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Wang X, Liu Z, Zhang F, Xiao H, Cao S, Xue H, Liu W, Su Y, Liu Z, Zhong H, Zhang F, Ahmad B, Long Q, Zhang Y, Liu Y, Gan Y, Hou T, Jin Z, Wu X, Liu G, Wang Y, Peng Y, Zhou Y. Integrative genomics reveals the polygenic basis of seedlessness in grapevine. Curr Biol 2024; 34:3763-3777.e5. [PMID: 39094571 DOI: 10.1016/j.cub.2024.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/04/2024] [Accepted: 07/03/2024] [Indexed: 08/04/2024]
Abstract
Seedlessness is a crucial quality trait in table grape (Vitis vinifera L.) breeding. However, the development of seeds involved intricate regulations, and the polygenic basis of seed abortion remains unclear. Here, we combine comparative genomics, population genetics, quantitative genetics, and integrative genomics to unravel the evolution and polygenic basis of seedlessness in grapes. We generated the haplotype-resolved genomes for two seedless grape cultivars, "Thompson Seedless" (TS, syn. "Sultania") and "Black Monukka" (BM). Comparative genomics identified a ∼4.25 Mb hemizygous inversion on Chr10 specific in seedless cultivars, with seedless-associated genes VvTT16 and VvSUS2 located at breakpoints. Population genomic analyses of 548 grapevine accessions revealed two distinct clusters of seedless cultivars, and the identity-by-descent (IBD) results indicated that the origin of the seedlessness trait could be traced back to "Sultania." Introgression, rather than convergent selection, shaped the evolutionary history of seedlessness in grape improvement. Genome-wide association study (GWAS) analysis identified 110 quantitative trait loci (QTLs) associated with 634 candidate genes, including previously unidentified candidate genes, such as three 11S GLOBULIN SEED STORAGE PROTEIN and two CYTOCHROME P450 genes, and well-known genes like VviAGL11. Integrative genomic analyses resulted in 339 core candidate genes categorized into 13 functional categories related to seed development. Machine learning-based genomic selection achieved a remarkable prediction accuracy of 97% for seedlessness in grapevines. Our findings highlight the polygenic nature of seedlessness and provide candidate genes for molecular genetics and an effective prediction for seedlessness in grape genomic breeding.
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Affiliation(s)
- Xu Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Fan Zhang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hui Xue
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wenwen Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ying Su
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhenya Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Haixia Zhong
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Fuchun Zhang
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Bilal Ahmad
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qiming Long
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yingchun Zhang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuting Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yu Gan
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ting Hou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhongxin Jin
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xinyu Wu
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Guotian Liu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yiwen Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
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Zhang J, Hu Z, Xie Q, Dong T, Li J, Chen G. Two SEPALLATA MADS-Box Genes, SlMBP21 and SlMADS1, Have Cooperative Functions Required for Sepal Development in Tomato. Int J Mol Sci 2024; 25:2489. [PMID: 38473738 PMCID: PMC10931843 DOI: 10.3390/ijms25052489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/08/2024] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
MADS-box transcription factors have crucial functions in numerous physiological and biochemical processes during plant growth and development. Previous studies have reported that two MADS-box genes, SlMBP21 and SlMADS1, play important regulatory roles in the sepal development of tomato, respectively. However, the functional relationships between these two genes are still unknown. In order to investigate this, we simultaneously studied these two genes in tomato. Phylogenetic analysis showed that they were classified into the same branch of the SEPALLATA (SEP) clade. qRT-PCR displayed that both SlMBP21 and SlMADS1 transcripts are preferentially accumulated in sepals, and are increased with flower development. During sepal development, SlMBP21 is increased but SlMADS1 is decreased. Using the RNAi, tomato plants with reduced SlMBP21 mRNA generated enlarged and fused sepals, while simultaneous inhibition of SlMBP21 and SlMADS1 led to larger (longer and wider) and fused sepals than that in SlMBP21-RNAi lines. qRT-PCR results exhibited that the transcripts of genes relating to sepal development, ethylene, auxin and cell expansion were dramatically changed in SlMBP21-RNAi sepals, especially in SlMBP21-SlMADS1-RNAi sepals. Yeast two-hybrid assay displayed that SlMBP21 can interact with SlMBP21, SlAP2a, TAGL1 and RIN, and SlMADS1 can interact with SlAP2a and RIN, respectively. In conclusion, SlMBP21 and SlMADS1 cooperatively regulate sepal development in tomato by impacting the expression or activities of other related regulators or via interactions with other regulatory proteins.
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Affiliation(s)
- Jianling Zhang
- Laboratory of Plant Germplasm Innovation and Utilization, School of Life Sciences, Liaocheng University, Liaocheng 252000, China;
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (Q.X.); (T.D.); (J.L.)
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (Q.X.); (T.D.); (J.L.)
| | - Qiaoli Xie
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (Q.X.); (T.D.); (J.L.)
| | - Tingting Dong
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (Q.X.); (T.D.); (J.L.)
- Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
| | - Jing Li
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (Q.X.); (T.D.); (J.L.)
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (Q.X.); (T.D.); (J.L.)
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Hyden B, Carper DL, Abraham PE, Yuan G, Yao T, Baumgart L, Zhang Y, Chen C, O'Malley R, Chen J, Yang X, Hettich RL, Tuskan GA, Smart LB. Functional analysis of Salix purpurea genes support roles for ARR17 and GATA15 as master regulators of sex determination. PLANT DIRECT 2023; 7:e3546. [PMID: 38028649 PMCID: PMC10651977 DOI: 10.1002/pld3.546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
The Salicaceae family is of growing interest in the study of dioecy in plants because the sex determination region (SDR) has been shown to be highly dynamic, with differing locations and heterogametic systems between species. Without the ability to transform and regenerate Salix in tissue culture, previous studies investigating the mechanisms regulating sex in the genus Salix have been limited to genome resequencing and differential gene expression, which are mostly descriptive in nature, and functional validation of candidate sex determination genes has not yet been conducted. Here, we used Arabidopsis to functionally characterize a suite of previously identified candidate genes involved in sex determination and sex dimorphism in the bioenergy shrub willow Salix purpurea. Six candidate master regulator genes for sex determination were heterologously expressed in Arabidopsis, followed by floral proteome analysis. In addition, 11 transcription factors with predicted roles in mediating sex dimorphism downstream of the SDR were tested using DAP-Seq in both male and female S. purpurea DNA. The results of this study provide further evidence to support models for the roles of ARR17 and GATA15 as master regulator genes of sex determination in S. purpurea, contributing to a regulatory system that is notably different from that of its sister genus Populus. Evidence was also obtained for the roles of two transcription factors, an AP2/ERF family gene and a homeodomain-like transcription factor, in downstream regulation of sex dimorphism.
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Affiliation(s)
- Brennan Hyden
- Horticulture Section, School of Integrative Plant ScienceCornell University, Cornell AgriTechGenevaNew YorkUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Dana L. Carper
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Paul E. Abraham
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Guoliang Yuan
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Tao Yao
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Leo Baumgart
- Lawrence Berkeley National LaboratoryUS Department of Energy Joint Genome InstituteBerkeleyCaliforniaUSA
| | - Yu Zhang
- Lawrence Berkeley National LaboratoryUS Department of Energy Joint Genome InstituteBerkeleyCaliforniaUSA
| | - Cindy Chen
- Lawrence Berkeley National LaboratoryUS Department of Energy Joint Genome InstituteBerkeleyCaliforniaUSA
| | - Ronan O'Malley
- Lawrence Berkeley National LaboratoryUS Department of Energy Joint Genome InstituteBerkeleyCaliforniaUSA
| | - Jin‐Gui Chen
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Xiaohan Yang
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Robert L. Hettich
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Gerald A. Tuskan
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Lawrence B. Smart
- Horticulture Section, School of Integrative Plant ScienceCornell University, Cornell AgriTechGenevaNew YorkUSA
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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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Becerra-García RE, Cruz-Valderrama JE, Cerbantez-Bueno VE, Marsch-Martínez N, de Folter S. A NanoLuc-Based Transactivation Assay in Plants. Methods Mol Biol 2023; 2686:553-565. [PMID: 37540377 DOI: 10.1007/978-1-0716-3299-4_26] [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
Protein-DNA interactions are determinant of the regulation of gene expression in living organisms. Luminescence studies have been used in a wide range of techniques to identify how gene transcription can be regulated by proteins such as transcription factors (TFs). Despite the great advances in the use of luciferases as reporters in the performance of this mechanism, some of them still have disadvantages that have been tried to be solved by the generation of new luciferases that induce a more stable and perfectly visualizable reaction. NanoLuc is a recently described luciferase that has been characterized by its efficient, stable, and powerful luminescence. These qualities have been considered to create a new and efficient reporter system to detect protein-DNA interactions. In this chapter, we take advantage of NanoLuc and describe its use in a reliable procedure to detect protein-DNA interactions in Nicotiana benthamiana extracts and entire leaves.
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Affiliation(s)
- Rosa Esmeralda Becerra-García
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - José Erik Cruz-Valderrama
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Vincent E Cerbantez-Bueno
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Nayelli Marsch-Martínez
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico.
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Nasrollahi V, Yuan ZC, Lu QSM, McDowell T, Kohalmi SE, Hannoufa A. Deciphering the role of SPL12 and AGL6 from a genetic module that functions in nodulation and root regeneration in Medicago sativa. PLANT MOLECULAR BIOLOGY 2022; 110:511-529. [PMID: 35976552 PMCID: PMC9684250 DOI: 10.1007/s11103-022-01303-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/17/2022] [Indexed: 05/11/2023]
Abstract
Our results show that SPL12 plays a crucial role in regulating nodule development in Medicago sativa L. (alfalfa), and that AGL6 is targeted and downregulated by SPL12. Root architecture in plants is critical because of its role in controlling nutrient cycling, water use efficiency and response to biotic and abiotic stress factors. The small RNA, microRNA156 (miR156), is highly conserved in plants, where it functions by silencing a group of SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors. We previously showed that transgenic Medicago sativa (alfalfa) plants overexpressing miR156 display increased nodulation, improved nitrogen fixation and enhanced root regenerative capacity during vegetative propagation. In alfalfa, transcripts of eleven SPLs, including SPL12, are targeted for cleavage by miR156. In this study, we characterized the role of SPL12 in root architecture and nodulation by investigating the transcriptomic and phenotypic changes associated with altered transcript levels of SPL12, and by determining SPL12 regulatory targets using SPL12-silencing and -overexpressing alfalfa plants. Phenotypic analyses showed that silencing of SPL12 in alfalfa caused an increase in root regeneration, nodulation, and nitrogen fixation. In addition, AGL6 which encodes AGAMOUS-like MADS box transcription factor, was identified as being directly targeted for silencing by SPL12, based on Next Generation Sequencing-mediated transcriptome analysis and chromatin immunoprecipitation assays. Taken together, our results suggest that SPL12 and AGL6 form a genetic module that regulates root development and nodulation in alfalfa.
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Affiliation(s)
- Vida Nasrollahi
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada
| | - Ze-Chun Yuan
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Qing Shi Mimmie Lu
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Tim McDowell
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Susanne E Kohalmi
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada.
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada.
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Nasrollahi V, Yuan ZC, Kohalmi SE, Hannoufa A. SPL12 Regulates AGL6 and AGL21 to Modulate Nodulation and Root Regeneration under Osmotic Stress and Nitrate Sufficiency Conditions in Medicago sativa. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223071. [PMID: 36432802 PMCID: PMC9697194 DOI: 10.3390/plants11223071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/26/2022] [Accepted: 11/10/2022] [Indexed: 06/12/2023]
Abstract
The highly conserved plant microRNA, miR156, affects root architecture, nodulation, symbiotic nitrogen fixation, and stress response. In Medicago sativa, transcripts of eleven SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE, SPLs, including SPL12, are targeted for cleavage by miR156. Our previous research revealed the role of SPL12 and its target gene, AGL6, in nodulation in alfalfa. Here, we investigated the involvement of SPL12, AGL6 and AGL21 in nodulation under osmotic stress and different nitrate availability conditions. Characterization of phenotypic and molecular parameters revealed that the SPL12/AGL6 module plays a negative role in maintaining nodulation under osmotic stress. While there was a decrease in the nodule numbers in WT plants under osmotic stress, the SPL12-RNAi and AGL6-RNAi genotypes maintained nodulation under osmotic stress. Moreover, the results showed that SPL12 regulates nodulation under a high concentration of nitrate by silencing AGL21. AGL21 transcript levels were increased under nitrate treatment in WT plants, but SPL12 was not affected throughout the treatment period. Given that AGL21 was significantly upregulated in SPL12-RNAi plants, we conclude that SPL12 may be involved in regulating nitrate inhibition of nodulation in alfalfa by targeting AGL21. Taken together, our results suggest that SPL12, AGL6, and AGL21 form a genetic module that regulates nodulation in alfalfa under osmotic stress and in response to nitrate.
