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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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Mostafavi AS, Omidi M, Azizinezhad R, Etminan A, Badi HN. Genetic diversity analysis in a mini core collection of Damask rose (Rosa damascena Mill.) germplasm from Iran using URP and SCoT markers. J Genet Eng Biotechnol 2021; 19:144. [PMID: 34591207 PMCID: PMC8484433 DOI: 10.1186/s43141-021-00247-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/14/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Rosa damascena Mill is a well-known species of the rose family. It is famous for its essential oil content. The aim of the present study was to assess the genetic diversity and population structure of a mini core collection of the Iranian Damask rose germplasm. This involved the use of universal rice primers (URP) and start codon targeted (SCoT) molecular markers. RESULTS Fourteen URP and twelve SCoT primers amplified 268 and 216 loci, with an average of 19.21 and 18.18 polymorphic fragments per primer, respectively. The polymorphic information content for URR and SCoT primers ranged from 0.38 to 0.48 and 0.11 to 0.45, with the resolving power ranging from 8.75 to 13.05 and 9.9 to 14.59, respectively. Clustering was based on neighbor-joining (NJ). The mini core collection contained 40 accessions and was divided into three distinct clusters, centered on both markers and on the combination of data. CONCLUSION Cluster analysis and principal coordinate analysis were consistent with genetic relationships derived by STRUCTURE analysis. The findings showed that patterns of grouping did not correlate with geographical origin. Both molecular markers demonstrated that the accessions were not genetically diverse as expected, thereby highlighting the possibility that gene flow occurred between populations.
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Affiliation(s)
- Atefeh Sadat Mostafavi
- Department of Plant Breeding and Biotechnology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mansour Omidi
- Department of Agronomy and Plant Breeding, Agricultural College, University of Tehran, Karaj, Iran
| | - Reza Azizinezhad
- Department of Plant Breeding and Biotechnology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Alireza Etminan
- Department of Plant breeding and Biotechnology, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Hassanali Naghdi Badi
- Department of Plant Breeding and Biotechnology, Science and Research Branch, Islamic Azad University, Tehran, Iran
- Medicinal Plants Research Center, Institute of Medicinal Plants, ACECR, Karaj, Iran
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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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Assessment of Genetic Relationships between Streptocarpus x hybridus V. Parents and F1 Progenies Using SRAP Markers and FT-IR Spectroscopy. PLANTS 2020; 9:plants9020160. [PMID: 32012949 PMCID: PMC7076643 DOI: 10.3390/plants9020160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/21/2020] [Accepted: 01/25/2020] [Indexed: 11/17/2022]
Abstract
The genetic relationship among three Streptocarpus parents and twelve F1 hybrids was assessed using sequence-related amplified polymorphism (SRAP) molecular markers and Fourier-transform infrared (FT-IR) spectroscopy. Both methods were able to discriminate F1 hybrids and parents as revealed by cluster analysis. For hybrid identification, the type III SRAP marker was the most effective due to the presence of male-specific bands in the hybrids. Different behaviors in the biochemical variability of DNA samples have been observed by FT-IR spectral analysis, which might be attributed to the inherent nature of the genomic DNA from parents and their F1 progenies. Mantel test was also carried out to compare morphological, SRAP, and FT-IR results based on genetic distances. The highest correlation coefficient was found between morphological and SRAP marker distances (R = 0.607; p ≤ 0.022). A lower correlation was observed between the morphological and FT-IR distance matrix (R = 0.231; p ≤0.008). Moreover, a positive correlation was found between the distances generated with SRAP and FT-IR analyses (R = 0.026) but was not statistically significant. These findings show that both SRAP and FT-IR techniques combined with morphological descriptions can be used effectively for nonconventional breeding programs for Streptocarpus to obtain new and valuable varieties.
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Veluru A, Bhat KV, Raju DVS, Prasad KV, Tolety J, Bharadwaj C, Mitra SVACR, Banyal N, Singh KP, Panwar S. Characterization of Indian bred rose cultivars using morphological and molecular markers for conservation and sustainable management. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:95-106. [PMID: 32158123 PMCID: PMC7036390 DOI: 10.1007/s12298-019-00735-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/27/2019] [Accepted: 11/19/2019] [Indexed: 05/25/2023]
Abstract
Rose (Rosa × hybrid L.) is one of the most important commercial ornamental crops cultivated worldwide for its beauty, fragrance and nutraceutical values. Characterization of rose germplasm provides precise information about the extent of diversity present among the cultivars. It also helps in cultivar identification, intellectual property right protection, variety improvement and genetic diversity conservation. In the present study, 109 Indian bred rose cultivars were characterized using 59 morphological and 48 SSR markers. Out of 48 SSRs used, 31 markers exhibited polymorphism and 96 alleles were identified with an average of 3.9 alleles per locus. Nei's expected heterozygosity value of each locus ranged from 0.08 (with SSR ABRII/RPU32) to 0.78 (SSR Rh58). The similarity coefficient values ranged from 0.42 to 0.90 which indicated presence of moderated diversity among Indian cultivars. The neighbor-joining tree based on morphological data grouped the cultivars into two major clusters and several minor clusters based on their morphological resemblance. However, UPGMA dendrogram constructed using matching coefficient values grouped the cultivars into eight different clusters. Interpopulation analysis revealed higher genetic similarities between Hybrid Tea and Floribunda cultivars. An analysis for presence of population sub-structure grouped the Indian cultivars into eight different genetic groups. Analysis of molecular variance revealed apportioning of 97.59% of the variation to within subgroup diversity and 3.07% to between the cultivar groups. We have demonstrated here successful utilization of robust SSR to distinguish cultivars and assess genetic diversity among Indian bred rose cultivars. The information provided here is useful for cultivar identification and protection, cultivar improvement and genetic diversity conservation.
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Affiliation(s)
- Aparna Veluru
- 1Division of Floriculture and Landscape Architecture, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
| | | | | | | | - Janakiram Tolety
- 3Assistant Director General, Horticulture, KAB-II, Indian Council of Agricultural Research, New Delhi, 110 012 India
| | - Chellapilla Bharadwaj
- 5Division of Genetics, ICAR- Indian Agricultural Research Institute, New Delhi, 110 012 India
| | | | - Namita Banyal
- 1Division of Floriculture and Landscape Architecture, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
| | - Kanwar Pal Singh
- 1Division of Floriculture and Landscape Architecture, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
| | - Sapna Panwar
- 1Division of Floriculture and Landscape Architecture, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
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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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Yan M, Byrne D, Klein P, van de Weg W, Yang J, Cai L. Black spot partial resistance in diploid roses:
QTL discovery and linkage map creation. ACTA ACUST UNITED AC 2019. [DOI: 10.17660/actahortic.2019.1232.21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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8
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da Silva Linge C, Antanaviciute L, Abdelghafar A, Arús P, Bassi D, Rossini L, Ficklin S, Gasic K. High-density multi-population consensus genetic linkage map for peach. PLoS One 2018; 13:e0207724. [PMID: 30462743 PMCID: PMC6248993 DOI: 10.1371/journal.pone.0207724] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/04/2018] [Indexed: 11/19/2022] Open
Abstract
Highly saturated genetic linkage maps are extremely helpful to breeders and are an essential prerequisite for many biological applications such as the identification of marker-trait associations, mapping quantitative trait loci (QTL), candidate gene identification, development of molecular markers for marker-assisted selection (MAS) and comparative genetic studies. Several high-density genetic maps, constructed using the 9K SNP peach array, are available for peach. However, each of these maps is based on a single mapping population and has limited use for QTL discovery and comparative studies. A consensus genetic linkage map developed from multiple populations provides not only a higher marker density and a greater genome coverage when compared to the individual maps, but also serves as a valuable tool for estimating genetic positions of unmapped markers. In this study, a previously developed linkage map from the cross between two peach cultivars 'Zin Dai' and 'Crimson Lady' (ZC2) was improved by genotyping additional progenies. In addition, a peach consensus map was developed based on the combination of the improved ZC2 genetic linkage map with three existing high-density genetic maps of peach and a reference map of Prunus. A total of 1,476 SNPs representing 351 unique marker positions were mapped across eight linkage groups on the ZC2 genetic map. The ZC2 linkage map spans 483.3 cM with an average distance between markers of 1.38 cM/marker. The MergeMap and LPmerge tools were used for the construction of a consensus map based on markers shared across five genetic linkage maps. The consensus linkage map contains a total of 3,092 molecular markers, consisting of 2,975 SNPs, 116 SSRs and 1 morphological marker associated with slow ripening in peach (SR). The consensus map provides valuable information on marker order and genetic position for QTL identification in peach and other genetic studies within Prunus and Rosaceae.
