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Genetic and Biochemical Aspects of Floral Scents in Roses. Int J Mol Sci 2022; 23:ijms23148014. [PMID: 35887360 PMCID: PMC9321236 DOI: 10.3390/ijms23148014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 12/12/2022] Open
Abstract
Floral scents possess high ornamental and economic values to rose production in the floricultural industry. In the past two decades, molecular bases of floral scent production have been studied in the rose as well as their genetic inheritance. Some significant achievements have been acquired, such as the comprehensive rose genome and the finding of a novel geraniol synthase in plants. In this review, we summarize the composition of floral scents in modern roses, focusing on the recent advances in the molecular mechanisms of floral scent production and emission, as well as the latest developments in molecular breeding and metabolic engineering of rose scents. It could provide useful information for both studying and improving the floral scent production in the rose.
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Davik J, Røen D, Lysøe E, Buti M, Rossman S, Alsheikh M, Aiden EL, Dudchenko O, Sargent DJ. A chromosome-level genome sequence assembly of the red raspberry (Rubus idaeus L.). PLoS One 2022; 17:e0265096. [PMID: 35294470 PMCID: PMC8926247 DOI: 10.1371/journal.pone.0265096] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
Rubus idaeus L. (red raspberry), is a perennial woody plant species of the Rosaceae family that is widely cultivated in the temperate regions of world and is thus an economically important soft fruit species. It is prized for its flavour and aroma, as well as a high content of healthful compounds such as vitamins and antioxidants. Breeding programs exist globally for red raspberry, but variety development is a long and challenging process. Genomic and molecular tools for red raspberry are valuable resources for breeding. Here, a chromosome-length genome sequence assembly and related gene predictions for the red raspberry cultivar 'Anitra' are presented, comprising PacBio long read sequencing scaffolded using Hi-C sequence data. The assembled genome sequence totalled 291.7 Mbp, with 247.5 Mbp (84.8%) incorporated into seven sequencing scaffolds with an average length of 35.4 Mbp. A total of 39,448 protein-coding genes were predicted, 75% of which were functionally annotated. The seven chromosome scaffolds were anchored to a previously published genetic linkage map with a high degree of synteny and comparisons to genomes of closely related species within the Rosoideae revealed chromosome-scale rearrangements that have occurred over relatively short evolutionary periods. A chromosome-level genomic sequence of R. idaeus will be a valuable resource for the knowledge of its genome structure and function in red raspberry and will be a useful and important resource for researchers and plant breeders.
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Affiliation(s)
- Jahn Davik
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
- * E-mail:
| | - Dag Røen
- Graminor Breeding Ltd., Ås, Norway
| | - Erik Lysøe
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Matteo Buti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Simeon Rossman
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Muath Alsheikh
- Graminor Breeding Ltd., Ås, Norway
- Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, Texas, United States of America
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, Australia
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Shanghai Institute for Advanced Immunochemical Studies, Shanghai Tech, Pudong, China
| | - Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, Texas, United States of America
| | - Daniel James Sargent
- Department of Genetics, Genomics and Breeding, NIAB-EMR, East Malling, United Kingdom
- Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom
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Du J, Ge C, Li T, Wang S, Gao Z, Sassa H, Qiao Y. Molecular characteristics of S-RNase alleles as the determinant of self-incompatibility in the style of Fragaria viridis. HORTICULTURE RESEARCH 2021; 8:185. [PMID: 34333550 PMCID: PMC8325692 DOI: 10.1038/s41438-021-00623-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/29/2021] [Accepted: 06/01/2021] [Indexed: 05/11/2023]
Abstract
Strawberry (Fragaria spp.) is a member of the Rosoideae subfamily in the family Rosaceae. The self-incompatibility (SI) of some diploid species is a key agronomic trait that acts as a basic pollination barrier; however, the genetic mechanism underlying SI control in strawberry remains unclear. Two candidate S-RNases (Sa- and Sb-RNase) identified in the transcriptome of the styles of the self-incompatible Fragaria viridis 42 were confirmed to be SI determinants at the S locus following genotype identification and intraspecific hybridization using selfing progenies. Whole-genome collinearity and RNase T2 family analysis revealed that only an S locus exists in Fragaria; however, none of the compatible species contained S-RNase. Although the results of interspecific hybridization experiments showed that F. viridis (SI) styles could accept pollen from F. mandshurica (self-compatible), the reciprocal cross was incompatible. Sa and Sb-RNase contain large introns, and their noncoding sequences (promotors and introns) can be transcribed into long noncoding RNAs (lncRNAs). Overall, the genus Fragaria exhibits S-RNase-based gametophytic SI, and S-RNase loss occurs at the S locus of compatible germplasms. In addition, a type of SI-independent unilateral incompatibility exists between compatible and incompatible Fragaria species. Furthermore, the large introns and neighboring lncRNAs in S-RNase in Fragaria could offer clues about S-RNase expression strategies.
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Affiliation(s)
- Jianke Du
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, 271-8510, Chiba, Japan
| | - Chunfeng Ge
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, Jiangsu, China
| | - Tingting Li
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Sanhong Wang
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhihong Gao
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Hidenori Sassa
- Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, 271-8510, Chiba, Japan
| | - Yushan Qiao
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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Recent Progress in Enhancing Fungal Disease Resistance in Ornamental Plants. Int J Mol Sci 2021; 22:ijms22157956. [PMID: 34360726 PMCID: PMC8348885 DOI: 10.3390/ijms22157956] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 01/19/2023] Open
Abstract
Fungal diseases pose a major threat to ornamental plants, with an increasing percentage of pathogen-driven host losses. In ornamental plants, management of the majority of fungal diseases primarily depends upon chemical control methods that are often non-specific. Host basal resistance, which is deficient in many ornamental plants, plays a key role in combating diseases. Despite their economic importance, conventional and molecular breeding approaches in ornamental plants to facilitate disease resistance are lagging, and this is predominantly due to their complex genomes, limited availability of gene pools, and degree of heterozygosity. Although genetic engineering in ornamental plants offers feasible methods to overcome the intrinsic barriers of classical breeding, achievements have mainly been reported only in regard to the modification of floral attributes in ornamentals. The unavailability of transformation protocols and candidate gene resources for several ornamental crops presents an obstacle for tackling the functional studies on disease resistance. Recently, multiomics technologies, in combination with genome editing tools, have provided shortcuts to examine the molecular and genetic regulatory mechanisms underlying fungal disease resistance, ultimately leading to the subsequent advances in the development of novel cultivars with desired fungal disease-resistant traits, in ornamental crops. Although fungal diseases constitute the majority of ornamental plant diseases, a comprehensive overview of this highly important fungal disease resistance seems to be insufficient in the field of ornamental horticulture. Hence, in this review, we highlight the representative mechanisms of the fungal infection-related resistance to pathogens in plants, with a focus on ornamental crops. Recent progress in molecular breeding, genetic engineering strategies, and RNAi technologies, such as HIGS and SIGS for the enhancement of fungal disease resistance in various important ornamental crops, is also described.
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Cheng B, Wan H, Han Y, Yu C, Luo L, Pan H, Zhang Q. Identification and QTL Analysis of Flavonoids and Carotenoids in Tetraploid Roses Based on an Ultra-High-Density Genetic Map. FRONTIERS IN PLANT SCIENCE 2021; 12:682305. [PMID: 34177997 PMCID: PMC8226220 DOI: 10.3389/fpls.2021.682305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/11/2021] [Indexed: 05/27/2023]
Abstract
Roses are highly valuable within the flower industry. The metabolites of anthocyanins, flavonols, and carotenoids in rose petals are not only responsible for the various visible petal colors but also important bioactive compounds that are important for human health. In this study, we performed a QTL analysis on pigment contents to locate major loci that determine the flower color traits. An F1 population of tetraploid roses segregating for flower color was used to construct an ultra-high-density genetic linkage map using whole-genome resequencing technology to detect genome-wide SNPs. Previously developed SSR and SNP markers were also utilized to increase the marker density. Thus, a total of 9,259 markers were mapped onto seven linkage groups (LGs). The final length of the integrated map was 1285.11 cM, with an average distance of 0.14 cM between adjacent markers. The contents of anthocyanins, flavonols and carotenoids of the population were assayed to enable QTL analysis. Across the 33 components, 46 QTLs were detected, explaining 11.85-47.72% of the phenotypic variation. The mapped QTLs were physically clustered and primarily distributed on four linkage groups, namely LG2, LG4, LG6, and LG7. These results improve the basis for flower color marker-assisted breeding of tetraploid roses and guide the development of rose products.