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Affiliation(s)
- Vida Nasrollahi
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
| | - Ze-Chun Yuan
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
| | - Susanne E. Kohalmi
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
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Li X, Liao J, Bai H, Bei J, Li K, Luo M, Shen W, Yang C, Gao C. Arabidopsis flowering integrator SOC1 transcriptionally regulates autophagy in response to long-term carbon starvation. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6589-6599. [PMID: 35852462 DOI: 10.1093/jxb/erac298] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/02/2022] [Indexed: 06/15/2023]
Abstract
Autophagy is a highly conserved, self-digestion process that is essential for plant adaptations to various environmental stresses. Although the core components of autophagy in plants have been well established, the molecular basis for its transcriptional regulation remains to be fully characterized. In this study, we demonstrate that SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), a MADS-box family transcription factor that determines flowering transition in Arabidopsis, functions as a transcriptional repressor of autophagy. EMSAs, ChIP-qPCR assays, and dual-luciferase receptor assays showed that SOC1 can bind to the promoters of ATG4b, ATG7, and ATG18c via the conserved CArG box. qRT-PCR analysis showed that the three ATG genes ATG4b, ATG7, and ATG18c were up-regulated in the soc1-2 mutant. In line with this, the mutant also displayed enhanced autophagy activity, as revealed by increased autophagosome formation and elevated autophagic flux compared with the wild type. More importantly, SOC1 negatively affected the tolerance of plants to long-term carbon starvation, and this process requires a functional autophagy pathway. Finally, we found that SOC1 was repressed upon carbon starvation at both the transcriptional and protein levels. Overall, our study not only uncovers an important transcriptional mechanism that contributes to the regulation of plant autophagy in response to nutrient starvation, but also highlights novel cellular functions of the flowering integrator SOC1.
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Affiliation(s)
- Xibao Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jun Liao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Haiyan Bai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jieying Bei
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Kailin Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Ming Luo
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Wenjin Shen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Chao Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- MOE & Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
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9
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Tang Y, Wang L, Qu Z, Huang C, Zhao T, Li Y, Zhang C. BSISTER transcription factors directly binds to the promoter of IAA19 and IAA29 genes to up-regulate gene expression and promote the root development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111324. [PMID: 35696924 DOI: 10.1016/j.plantsci.2022.111324] [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: 03/10/2022] [Revised: 04/24/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Roots play an important role in the growth and development of plants and auxin participates in regulating plant root development. Some studies have shown that BS (BSISTER) gene (the closest gene of class B gene) is involved in plant root development, but whether BS regulates root development via auxin signaling still not clear. To explore VviBS1 and VviBS2 roles in root development, VviBS1 and VviBS2 were overexpressedin Arabidopsis tt16 mutant and we found that they could restore the phenotype of shorter PR (primary roots) and high density of LR (lateral root) of tt16 compared with the wild type Ws Arabidopsis seedlings. However, the addition of exogenous NAA (naphthalene acetic acid) could not significantly promote the PR length of tt16 Arabidopsis, and the auxin signal transduction of tt16 may be blocked. The expression levels of auxin signal transduction pathway genes in Ws, tt16, p35s:VviBS1 in tt16 and p35s:VviBS2 in tt16 seedlings were detected. It was found that the expression of AtARF2, AtARF12, AtARF14, AtARF15, AtARF20, AtGH3, AtGH3-2 and AtSAUR51 genes in tt16 seedlings was higher than that in Ws, while the expression of AtIAA19 and AtIAA29 in Ws seedlings was higher than that of tt16. More importantly, BS may up regulate AtIAA19 and AtIAA29 expression directly by binding to their promoter. In addition, VviBS1 and VviBS2 also affect seed germination and may regulate leaf yellowing by regulating ethylene synthase. Therefore, our findings reveal a molecular mechanism that BS may modulate root system development via Aux/IAA-based auxin signaling, and provide insight into the BS function in regulation of leaf yellowing.
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Affiliation(s)
- Yujin Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling 712100, Shaanxi, China.
| | - Ling Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling 712100, Shaanxi, China.
| | - Ziyang Qu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling 712100, Shaanxi, China.
| | - Congbo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling 712100, Shaanxi, China.
| | - Ting Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling 712100, Shaanxi, China.
| | - Yan Li
- College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Chaohong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling 712100, Shaanxi, China.
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10
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Abstract
The zygote is a totipotent structure that develops into an embryo with all of the cells needed to produce an entire plant. The BABY BOOM (BBM) transcription factor induces spontaneous asexual embryo development on plant organs when ectopically expressed. Although BBM is at the top of a transcriptional network that promotes asexual embryo development, little is known about its expression and role during zygotic embryogenesis. Here we show in Arabidopsis that BBM regulates the progression of zygotic embryo development and embryo patterning, and division and cellularization of the filial endosperm. In line with its role as a totipotency factor, ectopic BBM expression in the egg cell is also sufficient to induce haploid embryo development in Arabidopsis and dicot crops. The BABY BOOM (BBM) AINTEGUMENTA-LIKE (AIL) AP2/ERF domain transcription factor is a major regulator of plant cell totipotency, as it induces asexual embryo formation when ectopically expressed. Surprisingly, only limited information is available on the role of BBM during zygotic embryogenesis. Here we reexamined BBM expression and function in the model plant Arabidopsis thaliana (Arabidopsis) using reporter analysis and newly developed CRISPR mutants. BBM was expressed in the embryo from the zygote stage and also in the maternal (nucellus) and filial (endosperm) seed tissues. Analysis of CRISPR mutant alleles for BBM (bbm-cr) and the redundantly acting AIL gene PLETHORA2 (PLT2) (plt2-cr) uncovered individual roles for these genes in the timing of embryo progression. We also identified redundant roles for BBM and PLT2 in endosperm proliferation and cellularization and the maintenance of zygotic embryo development. Finally, we show that ectopic BBM expression in the egg cell of Arabidopsis and the dicot crops Brassica napus and Solanum lycopersicon is sufficient to bypass the fertilization requirement for embryo development. Together these results highlight roles for BBM and PLT2 in seed development and demonstrate the utility of BBM genes for engineering asexual embryo development in dicot species.
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11
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Li F, Jia Y, Zhou S, Chen X, Xie Q, Hu Z, Chen G. SlMBP22 overexpression in tomato affects flower morphology and fruit development. JOURNAL OF PLANT PHYSIOLOGY 2022; 272:153687. [PMID: 35378388 DOI: 10.1016/j.jplph.2022.153687] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
MADS-domain transcription factors have been identified as key regulators involved in proper flower and fruit development in angiosperms. As members of the MADS-box subfamily, Bsister (Bs) genes have been observed to play an important role during the evolution of the reproductive organs in seed plants. However, their effects on reproductive development in fruit crops, such as tomato (Solanum lycopersicum), remain unclear. Here, we found that SlMBP22 overexpression (SlMBP22-OE) resulted in considerable alterations in floral morphology and affected the expression levels of several floral homeotic genes. Further analysis by yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays demonstrated that SlMBP22 forms dimers with class A protein MACROCALYX (MC) and SEPALLATA (SEP) floral homeotic proteins TM5 and TM29, respectively. In addition, pollen viability and cross-fertilization assays suggested that the defect in female reproductive development was responsible for the infertility phenotype observed in the strong overexpression transgenic plants. Transgenic fruits with mild overexpression exhibited reduced size as a result of reduced cell expansion, rather than impaired cell division. Additionally, SlMBP22 overexpression in tomato not only affected proanthocyanidin (PA) accumulation but also altered seed dormancy. Taken together, these findings may provide new insights into the knowledge of Bs MADS-box genes in flower and fruit development in tomato.
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Affiliation(s)
- Fenfen Li
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, PR China.
| | - Yanhua Jia
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, PR China.
| | - Shengen Zhou
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, PR China.
| | - Xinyu Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, PR China.
| | - Qiaoli Xie
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, PR China.
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, PR China.
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, PR China.
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12
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Zumajo-Cardona C, Ambrose BA. Fleshy or dry: transcriptome analyses reveal the genetic mechanisms underlying bract development in Ephedra. EvoDevo 2022; 13:10. [PMID: 35477429 PMCID: PMC9047513 DOI: 10.1186/s13227-022-00195-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 04/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gnetales have a key phylogenetic position in the evolution of seed plants. Among the Gnetales, there is an extraordinary morphological diversity of seeds, the genus Ephedra, in particular, exhibits fleshy, coriaceous or winged (dry) seeds. Despite this striking diversity, its underlying genetic mechanisms remain poorly understood due to the limited studies in gymnosperms. Expanding the genomic and developmental data from gymnosperms contributes to a better understanding of seed evolution and development. RESULTS We performed transcriptome analyses on different plant tissues of two Ephedra species with different seed morphologies. Anatomical observations in early developing ovules, show that differences in the seed morphologies are established early in their development. The transcriptomic analyses in dry-seeded Ephedra californica and fleshy-seeded Ephedra antisyphilitica, allowed us to identify the major differences between the differentially expressed genes in these species. We detected several genes known to be involved in fruit ripening as upregulated in the fleshy seed of Ephedra antisyphilitica. CONCLUSIONS This study allowed us to determine the differentially expressed genes involved in seed development of two Ephedra species. Furthermore, the results of this study of seeds with the enigmatic morphology in Ephedra californica and Ephedra antisyphilitica, allowed us to corroborate the hypothesis which suggest that the extra envelopes covering the seeds of Gnetales are not genetically similar to integument. Our results highlight the importance of carrying out studies on less explored species such as gymnosperms, to gain a better understanding of the evolutionary history of plants.
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Affiliation(s)
- Cecilia Zumajo-Cardona
- New York Botanical Garden, Bronx, NY, USA.,The Graduate Center, City University of New York, New York, NY, USA
| | - Barbara A Ambrose
- New York Botanical Garden, Bronx, NY, USA. .,The Graduate Center, City University of New York, New York, NY, USA.
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13
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Guan H, Wang H, Huang J, Liu M, Chen T, Shan X, Chen H, Shen J. Genome-Wide Identification and Expression Analysis of MADS-Box Family Genes in Litchi ( Litchi chinensis Sonn.) and Their Involvement in Floral Sex Determination. PLANTS 2021; 10:plants10102142. [PMID: 34685951 PMCID: PMC8540616 DOI: 10.3390/plants10102142] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/08/2021] [Accepted: 09/18/2021] [Indexed: 11/16/2022]
Abstract
Litchi possesses unique flower morphology and adaptive reproduction strategies. Although previous attention has been intensively devoted to the mechanisms underlying its floral induction, the molecular basis of flower sex determination remains largely unknown. MADS-box genes are promising candidates for this due to their significant roles in various aspects of inflorescence and flower organogenesis. Here, we present a detailed overview of phylogeny and expression profiles of 101 MADS-box genes that were identified in litchi. These LcMADSs are unevenly located across the 15 chromosomes and can be divided into type I and type II genes. Fifty type I MADS-box genes are subdivided into Mα, Mβ and Mγ subgroups, while fifty-one type II LcMADSs consist of 37 MIKCC -type and 14 MIKC *-type genes. Promoters of both types of LcMADS genes contain mainly ABA and MeJA response elements. Tissue-specific and development-related expression analysis reveal that LcMADS51 could be positively involved in litchi carpel formation, while six MADS-box genes, including LcMADS42/46/47/75/93/100, play a possible role in stamen development. GA is positively involved in the sex determination of litchi flowers by regulating the expression of LcMADS51 (LcSTK). However, JA down-regulates the expression of floral organ identity genes, suggesting a negative role in litchi flower development.
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Affiliation(s)
- Hongling Guan
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; (H.G.); (H.W.); (J.H.); (M.L.); (T.C.); (X.S.)
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Han Wang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; (H.G.); (H.W.); (J.H.); (M.L.); (T.C.); (X.S.)
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jianjun Huang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; (H.G.); (H.W.); (J.H.); (M.L.); (T.C.); (X.S.)
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Mingxin Liu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; (H.G.); (H.W.); (J.H.); (M.L.); (T.C.); (X.S.)
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Ting Chen
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; (H.G.); (H.W.); (J.H.); (M.L.); (T.C.); (X.S.)
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Xiaozhen Shan
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; (H.G.); (H.W.); (J.H.); (M.L.); (T.C.); (X.S.)
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Houbin Chen
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; (H.G.); (H.W.); (J.H.); (M.L.); (T.C.); (X.S.)
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
- Correspondence: (H.C.); (J.S.); Tel.: +86-20-85280231 (H.C. & J.S.)
| | - Jiyuan Shen
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; (H.G.); (H.W.); (J.H.); (M.L.); (T.C.); (X.S.)
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
- Correspondence: (H.C.); (J.S.); Tel.: +86-20-85280231 (H.C. & J.S.)
