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Hyma KE, Barba P, Wang M, Londo JP, Acharya CB, Mitchell SE, Sun Q, Reisch B, Cadle-Davidson L. Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine. PLoS One 2015; 10:e0134880. [PMID: 26244767 PMCID: PMC4526651 DOI: 10.1371/journal.pone.0134880] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/14/2015] [Indexed: 02/07/2023] Open
Abstract
Genotyping by sequencing (GBS) provides opportunities to generate high-resolution genetic maps at a low genotyping cost, but for highly heterozygous species, missing data and heterozygote undercalling complicate the creation of GBS genetic maps. To overcome these issues, we developed a publicly available, modular approach called HetMappS, which functions independently of parental genotypes and corrects for genotyping errors associated with heterozygosity. For linkage group formation, HetMappS includes both a reference-guided synteny pipeline and a reference-independent de novo pipeline. The de novo pipeline can be utilized for under-characterized or high diversity families that lack an appropriate reference. We applied both HetMappS pipelines in five half-sib F1 families involving genetically diverse Vitis spp. Starting with at least 116,466 putative SNPs per family, the HetMappS pipelines identified 10,440 to 17,267 phased pseudo-testcross (Pt) markers and generated high-confidence maps. Pt marker density exceeded crossover resolution in all cases; up to 5,560 non-redundant markers were used to generate parental maps ranging from 1,047 cM to 1,696 cM. The number of markers used was strongly correlated with family size in both de novo and synteny maps (r = 0.92 and 0.91, respectively). Comparisons between allele and tag frequencies suggested that many markers were in tandem repeats and mapped as single loci, while markers in regions of more than two repeats were removed during map curation. Both pipelines generated similar genetic maps, and genetic order was strongly correlated with the reference genome physical order in all cases. Independently created genetic maps from shared parents exhibited nearly identical results. Flower sex was mapped in three families and correctly localized to the known sex locus in all cases. The HetMappS pipeline could have wide application for genetic mapping in highly heterozygous species, and its modularity provides opportunities to adapt portions of the pipeline to other family types, genotyping technologies or applications.
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Affiliation(s)
- Katie E. Hyma
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Paola Barba
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, United States of America
| | - Minghui Wang
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Jason P. Londo
- USDA-ARS Grape Genetics Research Unit, Geneva, New York, United States of America
| | - Charlotte B. Acharya
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Sharon E. Mitchell
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Qi Sun
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Bruce Reisch
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America
| | - Lance Cadle-Davidson
- USDA-ARS Grape Genetics Research Unit, Geneva, New York, United States of America
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Vyskot B, Hobza R. The genomics of plant sex chromosomes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 236:126-35. [PMID: 26025526 DOI: 10.1016/j.plantsci.2015.03.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 02/27/2015] [Accepted: 03/26/2015] [Indexed: 05/18/2023]
Abstract
Around six percent of flowering species are dioecious, with separate female and male individuals. Sex determination is mostly based on genetics, but morphologically distinct sex chromosomes have only evolved in a few species. Of these, heteromorphic sex chromosomes have been most clearly described in the two model species - Silene latifolia and Rumex acetosa. In both species, the sex chromosomes are the largest chromosomes in the genome. They are hence easily distinguished, can be physically separated and analyzed. This review discusses some recent experimental data on selected model dioecious species, with a focus on S. latifolia. Phylogenetic analyses show that dioecy in plants originated independently and repeatedly even within individual genera. A cogent question is whether there is genetic degeneration of the non-recombining part of the plant Y chromosome, as in mammals, and, if so, whether reduced levels of gene expression in the heterogametic sex are equalized by dosage compensation. Current data provide no clear conclusion. We speculate that although some transcriptome analyses indicate the first signs of degeneration, especially in S. latifolia, the evolutionary processes forming plant sex chromosomes in plants may, to some extent, differ from those in animals.
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Affiliation(s)
- Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic.
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
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Geraldes A, Hefer CA, Capron A, Kolosova N, Martinez-Nuñez F, Soolanayakanahally RY, Stanton B, Guy RD, Mansfield SD, Douglas CJ, Cronk QCB. Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus). Mol Ecol 2015; 24:3243-56. [PMID: 25728270 DOI: 10.1111/mec.13126] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/15/2015] [Accepted: 02/19/2015] [Indexed: 12/16/2022]
Abstract
All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole-genome scans that the sex-associated region in Populus trichocarpa is small and much younger than the age of the genus. This indicates that sex determination is highly labile in poplar, consistent with recent evidence of 'turnover' of sex-determination regions in animals. We performed whole-genome resequencing of 52 P. trichocarpa (black cottonwood) and 34 Populus balsamifera (balsam poplar) individuals of known sex. Genomewide association studies in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex-linked region to be ~100 kbp. All SNPs significantly associated with sex were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex-associated SNPs revealed this to be an XY sex-determining system. Estimated divergence times of X and Y haplotype sequences (6-7 Ma) are much more recent than the divergence of P. trichocarpa (poplar) and Populus tremuloides (aspen). Consistent with this, in P. tremuloides, we found no XY haplotype divergence within the P. trichocarpa sex-determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past.
