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Minamikawa MF, Kunihisa M, Moriya S, Shimizu T, Inamori M, Iwata H. Genomic prediction and genome-wide association study using combined genotypic data from different genotyping systems: application to apple fruit quality traits. HORTICULTURE RESEARCH 2024; 11:uhae131. [PMID: 38979105 PMCID: PMC11228094 DOI: 10.1093/hr/uhae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/25/2024] [Indexed: 07/10/2024]
Abstract
With advances in next-generation sequencing technologies, various marker genotyping systems have been developed for genomics-based approaches such as genomic selection (GS) and genome-wide association study (GWAS). As new genotyping platforms are developed, data from different genotyping platforms must be combined. However, the potential use of combined data for GS and GWAS has not yet been clarified. In this study, the accuracy of genomic prediction (GP) and the detection power of GWAS increased for most fruit quality traits of apples when using combined data from different genotyping systems, Illumina Infinium single-nucleotide polymorphism array and genotyping by random amplicon sequencing-direct (GRAS-Di) systems. In addition, the GP model, which considered the inbreeding effect, further improved the accuracy of the seven fruit traits. Runs of homozygosity (ROH) islands overlapped with the significantly associated regions detected by the GWAS for several fruit traits. Breeders may have exploited these regions to select promising apples by breeders, increasing homozygosity. These results suggest that combining genotypic data from different genotyping platforms benefits the GS and GWAS of fruit quality traits in apples. Information on inbreeding could be beneficial for improving the accuracy of GS for fruit traits of apples; however, further analysis is required to elucidate the relationship between the fruit traits and inbreeding depression (e.g. decreased vigor).
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Affiliation(s)
- Mai F Minamikawa
- Institute for Advanced Academic Research (IAAR), Chiba University, 1-33 Yayoi, Inage, Chiba, Chiba 263-8522, Japan
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Miyuki Kunihisa
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Shigeki Moriya
- Institute of Fruit Tree and Tea Science, NARO, 92-24 Shimokuriyagawa Nabeyashiki, Morioka, Iwate 020-0123, Japan
| | - Tokurou Shimizu
- Institute of Fruit Tree and Tea Science, NARO, Okitsu Nakacho, Shimizu, Shizuoka 424-0292, Japan
| | - Minoru Inamori
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Hiroyoshi Iwata
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
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Hura T, Hura K, Ostrowska A, Gadzinowska J, Urban K, Pawłowska B. The role of invasive plant species in drought resilience in agriculture: the case of sweet briar (Rosa rubiginosa L.). JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2799-2810. [PMID: 36124695 DOI: 10.1093/jxb/erac377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/05/2022] [Indexed: 06/06/2023]
Abstract
Sweet briar (Rosa rubiginosa) belongs to the group of wild roses. Under natural conditions it grows throughout Europe, and was introduced also into the southern hemisphere, where it has efficiently adapted to dry lands. This review focuses on the high adaptation potential of sweet briar to soil drought in the context of global climatic changes, especially considering steppe formation and desertification of agricultural, orchard, and horticultural areas. We provide a comprehensive overview of current knowledge on sweet briar traits associated with drought tolerance and particularly water use efficiency, sugar accumulation, accumulation of CO2 in intercellular spaces, stomatal conductance, gibberellin level, effective electron transport between photosystem II and photosystem I, and protein content. We discuss the genetics and potential applications in plant breeding and suggest future directions of study concerning invasive populations of R. rubiginosa. Finally, we point out that sweet briar can provide new genes for breeding in the context of depleting gene pools of the crop plants.