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14
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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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15
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Paolo D, Orozco-Arroyo G, Rotasperti L, Masiero S, Colombo L, de Folter S, Ambrose BA, Caporali E, Ezquer I, Mizzotti C. Genetic Interaction of SEEDSTICK, GORDITA and AUXIN RESPONSE FACTOR 2 during Seed Development. Genes (Basel) 2021; 12:1189. [PMID: 34440362 PMCID: PMC8393894 DOI: 10.3390/genes12081189] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
Seed development is under the control of complex and coordinated molecular networks required for the formation of its different components. The seed coat development largely determines final seed size and shape, in addition to playing a crucial role in protecting the embryo and promoting germination. In this study, we investigated the role of three transcription factors known to be active during seed development in Arabidopsis thaliana: SEEDSTICK (STK) and GORDITA (GOA), two MADS-domain proteins, and AUXIN RESPONSE FACTOR 2 (ARF2), belonging to the ARF family. Through a reverse genetic approach, we characterized the seed phenotypes of all the single, double and triple loss-of-function mutants in relation to seed size/shape and the effects on metabolic pathways occurring in the seed coat. This approach revealed that dynamic networks involving these TFs are active throughout ovule and seed development, affecting the formation of the seed coat. Notably, while the genetic interaction among these genes results in synergies that control the promotion of cell expansion in the seed coat upon pollination and production of proanthocyanidins, functional antagonists arise in the control of cell proliferation and release of mucilage.
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Affiliation(s)
- Dario Paolo
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (G.O.-A.); (L.R.); (S.M.); (L.C.); (E.C.); (I.E.)
| | - Gregorio Orozco-Arroyo
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (G.O.-A.); (L.R.); (S.M.); (L.C.); (E.C.); (I.E.)
| | - Lisa Rotasperti
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (G.O.-A.); (L.R.); (S.M.); (L.C.); (E.C.); (I.E.)
| | - Simona Masiero
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (G.O.-A.); (L.R.); (S.M.); (L.C.); (E.C.); (I.E.)
| | - Lucia Colombo
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (G.O.-A.); (L.R.); (S.M.); (L.C.); (E.C.); (I.E.)
| | - Stefan de Folter
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato CP 36824, Guanajuato, Mexico;
| | | | - Elisabetta Caporali
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (G.O.-A.); (L.R.); (S.M.); (L.C.); (E.C.); (I.E.)
| | - Ignacio Ezquer
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (G.O.-A.); (L.R.); (S.M.); (L.C.); (E.C.); (I.E.)
| | - Chiara Mizzotti
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milano, Italy; (D.P.); (G.O.-A.); (L.R.); (S.M.); (L.C.); (E.C.); (I.E.)
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16
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Arellano-Villagómez FC, Guevara-Olvera L, Zuñiga-Mayo VM, E. Cerbantez-Bueno V, Verdugo-Perales M, R. Medina H, De Folter S, Acosta-García G. Arabidopsis cysteine-rich receptor-like protein kinase CRK33 affects stomatal density and drought tolerance. PLANT SIGNALING & BEHAVIOR 2021; 16:1905335. [PMID: 33769202 PMCID: PMC8143253 DOI: 10.1080/15592324.2021.1905335] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 05/19/2023]
Abstract
Cysteine-rich receptor-like protein kinases (CRKs) are transmembrane proteins containing two domains of unknown function 26 (DUF26) RLKs in their ectodomain. Despite that CRKs control important aspects of plant development, only few proteins have functionally been characterized. In this work, we analyzed the function of CRK33 by characterizing two insertional lines. The stomatal density and stomatal index were decreased in crk33-2 and crk33-3 plants in comparison to wild-type plants, correlating with a decreased transpiration in transgenic plants and a higher drought tolerance. Furthermore, photosynthesis and stomatal conductance changed. Finally, all four stomata cell fate genes were upregulated, especially the expression of TMM and SPCH in the mutant background, suggesting a role for CRK33 in stomatal spacing.
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Affiliation(s)
| | - Lorenzo Guevara-Olvera
- Laboratorio de Biología Molecular, Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México/ITCelaya, Celaya, México
| | - Víctor M. Zuñiga-Mayo
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro De Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, México
- Instituto de Fitosanidad, Colegio de Postgraduados, Campus Montecillo, Texcoco, Estado de México, México
| | - Vincent E. Cerbantez-Bueno
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro De Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, México
| | - Mercedes Verdugo-Perales
- Laboratorio de Biología Molecular, Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México/ITCelaya, Celaya, México
| | - Humberto R. Medina
- Laboratorio de Biología Molecular, Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México/ITCelaya, Celaya, México
| | - Stefan De Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro De Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, México
| | - Gerardo Acosta-García
- Laboratorio de Biología Molecular, Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México/ITCelaya, Celaya, México
- CONTACT Gerardo Acosta-García Laboratorio de Biología Molecular, Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México/ITCelaya, Celaya, México
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17
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Ye LX, Zhang JX, Hou XJ, Qiu MQ, Wang WF, Zhang JX, Hu CG, Zhang JZ. A MADS-Box Gene CiMADS43 Is Involved in Citrus Flowering and Leaf Development through Interaction with CiAGL9. Int J Mol Sci 2021; 22:ijms22105205. [PMID: 34069068 PMCID: PMC8156179 DOI: 10.3390/ijms22105205] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022] Open
Abstract
MADS-box genes are involved in various developmental processes including vegetative development, flower architecture, flowering, pollen formation, seed and fruit development. However, the function of most MADS-box genes and their regulation mechanism are still unclear in woody plants compared with model plants. In this study, a MADS-box gene (CiMADS43) was identified in citrus. Phylogenetic and sequence analysis showed that CiMADS43 is a GOA-like Bsister MADS-box gene. It was localized in the nucleus and as a transcriptional activator. Overexpression of CiMADS43 promoted early flowering and leaves curling in transgenic Arabidopsis. Besides, overexpression or knockout of CiMADS43 also showed leaf curl phenotype in citrus similar to that of CiMADS43 overexpressed in Arabidopsis. Protein–protein interaction found that a SEPALLATA (SEP)-like protein (CiAGL9) interacted with CiMADS43 protein. Interestingly, CiAGL9 also can bind to the CiMADS43 promoter and promote its transcription. Expression analysis also showed that these two genes were closely related to seasonal flowering and the development of the leaf in citrus. Our findings revealed the multifunctional roles of CiMADS43 in the vegetative and reproductive development of citrus. These results will facilitate our understanding of the evolution and molecular mechanisms of MADS-box genes in citrus.
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Orchid B sister gene PeMADS28 displays conserved function in ovule integument development. Sci Rep 2021; 11:1205. [PMID: 33441740 PMCID: PMC7806631 DOI: 10.1038/s41598-020-79877-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 12/14/2020] [Indexed: 11/21/2022] Open
Abstract
The ovules and egg cells are well developed to be fertilized at anthesis in many flowering plants. However, ovule development is triggered by pollination in most orchids. In this study, we characterized the function of a Bsister gene, named PeMADS28, isolated from Phalaenopsis equestris, the genome-sequenced orchid. Spatial and temporal expression analysis showed PeMADS28 predominantly expressed in ovules between 32 and 48 days after pollination, which synchronizes with integument development. Subcellular localization and protein–protein interaction analyses revealed that PeMADS28 could form a homodimer as well as heterodimers with D-class and E-class MADS-box proteins. In addition, ectopic expression of PeMADS28 in Arabidopsis thaliana induced small curled rosette leaves, short silique length and few seeds, similar to that with overexpression of other species’ Bsister genes in Arabidopsis. Furthermore, complementation test revealed that PeMADS28 could rescue the phenotype of the ABS/TT16 mutant. Together, these results indicate the conserved function of BsisterPeMADS28 associated with ovule integument development in orchid.
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Zeng D, Que C, Teixeira da Silva JA, Xu S, Li D. Comparative Transcriptomic and Metabolic Analyses Reveal the Molecular Mechanism of Ovule Development in the Orchid, Cymbidium sinense. FRONTIERS IN PLANT SCIENCE 2021; 12:814275. [PMID: 35126436 PMCID: PMC8813969 DOI: 10.3389/fpls.2021.814275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 12/27/2021] [Indexed: 05/04/2023]
Abstract
Ovule development is pivotal to plant reproduction and seed development. Cymbidium sinense (Orchidaceae) has high ornamental value due to its pleasant aroma and elegant floral morphology. The regulatory mechanism underlying ovule development in orchids, especially C. sinense, is largely unknown and information on the C. sinense genome is very scarce. In this study, a combined analysis was performed on the transcriptome and non-targeted metabolomes of 18 C. sinense 'Qi Jian Hei Mo' ovule samples. Transcriptome analysis assembled gene-related information related to six growth stages of C. sinense ovules (S1-S6, equivalent to 30, 35, 42, 46, 53, and 60 days after pollination). Illumina sequencing technology was used to obtain the complete set of transcriptome sequences of the 18 samples. A total of 81,585 unigene sequences were obtained after assembly, 24,860 (30.47%) of which were functionally annotated. Using transcriptome sequencing technology, a total of 9845 differentially expressed unigenes (DEUs) were identified in C. sinense ovules that were assigned to specific metabolic pathways according to the Kyoto Encyclopedia of Genes and Genomes (KEGG). DEUs associated with transcription factors (TFs) and phytohormones were identified and analyzed. The TFs homeobox and MADS-box were associated with C. sinense ovule development. In particular, the phytohormones associated with DEUs such as indole-3-acetic acid (IAA), cytokinin (CK), gibberellin (GA), abscisic acid (ABA), brassinosteroid (BR), and jasmonate (JA), may have important regulatory effects on C. sinense ovule development. Metabolomic analysis showed an inconsistent number of KEGG annotations of differential metabolites across comparisons (S2_vs_S4, S2_vs_S5, and S4_vs_S5 contained 23, 26, and 3 annotations, respectively) in C. sinense ovules. This study provides a valuable foundation for further understanding the regulation of orchid ovule development and formation, and establishes a theoretical background for future practical applications during orchid cultivation.
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Affiliation(s)
- Danqi Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Caixia Que
- Guangdong Provincial Research Center for Standardization of Production Engineering Technology of Orchids, Shunde Polytechnic, Foshan, China
| | | | - Shutao Xu
- College of Innovative Design, City University of Macau, Taipa, Macao SAR, China
| | - Dongmei Li
- Guangdong Provincial Research Center for Standardization of Production Engineering Technology of Orchids, Shunde Polytechnic, Foshan, China
- *Correspondence: Dongmei Li,
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20
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Yang S, Ma S, Qiu R, Guang Q, Lv Y, Dong Y, Wu J, Song L. Comparative analysis of RNA-Seq data reveals adventitious root development is mediated by ChIFNα in lotus japonicus. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1859946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Shimei Yang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Lab of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, People’s Republic of China
| | - Siyu Ma
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Lab of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, People’s Republic of China
| | - Riguang Qiu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Lab of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, People’s Republic of China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, Guangdong, People’s Republic of China
| | - Qiao Guang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Lab of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, People’s Republic of China
| | - Yun Lv
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Lab of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, People’s Republic of China
| | - Yaping Dong
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Lab of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, People’s Republic of China
| | - Jiahai Wu
- Institute of Fruit Research, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, People’s Republic of China
| | - Li Song
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Lab of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, People’s Republic of China
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21
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Li F, Chen X, Zhou S, Xie Q, Wang Y, Xiang X, Hu Z, Chen G. Overexpression of SlMBP22 in Tomato Affects Plant Growth and Enhances Tolerance to Drought Stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110672. [PMID: 33218637 DOI: 10.1016/j.plantsci.2020.110672] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
MADS-box transcription factors play crucial and diverse roles in plant growth and development, and the responses to biotic and abiotic stresses. However, the implementation of MADS-box transcription factors in regulating plant architecture and stress responses has not been fully explored in tomato. Here, we found that a novel MADS-box transcription factor, SlMBP22, participated in the control of agronomical traits, tolerance to abiotic stress, and regulation of auxin and gibberellin signalling. Transgenic plants overexpressing SlMBP22 (SlMBP22-OE) displayed pleiotropic phenotypes, including reduced plant height and leaf size, by affecting auxin and/or gibberellin signalling. SlMBP22 was induced by dehydration treatment, and SlMBP22-OE plants were more tolerant to drought stress than wild-type (WT). Furthermore, SlMBP22 overexpression plants accumulated more chlorophyll, starch and soluble sugar than WT, indicating that the darker green leaves might be attributed to increased chlorophyll levels in the transgenic plants. RNA-Seq results showed that the transcript levels of a series of genes related to chloroplast development, chlorophyll metabolism, starch and sucrose metabolism, hormone signalling, and stress responses were altered. Collectively, our data demonstrate that SlMBP22 plays an important role in both regulating tomato growth and resisting drought stress.
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Affiliation(s)
- Fenfen Li
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing, PR China.
| | - Xinyu Chen
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing, PR China.
| | - Shengen Zhou
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing, PR China.
| | - Qiaoli Xie
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing, PR China.
| | - Yunshu Wang
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing, PR China.
| | - Xiaoxue Xiang
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing, PR China.
| | - Zongli Hu
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing, PR China.
| | - Guoping Chen
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing, PR China.