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Affiliation(s)
- Bixuan Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Huihua Wan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Yu Han
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Chao Yu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Le Luo
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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Dos Reis MV, Rouhana LV, Sadeque A, Koga L, Clough SJ, Calla B, Paiva PDDO, Korban SS. Genome-wide expression of low temperature response genes in Rosa hybrida L. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 146:238-248. [PMID: 31765955 DOI: 10.1016/j.plaphy.2019.11.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/11/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
Plants respond to low temperature stress during cold acclimation, a complex process involving changes in physiological and biochemical modifications. The rose serves as a good model to investigate low temperature responses in perennial ornamentals. In this study, a heterologous apple microarray is used to investigate genome-wide expression profiles in Rosa hybrida subjected to low temperature dark treatment. Transcriptome profiles are determined in floral buds at 0h, 2h, and 12h of low temperature treatment (4 °C). It is observed that a total of 134 transcripts are up-regulated and 169 transcripts are down-regulated in response to low temperature. Interestingly, a total of eight up-regulated genes, including those coding for two cytochrome P450 proteins, two ankyrin repeat family proteins, two metal ion binding proteins, and two zinc finger protein-related transcription factors, along with a single down-regulated gene, coding for a dynamin-like protein, are detected. Transcript profiles of 12 genes known to be involved in cold stress response are also validated using qRT-PCR. Furthermore, expression patterns of the AP2/ERF gene family of transcription factors are investigated in both floral buds and leaves. Overall, AP2/ERFs genes are more rapidly induced in leaves than in floral buds. Moreover, differential expression of several AP2/ERF genes are detected earlier in vegetative rather than in reproductive tissues. These findings highlight important roles of various low temperature response genes in mediating cold acclimation, thereby allowing roses to adapt to low temperatures, but without adversely affecting flower bud development and subsequent flowering, while vegetative tissues undergo early adaptation to low temperatures.
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Affiliation(s)
- Michele Valquíria Dos Reis
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Agriculture, Federal University of Lavras, Lavras, MG, 37200-000, Brazil
| | - Laura Vaughn Rouhana
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ahmed Sadeque
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Lucimara Koga
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Steven J Clough
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; USDA-ARS, Urbana, IL, 61801, USA
| | - Bernanda Calla
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Schuyler S Korban
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Bourke PM, van Geest G, Voorrips RE, Jansen J, Kranenburg T, Shahin A, Visser RGF, Arens P, Smulders MJM, Maliepaard C. polymapR-linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. Bioinformatics 2019; 34:3496-3502. [PMID: 29722786 PMCID: PMC6184683 DOI: 10.1093/bioinformatics/bty371] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 05/09/2018] [Indexed: 12/20/2022] Open
Abstract
Motivation Polyploid species carry more than two copies of each chromosome, a condition found in many of the world’s most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realize all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops. Results polymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops. Availability and implementation polymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polymapR. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Peter M Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Geert van Geest
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands.,Deliflor Chrysanten B.V, Maasdijk, BS, The Netherlands
| | - Roeland E Voorrips
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Johannes Jansen
- Biometris, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Twan Kranenburg
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Arwa Shahin
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands.,Van Zanten Breeding B. V, Rijsenhout, EW, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Paul Arens
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Marinus J M Smulders
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Chris Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
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Li S, Yang G, Yang S, Just J, Yan H, Zhou N, Jian H, Wang Q, Chen M, Qiu X, Zhang H, Dong X, Jiang X, Sun Y, Zhong M, Bendahmane M, Ning G, Ge H, Hu JY, Tang K. The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose. Sci Rep 2019; 9:5985. [PMID: 30979937 PMCID: PMC6461668 DOI: 10.1038/s41598-019-42428-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 03/07/2019] [Indexed: 01/11/2023] Open
Abstract
Roses are important woody plants featuring a set of important traits that cannot be investigated in traditional model plants. Here, we used the restriction-site associated DNA sequencing (RAD-seq) technology to develop a high-density linkage map of the backcross progeny (BC1F1) between Rosa chinensis ‘Old Blush’ (OB) and R. wichuraiana ‘Basyes’ Thornless’ (BT). We obtained 643.63 million pair-end reads and identified 139,834 polymorphic tags that were distributed uniformly in the rose genome. 2,213 reliable markers were assigned to seven linkage groups (LGs). The length of the genetic map was 1,027.425 cM in total with a mean distance of 0.96 cM per marker locus. This new linkage map allowed anchoring an extra of 1.21/23.14 Mb (12.18/44.52%) of the unassembled OB scaffolds to the seven reference pseudo-chromosomes, thus significantly improved the quality of assembly of OB reference genome. We demonstrate that, while this new linkage map shares high collinearity level with strawberry genome, it also features two chromosomal rearrangements, indicating its usefulness as a resource for understanding the evolutionary scenario among Rosaceae genomes. Together with the newly released genome sequences for OB, this linkage map will facilitate the identification of genetic components underpinning key agricultural and biological traits, hence should greatly advance the studies and breeding efforts of rose.
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Affiliation(s)
- Shubin Li
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Guoqian Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan Province, China.,Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Shuhua Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jeremy Just
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69364, Lyon, France
| | - Huijun Yan
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Ningning Zhou
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Hongying Jian
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Qigang Wang
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Min Chen
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Xianqin Qiu
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Hao Zhang
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Xue Dong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiaodong Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan Province, China
| | - Yibo Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan Province, China
| | - Micai Zhong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan Province, China
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69364, Lyon, France
| | - Guogui Ning
- Key laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Ge
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Kaixue Tang
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China.
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9
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Bourke PM, van Geest G, Voorrips RE, Jansen J, Kranenburg T, Shahin A, Visser RGF, Arens P, Smulders MJM, Maliepaard C. polymapR-linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. BIOINFORMATICS (OXFORD, ENGLAND) 2019; 35:540. [PMID: 30629112 DOI: 10.1101/228817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
AbstractMotivationPolyploid species carry more than two copies of each chromosome, a condition found in many of the world’s most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realise all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops.ResultspolymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops.Availability and ImplementationpolymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) athttp://cran.r-project.org/packages=polymapR.ContactChris Maliepaard chris.maliepaard@wur.nl or Roeland E. Voorrips roeland.voorrips@wur.nl
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10
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Bourke PM, van Geest G, Voorrips RE, Jansen J, Kranenburg T, Shahin A, Visser RGF, Arens P, Smulders MJM, Maliepaard C. polymapR-linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. BIOINFORMATICS (OXFORD, ENGLAND) 2018. [PMID: 29722786 DOI: 10.1093/bioinformatica/bty371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
MOTIVATION Polyploid species carry more than two copies of each chromosome, a condition found in many of the world's most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realize all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops. RESULTS polymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops. AVAILABILITY AND IMPLEMENTATION polymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polymapR. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Peter M Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Geert van Geest
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
- Deliflor Chrysanten B.V, Maasdijk, BS, The Netherlands
| | - Roeland E Voorrips
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Johannes Jansen
- Biometris, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Twan Kranenburg
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Arwa Shahin
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
- Van Zanten Breeding B. V, Rijsenhout, EW, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Paul Arens
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Marinus J M Smulders
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Chris Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
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11
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Bourke PM, Gitonga VW, Voorrips RE, Visser RGF, Krens FA, Maliepaard C. Multi-environment QTL analysis of plant and flower morphological traits in tetraploid rose. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2055-2069. [PMID: 29961102 PMCID: PMC6154034 DOI: 10.1007/s00122-018-3132-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 06/20/2018] [Indexed: 05/09/2023]
Abstract
KEY MESSAGE Rose morphological traits such as prickles or petal number are influenced by a few key QTL which were detected across different growing environments-necessary for genomics-assisted selection in non-target environments. Rose, one of the world's most-loved and commercially important ornamental plants, is predominantly tetraploid, possessing four rather than two copies of each chromosome. This condition complicates genetic analysis, and so the majority of previous genetic studies in rose have been performed at the diploid level. However, there may be advantages to performing genetic analyses at the tetraploid level, not least because this is the ploidy level of most breeding germplasm. Here, we apply recently developed methods for quantitative trait loci (QTL) detection in a segregating tetraploid rose population (F1 = 151) to unravel the genetic control of a number of key morphological traits. These traits were measured both in the Netherlands and Kenya. Since ornamental plant breeding and selection are increasingly being performed at locations other than the production sites, environment-neutral QTL are required to maximise the effectiveness of breeding programmes. We detected a number of robust, multi-environment QTL for such traits as stem and petiole prickles, petal number and stem length that were localised on the recently developed high-density SNP linkage map for rose. Our work explores the complex genetic architecture of these important morphological traits at the tetraploid level, while helping to advance the methods for marker-trait exploration in polyploid species.
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Affiliation(s)
- Peter M Bourke
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Virginia W Gitonga
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
- Selecta Kenya GmbH & Co. KG, P. O. Box 64132, Nairobi, 00620, Kenya
| | - Roeland E Voorrips
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Frans A Krens
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Chris Maliepaard
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands.
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12
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Kishi-Kaboshi M, Aida R, Sasaki K. Genome engineering in ornamental plants: Current status and future prospects. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 131:47-52. [PMID: 29709514 DOI: 10.1016/j.plaphy.2018.03.015] [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: 12/26/2017] [Revised: 03/12/2018] [Accepted: 03/12/2018] [Indexed: 05/21/2023]
Abstract
Ornamental plants, like roses, carnations, and chrysanthemums, are economically important and are sold all over the world. In addition, numerous cut and garden flowers add colors to homes and gardens. Various strategies of plant breeding have been employed to improve traits of many ornamental plants. These approaches span from conventional techniques, such as crossbreeding and mutation breeding, to genetically modified plants. Recently, genome editing has become available as an efficient means for modifying traits in plant species. Genome editing technology is useful for genetic analysis and is poised to become a common breeding method for ornamental plants. In this review, we summarize the benefits and limitations of conventional breeding techniques and genome editing methods and discuss their future potential to accelerate the rate breeding programs in ornamental plants.
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Affiliation(s)
- Mitsuko Kishi-Kaboshi
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki, 305-0852, Japan
| | - Ryutaro Aida
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki, 305-0852, Japan
| | - Katsutomo Sasaki
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki, 305-0852, Japan.
