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Aggarwal PR, Pramitha L, Choudhary P, Singh RK, Shukla P, Prasad M, Muthamilarasan M. Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:892736. [PMID: 36119586 PMCID: PMC9470963 DOI: 10.3389/fpls.2022.892736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C4 photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.
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Affiliation(s)
- Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Lydia Pramitha
- School of Agriculture and Biosciences, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, India
| | - Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | | | - Pooja Shukla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Manoj Prasad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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Barcaccia G, Palumbo F, Sgorbati S, Albertini E, Pupilli F. A Reappraisal of the Evolutionary and Developmental Pathway of Apomixis and Its Genetic Control in Angiosperms. Genes (Basel) 2020; 11:E859. [PMID: 32731368 PMCID: PMC7466056 DOI: 10.3390/genes11080859] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 12/16/2022] Open
Abstract
Apomixis sensu stricto (agamospermy) is asexual reproduction by seed. In angiosperms it represents an easy byway of life cycle renewal through gamete-like cells that give rise to maternal embryos without ploidy reduction (meiosis) and ploidy restitution (syngamy). The origin of apomixis still represents an unsolved problem, as it may be either evolved from sex or the other way around. This review deals with a reappraisal of the origin of apomixis in order to deepen knowledge on such asexual mode of reproduction which seems mainly lacking in the most basal angiosperm orders (i.e., Amborellales, Nymphaeales and Austrobaileyales, also known as ANA-grade), while it clearly occurs in different forms and variants in many unrelated families of monocots and eudicots. Overall findings strengthen the hypothesis that apomixis as a whole may have evolved multiple times in angiosperm evolution following different developmental pathways deviating to different extents from sexuality. Recent developments on the genetic control of apomixis in model species are also presented and adequately discussed in order to shed additional light on the antagonist theories of gain- and loss-of-function over sexuality.
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Affiliation(s)
- Gianni Barcaccia
- Department of Agronomy Food Natural Resources Animals Environment, University of Padova, Campus of Agripolis, Viale dell’Università 16, Legnaro, 35020 Padova, Italy;
| | - Fabio Palumbo
- Department of Agronomy Food Natural Resources Animals Environment, University of Padova, Campus of Agripolis, Viale dell’Università 16, Legnaro, 35020 Padova, Italy;
| | - Sergio Sgorbati
- Department of Environmental and Territory Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy;
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy;
| | - Fulvio Pupilli
- Research Division of Perugia, Institute of Biosciences and Bioresources, National Research Council (CNR), Via Madonna Alta 130, 06128 Perugia, Italy;
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Scheben A, Hojsgaard D. Can We Use Gene-Editing to Induce Apomixis in Sexual Plants? Genes (Basel) 2020; 11:E781. [PMID: 32664641 PMCID: PMC7397034 DOI: 10.3390/genes11070781] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/12/2022] Open
Abstract
Apomixis, the asexual formation of seeds, is a potentially valuable agricultural trait. Inducing apomixis in sexual crop plants would, for example, allow breeders to fix heterosis in hybrid seeds and rapidly generate doubled haploid crop lines. Molecular models explain the emergence of functional apomixis, i.e., apomeiosis + parthenogenesis + endosperm development, as resulting from a combination of genetic or epigenetic changes that coordinate altered molecular and developmental steps to form clonal seeds. Apomixis-like features and synthetic clonal seeds have been induced with limited success in the sexual plants rice and maize by using gene editing to mutate genes related to meiosis and fertility or via egg-cell specific expression of embryogenesis genes. Inducing functional apomixis and increasing the penetrance of apomictic seed production will be important for commercial deployment of the trait. Optimizing the induction of apomixis with gene editing strategies that use known targets as well as identifying alternative targets will be possible by better understanding natural genetic variation in apomictic species. With the growing availability of genomic data and precise gene editing tools, we are making substantial progress towards engineering apomictic crops.
