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Niccolò T, Anderson AW, Emidio A. Apomixis: oh, what a tangled web we have! PLANTA 2023; 257:92. [PMID: 37000270 PMCID: PMC10066125 DOI: 10.1007/s00425-023-04124-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Apomixis is a complex evolutionary trait with many possible origins. Here we discuss various clues and causes, ultimately proposing a model harmonizing the three working hypotheses on the topic. Asexual reproduction through seeds, i.e., apomixis, is the holy grail of plant biology. Its implementation in modern breeding could be a game-changer for agriculture. It has the potential to generate clonal crops and maintain valuable complex genotypes and their associated heterotic traits without inbreeding depression. The genetic basis and origins of apomixis are still unclear. There are three central hypothesis for the development of apomixis that could be: i) a deviation from the sexual developmental program caused by an asynchronous development, ii) environmentally triggered through epigenetic regulations (a polyphenism of sex), iii) relying on one or more genes/alleles. Because of the ever-increasing complexity of the topic, the path toward a detailed understanding of the mechanisms underlying apomixis remains unclear. Here, we discuss the most recent advances in the evolution perspective of this multifaceted trait. We incorporated our understanding of the effect of endogenous effectors, such as small RNAs, epigenetic regulation, hormonal pathways, protein turnover, and cell wall modification in response to an upside stress. This can be either endogenous (hybridization or polyploidization) or exogenous environmental stress, mainly due to oxidative stress and the corresponding ROS (Reacting Oxygen Species) effectors. Finally, we graphically represented this tangled web.
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Affiliation(s)
- Terzaroli Niccolò
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy.
| | - Aaron W Anderson
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
- Fulbright Scholar From Department of Plant Sciences, University of California, Davis, USA
| | - Albertini Emidio
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
- Consorzio Interuniversitario per le Biotecnologie (CIB), Trieste, Italy
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Carballo J, Bellido AM, Selva JP, Zappacosta D, Gallo CA, Albertini E, Caccamo M, Echenique V. From tetraploid to diploid, a pangenomic approach to identify genes lost during synthetic diploidization of Eragrostis curvula. FRONTIERS IN PLANT SCIENCE 2023; 14:1133986. [PMID: 36993842 PMCID: PMC10040859 DOI: 10.3389/fpls.2023.1133986] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/24/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION In Eragrostis curvula, commonly known as weeping lovegrass, a synthetic diploidization event of the facultative apomictic tetraploid Tanganyika INTA cv. originated from the sexual diploid Victoria cv. Apomixis is an asexual reproduction by seeds in which the progeny is genetically identical to the maternal plant. METHODS To assess the genomic changes related to ploidy and to the reproductive mode occurring during diploidization, a mapping approach was followed to obtain the first E. curvula pangenome assembly. In this way, gDNA of Tanganyika INTA was extracted and sequenced in 2x250 Illumina pair-end reads and mapped against the Victoria genome assembly. The unmapped reads were used for variant calling, while the mapped reads were assembled using Masurca software. RESULTS The length of the assembly was 28,982,419 bp distributed in 18,032 contigs, and the variable genes annotated in these contigs rendered 3,952 gene models. Functional annotation of the genes showed that the reproductive pathway was differentially enriched. PCR amplification in gDNA and cDNA of Tanganyika INTA and Victoria was conducted to validate the presence/absence variation in five genes related to reproduction and ploidy. The polyploid nature of the Tanganyika INTA genome was also evaluated through the variant calling analysis showing the single nucleotide polymorphism (SNP) coverage and allele frequency distribution with a segmental allotetraploid pairing behavior. DISCUSSION The results presented here suggest that the genes were lost in Tanganyika INTA during the diploidization process that was conducted to suppress the apomictic pathway, affecting severely the fertility of Victoria cv.
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Affiliation(s)
- Jose Carballo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
| | - Andrés Martin Bellido
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
| | - Juan Pablo Selva
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - Diego Zappacosta
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - Cristian Andres Gallo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
| | - Emidio Albertini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | | | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
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Yang X, Wilkinson LG, Aubert MK, Houston K, Shirley NJ, Tucker MR. Ovule cell wall composition is a maternal determinant of grain size in barley. THE NEW PHYTOLOGIST 2023; 237:2136-2147. [PMID: 36600397 DOI: 10.1111/nph.18714] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
In cereal species, grain size is influenced by growth of the ovule integuments (seed coat), the spikelet hull (lemma and palea) and the filial endosperm. Whether a highly conserved ovule tissue, the nucellus, has any impact on grain size has remained unclear. Immunolabelling revealed that the barley nucellus comprises two distinct cell types that differ in terms of cell wall homogalacturonan (HG) accumulation. Transcriptional profiling of the nucellus identified two pectin methylesterase (PME) genes, OVULE PECTIN MODIFIER 1 (OPM1) and OPM2, which are expressed in the unfertilized ovule but absent from the seed. Ovules from an opm1 opm2 mutant and plants expressing an ovule-specific pectin methylesterase inhibitor (PMEI), exhibit reduced HG accumulation. This results in changes to ovule cell size and shape and ovules that are longer than wild-type (WT) controls. At grain maturity, this is manifested as significantly longer grain. These findings indicate that cell wall composition during ovule development acts to limit ovule and seed growth. The investigation of ovule PME and PMEI activity reveals an unexpected role of maternal tissues in controlling grain growth before fertilization, one that has been lacking from models exploring improvements in grain size.
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Affiliation(s)
- Xiujuan Yang
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Laura G Wilkinson
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Matthew K Aubert
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
- Australian Grain Technologies, 100 Byfield Street, Northam, WA, 6401, Australia
| | - Kelly Houston
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Neil J Shirley
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Matthew R Tucker
- Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, 5064, Australia
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Synthetic apomixis: the beginning of a new era. Curr Opin Biotechnol 2023; 79:102877. [PMID: 36628906 DOI: 10.1016/j.copbio.2022.102877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/24/2022] [Accepted: 12/05/2022] [Indexed: 01/11/2023]
Abstract
Apomixis is a process of asexual reproduction that enables plants to bypass meiosis and fertilization to generate clonal seeds that are identical to the maternal genotype. Apomixis has tremendous potential for breeding plants with desired characteristics, given its ability to fix any elite genotype. However, little is known about the origin and dynamics of natural apomictic plant systems. The introgression of apomixis-related genes from natural apomicts has achieved limited success. Therefore, synthetic apomixis, engineered to include apomeiosis, autonomous embryo formation, and autonomous endosperm development, has been proposed as a promising platform to effectuate apomixis in any crop. In this study, we have summarized recent advances in the understanding of synthetic apomixis and discussed the limitations of current synthetic apomixis systems and ways to overcome them.
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Bird DC, Ma C, Pinto S, Leong WH, Tucker MR. Genetic and Phenotypic Analysis of Ovule Development in Arabidopsis. Methods Mol Biol 2023; 2686:261-281. [PMID: 37540362 DOI: 10.1007/978-1-0716-3299-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The plant seed is a remarkable structure that represents the single most important energy source in global diets. The stages of reproductive growth preceding seed formation are particularly important since they influence the number, size, and quality of seed produced. The progenitor of the seed is the ovule, a multicellular organ that produces a female gametophyte while maintaining a range of somatic ovule cells to protect the seed and ensure it receives maternal nourishment. Ovule development has been well characterized in Arabidopsis using a range of molecular, genetic, and cytological assays. These can provide insight into the mechanistic basis for ovule development, and opportunities to explore its evolutionary conservation. In this chapter, we describe some of these methods and tools that can be used to investigate early ovule development and cell differentiation.
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Affiliation(s)
- Dayton C Bird
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
| | - Chao Ma
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
| | - Sara Pinto
- LAQV REQUIMTE, Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Weng Herng Leong
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
| | - Matthew R Tucker
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia.
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Jia HH, Xu YT, Yin ZP, Wu XM, Qing M, Fan YJ, Song X, Xie KD, Xie ZZ, Xu Q, Deng XX, Guo WW. Transcriptomes and DNA methylomes in apomictic cells delineate nucellar embryogenesis initiation in citrus. DNA Res 2021; 28:6356518. [PMID: 34424285 PMCID: PMC8476932 DOI: 10.1093/dnares/dsab014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022] Open
Abstract
Citrus nucellar poly-embryony (NPE) is a mode of sporophytic apomixis that asexual embryos formed in the seed through adventitious embryogenesis from the somatic nucellar cells. NPE allows clonal propagation of rootstocks, but it impedes citrus cross breeding. To understand the cellular processes involved in NPE initiation, we profiled the transcriptomes and DNA methylomes in laser microdissection captured citrus apomictic cells. In apomictic cells, ribosome biogenesis and protein degradation were activated, whereas auxin polar transport was repressed. Reactive oxygen species (ROS) accumulated in the poly-embryonic ovules, and response to oxidative stress was provoked. The global DNA methylation level, especially that of CHH context, was decreased, whereas the methylation level of the NPE-controlling key gene CitRWP was increased. A C2H2 domain-containing transcription factor gene and CitRWP co-expressed specifically in apomictic cells may coordinate to initiate NPE. The activated embryogenic development and callose deposition processes indicated embryogenic fate of nucellar embryo initial (NEI) cells. In our working model for citrus NPE initiation, DNA hyper-methylation may activate transcription of CitRWP, which increases C2H2 expression and ROS accumulation, triggers epigenetic regulation and regulates cell fate transition and NEI cell identity in the apomictic cells.
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Affiliation(s)
- Hui-Hui Jia
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuan-Tao Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhao-Ping Yin
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiao-Meng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mei Qing
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yan-Jie Fan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Song
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kai-Dong Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zong-Zhou Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiu-Xin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
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Janas AB, Szeląg Z, Musiał K. In search of female sterility causes in the tetraploid and pentaploid cytotype of Pilosella brzovecensis (Asteraceae). JOURNAL OF PLANT RESEARCH 2021; 134:803-810. [PMID: 33813645 PMCID: PMC8245384 DOI: 10.1007/s10265-021-01290-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Within the agamic Pilosella complex, apomixis (asexual reproduction through seed) involves apospory, parthenogenesis, and autonomous endosperm development. Observations of reproductive biology in P. brzovecensis throughout four growing seasons in the garden have shown that both tetraploid and pentaploid plants of this species do not produce viable seeds and reproduce exclusively vegetatively by underground stolons. The reasons for the seed development failure were unknown, therefore our research focused on the analysis of reproductive events in the ovules of this taxon. We found that apospory was initiated in the ovules of both cytotypes. Multiple aposporous initial (AI) cells differentiated in close proximity to the megaspore mother cell (MMC) and suppressed megasporogenesis at the stage of early prophase I. However, none of the AI cells was able to further develop into a multi-nucleate aposporous embryo sac (AES) due to the inhibition of mitotic divisions. It was unusual that callose was accumulated in the walls of AI cells and its synthesis was most likely associated with a response to the dysfunction of these cells. Callose is regarded as the isolating factor and its surprising deposition in the ovules of P. brzovecensis may signal disruption of reproductive processes that cause premature termination of the aposporous development pathway and ultimately lead to ovule sterility. The results of our embryological analysis may be the basis for undertaking advanced molecular studies aimed at fully understanding of the causes of female sterility in P. brzovecensis.
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Affiliation(s)
- Agnieszka Barbara Janas
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Gronostajowa 9, 30-387, Cracow, Poland.