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Affiliation(s)
- Cassia da Silva Linge
- Clemson University, Department of Plant and Environmental Sciences, Clemson, SC, United States of America
| | - Laima Antanaviciute
- Clemson University, Department of Plant and Environmental Sciences, Clemson, SC, United States of America
| | - Asma Abdelghafar
- Clemson University, Department of Plant and Environmental Sciences, Clemson, SC, United States of America
| | - Pere Arús
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica Consejo Superior de Investigaciones Científicas (CSIC)-IRTA–Universitat Autònoma de Barcelona (UAB)–University of Barcelona (UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Daniele Bassi
- Università degli Studi di Milano, Department of Agricultural and Environmental Sciences–Production, Landscape, Agroenergy, Milan, Italy
| | - Laura Rossini
- Università degli Studi di Milano, Department of Agricultural and Environmental Sciences–Production, Landscape, Agroenergy, Milan, Italy
| | - Stephen Ficklin
- Washington State University, Department of Horticulture, Pullman, WA, United States of America
| | - Ksenija Gasic
- Clemson University, Department of Plant and Environmental Sciences, Clemson, SC, United States of America
- * E-mail:
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Proteomic Analysis of Aphid-Resistant and -Sensitive Rose ( Rosa Hybrida) Cultivars at Two Developmental Stages. Proteomes 2018; 6:proteomes6020025. [PMID: 29799446 PMCID: PMC6027261 DOI: 10.3390/proteomes6020025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 01/05/2023] Open
Abstract
The rose is one the most commercially grown and costly ornamental plants because of its aesthetic beauty and aroma. A large number of pests attack its buds, flowers, leaves, and stem at every growing stage due to its high sugar content. The most common pest on roses are aphids which are considered to be the major cause for product loss. Aphid infestations lead to major changes in rose plants, such as large and irregular holes in petals, intact leaves and devouring tissues. It is hypothesized that different cut rose cultivars would have different levels of sensitivity or resistance to aphids, since different levels of infestation are observed in commercially cut rose production greenhouses. The present work compared four cut rose cultivars which were bred in Korea and were either resistant or sensitive to aphid infestation at different flower developmental stages. An integrative study was conducted using comprehensive proteome analyses. Proteins related to ubiquitin metabolism and the stress response were differentially expressed due to aphid infestation. The regulations and possible functions of identified proteins are presented in detail. The differential expressions of the identified proteins were validated by immunoblotting and blue native page. In addition, total sugar and carbohydrate content were also observed.
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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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11
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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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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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Yan X, Zhang X, Lu M, He Y, An H. De novo sequencing analysis of the Rosa roxburghii fruit transcriptome reveals putative ascorbate biosynthetic genes and EST-SSR markers. Gene 2015; 561:54-62. [PMID: 25701597 DOI: 10.1016/j.gene.2015.02.054] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/15/2015] [Accepted: 02/03/2015] [Indexed: 10/24/2022]
Abstract
Rosa roxburghii Tratt. is a well-known ornamental rose species native to China. In addition, the fruits of this species are valued for their nutritional and medicinal characteristics, especially their high ascorbic acid (AsA) levels. Nevertheless, AsA biosynthesis in R. roxburghii fruit has not been explored in detail because of a lack of genomic resources for this species. High-throughput transcriptomic sequencing generating large volumes of transcript sequence data can aid in gene discovery and molecular marker development. In this study, we generated more than 53 million clean reads using Illumina paired-end sequencing technology. De novo assembly yielded 106,590 unigenes, with an average length of 343 bp. On the basis of sequence similarity to known proteins, 9301 and 2393 unigenes were classified into Gene Ontology and Clusters of Orthologous Group categories, respectively. There were 7480 unigenes assigned to 124 pathways in the Kyoto Encyclopedia of Gene and Genome pathway database. BLASTx searches identified 498 unique putative transcripts encoding various transcription factors, some known to regulate fruit development. qRT-PCR validated the expressions of most of the genes encoding the main enzymes involved in ascorbate biosynthesis. In addition, 9131 potential simple sequence repeat (SSR) loci were identified among the unigenes. One hundred and two primer pairs were synthesized and 71 pairs produced an amplification product during initial screening. Among the amplified products, 30 were polymorphic in the 16 R. roxburghii germplasms tested. Our study was the first to produce a large volume of transcriptome data from R. roxburghii. The resulting sequence collection is a valuable resource for gene discovery and marker-assisted selective breeding in this rose species.
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Affiliation(s)
- Xiuqin Yan
- Guizhou Engineering Research Center for Fruit Crops, Agricultural College, Guizhou University, Guiyang 550025, PR China
| | - Xue Zhang
- Guizhou Engineering Research Center for Fruit Crops, Agricultural College, Guizhou University, Guiyang 550025, PR China
| | - Min Lu
- Guizhou Engineering Research Center for Fruit Crops, Agricultural College, Guizhou University, Guiyang 550025, PR China
| | - Yong He
- Guizhou Tongjitang Pharmaceutical Co. Ltd, Guiyang 550025, PR China
| | - Huaming An
- Guizhou Engineering Research Center for Fruit Crops, Agricultural College, Guizhou University, Guiyang 550025, PR China.
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Pootakham W, Ruang-Areerate P, Jomchai N, Sonthirod C, Sangsrakru D, Yoocha T, Theerawattanasuk K, Nirapathpongporn K, Romruensukharom P, Tragoonrung S, Tangphatsornruang S. Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS). FRONTIERS IN PLANT SCIENCE 2015; 6:367. [PMID: 26074933 PMCID: PMC4444744 DOI: 10.3389/fpls.2015.00367] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/09/2015] [Indexed: 05/18/2023]
Abstract
Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis), the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS) technique to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1704 and 1719 markers and encompassed 2041 cM and 1874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23-1.25 cM. A total of 1114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2321 markers and spanned the cumulative length of 2052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28,965 contigs, covering 135 Mb or 12% of the published rubber tree genome. We demonstrated that GBS is a robust and cost-effective approach for generating a common set of genome-wide SNP data suitable for constructing integrated linkage maps from multiple populations in a highly heterozygous agricultural species.
