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Auge G, Hankofer V, Groth M, Antoniou-Kourounioti R, Ratikainen I, Lampei C. Plant environmental memory: implications, mechanisms and opportunities for plant scientists and beyond. AOB PLANTS 2023; 15:plad032. [PMID: 37415723 PMCID: PMC10321398 DOI: 10.1093/aobpla/plad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 06/01/2023] [Indexed: 07/08/2023]
Abstract
Plants are extremely plastic organisms. They continuously receive and integrate environmental information and adjust their growth and development to favour fitness and survival. When this integration of information affects subsequent life stages or the development of subsequent generations, it can be considered an environmental memory. Thus, plant memory is a relevant mechanism by which plants respond adaptively to different environments. If the cost of maintaining the response is offset by its benefits, it may influence evolutionary trajectories. As such, plant memory has a sophisticated underlying molecular mechanism with multiple components and layers. Nonetheless, when mathematical modelling is combined with knowledge of ecological, physiological, and developmental effects as well as molecular mechanisms as a tool for understanding plant memory, the combined potential becomes unfathomable for the management of plant communities in natural and agricultural ecosystems. In this review, we summarize recent advances in the understanding of plant memory, discuss the ecological requirements for its evolution, outline the multilayered molecular network and mechanisms required for accurate and fail-proof plant responses to variable environments, point out the direct involvement of the plant metabolism and discuss the tremendous potential of various types of models to further our understanding of the plant's environmental memory. Throughout, we emphasize the use of plant memory as a tool to unlock the secrets of the natural world.
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Affiliation(s)
| | - Valentin Hankofer
- Institute of Biochemical Plant Pathology, Helmholtz Munich, Ingolstädter Landstraße 1, 85764 Oberschleißheim, Neuherberg, Germany
| | - Martin Groth
- Institute of Functional Epigenetics, Helmholtz Munich, Ingolstädter Landstraße 1, 85764 Oberschleißheim, Neuherberg, Germany
| | - Rea Antoniou-Kourounioti
- School of Molecular Biosciences, University of Glasgow, Sir James Black Building, University Ave, Glasgow G12 8QQ, UK
| | - Irja Ratikainen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Realfagbygget, NO-7491 Trondheim, Norway
| | - Christian Lampei
- Department of Biology (FB17), Plant Ecology and Geobotany Group, University of Marburg, Karl-von-Frisch-Straße 8, 35032 Marburg, Germany
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2
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Li J, Wang L, Wan J, Dang K, Lin Y, Meng S, Qiu X, Wang Q, Zhao J, Mu L, Luo H, Ding D, Chen Z, Tang J. Dynamic patterns of gene expression and regulatory variation in the maize seed coat. BMC PLANT BIOLOGY 2023; 23:82. [PMID: 36750803 PMCID: PMC9903604 DOI: 10.1186/s12870-023-04078-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Seed size is an important factor contributing to maize yield, but its molecular mechanism remains unclear. The seed coat, which serves as one of the three components of the maize grain, determines seed size to a certain extent. The seed coat also shares the maternal genotype and is an ideal material for studying heterosis. RESULTS In this study, the self-pollinated seeds of the maize hybrid Yudan888 and its parental lines were continuously collected from 0 day after pollination (DAP) to 15 DAP for phenotyping, cytological observation and RNA-seq. The phenotypic data showed that 3 DAP and 8 DAP are the best time points to study maize seed coat heterosis. Cytological observations indicated that maize seed coat heterosis might be the result of the coordination between cell number and cell size. Furthermore, the RNA-seq results showed that the nonadditive genes changed significantly between 3 and 8 DAP. However, the number of genes expressed additively was not significantly different. Our findings suggest that seed coat heterosis in hybrid is the result of nonadditive expression caused by dynamic changes in genes at different time points during seed expansion and seed coat development. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated that genes related to DNA replication, cell cycle regulation, circadian rhythms and metabolite accumulation contributed significantly to hybrid seed coat heterosis. CONCLUSION Maize seed coat phenotyping allowed us to infer that 3 DAP and 8 DAP are important time points in the study of seed coat heterosis. Our findings provide evidence for genes involved in DNA replication, cell cycle regulation, circadian rhythms and metabolite accumulation in hybrid with high or low parental expression as major contributors to hybrid seed coat heterosis.
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Affiliation(s)
- Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Liangfa Wang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Hebi Academy of Agricultural Sciences, Hebi, 458030, China
| | - Jiong Wan
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Kuntai Dang
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yuan Lin
- Hebi Academy of Agricultural Sciences, Hebi, 458030, China
| | - Shujun Meng
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoqian Qiu
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qiyue Wang
- Hebi Academy of Agricultural Sciences, Hebi, 458030, China
| | - Jiawen Zhao
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Liqin Mu
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongbing Luo
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Zehui Chen
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China.
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
- The Shennong Laboratory, Zhengzhou, 450002, China.
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3
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Dong E, Liu C, Bai Y, Mei X, Zhao Z, Zhu S, Zhang J, Cai Y. A new network containing MYB109-ZmCesA5 is involved in kernel development. Biochem Biophys Res Commun 2022; 602:15-20. [PMID: 35247699 DOI: 10.1016/j.bbrc.2022.02.104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 11/02/2022]
Abstract
MYB genes regulate several different aspects of metabolism and development. However, few studies have reported the involvement of MYBs-CesAs network in the regulation of maize kernel development. In this study, yeast one-hybrid (Y1H) assays and dual-luciferase reporter assays showed that ZmMYB109 activated the expression of ZmCesA5 by directly binding to its promoter. Real-time quantitative PCR (RT-qPCR) and transcriptome analyses showed that ZmMYB109 expression increased in ZmCesA5-OE kernels and decreased in ZmCesA5-KO kernels. Overexpression of ZmCesA5 produced heavier kernels, whereas loss of function of ZmCesA5 affected starch and sucrose metabolism, resulting in weight reduction of the maize kernels. Collectively, these findings suggest that a new network containing MYB109-ZmCesA5 is involved in kernel development.