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Cracow, Poland.
| | - Zbigniew Szeląg
- Institute of Biology, Pedagogical University of Cracow, Podchorążych 2, 30-084, Cracow, Poland
| | - Krystyna Musiał
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Gronostajowa 9, 30-387, Cracow, Poland
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Carballo J, Zappacosta D, Marconi G, Gallardo J, Di Marsico M, Gallo CA, Caccamo M, Albertini E, Echenique V. Differential Methylation Patterns in Apomictic vs. Sexual Genotypes of the Diplosporous Grass Eragrostis curvula. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10050946. [PMID: 34068493 PMCID: PMC8150776 DOI: 10.3390/plants10050946] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 05/05/2023]
Abstract
DNA methylation is an epigenetic mechanism by which a methyl group is added to a cytosine or an adenine. When located in a gene/regulatory sequence it may repress or de-repress genes, depending on the context and species. Eragrostis curvula is an apomictic grass in which facultative genotypes increases the frequency of sexual pistils triggered by epigenetic mechanisms. The aim of the present study was to look for correlations between the reproductive mode and specific methylated genes or genomic regions. To do so, plants with contrasting reproductive modes were investigated through MCSeEd (Methylation Context Sensitive Enzyme ddRad) showing higher levels of DNA methylation in apomictic genotypes. Moreover, an increased proportion of differentially methylated positions over the regulatory regions were observed, suggesting its possible role in regulation of gene expression. Interestingly, the methylation pathway was also found to be self-regulated since two of the main genes (ROS1 and ROS4), involved in de-methylation, were found differentially methylated between genotypes with different reproductive behavior. Moreover, this work allowed us to detect several genes regulated by methylation that were previously found as differentially expressed in the comparisons between apomictic and sexual genotypes, linking DNA methylation to differences in reproductive mode.
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Affiliation(s)
- Jose Carballo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, 8000 Bahía Blanca, Argentina; (J.C.); (D.Z.); (J.G.); (C.A.G.)
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000 Bahía Blanca, Argentina
| | - Diego Zappacosta
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, 8000 Bahía Blanca, Argentina; (J.C.); (D.Z.); (J.G.); (C.A.G.)
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000 Bahía Blanca, Argentina
| | - Gianpiero Marconi
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, 06121 Perugia, Italy; (G.M.); (M.D.M.)
| | - Jimena Gallardo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, 8000 Bahía Blanca, Argentina; (J.C.); (D.Z.); (J.G.); (C.A.G.)
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000 Bahía Blanca, Argentina
| | - Marco Di Marsico
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, 06121 Perugia, Italy; (G.M.); (M.D.M.)
| | - Cristian A. Gallo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, 8000 Bahía Blanca, Argentina; (J.C.); (D.Z.); (J.G.); (C.A.G.)
| | - Mario Caccamo
- NIAB, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK;
| | - Emidio Albertini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, 06121 Perugia, Italy; (G.M.); (M.D.M.)
- Correspondence: (E.A.); (V.E.); Tel.: +39-075-585-6206 (E.A.); +54-291-486-1124 (V.E.)
| | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS–CCT–CONICET Bahía Blanca), Camino de la Carrindanga km 7, 8000 Bahía Blanca, Argentina; (J.C.); (D.Z.); (J.G.); (C.A.G.)
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000 Bahía Blanca, Argentina
- Correspondence: (E.A.); (V.E.); Tel.: +39-075-585-6206 (E.A.); +54-291-486-1124 (V.E.)
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Ke Y, Podio M, Conner J, Ozias-Akins P. Single-cell transcriptome profiling of buffelgrass (Cenchrus ciliaris) eggs unveils apomictic parthenogenesis signatures. Sci Rep 2021; 11:9880. [PMID: 33972603 PMCID: PMC8110759 DOI: 10.1038/s41598-021-89170-y] [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: 02/11/2021] [Accepted: 04/15/2021] [Indexed: 12/04/2022] Open
Abstract
Apomixis, a type of asexual reproduction in angiosperms, results in progenies that are genetically identical to the mother plant. It is a highly desirable trait in agriculture due to its potential to preserve heterosis of F1 hybrids through subsequent generations. However, no major crops are apomictic. Deciphering mechanisms underlying apomixis becomes one of the alternatives to engineer self-reproducing capability into major crops. Parthenogenesis, a major component of apomixis, commonly described as the ability to initiate embryo formation from the egg cell without fertilization, also can be valuable in plant breeding for doubled haploid production. A deeper understanding of transcriptional differences between parthenogenetic and sexual or non-parthenogenetic eggs can assist with pathway engineering. By conducting laser capture microdissection-based RNA-seq on sexual and parthenogenetic egg cells on the day of anthesis, a de novo transcriptome for the Cenchrus ciliaris egg cells was created, transcriptional profiles that distinguish the parthenogenetic egg from its sexual counterpart were identified, and functional roles for a few transcription factors in promoting natural parthenogenesis were suggested. These transcriptome data expand upon previous gene expression studies and will be a resource for future research on the transcriptome of egg cells in parthenogenetic and sexual genotypes.
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Affiliation(s)
- Yuji Ke
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, 31793, USA
| | - Maricel Podio
- Department of Horticulture, University of Georgia, Tifton, GA, 31793, USA
| | - Joann Conner
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, 31793, USA.,Department of Horticulture, University of Georgia, Tifton, GA, 31793, USA
| | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, 31793, USA. .,Department of Horticulture, University of Georgia, Tifton, GA, 31793, USA.
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A study of the heterochronic sense/antisense RNA representation in florets of sexual and apomictic Paspalum notatum. BMC Genomics 2021; 22:185. [PMID: 33726667 PMCID: PMC7962388 DOI: 10.1186/s12864-021-07450-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/18/2021] [Indexed: 11/10/2022] Open
Abstract
Background Apomixis, an asexual mode of plant reproduction, is a genetically heritable trait evolutionarily related to sexuality, which enables the fixation of heterozygous genetic combinations through the development of maternal seeds. Recently, reference floral transcriptomes were generated from sexual and apomictic biotypes of Paspalum notatum, one of the most well-known plant models for the study of apomixis. However, the transcriptome dynamics, the occurrence of apomixis vs. sexual expression heterochronicity across consecutive developmental steps and the orientation of transcription (sense/antisense) remain unexplored. Results We produced 24 Illumina TruSeq®/ Hiseq 1500 sense/antisense floral transcriptome libraries covering four developmental stages (premeiosis, meiosis, postmeiosis, and anthesis) in biological triplicates, from an obligate apomictic and a full sexual genotype. De novo assemblies with Trinity yielded 103,699 and 100,114 transcripts for the apomictic and sexual samples respectively. A global comparative analysis involving reads from all developmental stages revealed 19,352 differentially expressed sense transcripts, of which 13,205 (68%) and 6147 (32%) were up- and down-regulated in apomictic samples with respect to the sexual ones. Interestingly, 100 differentially expressed antisense transcripts were detected, 55 (55%) of them up- and 45 (45%) down-regulated in apomictic libraries. A stage-by-stage comparative analysis showed a higher number of differentially expressed candidates due to heterochronicity discrimination: the highest number of differential sense transcripts was detected at premeiosis (23,651), followed by meiosis (22,830), postmeiosis (19,100), and anthesis (17,962), while the highest number of differential antisense transcripts were detected at anthesis (495), followed by postmeiosis (164), meiosis (120) and premeiosis (115). Members of the AP2, ARF, MYB and WRKY transcription factor families, as well as the auxin, jasmonate and cytokinin plant hormone families appeared broadly deregulated. Moreover, the chronological expression profile of several well-characterized apomixis controllers was examined in detail. Conclusions This work provides a quantitative sense/antisense gene expression catalogue covering several subsequent reproductive developmental stages from premeiosis to anthesis for apomictic and sexual P. notatum, with potential to reveal heterochronic expression between reproductive types and discover sense/antisense mediated regulation. We detected a contrasting transcriptional and hormonal control in apomixis and sexuality as well as specific sense/antisense modulation occurring at the onset of parthenogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07450-3.
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Xu Y, Jia H, Wu X, Koltunow AM, Deng X, Xu Q. Regulation of nucellar embryony, a mode of sporophytic apomixis in Citrus resembling somatic embryogenesis. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:101984. [PMID: 33418404 DOI: 10.1016/j.pbi.2020.101984] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/28/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Apomixis, is an asexual mode of seed formation resulting in genetically identical or clonal seed with a maternal genotype. Apomixis has not been reported in seed crops where its flexible application in plant breeding could accelerate delivery of new varieties. By contrast, a sporophytic form of apomixis termed nucellar or adventitious embryony is common in the Rutaceae containing Citrus crop species. Here, multiple embryos develop from the maternal, somatic, nucellar cells of the ovule. They are incorporated into the enlarging embryo sac containing the sexually derived zygotic embryo and endosperm, which are products of double fertilization. Recent research has provided insights to the molecular basis for nucellar embryony. Here, we review the current understanding of the initiation, genetic basis and evolution of nucellar embryony in Citrus, and discuss prospects for future study and breeding applications of Citrus sporophytic apomixis.
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Affiliation(s)
- Yuantao Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Huihui Jia
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xiaomeng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Anna Mg Koltunow
- Centre for Crop Sciences, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Queensland, 4702, Australia.
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
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12
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Płachno BJ, Kapusta M, Świątek P, Stolarczyk P, Kocki J. Immunodetection of Pectic Epitopes, Arabinogalactan Proteins, and Extensins in Mucilage Cells from the Ovules of Pilosella officinarum Vaill. and Taraxacum officinale Agg. (Asteraceae). Int J Mol Sci 2020; 21:E9642. [PMID: 33348898 PMCID: PMC7766254 DOI: 10.3390/ijms21249642] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022] Open
Abstract
The main aim of this study was to compare the cytological difference between ovular mucilage cells in two Asteraceae species-Pilosella officinarum and Taraxacum officinale-in order to determine whether pectic epitopes, arabinogalactan proteins, or extensins are present. The immunocytochemical technique was used. Both the Taracacum and Pilosella genera have been used recently as models for understanding the mechanisms of apomixis. Knowledge of the presence of signal molecules (pectic epitopes, arabinogalactan proteins, and extensins) can help better understand the developmental processes in these plants during seed growth. The results showed that in Pilosella officinarum, there was an accumulation of pectins in the mucilage, including both weakly and highly esterified pectins, which was in contrast to the mucilage of Taraxacum officinale, which had low amounts of these pectins. However, Taraxacum protoplasts of mucilage cells were rich in weakly methyl-esterified pectins. While the mucilage contained arabinogalactan proteins in both of the studied species, the types of arabinogalactan proteins were different. In both of the studied species, extensins were recorded in the transmitting tissues. Arabinogalactan proteins as well as weakly and highly esterified pectins and extensins occurred in close proximity to calcium oxalate crystals in both Taraxacum and Pilosella cells.
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Affiliation(s)
- Bartosz J. Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, 9 Gronostajowa St., 30-387 Kraków, Poland
| | - Małgorzata Kapusta
- Department of Plant Cytology and Embryology, University of Gdańsk, 59. Wita Stwosza St., 80-308 Gdańsk, Poland;
| | - Piotr Świątek
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 9 Bankowa St., 40-007 Katowice, Poland;
| | - Piotr Stolarczyk
- Department of Botany, Physiology and Plant Protection, Faculty of Biotechnology and Horticulture, University of Agriculture in Kraków, 29 Listopada 54 Ave., 31-425 Kraków, Poland;
| | - Janusz Kocki
- Department of Clinical Genetics, Medical University of Lublin, 11 Radziwiłowska St., 20-080 Lublin, Poland;
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Unequal contribution of two paralogous CENH3 variants in cowpea centromere function. Commun Biol 2020; 3:775. [PMID: 33319863 PMCID: PMC7738545 DOI: 10.1038/s42003-020-01507-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
In most diploids the centromere-specific histone H3 (CENH3), the assembly site of active centromeres, is encoded by a single copy gene. Persistance of two CENH3 paralogs in diploids species raises the possibility of subfunctionalization. Here we analysed both CENH3 genes of the diploid dryland crop cowpea. Phylogenetic analysis suggests that gene duplication of CENH3 occurred independently during the speciation of Vigna unguiculata. Both functional CENH3 variants are transcribed, and the corresponding proteins are intermingled in subdomains of different types of centromere sequences in a tissue-specific manner together with the kinetochore protein CENPC. CENH3.2 is removed from the generative cell of mature pollen, while CENH3.1 persists. CRISPR/Cas9-based inactivation of CENH3.1 resulted in delayed vegetative growth and sterility, indicating that this variant is needed for plant development and reproduction. By contrast, CENH3.2 knockout individuals did not show obvious defects during vegetative and reproductive development. Hence, CENH3.2 of cowpea is likely at an early stage of pseudogenization and less likely undergoing subfunctionalization.