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22
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Hoffmeier A, Gramzow L, Bhide AS, Kottenhagen N, Greifenstein A, Schubert O, Mummenhoff K, Becker A, Theißen G. A Dead Gene Walking: Convergent Degeneration of a Clade of MADS-Box Genes in Crucifers. Mol Biol Evol 2019; 35:2618-2638. [PMID: 30053121 DOI: 10.1093/molbev/msy142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Genes are "born," and eventually they "die." These processes shape the phenotypic evolution of organisms and are hence of great biological interest. If genes die in plants, they generally do so quite rapidly. Here, we describe the fate of GOA-like genes that evolve in a dramatically different manner. GOA-like genes belong to the subfamily of Bsister genes of MIKC-type MADS-box genes. Typical MIKC-type genes encode conserved transcription factors controlling plant development. We show that ABS-like genes, a clade of Bsister genes, are indeed highly conserved in crucifers (Brassicaceae) maintaining the ancestral function of Bsister genes in ovule and seed development. In contrast, their closest paralogs, the GOA-like genes, have been undergoing convergent gene death in Brassicaceae. Intriguingly, erosion of GOA-like genes occurred after millions of years of coexistence with ABS-like genes. We thus describe Delayed Convergent Asymmetric Degeneration, a so far neglected but possibly frequent pattern of duplicate gene evolution that does not fit classical scenarios. Delayed Convergent Asymmetric Degeneration of GOA-like genes may have been initiated by a reduction in the expression of an ancestral GOA-like gene in the stem group of Brassicaceae and driven by dosage subfunctionalization. Our findings have profound implications for gene annotations in genomics, interpreting patterns of gene evolution and using genes in phylogeny reconstructions of species.
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Affiliation(s)
- Andrea Hoffmeier
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
| | - Lydia Gramzow
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
| | - Amey S Bhide
- Plant Developmental Biology Group, Institute of Botany, Justus-Liebig-University Giessen, Giessen, Germany
| | - Nina Kottenhagen
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
| | - Andreas Greifenstein
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
| | - Olesia Schubert
- Plant Developmental Biology Group, Institute of Botany, Justus-Liebig-University Giessen, Giessen, Germany
| | - Klaus Mummenhoff
- Department of Biology/Botany, University of Osnabrück, Osnabrück, Germany
| | - Annette Becker
- Plant Developmental Biology Group, Institute of Botany, Justus-Liebig-University Giessen, Giessen, Germany
| | - Günter Theißen
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
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23
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Ali Z, Raza Q, Atif RM, Aslam U, Ajmal M, Chung G. Genetic and Molecular Control of Floral Organ Identity in Cereals. Int J Mol Sci 2019; 20:E2743. [PMID: 31167420 PMCID: PMC6600504 DOI: 10.3390/ijms20112743] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 12/22/2022] Open
Abstract
Grasses represent a major family of monocots comprising mostly cereals. When compared to their eudicot counterparts, cereals show a remarkable morphological diversity. Understanding the molecular basis of floral organ identity and inflorescence development is crucial to gain insight into the grain development for yield improvement purposes in cereals, however, the exact genetic mechanism of floral organogenesis remains elusive due to their complex inflorescence architecture. Extensive molecular analyses of Arabidopsis and other plant genera and species have established the ABCDE floral organ identity model. According to this model, hierarchical combinatorial activities of A, B, C, D, and E classes of homeotic genes regulate the identity of different floral organs with partial conservation and partial diversification between eudicots and cereals. Here, we review the developmental role of A, B, C, D, and E gene classes and explore the recent advances in understanding the floral development and subsequent organ specification in major cereals with reference to model plants. Furthermore, we discuss the evolutionary relationships among known floral organ identity genes. This comparative overview of floral developmental genes and associated regulatory factors, within and between species, will provide a thorough understanding of underlying complex genetic and molecular control of flower development and floral organ identity, which can be helpful to devise innovative strategies for grain yield improvement in cereals.
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Affiliation(s)
- Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Sharif University of Agriculture, Multan 66000, Pakistan.
| | - Qasim Raza
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku 39020, Pakistan.
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Usman Aslam
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
| | - Muhammad Ajmal
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea.
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24
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Zhou B, Wang J, Lou H, Wang H, Xu Q. Comparative transcriptome analysis of dioecious, unisexual floral development in Ribes diacanthum pall. Gene 2019; 699:43-53. [DOI: 10.1016/j.gene.2019.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 01/09/2023]
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25
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Land bridges in the Pleistocene contributed to flora assembly on the continental islands of South China: Insights from the evolutionary history of Quercus championii. Mol Phylogenet Evol 2019; 132:36-45. [DOI: 10.1016/j.ympev.2018.11.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/19/2018] [Accepted: 11/26/2018] [Indexed: 11/17/2022]
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26
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Zhang J, Wang Y, Naeem M, Zhu M, Li J, Yu X, Hu Z, Chen G. An AGAMOUS MADS-box protein, SlMBP3, regulates the speed of placenta liquefaction and controls seed formation in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:909-924. [PMID: 30481310 DOI: 10.1093/jxb/ery418] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 11/18/2018] [Indexed: 05/25/2023]
Abstract
AGAMOUS (AG) MADS-box transcription factors have been shown to play crucial roles in floral organ and fruit development in angiosperms. Here, we isolated a tomato (Solanum lycopersicum) AG MADS-box gene SlMBP3 and found that it is preferentially expressed in flowers and during early fruit developmental stages in the wild-type (WT), and in the Nr (never ripe) and rin (ripening inhibitor) mutants. Its transcripts are notably accumulated in the pistils; transcripts abundance decrease during seed and placental development, increasing again during flower development. SlMBP3-RNAi tomato plants displayed fleshy placenta without locular gel and extremely malformed seeds with no seed coat, while SlMBP3-overexpressing plants exhibited advanced liquefaction of the placenta and larger seeds. Enzymatic activities related to cell wall modification, and the contents of cell wall components and pigments were dramatically altered in the placentas of SlMBP3-RNAi compared with the WT. Alterations in these physiological features were also observed in the placentas of SlMBP3-overexpressing plants. The lignin content of mature seeds in SlMBP3-RNAi lines was markedly lower than that in the WT. RNA-seq and qRT-PCR analyses revealed that genes involved in seed development and the biosynthesis of enzymes related to cell wall modification, namely gibberellin, indole-3-acetic acid, and abscisic acid were down-regulated in the SlMBP3-RNAi lines. Taking together, our results demonstrate that SlMBP3 is involved in the regulation of placenta and seed development in tomato.
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Affiliation(s)
- Jianling Zhang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Yicong Wang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Muhammad Naeem
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Mingku Zhu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Jing Li
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Xiaohui Yu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
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27
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Herrera-Ubaldo H, Lozano-Sotomayor P, Ezquer I, Di Marzo M, Chávez Montes RA, Gómez-Felipe A, Pablo-Villa J, Diaz-Ramirez D, Ballester P, Ferrándiz C, Sagasser M, Colombo L, Marsch-Martínez N, de Folter S. New roles of NO TRANSMITTING TRACT and SEEDSTICK during medial domain development in Arabidopsis fruits. Development 2019; 146:dev.172395. [PMID: 30538100 DOI: 10.1242/dev.172395] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/03/2018] [Indexed: 01/11/2023]
Abstract
The gynoecium, the female reproductive part of the flower, is key for plant sexual reproduction. During its development, inner tissues such as the septum and the transmitting tract tissue, important for pollen germination and guidance, are formed. In Arabidopsis, several transcription factors are known to be involved in the development of these tissues. One of them is NO TRANSMITTING TRACT (NTT), essential for transmitting tract formation. We found that the NTT protein can interact with several gynoecium-related transcription factors, including several MADS-box proteins, such as SEEDSTICK (STK), known to specify ovule identity. Evidence suggests that NTT and STK control enzyme and transporter-encoding genes involved in cell wall polysaccharide and lipid distribution in gynoecial medial domain cells. The results indicate that the simultaneous loss of NTT and STK activity affects polysaccharide and lipid deposition and septum fusion, and delays entry of septum cells to their normal degradation program. Furthermore, we identified KAWAK, a direct target of NTT and STK, which is required for the correct formation of fruits in Arabidopsis These findings position NTT and STK as important factors in determining reproductive competence.
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Affiliation(s)
- Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - Paulina Lozano-Sotomayor
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - Ignacio Ezquer
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan 20133, Italy
| | - Maurizio Di Marzo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan 20133, Italy
| | - Ricardo Aarón Chávez Montes
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - Andrea Gómez-Felipe
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - Jeanneth Pablo-Villa
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - David Diaz-Ramirez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, CINVESTAV-IPN, Irapuato 36824, Guanajuato, México
| | - Patricia Ballester
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, 46022, Spain
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, 46022, Spain
| | - Martin Sagasser
- Bielefeld University, Faculty of Biology, Chair of Genetics and Genomics of Plants, Bielefeld 33615, Germany
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan 20133, Italy
| | - Nayelli Marsch-Martínez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, CINVESTAV-IPN, Irapuato 36824, Guanajuato, México
| | - Stefan de Folter
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
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28
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Sun CH, Yu JQ, Duan X, Wang JH, Zhang QY, Gu KD, Hu DG, Zheng CS. The MADS transcription factor CmANR1 positively modulates root system development by directly regulating CmPIN2 in chrysanthemum. HORTICULTURE RESEARCH 2018; 5:52. [PMID: 30302256 PMCID: PMC6165851 DOI: 10.1038/s41438-018-0061-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/23/2018] [Accepted: 05/28/2018] [Indexed: 05/20/2023]
Abstract
Plant root systems are essential for many physiological processes, including water and nutrient absorption. MADS-box transcription factor (TF) genes have been characterized as the important regulators of root development in plants; however, the underlying mechanism is largely unknown, including chrysanthemum. Here, it was found that the overexpression of CmANR1, a chrysanthemum MADS-box TF gene, promoted both adventitious root (AR) and lateral root (LR) development in chrysanthemum. Whole transcriptome sequencing analysis revealed a series of differentially expressed unigenes (DEGs) in the roots of CmANR1-transgenic chrysanthemum plants compared to wild-type plants. Functional annotation of these DEGs by alignment with Gene Ontology (GO) terms and biochemical pathway Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that CmANR1 TF exhibited "DNA binding" and "catalytic" activity, as well as participated in "phytohormone signal transduction". Both chromatin immunoprecipitation-polymerase chain reaction (ChIP-PCR) and gel electrophoresis mobility shift assays (EMSA) indicated the direct binding of CmPIN2 to the recognition site CArG-box motif by CmANR1. Finally, a firefly luciferase imaging assay demonstrated the transcriptional activation of CmPIN2 by CmANR1 in vivo. Overall, our results provide novel insights into the mechanisms of MADS-box TF CmANR1 modulation of both AR and LR development, which occurs by directly regulating auxin transport gene CmPIN2 in chrysanthemum.
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Affiliation(s)
- Cui-Hui Sun
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018 China
| | - Jian-Qiang Yu
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018 China
| | - Xi Duan
- Shandong Agricultural and Engineering University, Ji-Nan, Shandong China
| | - Jia-Hui Wang
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018 China
| | - Quan-Yan Zhang
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018 China
| | - Kai-Di Gu
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018 China
| | - Da-Gang Hu
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018 China
| | - Cheng-Shu Zheng
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018 China
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Lazcano-Ramírez HG, Gómez-Felipe A, Díaz-Ramírez D, Durán-Medina Y, Sánchez-Segura L, de Folter S, Marsch-Martínez N. Non-destructive Plant Morphometric and Color Analyses Using an Optoelectronic 3D Color Microscope. FRONTIERS IN PLANT SCIENCE 2018; 9:1409. [PMID: 30319671 PMCID: PMC6167917 DOI: 10.3389/fpls.2018.01409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/05/2018] [Indexed: 06/08/2023]
Abstract
Gene function discovery in plants, as other plant science quests, is aided by tools that image, document, and measure plant phenotypes. Tools that acquire images of plant organs and tissues at the microscopic level have evolved from qualitative documentation tools, to advanced tools where software-assisted analysis of images extracts quantitative information that allows statistical analyses. They are useful to perform morphometric studies that describe plant physical characteristics and quantify phenotypes, aiding gene function discovery. In parallel, non-destructive, versatile, robust, and user friendly technologies have also been developed for surface topography analysis and quality control in the industrial manufacture sector, such as optoelectronic three-dimensional (3D) color microscopes. These microscopes combine optical lenses, electronic image sensors, motorized stages, graphics engines, and user friendly software to allow the visualization and inspection of objects of diverse sizes and shapes from different angles. This allow the integration of different automatically obtained images along the Z axis of an object, into a single image with a large depth-of-field, or a 3D model in color. In this work, we explored the performance of an optoelectronic microscope to study plant morphological phenotypes and plant surfaces in different model species. Furthermore, as a "proof-of-concept," we included the phenotypic characterization (morphometric analyses at the organ level, color, and cell size measurements) of Arabidopsis mutant leaves. We found that the microscope tested is a suitable, practical, and fast tool to routinely and precisely analyze different plant organs and tissues, producing both high-quality, sharp color images and morphometric and color data in real time. It is fully compatible with live plant tissues (no sample preparation is required) and does not require special conditions, high maintenance, nor complex training. Therefore, though barely reported in plant scientific studies, optoelectronic microscopes should emerge as convenient and useful tools for phenotypic characterization in plant sciences.