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Affiliation(s)
- Erfei Dong
- Maize Research Institute, Southwest University, Tiansheng Road, No. 2, Beibei District, Chongqing, China
| | - Chaoxian Liu
- Maize Research Institute, Southwest University, Tiansheng Road, No. 2, Beibei District, Chongqing, China
| | - Yang Bai
- Maize Research Institute, Southwest University, Tiansheng Road, No. 2, Beibei District, Chongqing, China
| | - Xiupeng Mei
- Maize Research Institute, Southwest University, Tiansheng Road, No. 2, Beibei District, Chongqing, China
| | - Zikun Zhao
- Maize Research Institute, Southwest University, Tiansheng Road, No. 2, Beibei District, Chongqing, China
| | - Siying Zhu
- Maize Research Institute, Southwest University, Tiansheng Road, No. 2, Beibei District, Chongqing, China
| | - Jiahao Zhang
- Maize Research Institute, Southwest University, Tiansheng Road, No. 2, Beibei District, Chongqing, China
| | - Yilin Cai
- Maize Research Institute, Southwest University, Tiansheng Road, No. 2, Beibei District, Chongqing, China.
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Wang Y, Nie L, Ma J, Zhou B, Han X, Cheng J, Lu X, Fan Z, Li Y, Cao Y. Transcriptomic Variations and Network Hubs Controlling Seed Size and Weight During Maize Seed Development. FRONTIERS IN PLANT SCIENCE 2022; 13:828923. [PMID: 35237291 PMCID: PMC8882617 DOI: 10.3389/fpls.2022.828923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
To elucidate the mechanisms underlying seed development in maize, comprehensive RNA-seq analyses were conducted on Zhengdan1002 (ZD1002), Zhengdan958 (ZD958), and their parental lines during seven seed developmental stages. We found that gene expression levels were largely nonadditive in hybrids and that cis-only or trans × cis pattern played a large role in hybrid gene regulation during seed developmental stage. Weighted gene co-expression network (WGCNA) analysis showed that 36 modules were highly correlated (r = -0.90-0.92, p < 0.05) with kernel weight, length, and width during seed development. Forty-five transcription factors and 38 ribosomal protein genes were identified as major hub genes determining seed size/weight. We also described a network hub, Auxin Response Factor 12 of maize (ZmARF12), a member of a family of transcription factor that mediate gene expression in response to auxin, potentially links auxin signal pathways, cell division, and the size of the seeds. The ZmARF12 mutant exhibited larger seed size and higher grain weight. ZmARF12 transcription was negatively associated with cell division during seed development, which was confirmed by evaluating the yield of protoplasts that isolated from the kernels of the mutant and other inbred lines. Transient knock-down of ZmARF12 in maize plants facilitated cell expansion and division, whereas transient silencing of its potential interactor ZmIAA8 impaired cell division. ZmIAA8 expression was repressed in the ZmARF12 over-expressed protoplasts. The mutant phenotype and the genetics studies presented here illustrated evidence that ZmARF12 is a cell division repressor, and potentially determines the final seed size.
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Affiliation(s)
- Yanzhao Wang
- Henan Provincial Key Laboratory of Maize Biology, Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Lihong Nie
- Institute of Industrial Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Juan Ma
- Henan Provincial Key Laboratory of Maize Biology, Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Bo Zhou
- Henan Provincial Key Laboratory of Maize Biology, Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaohua Han
- Henan Provincial Key Laboratory of Maize Biology, Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Junling Cheng
- Henan Provincial Key Laboratory of Maize Biology, Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaomin Lu
- Henan Provincial Key Laboratory of Maize Biology, Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Zaifeng Fan
- State Kay Laboratory of Agro-biotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing, China
| | - Yuling Li
- Henan Maize Engineering Technology Joint Center, Henan Agricultural University, Zhengzhou, China
| | - Yanyong Cao
- Henan Provincial Key Laboratory of Maize Biology, Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
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Weighted gene co-expression network analysis unveils gene networks regulating folate biosynthesis in maize endosperm. 3 Biotech 2021; 11:441. [PMID: 34631342 DOI: 10.1007/s13205-021-02974-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/23/2021] [Indexed: 10/20/2022] Open
Abstract
Folates are essential elements for human growth and development, and their deficiency can lead to serious disorders. Waxy maize is a rich source of folates; however, the regulatory mechanism underlying folate biosynthesis in the endosperm remains unclear. Here, we examined changes in the folate content of maize endosperm collected at 15, 18, 21, 24, and 27 days after pollination (DAP) using liquid chromatograph-mass spectrometry and identified genes related to folate biosynthesis using transcriptome sequencing data. The results showed that 5-methyl-tetrahydrofolate and 5,10-methylene tetrahydrofolate were the main storage forms of folates in the endosperm, and their contents were relatively high at 21-24 days. We also identified 569, 3183, 4365, and 5513 differentially expressed genes (DEGs) in different days around milk stage. Functional annotation revealed 518 transcription factors (TFs) belonging to 33 families exhibiting specific expression in at least one sampling time. The key hub genes involved in folate biosynthesis were identified by weighted gene co-expression network analysis. In total, 24,976 genes were used to construct a co-expression network with 29 co-expression modules, among which the brown and purple modules were highly related to folate biosynthesis. Further, 187 transcription factors in the brown and purple modules were considered potential transcription factors related to endosperm folate biosynthesis. These results may improve the understanding of the molecular mechanism underlying folate biosynthesis in waxy maize and lead to the development of nutritionally fortified varieties. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02974-7.