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14
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Hojsgaard D, Schartl M. Skipping sex: A nonrecombinant genomic assemblage of complementary reproductive modules. Bioessays 2020; 43:e2000111. [PMID: 33169369 DOI: 10.1002/bies.202000111] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 02/03/2023]
Abstract
The unusual occurrence and developmental diversity of asexual eukaryotes remain a puzzle. De novo formation of a functioning asexual genome requires a unique assembly of sets of genes or gene states to disrupt cellular mechanisms of meiosis and gametogenesis, and to affect discrete components of sexuality and produce clonal or hemiclonal offspring. We highlight two usually overlooked but essential conditions to understand the molecular nature of clonal organisms, that is, a nonrecombinant genomic assemblage retaining modifiers of the sexual program, and a complementation between altered reproductive components. These subtle conditions are the basis for physiologically viable and genetically balanced transitions between generations. Genomic and developmental evidence from asexual animals and plants indicates the lack of complementation of molecular changes in the sexual reproductive program is likely the main cause of asexuals' rarity, and can provide an explanatory frame for the developmental diversity and lability of developmental patterns in some asexuals as well as for the discordant time to extinction estimations.
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Affiliation(s)
- Diego Hojsgaard
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Goettingen, Germany
| | - Manfred Schartl
- Department of Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany.,The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
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15
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Henderson SW, Henderson ST, Goetz M, Koltunow AMG. Efficient CRISPR/Cas9-Mediated Knockout of an Endogenous PHYTOENE DESATURASE Gene in T1 Progeny of Apomictic Hieracium Enables New Strategies for Apomixis Gene Identification. Genes (Basel) 2020; 11:E1064. [PMID: 32927657 PMCID: PMC7563859 DOI: 10.3390/genes11091064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 12/11/2022] Open
Abstract
Most Hieracium subgenus Pilosella species are self-incompatible. Some undergo facultative apomixis where most seeds form asexually with a maternal genotype. Most embryo sacs develop by mitosis, without meiosis and seeds form without fertilization. Apomixis is controlled by dominant loci where recombination is suppressed. Loci deletion by γ-irradiation results in reversion to sexual reproduction. Targeted mutagenesis of genes at identified loci would facilitate causal gene identification. In this study, the efficacy of CRISPR/Cas9 editing was examined in apomictic Hieracium by targeting mutations in the endogenous PHYTOENE DESATURASE (PDS) gene using Agrobacterium-mediated leaf disk transformation. In three experiments, the expected albino dwarf-lethal phenotype, characteristic of PDS knockout, was evident in 11% of T0 plants, 31.4% were sectorial albino chimeras, and the remainder were green. The chimeric plants flowered. Germinated T1 seeds derived from apomictic reproduction in two chimeric plants were phenotyped and sequenced to identify PDS gene edits. Up to 86% of seeds produced albino seedlings with complete PDS knockout. This was attributed to continuing Cas9-mediated editing in chimeric plants during apomictic seed formation preventing Cas9 segregation from the PDS target. This successful demonstration of efficient CRISPR/Cas9 gene editing in apomictic Hieracium, enabled development of the discussed strategies for future identification of causal apomixis genes.
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Affiliation(s)
- Sam W. Henderson
- Correspondence: (S.W.H.); (A.M.G.K.); Tel.: +61-407-323-260 (A.M.G.K.)
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16
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Genes Modulating the Increase in Sexuality in the Facultative Diplosporous Grass Eragrostis curvula under Water Stress Conditions. Genes (Basel) 2020; 11:genes11090969. [PMID: 32825586 PMCID: PMC7564825 DOI: 10.3390/genes11090969] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 01/23/2023] Open
Abstract
Eragrostis curvula presents mainly facultative genotypes that reproduce by diplosporous apomixis, retaining a percentage of sexual pistils that increase under drought and other stressful situations, indicating that some regulators activated by stress could be affecting the apomixis/sexual switch. Water stress experiments were performed in order to associate the increase in sexual embryo sacs with the differential expression of genes in a facultative apomictic cultivar using cytoembryology and RNA sequencing. The percentage of sexual embryo sacs increased from 4 to 24% and 501 out of the 201,011 transcripts were differentially expressed (DE) between control and stressed plants. DE transcripts were compared with previous transcriptomes where apomictic and sexual genotypes were contrasted. The results point as candidates to transcripts related to methylation, ubiquitination, hormone and signal transduction pathways, transcription regulation and cell wall biosynthesis, some acting as a general response to stress and some that are specific to the reproductive mode. We suggest that a DNA glycosylase EcROS1-like could be demethylating, thus de-repressing a gene or genes involved in the sexuality pathways. Many of the other DE transcripts could be part of a complex mechanism that regulates apomixis and sexuality in this grass, the ones in the intersection between control/stress and apo/sex being the strongest candidates.
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17
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Karunarathne P, Reutemann AV, Schedler M, Glücksberg A, Martínez EJ, Honfi AI, Hojsgaard DH. Sexual modulation in a polyploid grass: a reproductive contest between environmentally inducible sexual and genetically dominant apomictic pathways. Sci Rep 2020; 10:8319. [PMID: 32433575 PMCID: PMC7239852 DOI: 10.1038/s41598-020-64982-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 04/25/2020] [Indexed: 12/24/2022] Open
Abstract
In systems alternating between sexual and asexual reproduction, sex increases under unfavorable environmental conditions. In plants producing sexual and asexual (apomictic) seeds, studies on the influence of environmental factors on sex are equivocal. We used Paspalum intermedium to study environmental effects on the expression of sexual and apomictic developments, and on resulting reproductive fitness variables. Flow cytometric and embryological analyses were performed to characterize ploidy and reproductive modes, and effects of local climatic conditions on sexual and apomictic ovule and seed frequencies were determined. Seed set and germination data were collected and used to estimate reproductive fitness. Frequencies of sexual and apomictic ovules and seeds were highly variable within and among populations. Apomictic development exhibited higher competitive ability but lower overall fitness. Frequencies of sexual reproduction in facultative apomictic plants increased at lower temperatures and wider mean diurnal temperature ranges. We identified a two-fold higher fitness advantage of sexuality and a Tug of War between factors intrinsic to apomixis and environmental stressors promoting sexuality which influence the distribution of sex in apomictic populations. This points toward a crucial role of local ecological conditions in promoting a reshuffling of genetic variability that may be shaping the adaptative landscape in apomictic P. intermedium plants.
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Affiliation(s)
- Piyal Karunarathne
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Untere Karspuele 2, 37073, Goettingen, Germany.
- Georg-August University School of Science, University of Goettingen, Goettingen, Germany.
| | - Anna V Reutemann
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Untere Karspuele 2, 37073, Goettingen, Germany
- Instituto de Botánica del Nordeste (IBONE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste (FCA-UNNE), CC209, 3400, Corrientes, Argentina
| | - Mara Schedler
- Instituto de Botánica del Nordeste (IBONE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste (FCA-UNNE), CC209, 3400, Corrientes, Argentina
| | - Adriana Glücksberg
- Instituto de Botánica del Nordeste (IBONE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste (FCA-UNNE), CC209, 3400, Corrientes, Argentina
| | - Eric J Martínez
- Instituto de Botánica del Nordeste (IBONE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste (FCA-UNNE), CC209, 3400, Corrientes, Argentina
| | - Ana I Honfi
- Programa de Estudios Florísticos y Genética Vegetal, Instituto de Biología Subtropical (CONICET-UNaM), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Rivadavia 2370, 3300, Posadas, Misiones, Argentina
| | - Diego H Hojsgaard
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Untere Karspuele 2, 37073, Goettingen, Germany.
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18
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Hojsgaard D. Apomixis Technology: Separating the Wheat from the Chaff. Genes (Basel) 2020; 11:E411. [PMID: 32290084 PMCID: PMC7231277 DOI: 10.3390/genes11040411] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/03/2020] [Accepted: 04/08/2020] [Indexed: 02/06/2023] Open
Abstract
Projections indicate that current plant breeding approaches will be unable to incorporate the global crop yields needed to deliver global food security. Apomixis is a disruptive innovation by which a plant produces clonal seeds capturing heterosis and gene combinations of elite phenotypes. Introducing apomixis into hybrid cultivars is a game-changing development in the current plant breeding paradigm that will accelerate the generation of high-yield cultivars. However, apomixis is a developmentally complex and genetically multifaceted trait. The central problem behind current constraints to apomixis breeding is that the genomic configuration and molecular mechanism that initiate apomixis and guide the formation of a clonal seed are still unknown. Today, not a single explanation about the origin of apomixis offer full empirical coverage, and synthesizing apomixis by manipulating individual genes has failed or produced little success. Overall evidence suggests apomixis arise from a still unknown single event molecular mechanism with multigenic effects. Disentangling the genomic basis and complex genetics behind the emergence of apomixis in plants will require the use of novel experimental approaches benefiting from Next Generation Sequencing technologies and targeting not only reproductive genes, but also the epigenetic and genomic configurations associated with reproductive phenotypes in homoploid sexual and apomictic carriers. A comprehensive picture of most regulatory changes guiding apomixis emergence will be central for successfully installing apomixis into the target species by exploiting genetic modification techniques.
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Affiliation(s)
- Diego Hojsgaard
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, Georg-August-University of Göttingen, Untere Karspüle 2, D-37073-1 Göttingen, Germany
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19
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Controlling Apomixis: Shared Features and Distinct Characteristics of Gene Regulation. Genes (Basel) 2020; 11:genes11030329. [PMID: 32245021 PMCID: PMC7140868 DOI: 10.3390/genes11030329] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 02/06/2023] Open
Abstract
In higher plants, sexual and asexual reproduction through seeds (apomixis) have evolved as alternative strategies. As apomixis leads to the formation of clonal offspring, its great potential for agricultural applications has long been recognized. However, the genetic basis and the molecular control underlying apomixis and its evolutionary origin are to date not fully understood. Both in sexual and apomictic plants, reproduction is tightly controlled by versatile mechanisms regulating gene expression, translation, and protein abundance and activity. Increasing evidence suggests that interrelated pathways including epigenetic regulation, cell-cycle control, hormonal pathways, and signal transduction processes are relevant for apomixis. Additional molecular mechanisms are being identified that involve the activity of DNA- and RNA-binding proteins, such as RNA helicases which are increasingly recognized as important regulators of reproduction. Together with other factors including non-coding RNAs, their association with ribosomes is likely to be relevant for the formation and specification of the apomictic reproductive lineage. Subsequent seed formation appears to involve an interplay of transcriptional activation and repression of developmental programs by epigenetic regulatory mechanisms. In this review, insights into the genetic basis and molecular control of apomixis are presented, also taking into account potential relations to environmental stress, and considering aspects of evolution.
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20
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Wyder S, Rivera A, Valdés AE, Cañal MJ, Gagliardini V, Fernández H, Grossniklaus U. Differential gene expression profiling of one- and two-dimensional apogamous gametophytes of the fern Dryopteris affinis ssp. affinis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 148:302-311. [PMID: 32000107 DOI: 10.1016/j.plaphy.2020.01.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 12/16/2019] [Accepted: 01/15/2020] [Indexed: 05/01/2023]
Abstract
Apomixis was originally defined as the replacement of sexual reproduction by an asexual process that does not involve fertilization but, in angiosperms, it is often used in the more restricted sense of asexual reproduction through seeds. In ferns, apomixis combines the production of unreduced spores (diplospory) and the formation of sporophytes from somatic cells of the prothallium (apogamy). The genes that control the onset of apogamy in ferns are largely unknown. In this study, we describe the gametophyte transcriptome of the apogamous fern Dryopteris affinis ssp. affinis using an RNA-Seq approach to compare the gene expression profiles of one- and two-dimensional gametophytes, the latter containing apogamic centers. After collapsing highly similar de novo transcripts, we obtained 166,191 unigenes, of which 30% could be annotated using public databases. Multiple quality metrics indicate a good quality of the de novo transcriptome with a low level of fragmentation. Our data show a total of 10,679 genes (6% of all genes) to be differentially expressed between gametophytes of filamentous (one-dimensional) and prothallial (two-dimensional) architecture. 6,110 genes were up-regulated in two-dimensional relative to one-dimensional gametophytes, some of which are implicated in the regulation of meristem growth, auxin signaling, reproduction, and sucrose metabolism. 4,570 genes were down-regulated in two-dimensional versus one-dimensional gametophytes, which are enriched in stimulus and defense genes, as well as genes involved in epigenetic gene regulation and ubiquitin degradation. Our results provide insights into free-living gametophyte development, focusing on the filamentous-to-prothallus growth transition, and provide a useful resource for further investigations of asexual reproduction.