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Affiliation(s)
- Tomasz Hura
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Kraków, Niezapominajek 21, 30-239 Kraków, Poland
| | - Katarzyna Hura
- Department of Plant Breeding, Physiology and Seed Science, Faculty of Agriculture and Economics, Agricultural University, Podłużna 3, 30-239 Kraków, Poland
| | - Agnieszka Ostrowska
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Kraków, Niezapominajek 21, 30-239 Kraków, Poland
| | - Joanna Gadzinowska
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Kraków, Niezapominajek 21, 30-239 Kraków, Poland
| | - Karolina Urban
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Kraków, Niezapominajek 21, 30-239 Kraków, Poland
| | - Bożena Pawłowska
- Department of Ornamental Plants and Garden Arts, Agricultural University, 29 Listopada 54 Avenue, 31-425 Kraków, Poland
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3
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Wang R, Xing S, Bourke PM, Qi X, Lin M, Esselink D, Arens P, Voorrips RE, Visser RG, Sun L, Zhong Y, Gu H, Li Y, Li S, Maliepaard C, Fang J. Development of a 135K SNP genotyping array for Actinidia arguta and its applications for genetic mapping and QTL analysis in kiwifruit. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:369-380. [PMID: 36333116 PMCID: PMC9884011 DOI: 10.1111/pbi.13958] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/22/2022] [Accepted: 10/31/2022] [Indexed: 05/11/2023]
Abstract
Kiwifruit (Actinidia spp) is a woody, perennial and deciduous vine. In this genus, there are multiple ploidy levels but the main cultivated cultivars are polyploid. Despite the availability of many genomic resources in kiwifruit, SNP genotyping is still a challenge given these different levels of polyploidy. Recent advances in SNP array technologies have offered a high-throughput genotyping platform for genome-wide DNA polymorphisms. In this study, we developed a high-density SNP genotyping array to facilitate genetic studies and breeding applications in kiwifruit. SNP discovery was performed by genome-wide DNA sequencing of 40 kiwifruit genotypes. The identified SNPs were stringently filtered for sequence quality, predicted conversion performance and distribution over the available Actinidia chinensis genome. A total of 134 729 unique SNPs were put on the array. The array was evaluated by genotyping 400 kiwifruit individuals. We performed a multidimensional scaling analysis to assess the diversity of kiwifruit germplasm, showing that the array was effective to distinguish kiwifruit accessions. Using a tetraploid F1 population, we constructed an integrated linkage map covering 3060.9 cM across 29 linkage groups and performed QTL analysis for the sex locus that has been identified on Linkage Group 3 (LG3) in Actinidia arguta. Finally, our dataset presented evidence of tetrasomic inheritance with partial preferential pairing in A. arguta. In conclusion, we developed and evaluated a 135K SNP genotyping array for kiwifruit. It has the advantage of a comprehensive design that can be an effective tool in genetic studies and breeding applications in this high-value crop.
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Affiliation(s)
- Ran Wang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Siyuan Xing
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | - Peter M. Bourke
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Xiuquan Qi
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Miaomiao Lin
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Danny Esselink
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Paul Arens
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | | | | | - Leiming Sun
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Yunpeng Zhong
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Hong Gu
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Yukuo Li
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Sikai Li
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Chris Maliepaard
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Jinbao Fang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
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Lau J, Young EL, Collins S, Windham MT, Klein PE, Byrne DH, Riera-Lizarazu O. Rose Rosette Disease Resistance Loci Detected in Two Interconnected Tetraploid Garden Rose Populations. FRONTIERS IN PLANT SCIENCE 2022; 13:916231. [PMID: 35873988 PMCID: PMC9302375 DOI: 10.3389/fpls.2022.916231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/25/2022] [Indexed: 05/14/2023]
Abstract
Rose rosette disease (RRD), caused by the Rose rosette emaravirus (RRV), is a major threat to the garden rose industry in the United States. There has been limited work on the genetics of host plant resistance to RRV. Two interconnected tetraploid garden rose F1 biparental mapping populations were created to develop high-quality tetraploid rose linkage maps that allowed the discovery of RRD resistance quantitative trait loci (QTLs) on linkage groups (LGs) 5, 6, and 7. These QTLs individually accounted for around 18-40% of the phenotypic variance. The locus with the greatest effect on partial resistance was found in LG 5. Most individuals with the LG 5 QTL were in the simplex configuration; however, two individuals were duplex (likely due to double reduction). Identification of resistant individuals and regions of interest can help the development of diagnostic markers for marker-assisted selection in a breeding program.
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Affiliation(s)
- Jeekin Lau
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Ellen L. Young
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Sara Collins
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Mark T. Windham
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
| | - Patricia E. Klein
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - David H. Byrne
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Oscar Riera-Lizarazu
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
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5
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Fang P, Arens P, Liu X, Zhang X, Lakwani D, Foucher F, Clotault J, Geike J, Kaufmann H, Debener T, Bai Y, Zhang Z, Smulders MJM. Analysis of allelic variants of RhMLO genes in rose and functional studies on susceptibility to powdery mildew related to clade V homologs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2495-2515. [PMID: 33934211 PMCID: PMC8277636 DOI: 10.1007/s00122-021-03838-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
Rose has 19 MLO genes. Of these, RhMLO1 and RhMLO2 were shown to be required for powdery mildew infection, which suggests their potential as susceptibility targets towards disease resistance. Powdery mildew, caused by Podosphaera pannosa, is one of the most serious and widespread fungal diseases for roses, especially in greenhouse-grown cut roses. It has been shown that certain MLO genes are involved in powdery mildew susceptibility and that loss of function in these genes in various crops leads to broad-spectrum, long-lasting resistance against this fungal disease. For this reason, these MLO genes are called susceptibility genes. We carried out a genome-wide identification of the MLO gene family in the Rosa chinensis genome, and screened for allelic variants among 22 accessions from seven different Rosa species using re-sequencing and transcriptome data. We identified 19 MLO genes in rose, of which four are candidate genes for functional homologs in clade V, which is the clade containing all dicot MLO susceptibility genes. We detected a total of 198 different allelic variants in the set of Rosa species and accessions, corresponding to 5-15 different alleles for each of the genes. Some diploid Rosa species shared alleles with tetraploid rose cultivars, consistent with the notion that diploid species have contributed to the formation of tetraploid roses. Among the four RhMLO genes in clade V, we demonstrated using expression study, virus-induced gene silencing as well as transient RNAi silencing that two of them, RhMLO1 and RhMLO2, are required for infection by P. pannosa and suggest their potential as susceptibility targets for powdery mildew resistance breeding in rose.