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6
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Wang H, Sun J, Yang F, Weng Y, Chen P, Du S, Wei A, Li Y. CsKTN1 for a katanin p60 subunit is associated with the regulation of fruit elongation in cucumber (Cucumis sativus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2429-2441. [PMID: 34043036 DOI: 10.1007/s00122-021-03833-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/03/2021] [Indexed: 06/12/2023]
Abstract
We identified a short fruit3 (sf3) mutant in cucumber. Map-based cloning revealed that CsKTN1 gene encodes a katanin p60 subunit, which is associated with the regulation of fruit elongation. Fruit length is an important horticultural trait for both fruit yield and quality of cucumber (Cucumis sativus L.). Knowledge on the molecular regulation of fruit elongation in cucumber is very limited. In this study, we identified and characterized a cucumber short fruit3 (sf3) mutant. Histological examination indicated that the shorter fruit in the mutant was due to reduced cell numbers. Genetic analysis revealed that the phenotype of the sf3 mutant was controlled by a single gene with semi-dominant inheritance. By map-based cloning and Arabidopsis genetic transformation, we showed that Sf3 was a homolog of KTN1 (CsKTN1) encoding a katanin p60 subunit. A non-synonymous mutation in the fifth exon of CsKTN1 resulted in an amino acid substitution from Serine in the wild type to Phenylalanine in the sf3 mutant. CsKTN1 expressed in all tissues of both the wild type and the sf3 mutant. However, there was no significant difference in CsKTN1 expression levels between the wild type and the sf3 mutant. The hormone quantitation and RNA-seq analysis suggested that auxin and gibberellin contents are decreased in sf3 by changing the expression levels of genes related with auxin and gibberellin metabolism and signaling. This work helps understand the function of the katanin and the molecular mechanisms of fruit growth regulation in cucumber.
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Affiliation(s)
- Hui Wang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jing Sun
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fan Yang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yiqun Weng
- Horticulture Department, USDA-ARS Vegetable Crops Research Unit, University of Wisconsin, Madison, WI, 53706, USA
| | - Peng Chen
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shengli Du
- Tianjin Vegetable Research Center, Tianjin, 300192, China
- National Key Laboratory of Vegetable Germplasm Innovation, Tianjin, 300192, China
| | - Aimin Wei
- Tianjin Vegetable Research Center, Tianjin, 300192, China.
- National Key Laboratory of Vegetable Germplasm Innovation, Tianjin, 300192, China.
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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7
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Ma J, Wang L, Cao Y, Wang H, Li H. Association Mapping and Transcriptome Analysis Reveal the Genetic Architecture of Maize Kernel Size. FRONTIERS IN PLANT SCIENCE 2021; 12:632788. [PMID: 33815440 PMCID: PMC8013726 DOI: 10.3389/fpls.2021.632788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/04/2021] [Indexed: 05/05/2023]
Abstract
Kernel length, kernel width, and kernel thickness are important traits affecting grain yield and product quality. Here, the genetic architecture of the three kernel size traits was dissected in an association panel of 309 maize inbred lines using four statistical methods. Forty-two significant single nucleotide polymorphisms (SNPs; p < 1.72E-05) and 70 genes for the three traits were identified under five environments. One and eight SNPs were co-detected in two environments and by at least two methods, respectively, and they explained 5.87-9.59% of the phenotypic variation. Comparing the transcriptomes of two inbred lines with contrasting seed size, three and eight genes identified in the association panel showed significantly differential expression between the two genotypes at 15 and 39 days after pollination, respectively. Ten and 17 genes identified by a genome-wide association study were significantly differentially expressed between the two development stages in the two genotypes. Combining environment-/method-stable SNPs and differential expression analysis, ribosomal protein L7, jasmonate-regulated gene 21, serine/threonine-protein kinase RUNKEL, AP2-EREBP-transcription factor 16, and Zm00001d035222 (cell wall protein IFF6-like) were important candidate genes for maize kernel size and development.
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8
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Sun R, Gao L, Mi Z, Zheng Y, Li D. CnMADS1, a MADS transcription factor, positively modulates cell proliferation and lipid metabolism in the endosperm of coconut (Cocos nucifera L.). PLANTA 2020; 252:83. [PMID: 33040224 DOI: 10.1007/s00425-020-03490-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
The function of the first MADS-box transcription factor from endosperm of coconut, CnMADS1, was characterized via seed-specific overexpression in Arabidopsis seeds and further confirmed in protoplasts of coconut. Coconut (Cocos nucifera L.), which belongs to the palm family (Arecaceae), is one of the world's most useful economical tropical crops. However, few genes related to coconut endosperm development have been studied. In previous research, an AGAMOUS-like (AGL) MADS-box transcription factor, named CnMADS1, was identified in the endosperm of coconut through the SSH cDNA library. In this paper, functional characterization of the CnMADS1 gene was carried out by seed-specific overexpression in A. thaliana seeds and protoplasts of coconut. The results indicated that in the twelve independent T2 transgenic Arabidopsis lines with high overexpression of CnMADS1, the size of the mature seeds of transgenic plants was increased significantly (19.64% increase in the long axis and 8.6% increase in the short axis) compared to that of the wild-type seeds. Moreover, the total lipid content also increased significantly in mature seeds of transgenic plants. After comparing the expression of related genes in wild-type and transgenic plants and confirmation by EMSA, AtOSR1, a regulatory gene related to seed size, was proven to be significantly up-regulated by CnMADS1 in transgenic plants. Moreover, the transient transformation of protoplasts of coconut also proved that CnLECRK3 (the homologous gene of AtOSR1 in coconut) is up-regulated by the CnMADS1 gene in the same way. All these results indicated that a similar regulation mode existed in Arabidopsis and the endosperm of coconut and ultimately affected the yield and quality of coconut copra.