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Affiliation(s)
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Panthita Ruang-Areerate
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Nukoon Jomchai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Thippawan Yoocha
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Kanikar Theerawattanasuk
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Kanlaya Nirapathpongporn
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Phayao Romruensukharom
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
- *Correspondence: Sithichoke Tangphatsornruang, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
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15
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Koning-Boucoiran CFS, Esselink GD, Vukosavljev M, van 't Westende WPC, Gitonga VW, Krens FA, Voorrips RE, van de Weg WE, Schulz D, Debener T, Maliepaard C, Arens P, Smulders MJM. Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.). FRONTIERS IN PLANT SCIENCE 2015; 6:249. [PMID: 25954285 PMCID: PMC4404716 DOI: 10.3389/fpls.2015.00249] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/27/2015] [Indexed: 05/18/2023]
Abstract
In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs) within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array. Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L.) genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.
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Affiliation(s)
| | - G. Danny Esselink
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Mirjana Vukosavljev
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | | | - Virginia W. Gitonga
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Frans A. Krens
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Roeland E. Voorrips
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - W. Eric van de Weg
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Dietmar Schulz
- Abteilung Molekulare Pflanzenzüchtung, Institute for Plant Genetics, Leibnitz University HannoverHannover, Germany
| | - Thomas Debener
- Abteilung Molekulare Pflanzenzüchtung, Institute for Plant Genetics, Leibnitz University HannoverHannover, Germany
| | - Chris Maliepaard
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Paul Arens
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Marinus J. M. Smulders
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
- *Correspondence: Marinus J. M. Smulders, Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, NL-6708 PB Wageningen, Netherlands
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16
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Vukosavljev M, Esselink GD, van ’t Westende WPC, Cox P, Visser RGF, Arens P, Smulders MJM. Efficient development of highly polymorphic microsatellite markers based on polymorphic repeats in transcriptome sequences of multiple individuals. Mol Ecol Resour 2014; 15:17-27. [DOI: 10.1111/1755-0998.12289] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/29/2014] [Accepted: 05/30/2014] [Indexed: 11/26/2022]
Affiliation(s)
- M. Vukosavljev
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
- C.T. de Wit Graduate School for Production Ecology and Resource Conservation (PE&RC); Wageningen the Netherlands
| | - G. D. Esselink
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
| | - W. P. C. van ’t Westende
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
| | - P. Cox
- Roath BV; Eindhoven the Netherlands
| | - R. G. F. Visser
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
| | - P. Arens
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
| | - M. J. M. Smulders
- Wageningen UR Plant Breeding; Wageningen University & Research Centre; P.O. Box 386 NL-6700AJ Wageningen the Netherlands
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17
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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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Rusanov K, Kovacheva N, Atanassov A, Atanassov I. Rosa Damascena—Genetics of a Complex Allotetraploid Species and Perspectives for Molecular Breeding. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2009.10818495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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20
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van Dijk T, Pagliarani G, Pikunova A, Noordijk Y, Yilmaz-Temel H, Meulenbroek B, Visser RGF, van de Weg E. Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map. BMC PLANT BIOLOGY 2014; 14:55. [PMID: 24581289 PMCID: PMC3944823 DOI: 10.1186/1471-2229-14-55] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/18/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Breeders in the allo-octoploid strawberry currently make little use of molecular marker tools. As a first step of a QTL discovery project on fruit quality traits and resistance to soil-borne pathogens such as Phytophthora cactorum and Verticillium we built a genome-wide SSR linkage map for the cross Holiday x Korona. We used the previously published MADCE method to obtain full haplotype information for both of the parental cultivars, facilitating in-depth studies on their genomic organisation. RESULTS The linkage map incorporates 508 segregating loci and represents each of the 28 chromosome pairs of octoploid strawberry, spanning an estimated length of 2050 cM. The sub-genomes are denoted according to their sequence divergence from F. vesca as revealed by marker performance. The map revealed high overall synteny between the sub-genomes, but also revealed two large inversions on LG2C and LG2D, of which the latter was confirmed using a separate mapping population. We discovered interesting breeding features within the parental cultivars by in-depth analysis of our haplotype data. The linkage map-derived homozygosity level of Holiday was similar to the pedigree-derived inbreeding level (33% and 29%, respectively). For Korona we found that the observed homozygosity level was over three times higher than expected from the pedigree (13% versus 3.6%). This could indicate selection pressure on genes that have favourable effects in homozygous states. The level of kinship between Holiday and Korona derived from our linkage map was 2.5 times higher than the pedigree-derived value. This large difference could be evidence of selection pressure enacted by strawberry breeders towards specific haplotypes. CONCLUSION The obtained SSR linkage map provides a good base for QTL discovery. It also provides the first biologically relevant basis for the discernment and notation of sub-genomes. For the first time, we revealed genomic rearrangements that were verified in a separate mapping population. We believe that haplotype information will become increasingly important in identifying marker-trait relationships and regions that are under selection pressure within breeding material. Our attempt at providing a biological basis for the discernment of sub-genomes warrants follow-up studies to streamline the naming of the sub-genomes among different octoploid strawberry maps.
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Affiliation(s)
- Thijs van Dijk
- Wageningen-UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
- Graduate School Experimental Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Giulia Pagliarani
- Wageningen-UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
- Department of Agricultural Science, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Anna Pikunova
- Wageningen-UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
- The All-Russian Research Institute of Horticultural Breeding (VNIISPK), p/o Zhilina, Orel, Russia
| | - Yolanda Noordijk
- Wageningen-UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - Hulya Yilmaz-Temel
- Wageningen-UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
- Department of Bioengineering, Ege University, 35100 Izmir, Bornova, Turkey
| | - Bert Meulenbroek
- Fresh Forward Breeding B.V, Wielseweg 38a, Eck en Wiel, The Netherlands
| | - Richard GF Visser
- Wageningen-UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - Eric van de Weg
- Wageningen-UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands
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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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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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Yagi M, Yamamoto T, Isobe S, Hirakawa H, Tabata S, Tanase K, Yamaguchi H, Onozaki T. Construction of a reference genetic linkage map for carnation (Dianthus caryophyllus L.). BMC Genomics 2013; 14:734. [PMID: 24160306 PMCID: PMC3870981 DOI: 10.1186/1471-2164-14-734] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/25/2013] [Indexed: 02/07/2023] Open
Abstract
Background Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Dianthus caryophyllus L.) is an important ornamental flower worldwide. We previously reported a random amplified polymorphic DNA (RAPD)-based genetic linkage map derived from Dianthus capitatus ssp. andrezejowskianus and a simple sequence repeat (SSR)-based genetic linkage map constructed using data from intraspecific F2 populations; however, the number of markers was insufficient, and so the number of linkage groups (LGs) did not coincide with the number of chromosomes (x = 15). Therefore, we aimed to produce a high-density genetic map to improve its usefulness for breeding purposes and genetic research. Results We improved the SSR-based genetic linkage map using SSR markers derived from a genomic library, expression sequence tags, and RNA-seq data. Linkage analysis revealed that 412 SSR loci (including 234 newly developed SSR loci) could be mapped to 17 linkage groups (LGs) covering 969.6 cM. Comparison of five minor LGs covering less than 50 cM with LGs in our previous RAPD-based genetic map suggested that four LGs could be integrated into two LGs by anchoring common SSR loci. Consequently, the number of LGs corresponded to the number of chromosomes (x = 15). We added 192 new SSRs, eight RAPD, and two sequence-tagged site loci to refine the RAPD-based genetic linkage map, which comprised 15 LGs consisting of 348 loci covering 978.3 cM. The two maps had 125 SSR loci in common, and most of the positions of markers were conserved between them. We identified 635 loci in carnation using the two linkage maps. We also mapped QTLs for two traits (bacterial wilt resistance and anthocyanin pigmentation in the flower) and a phenotypic locus for flower-type by analyzing previously reported genotype and phenotype data. Conclusions The improved genetic linkage maps and SSR markers developed in this study will serve as reference genetic linkage maps for members of the genus Dianthus, including carnation, and will be useful for mapping QTLs associated with various traits, and for improving carnation breeding programs.