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Affiliation(s)
- Peihong Fang
- Plant Breeding, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Paul Arens
- Plant Breeding, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Xintong Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Xin Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Deepika Lakwani
- IRHS, Agrocampus-Ouest, INRAE, Université D’Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Fabrice Foucher
- IRHS, Agrocampus-Ouest, INRAE, Université D’Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Jérémy Clotault
- IRHS, Agrocampus-Ouest, INRAE, Université D’Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Juliane Geike
- Institute of Plant Genetics, Molecular Plant Breeding Unit, Leibniz Universität Hannover, Hannover, Germany
| | - Helgard Kaufmann
- Institute of Plant Genetics, Molecular Plant Breeding Unit, Leibniz Universität Hannover, Hannover, Germany
| | - Thomas Debener
- Institute of Plant Genetics, Molecular Plant Breeding Unit, Leibniz Universität Hannover, Hannover, Germany
| | - Yuling Bai
- Plant Breeding, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
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6
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Schulz D, Linde M, Debener T. Detection of Reproducible Major Effect QTL for Petal Traits in Garden Roses. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10050897. [PMID: 33946713 PMCID: PMC8145204 DOI: 10.3390/plants10050897] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/13/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
The detection of QTL by association genetics depends on the genetic architecture of the trait under study, the size and structure of the investigated population and the availability of phenotypic and marker data of sufficient quality and quantity. In roses, we previously demonstrated that major QTL could already be detected in small association panels. In this study, we analyzed petal number, petal size and fragrance in a small panel of 95 mostly tetraploid garden rose genotypes. After genotyping the panel with the 68 K Axiom WagRhSNP chip we detected major QTL for all three traits. Each trait was significantly influenced by several genomic regions. Some of the QTL span genomic regions that comprise several candidate genes. Selected markers from some of these regions were converted into KASP markers and were validated in independent populations of up to 282 garden rose genotypes. These markers demonstrate the robustness of the detected effects independent of the set of genotypes analyzed. Furthermore, the markers can serve as tools for marker-assisted breeding in garden roses. Over an extended timeframe, they may be used as a starting point for the isolation of the genes underlying the QTL.
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7
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Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops. PLANTS 2021; 10:plants10020415. [PMID: 33672381 PMCID: PMC7926561 DOI: 10.3390/plants10020415] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.
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Iezzoni AF, McFerson J, Luby J, Gasic K, Whitaker V, Bassil N, Yue C, Gallardo K, McCracken V, Coe M, Hardner C, Zurn JD, Hokanson S, van de Weg E, Jung S, Main D, da Silva Linge C, Vanderzande S, Davis TM, Mahoney LL, Finn C, Peace C. RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops. HORTICULTURE RESEARCH 2020; 7:177. [PMID: 33328430 PMCID: PMC7603521 DOI: 10.1038/s41438-020-00398-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/16/2020] [Accepted: 08/30/2020] [Indexed: 05/05/2023]
Abstract
The Rosaceae crop family (including almond, apple, apricot, blackberry, peach, pear, plum, raspberry, rose, strawberry, sweet cherry, and sour cherry) provides vital contributions to human well-being and is economically significant across the U.S. In 2003, industry stakeholder initiatives prioritized the utilization of genomics, genetics, and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural quality. However, rosaceous crop breeders lacked certain knowledge and tools to fully implement DNA-informed breeding-a "chasm" existed between existing genomics and genetic information and the application of this knowledge in breeding. The RosBREED project ("Ros" signifying a Rosaceae genomics, genetics, and breeding community initiative, and "BREED", indicating the core focus on breeding programs), addressed this challenge through a comprehensive and coordinated 10-year effort funded by the USDA-NIFA Specialty Crop Research Initiative. RosBREED was designed to enable the routine application of modern genomics and genetics technologies in U.S. rosaceous crop breeding programs, thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural quality. This review presents a synopsis of the approach, deliverables, and impacts of RosBREED, highlighting synergistic global collaborations and future needs. Enabling technologies and tools developed are described, including genome-wide scanning platforms and DNA diagnostic tests. Examples of DNA-informed breeding use by project participants are presented for all breeding stages, including pre-breeding for disease resistance, parental and seedling selection, and elite selection advancement. The chasm is now bridged, accelerating rosaceous crop genetic improvement.