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13
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Adhikari L, Lindstrom OM, Markham J, Missaoui AM. Dissecting Key Adaptation Traits in the Polyploid Perennial Medicago sativa Using GBS-SNP Mapping. FRONTIERS IN PLANT SCIENCE 2018; 9:934. [PMID: 30022989 PMCID: PMC6039623 DOI: 10.3389/fpls.2018.00934] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/11/2018] [Indexed: 05/18/2023]
Abstract
Understanding key adaptation traits is crucial to developing new cultivars with broad adaptations. The main objective of this research is to understand the genetic basis of winter hardiness (WH) and fall dormancy (FD) in alfalfa and the association between the two traits. QTL analysis was conducted in a pseudo-testcross F1 population developed from two cultivars contrasting in FD (3010 with FD = 2 and CW 1010 with FD = 10). The mapping population was evaluated in three replications at two locations (Watkinsville and Blairsville, GA). FD levels showed low to moderate correlations with WH (0.22-0.57). Assessing dormancy in winter is more reliable than in the fall in southern regions with warm winters. The mapping population was genotyped using Genotyping-by-sequencing (GBS). Single dose allele SNPs (SDA) were used for constructing linkage maps. The parental map (CW 1010) consisted of 32 linkage groups spanning 2127.5 cM with 1377 markers and an average marker density of 1.5 cM/SNP. The maternal map (3010) had 32 linkage groups spanning 2788.4 cM with 1837 SDA SNPs with an average marker density of 1.5 cM/SNP. Forty-five significant (P < 0.05) QTLs for FD and 35 QTLs for WH were detected on both male and female linkage maps. More than 75% (22/28) of the dormancy QTL detected from the 3010 parent did not share genomic regions with WH QTLs and more than 70% (12/17) dormancy QTLs detected from CW 1010 parent were localized in different genomic regions than WH QTLs. These results suggest that the two traits have independent inheritance and therefore can be improved separately in breeding programs.
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Affiliation(s)
- Laxman Adhikari
- Crop and Soil Sciences and Institute of Plant Breeding Genetics and Genomics, Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | | | - Jonathan Markham
- Crop and Soil Sciences and Institute of Plant Breeding Genetics and Genomics, Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Ali M. Missaoui
- Crop and Soil Sciences and Institute of Plant Breeding Genetics and Genomics, Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
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14
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Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Arens P, Voorrips RE, Maliepaard C, Neu E, Linde M, Le Paslier MC, Bérard A, Bounon R, Clotault J, Choisne N, Quesneville H, Kawamura K, Aubourg S, Sakr S, Smulders MJM, Schijlen E, Bucher E, Debener T, De Riek J, Foucher F. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. NATURE PLANTS 2018; 4:473-484. [PMID: 29892093 DOI: 10.1101/254102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/01/2018] [Indexed: 05/27/2023]
Abstract
Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.
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Affiliation(s)
- L Hibrand Saint-Oyant
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Ruttink
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - L Hamama
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - I Kirov
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
- Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - D Lakhwani
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N N Zhou
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - P M Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - N Daccord
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Leus
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - D Schulz
- Leibniz Universität, Hannover, Germany
| | - H Van de Geest
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - T Hesselink
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - K Van Laere
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - K Debray
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Balzergue
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Thouroude
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - A Chastellier
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - J Jeauffre
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Voisine
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Gaillard
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T J A Borm
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - P Arens
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - R E Voorrips
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - C Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Neu
- Leibniz Universität, Hannover, Germany
| | - M Linde
- Leibniz Universität, Hannover, Germany
| | - M C Le Paslier
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - A Bérard
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - R Bounon
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - J Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N Choisne
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - H Quesneville
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - K Kawamura
- Osaka Institute of Technology, Osaka, Japan
| | - S Aubourg
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Sakr
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - M J M Smulders
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Schijlen
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - E Bucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Debener
- Leibniz Universität, Hannover, Germany
| | - J De Riek
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - F Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France.
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15
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Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Arens P, Voorrips RE, Maliepaard C, Neu E, Linde M, Le Paslier MC, Bérard A, Bounon R, Clotault J, Choisne N, Quesneville H, Kawamura K, Aubourg S, Sakr S, Smulders MJM, Schijlen E, Bucher E, Debener T, De Riek J, Foucher F. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. NATURE PLANTS 2018; 4:473-484. [PMID: 29892093 PMCID: PMC6786968 DOI: 10.1038/s41477-018-0166-1] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/01/2018] [Indexed: 05/18/2023]
Abstract
Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.
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Affiliation(s)
- L Hibrand Saint-Oyant
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Ruttink
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - L Hamama
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - I Kirov
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
- Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - D Lakhwani
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N N Zhou
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - P M Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - N Daccord
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Leus
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - D Schulz
- Leibniz Universität, Hannover, Germany
| | - H Van de Geest
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - T Hesselink
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - K Van Laere
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - K Debray
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Balzergue
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Thouroude
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - A Chastellier
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - J Jeauffre
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Voisine
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Gaillard
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T J A Borm
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - P Arens
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - R E Voorrips
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - C Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Neu
- Leibniz Universität, Hannover, Germany
| | - M Linde
- Leibniz Universität, Hannover, Germany
| | - M C Le Paslier
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - A Bérard
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - R Bounon
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - J Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N Choisne
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - H Quesneville
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - K Kawamura
- Osaka Institute of Technology, Osaka, Japan
| | - S Aubourg
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Sakr
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - M J M Smulders
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Schijlen
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - E Bucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Debener
- Leibniz Universität, Hannover, Germany
| | - J De Riek
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - F Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France.
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16
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Yan M, Byrne DH, Klein PE, Yang J, Dong Q, Anderson N. Genotyping-by-sequencing application on diploid rose and a resulting high-density SNP-based consensus map. HORTICULTURE RESEARCH 2018; 5:17. [PMID: 29619228 PMCID: PMC5878828 DOI: 10.1038/s41438-018-0021-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/03/2017] [Accepted: 01/22/2018] [Indexed: 05/09/2023]
Abstract
Roses, which have been cultivated for at least 5000 years, are one of the most important ornamental crops in the world. Because of the interspecific nature and high heterozygosity in commercial roses, the genetic resources available for rose are limited. To effectively identify markers associated with QTL controlling important traits, such as disease resistance, abundant markers along the genome and careful phenotyping are required. Utilizing genotyping by sequencing technology and the strawberry genome (Fragaria vesca v2.0.a1) as a reference, we generated thousands of informative single nucleotide polymorphism (SNP) markers. These SNPs along with known bridge simple sequence repeat (SSR) markers allowed us to create the first high-density integrated consensus map for diploid roses. Individual maps were first created for populations J06-20-14-3×"Little Chief" (J14-3×LC), J06-20-14-3×"Vineyard Song" (J14-3×VS) and "Old Blush"×"Red Fairy" (OB×RF) and these maps were linked with 824 SNPs and 13 SSR bridge markers. The anchor SSR markers were used to determine the numbering of the rose linkage groups. The diploid consensus map has seven linkage groups (LGs), a total length of 892.2 cM, and an average distance of 0.25 cM between 3527 markers. By combining three individual populations, the marker density and the reliability of the marker order in the consensus map was improved over a single population map. Extensive synteny between the strawberry and diploid rose genomes was observed. This consensus map will serve as the tool for the discovery of marker-trait associations in rose breeding using pedigree-based analysis. The high level of conservation observed between the strawberry and rose genomes will help further comparative studies within the Rosaceae family and may aid in the identification of candidate genes within QTL regions.
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Affiliation(s)
- Muqing Yan
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
| | - David H. Byrne
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Patricia E. Klein
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843 USA
| | - Jizhou Yang
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843 USA
- Present Address: Department of Computer Science, San Francisco State University, San Francisco, CA 94132 USA
| | - Qianni Dong
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
- Present Address: Monsanto Company, 700 Chesterfield Parkway West, Chesterfield, MO 63017 USA
| | - Natalie Anderson
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
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17
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Nguyen THN, Schulz D, Winkelmann T, Debener T. Genetic dissection of adventitious shoot regeneration in roses by employing genome-wide association studies. PLANT CELL REPORTS 2017. [PMID: 28647832 DOI: 10.1007/s00299-017-2170-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We analysed the capacity to regenerate adventitious shoots in 96 rose genotypes and found 88 SNP markers associated with QTLs, some of which are derived from candidate genes for shoot regeneration. In an association panel of 96 rose genotypes previously analysed for petal colour, we conducted a genome-wide association study on the capacity of leaf petioles for direct shoot regeneration. Shoot regeneration rate and shoot ratio (number of shoots/total number of explants) were used as phenotypic descriptors for regeneration capacity. Two independent experiments were carried out with six replicates of ten explants each. We found significant variation between the genotypes ranging from 0.88 to 88.33% for the regeneration rate and from 0.008 to 1.2 for the shoot ratio, which exceeded the rates reported so far. Furthermore, we found 88 SNP markers associated with either the shoot regeneration rate or the shoot ratio. In this association analysis, we found 12 SNP markers from ESTs (expressed sequence tags) matching known candidate genes that are involved in shoot morphogenesis. The best markers explained more than 51% of the variance in the shoot regeneration rate and more than 0.65 of the variance in the shoot regeneration ratio between the homozygote marker classes. The genes underlying some of the best markers such as a GT-transcription factor or an LRR receptor-like protein kinase are novel candidate genes putatively involved in the observed phenotypic differences. The associated markers were mapped to the closely related genome of Fragaria vesca and revealed many distinct clusters, which also comprised the known candidate genes that functioned in the organogenesis of plant shoots. However, the validation of candidate genes and their functional relationship to shoot regeneration require further analysis in independent rose populations and functional analyses.