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Affiliation(s)
- Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA;
| | - Diego 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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Albertini E, Barcaccia G, Carman JG, Pupilli F. Did apomixis evolve from sex or was it the other way around? JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2951-2964. [PMID: 30854543 DOI: 10.1093/jxb/erz109] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/25/2019] [Indexed: 05/20/2023]
Abstract
In angiosperms, there are two pathways of reproduction through seeds: sexual, or amphimictic, and asexual, or apomictic. The essential feature of apomixis is that an embryo in an ovule is formed autonomously. It may form from a cell of the nucellus or integuments in an otherwise sexual ovule, a process referred to as adventitious embryony. Alternatively, the embryo may form by parthenogenesis from an unreduced egg that forms in an unreduced embryo sac. The latter may form from an ameiotic megasporocyte, in which case it is referred to as diplospory, or from a cell of the nucellus or integument, in which case it is referred to as apospory. Progeny of apomictic plants are generally identical to the mother plant. Apomixis has been seen over the years as either a gain- or loss-of-function over sexuality, implying that the latter is the default condition. Here, we consider an additional point of view, that apomixis may be anciently polyphenic with sex and that both reproductive phenisms involve anciently canalized components of complex molecular processes. This polyphenism viewpoint suggests that apomixis fails to occur in obligately sexual eukaryotes because genetic or epigenetic modifications have silenced the primitive sex apomixis switch and/or disrupted molecular capacities for apomixis. In eukaryotes where sex and apomixis are clearly polyphenic, apomixis exponentially drives clonal fecundity during reproductively favorable conditions, while stress induces sex for stress-tolerant spore or egg formation. The latter often guarantees species survival during environmentally harsh seasons.
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Affiliation(s)
- Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Gianni Barcaccia
- Laboratory of Genomics, Department of Agronomy, Food, Natural Resources, Animals and the Environment (DAFNAE), University of Padova Legnaro, PD, Italy
| | - John G Carman
- Department of Plants, Soils and Climate, Utah State University, Logan, Utah, USA
| | - Fulvio Pupilli
- Institute of Biosciences and Bioresources, Research Division of Perugia, National Research Council (CNR), Perugia, Italy
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Worthington M, Ebina M, Yamanaka N, Heffelfinger C, Quintero C, Zapata YP, Perez JG, Selvaraj M, Ishitani M, Duitama J, de la Hoz JF, Rao I, Dellaporta S, Tohme J, Arango J. Translocation of a parthenogenesis gene candidate to an alternate carrier chromosome in apomictic Brachiaria humidicola. BMC Genomics 2019. [PMID: 30642244 DOI: 10.1186/s12864-018-5392-5394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND The apomictic reproductive mode of Brachiaria (syn. Urochloa) forage species allows breeders to faithfully propagate heterozygous genotypes through seed over multiple generations. In Brachiaria, reproductive mode segregates as single dominant locus, the apospory-specific genomic region (ASGR). The AGSR has been mapped to an area of reduced recombination on Brachiaria decumbens chromosome 5. A primer pair designed within ASGR-BABY BOOM-like (BBML), the candidate gene for the parthenogenesis component of apomixis in Pennisetum squamulatum, was diagnostic for reproductive mode in the closely related species B. ruziziensis, B. brizantha, and B. decumbens. In this study, we used a mapping population of the distantly related commercial species B. humidicola to map the ASGR and test for conservation of ASGR-BBML sequences across Brachiaria species. RESULTS Dense genetic maps were constructed for the maternal and paternal genomes of a hexaploid (2n = 6x = 36) B. humidicola F1 mapping population (n = 102) using genotyping-by-sequencing, simple sequence repeat, amplified fragment length polymorphism, and transcriptome derived single nucleotide polymorphism markers. Comparative genomics with Setaria italica provided confirmation for x = 6 as the base chromosome number of B. humidicola. High resolution molecular karyotyping indicated that the six homologous chromosomes of the sexual female parent paired at random, whereas preferential pairing of subgenomes was observed in the apomictic male parent. Furthermore, evidence for compensated aneuploidy was found in the apomictic parent, with only five homologous linkage groups identified for chromosome 5 and seven homologous linkage groups of chromosome 6. The ASGR mapped to B. humidicola chromosome 1, a region syntenic with chromosomes 1 and 7 of S. italica. The ASGR-BBML specific PCR product cosegregated with the ASGR in the F1 mapping population, despite its location on a different carrier chromosome than B. decumbens. CONCLUSIONS The first dense molecular maps of B. humidicola provide strong support for cytogenetic evidence indicating a base chromosome number of six in this species. Furthermore, these results show conservation of the ASGR across the Paniceae in different chromosomal backgrounds and support postulation of the ASGR-BBML as candidate genes for the parthenogenesis component of apomixis.