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Affiliation(s)
- A Geraldes
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - C A Hefer
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - A Capron
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - N Kolosova
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - F Martinez-Nuñez
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - R Y Soolanayakanahally
- Agroforestry Development Centre, Agriculture and Agri-Food Canada, Indian Head, SK, S0G 2K0, Canada
| | - B Stanton
- Greenwood Resources, Portland, OR, 97201, USA
| | - R D Guy
- Department of Forest and Conservation Sciences, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - S D Mansfield
- Department of Wood Science, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - C J Douglas
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - Q C B Cronk
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
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Picq S, Santoni S, Lacombe T, Latreille M, Weber A, Ardisson M, Ivorra S, Maghradze D, Arroyo-Garcia R, Chatelet P, This P, Terral JF, Bacilieri R. A small XY chromosomal region explains sex determination in wild dioecious V. vinifera and the reversal to hermaphroditism in domesticated grapevines. BMC PLANT BIOLOGY 2014; 14:229. [PMID: 25179565 PMCID: PMC4167142 DOI: 10.1186/s12870-014-0229-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 08/18/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND In Vitis vinifera L., domestication induced a dramatic change in flower morphology: the wild sylvestris subspecies is dioecious while hermaphroditism is largely predominant in the domesticated subsp. V. v. vinifera. The characterisation of polymorphisms in genes underlying the sex-determining chromosomal region may help clarify the history of domestication in grapevine and the evolution of sex chromosomes in plants. In the genus Vitis, sex determination is putatively controlled by one major locus with three alleles, male M, hermaphrodite H and female F, with an allelic dominance M > H > F. Previous genetic studies located the sex locus on chromosome 2. We used DNA polymorphisms of geographically diverse V. vinifera genotypes to confirm the position of this locus, to characterise the genetic diversity and traces of selection in candidate genes, and to explore the origin of hermaphroditism. RESULTS In V. v. sylvestris, a sex-determining region of 154.8 kb, also present in other Vitis species, spans less than 1% of chromosome 2. It displays haplotype diversity, linkage disequilibrium and differentiation that typically correspond to a small XY sex-determining region with XY males and XX females. In male alleles, traces of purifying selection were found for a trehalose phosphatase, an exostosin and a WRKY transcription factor, with strikingly low polymorphism levels between distant geographic regions. Both diversity and network analysis revealed that H alleles are more closely related to M than to F alleles. CONCLUSIONS Hermaphrodite alleles appear to derive from male alleles of wild grapevines, with successive recombination events allowing import of diversity from the X into the Y chromosomal region and slowing down the expansion of the region into a full heteromorphic chromosome. Our data are consistent with multiple domestication events and show traces of introgression from other Asian Vitis species into the cultivated grapevine gene pool.