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Affiliation(s)
- Amy F Iezzoni
- Michigan State University, East Lansing, MI, 48824, USA.
| | - Jim McFerson
- Washington State University, Wenatchee, WA, 98801, USA
| | - James Luby
- University of Minnesota, St. Paul, MN, 55108, USA
| | | | | | | | - Chengyan Yue
- University of Minnesota, St. Paul, MN, 55108, USA
| | | | | | - Michael Coe
- Cedar Lake Research Group, Portland, OR, 97215, USA
| | | | | | | | - Eric van de Weg
- Wageningen University and Research, 6700 AA, Wageningen, The Netherlands
| | - Sook Jung
- Washington State University, Pullman, WA, 99164, USA
| | - Dorrie Main
- Washington State University, Pullman, WA, 99164, USA
| | | | | | | | | | | | - Cameron Peace
- Washington State University, Pullman, WA, 99164, USA
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Li C, Zheng Y, Huang P. Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling. Sci Rep 2020; 10:12188. [PMID: 32699274 PMCID: PMC7376030 DOI: 10.1038/s41598-020-68092-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 06/17/2020] [Indexed: 02/06/2023] Open
Abstract
The rose is one of the most important ornamental woody plants because of its extensive use and high economic value. Herein, we sequenced a complete chloroplast genome of the miniature rose variety Rosa 'Margo Koster' and performed comparative analyses with sequences previously published for other species in the Rosaceae family. The chloroplast genome of Rosa 'Margo Koster', with a size of 157,395 bp, has a circular quadripartite structure typical of angiosperm chloroplast genomes and contains a total of 81 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Conjunction regions in the chloroplast genome of Rosa 'Margo Koster' were verified and manually corrected by Sanger sequencing. Comparative genome analysis showed that the IR contraction and expansion events resulted in rps19 and ycf1 pseudogenes. The phylogenetic analysis within the Rosa genus showed that Rosa 'Margo Koster' is closer to Rosa odorata than to other Rosa species. Additionally, we identified and screened highly divergent sequences and cpSSRs and compared their power to discriminate rose varieties by Sanger sequencing and capillary electrophoresis. The results showed that 15 cpSSRs are polymorphic, but their discriminating power is only moderate among a set of rose varieties. However, more than 150 single nucleotide variations (SNVs) were discovered in the flanking region of cpSSRs, and the results indicated that these SNVs have a higher divergence and stronger power for profiling rose varieties. These findings suggest that nucleotide mutations in the chloroplast genome may be an effective and powerful tool for rose variety discrimination and DNA profiling. These molecular markers in the chloroplast genome sequence of Rosa spp. will facilitate population and phylogenetic studies and other related studies of this species.
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Affiliation(s)
- Changhong Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Silviculture and Tree Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Silviculture and Tree Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Ping Huang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Silviculture and Tree Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
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10
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Zurn JD, Zlesak DC, Holen M, Bradeen JM, Hokanson SC, Bassil NV. Mapping the black spot resistance locus Rdr3 in the shrub rose 'George Vancouver' allows for the development of improved diagnostic markers for DNA-informed breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2011-2020. [PMID: 32166372 DOI: 10.1007/s00122-020-03574-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 02/28/2020] [Indexed: 05/22/2023]
Abstract
Rdr3 is a novel resistance gene of black spot in roses that maps to a chromosome 6 homolog. A new DNA test was developed and can be used to pyramid black spot resistance in roses. Diplocarpon rosae, the cause of rose black spot, is one of the most devastating foliar pathogens of cultivated roses (Rosa spp.). The primary method of disease control is fungicides, and they are viewed unfavorably by home gardeners due to potential environmental and health impacts. Planting rose cultivars with genetic resistance to black spot can reduce many of the fungicide applications needed in an integrated pest management system. To date, four resistance genes have been identified in roses (Rdr1, Rdr2, Rdr3, and Rdr4). Rdr3 was never mapped and is thought to be unique from Rdr1 and Rdr2. It is unknown whether it is an allele of Rdr4. To assess the novelty of Rdr3, a mapping population was created by crossing the Rdr3 containing cultivar George Vancouver with the susceptible cultivar Morden Blush. The mapping population was genotyped with the WagRhSNP 68 K Axiom array and mapped using the 'polymapR' package. Rdr3 was mapped to a chromosome 6 homolog confirming it is different from Rdr1 and Rdr2, found on chromosome 1, and from Rdr4, found on chromosome 5. The mapping information was used in conjunction with the Rosa chinensis genome assembly to develop new tightly linked SSRs for marker-assisted breeding. Three markers were able to predict the presence of Rdr3 in a 63-cultivar validation set. Additionally, 12 cultivars appear to have resistance genes other than Rdr3. The improved diagnostic markers will be a great asset to the rose-breeding community toward developing new black spot-resistant cultivars.