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Affiliation(s)
- Masafumi Yagi
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan.
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Behrend A, Borchert T, Spiller M, Hohe A. AFLP-based genetic mapping of the "bud-flowering" trait in heather (Calluna vulgaris). BMC Genet 2013; 14:64. [PMID: 23915059 PMCID: PMC3751046 DOI: 10.1186/1471-2156-14-64] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 07/25/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Calluna vulgaris is one of the most important landscaping plants produced in Germany. Its enormous economic success is due to the prolonged flower attractiveness of mutants in flower morphology, the so-called bud-bloomers. In this study, we present the first genetic linkage map of C. vulgaris in which we mapped a locus of the economically highly desired trait "flower type". RESULTS The map was constructed in JoinMap 4.1. using 535 AFLP markers from a single mapping population. A large fraction (40%) of markers showed distorted segregation. To test the effect of segregation distortion on linkage estimation, these markers were sorted regarding their segregation ratio and added in groups to the data set. The plausibility of group formation was evaluated by comparison of the "two-way pseudo-testcross" and the "integrated" mapping approach. Furthermore, regression mapping was compared to the multipoint-likelihood algorithm. The majority of maps constructed by different combinations of these methods consisted of eight linkage groups corresponding to the chromosome number of C. vulgaris. CONCLUSIONS All maps confirmed the independent inheritance of the most important horticultural traits "flower type", "flower colour", and "leaf colour". An AFLP marker for the most important breeding target "flower type" was identified. The presented genetic map of C. vulgaris can now serve as a basis for further molecular marker selection and map-based cloning of the candidate gene encoding the unique flower architecture of C. vulgaris bud-bloomers.
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Affiliation(s)
- Anne Behrend
- Department Plant Propagation, Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Kuehnhaueser Strasse 101, 99090, Erfurt, Germany
| | - Thomas Borchert
- Department Plant Propagation, Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Kuehnhaueser Strasse 101, 99090, Erfurt, Germany
- Present address: Siemens Healthcare Diagnostics Holding GmbH, Ludwig-Erhard-Straße 12, 65760, Eschborn, Germany
| | - Monika Spiller
- Department Molecular Plant Breeding, Leibniz University Hannover, Herrenhaeuser Strasse 2, 30419, Hannover, Germany
| | - Annette Hohe
- Department Plant Propagation, Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Kuehnhaueser Strasse 101, 99090, Erfurt, Germany
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QTL mapping of growth-related traits in a full-sib family of rubber tree (Hevea brasiliensis) evaluated in a sub-tropical climate. PLoS One 2013; 8:e61238. [PMID: 23620732 PMCID: PMC3631230 DOI: 10.1371/journal.pone.0061238] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 03/06/2013] [Indexed: 11/23/2022] Open
Abstract
The rubber tree (Hevea spp.), cultivated in equatorial and tropical countries, is the primary plant used in natural rubber production. Due to genetic and physiological constraints, inbred lines of this species are not available. Therefore, alternative approaches are required for the characterization of this species, such as the genetic mapping of full-sib crosses derived from outbred parents. In the present study, an integrated genetic map was obtained for a full-sib cross family with simple sequence repeats (SSRs) and expressed sequence tag (EST-SSR) markers, which can display different segregation patterns. To study the genetic architecture of the traits related to growth in two different conditions (winter and summer), quantitative trait loci (QTL) mapping was also performed using the integrated map. Traits evaluated were height and girth growth, and the statistical model was based in an extension of composite interval mapping. The obtained molecular genetic map has 284 markers distributed among 23 linkage groups with a total length of 2688.8 cM. A total of 18 QTLs for growth traits during the summer and winter seasons were detected. A comparison between the different seasons was also conducted. For height, QTLs detected during the summer season were different from the ones detected during winter season. This type of difference was also observed for girth. Integrated maps are important for genetics studies in outbred species because they represent more accurately the polymorphisms observed in the genitors. QTL mapping revealed several interesting findings, such as a dominance effect and unique segregation patterns that each QTL could exhibit, which were independent of the flanking markers. The QTLs identified in this study, especially those related to phenotypic variation associated with winter could help studies of marker-assisted selection that are particularly important when the objective of a breeding program is to obtain phenotypes that are adapted to sub-optimal regions.
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Bendahmane M, Dubois A, Raymond O, Bris ML. Genetics and genomics of flower initiation and development in roses. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:847-57. [PMID: 23364936 PMCID: PMC3594942 DOI: 10.1093/jxb/ers387] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Roses hold high symbolic value and great cultural importance in different societies throughout human history. They are widely used as garden ornamental plants, as cut flowers, and for the production of essential oils for the perfume and cosmetic industries. Domestication of roses has a long and complex history, and the rose species have been hybridized across vast geographic areas such as Europe, Asia, and the Middle East. The domestication processes selected several flower characters affecting floral quality, such as recurrent flowering, double flowers, petal colours, and fragrance. The molecular and genetic events that determine some of these flower characters cannot be studied using model species such as Arabidopsis thaliana, or at least only in a limited manner. In this review, we comment on the recent development of genetic, genomic, and transcriptomic tools for roses, and then focus on recent advances that have helped unravel the molecular mechanisms underlying several rose floral traits.
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Affiliation(s)
- Mohammed Bendahmane
- Reproduction et Développement des Plantes UMR INRA-CNRS-Université Lyon 1-ENSL, IFR128 BioSciences-Gerland Lyon sud, Ecole Normale Supérieure, 46 allée d'Italie, Lyon Cedex 07, France.
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Kelager A, Pedersen JS, Bruun HH. Multiple introductions and no loss of genetic diversity: invasion history of Japanese Rose, Rosa rugosa, in Europe. Biol Invasions 2012. [DOI: 10.1007/s10530-012-0356-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Nakatsuka T, Yamada E, Saito M, Hikage T, Ushiku Y, Nishihara M. Construction of the first genetic linkage map of Japanese gentian (Gentianaceae). BMC Genomics 2012. [PMID: 23186361 PMCID: PMC3561071 DOI: 10.1186/1471-2164-13-672] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Background Japanese gentians (Gentiana triflora and Gentiana scabra) are amongst the most popular floricultural plants in Japan. However, genomic resources for Japanese gentians have not yet been developed, mainly because of the heterozygous genome structure conserved by outcrossing, the long juvenile period, and limited knowledge about the inheritance of important traits. In this study, we developed a genetic linkage map to improve breeding programs of Japanese gentians. Results Enriched simple sequence repeat (SSR) libraries from a G. triflora double haploid line yielded almost 20,000 clones using 454 pyrosequencing technology, 6.7% of which could be used to design SSR markers. To increase the number of molecular markers, we identified three putative long terminal repeat (LTR) sequences using the recently developed inter-primer binding site (iPBS) method. We also developed retrotransposon microsatellite amplified polymorphism (REMAP) markers combining retrotransposon and inter-simple sequence repeat (ISSR) markers. In addition to SSR and REMAP markers, modified amplified fragment length polymorphism (AFLP) and random amplification polymorphic DNA (RAPD) markers were developed. Using 93 BC1 progeny from G. scabra backcrossed with a G. triflora double haploid line, 19 linkage groups were constructed with a total of 263 markers (97 SSR, 97 AFLP, 39 RAPD, and 30 REMAP markers). One phenotypic trait (stem color) and 10 functional markers related to genes controlling flower color, flowering time and cold tolerance were assigned to the linkage map, confirming its utility. Conclusions This is the first reported genetic linkage map for Japanese gentians and for any species belonging to the family Gentianaceae. As demonstrated by mapping of functional markers and the stem color trait, our results will help to explain the genetic basis of agronomic important traits, and will be useful for marker-assisted selection in gentian breeding programs. Our map will also be an important resource for further genetic analyses such as mapping of quantitative trait loci and map-based cloning of genes in this species.