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Affiliation(s)
- Sandrine Picq
- />Centre de Bio-Archéologie et d’Ecologie CBAE (UMR 5059 CNRS/Université Montpellier 2/EPHE/INRAP). Equipe Interactions, Biodiversité, Sociétés, Institut de Botanique, 163 rue Auguste Broussonet, 34090 Montpellier, France
| | - Sylvain Santoni
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Thierry Lacombe
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Muriel Latreille
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Audrey Weber
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Morgane Ardisson
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Sarah Ivorra
- />Centre de Bio-Archéologie et d’Ecologie CBAE (UMR 5059 CNRS/Université Montpellier 2/EPHE/INRAP). Equipe Interactions, Biodiversité, Sociétés, Institut de Botanique, 163 rue Auguste Broussonet, 34090 Montpellier, France
| | - David Maghradze
- />Institute of Horticulture, Viticulture and Oenology, Agrarian University of Georgia, University Campus at Digomi, David Aghmashenebeli Alley, 13-th km. 0159, Tbilisi, Georgia
| | - Rosa Arroyo-Garcia
- />CBGP-INIA. Dpto Biotecnología, Campus de Montegancedo, Autovía M40, km38, 28223 Pozuelo de Alarcón, Madrid Spain
| | - Philippe Chatelet
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Patrice This
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
| | - Jean-Frédéric Terral
- />Centre de Bio-Archéologie et d’Ecologie CBAE (UMR 5059 CNRS/Université Montpellier 2/EPHE/INRAP). Equipe Interactions, Biodiversité, Sociétés, Institut de Botanique, 163 rue Auguste Broussonet, 34090 Montpellier, France
- />Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier, France
| | - Roberto Bacilieri
- />INRA, UMR 1334 AGAP, Equipe Diversité, Adaptation et Amélioration de la Vigne, F34060 Montpellier, France
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Fechter I, Hausmann L, Zyprian E, Daum M, Holtgräwe D, Weisshaar B, Töpfer R. QTL analysis of flowering time and ripening traits suggests an impact of a genomic region on linkage group 1 in Vitis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1857-72. [PMID: 25112201 PMCID: PMC4145202 DOI: 10.1007/s00122-014-2310-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 04/05/2014] [Indexed: 05/21/2023]
Abstract
In the recent past, genetic analyses of grapevine focused mainly on the identification of resistance loci for major diseases such as powdery and downy mildew. Currently, breeding programs make intensive use of these results by applying molecular markers linked to the resistance traits. However, modern genetics also allows to address additional agronomic traits that have considerable impact on the selection of grapevine cultivars. In this study, we have used linkage mapping for the identification and characterization of flowering time and ripening traits in a mapping population from a cross of V3125 ('Schiava Grossa' × 'Riesling') and the interspecific rootstock cultivar 'Börner' (Vitis riparia × Vitis cinerea). Comparison of the flowering time QTL mapping with data derived from a second independent segregating population identified several common QTLs. Especially a large region on linkage group 1 proved to be of special interest given the genetic divergence of the parents of the two populations. The proximity of the QTL region contains two CONSTANS-like genes. In accordance with data from other plants such as Arabidopsis thaliana and Oryza sativa, we hypothesize that these genes are major contributors to control the time of flowering in Vitis.
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Affiliation(s)
- Iris Fechter
- Institute for Grapevine Breeding, Julius Kuehn-Institute, Federal Research Centre for Cultivated Plants, Geilweilerhof, 76833, Siebeldingen, Germany,
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Kersten B, Pakull B, Groppe K, Lueneburg J, Fladung M. The sex-linked region in Populus tremuloides Turesson 141 corresponds to a pericentromeric region of about two million base pairs on P. trichocarpa chromosome 19. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16:411-8. [PMID: 23710995 DOI: 10.1111/plb.12048] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 04/11/2013] [Indexed: 05/20/2023]
Abstract
In the dioecious genus Populus, sex determination has been located to chromosome 19. However, despite a high degree of genome collinearity, various Populus species seem to differ with regard to the location of the sex-determining region on the respective chromosome and the apparent heterogametic sex. In this study, the boundaries of the recombination-suppressed, sex-linked region of the male P. tremuloides clone Turesson 141 were localised by genetic mapping using new SNP and InDel markers. The respective region seems to be located in a pericentromeric position. The corresponding P. trichocarpa genome region spans about two million bp and comprises 65 gene loci, which were bioinformatically evaluated for their potential as candidate genes for sex determination. Three putative transcription factor genes and four genes that are potentially involved in flower development processes, e.g. meristem transition from the vegetative to the reproductive phase, were identified. Populus tremuloides sequence data of the sex-linked region is required for a final search for candidate genes.
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Affiliation(s)
- B Kersten
- Department of Genome Research, Thuenen-Institute of Forest Genetics, Grosshansdorf, Germany
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Aryal R, Ming R. Sex determination in flowering plants: papaya as a model system. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 217-218:56-62. [PMID: 24467896 DOI: 10.1016/j.plantsci.2013.10.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 10/28/2013] [Accepted: 10/29/2013] [Indexed: 05/23/2023]
Abstract
Unisexuality in flowering plants evolved from a hermaphrodite ancestor. Transition from hermaphrodite to unisexual flowers has occurred multiple times across the different lineages of the angiosperms. Sexuality in plants is regulated by genetic, epigenetic and physiological mechanisms. The most specialized mechanism of sex determination is sex chromosomes. The sex chromosomes ensure the stable segregation of sexual phenotypes by preventing the recombination of sex determining genes. Despite continuous efforts, sex determining genes of dioecious plants have not yet been cloned. Concerted efforts with various model systems are necessary to understand the complex mechanism of sex determination in plants. Papaya (Carica papaya L.) is a tropical fruit tree with three sex forms, male, hermaphrodite, and female. Sexuality in papaya is determined by an XY chromosome system that is in an early evolutionary stage. The male and hermaphrodite of papaya are controlled by two different types of Y chromosomes: Y and Y(h). Large amounts of information in the area of genetics, genomics, and epigenetics of papaya have been accumulated over the last few decades. Relatively short lifecycle, small genome size, and readily available genetic and genomic resources render papaya an excellent model system to study sex determination and sex chromosomes in flowering plants.