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Affiliation(s)
- Stefan Wyder
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | - Alejandro Rivera
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, c) Catedrático R Uría s/n, 33071, Oviedo, Spain
| | - Ana E Valdés
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - María Jesús Cañal
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, c) Catedrático R Uría s/n, 33071, Oviedo, Spain
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | - Helena Fernández
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, c) Catedrático R Uría s/n, 33071, Oviedo, Spain.
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
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21
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Coexpression and Transcriptome analyses identify active Apomixis-related genes in Paspalum notatum leaves. BMC Genomics 2020; 21:78. [PMID: 31992196 PMCID: PMC6986084 DOI: 10.1186/s12864-020-6518-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 01/20/2020] [Indexed: 11/12/2022] Open
Abstract
Background Paspalum notatum exhibits both sexual and apomictic cytotypes and, thus, is considered a good model for studies of apomixis because it facilitates comparative approaches. In this work, transcriptome sequencing was used to compare contrasting P. notatum cytotypes to identify differential expression patterns and candidate genes involved in the regulation of expression of this trait. Results We built a comprehensive transcriptome using leaf and inflorescence from apomictic tetraploids and sexual diploids/tetraploids and a coexpression network based on pairwise correlations between transcript expression profiles. We identified genes exclusively expressed in each cytotype and genes differentially expressed between pairs of cytotypes. Gene Ontology enrichment analyses were performed to better interpret the data. We de novo assembled 114,306 reference transcripts. In total, 536 candidate genes possibly associated with apomixis were detected through statistical analyses of the differential expression data, and several interacting genes potentially linked to the apomixis-controlling region, genes that have already been reported in the literature, and their neighbors were transcriptionally related in the coexpression network. Conclusions Apomixis is a highly desirable trait in modern agriculture due to the maintenance of the characteristics of the mother plant in the progeny. The reference transcriptome, candidate genes and their coexpression network identified in this work represent rich resources for future grass breeding programs.
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Tang Q, Xu Y, Deng C, Cheng C, Dai Z, Yang Z, Liu C, Su J. A Full-Length Reference Floral Transcriptome of Boehmeria tricuspis Provides Insights into Apomeiosis and Polyploidy. Int J Genomics 2019; 2019:4025747. [PMID: 31950027 PMCID: PMC6948294 DOI: 10.1155/2019/4025747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/21/2019] [Indexed: 01/27/2023] Open
Abstract
Boehmeria tricuspis (Hance) Makino constitutes a hardy herbaceous or shrubby perennial native to East Asia that includes different ploidy levels and reproductive modes (diplosporous to sexual). Although several apomeiosis-associated genes have been described, the genetic control and molecular mechanisms underlying apomeiosis remain poorly understood. Moreover, the basis of the correlation between polyploidy and apomixis has not yet been clarified. We utilized long-read sequencing to produce a full-length reference floral transcriptome of B. tricuspis. Based on the generated database, gene expression of the female flowers of different ploidy levels and reproductive mode cytotypes was compared. Overall, 1,387 genes related to apomeiosis, 217 genes related to ploidy, and 9 genes associated with both apomixis and ploidy were identified. Gene Ontology analyses of this set of transcripts indicated reproductive genes, especially those related to "cell differentiation" and "cell cycle process," as significant factors regulating apomeiosis. Furthermore, our results suggested that different expressions of stress response genes might be important in the preparation for apomeiosis transition. In addition, our observations indicated that the expression of apomeiosis may not depend on polyploidy but rather on deregulation of the sexual pathway in B. tricuspis.
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Affiliation(s)
- Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Canhui Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Chaohua Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Zhigang Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Chan Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
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Garbus I, Selva JP, Pasten MC, Bellido AM, Carballo J, Albertini E, Echenique V. Characterization and discovery of miRNA and miRNA targets from apomictic and sexual genotypes of Eragrostis curvula. BMC Genomics 2019; 20:839. [PMID: 31718556 PMCID: PMC6852985 DOI: 10.1186/s12864-019-6169-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 10/02/2019] [Indexed: 01/01/2023] Open
Abstract
Background Weeping lovegrass (Eragrostis curvula [Shrad.] Nees) is a perennial grass found in semi-arid regions that is well adapted for growth in sandy soils and drought conditions. E. curvula constitutes a polymorphic complex that includes cytotypes with different ploidy levels (from 2x to 8x), where most polyploids are facultative apomicts, although both sexual reproduction and full apomixis have been reported in this species. Apomixis is thought to be associated with silencing of the sexual pathway, which would involve epigenetic mechanisms. However, a correlation between small RNAs and apomixis has not yet been conclusively established. Results Aiming to contribute to the elucidation of their role in the expression of apomixis, we constructed small RNA libraries from sexual and apomictic E. curvula genotypes via Illumina technology, characterized the small RNA populations, and conducted differential expression analysis by comparing these small RNAs with the E. curvula reference transcriptome. We found that the expression of two genes is repressed in the sexual genotype, which is associated with specific microRNA expression. Conclusion Our results support the hypothesis that in E. curvula the expression of apomixis leads to sexual repression.
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Affiliation(s)
- Ingrid Garbus
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina.
| | - Juan Pablo Selva
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina
| | - María Cielo Pasten
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina
| | - Andrés Martín Bellido
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina
| | - José Carballo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina
| | - Emidio Albertini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS); CONICET, Bahía Blanca, Argentina
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Ortiz JPA, Leblanc O, Rohr C, Grisolia M, Siena LA, Podio M, Colono C, Azzaro C, Pessino SC. Small RNA-seq reveals novel regulatory components for apomixis in Paspalum notatum. BMC Genomics 2019; 20:487. [PMID: 31195966 PMCID: PMC6567921 DOI: 10.1186/s12864-019-5881-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/04/2019] [Indexed: 12/31/2022] Open
Abstract
Background Apomixis is considered an evolutionary deviation of the sexual reproductive pathway leading to the generation of clonal maternal progenies by seeds. Recent evidence from model and non-model species suggested that this trait could be modulated by epigenetic mechanisms involving small RNAs (sRNAs). Here we profiled floral sRNAs originated from apomictic and sexual Paspalum notatum genotypes in order to identify molecular pathways under epigenetic control that might be involved in the transition from sexuality to agamospermy. Results The mining of genes participating in sRNA-directed pathways from floral Paspalum transcriptomic resources showed these routes are functional during reproductive development, with several members differentially expressed in apomictic and sexual plants. Triplicate floral sRNA libraries derived from apomictic and a sexual genotypes were characterized by using high-throughput sequencing technology. EdgeR was apply to compare the number of sRNA reads between sexual and apomictic libraries that map over all Paspalum floral transcripts. A total of 1525 transcripts showed differential sRNA representation, including genes related to meiosis, plant hormone signaling, biomolecules transport, transcription control and cell cycle. Survey for miRNA precursors on transcriptome and genome references allowed the discovery of 124 entities, including 40 conserved and 8 novel ones. Fifty-six clusters were differentially represented in apomictic and sexual plants. All differentially expressed miRNAs were up-regulated in apomictic libraries but miR2275, which showed different family members with opposed representation. Examination of predicted miRNAs targets detected 374 potential candidates. Considering sRNA, miRNAs and target surveys together, 14 genes previously described as related with auxin metabolism, transport and signaling were detected, including AMINO ACID/AUXIN PERMEASE 15, IAA-AMIDO SYNTHETASE GH3–8, IAA30, miR160, miR167, miR164, miR319, ARF2, ARF8, ARF10, ARF12, AFB2, PROLIFERATING CELL FACTOR 6 and NITRATE TRANSPORTER 1.1. Conclusions This work provides a comprehensive survey of the sRNA differential representation in flowers of sexual and apomictic Paspalum notatum plants. An integration of the small RNA profiling data presented here and previous transcriptomic information suggests that sRNA-mediated regulation of auxin pathways is pivotal in promoting apomixis. These results will underlie future functional characterization of the molecular components mediating the switch from sexuality to apomixis. Electronic supplementary material The online version of this article (10.1186/s12864-019-5881-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan Pablo A Ortiz
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR, CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Olivier Leblanc
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | - Cristian Rohr
- Instituto de Agrobiotecnología de Rosario (INDEAR), Rosario, Argentina
| | - Mauricio Grisolia
- Instituto de Agrobiotecnología de Rosario (INDEAR), Rosario, Argentina
| | - Lorena A Siena
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR, CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Maricel Podio
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR, CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Carolina Colono
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR, CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Celeste Azzaro
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR, CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Silvina C Pessino
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR, CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina.
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25
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Juranić M, Johnson SD, Koltunow AM. Phenotypic plasticity of aposporous embryo sac development in Hieracium praealtum. PLANT SIGNALING & BEHAVIOR 2019; 14:1622981. [PMID: 31161899 PMCID: PMC6620000 DOI: 10.1080/15592324.2019.1622981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
Apomixis in Hieracium praealtum follows a developmental pathway of apospory, where an unreduced embryo sac develops from a somatic ovule cell without meiosis. The avoidance of meiosis together with fertilization-independent seed formation leads to clonal progeny genetically identical to the maternal plant. We have previously described the initial developmental steps of aposporous embryo sac formation in H. praealtum and here, we cytologically observed more than 500 ovules with a focus on the later stages of embryo sac maturation. Aposporous embryo sac maturation is a stochastic process in H. praealtum with single or multiple embryo sacs formed, in addition to off-types and embryo sac abortion. The frequency of twin embryo sacs growing at the same rate is a rare event and, in most ovules, the additional embryo sac undergoes developmental arrest suggesting dominance or growth promotion of a single embryo sac. Observed deviations from the Polygonum-type embryo sac in H. praealtum indicate developmental plasticity during embryo sac maturation. Nevertheless, fertilization-independent seed formation successfully occurs.
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Affiliation(s)
- Martina Juranić
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Urrbrae, South Australia, Australia
| | - Susan D. Johnson
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Urrbrae, South Australia, Australia
| | - Anna M. Koltunow
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Urrbrae, South Australia, Australia
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Fei X, Shi J, Liu Y, Niu J, Wei A. The steps from sexual reproduction to apomixis. PLANTA 2019; 249:1715-1730. [PMID: 30963237 DOI: 10.1007/s00425-019-03113-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/18/2019] [Indexed: 05/03/2023]
Abstract
In this paper, an interaction model of apomixis-related genes was constructed to analyze the emergence of apomictic types. It is speculated that apomixis technology will be first implemented in gramineous plants. Apomixis (asexual seed formation) is a phenomenon in which a plant bypasses the most fundamental aspects of sexual reproduction-meiosis and fertilization-to form a viable seed. Plants can form seeds without fertilization, and the seed genotype is consistent with the female parent. The development of apomictic technology would be revolutionary for agriculture and for food production as it would reduce costs and breeding times and also avoid many complications typical of sexual reproduction (e.g. incompatibility barriers) and of vegetative propagation (e.g. viral transfer). The application of apomictic reproductive technology has the potential to revolutionize crop breeding. This article reviews recent advances in apomixis in cytology and molecular biology. The general idea of identifying apomixis was proposed and the process of the emergence of non-fusion types was discussed. To better understand the apomixis mechanism, an apomixis regulatory model was established. At the same time, the realization of apomixis technology is proposed, which provides reference for the research and application of apomixis.
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Affiliation(s)
- Xitong Fei
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Jingwei Shi
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Yulin Liu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Jinshuang Niu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Anzhi Wei
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China.