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Affiliation(s)
- Thi Hong Nhung Nguyen
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
- Institute of Agricultural Genetics, Hanoi, Vietnam
| | - Dietmar Schulz
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Woody Plant and Propagation Physiology, Leibniz Universität Hannover, Hannover, Germany
| | - Thomas Debener
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany.
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18
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Bourke PM, Arens P, Voorrips RE, Esselink GD, Koning-Boucoiran CFS, Van't Westende WPC, Santos Leonardo T, Wissink P, Zheng C, van Geest G, Visser RGF, Krens FA, Smulders MJM, Maliepaard C. Partial preferential chromosome pairing is genotype dependent in tetraploid rose. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:330-343. [PMID: 28142191 DOI: 10.1111/tpj.13496] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 05/18/2023]
Abstract
It has long been recognised that polyploid species do not always neatly fall into the categories of auto- or allopolyploid, leading to the term 'segmental allopolyploid' to describe everything in between. The meiotic behaviour of such intermediate species is not fully understood, nor is there consensus as to how to model their inheritance patterns. In this study we used a tetraploid cut rose (Rosa hybrida) population, genotyped using the 68K WagRhSNP array, to construct an ultra-high-density linkage map of all homologous chromosomes using methods previously developed for autotetraploids. Using the predicted bivalent configurations in this population we quantified differences in pairing behaviour among and along homologous chromosomes, leading us to correct our estimates of recombination frequency to account for this behaviour. This resulted in the re-mapping of 25 695 SNP markers across all homologues of the seven rose chromosomes, tailored to the pairing behaviour of each chromosome in each parent. We confirmed the inferred differences in pairing behaviour among chromosomes by examining repulsion-phase linkage estimates, which also carry information about preferential pairing and recombination. Currently, the closest sequenced relative to rose is Fragaria vesca. Aligning the integrated ultra-dense rose map with the strawberry genome sequence provided a detailed picture of the synteny, confirming overall co-linearity but also revealing new genomic rearrangements. Our results suggest that pairing affinities may vary along chromosome arms, which broadens our current understanding of segmental allopolyploidy.
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Affiliation(s)
- Peter M Bourke
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Paul Arens
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Roeland E Voorrips
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - G Danny Esselink
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | | | - Wendy P C Van't Westende
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Tiago Santos Leonardo
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Patrick Wissink
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Chaozhi Zheng
- Biometris, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Geert van Geest
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Horticulture and Product Physiology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Frans A Krens
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Marinus J M Smulders
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Chris Maliepaard
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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19
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Shirasawa K, Tanaka M, Takahata Y, Ma D, Cao Q, Liu Q, Zhai H, Kwak SS, Cheol Jeong J, Yoon UH, Lee HU, Hirakawa H, Isobe S. A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas). Sci Rep 2017; 7:44207. [PMID: 28281636 PMCID: PMC5345071 DOI: 10.1038/srep44207] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/06/2017] [Indexed: 12/14/2022] Open
Abstract
Sweetpotato (Ipomoea batatas) is an autohexaploid species with 90 chromosomes (2n = 6x = 90) and a basic chromosome number of 15, and is therefore regarded as one of the most challenging species for high-density genetic map construction. Here, we used single nucleotide polymorphisms (SNPs) identified by double-digest restriction site-associated DNA sequencing based on next-generation sequencing technology to construct a map for sweetpotato. We then aligned the sequence reads onto the reference genome sequence of I. trifida, a likely diploid ancestor of sweetpotato, to detect SNPs. In addition, to simplify analysis of the complex genetic mode of autohexaploidy, we used an S1 mapping population derived from self-pollination of a single parent. As a result, 28,087 double-simplex SNPs showing a Mendelian segregation ratio in the S1 progeny could be mapped onto 96 linkage groups (LGs), covering a total distance of 33,020.4 cM. Based on the positions of the SNPs on the I. trifida genome, the LGs were classified into 15 groups, each with roughly six LGs and six small extra groups. The molecular genetic techniques used in this study are applicable to high-density mapping of other polyploid plant species, including important crops.
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Affiliation(s)
| | - Masaru Tanaka
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Japan
| | - Yasuhiro Takahata
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Japan
| | - Daifu Ma
- Chinese Academy of Agricultural Sciences, China
| | - Qinghe Cao
- Chinese Academy of Agricultural Sciences, China
| | | | - Hong Zhai
- China Agricultural University, China
| | - Sang-Soo Kwak
- Korea Research Institute of Bioscience &Biotechnology, South Korea
| | - Jae Cheol Jeong
- Korea Research Institute of Bioscience &Biotechnology, South Korea
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20
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Grandke F, Ranganathan S, van Bers N, de Haan JR, Metzler D. PERGOLA: fast and deterministic linkage mapping of polyploids. BMC Bioinformatics 2017; 18:12. [PMID: 28049428 PMCID: PMC5210299 DOI: 10.1186/s12859-016-1416-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 12/09/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A large share of agriculturally and horticulturally important plant species are polyploid. Linkage maps are used to locate associations between genes and traits by breeders and geneticists. Linkage map creation for polyploid species is not supported by standard tools. We want to overcome this limitation and validate our results with simulation studies. RESULTS We developed PERGOLA, a deterministic and heuristic method that addresses this problem. We show that it creates correct linkage groups, marker orders and distances for simulated and real datasets. We compare it to existing tools and demonstrate that it overcomes limitations in ploidy and outperforms them in computational time and mapping accuracy. We represent linkage maps as dendrograms and show that this has advantages in the comparison of different maps. CONCLUSIONS PERGOLA can be used successfully to calculate linkage maps for diploid and polyploid species and outperforms existing tools.
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Affiliation(s)
- Fabian Grandke
- Genetwister Technologies B.V., Wageningen, The Netherlands. .,Fakultät für Biologie, University of Munich (LMU), Munich, Germany.
| | | | | | - Jorn R de Haan
- Genetwister Technologies B.V., Wageningen, The Netherlands
| | - Dirk Metzler
- Fakultät für Biologie, University of Munich (LMU), Munich, Germany
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21
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Lenz RR, Dai W. Mapping X-Disease Phytoplasma Resistance in Prunus virginiana. FRONTIERS IN PLANT SCIENCE 2017; 8:2057. [PMID: 29238359 PMCID: PMC5712551 DOI: 10.3389/fpls.2017.02057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/17/2017] [Indexed: 05/10/2023]
Abstract
Phytoplasmas such as "Candidatus Phytoplasma pruni," the causal agent of X-disease of stone fruits, lack detailed biological analysis. This has limited the understanding of plant resistance mechanisms. Chokecherry (Prunus virginiana L.) is a promising model to be used for the plant-phytoplasma interaction due to its documented ability to resist X-disease infection. A consensus chokecherry genetic map "Cho" was developed with JoinMap 4.0 by joining two parental maps. The new map contains a complete set of 16 linkage groups, spanning a genetic distance of 2,172 cM with an average marker density of 3.97 cM. Three significant quantitative trait loci (QTL) associated with X-disease resistance were identified contributing to a total of 45.9% of the phenotypic variation. This updated genetic linkage map and the identified QTL will provide the framework needed to facilitate molecular genetics, genomics, breeding, and biotechnology research concerning X-disease in chokecherry and other Prunus species.
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22
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Liorzou M, Pernet A, Li S, Chastellier A, Thouroude T, Michel G, Malécot V, Gaillard S, Briée C, Foucher F, Oghina-Pavie C, Clotault J, Grapin A. Nineteenth century French rose (Rosa sp.) germplasm shows a shift over time from a European to an Asian genetic background. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4711-25. [PMID: 27406785 PMCID: PMC4973750 DOI: 10.1093/jxb/erw269] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Hybridization with introduced genetic resources is commonly practiced in ornamental plant breeding to introgress desired traits. The 19th century was a golden age for rose breeding in France. The objective here was to study the evolution of rose genetic diversity over this period, which included the introduction of Asian genotypes into Europe. A large sample of 1228 garden roses encompassing the conserved diversity cultivated during the 18th and 19th centuries was genotyped with 32 microsatellite primer pairs. Its genetic diversity and structure were clarified. Wide diversity structured in 16 genetic groups was observed. Genetic differentiation was detected between ancient European and Asian accessions, and a temporal shift from a European to an Asian genetic background was observed in cultivated European hybrids during the 19th century. Frequent crosses with Asian roses throughout the 19th century and/or selection for Asiatic traits may have induced this shift. In addition, the consistency of the results with respect to a horticultural classification is discussed. Some horticultural groups, defined according to phenotype and/or knowledge of their pedigree, seem to be genetically more consistent than others, highlighting the difficulty of classifying cultivated plants. Therefore, the horticultural classification is probably more appropriate for commercial purposes rather than genetic relatedness, especially to define preservation and breeding strategies.