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Affiliation(s)
- Jason D Zurn
- USDA-ARS National Clonal Germplasm Repository, Corvallis, OR, USA
| | - David C Zlesak
- Department of Plant and Earth Science, University of Wisconsin-River Falls, River Falls, WI, USA
| | - Matthew Holen
- Department of Horticulture, University of Minnesota, St. Paul, MN, USA
| | - James M Bradeen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Stan C Hokanson
- Department of Horticulture, University of Minnesota, St. Paul, MN, USA
| | - Nahla V Bassil
- USDA-ARS National Clonal Germplasm Repository, Corvallis, OR, USA.
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11
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Howe GT, Jayawickrama K, Kolpak SE, Kling J, Trappe M, Hipkins V, Ye T, Guida S, Cronn R, Cushman SA, McEvoy S. An Axiom SNP genotyping array for Douglas-fir. BMC Genomics 2020; 21:9. [PMID: 31900111 PMCID: PMC6942338 DOI: 10.1186/s12864-019-6383-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 12/10/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND In forest trees, genetic markers have been used to understand the genetic architecture of natural populations, identify quantitative trait loci, infer gene function, and enhance tree breeding. Recently, new, efficient technologies for genotyping thousands to millions of single nucleotide polymorphisms (SNPs) have finally made large-scale use of genetic markers widely available. These methods will be exceedingly valuable for improving tree breeding and understanding the ecological genetics of Douglas-fir, one of the most economically and ecologically important trees in the world. RESULTS We designed SNP assays for 55,766 potential SNPs that were discovered from previous transcriptome sequencing projects. We tested the array on ~ 2300 related and unrelated coastal Douglas-fir trees (Pseudotsuga menziesii var. menziesii) from Oregon and Washington, and 13 trees of interior Douglas-fir (P. menziesii var. glauca). As many as ~ 28 K SNPs were reliably genotyped and polymorphic, depending on the selected SNP call rate. To increase the number of SNPs and improve genome coverage, we developed protocols to 'rescue' SNPs that did not pass the default Affymetrix quality control criteria (e.g., 97% SNP call rate). Lowering the SNP call rate threshold from 97 to 60% increased the number of successful SNPs from 20,669 to 28,094. We used a subset of 395 unrelated trees to calculate SNP population genetic statistics for coastal Douglas-fir. Over a range of call rate thresholds (97 to 60%), the median call rate for SNPs in Hardy-Weinberg equilibrium ranged from 99.2 to 99.7%, and the median minor allele frequency ranged from 0.198 to 0.233. The successful SNPs also worked well on interior Douglas-fir. CONCLUSIONS Based on the original transcriptome assemblies and comparisons to version 1.0 of the Douglas-fir reference genome, we conclude that these SNPs can be used to genotype about 10 K to 15 K loci. The Axiom genotyping array will serve as an excellent foundation for studying the population genomics of Douglas-fir and for implementing genomic selection. We are currently using the array to construct a linkage map and test genomic selection in a three-generation breeding program for coastal Douglas-fir.
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Affiliation(s)
- Glenn T Howe
- Pacific Northwest Tree Improvement Research Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA.
| | - Keith Jayawickrama
- Northwest Tree Improvement Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Scott E Kolpak
- Pacific Northwest Tree Improvement Research Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Jennifer Kling
- Pacific Northwest Tree Improvement Research Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Matt Trappe
- Northwest Tree Improvement Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Valerie Hipkins
- USDA Forest Service, National Forest Genetics Laboratory, Placerville, CA, USA
| | - Terrance Ye
- Northwest Tree Improvement Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | | | - Richard Cronn
- USDA Forest Service, Pacific Northwest Research Station, Corvallis, OR, USA
| | - Samuel A Cushman
- USDA Forest Service, Rocky Mountain Research Station, Flagstaff, AZ, USA
| | - Susan McEvoy
- Pacific Northwest Tree Improvement Research Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
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12
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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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13
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Matias FI, Xavier Meireles KG, Nagamatsu ST, Lima Barrios SC, Borges do Valle C, Carazzolle MF, Fritsche-Neto R, Endelman JB. Expected Genotype Quality and Diploidized Marker Data from Genotyping-by-Sequencing of Urochloa spp. Tetraploids. THE PLANT GENOME 2019; 12:1-9. [PMID: 33016594 DOI: 10.3835/plantgenome2019.01.0002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/29/2019] [Indexed: 05/08/2023]
Abstract