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Affiliation(s)
- Hugo G. Lazcano-Ramírez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Mexico
| | - Andrea Gómez-Felipe
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Guanajuato, Mexico
| | - David Díaz-Ramírez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Mexico
| | - Yolanda Durán-Medina
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Mexico
| | - Lino Sánchez-Segura
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Mexico
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Guanajuato, Mexico
| | - Nayelli Marsch-Martínez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Mexico
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Zhang J, Hu Z, Wang Y, Yu X, Liao C, Zhu M, Chen G. Suppression of a tomato SEPALLATA MADS-box gene, SlCMB1, generates altered inflorescence architecture and enlarged sepals. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 272:75-87. [PMID: 29807608 DOI: 10.1016/j.plantsci.2018.03.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/20/2018] [Accepted: 03/29/2018] [Indexed: 06/08/2023]
Abstract
The SEPALLATA (SEP) MADS-box transcription factors play essential roles in reproductive growth, especially in floral organ differentiation. Here, SlCMB1, a tomato SEP MADS-box gene, was isolated. SlCMB1 is noticeably expressed in inflorescences and flowers. Its transcript levels were higher in sepals than in other floral organs and decreased during sepal development. Tomato plants with reduced SlCMB1 mRNA levels displayed longer, branched and indeterminate inflorescences that exhibited a transition from reproductive to vegetative growth and enlarged and abnormally fused sepals. The transcript levels of genes known to regulate the development of inflorescence architecture and sepal size in tomato were dramatically changed. In addition, the expression levels of cell elongation-related and gibberellin biosynthetic genes also showed significant differences between the transgenic lines and the wild type, and the GA content of the peduncle in the transgenic lines was higher than that in the wild type. Yeast two-hybrid assay showed that SlCMB1 could interact individually with MC, J, AP2a and SlMBP21. Overall, our results indicate that SlCMB1 is an important regulator involved in the development of inflorescence architecture and sepal size in tomato plants.
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Affiliation(s)
- Jianling Zhang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Yunshu Wang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Xiaohui Yu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Changguang Liao
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Mingku Zhu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
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Nardeli SM, Artico S, Aoyagi GM, de Moura SM, da Franca Silva T, Grossi-de-Sa MF, Romanel E, Alves-Ferreira M. Genome-wide analysis of the MADS-box gene family in polyploid cotton (Gossypium hirsutum) and in its diploid parental species (Gossypium arboreum and Gossypium raimondii). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:169-184. [PMID: 29604523 DOI: 10.1016/j.plaphy.2018.03.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/27/2018] [Accepted: 03/18/2018] [Indexed: 06/08/2023]
Abstract
The MADS-box gene family encodes transcription factors that share a highly conserved domain known to bind to DNA. Members of this family control various processes of development in plants, from root formation to fruit ripening. In this work, a survey of diploid (Gossypium raimondii and Gossypium arboreum) and tetraploid (Gossypium hirsutum) cotton genomes found a total of 147, 133 and 207 MADS-box genes, respectively, distributed in the MIKC, Mα, Mβ, Mγ, and Mδ subclades. A comparative phylogenetic analysis among cotton species, Arabidopsis, poplar and grapevine MADS-box homologous genes allowed us to evaluate the evolution of each MADS-box lineage in cotton plants and identify sequences within well-established subfamilies. Chromosomal localization and phylogenetic analysis revealed that G. raimondii and G. arboreum showed a conserved evolution of the MIKC subclade and a distinct pattern of duplication events in the Mα, Mγ and Mδ subclades. Additionally, G. hirsutum showed a combination of its parental subgenomes followed by a distinct evolutionary history including gene gain and loss in each subclade. qPCR analysis revealed the expression patterns of putative homologs in the AP1, AP3, AGL6, SEP4, AGL15, AG, AGL17, TM8, SVP, SOC and TT16 subfamilies of G. hirsutum. The identification of putative cotton orthologs is discussed in the light of evolution and gene expression data from other plants. This analysis of the MADS-box genes in Gossypium species opens an avenue to understanding the origin and evolution of each gene subfamily within diploid and polyploid species and paves the way for functional studies in cotton species.
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Affiliation(s)
- Sarah Muniz Nardeli
- Laboratório de Genética Molecular Vegetal, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), CEP 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Sinara Artico
- Laboratório de Genética Molecular Vegetal, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), CEP 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Gustavo Mitsunori Aoyagi
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo (EEL-USP), CEP 12602-810, Lorena, SP, Brazil.
| | - Stéfanie Menezes de Moura
- Laboratório de Genética Molecular Vegetal, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), CEP 21941-617, Rio de Janeiro, RJ, Brazil.
| | - Tatiane da Franca Silva
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo (EEL-USP), CEP 12602-810, Lorena, SP, Brazil.
| | | | - Elisson Romanel
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo (EEL-USP), CEP 12602-810, Lorena, SP, Brazil.
| | - Marcio Alves-Ferreira
- Laboratório de Genética Molecular Vegetal, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), CEP 21941-617, Rio de Janeiro, RJ, Brazil.
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Identification and Characterization of the MADS-Box Genes and Their Contribution to Flower Organ in Carnation (Dianthus caryophyllus L.). Genes (Basel) 2018; 9:genes9040193. [PMID: 29617274 PMCID: PMC5924535 DOI: 10.3390/genes9040193] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 03/22/2018] [Accepted: 03/22/2018] [Indexed: 01/22/2023] Open
Abstract
Dianthus is a large genus containing many species with high ornamental economic value. Extensive breeding strategies permitted an exploration of an improvement in the quality of cultivated carnation, particularly in flowers. However, little is known on the molecular mechanisms of flower development in carnation. Here, we report the identification and description of MADS-box genes in carnation (DcaMADS) with a focus on those involved in flower development and organ identity determination. In this study, 39 MADS-box genes were identified from the carnation genome and transcriptome by the phylogenetic analysis. These genes were categorized into four subgroups (30 MIKCc, two MIKC*, two Mα, and five Mγ). The MADS-box domain, gene structure, and conserved motif compositions of the carnation MADS genes were analysed. Meanwhile, the expression of DcaMADS genes were significantly different in stems, leaves, and flower buds. Further studies were carried out for exploring the expression of DcaMADS genes in individual flower organs, and some crucial DcaMADS genes correlated with their putative function were validated. Finally, a new expression pattern of DcaMADS genes in flower organs of carnation was provided: sepal (three class E genes and two class A genes), petal (two class B genes, two class E genes, and one SHORT VEGETATIVE PHASE (SVP)), stamen (two class B genes, two class E genes, and two class C), styles (two class E genes and two class C), and ovary (two class E genes, two class C, one AGAMOUS-LIKE 6 (AGL6), one SEEDSTICK (STK), one B sister, one SVP, and one Mα). This result proposes a model in floral organ identity of carnation and it may be helpful to further explore the molecular mechanism of flower organ identity in carnation.
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A tomato MADS-box protein, SlCMB1, regulates ethylene biosynthesis and carotenoid accumulation during fruit ripening. Sci Rep 2018; 8:3413. [PMID: 29467500 PMCID: PMC5821886 DOI: 10.1038/s41598-018-21672-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 02/07/2018] [Indexed: 12/30/2022] Open
Abstract
The MADS-box transcription factors play essential roles in many physiological and biochemical processes of plants, especially in fruit ripening. Here, a tomato MADS-box gene, SlCMB1, was isolated. SlCMB1 expression declined with the fruit ripening from immature green to B + 7 (7 days after Breaker) fruits in the wild type (WT) and was lower in Nr and rin mutants fruits. Tomato plants with reduced SlCMB1 mRNA displayed delayed fruit ripening, reduced ethylene production and carotenoid accumulation. The ethylene production in SlCMB1-RNAi fruits decreased by approximately 50% as compared to WT. The transcripts of ethylene biosynthesis genes (ACS2, ACS4, ACO1 and ACO3), ethylene-responsive genes (E4, E8 and ERF1) and fruit ripening-related genes (RIN, TAGL1, FUL1, FUL2, LoxC and PE) were inhibited in SlCMB1-RNAi fruits. The carotenoid accumulation was decreased and two carotenoid synthesis-related genes (PSY1 and PDS) were down-regulated while three lycopene cyclase genes (CYCB, LCYB and LCYE) were up-regulated in transgenic fruits. Furthermore, yeast two-hybrid assay showed that SlCMB1 could interact with SlMADS-RIN, SlMADS1, SlAP2a and TAGL1, respectively. Collectively, these results indicate that SlCMB1 is a new component to the current model of regulatory network that regulates ethylene biosynthesis and carotenoid accumulation during fruit ripening.
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Huang B, Routaboul JM, Liu M, Deng W, Maza E, Mila I, Hu G, Zouine M, Frasse P, Vrebalov JT, Giovannoni JJ, Li Z, van der Rest B, Bouzayen M. Overexpression of the class D MADS-box gene Sl-AGL11 impacts fleshy tissue differentiation and structure in tomato fruits. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4869-4884. [PMID: 28992179 DOI: 10.1093/jxb/erx303] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
MADS-box transcription factors are key elements of the genetic networks controlling flower and fruit development. Among these, the class D clade gathers AGAMOUS-like genes which are involved in seed, ovule, and funiculus development. The tomato genome comprises two class D genes, Sl-AGL11 and Sl-MBP3, both displaying high expression levels in seeds and in central tissues of young fruits. The potential effects of Sl-AGL11 on fruit development were addressed through RNAi silencing and ectopic expression strategies. Sl-AGL11-down-regulated tomato lines failed to show obvious phenotypes except a slight reduction in seed size. In contrast, Sl-AGL11 overexpression triggered dramatic modifications of flower and fruit structure that include: the conversion of sepals into fleshy organs undergoing ethylene-dependent ripening, a placenta hypertrophy to the detriment of locular space, starch and sugar accumulation, and an extreme softening that occurs well before the onset of ripening. RNA-Seq transcriptomic profiling highlighted substantial metabolic reprogramming occurring in sepals and fruits, with major impacts on cell wall-related genes. While several Sl-AGL11-related phenotypes are reminiscent of class C MADS-box genes (TAG1 and TAGL1), the modifications observed on the placenta and cell wall and the Sl-AGL11 expression pattern suggest an action of this class D MADS-box factor on early fleshy fruit development.
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Affiliation(s)
- Baowen Huang
- Université de Toulouse, Institut National Polytechnique de Toulouse-Ecole Nationale Supérieure Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
- Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, Chongqing, 400044, PR China
| | - Jean-Marc Routaboul
- Université de Toulouse, Institut National Polytechnique de Toulouse-Ecole Nationale Supérieure Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
| | - Mingchun Liu
- Université de Toulouse, Institut National Polytechnique de Toulouse-Ecole Nationale Supérieure Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
| | - Wei Deng
- Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, Chongqing, 400044, PR China
| | - Elie Maza
- Université de Toulouse, Institut National Polytechnique de Toulouse-Ecole Nationale Supérieure Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
| | - Isabelle Mila
- Université de Toulouse, Institut National Polytechnique de Toulouse-Ecole Nationale Supérieure Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
| | - Guojian Hu
- Université de Toulouse, Institut National Polytechnique de Toulouse-Ecole Nationale Supérieure Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
| | - Mohamed Zouine
- Université de Toulouse, Institut National Polytechnique de Toulouse-Ecole Nationale Supérieure Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
| | - Pierre Frasse
- Université de Toulouse, Institut National Polytechnique de Toulouse-Ecole Nationale Supérieure Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
| | - Julia T Vrebalov
- Boyce Thompson Institute and USDA-ARS Robert W. Holley Center, Cornell University campus, Ithaca, NY 14853,USA
| | - James J Giovannoni
- Boyce Thompson Institute and USDA-ARS Robert W. Holley Center, Cornell University campus, Ithaca, NY 14853,USA
| | - Zhengguo Li
- Genetic Engineering Research Centre, School of Life Sciences, Chongqing University, Chongqing, 400044, PR China
| | - Benoît van der Rest
- Université de Toulouse, Institut National Polytechnique de Toulouse-Ecole Nationale Supérieure Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
| | - Mondher Bouzayen
- Université de Toulouse, Institut National Polytechnique de Toulouse-Ecole Nationale Supérieure Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
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Moyroud E, Monniaux M, Thévenon E, Dumas R, Scutt CP, Frohlich MW, Parcy F. A link between LEAFY and B-gene homologues in Welwitschia mirabilis sheds light on ancestral mechanisms prefiguring floral development. THE NEW PHYTOLOGIST 2017; 216:469-481. [PMID: 28233912 DOI: 10.1111/nph.14483] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 01/05/2017] [Indexed: 05/26/2023]
Abstract
Flowering plants evolved from an unidentified gymnosperm ancestor. Comparison of the mechanisms controlling development in angiosperm flowers and gymnosperm cones may help to elucidate the mysterious origin of the flower. We combined gene expression studies with protein behaviour characterization in Welwitschia mirabilis to test whether the known regulatory links between LEAFY and its MADS-box gene targets, central to flower development, might also contribute to gymnosperm reproductive development. We found that WelLFY, one of two LEAFY-like genes in Welwitschia, could be an upstream regulator of the MADS-box genes APETALA3/PISTILLATA-like (B-genes). We demonstrated that, even though their DNA-binding domains are extremely similar, WelLFY and its paralogue WelNDLY exhibit distinct DNA-binding specificities, and that, unlike WelNDLY, WelLFY shares with its angiosperm orthologue the capacity to bind promoters of Welwitschia B-genes. Finally, we identified several cis-elements mediating these interactions in Welwitschia and obtained evidence that the link between LFY homologues and B-genes is also conserved in two other gymnosperms, Pinus and Picea. Although functional approaches to investigate cone development in gymnosperms are limited, our state-of-the-art biophysical techniques, coupled with expression studies, provide evidence that crucial links, central to the control of floral development, may already have existed before the appearance of flowers.