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Affiliation(s)
- Mathilde Liorzou
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Alix Pernet
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Shubin Li
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Annie Chastellier
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Tatiana Thouroude
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Gilles Michel
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Valéry Malécot
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Sylvain Gaillard
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Céline Briée
- Université d'Angers, UMR CNRS 6258 CERHIO, Centre de recherches historiques de l'Ouest, 5 bis Bd Lavoisier 49045 Angers, France
| | - Fabrice Foucher
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Cristiana Oghina-Pavie
- Université d'Angers, UMR CNRS 6258 CERHIO, Centre de recherches historiques de l'Ouest, 5 bis Bd Lavoisier 49045 Angers, France
| | - Jérémy Clotault
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Agnès Grapin
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
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23
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Vukosavljev M, Arens P, Voorrips RE, van ‘t Westende WPC, Esselink GD, Bourke PM, Cox P, van de Weg WE, Visser RGF, Maliepaard C, Smulders MJM. High-density SNP-based genetic maps for the parents of an outcrossed and a selfed tetraploid garden rose cross, inferred from admixed progeny using the 68k rose SNP array. HORTICULTURE RESEARCH 2016; 3:16052. [PMID: 27818777 PMCID: PMC5080978 DOI: 10.1038/hortres.2016.52] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 09/26/2016] [Accepted: 09/30/2016] [Indexed: 05/21/2023]
Abstract
Dense genetic maps create a base for QTL analysis of important traits and future implementation of marker-assisted breeding. In tetraploid rose, the existing linkage maps include <300 markers to cover 28 linkage groups (4 homologous sets of 7 chromosomes). Here we used the 68k WagRhSNP Axiom single-nucleotide polymorphism (SNP) array for rose, in combination with SNP dosage calling at the tetraploid level, to genotype offspring from the garden rose cultivar 'Red New Dawn'. The offspring proved to be not from a single bi-parental cross. In rose breeding, crosses with unintended parents occur regularly. We developed a strategy to separate progeny into putative populations, even while one of the parents was unknown, using principle component analysis on pairwise genetic distances based on sets of selected SNP markers that were homozygous, and therefore uninformative for one parent. One of the inferred populations was consistent with self-fertilization of 'Red New Dawn'. Subsequently, linkage maps were generated for a bi-parental and a self-pollinated population with 'Red New Dawn' as the common maternal parent. The densest map, for the selfed parent, had 1929 SNP markers on 25 linkage groups, covering 1765.5 cM at an average marker distance of 0.9 cM. Synteny with the strawberry (Fragaria vesca) genome was extensive. Rose ICM1 corresponded to F. vesca pseudochromosome 7 (Fv7), ICM4 to Fv4, ICM5 to Fv3, ICM6 to Fv2 and ICM7 to Fv5. Rose ICM2 corresponded to parts of F. vesca pseudochromosomes 1 and 6, whereas ICM3 is syntenic to the remainder of Fv6.
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Affiliation(s)
- Mirjana Vukosavljev
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - Paul Arens
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - Roeland E Voorrips
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - Wendy PC van ‘t Westende
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - GD Esselink
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - Peter M Bourke
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - Peter Cox
- Roath BV, Eindhoven, The Netherlands
| | - W Eric van de Weg
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - Richard GF Visser
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - Chris Maliepaard
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
| | - Marinus JM Smulders
- Wageningen UR Plant Breeding, Wageningen University & Research, NL-6700 AJ Wageningen, The Netherlands
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24
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Schulz DF, Schott RT, Voorrips RE, Smulders MJM, Linde M, Debener T. Genome-Wide Association Analysis of the Anthocyanin and Carotenoid Contents of Rose Petals. FRONTIERS IN PLANT SCIENCE 2016; 7:1798. [PMID: 27999579 PMCID: PMC5138216 DOI: 10.3389/fpls.2016.01798] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/15/2016] [Indexed: 05/18/2023]
Abstract
Petal color is one of the key characteristics determining the attractiveness and therefore the commercial value of an ornamental crop. Here, we present the first genome-wide association study for the important ornamental crop rose, focusing on the anthocyanin and carotenoid contents in petals of 96 diverse tetraploid garden rose genotypes. Cultivated roses display a vast phenotypic and genetic diversity and are therefore ideal targets for association genetics. For marker analysis, we used a recently designed Axiom SNP chip comprising 68,000 SNPs with additionally 281 SSRs, 400 AFLPs and 246 markers from candidate genes. An analysis of the structure of the rose population revealed three subpopulations with most of the genetic variation between individual genotypes rather than between clusters and with a high average proportion of heterozygous loci. The mapping of markers significantly associated with anthocyanin and carotenoid content to the related Fragaria and Prunus genomes revealed clusters of associated markers indicating five genomic regions associated with the total anthocyanin content and two large clusters associated with the carotenoid content. Among the marker clusters associated with the phenotypes, we found several candidate genes with known functions in either the anthocyanin or the carotenoid biosynthesis pathways. Among others, we identified a glutathione-S-transferase, 4CL, an auxin response factor and F3'H as candidate genes affecting anthocyanin concentration, and CCD4 and Zeaxanthine epoxidase as candidates affecting the concentration of carotenoids. These markers are starting points for future validation experiments in independent populations as well as for functional genomic studies to identify the causal factors for the observed color phenotypes. Furthermore, validated markers may be interesting tools for marker-assisted selection in commercial breeding programmes in that they provide the tools to identify superior parental combinations that combine several associated markers in higher dosages.
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Affiliation(s)
- Dietmar F. Schulz
- Abteilung Molekulare Pflanzenzüchtung, Institute for Plant Genetics, Leibnitz University HannoverHannover, Germany
| | - Rena T. Schott
- Abteilung Molekulare Pflanzenzüchtung, Institute for Plant Genetics, Leibnitz University HannoverHannover, Germany
| | - Roeland E. Voorrips
- Wageningen University and Research Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Marinus J. M. Smulders
- Wageningen University and Research Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Marcus Linde
- Abteilung Molekulare Pflanzenzüchtung, Institute for Plant Genetics, Leibnitz University HannoverHannover, Germany
| | - Thomas Debener
- Abteilung Molekulare Pflanzenzüchtung, Institute for Plant Genetics, Leibnitz University HannoverHannover, Germany
- *Correspondence: Thomas Debener
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25
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Kirov IV, Van Laere K, Khrustaleva LI. High resolution physical mapping of single gene fragments on pachytene chromosome 4 and 7 of Rosa. BMC Genet 2015; 16:74. [PMID: 26134672 PMCID: PMC4488978 DOI: 10.1186/s12863-015-0233-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 06/16/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rosaceae is a family containing many economically important fruit and ornamental species. Although fluorescence in situ hybridization (FISH)-based physical mapping of plant genomes is a valuable tool for map-based cloning, comparative genomics and evolutionary studies, no studies using high resolution physical mapping have been performed in this family. Previously we proved that physical mapping of single-copy genes as small as 1.1 kb is possible on mitotic metaphase chromosomes of Rosa wichurana using Tyramide-FISH. In this study we aimed to further improve the physical map of Rosa wichurana by applying high resolution FISH to pachytene chromosomes. RESULTS Using high resolution Tyramide-FISH and multicolor Tyramide-FISH, 7 genes (1.7-3 kb) were successfully mapped on pachytene chromosomes 4 and 7 of Rosa wichurana. Additionally, by using multicolor Tyramide-FISH three closely located genes were simultaneously visualized on chromosome 7. A detailed map of heterochromatine/euchromatine patterns of chromosome 4 and 7 was developed with indication of the physical position of these 7 genes. Comparison of the gene order between Rosa wichurana and Fragaria vesca revealed a poor collinearity for chromosome 7, but a perfect collinearity for chromosome 4. CONCLUSIONS High resolution physical mapping of short probes on pachytene chromosomes of Rosa wichurana was successfully performed for the first time. Application of Tyramide-FISH on pachytene chromosomes allowed the mapping resolution to be increased up to 20 times compared to mitotic metaphase chromosomes. High resolution Tyramide-FISH and multicolor Tyramide-FISH might become useful tools for further physical mapping of single-copy genes and for the integration of physical and genetic maps of Rosa wichurana and other members of the Rosaceae.
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Affiliation(s)
- Ilya V Kirov
- Department of Genetics, Biotechnology, Plant Breeding and Seed Science, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str.49, 127550, Moscow, Russia. .,Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Listvennichnaya Alleya 5, 127550, Moscow, Russia. .,Plant Sciences Unit, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research (ILVO), Caritasstraat 21, 9090, Melle, Belgium.
| | - Katrijn Van Laere
- Plant Sciences Unit, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research (ILVO), Caritasstraat 21, 9090, Melle, Belgium.
| | - Ludmila I Khrustaleva
- Department of Genetics, Biotechnology, Plant Breeding and Seed Science, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str.49, 127550, Moscow, Russia. .,Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Listvennichnaya Alleya 5, 127550, Moscow, Russia.