Introduced concept of expected genotype quality (EGQ) and software to calculate it Provided read depth guidelines for GBS in tetraploids Developed software to generate diploidized genotype calls from VCF files Demonstrated value of aligning GBS reads to a mock reference genome for SNP discovery Recommend filtering based on GQ and read depth to prevent genotype bias Although genotyping-by-sequencing (GBS) is a well-established marker technology in diploids, the development of best practices for tetraploid species is a topic of current research. We determined the theoretical relationship between read depth and the phred-scaled probability of genotype misclassification conditioned on the true genotype, which we call expected genotype quality (EGQ). If the GBS method has 0.5% allelic error, then 17 reads are needed to classify simplex tetraploids as heterozygous with 95% accuracy (EGQ = 13) vs. 61 reads to determine allele dosage. We developed an R script to convert tetraploid GBS data in variant call format (VCF) into diploidized genotype calls and applied it to 267 interspecific hybrids of the tetraploid forage grass Urochloa. When reads were aligned to a mock reference genome created from GBS data of the Urochloa brizantha (Hochst. ex A. Rich.) R. D. Webster cultivar Marandu, 25,678 biallelic single nucleotide polymorphism (SNPs) were discovered, compared with ∼3000 SNPs when aligning to the closest true reference genomes, Setaria viridis (L.) P. Beauv. and S. italica (L.) P. Beauv. Cross-validation revealed that missing genotypes were imputed by the random forest method with a median accuracy of 0.85 regardless of heterozygote frequency. Using the Urochloa spp. hybrids, we illustrated how filtering samples based only on genotype quality (GQ) creates genotype bias; a depth threshold based on EGQ is also needed regardless of whether genotypes are called using a diploidized or allele dosage model.
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Affiliation(s)
- Filipe Inácio Matias
- Genetics Dep., Luiz de Queiroz College of Agriculture, Univ. of São Paulo, Av. Pádua Dias, 11, C. P. 9, 13.418-900, Piracicaba, São Paulo, Brazil
| | | | - Sheila Tiemi Nagamatsu
- Genetics and Evolution Dep., Univ. of Campinas, Cidade Univ. Zeferino Vaz, 13.083-970, Campinas, São Paulo, Brazil
| | | | - Cacilda Borges do Valle
- Embrapa Beef Cattle, Av. Rádio Maia, 830, Zona Rural, 79.106-550, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Roberto Fritsche-Neto
- Genetics Dep., Luiz de Queiroz College of Agriculture, Univ. of São Paulo, Av. Pádua Dias, 11, C. P. 9, 13.418-900, Piracicaba, São Paulo, Brazil
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14
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Bourke PM, van Geest G, Voorrips RE, Jansen J, Kranenburg T, Shahin A, Visser RGF, Arens P, Smulders MJM, Maliepaard C. polymapR-linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. Bioinformatics 2019; 34:3496-3502. [PMID: 29722786 PMCID: PMC6184683 DOI: 10.1093/bioinformatics/bty371] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 05/09/2018] [Indexed: 12/20/2022] Open
Abstract
Motivation Polyploid species carry more than two copies of each chromosome, a condition found in many of the world’s most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realize all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops. Results polymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops. Availability and implementation polymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polymapR. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Peter M Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Geert van Geest
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands.,Deliflor Chrysanten B.V, Maasdijk, BS, The Netherlands
| | - Roeland E Voorrips
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Johannes Jansen
- Biometris, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Twan Kranenburg
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Arwa Shahin
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands.,Van Zanten Breeding B. V, Rijsenhout, EW, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Paul Arens
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Marinus J M Smulders
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Chris Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
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15
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Huang P, Lin F, Li B, Zheng Y. Hybrid-Transcriptome Sequencing and Associated Metabolite Analysis Reveal Putative Genes Involved in Flower Color Difference in Rose Mutants. PLANTS (BASEL, SWITZERLAND) 2019; 8:E267. [PMID: 31387222 PMCID: PMC6724100 DOI: 10.3390/plants8080267] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/21/2019] [Accepted: 07/29/2019] [Indexed: 02/04/2023]
Abstract
Gene mutation is a common phenomenon in nature that often leads to phenotype differences, such as the variations in flower color that frequently occur in roses. With the aim of revealing the genomic information and inner mechanisms, the differences in the levels of both transcription and secondary metabolism between a pair of natural rose mutants were investigated by using hybrid RNA-sequencing and metabolite analysis. Metabolite analysis showed that glycosylated derivatives of pelargonidin, e.g., pelargonidin 3,5 diglucoside and pelargonidin 3-glucoside, which were not detected in white flowers (Rosa 'Whilte Mrago Koster'), constituted the major pigments in pink flowers. Conversely, the flavonol contents of petal, such as kaempferol-3-glucoside, quercetin 3-glucoside, and rutin, were higher in white flowers. Hybrid RNA-sequencing obtained a total of 107,280 full-length transcripts in rose petal which were annotated in major databases. Differentially expressed gene (DEG) analysis showed that the expression of genes involved in the flavonoid biosynthesis pathway was significantly different, e.g., CHS, FLS, DFR, LDOX, which was verified by qRT-PCR during flowering. Additionally, two MYB transcription factors were found and named RmMYBAN2 and RmMYBPA1, and their expression patterns during flowering were also analyzed. These findings indicate that these genes may be involved in the flower color difference in the rose mutants, and competition between anthocyanin and flavonol biosynthesis is a primary cause of flower color variation, with its regulation reflected by transcriptional and secondary metabolite levels.
