [PMID: 29718461 DOI: 10.1093/jxb/ery086] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/16/2018] [Indexed: 05/05/2023]
Abstract
Many monocot plants have high social and economic value. These include grasses such as rice (Oryza sativa), wheat (Triticum aestivum), and barley (Hordeum vulgare), which produce soft commodities for many food and beverage industries, and ornamental flowers such ase lily (Lilium longiflorum) and orchid (Oncidium Gower Ramsey), which represent an important component of international flower markets. There is constant pressure to improve the development and diversity of these species, with a significant emphasis on flower development, and this is particularly relevant considering the impact of changing environments on reproduction and thus yield. MADS-box proteins are a family of transcription factors that contain a conserved 60 amino acid MADS-box motif. In plants, attention has been devoted to characterization of this family due to their roles in inflorescence and flower development, which holds promise for the modification of floral architecture for plant breeding. This has been explored in diverse angiosperms, but particularly the dicot model Arabidopsis thaliana. The focus of this review is on the less well characterized roles of the MADS-box proteins in monocot flower development and how changes in MADS-box proteins throughout evolution may have contributed to creating a diverse range of flowers. Examining these changes within the monocots can identify the importance of certain genes and pinpoint those which might be useful in future crop improvement and breeding strategies.
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Affiliation(s)
- Cindy Callens
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
| | - Matthew R Tucker
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
| | - Dabing Zhang
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zoe A Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
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Xiang L, Chen Y, Chen L, Fu X, Zhao K, Zhang J, Sun C. B and E MADS-box genes determine the perianth formation in Cymbidium goeringii Rchb.f. PHYSIOLOGIA PLANTARUM 2018; 162:353-369. [PMID: 28967227 DOI: 10.1111/ppl.12647] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 05/09/2023]
Abstract
Cymbidium goeringii Rchb.f. is an important ornamental plant with a striking well-differentiated lip. Its complex floral architecture presents an exciting opportunity to examine perianth development. In flowering plants, class A, B and E floral homeotic genes play key roles in the specification of perianth identity. In this study, we used a cDNA library of wild-type C. goeringii flower buds for transcriptome sequencing. Eighteen candidate class A, B and E genes (including AP1/FUL-, AP2-, DEF-, GLO-, SEP- and AGL6-like genes) were identified. Quantitative real time polymerase chain reaction (qRT-PCR) results showed that CgDEF1, CgSEP2 and CgAGL6-1 were strongly detected only in the sepals and petals and were significantly downregulated in the lips. CgDEF3, CgDEF4 and CgAGL6-3 were highly expressed in the lips and lip-like petals but were only minimally detected in the sepals. Yeast two-hybrid analysis indicated that CgDEF1 and CgGLO formed a heterodimer. CgAGL6-1/CgSEP2 and CgDEF1 formed higher-order protein complexes with the assistance of the CgGLO protein, and both CgAGL6-1 and CgSEP2 formed a heterodimer. CgDEF3/CgDEF4 could interact independently with CgGLO and CgAGL6-3, respectively, while CgDEF3 and CgDEF4 also formed heterodimers with the assistance of the CgGLO. Based on a comprehensive analysis relating these gene expression patterns to protein interaction profiles, the mechanism of sepal/petal/lip determination was studied in C. goeringii. Furthermore, a hypothesis explaining the sepal/petal/lip determination of C. goeringii is proposed. The lip-quartet (CgDEF3/CgDEF4/CgAGL6-3/CgGLO) promoted lip formation, whereas the sepal/petal-quartet (CgDEF1/CgAGL6-1/CgSEP2/CgGLO) promoted sepal/petal formation. These results enrich the current knowledge regarding the mechanism and pathways of perianth formation in orchids.