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Gitonga VW, Koning-Boucoiran CFS, Verlinden K, Dolstra O, Visser RGF, Maliepaard C, Krens FA. Genetic variation, heritability and genotype by environment interaction of morphological traits in a tetraploid rose population. BMC Genet 2014; 15:146. [PMID: 25526782 PMCID: PMC4293809 DOI: 10.1186/s12863-014-0146-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 12/08/2014] [Indexed: 11/29/2022] Open
Abstract
Background Global trade has ensured that the ornamental horticulture continues to grow worldwide, with rose hybrids being the most economically important genus (Rosa x hybrida). Due to changes in global trade and an increase in energy costs the ornamental industry has seen a shift in the production and sale of flowers from the US and Europe alone to production in Africa and Latin America. As Kenya is a major exporter of roses to Europe we studied the genetic variation and heritability of specific morphological traits in a tetraploid population grown in the Netherlands and in Kenya. The aim was to estimate genotype by environment interaction (G × E) and to investigate the implications of (G × E) for rose breeding. Results A tetraploid rose population (K5) from a cross between two tetraploid parents was field tested over two seasons in the Netherlands (summer and winter) and two locations in Kenya (Nairobi and Njoro). Ten traits were compared per genotype across the four environments. There were differences in trait association across the four environments showing that the traits were partially influenced by the environment. The traits that had a low ratio of σ2ge/σ2g also showed a high value for heritability. For the traits number of petals, prickles on petioles, prickles on stems the interaction is minimal. For the traits chlorophyll content, stem width and side shoots we observed a much higher interaction ratio of 0.83, 1.43 and 3.13 respectively. The trait number of petals had the highest heritability of 0.96 and the lowest σ2ge/σ2g ratio (0.08). The trait number of side shoots (SS) with the lowest heritability (0.40) also had the highest σ2ge/σ2g ratio of 3.13. Conclusion Attained by this experiment showed that we have different magnitudes of non-crossover G × E interactions. For the traits number of petals, prickles on stems and prickles on petioles with a low interaction and high heritability, selection can be done at any of the environments. Thus, these traits can be confirmed at the breeding site. For the traits stem width, side shoots and chlorophyll content that had a higher interaction selection for or against these traits should be done at the production location or at least be verified there. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0146-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Virginia W Gitonga
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ, Wageningen, the Netherlands. .,Present address: Lex + East Africa, PO Box 1739, Naivasha, 20117, Kenya.
| | - Carole F S Koning-Boucoiran
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ, Wageningen, the Netherlands.
| | - Kathryn Verlinden
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ, Wageningen, the Netherlands. .,Present address: Syngenta Seeds B.V, PO Box 2, 1600 AA, Enkhuizen, the Netherlands.
| | - Oene Dolstra
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ, Wageningen, the Netherlands.
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ, Wageningen, the Netherlands.
| | - Chris Maliepaard
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ, Wageningen, the Netherlands.
| | - Frans A Krens
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ, Wageningen, the Netherlands.
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Debener T, Byrne DH. Disease resistance breeding in rose: current status and potential of biotechnological tools. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 228:107-17. [PMID: 25438791 DOI: 10.1016/j.plantsci.2014.04.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/30/2014] [Accepted: 04/03/2014] [Indexed: 05/09/2023]
Abstract
The cultivated rose is a multispecies complex for which a high level of disease protection is needed due to the low tolerance of blemishes in ornamental plants. The most important fungal diseases are black spot, powdery mildew, botrytis and downy mildew. Rose rosette, a lethal viral pathogen, is emerging as a devastating disease in North America. Currently rose breeders use a recurrent phenotypic selection approach and perform selection for disease resistance for most pathogen issues in a 2-3 year field trial. Marker assisted selection could accelerate this breeding process. Thus far markers have been identified for resistance to black spot (Rdrs) and powdery mildew and with the ability of genotyping by sequencing to generate 1000s of markers our ability to identify markers useful in plant improvement should increase exponentially. Transgenic rose lines with various fungal resistance genes inserted have shown limited success and RNAi technology has potential to provide virus resistance. Roses, as do other plants, have sequences homologous to characterized R-genes in their genomes, some which have been related to specific disease resistance. With improving next generation sequencing technology, our ability to do genomic and transcriptomic studies of the resistance related genes in both the rose and the pathogens to reveal novel gene targets to develop resistant roses will accelerate. Finally, the development of designer nucleases opens up a potentially non-GMO approach to directly modify a rose's DNA to create a disease resistant rose. Although there is much potential, at present rose breeders are not using marker assisted breeding primarily because a good suite of marker/trait associations (MTA) that would ensure a path to stable disease resistance is not available. As our genomic analytical tools improve, so will our ability to identify useful genes and linked markers. Once these MTAs are available, it will be the cost savings, both in time and money, that will convince the breeders to use the technology.
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Affiliation(s)
- Thomas Debener
- Leibniz University of Hannover, Faculty of Natural Sciences, Institute for Plant Genetics, Hannover, Germany
| | - David H Byrne
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-2133, USA.
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Kirov I, Van Laere K, De Riek J, De Keyser E, Van Roy N, Khrustaleva L. Anchoring linkage groups of the Rosa genetic map to physical chromosomes with tyramide-FISH and EST-SNP markers. PLoS One 2014; 9:e95793. [PMID: 24755945 PMCID: PMC3995938 DOI: 10.1371/journal.pone.0095793] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 03/31/2014] [Indexed: 11/29/2022] Open
Abstract
In order to anchor Rosa linkage groups to physical chromosomes, a combination of the Tyramide-FISH technology and the modern molecular marker system based on High Resolution Melting (HRM) is an efficient approach. Although, Tyramide-FISH is a very promising technique for the visualization of short DNA probes, it is very challenging for plant species with small chromosomes such as Rosa. In this study, we successfully applied the Tyramide-FISH technique for Rosa and compared different detection systems. An indirect detection system exploiting biotinylated tyramides was shown to be the most suitable technique for reliable signal detection. Three gene fragments with a size of 1100 pb–1700 bp (Phenylalanine Ammonia Lyase, Pyrroline-5-Carboxylate Synthase and Orcinol O-Methyl Transferase) have been physically mapped on chromosomes 7, 4 and 1, respectively, of Rosa wichurana. The signal frequency was between 25% and 40%. HRM markers of these 3 gene fragments were used to include the gene fragments on the existing genetic linkage map of Rosa wichurana. As a result, three linkage groups could be anchored to their physical chromosomes. The information was used to check for synteny between the Rosa chromosomes and Fragaria.
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Affiliation(s)
- Ilya Kirov
- Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
- Department of Genetics and Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Melle, Belgium
| | - Katrijn Van Laere
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Melle, Belgium
- * E-mail:
| | - Jan De Riek
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Melle, Belgium
| | - Ellen De Keyser
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Melle, Belgium
| | - Nadine Van Roy
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Ludmila Khrustaleva
- Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
- Department of Genetics and Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
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Djennane S, Hibrand-Saint Oyant L, Kawamura K, Lalanne D, Laffaire M, Thouroude T, Chalain S, Sakr S, Boumaza R, Foucher F, Leduc N. Impacts of light and temperature on shoot branching gradient and expression of strigolactone synthesis and signalling genes in rose. PLANT, CELL & ENVIRONMENT 2014; 37:742-57. [PMID: 23992149 DOI: 10.1111/pce.12191] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 07/08/2013] [Accepted: 08/17/2013] [Indexed: 05/06/2023]
Abstract
Light and temperature are two environmental factors that deeply affect bud outgrowth. However, little is known about their impact on the bud burst gradient along a stem and their interactions with the molecular mechanisms of bud burst control. We investigated this question in two acrotonic rose cultivars. We demonstrated that the darkening of distal buds or exposure to cold (5 °C) prior to transfer to mild temperatures (20 °C) both repress acrotony, allowing the burst of quiescent medial and proximal buds. We sequenced the strigolactone pathway MAX-homologous genes in rose and studied their expression in buds and internodes along the stem. Only expressions of RwMAX1, RwMAX2 and RwMAX4 were detected. Darkening of the distal part of the shoot triggered a strong increase of RwMAX2 expression in darkened buds and bark-phloem samples, whereas it suppressed the acropetal gradient of the expression of RwMAX1 observed in stems fully exposed to light. Cold treatment induced an acropetal gradient of expression of RwMAX1 in internodes and of RwMAX2 in buds along the stem. Our results suggest that the bud burst gradient along the stem cannot be explained by a gradient of expression of RwMAX genes but rather by their local level of expression at each individual position.
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Affiliation(s)
- Samia Djennane
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L'UNAM, F-49045, Angers, France; INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
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Yu C, Luo L, Pan H, Guo X, Wan H, Zhang Q. Filling gaps with construction of a genetic linkage map in tetraploid roses. FRONTIERS IN PLANT SCIENCE 2014; 5:796. [PMID: 25628638 PMCID: PMC4292389 DOI: 10.3389/fpls.2014.00796] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 12/21/2014] [Indexed: 05/21/2023]
Abstract
Rose (Rosa sp.) is one of the most economically important ornamental crops worldwide. The present work contains a genetic linkage map for tetraploid roses that was constructed from an F1 segregation population using AFLPs and SSRs on 189 individuals. The preliminary 'Yunzheng Xiawei' and 'Sun City' maps consisted of 298 and 255 markers arranged into 26 and 32 linkage groups, respectively. The recombined parental maps covered 737 and 752 cM of the genome, respectively. The integrated linkage map was composed of 295 polymorphic markers that spanned 874 cM, and it had a mean intermarker distance of 2.9 cM. In addition, a set of newly developed EST-SSRs that are distributed evenly throughout the mapping population were released. The work identified 67 anchoring points that came from 43 common SSRs. The results that were produced from a large number of individuals (189) and polymorphic SSRs (242) will enhance the ability to construct higher density consensus maps with the available diploid level rose maps, and they will definitely serve as a tool for accurate QTL detection and marker assisted selection.