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Affiliation(s)
- Ping Huang
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Furong Lin
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Bin Li
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
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16
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Montanari S, Bianco L, Allen BJ, Martínez-García PJ, Bassil NV, Postman J, Knäbel M, Kitson B, Deng CH, Chagné D, Crepeau MW, Langley CH, Evans K, Dhingra A, Troggio M, Neale DB. Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization. BMC Genomics 2019; 20:331. [PMID: 31046664 PMCID: PMC6498479 DOI: 10.1186/s12864-019-5712-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 04/17/2019] [Indexed: 12/20/2022] Open
Abstract
Background Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are equally important to enable faster progress in plant breeding. Pear (Pyrus spp.) lags far behind other fruit and nut crops in terms of employment of available genetic resources for new cultivar development. To address this gap, we designed a high-density, high-efficiency and robust single nucleotide polymorphism (SNP) array for pear, with the main objectives of conducting genetic diversity and genome-wide association studies. Results By applying a two-step design process, which consisted of the construction of a first ‘draft’ array for the screening of a small subset of samples, we were able to identify the most robust and informative SNPs to include in the Applied Biosystems™ Axiom™ Pear 70 K Genotyping Array, currently the densest SNP array for pear. Preliminary evaluation of this 70 K array in 1416 diverse pear accessions from the USDA National Clonal Germplasm Repository (NCGR) in Corvallis, OR identified 66,616 SNPs (93% of all the tiled SNPs) as high quality and polymorphic (PolyHighResolution). We further used the Axiom Pear 70 K Genotyping Array to construct high-density linkage maps in a bi-parental population, and to make a direct comparison with available genotyping-by-sequencing (GBS) data, which suggested that the SNP array is a more robust method of screening for SNPs than restriction enzyme reduced representation sequence-based genotyping. Conclusions The Axiom Pear 70 K Genotyping Array, with its high efficiency in a widely diverse panel of Pyrus species and cultivars, represents a valuable resource for a multitude of molecular studies in pear. The characterization of the USDA-NCGR collection with this array will provide important information for pear geneticists and breeders, as well as for the optimization of conservation strategies for Pyrus. Electronic supplementary material The online version of this article (10.1186/s12864-019-5712-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara Montanari
- Department of Plant Sciences, University of California, Davis, CA, USA.
| | - Luca Bianco
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, CA, USA
| | | | - Nahla V Bassil
- USDA Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, OR, USA
| | - Joseph Postman
- USDA Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, OR, USA
| | - Mareike Knäbel
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North, New Zealand
| | - Biff Kitson
- Motueka Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Motueka, New Zealand
| | - Cecilia H Deng
- Auckland Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
| | - David Chagné
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North, New Zealand
| | - Marc W Crepeau
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Charles H Langley
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Kate Evans
- Tree Fruit Research and Extension Center, Washington State University, Wenatchee, WA, USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA, USA
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17
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Dhandapani S, Jin J, Sridhar V, Chua NH, Jang IC. CYP79D73 Participates in Biosynthesis of Floral Scent Compound 2-Phenylethanol in Plumeria rubra. PLANT PHYSIOLOGY 2019; 180:171-184. [PMID: 30804010 PMCID: PMC6501094 DOI: 10.1104/pp.19.00098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 02/12/2019] [Indexed: 05/19/2023]
Abstract
Plumeria (Plumeria rubra), well known for its brightly colored and fragrant flowers, emits a number of floral volatile organic compounds (VOCs). Plumeria flowers emit a total of 43 VOCs including nine phenylpropanoids/benzenoids, such as 2-phenylethanol (2PE), benzaldehyde, 2-phenylacetaldehyde (PAld), (E/Z)-phenylacetaldoxime (PAOx), benzyl nitrile (BN), and 2-phenylnitroethane (PN). To identify genes and pathways involved in the production of the major compound 2PE, we analyzed the plumeria floral transcriptome and found a highly expressed, flower-specific gene encoding a cytochrome P450 family 79D protein (PrCYP79D73), which catalyzed the formation of (E/Z)-PAOx. Feeding experiments with deuterated phenylalanine or deuterated (E/Z)-PAOx showed that (E/Z)-PAOx is an intermediate in the biosynthesis of 2PE, as are two nitrogen-containing volatiles, BN and PN, in plumeria flowers. Crude enzyme extracts from plumeria flowers converted l-phenylalanine to (E/Z)-PAOx, PAld, 2PE, BN, and PN. The biosynthesis of these compounds increased with addition of PrCYP79D73-enriched microsomes but was blocked by pretreatment with 4-phenylimidazole, an inhibitor of cytochrome P450 enzymes. Moreover, overexpression of PrCYP79D73 in Nicotiana benthamiana resulted in the emission of (E/Z)-PAOx as well as PAld, 2PE, BN, and PN, all of which were also found among plumeria floral VOCs. Taken together, our results demonstrate that PrCYP79D73 is a crucial player in the biosynthesis of the major floral VOC 2PE and other nitrogen-containing volatiles. These volatiles may be required for plant defense as well as to attract pollinators for the successful reproduction of plumeria.