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Affiliation(s)
- Lin Xiang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Yue Chen
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Liping Chen
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaopeng Fu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Kaige Zhao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Jie Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Chongbo Sun
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Ma X, Zheng Z, Lin F, Ge T, Sun H. Genetic analysis and gene mapping of a low stigma exposed mutant gene by high-throughput sequencing. PLoS One 2018; 13:e0186942. [PMID: 29298308 PMCID: PMC5751978 DOI: 10.1371/journal.pone.0186942] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 10/10/2017] [Indexed: 12/02/2022] Open
Abstract
Rice is one of the main food crops and several studies have examined the molecular mechanism of the exposure of the rice plant stigma. The improvement in the exposure of the stigma in female parent hybrid combinations can enhance the efficiency of hybrid breeding. In the present study, a mutant plant with low exposed stigma (lesr) was discovered among the descendants of the indica thermo-sensitive sterile line 115S. The ES% rate of the mutant decreased by 70.64% compared with the wild type variety. The F2 population was established by genetic analysis considering the mutant as the female parent and the restorer line 93S as the male parent. The results indicated a normal F1 population, while a clear division was noted for the high and low exposed stigma groups, respectively. This process was possible only by a ES of 25% in the F2 population. This was in agreement with the ratio of 3:1, which indicated that the mutant was controlled by a recessive main-effect QTL locus, temporarily named as LESR. Genome-wide comparison of the SNP profiles between the early, high and low production bulks were constructed from F2 plants using bulked segregant analysis in combination with high-throughput sequencing technology. The results demonstrated that the candidate loci was located on the chromosome 10 of the rice. Following screening of the recombinant rice plants with newly developed molecular markers, the genetic region was narrowed down to 0.25 Mb. This region was flanked by InDel-2 and InDel-2 at the physical location from 13.69 to 13.94 Mb. Within this region, 7 genes indicated base differences between parents. A total of 2 genes exhibited differences at the coding region and upstream of the coding region, respectively. The present study aimed to further clone the LESR gene, verify its function and identify the stigma variation.
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Affiliation(s)
- Xiao Ma
- College of Life Science, Jinggangshan University, Ji’ an, China
| | - Zhuo Zheng
- College of Life Science, Jinggangshan University, Ji’ an, China
| | - Fanshu Lin
- College of Life Science, Jinggangshan University, Ji’ an, China
| | - Tingting Ge
- College of Life Science, Jinggangshan University, Ji’ an, China
| | - Huimin Sun
- College of Life Science, Jinggangshan University, Ji’ an, China
- * E-mail:
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Kostyun JL, Moyle LC. Multiple strong postmating and intrinsic postzygotic reproductive barriers isolate florally diverse species of Jaltomata (Solanaceae). Evolution 2017; 71:1556-1571. [PMID: 28432763 PMCID: PMC5502772 DOI: 10.1111/evo.13253] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/31/2017] [Indexed: 12/22/2022]
Abstract
Divergence in phenotypic traits often contributes to premating isolation between lineages, but could also promote isolation at postmating stages. Phenotypic differences could directly result in mechanical isolation or hybrids with maladapted traits; alternatively, when alleles controlling these trait differences pleiotropically affect other components of development, differentiation could indirectly produce genetic incompatibilities in hybrids. Here, we determined the strength of nine postmating and intrinsic postzygotic reproductive barriers among 10 species of Jaltomata (Solanaceae), including species with highly divergent floral traits. To evaluate the relative importance of floral trait diversification for the strength of these postmating barriers, we assessed their relationship to floral divergence, genetic distance, geographical context, and ecological differences, using conventional tests and a new linear-mixed modeling approach. Despite close evolutionary relationships, all species pairs showed moderate to strong isolation. Nonetheless, floral trait divergence was not a consistent predictor of the strength of isolation; instead this was best explained by genetic distance, although we found evidence for mechanical isolation in one species, and a positive relationship between floral trait divergence and fruit set isolation across species pairs. Overall, our data indicate that intrinsic postzygotic isolation is more strongly associated with genome-wide genetic differentiation, rather than floral divergence.
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Affiliation(s)
- Jamie L. Kostyun
- Department of Biology, Indiana University, Bloomington, Indiana
47405, USA
| | - Leonie C. Moyle
- Department of Biology, Indiana University, Bloomington, Indiana
47405, USA
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