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Affiliation(s)
- Takashi Nakatsuka
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate 024-0003, Japan
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Khan MA, Han Y, Zhao YF, Troggio M, Korban SS. A multi-population consensus genetic map reveals inconsistent marker order among maps likely attributed to structural variations in the apple genome. PLoS One 2012; 7:e47864. [PMID: 23144832 PMCID: PMC3489900 DOI: 10.1371/journal.pone.0047864] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 09/19/2012] [Indexed: 12/26/2022] Open
Abstract
Genetic maps serve as frameworks for determining the genetic architecture of quantitative traits, assessing structure of a genome, as well as aid in pursuing association mapping and comparative genetic studies. In this study, a dense genetic map was constructed using a high-throughput 1,536 EST-derived SNP GoldenGate genotyping platform and a global consensus map established by combining the new genetic map with four existing reliable genetic maps of apple. The consensus map identified markers with both major and minor conflicts in positioning across all five maps. These major inconsistencies among marker positions were attributed either to structural variations within the apple genome, or among mapping populations, or genotyping technical errors. These also highlighted problems in assembly and anchorage of the reference draft apple genome sequence in regions with known segmental duplications. Markers common across all five apple genetic maps resulted in successful positioning of 2875 markers, consisting of 2033 SNPs and 843 SSRs as well as other specific markers, on the global consensus map. These markers were distributed across all 17 linkage groups, with an average of 169±33 marker per linkage group and with an average distance of 0.70±0.14 cM between markers. The total length of the consensus map was 1991.38 cM with an average length of 117.14±24.43 cM per linkage group. A total of 569 SNPs were mapped onto the genetic map, consisting of 140 recombinant individuals, from our recently developed apple Oligonucleotide pool assays (OPA). The new functional SNPs, along with the dense consensus genetic map, will be useful for high resolution QTL mapping of important traits in apple and for pursuing comparative genetic studies in Rosaceae.
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Affiliation(s)
- Muhammad Awais Khan
- Department of Natural Resources & Environmental Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Moshan, Wuhan, People's Republic of China
| | - Youfu Frank Zhao
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Michela Troggio
- Istituto Agrario San Michele all'Adige Research and Innovation Centre, Foundation Edmund Mach, Trento, Italy
| | - Schuyler S. Korban
- Department of Natural Resources & Environmental Sciences, University of Illinois, Urbana, Illinois, United States of America
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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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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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Riaz S, Sadia B, Awan FS, Khan IA, Sadaqat HA, Khan IA. Development of a species-specific sequence-characterized amplified region marker for roses. GENETICS AND MOLECULAR RESEARCH 2012; 11:440-7. [PMID: 22427036 DOI: 10.4238/2012.february.24.3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
DNA fingerprints of four rose species, Rosa centifolia, R. Gruss-an-Teplitz, R. bourboniana, and R. damascena, were developed using RAPD-PCR. We identified a unique polymorphic band in R. centifolia. This 762-bp fragment was produced by the random primer GLI-2. The fragment was eluted and directly cloned in a TA cloning vector, pTZ57R/T. Digestion of the plasmid with EcoRI confirmed the cloning of GLI-2(762) in pTZ57R/T. A second enzyme, PstI, used in combination with EcoRI, gave complete digestion of the plasmid, and the 762-bp fragment was confirmed on the gel. Subsequently, the polymorphic amplicon was sequenced with an AB1 373 DNA sequencer system using the PRISM(TM) Ready Reaction DyeDeoxy(TM) Terminator Cycle Sequencing kit. After sequencing, specific primers (23 bp long) were designed based on the sequence of the flanking regions of the original RAPD fragment. These primers will effectively allow fingerprinting for the identification of R. centifolia species. In essence, we developed an SCAR marker to authenticate the identity of R. centifolia species and to distinguish it from its substitutes. Such techniques are required not only to complement conventional parameters in creating the passport data of commercial and medicinal products of rose, but also for routine quality control in commercial and government rosaries and rose nurseries.
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Affiliation(s)
- S Riaz
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
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Zhao P, Woeste KE. DNA markers identify hybrids between butternut (Juglans cinerea L.) and Japanese walnut (Juglans ailantifolia Carr.). TREE GENETICS & GENOMES 2011; 7:511-533. [PMID: 0 DOI: 10.1007/s11295-010-0352-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Gar O, Sargent DJ, Tsai CJ, Pleban T, Shalev G, Byrne DH, Zamir D. An autotetraploid linkage map of rose (Rosa hybrida) validated using the strawberry (Fragaria vesca) genome sequence. PLoS One 2011; 6:e20463. [PMID: 21647382 PMCID: PMC3103584 DOI: 10.1371/journal.pone.0020463] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 04/24/2011] [Indexed: 01/21/2023] Open
Abstract
Polyploidy is a pivotal process in plant evolution as it increase gene redundancy and morphological intricacy but due to the complexity of polysomic inheritance we have only few genetic maps of autopolyploid organisms. A robust mapping framework is particularly important in polyploid crop species, rose included (2n = 4x = 28), where the objective is to study multiallelic interactions that control traits of value for plant breeding. From a cross between the garden, peach red and fragrant cultivar Fragrant Cloud (FC) and a cut-rose yellow cultivar Golden Gate (GG), we generated an autotetraploid GGFC mapping population consisting of 132 individuals. For the map we used 128 sequence-based markers, 141 AFLP, 86 SSR and three morphological markers. Seven linkage groups were resolved for FC (Total 632 cM) and GG (616 cM) which were validated by markers that segregated in both parents as well as the diploid integrated consensus map.The release of the Fragaria vesca genome, which also belongs to the Rosoideae, allowed us to place 70 rose sequenced markers on the seven strawberry pseudo-chromosomes. Synteny between Rosa and Fragaria was high with an estimated four major translocations and six inversions required to place the 17 non-collinear markers in the same order. Based on a verified linear order of the rose markers, we could further partition each of the parents into its four homologous groups, thus providing an essential framework to aid the sequencing of an autotetraploid genome.