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Affiliation(s)
- RuHao Sun
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Li Gao
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Zhiqi Mi
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Yusheng Zheng
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Dongdong Li
- College of Tropical Crops, Hainan University, Hainan, 570228, China.
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Botet R, Keurentjes JJB. The Role of Transcriptional Regulation in Hybrid Vigor. FRONTIERS IN PLANT SCIENCE 2020; 11:410. [PMID: 32351526 PMCID: PMC7174566 DOI: 10.3389/fpls.2020.00410] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/23/2020] [Indexed: 05/19/2023]
Abstract
The genetic basis of hybrid vigor in plants remains largely unsolved but strong evidence suggests that variation in transcriptional regulation can explain many aspects of this phenomenon. Natural variation in transcriptional regulation is highly abundant in virtually all species and thus a potential source of heterotic variability. Allele Specific Expression (ASE), which is tightly linked to parent of origin effects and modulated by complex interactions in cis and in trans, is generally considered to play a key role in explaining the differences between hybrids and parental lines. Here we discuss the recent developments in elucidating the role of transcriptional variation in a number of aspects of hybrid vigor, thereby bridging old paradigms and hypotheses with contemporary research in various species.
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Affiliation(s)
- Ramon Botet
- Laboratory of Genetics, Wageningen University & Research, Wageningen, Netherlands
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10
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Chen L, Li Y, Li C, Shi Y, Song Y, Zhang D, Wang H, Li Y, Wang T. The retromer protein ZmVPS29 regulates maize kernel morphology likely through an auxin-dependent process(es). PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1004-1014. [PMID: 31553822 PMCID: PMC7061865 DOI: 10.1111/pbi.13267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 07/28/2019] [Accepted: 09/22/2019] [Indexed: 05/13/2023]
Abstract
Kernel size and morphology are two important yield-determining traits in maize, but their molecular and genetic mechanisms are poorly characterized. Here, we identified a major QTL, qKM4.08, which explains approximately 24.20% of the kernel morphology variance in a recombinant population derived from two elite maize inbred lines, Huangzaosi (HZS, round kernel) and LV28 (slender kernel). Positional cloning and transgenic analysis revealed that qKM4.08 encodes ZmVPS29, a retromer complex component. Compared with the ZmVPS29 HZS allele, the ZmVPS29 LV28 allele showed higher expression in developing kernels. Overexpression of ZmVPS29 conferred a slender kernel morphology and increased the yield per plant in different maize genetic backgrounds. Sequence analysis revealed that ZmVPS29 has been under purifying selection during maize domestication. Association analyses identified two significant kernel morphology-associated polymorphic sites in the ZmVPS29 promoter region that were significantly enriched in modern maize breeding lines. Further study showed that ZmVPS29 increased auxin accumulation during early kernel development by enhancing auxin biosynthesis and transport and reducing auxin degradation and thereby improved kernel development. Our results suggest that ZmVPS29 regulates kernel morphology, most likely through an auxin-dependent process(es).
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Affiliation(s)
- Lin Chen
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yong‐Xiang Li
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Chunhui Li
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yunsu Shi
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yanchun Song
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Dengfeng Zhang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Haiyang Wang
- School of Life SciencesState Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Yu Li
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Tianyu Wang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
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11
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Yu A, Li F, Xu W, Wang Z, Sun C, Han B, Wang Y, Wang B, Cheng X, Liu A. Application of a high-resolution genetic map for chromosome-scale genome assembly and fine QTLs mapping of seed size and weight traits in castor bean. Sci Rep 2019; 9:11950. [PMID: 31420567 PMCID: PMC6697702 DOI: 10.1038/s41598-019-48492-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/07/2019] [Indexed: 01/27/2023] Open
Abstract
Castor bean (Ricinus communis L., Euphorbiaceae) is a critical biodiesel crop and its seed derivatives have important industrial applications. Due to lack of a high-density genetic map, the breeding and genetic improvement of castor bean has been largely restricted. In this study, based on a recombinant inbred line (RIL) population consisting of 200 individuals, we generated 8,896 high-quality genomic SNP markers and constructed a high-resolution genetic map with 10 linkage groups (LGs), spanning 1,852.33 centiMorgan (cM). Based on the genetic map, 996 scaffolds from the draft reference genome were anchored onto 10 pseudo-chromosomes, covering 84.43% of the castor bean genome. Furthermore, the quality of the pseudo-chromosome scale assembly genome was confirmed via genome collinearity analysis within the castor bean genome as well as between castor bean and cassava. Our results provide new evidence that the phylogenetic position of castor bean is relatively solitary from other taxa in the Euphorbiaceae family. Based on the genetic map, we identified 16 QTLs that control seed size and weight (covering 851 candidate genes). The findings will be helpful for further research into potential new mechanisms controlling seed size and weight in castor bean. The genetic map and improved pseudo-chromosome scale genome provide crucial foundations for marker-assisted selection (MAS) of QTL governing important agronomic traits, as well as the accelerated molecular breeding of castor bean in a cost-effective pattern.