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Affiliation(s)
- Edwige Moyroud
- LPCV, CEA, CNRS, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France
| | - Marie Monniaux
- LPCV, CEA, CNRS, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France
| | - Emmanuel Thévenon
- LPCV, CEA, CNRS, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France
| | - Renaud Dumas
- LPCV, CEA, CNRS, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France
| | - Charles P Scutt
- Laboratoire de Reproduction et Développement des Plantes, UMR5667, CNRS, INRA, Université de Lyon, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon Cedex 07, France
| | - Michael W Frohlich
- Laboratoire de Reproduction et Développement des Plantes, UMR5667, CNRS, INRA, Université de Lyon, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364, Lyon Cedex 07, France
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
| | - François Parcy
- LPCV, CEA, CNRS, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France
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Xu W, Bobet S, Le Gourrierec J, Grain D, De Vos D, Berger A, Salsac F, Kelemen Z, Boucherez J, Rolland A, Mouille G, Routaboul JM, Lepiniec L, Dubos C. TRANSPARENT TESTA 16 and 15 act through different mechanisms to control proanthocyanidin accumulation in Arabidopsis testa. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2859-2870. [PMID: 28830101 PMCID: PMC5853933 DOI: 10.1093/jxb/erx151] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 04/07/2017] [Indexed: 05/27/2023]
Abstract
Flavonoids are secondary metabolites that fulfil a multitude of functions during the plant life cycle. In Arabidopsis proanthocyanidins (PAs) are flavonoids that specifically accumulate in the innermost integuments of the seed testa (i.e. endothelium), as well as in the chalaza and micropyle areas, and play a vital role in protecting the embryo against various biotic and abiotic stresses. PAs accumulation in the endothelium requires the activity of the MADS box transcription factor TRANSPARENT TESTA (TT) 16 (ARABIDOPSIS B-SISTER/AGAMOUS-LIKE 32) and the UDP-glycosyltransferase TT15 (UGT80B1). Interestingly tt16 and tt15 mutants display a very similar flavonoid profiles and patterns of PA accumulation. By using a combination of genetic, molecular, biochemical, and histochemical methods, we showed that both TT16 and TT15 act upstream the PA biosynthetic pathway, but through two distinct genetic routes. We also demonstrated that the activity of TT16 in regulating cell fate determination and PA accumulation in the endothelium is required in the chalaza prior to the globular stage of embryo development. Finally this study provides new insight showing that TT16 and TT15 functions extend beyond PA biosynthesis in the inner integuments of the Arabidopsis seed coat.
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Affiliation(s)
- W Xu
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Saclay Plant Sciences, Université Paris-Saclay, Versailles, France
| | - S Bobet
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Saclay Plant Sciences, Université Paris-Saclay, Versailles, France
| | - J Le Gourrierec
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Saclay Plant Sciences, Université Paris-Saclay, Versailles, France
| | - D Grain
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Saclay Plant Sciences, Université Paris-Saclay, Versailles, France
| | - D De Vos
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Saclay Plant Sciences, Université Paris-Saclay, Versailles, France
| | - A Berger
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Saclay Plant Sciences, Université Paris-Saclay, Versailles, France
| | - F Salsac
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Saclay Plant Sciences, Université Paris-Saclay, Versailles, France
| | - Z Kelemen
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Saclay Plant Sciences, Université Paris-Saclay, Versailles, France
| | - J Boucherez
- Biochimie et Physiologie Moleculaire des Plantes (BPMP), INRA, CNRS, SupAgro-M, Université de Montpellier, Montpellier Cedex, France
| | - A Rolland
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Saclay Plant Sciences, Université Paris-Saclay, Versailles, France
| | - G Mouille
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Saclay Plant Sciences, Université Paris-Saclay, Versailles, France
| | - J M Routaboul
- Genomic and Biotechnology of Fruit, UMR 990 INRA/INP-ENSAT, 24 Chemin de Borderouge-Auzeville, CS, Castanet-Tolosan Cedex, France
| | - L Lepiniec
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Saclay Plant Sciences, Université Paris-Saclay, Versailles, France
| | - C Dubos
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Saclay Plant Sciences, Université Paris-Saclay, Versailles, France
- Biochimie et Physiologie Moleculaire des Plantes (BPMP), INRA, CNRS, SupAgro-M, Université de Montpellier, Montpellier Cedex, France
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Burrows BA, McCubbin AG. Sequencing the genomic regions flanking S-linked PvGLO sequences confirms the presence of two GLO loci, one of which lies adjacent to the style-length determinant gene CYP734A50. PLANT REPRODUCTION 2017; 30:53-67. [PMID: 28229234 DOI: 10.1007/s00497-017-0299-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/10/2017] [Indexed: 06/06/2023]
Abstract
Primula vulgaris contains two GLOBOSA loci, one located adjacent to the style length determinant gene CYP734A50 which lies within the S -locus. Using a combination of BAC walking and PacBio sequencing, we have sequenced two substantial genomic contigs in and around the S-locus of Primula vulgaris. Using these data, we were able to demonstrate that two alleles of PvGlo P as well as PvGlo T can be present in the genome of a single plant, providing empirical evidence that these two forms of the MADS-box gene GLOBOSA are separate loci and not allelic as previously reported. We propose they should be renamed PvGLO1 and PvGLO2. BAC contigs extending from each GLOBOSA locus were identified and fully sequenced. No homologous genes were found between the contigs other than the GLOBOSA genes themselves, consistent with their identity as separate loci. Exons of the recently identified style-length determinant gene CYP734A50 were identified on one end of the contig containing PvGLO2 and these genes are adjacent in the genome, suggesting that PvGLO2 lies either within or at least very close to the S-locus. Current evidence suggests that both CYP734A50 and GLO2 are specific to the S-morph mating type and are hemizygous rather than heterozygous in the Primula genome. This finding contrasts classical models of the HSI locus, which propose that components of the S-locus are allelic, suggesting that these models may need to be reconsidered.
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Affiliation(s)
- Benjamin A Burrows
- School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Andrew G McCubbin
- School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA.
- Center for Reproductive Biology, Washington State University, Pullman, WA, 99164-4236, USA.
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Ren Z, Yu D, Yang Z, Li C, Qanmber G, Li Y, Li J, Liu Z, Lu L, Wang L, Zhang H, Chen Q, Li F, Yang Z. Genome-Wide Identification of the MIKC-Type MADS-Box Gene Family in Gossypium hirsutum L. Unravels Their Roles in Flowering. FRONTIERS IN PLANT SCIENCE 2017; 8:384. [PMID: 28382045 PMCID: PMC5360754 DOI: 10.3389/fpls.2017.00384] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 03/06/2017] [Indexed: 05/22/2023]
Abstract
Cotton is one of the major world oil crops. Cottonseed oil meets the increasing demand of fried food, ruminant feed, and renewable bio-fuels. MADS intervening keratin-like and C-terminal (MIKC)-type MADS-box genes encode transcription factors that have crucial roles in various plant developmental processes. Nevertheless, this gene family has not been characterized, nor its functions investigated, in cotton. Here, we performed a comprehensive analysis of MIKC-type MADS genes in the tetraploid Gossypium hirsutum L., which is the most widely cultivated cotton species. In total, 110 GhMIKC genes were identified and phylogenetically classified into 13 subfamilies. The Flowering locus C (FLC) subfamily was absent in the Gossypium hirsutum L. genome but is found in Arabidopsis and Vitis vinifera L. Among the genes, 108 were distributed across the 13 A and 12 of the D genome's chromosomes, while two were located in scaffolds. GhMIKCs within subfamilies displayed similar exon/intron characteristics and conserved motif compositions. According to RNA-sequencing, most MIKC genes exhibited high flowering-associated expression profiles. A quantitative real-time PCR analysis revealed that some crucial MIKC genes determined the identities of the five flower organs. Furthermore, the overexpression of GhAGL17.9 in Arabidopsis caused an early flowering phenotype. Meanwhile, the expression levels of the flowering-related genes CONSTANS (CO), LEAFY (LFY) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) were significantly increased in these lines. These results provide useful information for future studies of GhMIKCs' regulation of cotton flowering.
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Affiliation(s)
- Zhongying Ren
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Daoqian Yu
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Zhaoen Yang
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Changfeng Li
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
- Cotton Research Institute, Anhui Academy of Agricultural SciencesHefei, China
| | - Ghulam Qanmber
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Yi Li
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Jie Li
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Zhao Liu
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Lili Lu
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Lingling Wang
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Hua Zhang
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
| | - Quanjia Chen
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
| | - Fuguang Li
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
- *Correspondence: Zuoren Yang
| | - Zuoren Yang
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agriculture UniversityUrumqi, China
- Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
- Fuguang Li
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Li W, Zhang L, Zhang Y, Wang G, Song D, Zhang Y. Selection and Validation of Appropriate Reference Genes for Quantitative Real-Time PCR Normalization in Staminate and Perfect Flowers of Andromonoecious Taihangia rupestris. FRONTIERS IN PLANT SCIENCE 2017; 8:729. [PMID: 28579993 PMCID: PMC5437146 DOI: 10.3389/fpls.2017.00729] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 04/19/2017] [Indexed: 05/19/2023]
Abstract
Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is the most commonly used and powerful method for gene expression analysis due to its high sensitivity, specificity, and high throughput, and the accuracy of this approach depends on the stability of reference genes used for normalization. Taihangia rupestris Yu and Li (Rosaceae), an andromonoecious plant, produces both bisexual flowers and unisexual male flowers within the same individual. Using qRT-PCR technique, investigation of the gene expression profiling in staminate and perfect flowers would improve our understanding of the molecular mechanism in regulation of flower formation and sex differentiation in andromonoecious T. rupestris. To accurate normalize the gene expression level in Taihangia flower, 16 candidate reference genes, including 10 traditional housekeeping genes, and 6 newly stable genes, were selected based on transcriptome sequence data and previous studies. The expressions of these genes were assessed by qRT-PCR analysis in 51 samples, including 30 staminate and perfect flower samples across developmental stages and 21 different floral tissue samples from mature flowers. By using geNorm, NormFinder, BestKeeper, and comprehensive RefFinder algorithms, ADF3 combined with UFD1 were identified as the optimal reference genes for staminate flowers, while the combination of HIS3/ADF3 was the most accurate reference genes for perfect floral samples. For floral tissues, HIS3, UFD1, and TMP50 were the most suitable reference genes. Furthermore, two target genes, TruPI, and TruFBP24, involved in floral organ identity were selected to validate the most and least stable reference genes in staminate flowers, perfect flowers, and different floral tissues, indicating that the use of inappropriate reference genes for normalization will lead to the adverse results. The reference genes identified in this study will improve the accuracy of qRT-PCR quantification of target gene expression in andromonoecious T. rupestris flowers, and will facilitate the functional genomics studies on flower development and sex differentiation in the future.
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Affiliation(s)
- Weiguo Li
- College of Life Sciences, Changchun Normal UniversityChangchun, China
- College of Resource and Environment, Henan Polytechnic UniversityJiaozuo, China
- *Correspondence: Weiguo Li
| | - Lihui Zhang
- College of Life Sciences, Changchun Normal UniversityChangchun, China
| | - Yandi Zhang
- College of Resource and Environment, Henan Polytechnic UniversityJiaozuo, China
| | - Guodong Wang
- College of Resource and Environment, Henan Polytechnic UniversityJiaozuo, China
| | - Dangyu Song
- College of Resource and Environment, Henan Polytechnic UniversityJiaozuo, China
| | - Yanwen Zhang
- College of Life Sciences, Changchun Normal UniversityChangchun, China
- Yanwen Zhang
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Schilling S, Gramzow L, Lobbes D, Kirbis A, Weilandt L, Hoffmeier A, Junker A, Weigelt-Fischer K, Klukas C, Wu F, Meng Z, Altmann T, Theißen G. Non-canonical structure, function and phylogeny of the Bsister MADS-box gene OsMADS30 of rice (Oryza sativa). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:1059-1072. [PMID: 26473514 DOI: 10.1111/tpj.13055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/02/2015] [Accepted: 10/06/2015] [Indexed: 06/05/2023]
Abstract
Bsister MADS-box genes play key roles in female reproductive organ and seed development throughout seed plants. This view is supported by their high conservation in terms of sequence, expression and function. In grasses, there are three subclades of Bsister genes: the OsMADS29-, the OsMADS30- and the OsMADS31-like genes. Here, we report on the evolution of the OsMADS30-like genes. Our analyses indicate that these genes evolved under relaxed purifying selection and are rather weakly expressed. OsMADS30, the representative of the OsMADS30-like genes from rice (Oryza sativa), shows strong sequence deviations in its 3' region when compared to orthologues from other grass species. We show that this is due to a 2.4-kbp insertion, possibly of a hitherto unknown helitron, which confers a heterologous C-terminal domain to OsMADS30. This putative helitron is not present in the OsMADS30 orthologues from closely related wild rice species, pointing to a relatively recent insertion event. Unlike other Bsister mutants O. sativa plants carrying a T-DNA insertion in the OsMADS30 gene do not show aberrant seed phenotypes, indicating that OsMADS30 likely does not have a canonical 'Bsister function'. However, imaging-based phenotyping of the T-DNA carrying plants revealed alterations in shoot size and architecture. We hypothesize that sequence deviations that accumulated during a period of relaxed selection in the gene lineage that led to OsMADS30 and the alteration of the C-terminal domain might have been a precondition for a potential neo-functionalization of OsMADS30 in O. sativa.