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Affiliation(s)
| | | | | | | | | | - Qixiang Zhang
- *Correspondence: Qixiang Zhang, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and rural ecological environment and College of Landscape Architecture, Beijing Forestry University, 35# Qinghua East Road, Beijing, 100083, China e-mail:
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31
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Longhi S, Giongo L, Buti M, Surbanovski N, Viola R, Velasco R, Ward JA, Sargent DJ. Molecular genetics and genomics of the Rosoideae: state of the art and future perspectives. HORTICULTURE RESEARCH 2014; 1:1. [PMID: 26504527 PMCID: PMC4591673 DOI: 10.1038/hortres.2014.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 11/24/2013] [Indexed: 05/04/2023]
Abstract
The Rosoideae is a subfamily of the Rosaceae that contains a number of species of economic importance, including the soft fruit species strawberry (Fragaria ×ananassa), red (Rubus idaeus) and black (Rubus occidentalis) raspberries, blackberries (Rubus spp.) and one of the most economically important cut flower genera, the roses (Rosa spp.). Molecular genetics and genomics resources for the Rosoideae have developed rapidly over the past two decades, beginning with the development and application of a number of molecular marker types including restriction fragment length polymorphisms, amplified fragment length polymorphisms and microsatellites, and culminating in the recent publication of the genome sequence of the woodland strawberry, Fragaria vesca, and the development of high throughput single nucleotide polymorphism (SNP)-genotyping resources for Fragaria, Rosa and Rubus. These tools have been used to identify genes and other functional elements that control traits of economic importance, to study the evolution of plant genome structure within the subfamily, and are beginning to facilitate genomic-assisted breeding through the development and deployment of markers linked to traits such as aspects of fruit quality, disease resistance and the timing of flowering. In this review, we report on the developments that have been made over the last 20 years in the field of molecular genetics and structural genomics within the Rosoideae, comment on how the knowledge gained will improve the efficiency of cultivar development and discuss how these advances will enhance our understanding of the biological processes determining agronomically important traits in all Rosoideae species.
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Affiliation(s)
- Sara Longhi
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Lara Giongo
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Matteo Buti
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Nada Surbanovski
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Roberto Viola
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Riccardo Velasco
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | | | - Daniel J Sargent
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
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Castro P, Stafne ET, Clark JR, Lewers KS. Genetic map of the primocane-fruiting and thornless traits of tetraploid blackberry. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2521-32. [PMID: 23856741 DOI: 10.1007/s00122-013-2152-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 07/01/2013] [Indexed: 05/23/2023]
Abstract
Blackberry primocane fruiting, fruiting on first-year canes, has the potential to expand blackberry production both seasonally and geographically. The incorporation of the primocane-fruiting trait into cultivars with desirable horticultural attributes is challenging due to its recessive nature and tetrasomic inheritance. Molecular marker-assisted selection has high potential to facilitate incorporation, because breeders already use morphological marker-assisted selection of seedlings without marginal cotyledonary hairs to identify progeny that will be thornless when mature. The development of a genetic linkage map with these two traits is the first step to utilizing molecular markers in breeding for thornless primocane-fruiting blackberry cultivars. A full-sib family segregating for thornlessness and primocane fruiting, from a cross between 'APF-12' and 'Arapaho', was used to construct the first genetic map of tetraploid blackberry. Segregation patterns of several dominant markers and the two phenotypic traits fit those expected uniquely with tetrasomic inheritance (e.g., 5:1, 11:1 and 35:1). Some loci showed significant double reduction frequencies, but genotypes that could have originated only from double reduction were not found. The map consists of seven linkage groups (LG) in each parent, consistent with the basic number of chromosomes (2n = 4x = 28). Naming of LG1-LG6 followed that of the recently revised system for raspberry using SSR markers in common between blackberry and raspberry, and LG7 was tentatively defined by default. The loci controlling primocane fruiting and thornlessness were not linked to each other; thornless/thorny, the S Locus, was mapped on LG4, and the primocane-/floricane-fruiting locus, named in this work the F Locus, on LG7.
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Affiliation(s)
- P Castro
- IFAPA, Centro 'Alameda del Obispo', Mejora y Biotecnologia, Avenida Menendez Pidal, s/n, 14080, Córdoba, Spain
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Linkage analysis and QTL mapping using SNP dosage data in a tetraploid potato mapping population. PLoS One 2013; 8:e63939. [PMID: 23704960 PMCID: PMC3660524 DOI: 10.1371/journal.pone.0063939] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 04/08/2013] [Indexed: 11/19/2022] Open
Abstract
New sequencing and genotyping technologies have enabled researchers to generate high density SNP genotype data for mapping populations. In polyploid species, SNP data usually contain a new type of information, the allele dosage, which is not used by current methodologies for linkage analysis and QTL mapping. Here we extend existing methodology to use dosage data on SNPs in an autotetraploid mapping population. The SNP dosages are inferred from allele intensity ratios using normal mixture models. The steps of the linkage analysis (testing for distorted segregation, clustering SNPs, calculation of recombination fractions and LOD scores, ordering of SNPs and inference of parental phase) are extended to use the dosage information. For QTL analysis, the probability of each possible offspring genotype is inferred at a grid of locations along the chromosome from the ordered parental genotypes and phases and the offspring dosages. A normal mixture model is then used to relate trait values to the offspring genotypes and to identify the most likely locations for QTLs. These methods are applied to analyse a tetraploid potato mapping population of parents and 190 offspring, genotyped using an Infinium 8300 Potato SNP Array. Linkage maps for each of the 12 chromosomes are constructed. The allele intensity ratios are mapped as quantitative traits to check that their position and phase agrees with that of the corresponding SNP. This analysis confirms most SNP positions, and eliminates some problem SNPs to give high-density maps for each chromosome, with between 74 and 152 SNPs mapped and between 100 and 300 further SNPs allocated to approximate bins. Low numbers of double reduction products were detected. Overall 3839 of the 5378 polymorphic SNPs can be assigned putative genetic locations. This methodology can be applied to construct high-density linkage maps in any autotetraploid species, and could also be extended to higher autopolyploids.
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Kim J, Park JH, Lim CJ, Lim JY, Ryu JY, Lee BW, Choi JP, Kim WB, Lee HY, Choi Y, Kim D, Hur CG, Kim S, Noh YS, Shin C, Kwon SY. Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars. BMC Genomics 2012; 13:657. [PMID: 23171001 PMCID: PMC3527192 DOI: 10.1186/1471-2164-13-657] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 10/22/2012] [Indexed: 12/21/2022] Open
Abstract
Background Roses (Rosa sp.), which belong to the family Rosaceae, are the most economically important ornamental plants—making up 30% of the floriculture market. However, given high demand for roses, rose breeding programs are limited in molecular resources which can greatly enhance and speed breeding efforts. A better understanding of important genes that contribute to important floral development and desired phenotypes will lead to improved rose cultivars. For this study, we analyzed rose miRNAs and the rose flower transcriptome in order to generate a database to expound upon current knowledge regarding regulation of important floral characteristics. A rose genetic database will enable comprehensive analysis of gene expression and regulation via miRNA among different Rosa cultivars. Results We produced more than 0.5 million reads from expressed sequences, totalling more than 110 million bp. From these, we generated 35,657, 31,434, 34,725, and 39,722 flower unigenes from Rosa hybrid: ‘Vital’, ‘Maroussia’, and ‘Sympathy’ and Rosa rugosa Thunb. , respectively. The unigenes were assigned functional annotations, domains, metabolic pathways, Gene Ontology (GO) terms, Plant Ontology (PO) terms, and MIPS Functional Catalogue (FunCat) terms. Rose flower transcripts were compared with genes from whole genome sequences of Rosaceae members (apple, strawberry, and peach) and grape. We also produced approximately 40 million small RNA reads from flower tissue for Rosa, representing 267 unique miRNA tags. Among identified miRNAs, 25 of them were novel and 242 of them were conserved miRNAs. Statistical analyses of miRNA profiles revealed both shared and species-specific miRNAs, which presumably effect flower development and phenotypes. Conclusions In this study, we constructed a Rose miRNA and transcriptome database, and we analyzed the miRNAs and transcriptome generated from the flower tissues of four Rosa cultivars. The database provides a comprehensive genetic resource which can be used to better understand rose flower development and to identify candidate genes for important phenotypes.
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Affiliation(s)
- Jungeun Kim
- Green Bio Research Center, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
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Dubois A, Carrere S, Raymond O, Pouvreau B, Cottret L, Roccia A, Onesto JP, Sakr S, Atanassova R, Baudino S, Foucher F, Le Bris M, Gouzy J, Bendahmane M. Transcriptome database resource and gene expression atlas for the rose. BMC Genomics 2012; 13:638. [PMID: 23164410 PMCID: PMC3518227 DOI: 10.1186/1471-2164-13-638] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/06/2012] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND For centuries roses have been selected based on a number of traits. Little information exists on the genetic and molecular basis that contributes to these traits, mainly because information on expressed genes for this economically important ornamental plant is scarce. RESULTS Here, we used a combination of Illumina and 454 sequencing technologies to generate information on Rosa sp. transcripts using RNA from various tissues and in response to biotic and abiotic stresses. A total of 80714 transcript clusters were identified and 76611 peptides have been predicted among which 20997 have been clustered into 13900 protein families. BLASTp hits in closely related Rosaceae species revealed that about half of the predicted peptides in the strawberry and peach genomes have orthologs in Rosa dataset. Digital expression was obtained using RNA samples from organs at different development stages and under different stress conditions. qPCR validated the digital expression data for a selection of 23 genes with high or low expression levels. Comparative gene expression analyses between the different tissues and organs allowed the identification of clusters that are highly enriched in given tissues or under particular conditions, demonstrating the usefulness of the digital gene expression analysis. A web interface ROSAseq was created that allows data interrogation by BLAST, subsequent analysis of DNA clusters and access to thorough transcript annotation including best BLAST matches on Fragaria vesca, Prunus persica and Arabidopsis. The rose peptides dataset was used to create the ROSAcyc resource pathway database that allows access to the putative genes and enzymatic pathways. CONCLUSIONS The study provides useful information on Rosa expressed genes, with thorough annotation and an overview of expression patterns for transcripts with good accuracy.