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Affiliation(s)
- Anmin Yu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Li
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Wei Xu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zaiqing Wang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Sun
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Bing Han
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue Wang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Bo Wang
- Wuhan Genoseq Technology Co., Ltd, Wuhan, 430070, China
| | - Xiaomao Cheng
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China.
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12
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Zhang X, Xie S, Han J, Zhou Y, Liu C, Zhou Z, Wang F, Cheng Z, Zhang J, Hu Y, Hao Z, Li M, Zhang D, Yong H, Huang Y, Weng J, Li X. Integrated transcriptome, small RNA, and degradome analysis reveals the complex network regulating starch biosynthesis in maize. BMC Genomics 2019; 20:574. [PMID: 31296166 PMCID: PMC6625009 DOI: 10.1186/s12864-019-5945-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/30/2019] [Indexed: 12/18/2022] Open
Abstract
Background Starch biosynthesis in endosperm is a key process influencing grain yield and quality in maize. Although a number of starch biosynthetic genes have been well characterized, the mechanisms by which the expression of these genes is regulated, especially in regard to microRNAs (miRNAs), remain largely unclear. Results Sequence data for small RNAs, degradome, and transcriptome of maize endosperm at 15 and 25 d after pollination (DAP) from inbred lines Mo17 and Ji419, which exhibit distinct starch content and starch granule structure, revealed the mediation of starch biosynthetic pathways by miRNAs. Transcriptome analysis of these two lines indicated that 33 of 40 starch biosynthetic genes were differentially expressed, of which 12 were up-regulated in Ji419 at 15 DAP, one was up-regulated in Ji419 at 25 DAP, 14 were up-regulated in Ji419 at both 15 and 25 DAP, one was down-regulated in Ji419 at 15 DAP, two were down-regulated in Ji419 at 25 DAP, and three were up-regulated in Ji419 at 15 DAP and down-regulated in Ji419 at 25 DAP, compared with Mo17. Through combined analyses of small RNA and degradome sequences, 22 differentially expressed miRNAs were identified, including 14 known and eight previously unknown miRNAs that could target 35 genes. Furthermore, a complex co-expression regulatory network was constructed, in which 19 miRNAs could modulate starch biosynthesis in endosperm by tuning the expression of 19 target genes. Moreover, the potential operation of four miRNA-mediated pathways involving transcription factors, miR169a-NF-YA1-GBSSI/SSIIIa and miR169o-GATA9-SSIIIa/SBEIIb, was validated via analyses of expression pattern, transient transformation assays, and transactivation assays. Conclusion Our results suggest that miRNAs play a critical role in starch biosynthesis in endosperm, and that miRNA-mediated networks could modulate starch biosynthesis in this tissue. These results have provided important insights into the molecular mechanism of starch biosynthesis in developing maize endosperm. Electronic supplementary material The online version of this article (10.1186/s12864-019-5945-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaocong Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sidi Xie
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jienan Han
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Chang Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Feifei Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zixiang Cheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Yufeng Hu
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhuanfang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Degui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongjun Yong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yubi Huang
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
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13
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Li N, Song D, Peng W, Zhan J, Shi J, Wang X, Liu G, Wang H. Maternal control of seed weight in rapeseed (Brassica napus L.): the causal link between the size of pod (mother, source) and seed (offspring, sink). PLANT BIOTECHNOLOGY JOURNAL 2019; 17:736-749. [PMID: 30191657 PMCID: PMC6419582 DOI: 10.1111/pbi.13011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 08/26/2018] [Accepted: 09/04/2018] [Indexed: 05/16/2023]
Abstract
Seed size/weight is one of the key traits related to plant domestication and crop improvement. In rapeseed (Brassica napus L.) germplasm, seed weight shows extensive variation, but its regulatory mechanism is poorly understood. To identify the key mechanism of seed weight regulation, a systematic comparative study was performed. Genetic, morphological and cytological evidence showed that seed weight was controlled by maternal genotype, through the regulation of seed size mainly via cell number. The physiological evidence indicated that differences in the pod length might result in differences in pod wall photosynthetic area, carbohydrates and the final seed weight. We also identified two pleiotropic major quantitative trait loci that acted indirectly on seed weight via their effects on pod length. RNA-seq results showed that genes related to pod development and hormones were significantly differentially expressed in the pod wall; genes related to development, cell division, nutrient reservoir and ribosomal proteins were all up-regulated in the seeds of the large-seed pool. Finally, we proposed a potential seed weight regulatory mechanism that is specific to rapeseed and novel in plants. The results demonstrate a causal link between the size of the pod (mother, source) and the seed (offspring, sink) in rapeseed, which provides novel insight into the maternal control of seed weight and will open a new research field in plants.