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Affiliation(s)
- Oron Gar
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Ching-Jung Tsai
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Tzili Pleban
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Gil Shalev
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - David H. Byrne
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Dani Zamir
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- * E-mail:
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Genomic resources in horticultural crops: Status, utility and challenges. Biotechnol Adv 2011; 29:199-209. [DOI: 10.1016/j.biotechadv.2010.11.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2010] [Revised: 09/04/2010] [Accepted: 09/26/2010] [Indexed: 01/02/2023]
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Kawamura K, Hibrand-Saint Oyant L, Crespel L, Thouroude T, Lalanne D, Foucher F. Quantitative trait loci for flowering time and inflorescence architecture in rose. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:661-75. [PMID: 21046064 DOI: 10.1007/s00122-010-1476-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 09/30/2010] [Indexed: 05/09/2023]
Abstract
The pattern of development of the inflorescence is an important characteristic in ornamental plants, where the economic value is in the flower. The genetic determinism of inflorescence architecture is poorly understood, especially in woody perennial plants with long life cycles. Our objective was to study the genetic determinism of this characteristic in rose. The genetic architectures of 10 traits associated with the developmental timing and architecture of the inflorescence, and with flower production were investigated in a F(1) diploid garden rose population, based on intensive measurements of phenological and morphological traits in a field. There were substantial genetic variations in inflorescence development traits, with broad-sense heritabilities ranging from 0.82 to 0.93. Genotypic correlations were significant for most (87%) pairs of traits, suggesting either pleiotropy or tight linkage among loci. However, non-significant and low correlations between some pairs of traits revealed two independent developmental pathways controlling inflorescence architecture: (1) the production of inflorescence nodes increased the number of branches and the production of flowers; (2) internode elongation connected with frequent branching increased the number of branches and the production of flowers. QTL mapping identified six common QTL regions (cQTL) for inflorescence developmental traits. A QTL for flowering time and many inflorescence traits were mapped to the same cQTL. Several candidate genes that are known to control inflorescence developmental traits and gibberellin signaling in Arabidopsis thaliana were mapped in rose. Rose orthologues of FLOWERING LOCUS T (RoFT), TERMINAL FLOWER 1 (RoKSN), SPINDLY (RoSPINDLY), DELLA (RoDELLA), and SLEEPY (RoSLEEPY) co-localized with cQTL for relevant traits. This is the first report on the genetic basis of complex inflorescence developmental traits in rose.
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Affiliation(s)
- Koji Kawamura
- INRA d'Angers Nantes, IFR 149 Quasav, UMR 1259 GenHort, Beaucouzé, France
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Gaur R, Sethy NK, Choudhary S, Shokeen B, Gupta V, Bhatia S. Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.). BMC Genomics 2011; 12:117. [PMID: 21329497 PMCID: PMC3050819 DOI: 10.1186/1471-2164-12-117] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 02/17/2011] [Indexed: 11/10/2022] Open
Abstract
Background Chickpea (Cicer arietinum L.) is an economically important cool season grain legume crop that is valued for its nutritive seeds having high protein content. However, several biotic and abiotic stresses and the low genetic variability in the chickpea genome have continuously hindered the chickpea molecular breeding programs. STMS (Sequence Tagged Microsatellite Sites) markers which are preferred for the construction of saturated linkage maps in several crop species, have also emerged as the most efficient and reliable source for detecting allelic diversity in chickpea. However, the number of STMS markers reported in chickpea is still limited and moreover exhibit low rates of both inter and intraspecific polymorphism, thereby limiting the positions of the SSR markers especially on the intraspecific linkage maps of chickpea. Hence, this study was undertaken with the aim of developing additional STMS markers and utilizing them for advancing the genetic linkage map of chickpea which would have applications in QTL identification, MAS and for de novo assembly of high throughput whole genome sequence data. Results A microsatellite enriched library of chickpea (enriched for (GT/CA)n and (GA/CT)n repeats) was constructed from which 387 putative microsatellite containing clones were identified. From these, 254 STMS primers were designed of which 181 were developed as functional markers. An intraspecific mapping population of chickpea, [ICCV-2 (single podded) × JG-62 (double podded)] and comprising of 126 RILs, was genotyped for mapping. Of the 522 chickpea STMS markers (including the double-podding trait, screened for parental polymorphism, 226 (43.3%) were polymorphic in the parents and were used to genotype the RILs. At a LOD score of 3.5, eight linkage groups defining the position of 138 markers were obtained that spanned 630.9 cM with an average marker density of 4.57 cM. Further, based on the common loci present between the current map and the previously published chickpea intraspecific map, integration of maps was performed which revealed improvement of marker density and saturation of the region in the vicinity of sfl (double-podding) gene thereby bringing about an advancement of the current map. Conclusion An arsenal of 181 new chickpea STMS markers was reported. The developed intraspecific linkage map defined map positions of 138 markers which included 101 new locations.Map integration with a previously published map was carried out which revealed an advanced map with improved density. This study is a major contribution towards providing advanced genomic resources which will facilitate chickpea geneticists and molecular breeders in developing superior genotypes with improved traits.
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Affiliation(s)
- Rashmi Gaur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No, 10531, New Delhi 110067, India
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Spiller M, Linde M, Hibrand-Saint Oyant L, Tsai CJ, Byrne DH, Smulders MJM, Foucher F, Debener T. Towards a unified genetic map for diploid roses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:489-500. [PMID: 20936462 DOI: 10.1007/s00122-010-1463-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 09/24/2010] [Indexed: 05/03/2023]
Abstract
We have constructed the first integrated consensus map (ICM) for rose, based on the information of four diploid populations and more than 1,000 initial markers. The single population maps are linked via 59 bridge markers, on average 8.4 per linkage group (LG). The integrated map comprises 597 markers, 206 of which are sequence-based, distributed over a length of 530 cM on seven LGs. By using a larger effective population size and therefore higher marker density, the marker order in the ICM is more reliable than in the single population maps. This is supported by a more even marker distribution and a decrease in gap sizes in the consensus map as compared to the single population maps. This unified map establishes a standard nomenclature for rose LGs, and presents the location of important ornamental traits, such as self-incompatibility, black spot resistance (Rdr1), scent production and recurrent blooming. In total, the consensus map includes locations for 10 phenotypic single loci, QTLs for 7 different traits and 51 ESTs or gene-based molecular markers. This consensus map combines for the first time the information for traits with high relevance for rose variety development. It will serve as a tool for selective breeding and marker assisted selection. It will benefit future efforts of the rose community to sequence the whole rose genome and will be useful for synteny studies in the Rosaceae family and especially in the section Rosoideae.
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Affiliation(s)
- Monika Spiller
- Institute for Plant Genetics, Leibniz University Hannover, Herrenhaeuser Strasse 2, Hannover, Germany
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Spiller M, Berger RG, Debener T. Genetic dissection of scent metabolic profiles in diploid rose populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:1461-71. [PMID: 20084491 DOI: 10.1007/s00122-010-1268-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 12/23/2009] [Indexed: 05/15/2023]
Abstract
The scent of flowers is a very important trait in ornamental roses in terms of both quantity and quality. In cut roses, scented varieties are a rare exception. Although metabolic profiling has identified more than 500 scent volatiles from rose flowers so far, nothing is known about the inheritance of scent in roses. Therefore, we analysed scent volatiles and molecular markers in diploid segregating populations. We resolved the patterns of inheritance of three volatiles (nerol, neryl acetate and geranyl acetate) into single Mendelian traits, and we mapped these as single or oligogenic traits in the rose genome. Three other volatiles (geraniol, beta-citronellol and 2-phenylethanol) displayed quantitative variation in the progeny, and we mapped a total of six QTLs influencing the amounts of these volatiles onto the rose marker map. Because we included known scent related genes and newly generated ESTs for scent volatiles as markers, we were able to link scent related QTLs with putative candidate genes. Our results serve as a starting point for both more detailed analyses of complex scent biosynthetic pathways and the development of markers for marker-assisted breeding of scented rose varieties.