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Pinto SC, Mendes MA, Coimbra S, Tucker MR. Revisiting the Female Germline and Its Expanding Toolbox. TRENDS IN PLANT SCIENCE 2019; 24:455-467. [PMID: 30850278 DOI: 10.1016/j.tplants.2019.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 01/28/2019] [Accepted: 02/04/2019] [Indexed: 05/27/2023]
Abstract
The Arabidopsis thaliana ovule arises as a female reproductive organ composed solely of somatic diploid cells. Among them, one cell will acquire a unique identity and initiate female germline development. In this review we explore the complex network that facilitates differentiation of this single cell, and consider how it becomes committed to a distinct developmental program. We highlight recent progress towards understanding the role of intercellular communication, cell competency, and cell-cycle regulation in the ovule primordium, and we discuss the possibility that distinct pathways restrict germline development at different stages. Importantly, these recent findings suggest a renaissance in plant ovule research, restoring the female germline as an attractive model to study cell communication and cell fate establishment in multicellular organs.
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Affiliation(s)
- Sara C Pinto
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal; GreenUPorto, Sustainable AgriFood Production Research Centre, Rua da Agrária 747, 4485-646 Vairão, Portugal
| | - Marta A Mendes
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Sílvia Coimbra
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal; GreenUPorto, Sustainable AgriFood Production Research Centre, Rua da Agrária 747, 4485-646 Vairão, Portugal
| | - Matthew R Tucker
- School of Agriculture, Food, and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia.
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28
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Kaushal P, Dwivedi KK, Radhakrishna A, Srivastava MK, Kumar V, Roy AK, Malaviya DR. Partitioning Apomixis Components to Understand and Utilize Gametophytic Apomixis. FRONTIERS IN PLANT SCIENCE 2019; 10:256. [PMID: 30906306 PMCID: PMC6418048 DOI: 10.3389/fpls.2019.00256] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/18/2019] [Indexed: 05/07/2023]
Abstract
Apomixis is a method of reproduction to generate clonal seeds and offers tremendous potential to fix heterozygosity and hybrid vigor. The process of apomictic seed development is complex and comprises three distinct components, viz., apomeiosis (leading to formation of unreduced egg cell), parthenogenesis (development of embryo without fertilization) and functional endosperm development. Recently, in many crops, these three components are reported to be uncoupled leading to their partitioning. This review provides insight into the recent status of our understanding surrounding partitioning apomixis components in gametophytic apomictic plants and research avenues that it offers to help understand the biology of apomixis. Possible consequences leading to diversity in seed developmental pathways, resources to understand apomixis, inheritance and identification of candidate gene(s) for partitioned components, as well as contribution towards creation of variability are all discussed. The potential of Panicum maximum, an aposporous crop, is also discussed as a model crop to study partitioning principle and effects. Modifications in cytogenetic status, as well as endosperm imprinting effects arising due to partitioning effects, opens up new opportunities to understand and utilize apomixis components, especially towards synthesizing apomixis in crops.
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Affiliation(s)
- Pankaj Kaushal
- ICAR-National Institute of Biotic Stress Management, Raipur, India
| | | | | | | | - Vinay Kumar
- ICAR-National Institute of Biotic Stress Management, Raipur, India
| | - Ajoy Kumar Roy
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
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Galla G, Basso A, Grisan S, Bellucci M, Pupilli F, Barcaccia G. Ovule Gene Expression Analysis in Sexual and Aposporous Apomictic Hypericum perforatum L. (Hypericaceae) Accessions. FRONTIERS IN PLANT SCIENCE 2019; 10:654. [PMID: 31178879 PMCID: PMC6543059 DOI: 10.3389/fpls.2019.00654] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 05/01/2019] [Indexed: 05/09/2023]
Abstract
Hypericum perforatum L. (2n = 4x = 32) is an attractive model system for the study of aposporous apomixis. The earliest phenotypic features of aposporous apomixis in this species are the mitotic formation of unreduced embryo sacs from a somatic cell of the ovule nucellus and the avoidance of meiosis. In this research we addressed gene expression variation in sexual and apomictic plants, by focusing on the ovule nucellus, which is the cellular domain primarily involved into the differentiation of meiocyte precursors and aposporous embryo sacs, at a pre-meiotic developmental stage. Gene expression analyses performed by RNAseq identified 396 differentially expressed genes and 1834 transcripts displaying phenotype-specific expression. Furthermore, the sequencing and assembly of the genome from a diploid sexual accession allowed the annotation of a 50 kb sequence portion located upstream the HAPPY locus and to address the extent to which single transcripts were assembled in multiple variants and their co-expression levels. About one third of identified DEGs and phenotype-specific transcripts were associated to transcript variants with alternative expression patterns. Additionally, considering DEGs and phenotype-specific transcript, the co-expression level was estimated in about two transcripts per locus. Our gene expression study shows massive differences in the expression of several genes encoding for transposable elements. Transcriptional differences in the ovule nucellus and pistil terminal developmental stages were also found for subset of genes encoding for potentially interacting proteins involved in pre-mRNA splicing. Furthermore, the sexual and aposporous ovule transcriptomes were characterized by differential expression in genes operating in RNA silencing, RNA-mediated DNA methylation (RdDM) and histone and chromatin modifications. These findings are consistent with a role of these processes in regulating cell fate determination in the ovule, as indicated by forward genetic studies in sexual model species. The association between aposporous apomixis, pre-mRNA splicing and DNA methylation mediated by sRNAs, which is supported by expression data and by the enrichment in GO terms related to these processes, is consistent with the massive differential expression of multiple transposon-related sequences observed in ovules collected from both sexual and aposporous apomictic accessions. Overall, our data suggest that phenotypic expression of aposporous apomixis is concomitant with the modulation of key genes involved in the two interconnected processes: RNA splicing and RNA-directed DNA methylation.
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Affiliation(s)
- Giulio Galla
- Laboratory of Genetics and Genomics, Dipartimento di Agronomia, Animali, Alimenti, Risorse Naturali e Ambiente, University of Padova, Padua, Italy
- *Correspondence: Giulio Galla,
| | - Andrea Basso
- Laboratory of Genetics and Genomics, Dipartimento di Agronomia, Animali, Alimenti, Risorse Naturali e Ambiente, University of Padova, Padua, Italy
| | - Simone Grisan
- Institute of Biosciences and Bioresources, Research Division of Perugia, National Research Council, Perugia, Italy
| | - Michele Bellucci
- Institute of Biosciences and Bioresources, Research Division of Perugia, National Research Council, Perugia, Italy
| | - Fulvio Pupilli
- Institute of Biosciences and Bioresources, Research Division of Perugia, National Research Council, Perugia, Italy
| | - Gianni Barcaccia
- Laboratory of Genetics and Genomics, Dipartimento di Agronomia, Animali, Alimenti, Risorse Naturali e Ambiente, University of Padova, Padua, Italy
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30
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Colono C, Ortiz JPA, Permingeat HR, Souza Canada ED, Siena LA, Spoto N, Galdeano F, Espinoza F, Leblanc O, Pessino SC. A Plant-Specific TGS1 Homolog Influences Gametophyte Development in Sexual Tetraploid Paspalum notatum Ovules. FRONTIERS IN PLANT SCIENCE 2019; 10:1566. [PMID: 31850040 PMCID: PMC6895069 DOI: 10.3389/fpls.2019.01566] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 11/08/2019] [Indexed: 05/04/2023]
Abstract
Aposporous apomictic plants form clonal maternal seeds by inducing the emergence of non-reduced (2n) embryo sacs in the ovule nucellus and the development of embryos by parthenogenesis. In previous work, we reported a plant-specific TRIMETHYLGUANOSINE SYNTHASE 1 (TGS1) gene (PN_TGS1-like) showing expression levels positively correlated with sexuality rates in facultative apomictic Paspalum notatum. PN_ TGS1-like displayed contrasting in situ hybridization patterns in apomictic and sexual plant ovules from premeiosis to anthesis. Here we transformed sexual P. notatum with a TGS1-like antisense construction under a constitutive promoter, in order to produce lines with reduced transcript representation. Antisense plants developed prominent trichomes on the adaxial leaf surface, a trait absent from control genotypes. Reproductive development analysis revealed occasional formation of twin ovules. While control individuals typically displayed a single meiotic embryo sac per ovule, antisense lines showed 12.93-15.79% of ovules bearing extra nuclei, which can be assigned to aposporous-like embryo sacs (AES-like) or, alternatively, to gametophytes with a misguided cell fate development. Moreover, around 8.42-9.52% of ovules showed what looked like a combination of meiotic and aposporous-like sacs. Besides, 32.5% of ovules at early developmental stages displayed nucellar cells with prominent nuclei resembling apospory initials (AIs), which surrounded the megaspore mother cell (MMC) or the MMC-derived meiotic products. Two or more concurrent meiosis events were never detected, which suggest a non-reduced nature for the extra nuclei observed in the mature ovules, unless they were generated by proliferation and misguided differentiation of the legitimate meiotic products. The antisense lines produced a similar amount of viable even-sized pollen with respect to control genotypes, and formed an equivalent full seed set (∼9% of total seeds) after self-pollination. Flow cytometry analyses of caryopses derived from antisense lines revealed that all full seeds had originated from meiotic embryo sacs (i.e. by sexuality). A reduction of 25.55% in the germination percentage was detected when comparing antisense lines with controls. Our results indicate that PN_ TGS1-like influences ovule, gametophyte and possibly embryo development.
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Affiliation(s)
- Carolina Colono
- Molecular Biology Laboratory, IICAR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Juan Pablo A. Ortiz
- Molecular Biology Laboratory, IICAR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Hugo R. Permingeat
- Molecular Biology Laboratory, IICAR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | | | - Lorena A. Siena
- Molecular Biology Laboratory, IICAR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Nicolás Spoto
- Molecular Biology Laboratory, IICAR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
| | - Florencia Galdeano
- Genetics Laboratory, IBONE, CONICET, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - Francisco Espinoza
- Genetics Laboratory, IBONE, CONICET, Universidad Nacional del Nordeste, Corrientes, Argentina
| | | | - Silvina C. Pessino
- Molecular Biology Laboratory, IICAR, CONICET, Universidad Nacional de Rosario, Rosario, Argentina
- *Correspondence: Silvina C. Pessino,
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Mancini M, Permingeat H, Colono C, Siena L, Pupilli F, Azzaro C, de Alencar Dusi DM, de Campos Carneiro VT, Podio M, Seijo JG, González AM, Felitti SA, Ortiz JPA, Leblanc O, Pessino SC. The MAP3K-Coding QUI-GON JINN ( QGJ) Gene Is Essential to the Formation of Unreduced Embryo Sacs in Paspalum. FRONTIERS IN PLANT SCIENCE 2018; 9:1547. [PMID: 30405677 PMCID: PMC6207905 DOI: 10.3389/fpls.2018.01547] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/03/2018] [Indexed: 05/20/2023]
Abstract
Apomixis is a clonal mode of reproduction via seeds, which results from the failure of meiosis and fertilization in the sexual female reproductive pathway. In previous transcriptomic surveys, we identified a mitogen-activated protein kinase kinase kinase (N46) displaying differential representation in florets of sexual and apomictic Paspalum notatum genotypes. Here, we retrieved and characterized the N46 full cDNA sequence from sexual and apomictic floral transcriptomes. Phylogenetic analyses showed that N46 was a member of the YODA family, which was re-named QUI-GON JINN (QGJ). Differential expression in florets of sexual and apomictic plants was confirmed by qPCR. In situ hybridization experiments revealed expression in the nucellus of aposporous plants' ovules, which was absent in sexual plants. RNAi inhibition of QGJ expression in two apomictic genotypes resulted in significantly reduced rates of aposporous embryo sac formation, with respect to the level detected in wild type aposporous plants and transformation controls. The QGJ locus segregated independently of apospory. However, a probe derived from a related long non-coding RNA sequence (PN_LNC_QGJ) revealed RFLP bands cosegregating with the Paspalum apospory-controlling region (ACR). PN_LNC_QGJ is expressed in florets of apomictic plants only. Our results indicate that the activity of QGJ in the nucellus of apomictic plants is necessary to form non-reduced embryo sacs and that a long non-coding sequence with regulatory potential is similar to sequences located within the ACR.