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Affiliation(s)
- Rishi Aryal
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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Akagi T, Kajita K, Kibe T, Morimura H, Tsujimoto T, Nishiyama S, Kawai T, Yamane H, Tao R. Development of Molecular Markers Associated with Sexuality in Diospyros lotus L. and Their Application in D. kaki Thunb. ACTA ACUST UNITED AC 2014. [DOI: 10.2503/jjshs1.ch-109] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Battilana J, Lorenzi S, Moreira FM, Moreno-Sanz P, Failla O, Emanuelli F, Grando MS. Linkage mapping and molecular diversity at the flower sex locus in wild and cultivated grapevine reveal a prominent SSR haplotype in hermaphrodite plants. Mol Biotechnol 2013; 54:1031-7. [PMID: 23532385 PMCID: PMC3641292 DOI: 10.1007/s12033-013-9657-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cultivars used for wine and table grape have self-fertile hermaphrodite flowers whereas wild European vines and American and Asian species are dioecious, having either male or female flowers. Consistent with previous studies, the flower sex trait was mapped as a single major locus on chromosome 2 based on a pure Vitis vinifera population segregating for hermaphrodite and female progeny, and a hybrid population producing all three flower sex types. The sex locus was placed between the same SSR and SNP markers on both genetic maps, although abnormal segregation hampered to fine map the genomic region. From a total of 55 possible haplotypes inferred for three SSR markers around the sex locus, in a population of 132 V. sylvestris accessions and 171 V. vinifera cultivars, one of them accounted for 66 % of the hermaphrodite individuals and may be the result of domestication. Specific size variants of the VVIB23 microsatellite sequence within the 3'-UTR of a putative YABBY1 gene were found to be statistically significantly associated with the sex alleles M, H and f; these markers can provide assistance in defining the status of wild grapevine germplasm.
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Affiliation(s)
- Juri Battilana
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach Via E. Mach 1, 38010 San Michele all’Adige, TN Italy
| | - Silvia Lorenzi
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach Via E. Mach 1, 38010 San Michele all’Adige, TN Italy
| | - Flavia M. Moreira
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach Via E. Mach 1, 38010 San Michele all’Adige, TN Italy
- Present Address: Instituto Federal de Santa Catarina, Rua José Lino Kretzer 608–Praia Comprida, São José, Santa Catarina 88130-310 Brazil
| | - Paula Moreno-Sanz
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach Via E. Mach 1, 38010 San Michele all’Adige, TN Italy
| | - Osvaldo Failla
- Department of Crop Production, Faculty of Agriculture, University of Milano, Via Celoria 2, 20133 Milan, Italy
| | - Francesco Emanuelli
- Department of Crop Production, Faculty of Agriculture, University of Milano, Via Celoria 2, 20133 Milan, Italy
| | - M. Stella Grando
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach Via E. Mach 1, 38010 San Michele all’Adige, TN Italy
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Riaz S, Boursiquot JM, Dangl GS, Lacombe T, Laucou V, Tenscher AC, Walker MA. Identification of mildew resistance in wild and cultivated Central Asian grape germplasm. BMC PLANT BIOLOGY 2013; 13:149. [PMID: 24093598 PMCID: PMC3851849 DOI: 10.1186/1471-2229-13-149] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 09/30/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Cultivated grapevines, Vitis vinifera subsp. sativa, evolved from their wild relative, V. vinifera subsp. sylvestris. They were domesticated in Central Asia in the absence of the powdery mildew fungus, Erysiphe necator, which is thought to have originated in North America. However, powdery mildew resistance has previously been discovered in two Central Asian cultivars and in Chinese Vitis species. RESULTS A set of 380 unique genotypes were evaluated with data generated from 34 simple sequence repeat (SSR) markers. The set included 306 V. vinifera cultivars, 40 accessions of V. vinifera subsp. sylvestris, and 34 accessions of Vitis species from northern Pakistan, Afghanistan and China. Based on the presence of four SSR alleles previously identified as linked to the powdery mildew resistance locus, Ren1, 10 new mildew resistant genotypes were identified in the test set: eight were V. vinifera cultivars and two were V. vinifera subsp. sylvestris based on flower and seed morphology. Sequence comparison of a 620 bp region that includes the Ren1-linked allele (143 bp) of the co-segregating SSR marker SC8-0071-014, revealed that the ten newly identified genotypes have sequences that are essentially identical to the previously identified mildew resistant V. vinifera cultivars: 'Kishmish vatkana' and 'Karadzhandal'. Kinship analysis determined that three of the newly identified powdery mildew resistant accessions had a relationship with 'Kishmish vatkana' and 'Karadzhandal', and that six were not related to any other accession in this study set. Clustering procedures assigned accessions into three groups: 1) Chinese species; 2) a mixed group of cultivated and wild V. vinifera; and 3) table grape cultivars, including nine of the powdery mildew resistant accessions. Gene flow was detected among the groups. CONCLUSIONS This study provides evidence that powdery mildew resistance is present in V. vinifera subsp. sylvestris, the dioecious wild progenitor of the cultivated grape. Four first-degree parent progeny relationships were discovered among the hermaphroditic powdery mildew resistant cultivars, supporting the existence of intentional grape breeding efforts. Although several Chinese grape species are resistant to powdery mildew, no direct genetic link to the resistance found in V. vinifera could be established.