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Affiliation(s)
- M Spiller
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz University Hannover, Herrenhaeuser Str. 2, 30419, Hannover, Germany
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Whitaker VM, Bradeen JM, Debener T, Biber A, Hokanson SC. Rdr3, a novel locus conferring black spot disease resistance in tetraploid rose: genetic analysis, LRR profiling, and SCAR marker development. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:573-85. [PMID: 19847388 DOI: 10.1007/s00122-009-1177-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 09/30/2009] [Indexed: 05/20/2023]
Abstract
Black spot disease of rose, incited by the fungus Diplocarpon rosae, is found worldwide and is the most important disease of garden roses. A gene-for-gene interaction in this pathosystem is evidenced by the presence of pathogenic races of D. rosae and the previous discovery of a dominant resistance allele at the Rdr1 locus in the diploid Rosa multiflora. The objective of the present study was to genetically analyze resistances to North American black spot races 3, 8, and 9 previously reported in tetraploid roses. Resistance to North American races 3 and 8 segregated 1:1 in multiple F(1) populations, indicating that both are conferred by dominant alleles at single loci and are present in simplex (Rrrr) configuration. Gene pyramiding was demonstrated by combining both resistances into single genotypes. Resistance to race 9 was partial and segregated in a quantitative fashion. Analysis of these populations with microsatellite markers previously developed for Rdr1 revealed that the gene conferring race 3 resistance resides within the same R gene cluster as Rdr1. Race 8 resistance segregated independently and is, therefore, a novel locus for black spot resistance in rose which we have named Rdr3. NBS and LRR profiling were used in a bulked segregant analysis to identify a marker 9.1 cM from Rdr3, which was converted to a SCAR marker form for marker-assisted breeding.
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Affiliation(s)
- Vance M Whitaker
- Department of Horticultural Science, Gulf Coast Research and Education Center, University of Florida, 14625 CR 672, Wimauma, FL 33598, USA.
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Biber A, Kaufmann H, Linde M, Spiller M, Terefe D, Debener T. Molecular markers from a BAC contig spanning the Rdr1 locus: a tool for marker-assisted selection in roses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:765-73. [PMID: 19911159 DOI: 10.1007/s00122-009-1197-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 10/17/2009] [Indexed: 05/03/2023]
Abstract
We constructed a BAC contig of about 300 kb spanning the Rdr1 locus for black spot resistance in Rosa multiflora hybrids, using a new BIBAC library from DNA of this species. From this contig, we developed broadly applicable simple sequence repeat (SSR) markers tightly linked to Rdr1, which are suitable for genetic analyses and marker-assisted selection in roses. As a source for the high molecular weight DNA, we chose the homozygous resistant R. multiflora hybrid 88/124-46. For the assembly of the BAC contig, we made use of molecular markers derived from a previously established R. rugosa contig. In order to increase the resolution for fine mapping, the size of the population was increased to 974 plants. The genomic region spanning Rdr1 is now genetically restricted to 0.2 cM, corresponding to a physical distance of about 300 kb. One single-stranded conformational polymorphism (SSCP) and one SSR marker cosegregate with the Rdr1-mediated black spot resistance, while one SSR and several cleaved amplified polymorphic sequence or SSCP markers are very tightly linked with one to three recombinants among the 974 plants. The benefits of the molecular markers developed from the R. multiflora contig for the genetic analysis of roses and the integration of rose genetic maps are discussed.
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Affiliation(s)
- Anja Biber
- Institute for Plant Genetics, Leibniz University Hannover, Herrenhaeuser Strasse 2, Hannover, Germany
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Multipoint-likelihood maximization mapping on 4 segregating populations to achieve an integrated framework map for QTL analysis in pot azalea (Rhododendron simsii hybrids). BMC Mol Biol 2010; 11:1. [PMID: 20070894 PMCID: PMC2837023 DOI: 10.1186/1471-2199-11-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Accepted: 01/13/2010] [Indexed: 11/25/2022] Open
Abstract
Background Azalea (Rhododendron simsii hybrids) is the most important flowering pot plant produced in Belgium, being exported world-wide. In the breeding program, flower color is the main feature for selection, only in later stages cultivation related plant quality traits are evaluated. As a result, plants with attractive flowering are kept too long in the breeding cycle. The inheritance of flower color has been well studied; information on the heritability of cultivation related quality traits is lacking. For this purpose, QTL mapping in diverse genetic backgrounds appeared to be a must and therefore 4 mapping populations were made and analyzed. Results An integrated framework map on four individual linkage maps in Rhododendron simsii hybrids was constructed. For genotyping, mainly dominant scored AFLP (on average 364 per population) and MYB-based markers (15) were combined with co-dominant SSR (23) and EST markers (12). Linkage groups were estimated in JoinMap. A consensus grouping for the 4 mapping populations was made and applied in each individual mapping population. Finally, 16 stable linkage groups were set for the 4 populations; the azalea chromosome number being 13. A combination of regression mapping (JoinMap) and multipoint-likelihood maximization (Carthagène) enabled the construction of 4 maps and their alignment. A large portion of loci (43%) was common to at least two populations and could therefore serve as bridging markers. The different steps taken for map optimization and integration into a reference framework map for QTL mapping are discussed. Conclusions This is the first map of azalea up to our knowledge. AFLP and SSR markers are used as a reference backbone and functional markers (EST and MYB) were added as candidate genes for QTL analysis. The alignment of the 4 maps on the basis of framework markers will facilitate in turn the alignment of QTL regions detected in each of the populations. The approach we took is thoroughly different than the recently published integrated maps and well-suited for mapping in a non-model crop.
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Development of new SSR markers from EST of SSH cDNA libraries on rose fragrance. YI CHUAN = HEREDITAS 2009; 31:962-6. [DOI: 10.3724/sp.j.1005.2009.00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Blas AL, Yu Q, Chen C, Veatch O, Moore PH, Paull RE, Ming R. Enrichment of a papaya high-density genetic map with AFLP markers. Genome 2009; 52:716-25. [DOI: 10.1139/g09-043] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A high-density genetic linkage map of papaya, previously developed using an F2mapping population derived from the intraspecific cross AU9 × SunUp, was enriched with AFLP markers. The comprehensive genetic map presented here spans 945.2 cM and covers 9 major and 5 minor linkage groups containing 712 SSR, 277 AFLP, and 1 morphological markers. The average marker density for the 9 major linkage groups is 0.9 cM between adjacent markers, and the total number of gaps >5 cM was reduced from 48 to 27 in the current map. AFLPs generated by EcoRI/MseI primer combinations were distributed throughout the 14 linkage groups and resulted in several large locus order rearrangements within the 9 major linkage groups. Integration of AFLP markers provided tighter linkage association between loci, leading to a reduction in map distance on LGs 1, 2, and 4, which were inflated in the previous map, and correction of the marker order on LG8. Suppression of recombination in the male-specific Y region (MSY) of LG1 is further validated by the addition of 27 sex co-segregating AFLP markers. A large region of distorted segregation surrounding the MSY spans 54.4 cM and represents ∼71% of the linkage group. This comprehensive high-density genetic map provides a framework for mapping quantitative trait loci and for fine mapping as well as for comparative genomic studies of crop plant development and evolution.
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Affiliation(s)
- Andrea L. Blas
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA
- Hawaii Agriculture Research Center, Aiea, HI 96701, USA
- Department of Plant Biology, 148 ERML, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Qingyi Yu
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA
- Hawaii Agriculture Research Center, Aiea, HI 96701, USA
- Department of Plant Biology, 148 ERML, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Cuixia Chen
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA
- Hawaii Agriculture Research Center, Aiea, HI 96701, USA
- Department of Plant Biology, 148 ERML, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Olivia Veatch
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA
- Hawaii Agriculture Research Center, Aiea, HI 96701, USA
- Department of Plant Biology, 148 ERML, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Paul H. Moore
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA
- Hawaii Agriculture Research Center, Aiea, HI 96701, USA
- Department of Plant Biology, 148 ERML, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Robert E. Paull
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA
- Hawaii Agriculture Research Center, Aiea, HI 96701, USA
- Department of Plant Biology, 148 ERML, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Ray Ming
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA
- Hawaii Agriculture Research Center, Aiea, HI 96701, USA
- Department of Plant Biology, 148 ERML, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
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Papdi C, Joseph MP, Salamó IP, Vidal S, Szabados L. Genetic technologies for the identification of plant genes controlling environmental stress responses. FUNCTIONAL PLANT BIOLOGY : FPB 2009; 36:696-720. [PMID: 32688681 DOI: 10.1071/fp09047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 06/11/2009] [Indexed: 06/11/2023]
Abstract
Abiotic conditions such as light, temperature, water availability and soil parameters determine plant growth and development. The adaptation of plants to extreme environments or to sudden changes in their growth conditions is controlled by a well balanced, genetically determined signalling system, which is still far from being understood. The identification and characterisation of plant genes which control responses to environmental stresses is an essential step to elucidate the complex regulatory network, which determines stress tolerance. Here, we review the genetic approaches, which have been used with success to identify plant genes which control responses to different abiotic stress factors. We describe strategies and concepts for forward and reverse genetic screens, conventional and insertion mutagenesis, TILLING, gene tagging, promoter trapping, activation mutagenesis and cDNA library transfer. The utility of the various genetic approaches in plant stress research we review is illustrated by several published examples.