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Affiliation(s)
- Na Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
- Zhengzhou Fruit Research Institute of the Chinese Academy of Agricultural SciencesThe Laboratory of Melon CropsZhengzhouHenan ProvinceChina
| | - Dongji Song
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Wei Peng
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Jiepeng Zhan
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Jiaqin Shi
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Guihua Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhanHubei ProvinceChina
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14
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Yu A, Wang Z, Zhang Y, Li F, Liu A. Global Gene Expression of Seed Coat Tissues Reveals a Potential Mechanism of Regulating Seed Size Formation in Castor Bean. Int J Mol Sci 2019; 20:E1282. [PMID: 30875738 PMCID: PMC6471003 DOI: 10.3390/ijms20061282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 01/19/2023] Open
Abstract
The physiological and molecular basis of seed size formation is complex, and the development of seed coat (derived from integument cells) might be a critical factor that determines seed size formation for many endospermic seeds. Castor bean (Ricinus communis L.), a model system of studying seed biology, has large and persistent endosperm with a hard seed coat at maturity. Here, we investigated the potential molecular mechanisms underlying seed size formation in castor bean by comparing the difference between global gene expression within developing seed coat tissues between the large-seed ZB107 and small-seed ZB306. First, we observed the cell size of seed coat and concluded that the large seed coat area of ZB107 resulted from more cell numbers (rather than cell size). Furthermore, we found that the lignin proportion of seed coat was higher in ZB306. An investigation into global gene expression of developing seed coat tissues revealed that 815 genes were up-regulated and 813 were down-regulated in ZB306 relative to ZB107. Interestingly, we found that many genes involved in regulating cell division were up-regulated in ZB107, whereas many genes involved in regulating lignin biosynthesis (including several NAC members, as well as MYB46/83 and MYB58/63) and in mediating programmed cell death (such as CysEP1 and βVPE) were up-regulated in ZB306. Furthermore, the expression patterns of the genes mentioned above indicated that the lignification of seed coat tissues was enhanced and occurred earlier in the developing seeds of ZB306. Taken together, we tentatively proposed a potential scenario for explaining the molecular mechanisms of seed coat governing seed size formation in castor bean by increasing the cell number and delaying the onset of lignification in seed coat tissues in large-seed ZB107. This study not only presents new information for possible modulation of seed coat related genes to improve castor seed yield, but also provides new insights into understanding the molecular basis of seed size formation in endospermic seeds with hard seed coat.
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Affiliation(s)
- Anmin Yu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
- University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Zaiqing Wang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
- University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Yang Zhang
- Jiangxi Province Key Laboratory of Oil Crops Biology, Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China.
| | - Fei Li
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.
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15
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Brinton J, Uauy C. A reductionist approach to dissecting grain weight and yield in wheat. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:337-358. [PMID: 30421518 PMCID: PMC6492019 DOI: 10.1111/jipb.12741] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/07/2018] [Indexed: 05/20/2023]
Abstract
Grain yield is a highly polygenic trait that is influenced by the environment and integrates events throughout the life cycle of a plant. In wheat, the major grain yield components often present compensatory effects among them, which alongside the polyploid nature of wheat, makes their genetic and physiological study challenging. We propose a reductionist and systematic approach as an initial step to understand the gene networks regulating each individual yield component. Here, we focus on grain weight and discuss the importance of examining individual sub-components, not only to help in their genetic dissection, but also to inform our mechanistic understanding of how they interrelate. This knowledge should allow the development of novel combinations, across homoeologs and between complementary modes of action, thereby advancing towards a more integrated strategy for yield improvement. We argue that this will break barriers in terms of phenotypic variation, enhance our understanding of the physiology of yield, and potentially deliver improved on-farm yield.
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Affiliation(s)
- Jemima Brinton
- John Innes CentreNorwich Research ParkNorwich NR4 7UHUnited Kingdom
| | - Cristobal Uauy
- John Innes CentreNorwich Research ParkNorwich NR4 7UHUnited Kingdom
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16
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Castillo FM, Canales J, Claude A, Calderini DF. Expansin genes expression in growing ovaries and grains of sunflower are tissue-specific and associate with final grain weight. BMC PLANT BIOLOGY 2018; 18:327. [PMID: 30514222 PMCID: PMC6280438 DOI: 10.1186/s12870-018-1535-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 11/19/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Grain weight (GW) is a key component of sunflower yield and quality, but may be limited by maternal tissues. Cell growth is influenced by expansin proteins that loosen the plant cell wall. This study aimed to identify spatio-temporal expression of EXPN genes in sunflower reproductive organ tissues (ovary, pericarp, and embryo) and evaluate correlations between reproductive organ growth and expansin genes expression. Evaluations involved eight different developmental stages, two genotypes, two source-sink treatments and two experiments. The genotypes evaluated are contrasting in GW (Alybro and confection variety RHA280) under two source-sink treatments (control and shaded) to study the interactions between grain growth and expansin genes expression. RESULTS Ovaries and grains were sampled at pre- and post-anthesis, respectively. Final GW differed between genotypes and shading treatments. Shading treatment decreased final GW by 16.4 and 19.5% in RHA280 and Alybro, respectively. Relative expression of eight expansin genes were evaluated in grain tissues. EXPN4 was the most abundant expansin in the ovary tissue, while EXPN10 and EXPN7 act predominantly in ovary and pericarp tissues, and EXPN1 and EXPN15 in the embryo tissues. CONCLUSIONS Specific expansin genes were expressed in ovary, pericarp and embryo in a tissue-specific manner. Differential expression among grain tissues was consistent between genotypes, source-sink treatments and experiments. The correlation analysis suggests that EXPN genes could be specifically involved in grain tissue extension, and their expression could be linked to grain size in sunflower.