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Affiliation(s)
- Micaela Mancini
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Hugo Permingeat
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Carolina Colono
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Lorena Siena
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Fulvio Pupilli
- Istituto di Bioscienze e BioRisorse, Consiglio Nazionale delle Ricerche, Perugia, Italy
| | - Celeste Azzaro
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | | | | | - Maricel Podio
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - José Guillermo Seijo
- Instituto de Botánica del Nordeste, CONICET-UNNE, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - Ana María González
- Instituto de Botánica del Nordeste, CONICET-UNNE, Corrientes, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - Silvina A. Felitti
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Juan Pablo A. Ortiz
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | | | - Silvina C. Pessino
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
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Rojek J, Kapusta M, Kozieradzka-Kiszkurno M, Majcher D, Górniak M, Sliwinska E, Sharbel TF, Bohdanowicz J. Establishing the cell biology of apomictic reproduction in diploid Boechera stricta (Brassicaceae). ANNALS OF BOTANY 2018. [PMID: 29982367 DOI: 10.1093/aob/mcy11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
BACKGROUND AND AIMS In the Brassicaceae family, apomictic development is characteristic of the genus Boechera. Hybridization, polyploidy and environmental adaptation that arose during the evolution of Boechera may serve as (epi)genetic regulators of apomictic initiation in this genus. Here we focus on Boechera stricta, a predominantly diploid species that reproduces sexually. However, apomictic development in this species has been reported in several studies, indicating non-obligate sexuality. METHODS A progressive investigation of flower development was conducted using three accessions to assess the reproductive system of B. stricta. We employed molecular and cyto-embryological identification using histochemistry, transmission electron microscopy and Nomarski and epifluorescence microscopy. KEY RESULTS Data from internal transcribed spacer (ITS) and chloroplast haplotype sequencing, in addition to microsatellite variation, confirmed the B. stricta genotype for all lines. Embryological data indicated irregularities in sexual reproduction manifested by heterochronic ovule development, longevity of meiocyte and dyad stages, diverse callose accumulation during meiocyte-to-gametophyte development, and the formation of triads and tetrads in several patterns. The arabinogalactan-related sugar epitope recognized by JIM13 immunolocalized to one or more megaspores. Furthermore, pollen sterility and a high frequency of seed abortion appeared to accompany reproduction of the accession ES512, along with the initiation of parthenogenesis. Data from flow cytometric screening revealed both sexual and apomictic seed formation. CONCLUSION These results imply that B. stricta is a species with an underlying ability to initiate apomixis, at least with respect to the lines examined here. The existence of apomixis in an otherwise diploid sexual B. stricta may provide the genomic building blocks for establishing highly penetrant apomictic diploids and hybrid relatives. Our findings demonstrate that apomixis per se is a variable trait upon which natural selection could act.
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Affiliation(s)
- Joanna Rojek
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdansk, Poland
| | - Malgorzata Kapusta
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdansk, Poland
| | | | - Daria Majcher
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdansk, Poland
| | - Marcin Górniak
- Department of Molecular Evolution, Faculty of Biology, University of Gdansk, Poland
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Technology and Life Sciences in Bydgoszcz, Poland
| | - Timothy F Sharbel
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Jerzy Bohdanowicz
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdansk, Poland
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Rojek J, Kapusta M, Kozieradzka-Kiszkurno M, Majcher D, Górniak M, Sliwinska E, Sharbel TF, Bohdanowicz J. Establishing the cell biology of apomictic reproduction in diploid Boechera stricta (Brassicaceae). ANNALS OF BOTANY 2018; 122:513-539. [PMID: 29982367 PMCID: PMC6153484 DOI: 10.1093/aob/mcy114] [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: 02/08/2018] [Accepted: 06/21/2018] [Indexed: 05/15/2023]
Abstract
Background and aims In the Brassicaceae family, apomictic development is characteristic of the genus Boechera. Hybridization, polyploidy and environmental adaptation that arose during the evolution of Boechera may serve as (epi)genetic regulators of apomictic initiation in this genus. Here we focus on Boechera stricta, a predominantly diploid species that reproduces sexually. However, apomictic development in this species has been reported in several studies, indicating non-obligate sexuality. Methods A progressive investigation of flower development was conducted using three accessions to assess the reproductive system of B. stricta. We employed molecular and cyto-embryological identification using histochemistry, transmission electron microscopy and Nomarski and epifluorescence microscopy. Key Results Data from internal transcribed spacer (ITS) and chloroplast haplotype sequencing, in addition to microsatellite variation, confirmed the B. stricta genotype for all lines. Embryological data indicated irregularities in sexual reproduction manifested by heterochronic ovule development, longevity of meiocyte and dyad stages, diverse callose accumulation during meiocyte-to-gametophyte development, and the formation of triads and tetrads in several patterns. The arabinogalactan-related sugar epitope recognized by JIM13 immunolocalized to one or more megaspores. Furthermore, pollen sterility and a high frequency of seed abortion appeared to accompany reproduction of the accession ES512, along with the initiation of parthenogenesis. Data from flow cytometric screening revealed both sexual and apomictic seed formation. Conclusion These results imply that B. stricta is a species with an underlying ability to initiate apomixis, at least with respect to the lines examined here. The existence of apomixis in an otherwise diploid sexual B. stricta may provide the genomic building blocks for establishing highly penetrant apomictic diploids and hybrid relatives. Our findings demonstrate that apomixis per se is a variable trait upon which natural selection could act.
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Affiliation(s)
- Joanna Rojek
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdańsk, Poland
| | - Małgorzata Kapusta
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdańsk, Poland
| | | | - Daria Majcher
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdańsk, Poland
| | - Marcin Górniak
- Department of Molecular Evolution, Faculty of Biology, University of Gdańsk, Poland
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Technology and Life Sciences in Bydgoszcz, Poland
| | - Timothy F Sharbel
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Jerzy Bohdanowicz
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdańsk, Poland
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Bräuning S, Catanach A, Lord JM, Bicknell R, Macknight RC. Comparative transcriptome analysis of the wild-type model apomict Hieracium praealtum and its loss of parthenogenesis (lop) mutant. BMC PLANT BIOLOGY 2018; 18:206. [PMID: 30249189 PMCID: PMC6154955 DOI: 10.1186/s12870-018-1423-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 09/10/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Asexual seed formation (apomixis) has been observed in diverse plant families but is rare in crop plants. The generation of apomictic crops would revolutionize agriculture, as clonal seed production provides a low cost and efficient way to produce hybrid seed. Hieracium (Asteraceae) is a model system for studying the molecular components of gametophytic apomixis (asexual seed reproduction). RESULTS In this study, a reference transcriptome was produced from apomictic Hieracium undergoing the key apomictic events of apomeiosis, parthenogenesis and autonomous endosperm development. In addition, transcriptome sequences from pre-pollination and post-pollination stages were generated from a loss of parthenogenesis (lop) mutant accession that exhibits loss of parthenogenesis and autonomous endosperm development. The transcriptome is composed of 147,632 contigs, 50% of which were annotated with orthologous genes and their probable function. The transcriptome was used to identify transcripts differentially expressed during apomictic and pollination dependent (lop) seed development. Gene Ontology enrichment analysis of differentially expressed transcripts showed that an important difference between apomictic and pollination dependent seed development was the expression of genes relating to epigenetic gene regulation. Genes that mark key developmental stages, i.e. aposporous embryo sac development and seed development, were also identified through their enhanced expression at those stages. CONCLUSION The production of a comprehensive floral reference transcriptome for Hieracium provides a valuable resource for research into the molecular basis of apomixis and the identification of the genes underlying the LOP locus.
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Affiliation(s)
- Sophia Bräuning
- Department of Biochemistry, University of Otago, 710 Cumberland St, Dunedin, 9016 New Zealand
- Department of Botany, University of Otago, 464 Great King St, Dunedin, 9016 New Zealand
| | - Andrew Catanach
- New Zealand Institute for Plant and Food Research, Gerald St, Lincoln, 7608 New Zealand
| | - Janice M. Lord
- Department of Botany, University of Otago, 464 Great King St, Dunedin, 9016 New Zealand
| | - Ross Bicknell
- New Zealand Institute for Plant and Food Research, Gerald St, Lincoln, 7608 New Zealand
| | - Richard C. Macknight
- Department of Biochemistry, University of Otago, 710 Cumberland St, Dunedin, 9016 New Zealand
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Aubert MK, Coventry S, Shirley NJ, Betts NS, Würschum T, Burton RA, Tucker MR. Differences in hydrolytic enzyme activity accompany natural variation in mature aleurone morphology in barley (Hordeum vulgare L.). Sci Rep 2018; 8:11025. [PMID: 30038399 DOI: 10.1038/s41598-018-29068-29064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/04/2018] [Indexed: 05/27/2023] Open
Abstract
The aleurone is a critical component of the cereal seed and is located at the periphery of the starchy endosperm. During germination, the aleurone is responsible for releasing hydrolytic enzymes that degrade cell wall polysaccharides and starch granules, which is a key requirement for barley malt production. Inter- and intra-species differences in aleurone layer number have been identified in the cereals but the significance of this variation during seed development and germination remains unclear. In this study, natural variation in mature aleurone features was examined in a panel of 33 Hordeum vulgare (barley) genotypes. Differences were identified in the number of aleurone cell layers, the transverse thickness of the aleurone and the proportion of aleurone relative to starchy endosperm. In addition, variation was identified in the activity of hydrolytic enzymes that are associated with germination. Notably, activity of the free fraction of β-amylase (BMY), but not the bound fraction, was increased at grain maturity in barley varieties possessing more aleurone. Laser capture microdissection (LCM) and transcriptional profiling confirmed that HvBMY1 is the most abundant BMY gene in developing grain and accumulates in the aleurone during early stages of grain fill. The results reveal a link between molecular pathways influencing early aleurone development and increased levels of free β-amylase enzyme, potentially highlighting the aleurone as a repository of free β-amylase at grain maturity.
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Affiliation(s)
- Matthew K Aubert
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
- Australian Research Council Centre of Excellence in Plant Cell Walls, the University of Adelaide, Adelaide, Australia
| | - Stewart Coventry
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Neil J Shirley
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
- Australian Research Council Centre of Excellence in Plant Cell Walls, the University of Adelaide, Adelaide, Australia
| | - Natalie S Betts
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia
| | - Tobias Würschum
- State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany
| | - Rachel A Burton
- Australian Research Council Centre of Excellence in Plant Cell Walls, the University of Adelaide, Adelaide, Australia
| | - Matthew R Tucker
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA, Australia.
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Differences in hydrolytic enzyme activity accompany natural variation in mature aleurone morphology in barley (Hordeum vulgare L.). Sci Rep 2018; 8:11025. [PMID: 30038399 PMCID: PMC6056469 DOI: 10.1038/s41598-018-29068-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/04/2018] [Indexed: 12/11/2022] Open
Abstract
The aleurone is a critical component of the cereal seed and is located at the periphery of the starchy endosperm. During germination, the aleurone is responsible for releasing hydrolytic enzymes that degrade cell wall polysaccharides and starch granules, which is a key requirement for barley malt production. Inter- and intra-species differences in aleurone layer number have been identified in the cereals but the significance of this variation during seed development and germination remains unclear. In this study, natural variation in mature aleurone features was examined in a panel of 33 Hordeum vulgare (barley) genotypes. Differences were identified in the number of aleurone cell layers, the transverse thickness of the aleurone and the proportion of aleurone relative to starchy endosperm. In addition, variation was identified in the activity of hydrolytic enzymes that are associated with germination. Notably, activity of the free fraction of β-amylase (BMY), but not the bound fraction, was increased at grain maturity in barley varieties possessing more aleurone. Laser capture microdissection (LCM) and transcriptional profiling confirmed that HvBMY1 is the most abundant BMY gene in developing grain and accumulates in the aleurone during early stages of grain fill. The results reveal a link between molecular pathways influencing early aleurone development and increased levels of free β-amylase enzyme, potentially highlighting the aleurone as a repository of free β-amylase at grain maturity.