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Affiliation(s)
- Csaba Papdi
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Mary Prathiba Joseph
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Imma Pérez Salamó
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Sabina Vidal
- Facultad de Ciencias, Universidad de la República, Iguá 4225, CP 11400, Montevideo, Uruguay
| | - László Szabados
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
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Lee HR, Bae IH, Park SW, Kim HJ, Min WK, Han JH, Kim KT, Kim BD. Construction of an integrated pepper map using RFLP, SSR, CAPS, AFLP, WRKY, rRAMP, and BAC end sequences. Mol Cells 2009; 27:21-37. [PMID: 19214431 DOI: 10.1007/s10059-009-0002-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 10/01/2008] [Accepted: 10/02/2008] [Indexed: 11/29/2022] Open
Abstract
Map-based cloning to find genes of interest, markerassisted selection (MAS), and marker-assisted breeding (MAB) all require good genetic maps with high reproducible markers. For map construction as well as chromosome assignment, development of single copy PCR-based markers and map integration process are necessary. In this study, the 132 markers (57 STS from BAC-end sequences, 13 STS from RFLP, and 62 SSR) were newly developed as single copy type PCR-based markers. They were used together with 1830 markers previously developed in our lab to construct an integrated map with the Joinmap 3.0 program. This integrated map contained 169 SSR, 354 RFLP, 23 STS from BAC-end sequences, 6 STS from RFLP, 152 AFLP, 51 WRKY, and 99 rRAMP markers on 12 chromosomes. The integrated map contained four genetic maps of two interspecific (Capsicum annuum 'TF68' and C. chinense 'Habanero') and two intraspecific (C. annuum 'CM334' and C. annuum 'Chilsungcho') populations of peppers. This constructed integrated map consisted of 805 markers (map distance of 1858 cM) in interspecific populations and 745 markers (map distance of 1892 cM) in intraspecific populations. The used pepper STS were first developed from end sequences of BAC clones from Capsicum annuum 'CM334'. This integrated map will provide useful information for construction of future pepper genetic maps and for assignment of linkage groups to pepper chromosomes.
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Affiliation(s)
- Heung-Ryul Lee
- Department of Plant Science, Seoul National University, Seoul, 151-921, Korea
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Kakizaki Y, Nakatsuka T, Kawamura H, Abe J, Abe Y, Yamamura S, Nishihara M. Development of codominant DNA marker distinguishing pink from blue flowers in Gentiana scabra. ACTA ACUST UNITED AC 2009. [DOI: 10.1270/jsbbr.11.9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
| | | | | | - Jun Abe
- Iwate Agriculture Research Center
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Koopman WJM, Wissemann V, De Cock K, Van Huylenbroeck J, De Riek J, Sabatino GJH, Visser D, Vosman B, Ritz CM, Maes B, Werlemark G, Nybom H, Debener T, Linde M, Smulders MJM. AFLP markers as a tool to reconstruct complex relationships: A case study in Rosa (Rosaceae). AMERICAN JOURNAL OF BOTANY 2008; 95:353-66. [PMID: 21632360 DOI: 10.3732/ajb.95.3.353] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The genus Rosa has a complex evolutionary history caused by several factors, often in conjunction: extensive hybridization, recent radiation, incomplete lineage sorting, and multiple events of polyploidy. We examined the applicability of AFLP markers for reconstructing (species) relationships in Rosa, using UPGMA clustering, Wagner parsimony, and Bayesian inference. All trees were well resolved, but many of the deeper branches were weakly supported. The cluster analysis showed that the rose cultivars can be separated into a European and an Oriental cluster, each being related to different wild species. The phylogenetic analyses showed that (1) two of the four subgenera (Hulthemia and Platyrhodon) do not deserve subgeneric status; (2) section Carolinae should be merged with sect. Cinnamomeae; (3) subsection Rubigineae is a monophyletic group within sect. Caninae, making sect. Caninae paraphyletic; and (4) there is little support for the distinction of the five other subsections within sect. Caninae. Comparison of the trees with morphological classifications and with previous molecular studies showed that all methods yielded reliable trees. Bayesian inference proved to be a useful alternative to parsimony analysis of AFLP data. Because of their genome-wide sampling, AFLPs are the markers of choice to reconstruct (species) relationships in evolutionary complex groups.
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Affiliation(s)
- Wim J M Koopman
- Plant Research International, Wageningen UR, P.O. Box 16, 6700 AA Wageningen, The Netherlands
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Sun J, Xie Y, Zhang H, Faloutsos C. Less is More: Sparse Graph Mining with Compact Matrix Decomposition. Stat Anal Data Min 2007. [DOI: 10.1002/sam.102] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Troggio M, Malacarne G, Coppola G, Segala C, Cartwright DA, Pindo M, Stefanini M, Mank R, Moroldo M, Morgante M, Grando MS, Velasco R. A dense single-nucleotide polymorphism-based genetic linkage map of grapevine (Vitis vinifera L.) anchoring Pinot Noir bacterial artificial chromosome contigs. Genetics 2007; 176:2637-50. [PMID: 17603124 PMCID: PMC1950661 DOI: 10.1534/genetics.106.067462] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2006] [Accepted: 06/14/2007] [Indexed: 11/18/2022] Open
Abstract
The construction of a dense genetic map for Vitis vinifera and its anchoring to a BAC-based physical map is described: it includes 994 loci mapped onto 19 linkage groups, corresponding to the basic chromosome number of Vitis. Spanning 1245 cM with an average distance of 1.3 cM between adjacent markers, the map was generated from the segregation of 483 single-nucleotide polymorphism (SNP)-based genetic markers, 132 simple sequence repeats (SSRs), and 379 AFLP markers in a mapping population of 94 F(1) individuals derived from a V. vinifera cross of the cultivars Syrah and Pinot Noir. Of these markers, 623 were anchored to 367 contigs that are included in a physical map produced from the same clone of Pinot Noir and covering 352 Mbp. On the basis of contigs containing two or more genetically mapped markers, region-dependent estimations of physical and recombinational distances are presented. The markers used in this study include 118 SSRs common to an integrated map derived from five segregating populations of V. vinifera. The positions of these SSR markers in the two maps are conserved across all Vitis linkage groups. The addition of SNP-based markers introduces polymorphisms that are easy to database, are useful for evolutionary studies, and significantly increase the density of the map. The map provides the most comprehensive view of the Vitis genome reported to date and will be relevant for future studies on structural and functional genomics and genetic improvement.
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Affiliation(s)
- Michela Troggio
- IASMA Research Center, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy.
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