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Affiliation(s)
- Susanne Schilling
- Department of Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Lydia Gramzow
- Department of Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Dajana Lobbes
- Department of Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Alexander Kirbis
- Department of Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Lisa Weilandt
- Department of Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Andrea Hoffmeier
- Department of Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Astrid Junker
- Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466, Germany
| | - Kathleen Weigelt-Fischer
- Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466, Germany
| | - Christian Klukas
- Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466, Germany
| | - Feng Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zheng Meng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Thomas Altmann
- Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466, Germany
| | - Günter Theißen
- Department of Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
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Lovisetto A, Masiero S, Rahim MA, Mendes MAM, Casadoro G. Fleshy seeds form in the basal Angiosperm Magnolia grandiflora and several MADS-box genes are expressed as fleshy seed tissues develop. Evol Dev 2015; 17:82-91. [PMID: 25627715 DOI: 10.1111/ede.12106] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
One successful mechanism of seed dispersal in plants involves production of edible fleshy structures which attract frugivorous animals and transfer this task to them. Not only Angiosperms but also Gymnosperms may use the fleshy fruit habit for seed dispersal, and a similar suite of MADS-box genes may be expressed as these structures form. Magnolia grandiflora produces dry follicles which, at maturity, open to reveal brightly colored fleshy seeds. This species thus also employs endozoochory for seed dispersal, although it produces dry fruits. Molecular analysis reveals that genes involved in softening and color changes are expressed at late stages of seed development, when the fleshy seed sarcotesta softens and accumulates carotenoids. Several MADS-box genes have also been studied and results highlight the existence of a basic genetic toolkit which may be common to all fleshy fruit-like structures, independently of their anatomic origin. According to their expression patterns, one of two AGAMOUS genes and the three SEPALLATA genes known so far in Magnolia are of particular interest. Duplication of AGAMOUS already occurs in both Nymphaeales and Magnoliids, although the lack of functional gene analysis prevents comparisons with known duplications in the AGAMOUS lineage of core Eudicots.
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Affiliation(s)
- Alessandro Lovisetto
- Dipartimento di Biologia, Università di Padova, Via U. Bassi 58/B, 35131, Padova, Italy
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Pérez-Ruiz RV, García-Ponce B, Marsch-Martínez N, Ugartechea-Chirino Y, Villajuana-Bonequi M, de Folter S, Azpeitia E, Dávila-Velderrain J, Cruz-Sánchez D, Garay-Arroyo A, Sánchez MDLP, Estévez-Palmas JM, Álvarez-Buylla ER. XAANTAL2 (AGL14) Is an Important Component of the Complex Gene Regulatory Network that Underlies Arabidopsis Shoot Apical Meristem Transitions. MOLECULAR PLANT 2015; 8:796-813. [PMID: 25636918 DOI: 10.1016/j.molp.2015.01.017] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 12/10/2014] [Accepted: 01/05/2015] [Indexed: 05/21/2023]
Abstract
In Arabidopsis thaliana, multiple genes involved in shoot apical meristem (SAM) transitions have been characterized, but the mechanisms required for the dynamic attainment of vegetative, inflorescence, and floral meristem (VM, IM, FM) cell fates during SAM transitions are not well understood. Here we show that a MADS-box gene, XAANTAL2 (XAL2/AGL14), is necessary and sufficient to induce flowering, and its regulation is important in FM maintenance and determinacy. xal2 mutants are late flowering, particularly under short-day (SD) condition, while XAL2 overexpressing plants are early flowering, but their flowers have vegetative traits. Interestingly, inflorescences of the latter plants have higher expression levels of LFY, AP1, and TFL1 than wild-type plants. In addition we found that XAL2 is able to bind the TFL1 regulatory regions. On the other hand, the basipetal carpels of the 35S::XAL2 lines lose determinacy and maintain high levels of WUS expression under SD condition. To provide a mechanistic explanation for the complex roles of XAL2 in SAM transitions and the apparently paradoxical phenotypes of XAL2 and other MADS-box (SOC1, AGL24) overexpressors, we conducted dynamic gene regulatory network (GRN) and epigenetic landscape modeling. We uncovered a GRN module that underlies VM, IM, and FM gene configurations and transition patterns in wild-type plants as well as loss and gain of function lines characterized here and previously. Our approach thus provides a novel mechanistic framework for understanding the complex basis of SAM development.
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Affiliation(s)
- Rigoberto V Pérez-Ruiz
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Berenice García-Ponce
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico.
| | - Nayelli Marsch-Martínez
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Yamel Ugartechea-Chirino
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Mitzi Villajuana-Bonequi
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Stefan de Folter
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Carretera Irapuato - León, AP 629, 36821 Irapuato, Guanajuato, Mexico
| | - Eugenio Azpeitia
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - José Dávila-Velderrain
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - David Cruz-Sánchez
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Adriana Garay-Arroyo
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - María de la Paz Sánchez
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Juan M Estévez-Palmas
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Elena R Álvarez-Buylla
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico; University of California, 431 Koshland Hall, Berkeley, CA 94720, USA.
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43
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Tang N, Deng W, Hu G, Hu N, Li Z. Transcriptome profiling reveals the regulatory mechanism underlying pollination dependent and parthenocarpic fruit set mainly mediated by auxin and gibberellin. PLoS One 2015; 10:e0125355. [PMID: 25909657 PMCID: PMC4409352 DOI: 10.1371/journal.pone.0125355] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 03/11/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Fruit set is a key process for crop production in tomato which occurs after successful pollination and fertilization naturally. However, parthenocarpic fruit development can be uncoupled from fertilization triggered by exogenous auxin or gibberellins (GAs). Global transcriptome knowledge during fruit initiation would help to characterize the molecular mechanisms by which these two hormones regulate pollination-dependent and -independent fruit set. PRINCIPAL FINDINGS In this work, digital gene expression tag profiling (DGE) technology was applied to compare the transcriptomes from pollinated and 2, 4-D/GA3-treated ovaries. Activation of carbohydrate metabolism, cell division and expansion as well as the down-regulation of MADS-box is a comprehensive regulatory pathway during pollination-dependent and parthenocarpic fruit set. The signaling cascades of auxin and GA are significantly modulated. The feedback regulations of Aux/IAAs and DELLA genes which functioned to fine-tune auxin and GA response respectively play fundamental roles in triggering fruit initiation. In addition, auxin regulates GA synthesis via up-regulation of GA20ox1 and down-regulation of KNOX. Accordingly, the effect of auxin on fruit set is mediated by GA via ARF2 and IAA9 down-regulation, suggesting that both pollination-dependent and parthenocarpic fruit set depend on the crosstalk between auxin and GA. SIGNIFICANCE This study characterizes the transcriptomic features of ovary development and more importantly unravels the integral roles of auxin and GA on pollination-dependent and parthenocarpic fruit set.
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Affiliation(s)
- Ning Tang
- Genetic Engineering Research Center, School of Life Sciences, Key Laboratory of Functional Gene and New Regulation Technologies Under Chongqing Municipal Education Commission, Chongqing University, Chongqing 400030, China
| | - Wei Deng
- Genetic Engineering Research Center, School of Life Sciences, Key Laboratory of Functional Gene and New Regulation Technologies Under Chongqing Municipal Education Commission, Chongqing University, Chongqing 400030, China
| | - Guojian Hu
- Genetic Engineering Research Center, School of Life Sciences, Key Laboratory of Functional Gene and New Regulation Technologies Under Chongqing Municipal Education Commission, Chongqing University, Chongqing 400030, China
| | - Nan Hu
- Genetic Engineering Research Center, School of Life Sciences, Key Laboratory of Functional Gene and New Regulation Technologies Under Chongqing Municipal Education Commission, Chongqing University, Chongqing 400030, China
| | - Zhengguo Li
- Genetic Engineering Research Center, School of Life Sciences, Key Laboratory of Functional Gene and New Regulation Technologies Under Chongqing Municipal Education Commission, Chongqing University, Chongqing 400030, China
- * E-mail:
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44
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Mizzotti C, Ezquer I, Paolo D, Rueda-Romero P, Guerra RF, Battaglia R, Rogachev I, Aharoni A, Kater MM, Caporali E, Colombo L. SEEDSTICK is a master regulator of development and metabolism in the Arabidopsis seed coat. PLoS Genet 2014; 10:e1004856. [PMID: 25521508 PMCID: PMC4270456 DOI: 10.1371/journal.pgen.1004856] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/28/2014] [Indexed: 11/19/2022] Open
Abstract
The role of secondary metabolites in the determination of cell identity has been an area of particular interest over recent years, and studies strongly indicate a connection between cell fate and the regulation of enzymes involved in secondary metabolism. In Arabidopsis thaliana, the maternally derived seed coat plays pivotal roles in both the protection of the developing embryo and the first steps of germination. In this regard, a characteristic feature of seed coat development is the accumulation of proanthocyanidins (PAs - a class of phenylpropanoid metabolites) in the innermost layer of the seed coat. Our genome-wide transcriptomic analysis suggests that the ovule identity factor SEEDSTICK (STK) is involved in the regulation of several metabolic processes, providing a strong basis for a connection between cell fate determination, development and metabolism. Using phenotypic, genetic, biochemical and transcriptomic approaches, we have focused specifically on the role of STK in PA biosynthesis. Our results indicate that STK exerts its effect by direct regulation of the gene encoding BANYULS/ANTHOCYANIDIN REDUCTASE (BAN/ANR), which converts anthocyanidins into their corresponding 2,3-cis-flavan-3-ols. Our study also demonstrates that the levels of H3K9ac chromatin modification directly correlate with the active state of BAN in an STK-dependent way. This is consistent with the idea that MADS-domain proteins control the expression of their target genes through the modification of chromatin states. STK might thus recruit or regulate histone modifying factors to control their activity. In addition, we show that STK is able to regulate other BAN regulators. Our study demonstrates for the first time how a floral homeotic gene controls tissue identity through the regulation of a wide range of processes including the accumulation of secondary metabolites. Plant secondary metabolites accumulate in seeds to protect the developing embryo. Using an RNA sequencing approach in conjunction with enrichment analyses we identified the homeotic MADS-domain gene SEEDSTICK (STK) as a regulator of metabolic processes during seed development. We analyzed the role of STK as a key regulator of the production of proanthocyanidins, compounds which are important for the pigmentation of the seed. STK directly regulates a network of metabolic genes, and is also implicated in changes occurring in the chromatin landscape. Our work demonstrates that a key homeotic transcription factor not only determines the identity of ovules but also controls metabolic processes that occur subsequent to the initial identity determination process, thus suggesting a link between identity determination and cell-specific (metabolic) processes.
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Affiliation(s)
- Chiara Mizzotti
- Dipartimento di BioScienze, Università degli Studi di Milano, Milan, Italy
| | - Ignacio Ezquer
- Dipartimento di BioScienze, Università degli Studi di Milano, Milan, Italy
- Consiglio Nazionale delle Ricerche, Istituto di Biofisica, Milan, Italy
| | - Dario Paolo
- Dipartimento di BioScienze, Università degli Studi di Milano, Milan, Italy
| | - Paloma Rueda-Romero
- Centro de Biotecnología y Genómica de Plantas-UPM-INIA, ETSI Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Madrid, Spain
| | | | | | - Ilana Rogachev
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Martin M. Kater
- Dipartimento di BioScienze, Università degli Studi di Milano, Milan, Italy
| | | | - Lucia Colombo
- Dipartimento di BioScienze, Università degli Studi di Milano, Milan, Italy
- Consiglio Nazionale delle Ricerche, Istituto di Biofisica, Milan, Italy
- * E-mail:
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Yu LH, Miao ZQ, Qi GF, Wu J, Cai XT, Mao JL, Xiang CB. MADS-box transcription factor AGL21 regulates lateral root development and responds to multiple external and physiological signals. MOLECULAR PLANT 2014; 7:1653-1669. [PMID: 25122697 PMCID: PMC4228986 DOI: 10.1093/mp/ssu088] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plant root system morphology is dramatically influenced by various environmental cues. The adaptation of root system architecture to environmental constraints, which mostly depends on the formation and growth of lateral roots, is an important agronomic trait. Lateral root development is regulated by the external signals coordinating closely with intrinsic signaling pathways. MADS-box transcription factors are known key regulators of the transition to flowering and flower development. However, their functions in root development are still poorly understood. Here we report that AGL21, an AGL17-clade MADS-box gene, plays a crucial role in lateral root development. AGL21 was highly expressed in root, particularly in the root central cylinder and lateral root primordia. AGL21 overexpression plants produced more and longer lateral roots while agl21 mutants showed impaired lateral root development, especially under nitrogen-deficient conditions. AGL21 was induced by many plant hormones and environmental stresses, suggesting a function of this gene in root system plasticity in response to various signals. Furthermore, AGL21 was found positively regulating auxin accumulation in lateral root primordia and lateral roots by enhancing local auxin biosynthesis, thus stimulating lateral root initiation and growth. We propose that AGL21 may be involved in various environmental and physiological signals-mediated lateral root development and growth.