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Juranić M, Tucker MR, Schultz CJ, Shirley NJ, Taylor JM, Spriggs A, Johnson SD, Bulone V, Koltunow AM. Asexual Female Gametogenesis Involves Contact with a Sexually-Fated Megaspore in Apomictic Hieracium. PLANT PHYSIOLOGY 2018; 177:1027-1049. [PMID: 29844228 PMCID: PMC6052994 DOI: 10.1104/pp.18.00342] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/16/2018] [Indexed: 05/03/2023]
Abstract
Apomixis results in asexual seed formation where progeny are identical to the maternal plant. In ovules of apomictic species of the Hieracium subgenus Pilosella, meiosis of the megaspore mother cell generates four megaspores. Aposporous initial (AI) cells form during meiosis in most ovules. The sexual pathway terminates during functional megaspore (FM) differentiation, when an enlarged AI undergoes mitosis to form an aposporous female gametophyte. Then, the mitotically programmed FM dies along with the three other megaspores by unknown mechanisms. Transcriptomes of laser-dissected AIs, ovule cells, and ovaries from apomicts and AI-deficient mutants were analyzed to understand the pathways involved. The steps leading to AI mitosis and sexual pathway termination were determined using antibodies against arabinogalactan protein epitopes found to mark both sexual and aposporous female gametophyte lineages at inception. At most, four AIs differentiated near developing megaspores. The first expanding AI cell to contact the FM formed a functional AI that underwent mitosis soon after megaspore degeneration. Transcriptome analyses indicated that the enlarged, laser-captured AIs were arrested in the S/G2 phase of the cell cycle and were metabolically active. Further comparisons with AI-deficient mutants showed that AIs were enriched in transcripts encoding homologs of genes involved in, and potentially antagonistic to, known FM specification pathways. We propose that AI and FM cell contact provides cues required for AI mitosis and megaspore degeneration. Specific candidates to further interrogate AI-FM interactions were identified here and include Hieracium arabinogalactan protein family genes.
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Affiliation(s)
- Martina Juranić
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Urrbrae, South Australia 5064, Australia
| | - Matthew R Tucker
- School of Agriculture, Food, and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Carolyn J Schultz
- School of Agriculture, Food, and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Neil J Shirley
- School of Agriculture, Food, and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia
- Australian Research Council Centre of Excellence in Plant Cell Walls, Wine Innovation Central, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Jennifer M Taylor
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Black Mountain Laboratories, Black Mountain, Australian Capital Territory 2601, Australia
| | - Andrew Spriggs
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Black Mountain Laboratories, Black Mountain, Australian Capital Territory 2601, Australia
| | - Susan D Johnson
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Urrbrae, South Australia 5064, Australia
| | - Vincent Bulone
- School of Agriculture, Food, and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia
- Australian Research Council Centre of Excellence in Plant Cell Walls, Wine Innovation Central, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Anna M Koltunow
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Urrbrae, South Australia 5064, Australia
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Płachno BJ, Świątek P, Kozieradzka-Kiszkurno M, Szeląg Z, Stolarczyk P. Integument cell gelatinisation-the fate of the integumentary cells in Hieracium and Pilosella (Asteraceae). PROTOPLASMA 2017; 254:2287-2294. [PMID: 28508157 PMCID: PMC5653734 DOI: 10.1007/s00709-017-1120-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 05/02/2017] [Indexed: 05/27/2023]
Abstract
Members of the genera Hieracium and Pilosella are model plants that are used to study the mechanisms of apomixis. In order to have a proper understanding of apomixis, knowledge about the relationship between the maternal tissue and the gametophyte is needed. In the genus Pilosella, previous authors have described the specific process of the "liquefaction" of the integument cells that surround the embryo sac. However, these observations were based on data only at the light microscopy level. The main aim of our paper was to investigate the changes in the integument cells at the ultrastructural level in Pilosella officinarum and Hieracium alpinum. We found that the integument peri-endothelial zone in both species consisted of mucilage cells. The mucilage was deposited as a thick layer between the plasma membrane and the cell wall. The mucilage pushed the protoplast to the centre of the cell, and cytoplasmic bridges connected the protoplast to the plasmodesmata through the mucilage layers. Moreover, an elongation of the plasmodesmata was observed in the mucilage cells. The protoplasts had an irregular shape and were finally degenerated. After the cell wall breakdown of the mucilage cells, lysigenous cavities that were filled with mucilage were formed.
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Affiliation(s)
- Bartosz J Płachno
- Department of Plant Cytology and Embryology, Jagiellonian University in Kraków, 9 Gronostajowa St., 30-387, Kraków, Poland.
| | - Piotr Świątek
- Department of Animal Histology and Embryology, University of Silesia in Katowice, 9 Bankowa St., 40-007, Katowice, Poland
| | | | - Zbigniew Szeląg
- Department of Botany, Pedagogical University of Kraków, 3 Podchorążych St., 30-084, Kraków, Poland
| | - Piotr Stolarczyk
- Unit of Botany and Plant Physiology, Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Kraków, 29 Listopada 54 Street, 31-425, Kraków, Poland
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Ortiz JPA, Revale S, Siena LA, Podio M, Delgado L, Stein J, Leblanc O, Pessino SC. A reference floral transcriptome of sexual and apomictic Paspalum notatum. BMC Genomics 2017; 18:318. [PMID: 28431521 PMCID: PMC5399859 DOI: 10.1186/s12864-017-3700-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/11/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Paspalum notatum Flügge is a subtropical grass native to South America, which includes sexual diploid and apomictic polyploid biotypes. In the past decade, a number of apomixis-associated genes were discovered in this species through genetic mapping and differential expression surveys. However, the scarce information on Paspalum sequences available in public databanks limited annotations and functional predictions for these candidates. RESULTS We used a long-read 454/Roche FLX+ sequencing strategy to produce robust reference transcriptome datasets from florets of sexual and apomictic Paspalum notatum genotypes and delivered a list of transcripts showing differential representation in both reproductive types. Raw data originated from floral samples collected from premeiosis to anthesis was assembled in three libraries: i) sexual (SEX), ii) apomictic (APO) and iii) global (SEX + APO). A group of physically-supported Paspalum mRNA and EST sequences matched with high level of confidence to both sexual and apomictic libraries. A preliminary trial allowed discovery of the whole set of putative alleles/paralogs corresponding to 23 previously identified apomixis-associated candidate genes. Moreover, a list of 3,732 transcripts and several co-expression and protein -protein interaction networks associated with apomixis were identified. CONCLUSIONS The use of the 454/Roche FLX+ transcriptome database will allow the detailed characterization of floral alleles/paralogs of apomixis candidate genes identified in prior and future work. Moreover, it was used to reveal additional candidate genes differentially represented in apomictic and sexual flowers. Gene ontology (GO) analyses of this set of transcripts indicated that the main molecular pathways altered in the apomictic genotype correspond to specific biological processes, like biotic and abiotic stress responses, growth, development, cell death and senescence. This data collection will be of interest to the plant reproduction research community and, particularly, to Paspalum breeding projects.
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Affiliation(s)
- Juan Pablo A Ortiz
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR)-CONICET/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, Provincia de Santa Fe, Zavalla, S2125ZAA, Argentina
| | - Santiago Revale
- Instituto de Agrobiotecnología de Rosario (INDEAR), Ocampo 210 bis, Provincia de Santa Fe, Rosario, 2000, Argentina.,Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Lorena A Siena
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR)-CONICET/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, Provincia de Santa Fe, Zavalla, S2125ZAA, Argentina
| | - Maricel Podio
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR)-CONICET/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, Provincia de Santa Fe, Zavalla, S2125ZAA, Argentina
| | - Luciana Delgado
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR)-CONICET/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, Provincia de Santa Fe, Zavalla, S2125ZAA, Argentina
| | - Juliana Stein
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR)-CONICET/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, Provincia de Santa Fe, Zavalla, S2125ZAA, Argentina
| | - Olivier Leblanc
- UMR 232, Institut de Recherche pour le Développement, Université de Montpellier, Montpellier, 34394, France
| | - Silvina C Pessino
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR)-CONICET/Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, Provincia de Santa Fe, Zavalla, S2125ZAA, Argentina.
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Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction. Nat Genet 2017; 49:765-772. [DOI: 10.1038/ng.3839] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/17/2017] [Indexed: 12/17/2022]
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Tang Q, Zang G, Cheng C, Luan M, Dai Z, Xu Y, Yang Z, Zhao L, Su J. Diplosporous development in Boehmeria tricuspis: Insights from de novo transcriptome assembly and comprehensive expression profiling. Sci Rep 2017; 7:46043. [PMID: 28382950 PMCID: PMC5382578 DOI: 10.1038/srep46043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/07/2017] [Indexed: 01/05/2023] Open
Abstract
Boehmeria tricuspis includes sexually reproducing diploid and apomictic triploid individuals. Previously, we established that triploid B. tricuspis reproduces through obligate diplospory. To understand the molecular basis of apomictic development in B. tricuspis, we sequenced and compared transcriptomic profiles of the flowers of sexual and apomictic plants at four key developmental stages. A total of 283,341 unique transcripts were obtained from 1,463 million high-quality paired-end reads. In total, 18,899 unigenes were differentially expressed between the reproductive types at the four stages. By classifying the transcripts into gene ontology categories of differentially expressed genes, we showed that differential plant hormone signal transduction, cell cycle regulation, and transcription factor regulation are possibly involved in apomictic development and/or a polyploidization response in B. tricuspis. Furthermore, we suggest that specific gene families are possibly related to apomixis and might have important effects on diplosporous floral development. These results make a notable contribution to our understanding of the molecular basis of diplosporous development in B. tricuspis.
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Affiliation(s)
- Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Gonggu Zang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Chaohua Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Mingbao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Zhigang Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Lining Zhao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, 348 West Xianjiahu Road, Changsha, Hunan, China
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Abstract
Apomixis, commonly defined as asexual reproduction through seed, is a reproductive trait that occurs in only a few minor crops, but would be highly valuable in major crops. Apomixis results in seed-derived progenies that are genetically identical to their maternal parent. The advantage of apomixis would lie in seed propagation of elite food, feed, and biofuel crops that are heterozygous such as hybrid corn and switchgrass or self-pollinating crops for which no commercial-scale hybrid production system is available. While hybrid plants often outperform parental lines in growth and higher yields, production of hybrid seed is accomplished through carefully controlled, labor intensive crosses. Both small farmers in developing countries who produce their own seed and commercial companies that market hybrid seed could benefit from the establishment of engineered apomixis in plants. In this chapter, we review what has been learned from studying natural apomicts and mutations in sexual plants leading to apomixis-like development, plus discuss how the components of apomixis could be successfully engineered in plants.
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Affiliation(s)
- Joann A Conner
- Horticulture Department, NESPAL/University of Georgia-Tifton Campus, 2356 Rainwater Road, Tifton, GA, 31794, USA.
| | - Peggy Ozias-Akins
- Horticulture Department, NESPAL/University of Georgia-Tifton Campus, 2356 Rainwater Road, Tifton, GA, 31794, USA
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia-Tifton Campus, Tifton, GA, USA
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Rabiger DS, Taylor JM, Spriggs A, Hand ML, Henderson ST, Johnson SD, Oelkers K, Hrmova M, Saito K, Suzuki G, Mukai Y, Carroll BJ, Koltunow AMG. Generation of an integrated Hieracium genomic and transcriptomic resource enables exploration of small RNA pathways during apomixis initiation. BMC Biol 2016; 14:86. [PMID: 27716180 PMCID: PMC5054587 DOI: 10.1186/s12915-016-0311-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/21/2016] [Indexed: 11/23/2022] Open
Abstract
Background Application of apomixis, or asexual seed formation, in crop breeding would allow rapid fixation of complex traits, economizing improved crop delivery. Identification of apomixis genes is confounded by the polyploid nature, high genome complexity and lack of genomic sequence integration with reproductive tissue transcriptomes in most apomicts. Results A genomic and transcriptomic resource was developed for Hieracium subgenus Pilosella (Asteraceae) which incorporates characterized sexual, apomictic and mutant apomict plants exhibiting reversion to sexual reproduction. Apomicts develop additional female gametogenic cells that suppress the sexual pathway in ovules. Disrupting small RNA pathways in sexual Arabidopsis also induces extra female gametogenic cells; therefore, the resource was used to examine if changes in small RNA pathways correlate with apomixis initiation. An initial characterization of small RNA pathway genes within Hieracium was undertaken, and ovary-expressed ARGONAUTE genes were identified and cloned. Comparisons of whole ovary transcriptomes from mutant apomicts, relative to the parental apomict, revealed that differentially expressed genes were enriched for processes involved in small RNA biogenesis and chromatin silencing. Small RNA profiles within mutant ovaries did not reveal large-scale alterations in composition or length distributions; however, a small number of differentially expressed, putative small RNA targets were identified. Conclusions The established Hieracium resource represents a substantial contribution towards the investigation of early sexual and apomictic female gamete development, and the generation of new candidate genes and markers. Observed changes in small RNA targets and biogenesis pathways within sexual and apomictic ovaries will underlie future functional research into apomixis initiation in Hieracium. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0311-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David S Rabiger
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Jennifer M Taylor
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Bellenden Street, Crace, Australian Capital Territory, 2911, Australia
| | - Andrew Spriggs
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Bellenden Street, Crace, Australian Capital Territory, 2911, Australia
| | - Melanie L Hand
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Steven T Henderson
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Susan D Johnson
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Karsten Oelkers
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Maria Hrmova
- Australian Centre for Plant Functional Genomics, University of Adelaide PMB 1, Glen Osmond, South Australia, 5064, Australia
| | - Keisuke Saito
- Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan
| | - Go Suzuki
- Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan
| | - Yasuhiko Mukai
- Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Anna M G Koltunow
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia.