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Affiliation(s)
- Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
| | - Jean-Michel Boursiquot
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes, Montpellier SupAgro, 2 Place Viala, Montpellier 34060, France
| | - Gerald S Dangl
- Foundation Plant Services, University of California, Davis, CA 95616, USA
| | - Thierry Lacombe
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes, INRA, 2 Place Viala, Montpellier 34060, France
| | - Valerie Laucou
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes, INRA, 2 Place Viala, Montpellier 34060, France
| | - Alan C Tenscher
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
| | - M Andrew Walker
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
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Identification of promoter motifs regulating ZmeIF4E expression level involved in maize rough dwarf disease resistance in maize (Zea Mays L.). Mol Genet Genomics 2013; 288:89-99. [PMID: 23474695 DOI: 10.1007/s00438-013-0737-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 02/21/2013] [Indexed: 01/02/2023]
Abstract
Maize rough dwarf disease (MRDD, a viral disease) results in significant grain yield losses, while genetic basis of which is largely unknown. Based on comparative genomics, eukaryotic translation initiation factor 4E (eIF4E) was considered as a candidate gene for MRDD resistance, validation of which will help to understand the possible genetic mechanism of this disease. ZmeIF4E (orthologs of eIF4E gene in maize) encodes a protein of 218 amino acids, harboring five exons and no variation in the cDNA sequence is identified between the resistant inbred line, X178 and susceptible one, Ye478. ZmeIF4E expression was different in the two lines plants treated with three plant hormones, ethylene, salicylic acid, and jasmonates at V3 developmental stage, suggesting that ZmeIF4E is more likely to be involved in the regulation of defense gene expression and induction of local and systemic resistance. Moreover, four cis-acting elements related to plant defense responses, including DOFCOREZM, EECCRCAH1, GT1GAMSCAM4, and GT1CONSENSUS were detected in ZmeIF4E promoter for harboring sequence variation in the two lines. Association analysis with 163 inbred lines revealed that one SNP in EECCRCAH1 is significantly associated with CSI of MRDD in two environments, which explained 3.33 and 9.04 % of phenotypic variation, respectively. Meanwhile, one SNP in GT-1 motif was found to affect MRDD resistance only in one of the two environments, which explained 5.17 % of phenotypic variation. Collectively, regulatory motifs respectively harboring the two significant SNPs in ZmeIF4E promoter could be involved in the defense process of maize after viral infection. These results contribute to understand maize defense mechanisms against maize rough dwarf virus.
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Abstract
It is now well established that plants have an important place in studies of sex chromosome evolution because of the repeated independent evolution of separate sexes and sex chromosomes. There has been considerable recent progress in studying plant sex chromosomes. In this review, I focus on how these recent studies have helped clarify or answer several important questions about sex chromosome evolution, and I shall also try to clarify some common misconceptions. I also outline future work that will be needed to make further progress, including testing some important ideas by genetic, molecular, and developmental approaches. Systems with different ages can clearly help show the time course of events during changes from an ancestral co-sexual state (hermaphroditism or monoecy), and I will also explain how different questions can be studied in lineages whose dioecy or sex chromosomes evolved at different times in the past.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, The King's Buildings, West Mains Road, Edinburgh EH9 3JT, UK.
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