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Affiliation(s)
- Lin-Hui Yu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China
| | - Zi-Qing Miao
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China
| | - Guo-Feng Qi
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China
| | - Jie Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China
| | - Xiao-Teng Cai
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China
| | - Jie-Li Mao
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China
| | - Cheng-Bin Xiang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China.
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Nayar S, Sharma R, Tyagi AK, Kapoor S. Functional delineation of rice MADS29 reveals its role in embryo and endosperm development by affecting hormone homeostasis. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:4239-53. [PMID: 23929654 PMCID: PMC3808311 DOI: 10.1093/jxb/ert231] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Rice MADS29 has recently been reported to cause programmed cell death of maternal tissues, the nucellus, and the nucellar projection during early stages of seed development. However, analyses involving OsMADS29 protein expression domains and characterization of OsMADS29 gain-of-function and knockdown phenotypes revealed novel aspects of its function in maintaining hormone homeostasis, which may have a role in the development of embryo and plastid differentiation and starch filling in endosperm cells. The MADS29 transcripts accumulated to high levels soon after fertilization; however, protein accumulation was found to be delayed by at least 4 days. Immunolocalization studies revealed that the protein accumulated initially in the dorsal-vascular trace and the outer layers of endosperm, and subsequently in the embryo and aleurone and subaleurone layers of the endosperm. Ectopic expression of MADS29 resulted in a severely dwarfed phenotype, exhibiting elevated levels of cytokinin, thereby suggesting that cytokinin biosynthesis pathway could be one of the major targets of OsMADS29. Overexpression of OsMADS29 in heterologous BY2 cells was found to mimic the effects of exogenous application of cytokinins that causes differentiation of proplastids to starch-containing amyloplasts and activation of genes involved in the starch biosynthesis pathway. Suppression of MADS29 expression by RNAi severely affected seed set. The surviving seeds were smaller in size, with developmental abnormalities in the embryo and reduced size of endosperm cells, which also contained loosely packed starch granules. Microarray analysis of overexpression and knockdown lines exhibited altered expression of genes involved in plastid biogenesis, starch biosynthesis, cytokinin signalling and biosynthesis.
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Affiliation(s)
- Saraswati Nayar
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Rita Sharma
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
- *Present address: Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Akhilesh Kumar Tyagi
- National Institute for Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
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Carlsbecker A, Sundström JF, Englund M, Uddenberg D, Izquierdo L, Kvarnheden A, Vergara-Silva F, Engström P. Molecular control of normal and acrocona mutant seed cone development in Norway spruce (Picea abies) and the evolution of conifer ovule-bearing organs. THE NEW PHYTOLOGIST 2013; 200:261-275. [PMID: 0 DOI: 10.1111/nph.12360] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/03/2013] [Indexed: 05/03/2023]
Abstract
Reproductive organs in seed plants are morphologically divergent and their evolutionary history is often unclear. The mechanisms controlling their development have been extensively studied in angiosperms but are poorly understood in conifers and other gymnosperms. Here, we address the molecular control of seed cone development in Norway spruce, Picea abies. We present expression analyses of five novel MADS-box genes in comparison with previously identified MADS and LEAFY genes at distinct developmental stages. In addition, we have characterized the homeotic transformation from vegetative shoot to female cone and associated changes in regulatory gene expression patterns occurring in the acrocona mutant. The analyses identified genes active at the onset of ovuliferous and ovule development and identified expression patterns marking distinct domains of the ovuliferous scale. The reproductive transformation in acrocona involves the activation of all tested genes normally active in early cone development, except for an AGAMOUS-LIKE6/SEPALLATA (AGL6/SEP) homologue. This absence may be functionally associated with the nondeterminate development of the acrocona ovule-bearing scales. Our morphological and gene expression analyses give support to the hypothesis that the modern cone is a complex structure, and the ovuliferous scale the result of reductions and compactions of an ovule-bearing axillary short shoot in cones of Paleozoic conifers.
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Affiliation(s)
- Annelie Carlsbecker
- Department of Organismal Biology, Physiological Botany, Uppsala University, and The Linnean Center for Plant Biology, Ullsv. 24E, SE-756 51, Uppsala, Sweden
| | - Jens F Sundström
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and The Linnean Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
| | - Marie Englund
- Department of Organismal Biology, Physiological Botany, Uppsala University, and The Linnean Center for Plant Biology, Ullsv. 24E, SE-756 51, Uppsala, Sweden
| | - Daniel Uddenberg
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and The Linnean Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
| | - Liz Izquierdo
- Department of Organismal Biology, Physiological Botany, Uppsala University, and The Linnean Center for Plant Biology, Ullsv. 24E, SE-756 51, Uppsala, Sweden
| | - Anders Kvarnheden
- Department of Organismal Biology, Physiological Botany, Uppsala University, and The Linnean Center for Plant Biology, Ullsv. 24E, SE-756 51, Uppsala, Sweden
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and The Linnean Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
| | - Francisco Vergara-Silva
- Laboratorio de Sistemática Molecular (Jardín Botánico), Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, México DF, 04510, Mexico
| | - Peter Engström
- Department of Organismal Biology, Physiological Botany, Uppsala University, and The Linnean Center for Plant Biology, Ullsv. 24E, SE-756 51, Uppsala, Sweden
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Lovisetto A, Guzzo F, Busatto N, Casadoro G. Gymnosperm B-sister genes may be involved in ovule/seed development and, in some species, in the growth of fleshy fruit-like structures. ANNALS OF BOTANY 2013; 112:535-44. [PMID: 23761686 PMCID: PMC3718214 DOI: 10.1093/aob/mct124] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 04/17/2013] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS The evolution of seeds together with the mechanisms related to their dispersal into the environment represented a turning point in the evolution of plants. Seeds are produced by gymnosperms and angiosperms but only the latter have an ovary to be transformed into a fruit. Yet some gymnosperms produce fleshy structures attractive to animals, thus behaving like fruits from a functional point of view. The aim of this work is to increase our knowledge of possible mechanisms common to the development of both gymnosperm and angiosperm fruits. METHODS B-sister genes from two gymnosperms (Ginkgo biloba and Taxus baccata) were isolated and studied. The Ginkgo gene was also functionally characterized by ectopically expressing it in tobacco. KEY RESULTS In Ginkgo the fleshy structure derives from the outer seed integument and the B-sister gene is involved in its growth. In Taxus the fleshy structure is formed de novo as an outgrowth of the ovule peduncle, and the B-sister gene is not involved in this growth. In transgenic tobacco the Ginkgo gene has a positive role in tissue growth and confirms its importance in ovule/seed development. CONCLUSIONS This study suggests that B-sister genes have a main function in ovule/seed development and a subsidiary role in the formation of fleshy fruit-like structures when the latter have an ovular origin, as occurs in Ginkgo. Thus, the 'fruit function' of B-sister genes is quite old, already being present in Gymnosperms as ancient as Ginkgoales, and is also present in Angiosperms where a B-sister gene has been shown to be involved in the formation of the Arabidopsis fruit.
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Affiliation(s)
| | - Flavia Guzzo
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Nicola Busatto
- Department of Biology, University of Padua, 35131 Padua, Italy
| | - Giorgio Casadoro
- Department of Biology, University of Padua, 35131 Padua, Italy
- Botanic Garden of Padua, 35123 Padua, Italy
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Chen G, Deng W, Peng F, Truksa M, Singer S, Snyder CL, Mietkiewska E, Weselake RJ. Brassica napus TT16 homologs with different genomic origins and expression levels encode proteins that regulate a broad range of endothelium-associated genes at the transcriptional level. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:663-77. [PMID: 23425240 DOI: 10.1111/tpj.12151] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 02/08/2013] [Accepted: 02/14/2013] [Indexed: 05/14/2023]
Abstract
The transcription factor TRANSPARENT TESTA 16 (TT16) plays an important role in endothelial cell specification and proanthocyanidin (PA) accumulation. However, its precise regulatory function with regard to the expression of endothelial-associated genes in developing seeds, and especially in the PA-producing inner integument, remains largely unknown. Therefore, we endeavored to characterize four TT16 homologs from the allotetraploid oil crop species Brassica napus, and systematically explore their regulatory function in endothelial development. Our results indicated that all four BnTT16 genes were predominantly expressed in the early stages of seed development, but at distinct levels, and encoded functional proteins. Bntt16 RNA interference lines exhibited abnormal endothelial development and decreased PA content, while PA polymerization was not affected. In addition to the previously reported function of TT16 in the transcriptional regulation of anthocyanidin reductase (ANR) and dihydroflavonol reductase (TT3), we also determined that BnTT16 proteins played a significant role in the transcriptional regulation of five other genes involved in the PA biosynthetic pathway (P < 0.01). Moreover, we identified two genes involved in inner integument development that were strongly regulated by the BnTT16 proteins (TT2 and δ-vacuolar processing enzyme). These results will better our understanding of the precise role of TT16 in endothelial development in Brassicaceae species, and could potentially be used for the future improvement of oilseed crops.
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Affiliation(s)
- Guanqun Chen
- Alberta Innovates Phytola Centre, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
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Lee DS, Chen LJ, Li CY, Liu Y, Tan XL, Lu BR, Li J, Gan SX, Kang SG, Suh HS, Zhu Y. The Bsister MADS gene FST determines ovule patterning and development of the zygotic embryo and endosperm. PLoS One 2013; 8:e58748. [PMID: 23527017 PMCID: PMC3602522 DOI: 10.1371/journal.pone.0058748] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 02/05/2013] [Indexed: 11/19/2022] Open
Abstract
Many homeotic MADS-box genes have been identified as controllers of the floral transition and floral development. However, information regarding Bsister (Bs)-function genes in monocots is still limited. Here, we describe the functional characterization of a Bs-group MADS-box gene FEMALE-STERILE (FST), whose frame-shift mutation (fst) results in abnormal ovules and the complete abortion of zygotic embryos and endosperms in rice. Anatomical analysis showed that the defective development in the fst mutant exclusively occurred in sporophytic tissues including integuments, fertilized proembryos and endosperms. Analyses of the spatio-temporal expression pattern revealed that the prominent FST gene products accumulated in the inner integument, nucellar cell of the micropylar side, apical and base of the proembryos and free endosperm nuclei. Microarray and gene ontology analysis unraveled substantial changes in the expression level of many genes in the fst mutant ovules and seeds, with a subset of genes involved in several developmental and hormonal pathways appearing to be down-regulated. Using both forward and reverse genetics approaches, we demonstrated that rice FST plays indispensable roles and multiple functions during ovule and early seed development. These findings support a novel function for the Bs-group MADS-box genes in plants.
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Affiliation(s)
- Dong Sun Lee
- Key Lab of Agro-Biodiversity and Pest Management of Education Ministry, Yunnan Agricultural University, Kunming, China
- Rice Research Institute, Yunnan Agricultural University, Kunming, China
| | - Li Juan Chen
- Rice Research Institute, Yunnan Agricultural University, Kunming, China
- Key Lab of Molecular Breeding for Dian-Type Japonica Hybrid Rice of Yunnan Education Department, Yunnan Agricultural University, Kunming, China
| | - Cheng Yun Li
- Key Lab of Agro-Biodiversity and Pest Management of Education Ministry, Yunnan Agricultural University, Kunming, China
| | - Yongsheng Liu
- Ministry of Education Key Lab for Bio-resource and Eco-environment, College of Life Science, State Key Lab of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Xue Lin Tan
- Rice Research Institute, Yunnan Agricultural University, Kunming, China
- Key Lab of Molecular Breeding for Dian-Type Japonica Hybrid Rice of Yunnan Education Department, Yunnan Agricultural University, Kunming, China
| | - Bao-Rong Lu
- Ministry of Education Key Lab for Biodiversity and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Juan Li
- Rice Research Institute, Yunnan Agricultural University, Kunming, China
- Key Lab of Molecular Breeding for Dian-Type Japonica Hybrid Rice of Yunnan Education Department, Yunnan Agricultural University, Kunming, China
| | - Shu Xian Gan
- Rice Research Institute, Yunnan Agricultural University, Kunming, China
- Key Lab of Molecular Breeding for Dian-Type Japonica Hybrid Rice of Yunnan Education Department, Yunnan Agricultural University, Kunming, China
| | - Sang Gu Kang
- School of Biotechnology, Yeungnam University, Gyeongsan, Korea
| | - Hak Soo Suh
- School of Biological Resources, Yeungnam University, Gyeongsan, Korea
| | - Youyong Zhu
- Key Lab of Agro-Biodiversity and Pest Management of Education Ministry, Yunnan Agricultural University, Kunming, China
- * E-mail:
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