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Florez Rueda AM, Grossniklaus U, Schmidt A. Laser-assisted Microdissection (LAM) as a Tool for Transcriptional Profiling of Individual Cell Types. J Vis Exp 2016. [PMID: 27213843 DOI: 10.3791/53916] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The understanding of developmental processes at the molecular level requires insights into transcriptional regulation, and thus the transcriptome, at the level of individual cell types. While the methods described here are generally applicable to a wide range of species and cell types, our research focuses on plant reproduction. Plant cultivation and seed production is of crucial importance for human and animal nutrition. A detailed understanding of the regulatory networks that govern the formation of the reproductive lineage (germline) and ultimately of seeds is a precondition for the targeted manipulation of plant reproduction. In particular, the engineering of apomixis (asexual reproduction through seeds) into crop plants promises great improvements, as it leads to the formation of clonal seeds that are genetically identical to the mother plant. Consequently, the cell types of the female germline are of major importance for the understanding and engineering of apomixis. However, as the corresponding cells are deeply embedded within the floral tissues, they are very difficult to access for experimental analyses, including cell-type specific transcriptomics. To overcome this limitation, sections of individual cells can be isolated by laser-assisted microdissection (LAM). While LAM in combination with transcriptional profiling allows the identification of genes and pathways active in any cell type with high specificity, establishing a suitable protocol can be challenging. Specifically, the quality of RNA obtained after LAM can be compromised, especially when small, single cells are targeted. To circumvent this problem, we have established a workflow for LAM that reproducibly results in high RNA quality that is well suitable for transcriptomics, as exemplified here by the isolation of cells of the female germline in apomictic Boechera. In this protocol, procedures are described for tissue preparation and LAM, also with regard to RNA extraction and quality control.
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Affiliation(s)
| | | | - Anja Schmidt
- University of Zürich & Zürich-Basel Plant Science Center;
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Schmid MW, Schmidt A, Grossniklaus U. The female gametophyte: an emerging model for cell type-specific systems biology in plant development. FRONTIERS IN PLANT SCIENCE 2015; 6:907. [PMID: 26579157 PMCID: PMC4630298 DOI: 10.3389/fpls.2015.00907] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/10/2015] [Indexed: 05/03/2023]
Abstract
Systems biology, a holistic approach describing a system emerging from the interactions of its molecular components, critically depends on accurate qualitative determination and quantitative measurements of these components. Development and improvement of large-scale profiling methods ("omics") now facilitates comprehensive measurements of many relevant molecules. For multicellular organisms, such as animals, fungi, algae, and plants, the complexity of the system is augmented by the presence of specialized cell types and organs, and a complex interplay within and between them. Cell type-specific analyses are therefore crucial for the understanding of developmental processes and environmental responses. This review first gives an overview of current methods used for large-scale profiling of specific cell types exemplified by recent advances in plant biology. The focus then lies on suitable model systems to study plant development and cell type specification. We introduce the female gametophyte of flowering plants as an ideal model to study fundamental developmental processes. Moreover, the female reproductive lineage is of importance for the emergence of evolutionary novelties such as an unequal parental contribution to the tissue nurturing the embryo or the clonal production of seeds by asexual reproduction (apomixis). Understanding these processes is not only interesting from a developmental or evolutionary perspective, but bears great potential for further crop improvement and the simplification of breeding efforts. We finally highlight novel methods, which are already available or which will likely soon facilitate large-scale profiling of the specific cell types of the female gametophyte in both model and non-model species. We conclude that it may take only few years until an evolutionary systems biology approach toward female gametogenesis may decipher some of its biologically most interesting and economically most valuable processes.
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Affiliation(s)
| | | | - Ueli Grossniklaus
- Department of Plant & Microbial Biology and Zurich-Basel Plant Science Center, University of ZurichZurich, Switzerland
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Płachno BJ, Świątek P, Kozieradzka-Kiszkurno M, Majeský Ľ, Marciniuk J, Stolarczyk P. Are obligatory apomicts invested in the pollen tube transmitting tissue? Comparison of the micropyle ultrastructure between sexual and apomictic dandelions (Asteraceae, Lactuceae). PROTOPLASMA 2015; 252:1325-33. [PMID: 25652809 PMCID: PMC4561075 DOI: 10.1007/s00709-015-0765-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/20/2015] [Indexed: 05/07/2023]
Abstract
With the exception of the sunflower, little information concerning the micropyle ultrastructure of the family Asteraceae is available. The aim of our study was to compare the micropyle structure in amphimictic and apomictic dandelions. Ultrastructural studies using buds and flowers during anthesis have been done on the micropyle of the sexual and apomictic Taraxacum. In all of the species that were examined, the micropylar canal was completely filled with ovule transmitting tissue and the matrix that was produced by these cells. The ovule transmitting tissue was connected to the ovarian transmitting tissue. The micropyle was asymmetrical because the integument epidermis that forms the transmitting tissue was only on the funicular side. There was a cuticle between the obturator cells and epidermal cells on the other side of integument. The micropylar transmitting tissue cells and theirs matrix reached the synergid apex. The cytoplasm of the transmitting tissue cells was especially rich in rough endoplasmic reticulum (ER), dictyosomes, and mitochondria. No major differences were detected between the micropyle structure of the amphimictic and apomictic species; thus, a structural reduction of obturator does not exist. The ovule transmitting tissue is still active in apomictic dandelions despite the presence of the embryo and endosperm. Differences and similarities between the micropyle structure in the Asteraceae that have been studied to date are discussed.
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Affiliation(s)
- Bartosz J Płachno
- Department of Plant Cytology and Embryology, Jagiellonian University in Kraków, Kraków, 9 Gronostajowa St., 30-387, Kraków, Poland,
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Abstract
Apomixis (asexual seed formation) is the result of a plant gaining the ability to bypass the most fundamental aspects of sexual reproduction: meiosis and fertilization. Without the need for male fertilization, the resulting seed germinates a plant that develops as a maternal clone. This dramatic shift in reproductive process has been documented in many flowering plant species, although no major seed crops have been shown to be capable of apomixis. The ability to generate maternal clones and therefore rapidly fix desirable genotypes in crop species could accelerate agricultural breeding strategies. The potential of apomixis as a next-generation breeding technology has contributed to increasing interest in the mechanisms controlling apomixis. In this review, we discuss the progress made toward understanding the genetic and molecular control of apomixis. Research is currently focused on two fronts. One aims to identify and characterize genes causing apomixis in apomictic species that have been developed as model species. The other aims to engineer or switch the sexual seed formation pathway in non-apomictic species, to one that mimics apomixis. Here we describe the major apomictic mechanisms and update knowledge concerning the loci that control them, in addition to presenting candidate genes that may be used as tools for switching the sexual pathway to an apomictic mode of reproduction in crops.
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Schmidt A, Schmid MW, Grossniklaus U. Plant germline formation: common concepts and developmental flexibility in sexual and asexual reproduction. Development 2015; 142:229-41. [PMID: 25564620 DOI: 10.1242/dev.102103] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The life cycle of flowering plants alternates between two heteromorphic generations: a diploid sporophytic generation and a haploid gametophytic generation. During the development of the plant reproductive lineages - the germlines - typically, single sporophytic (somatic) cells in the flower become committed to undergo meiosis. The resulting spores subsequently develop into highly polarized and differentiated haploid gametophytes that harbour the gametes. Recent studies have provided insights into the genetic basis and regulatory programs underlying cell specification and the acquisition of reproductive fate during both sexual reproduction and asexual (apomictic) reproduction. As we review here, these recent advances emphasize the importance of transcriptional, translational and post-transcriptional regulation, and the role of epigenetic regulatory pathways and hormonal activity.
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Affiliation(s)
- Anja Schmidt
- Institute of Plant Biology and Zürich-Basel Plant Science Centre, University of Zürich, Zollikerstrasse 107, Zürich CH-8008, Switzerland
| | - Marc W Schmid
- Institute of Plant Biology and Zürich-Basel Plant Science Centre, University of Zürich, Zollikerstrasse 107, Zürich CH-8008, Switzerland
| | - Ueli Grossniklaus
- Institute of Plant Biology and Zürich-Basel Plant Science Centre, University of Zürich, Zollikerstrasse 107, Zürich CH-8008, Switzerland
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Shirasawa K, Hand ML, Henderson ST, Okada T, Johnson SD, Taylor JM, Spriggs A, Siddons H, Hirakawa H, Isobe S, Tabata S, Koltunow AMG. A reference genetic linkage map of apomictic Hieracium species based on expressed markers derived from developing ovule transcripts. ANNALS OF BOTANY 2015; 115:567-80. [PMID: 25538115 PMCID: PMC4343286 DOI: 10.1093/aob/mcu249] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
BACKGROUND AND AIMS Apomixis in plants generates clonal progeny with a maternal genotype through asexual seed formation. Hieracium subgenus Pilosella (Asteraceae) contains polyploid, highly heterozygous apomictic and sexual species. Within apomictic Hieracium, dominant genetic loci independently regulate the qualitative developmental components of apomixis. In H. praealtum, LOSS OF APOMEIOSIS (LOA) enables formation of embryo sacs without meiosis and LOSS OF PARTHENOGENESIS (LOP) enables fertilization-independent seed formation. A locus required for fertilization-independent endosperm formation (AutE) has been identified in H. piloselloides. Additional quantitative loci appear to influence the penetrance of the qualitative loci, although the controlling genes remain unknown. This study aimed to develop the first genetic linkage maps for sexual and apomictic Hieracium species using simple sequence repeat (SSR) markers derived from expressed transcripts within the developing ovaries. METHODS RNA from microdissected Hieracium ovule cell types and ovaries was sequenced and SSRs were identified. Two different F1 mapping populations were created to overcome difficulties associated with genome complexity and asexual reproduction. SSR markers were analysed within each mapping population to generate draft linkage maps for apomictic and sexual Hieracium species. KEY RESULTS A collection of 14 684 Hieracium expressed SSR markers were developed and linkage maps were constructed for Hieracium species using a subset of the SSR markers. Both the LOA and LOP loci were successfully assigned to linkage groups; however, AutE could not be mapped using the current populations. Comparisons with lettuce (Lactuca sativa) revealed partial macrosynteny between the two Asteraceae species. CONCLUSIONS A collection of SSR markers and draft linkage maps were developed for two apomictic and one sexual Hieracium species. These maps will support cloning of controlling genes at LOA and LOP loci in Hieracium and should also assist with identification of quantitative loci that affect the expressivity of apomixis. Future work will focus on mapping AutE using alternative populations.
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Affiliation(s)
- Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Melanie L Hand
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Steven T Henderson
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Takashi Okada
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Susan D Johnson
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Jennifer M Taylor
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Andrew Spriggs
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Hayley Siddons
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Sachiko Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
| | - Anna M G Koltunow
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan and Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture Flagship, Waite Campus, Hartley Grove, Urrbrae, South Australia 5064, Australia
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