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Affiliation(s)
- Margaret Worthington
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia.
- Present address: Department of Horticulture, University of Arkansas, 306 Plant Sciences Bldg, Fayetteville, AR, 72701, USA.
| | - Masumi Ebina
- National Agriculture and Food Research Organization (NARO), Institute of Livestock and Grassland Science, Nasushiobara, Tochigi, 392-2793, Japan
| | - Naoki Yamanaka
- Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Christopher Heffelfinger
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Constanza Quintero
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | | | | | - Michael Selvaraj
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Manabu Ishitani
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Jorge Duitama
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
- Present address: Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Juan Fernando de la Hoz
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
- Present address: Bioinformatics Interdepartmental Ph.D. Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Idupulapati Rao
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
- Present address: Plant Polymer Research Unit (PPL), National Center for Agricultural Utilization Research (NCAUR), Agricultural Research Service, United States Department of Agriculture (ARS-USDA), 1815 N. University St., Peoria, IL, 61604, USA
| | - Stephen Dellaporta
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Joe Tohme
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Jacobo Arango
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
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Worthington M, Ebina M, Yamanaka N, Heffelfinger C, Quintero C, Zapata YP, Perez JG, Selvaraj M, Ishitani M, Duitama J, de la Hoz JF, Rao I, Dellaporta S, Tohme J, Arango J. Translocation of a parthenogenesis gene candidate to an alternate carrier chromosome in apomictic Brachiaria humidicola. BMC Genomics 2019; 20:41. [PMID: 30642244 PMCID: PMC6332668 DOI: 10.1186/s12864-018-5392-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 12/18/2018] [Indexed: 12/05/2022] Open
Abstract
Background The apomictic reproductive mode of Brachiaria (syn. Urochloa) forage species allows breeders to faithfully propagate heterozygous genotypes through seed over multiple generations. In Brachiaria, reproductive mode segregates as single dominant locus, the apospory-specific genomic region (ASGR). The AGSR has been mapped to an area of reduced recombination on Brachiaria decumbens chromosome 5. A primer pair designed within ASGR-BABY BOOM-like (BBML), the candidate gene for the parthenogenesis component of apomixis in Pennisetum squamulatum, was diagnostic for reproductive mode in the closely related species B. ruziziensis, B. brizantha, and B. decumbens. In this study, we used a mapping population of the distantly related commercial species B. humidicola to map the ASGR and test for conservation of ASGR-BBML sequences across Brachiaria species. Results Dense genetic maps were constructed for the maternal and paternal genomes of a hexaploid (2n = 6x = 36) B. humidicola F1 mapping population (n = 102) using genotyping-by-sequencing, simple sequence repeat, amplified fragment length polymorphism, and transcriptome derived single nucleotide polymorphism markers. Comparative genomics with Setaria italica provided confirmation for x = 6 as the base chromosome number of B. humidicola. High resolution molecular karyotyping indicated that the six homologous chromosomes of the sexual female parent paired at random, whereas preferential pairing of subgenomes was observed in the apomictic male parent. Furthermore, evidence for compensated aneuploidy was found in the apomictic parent, with only five homologous linkage groups identified for chromosome 5 and seven homologous linkage groups of chromosome 6. The ASGR mapped to B. humidicola chromosome 1, a region syntenic with chromosomes 1 and 7 of S. italica. The ASGR-BBML specific PCR product cosegregated with the ASGR in the F1 mapping population, despite its location on a different carrier chromosome than B. decumbens. Conclusions The first dense molecular maps of B. humidicola provide strong support for cytogenetic evidence indicating a base chromosome number of six in this species. Furthermore, these results show conservation of the ASGR across the Paniceae in different chromosomal backgrounds and support postulation of the ASGR-BBML as candidate genes for the parthenogenesis component of apomixis. Electronic supplementary material The online version of this article (10.1186/s12864-018-5392-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Margaret Worthington
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia. .,Present address: Department of Horticulture, University of Arkansas, 306 Plant Sciences Bldg, Fayetteville, AR, 72701, USA.