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Affiliation(s)
- Francisca M. Castillo
- Graduate School, Faculty of Agricultural Sciences, Universidad Austral de Chile, Valdivia, Chile
- Plant Production and Plant Protection Institute, Faculty of Agricultural Sciences, Universidad Austral de Chile, Valdivia, Chile
| | - Javier Canales
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Alejandro Claude
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia, Chile
| | - Daniel F. Calderini
- Plant Production and Plant Protection Institute, Faculty of Agricultural Sciences, Universidad Austral de Chile, Valdivia, Chile
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17
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Ma J, Zhang D, Cao Y, Wang L, Li J, Lübberstedt T, Wang T, Li Y, Li H. Heterosis-related genes under different planting densities in maize. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5077-5087. [PMID: 30085089 DOI: 10.1093/jxb/ery282] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/23/2018] [Indexed: 05/23/2023]
Abstract
Heterosis and increasing planting density have contributed to improving maize grain yield (GY) for several decades. As planting densities increase, the GY per plot also increases, whereas the contribution of heterosis to GY decreases. There are trade-offs between heterosis and planting density, and the transcriptional characterization of heterosis may explain the mechanism involved. In this study, 48 transcriptome libraries were sequenced from four inbred Chinese maize lines and their F1 hybrids. They were planted at densities of 45000 and 67500 plants ha-1. Maternal-effect differentially expressed genes (DEGs) played important roles in processes related to photosynthesis and carbohydrate biosynthesis and metabolism. Paternal-effect DEGs participated in abiotic/biotic stress response and plant hormone production under high planting density. Weighted gene co-expression network analysis revealed that high planting density induced heterosis-related genes regulating abiotic/biotic stress response, plant hormone biosynthesis, and ubiquitin-mediated proteolysis, but repressed other genes regulating energy formation. Under high planting density, maternal genes were mainly enriched in the photosynthesis reaction center, while paternal genes were mostly concentrated in the peripheral antenna system. Four important genes were identified in maize heterosis and high planting density, all with functions in photosynthesis, starch biosynthesis, auxin metabolism, gene silencing, and RNAi.
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Affiliation(s)
- Juan Ma
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, PR China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Yanyong Cao
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, PR China
| | - Lifeng Wang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, PR China
| | - Jingjing Li
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, PR China
| | | | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Huiyong Li
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, PR China
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18
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Bergareche D, Royo J, Muñiz LM, Hueros G. Cell wall invertase activity regulates the expression of the transfer cell-specific transcription factor ZmMRP-1. PLANTA 2018; 247:429-442. [PMID: 29071379 DOI: 10.1007/s00425-017-2800-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 10/18/2017] [Indexed: 05/08/2023]
Abstract
Studies in cell wall bound invertase mutants indicate that the promoter of the transfer cell-specific transcription factor, ZmMRP - 1 , is modulated by the carbohydrate balance. Transfer cells are highly specialized plant cells located at the surfaces that need to support an intensive exchange of nutrients, such as the entrance of fruits, seeds and nodules or the young branching points along the stem. ZmMRP-1 is a one-domain MYB-related transcription factor specifically expressed at the transfer cell layer of the maize endosperm. Previous studies demonstrated that this factor regulates the expression of a large number of transfer cell-specific genes, and suggested that ZmMRP-1 is a key regulator of the differentiation of this tissue. The expression of this gene is largely dominated by positional cues, but within the ZmMRP-1 expressing cells the promoter appears to be modulated by sugars. Here we have investigated in vivo this modulation. Using maize and Arabidopsis mutants for cell wall invertase genes, we found that the absence of cell wall invertase activity is a major inductive signal of the ZmMRP-1 expression.
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Affiliation(s)
- Diego Bergareche
- Dpto. Biomedicina y Biotecnología, Universidad de Alcalá, Campus Universitario, Alcalá de Henares, 28805, Madrid, Spain
| | - Joaquín Royo
- Dpto. Biomedicina y Biotecnología, Universidad de Alcalá, Campus Universitario, Alcalá de Henares, 28805, Madrid, Spain
| | - Luis M Muñiz
- Dpto. Biomedicina y Biotecnología, Universidad de Alcalá, Campus Universitario, Alcalá de Henares, 28805, Madrid, Spain
| | - Gregorio Hueros
- Dpto. Biomedicina y Biotecnología, Universidad de Alcalá, Campus Universitario, Alcalá de Henares, 28805, Madrid, Spain.
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19
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Noble TJ, Tao Y, Mace ES, Williams B, Jordan DR, Douglas CA, Mundree SG. Characterization of Linkage Disequilibrium and Population Structure in a Mungbean Diversity Panel. FRONTIERS IN PLANT SCIENCE 2018; 8:2102. [PMID: 29375590 PMCID: PMC5770403 DOI: 10.3389/fpls.2017.02102] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/27/2017] [Indexed: 05/28/2023]
Abstract
Mungbean [Vigna radiata (L.) R. Wilczek var. radiata] is an important grain legume globally, providing a high-quality plant protein source largely produced and consumed in South and East Asia. This study aimed to characterize a mungbean diversity panel consisting of 466 cultivated accessions and demonstrate its utility by conducting a pilot genome-wide association study of seed coat color. In addition 16 wild accessions were genotyped for comparison and in total over 22,000 polymorphic genome-wide SNPs were identified and used to analyze the genetic diversity, population structure, linkage disequilibrium (LD) of mungbean. Polymorphism was lower in the cultivated accessions in comparison to the wild accessions, with average polymorphism information content values 0.174, versus 0.305 in wild mungbean. LD decayed in ∼100 kb in cultivated lines, a distance higher than the linkage decay of ∼60 kb estimated in wild mungbean. Four distinct subgroups were identified within the cultivated lines, which broadly corresponded to geographic origin and seed characteristics. In a pilot genome-wide association mapping study of seed coat color, five genomic regions associated were identified, two of which were close to seed coat color genes in other species. This mungbean diversity panel constitutes a valuable resource for genetic dissection of important agronomical traits to accelerate mungbean breeding.