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Affiliation(s)
- Annick Dubois
- Reproduction et Développement des Plantes UMR INRA-CNRS- Université Lyon 1-ENSL, Ecole Normale Supérieure, 46 allée d'Italie, Lyon Cedex 07 69364, France
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Kaufmann H, Qiu X, Wehmeyer J, Debener T. Isolation, Molecular Characterization, and Mapping of Four Rose MLO Orthologs. FRONTIERS IN PLANT SCIENCE 2012; 3:244. [PMID: 23130018 PMCID: PMC3487107 DOI: 10.3389/fpls.2012.00244] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 10/12/2012] [Indexed: 05/24/2023]
Abstract
Powdery mildew is a major disease of economic importance in cut and pot roses. As an alternative to conventional resistance breeding strategies utilizing single-dominant genes or QTLs, mildew resistance locus o (MLO)-based resistance might offer some advantages. In dicots such as Arabidopsis, pea, and tomato, loss-of-function mutations in MLO genes confer high levels of broad-spectrum resistance. Here, we report the isolation and characterization of four MLO homologs from a large rose EST collection isolated from leaves. These genes are phylogenetically closely related to other dicot MLO genes that are involved in plant powdery mildew interactions. Therefore, they are candidates for MLO genes involved in rose powdery mildew interactions. Two of the four isolated genes contain all of the sequence signatures considered to be diagnostic for MLO genes. We mapped all four genes to three linkage groups and conducted the first analysis of alternative alleles. This information is discussed in regards to a reverse genetics approach aimed at the selection of rose plants that are homozygous for loss-of-function in one or more MLO genes.
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Affiliation(s)
- Helgard Kaufmann
- Department of Molecular Breeding, Institute for Plant Genetics, Leibniz University of Hannover Hannover, Germany
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Terefe-Ayana D, Kaufmann H, Linde M, Debener T. Evolution of the Rdr1 TNL-cluster in roses and other Rosaceous species. BMC Genomics 2012; 13:409. [PMID: 22905676 PMCID: PMC3503547 DOI: 10.1186/1471-2164-13-409] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 08/06/2012] [Indexed: 12/03/2022] Open
Abstract
Background The resistance of plants to pathogens relies on two lines of defense: a basal defense response and a pathogen-specific system, in which resistance (R) genes induce defense reactions after detection of pathogen-associated molecular patterns (PAMPS). In the specific system, a so-called arms race has developed in which the emergence of new races of a pathogen leads to the diversification of plant resistance genes to counteract the pathogens’ effect. The mechanism of resistance gene diversification has been elucidated well for short-lived annual species, but data are mostly lacking for long-lived perennial and clonally propagated plants, such as roses. We analyzed the rose black spot resistance gene, Rdr1, in five members of the Rosaceae: Rosa multiflora, Rosa rugosa, Fragaria vesca (strawberry), Malus x domestica (apple) and Prunus persica (peach), and we present the deduced possible mechanism of R-gene diversification. Results We sequenced a 340.4-kb region from R. rugosa orthologous to the Rdr1 locus in R. multiflora. Apart from some deletions and rearrangements, the two loci display a high degree of synteny. Additionally, less pronounced synteny is found with an orthologous locus in strawberry but is absent in peach and apple, where genes from the Rdr1 locus are distributed on two different chromosomes. An analysis of 20 TIR-NBS-LRR (TNL) genes obtained from R. rugosa and R. multiflora revealed illegitimate recombination, gene conversion, unequal crossing over, indels, point mutations and transposable elements as mechanisms of diversification. A phylogenetic analysis of 53 complete TNL genes from the five Rosaceae species revealed that with the exception of some genes from apple and peach, most of the genes occur in species-specific clusters, indicating that recent TNL gene diversification began prior to the split of Rosa from Fragaria in the Rosoideae and peach from apple in the Spiraeoideae and continued after the split in individual species. Sequence similarity of up to 99% is obtained between two R. multiflora TNL paralogs, indicating a very recent duplication. Conclusions The mechanisms by which TNL genes from perennial Rosaceae diversify are mainly similar to those from annual plant species. However, most TNL genes appear to be of recent origin, likely due to recent duplications, supporting the hypothesis that TNL genes in woody perennials are generally younger than those from annuals. This recent origin might facilitate the development of new resistance specificities, compensating for longer generation times in woody perennials.
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Affiliation(s)
- Diro Terefe-Ayana
- Institute for Plant Genetics, Leibniz University Hannover, Herrenhaeuser Str, 2, Hannover, 30419, Germany
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Koning-Boucoiran CFS, Gitonga VW, Yan Z, Dolstra O, van der Linden CG, van der Schoot J, Uenk GE, Verlinden K, Smulders MJM, Krens FA, Maliepaard C. The mode of inheritance in tetraploid cut roses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:591-607. [PMID: 22526522 PMCID: PMC3397129 DOI: 10.1007/s00122-012-1855-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 03/21/2012] [Indexed: 05/18/2023]
Abstract
Tetraploid hybrid tea roses (Rosa hybrida) represent most of the commercial cultivars of cut roses and form the basis for breeding programmes. Due to intensive interspecific hybridizations, modern cut roses are complex tetraploids for which the mode of inheritance is not exactly known. The segregation patterns of molecular markers in a tetraploid mapping population of 184 genotypes, an F(1) progeny from a cross of two heterozygous parents, were investigated for disomic and tetrasomic inheritance. The possible occurrence of double reduction was studied as well. We can exclude disomic inheritance, but while our observations are more in line with a tetrasomic inheritance, we cannot exclude that there is a mixture of both inheritance modes. Two novel parental tetraploid linkage maps were constructed using markers known from literature, combined with newly generated markers. Comparison with the integrated consensus diploid map (ICM) of Spiller et al. (Theor Appl Genet 122:489-500, 2010) allowed assigning numbers to each of the linkage groups of both maps and including small linkage groups. So far, the possibility of using marker-assisted selection in breeding of tetraploid cut roses and of other species with a tetrasomic or partly tetrasomic inheritance, is still limited due to the difficulties in establishing marker-trait associations. We used these tetraploid linkage maps to determine associations between markers, two morphological traits and powdery mildew resistance. The knowledge on inheritance and marker-trait associations in tetraploid cut roses will be of direct use to cut rose breeding.
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Affiliation(s)
- C F S Koning-Boucoiran
- Wageningen University and Research Centre, Plant Breeding, P.O. Box 16, 6700 AA, Wageningen, The Netherlands.
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Zorrilla-Fontanesi Y, Rambla JL, Cabeza A, Medina JJ, Sánchez-Sevilla JF, Valpuesta V, Botella MA, Granell A, Amaya I. Genetic analysis of strawberry fruit aroma and identification of O-methyltransferase FaOMT as the locus controlling natural variation in mesifurane content. PLANT PHYSIOLOGY 2012; 159:851-70. [PMID: 22474217 PMCID: PMC3375946 DOI: 10.1104/pp.111.188318] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Accepted: 04/02/2012] [Indexed: 05/18/2023]
Abstract
Improvement of strawberry (Fragaria × ananassa) fruit flavor is an important goal in breeding programs. To investigate genetic factors controlling this complex trait, a strawberry mapping population derived from genotype '1392', selected for its superior flavor, and '232' was profiled for volatile compounds over 4 years by headspace solid phase microextraction coupled to gas chromatography and mass spectrometry. More than 300 volatile compounds were detected, of which 87 were identified by comparison of mass spectrum and retention time to those of pure standards. Parental line '1392' displayed higher volatile levels than '232', and these and many other compounds with similar levels in both parents segregated in the progeny. Cluster analysis grouped the volatiles into distinct chemically related families and revealed a complex metabolic network underlying volatile production in strawberry fruit. Quantitative trait loci (QTL) detection was carried out over 3 years based on a double pseudo-testcross strategy. Seventy QTLs covering 48 different volatiles were detected, with several of them being stable over time and mapped as major QTLs. Loci controlling γ-decalactone and mesifurane content were mapped as qualitative traits. Using a candidate gene approach we have assigned genes that are likely responsible for several of the QTLs. As a proof of concept we show that one homoeolog of the O-methyltransferase gene (FaOMT) is the locus responsible for the natural variation of mesifurane content. Sequence analysis identified 30 bp in the promoter of this FaOMT homoeolog containing putative binding sites for basic/helix-loop-helix, MYB, and BZIP transcription factors. This polymorphism fully cosegregates with both the presence of mesifurane and the high expression of FaOMT during ripening.
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Affiliation(s)
- Yasmín Zorrilla-Fontanesi
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
| | - José-Luis Rambla
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
| | - Amalia Cabeza
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
| | - Juan J. Medina
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
| | - José F. Sánchez-Sevilla
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
| | - Victoriano Valpuesta
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
| | - Miguel A. Botella
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
| | - Antonio Granell
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
| | - Iraida Amaya
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
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