| | - Masumi Ebina
- National Agriculture and Food Research Organization (NARO), Institute of Livestock and Grassland Science, Nasushiobara, Tochigi, 392-2793, Japan
| | - Naoki Yamanaka
- Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Christopher Heffelfinger
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Constanza Quintero
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | | | | | - Michael Selvaraj
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Manabu Ishitani
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Jorge Duitama
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia.,Present address: Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Juan Fernando de la Hoz
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia.,Present address: Bioinformatics Interdepartmental Ph.D. Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Idupulapati Rao
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia.,Present address: Plant Polymer Research Unit (PPL), National Center for Agricultural Utilization Research (NCAUR), Agricultural Research Service, United States Department of Agriculture (ARS-USDA), 1815 N. University St., Peoria, IL, 61604, USA
| | - Stephen Dellaporta
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Joe Tohme
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
| | - Jacobo Arango
- International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia
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Zappacosta D, Gallardo J, Carballo J, Meier M, Rodrigo JM, Gallo CA, Selva JP, Stein J, Ortiz JPA, Albertini E, Echenique V. A High-Density Linkage Map of the Forage Grass Eragrostis curvula and Localization of the Diplospory Locus. FRONTIERS IN PLANT SCIENCE 2019; 10:918. [PMID: 31354781 PMCID: PMC6640543 DOI: 10.3389/fpls.2019.00918] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 06/28/2019] [Indexed: 05/05/2023]
Abstract
Eragrostis curvula (Schrad.) Nees (weeping lovegrass) is an apomictic species native to Southern Africa that is used as forage grass in semiarid regions of Argentina. Apomixis is a mechanism for clonal propagation through seeds that involves the avoidance of meiosis to generate an unreduced embryo sac (apomeiosis), parthenogenesis, and viable endosperm formation in a fertilization-dependent or -independent manner. Here, we constructed the first saturated linkage map of tetraploid E. curvula using both traditional (AFLP and SSR) and high-throughput molecular markers (GBS-SNP) and identified the locus controlling diplospory. We also identified putative regulatory regions affecting the expressivity of this trait and syntenic relationships with genomes of other grass species. We obtained a tetraploid mapping population from a cross between a full sexual genotype (OTA-S) with a facultative apomictic individual of cv. Don Walter. Phenotypic characterization of F1 hybrids by cytoembryological analysis yielded a 1:1 ratio of apomictic vs. sexual plants (34:27, X 2 = 0.37), which agrees with the model of inheritance of a single dominant genetic factor. The final number of markers was 1,114 for OTA-S and 2,019 for Don Walter. These markers were distributed into 40 linkage groups per parental genotype, which is consistent with the number of E. curvula chromosomes (containing 2 to 123 markers per linkage group). The total length of the OTA-S map was 1,335 cM, with an average marker density of 1.22 cM per marker. The Don Walter map was 1,976.2 cM, with an average marker density of 0.98 cM/marker. The locus responsible for diplospory was mapped on Don Walter linkage group 3, with other 65 markers. QTL analyses of the expressivity of diplospory in the F1 hybrids revealed the presence of two main QTLs, located 3.27 and 15 cM from the diplospory locus. Both QTLs explained 28.6% of phenotypic variation. Syntenic analysis allowed us to establish the groups of homologs/homeologs for each linkage map. The genetic linkage map reported in this study, the first such map for E. curvula, is the most saturated map for the genus Eragrostis and one of the most saturated maps for a polyploid forage grass species.