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Affiliation(s)
- Thomas J. Noble
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, Australia
| | - Emma S. Mace
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, Australia
| | - Brett Williams
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - David R. Jordan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, Australia
| | - Colin A. Douglas
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, Australia
| | - Sagadevan G. Mundree
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
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20
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Xie G, Li Z, Ran Q, Wang H, Zhang J. Over-expression of mutated ZmDA1 or ZmDAR1 gene improves maize kernel yield by enhancing starch synthesis. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:234-244. [PMID: 28557341 PMCID: PMC5785342 DOI: 10.1111/pbi.12763] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 05/13/2017] [Accepted: 05/23/2017] [Indexed: 05/03/2023]
Abstract
Grain weight and grain number are important crop yield determinants. DA1 and DAR1 are the ubiquitin receptors that function as the negative regulators of cell proliferation during development in Arabidopsis. An arginine to lysine mutant at amino acid site 358 could lead to the da1-1 phenotype, which results in an increased organ size and larger seeds. In this study, the mutated ZmDA1 (Zmda1) and mutated ZmDAR1 (Zmdar1) driven by the maize ubiquitin promoter were separately introduced into maize elite inbred line DH4866. The grain yield of the transgenic plants was 15% greater than that of the wild-type in 3 years of field trials due to improvements in the grain number, weight and starch content. Interestingly, the over-expression of Zmda1 and Zmdar1 promoted kernel development, resulting in a more developed basal endosperm transfer cell layer (BETL) than WT and enhanced expression of starch synthase genes. This study suggests that the over-expression of the mutated ZmDA1 or ZmDAR1 genes improves the sugar imports into the sink organ and starch synthesis in maize kernels.
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Affiliation(s)
- Guangning Xie
- School of Life SciencesShandong UniversityJinanShandongChina
| | - Zhaoxia Li
- School of Life SciencesShandong UniversityJinanShandongChina
| | - Qijun Ran
- School of Life SciencesShandong UniversityJinanShandongChina
| | - Hui Wang
- School of Life SciencesShandong UniversityJinanShandongChina
| | - Juren Zhang
- School of Life SciencesShandong UniversityJinanShandongChina
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21
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Hernández-Terán A, Wegier A, Benítez M, Lira R, Escalante AE. Domesticated, Genetically Engineered, and Wild Plant Relatives Exhibit Unintended Phenotypic Differences: A Comparative Meta-Analysis Profiling Rice, Canola, Maize, Sunflower, and Pumpkin. FRONTIERS IN PLANT SCIENCE 2017; 8:2030. [PMID: 29259610 PMCID: PMC5723393 DOI: 10.3389/fpls.2017.02030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/14/2017] [Indexed: 05/29/2023]
Abstract
Agronomic management of plants is a powerful evolutionary force acting on their populations. The management of cultivated plants is carried out by the traditional process of human selection or plant breeding and, more recently, by the technologies used in genetic engineering (GE). Even though crop modification through GE is aimed at specific traits, it is possible that other non-target traits can be affected by genetic modification due to the complex regulatory processes of plant metabolism and development. In this study, we conducted a meta-analysis profiling the phenotypic consequences of plant breeding and GE, and compared modified cultivars with wild relatives in five crops of global economic and cultural importance: rice, maize, canola, sunflower, and pumpkin. For these five species, we analyzed the literature with documentation of phenotypic traits that are potentially related to fitness for the same species in comparable conditions. The information was analyzed to evaluate whether the different processes of modification had influenced the phenotype in such a way as to cause statistical differences in the state of specific phenotypic traits or grouping of the organisms depending on their genetic origin [wild, domesticated with genetic engineering (domGE), and domesticated without genetic engineering (domNGE)]. In addition, we tested the hypothesis that, given that transgenic plants are a construct designed to impact, in many cases, a single trait of the plant (e.g., lepidopteran resistance), the phenotypic differences between domGE and domNGE would be either less (or inexistent) than between the wild and domesticated relatives (either domGE or domNGE). We conclude that (1) genetic modification (either by selective breeding or GE) can be traced phenotypically when comparing wild relatives with their domesticated relatives (domGE and domNGE) and (2) the existence and the magnitude of the phenotypic differences between domGE and domNGE of the same crop suggest consequences of genetic modification beyond the target trait(s).
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Affiliation(s)
- Alejandra Hernández-Terán
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ana Wegier
- Laboratorio de Genética de la Conservación, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rafael Lira
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ana E. Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Gehring M, Satyaki PR. Endosperm and Imprinting, Inextricably Linked. PLANT PHYSIOLOGY 2017; 173:143-154. [PMID: 27895206 PMCID: PMC5210735 DOI: 10.1104/pp.16.01353] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/22/2016] [Indexed: 05/21/2023]
Abstract
Recent developments advance our understanding of imprinted gene expression in plants.
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Affiliation(s)
- Mary Gehring
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142 (M.G., P.R.S.); and
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (M.G.)
| | - P R Satyaki
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142 (M.G., P.R.S.); and
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (M.G.)
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