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Affiliation(s)
- Diego Zappacosta
- Departamento de Agronomía, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CONICET, CCT Bahía Blanca), Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Jimena Gallardo
- Departamento de Agronomía, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CONICET, CCT Bahía Blanca), Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - José Carballo
- Departamento de Agronomía, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CONICET, CCT Bahía Blanca), Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Mauro Meier
- Laboratorio Biotecnológico, Asociación de Cooperativas Argentinas Coop. Ltd., Pergamino, Argentina
| | - Juan Manuel Rodrigo
- Departamento de Agronomía, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CONICET, CCT Bahía Blanca), Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Cristian A. Gallo
- Departamento de Agronomía, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CONICET, CCT Bahía Blanca), Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Juan Pablo Selva
- Departamento de Agronomía, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CONICET, CCT Bahía Blanca), Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Juliana Stein
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR, CONICET-UNR), Zavalla, Argentina
| | - Juan Pablo A. Ortiz
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR, CONICET-UNR), Zavalla, Argentina
| | - Emidio Albertini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
- Emidio Albertini,
| | - Viviana Echenique
- Departamento de Agronomía, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CONICET, CCT Bahía Blanca), Universidad Nacional del Sur, Bahía Blanca, Argentina
- *Correspondence: Viviana Echenique,
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A Parthenogenesis Gene Candidate and Evidence for Segmental Allopolyploidy in Apomictic Brachiaria decumbens. Genetics 2016; 203:1117-32. [PMID: 27206716 PMCID: PMC4937464 DOI: 10.1534/genetics.116.190314] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/14/2016] [Indexed: 12/19/2022] Open
Abstract
Apomixis, asexual reproduction through seed, enables breeders to identify and faithfully propagate superior heterozygous genotypes by seed without the disadvantages of vegetative propagation or the expense and complexity of hybrid seed production. The availability of new tools such as genotyping by sequencing and bioinformatics pipelines for species lacking reference genomes now makes the construction of dense maps possible in apomictic species, despite complications including polyploidy, multisomic inheritance, self-incompatibility, and high levels of heterozygosity. In this study, we developed saturated linkage maps for the maternal and paternal genomes of an interspecific Brachiaria ruziziensis (R. Germ. and C. M. Evrard) × B. decumbens Stapf. F1 mapping population in order to identify markers linked to apomixis. High-resolution molecular karyotyping and comparative genomics with Setaria italica (L.) P. Beauv provided conclusive evidence for segmental allopolyploidy in B. decumbens, with strong preferential pairing of homologs across the genome and multisomic segregation relatively more common in chromosome 8. The apospory-specific genomic region (ASGR) was mapped to a region of reduced recombination on B. decumbens chromosome 5. The Pennisetum squamulatum (L.) R.Br. PsASGR-BABY BOOM-like (psASGR–BBML)-specific primer pair p779/p780 was in perfect linkage with the ASGR in the F1 mapping population and diagnostic for reproductive mode in a diversity panel of known sexual and apomict Brachiaria (Trin.) Griseb. and P. maximum Jacq. germplasm accessions and cultivars. These findings indicate that ASGR–BBML gene sequences are highly conserved across the Paniceae and add further support for the postulation of the ASGR–BBML as candidate genes for the apomictic function of parthenogenesis.
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