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Affiliation(s)
- Savitha Dhandapani
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Jingjing Jin
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604
| | - Vishweshwaran Sridhar
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604
| | - Nam-Hai Chua
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604
| | - In-Cheol Jang
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604
- Department of Biological Sciences, National University of Singapore, Singapore 117543
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18
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Jung S, Lee T, Cheng CH, Buble K, Zheng P, Yu J, Humann J, Ficklin SP, Gasic K, Scott K, Frank M, Ru S, Hough H, Evans K, Peace C, Olmstead M, DeVetter LW, McFerson J, Coe M, Wegrzyn JL, Staton ME, Abbott AG, Main D. 15 years of GDR: New data and functionality in the Genome Database for Rosaceae. Nucleic Acids Res 2019; 47:D1137-D1145. [PMID: 30357347 PMCID: PMC6324069 DOI: 10.1093/nar/gky1000] [Citation(s) in RCA: 198] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 10/09/2018] [Indexed: 12/13/2022] Open
Abstract
The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding data and data-mining tools to facilitate basic, translational and applied research in Rosaceae. The volume of data in GDR has increased greatly over the last 5 years. The GDR now houses multiple versions of whole genome assembly and annotation data from 14 species, made available by recent advances in sequencing technology. Annotated and searchable reference transcriptomes, RefTrans, combining peer-reviewed published RNA-Seq as well as EST datasets, are newly available for major crop species. Significantly more quantitative trait loci, genetic maps and markers are available in MapViewer, a new visualization tool that better integrates with other pages in GDR. Pathways can be accessed through the new GDR Cyc Pathways databases, and synteny among the newest genome assemblies from eight species can be viewed through the new synteny browser, SynView. Collated single-nucleotide polymorphism diversity data and phenotypic data from publicly available breeding datasets are integrated with other relevant data. Also, the new Breeding Information Management System allows breeders to upload, manage and analyze their private breeding data within the secure GDR server with an option to release data publicly.
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Affiliation(s)
- Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Taein Lee
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Chun-Huai Cheng
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Katheryn Buble
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Jing Yu
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Jodi Humann
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Stephen P Ficklin
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Ksenija Gasic
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634-0310, USA
| | - Kristin Scott
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Morgan Frank
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Sushan Ru
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN 55108, USA
| | - Heidi Hough
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Kate Evans
- Department of Horticulture, Washington State University Tree Fruit Research and Extension Center, Wenatchee, WA 98801, USA
| | - Cameron Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Mercy Olmstead
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Lisa W DeVetter
- Department of Horticulture, Washington State University, Northwestern Washington Research and Extension Center, Mount Vernon, WA 98273, USA
| | - James McFerson
- Department of Horticulture, Washington State University Tree Fruit Research and Extension Center, Wenatchee, WA 98801, USA
| | - Michael Coe
- Cedar Lake Research Group, LLC, Portland, OR 97293, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Margaret E Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Albert G Abbott
- Forest Health Research and Extension Center, University of Kentucky, Lexington, KY 40546-0091, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
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19
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Smulders MJM, Arens P, Bourke PM, Debener T, Linde M, Riek JD, Leus L, Ruttink T, Baudino S, Hibrant Saint-Oyant L, Clotault J, Foucher F. In the name of the rose: a roadmap for rose research in the genome era. HORTICULTURE RESEARCH 2019; 6:65. [PMID: 31069087 PMCID: PMC6499834 DOI: 10.1038/s41438-019-0156-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/18/2019] [Indexed: 05/07/2023]
Abstract
The recent completion of the rose genome sequence is not the end of a process, but rather a starting point that opens up a whole set of new and exciting activities. Next to a high-quality genome sequence other genomic tools have also become available for rose, including transcriptomics data, a high-density single-nucleotide polymorphism array and software to perform linkage and quantitative trait locus mapping in polyploids. Rose cultivars are highly heterogeneous and diverse. This vast diversity in cultivated roses can be explained through the genetic potential of the genus, introgressions from wild species into commercial tetraploid germplasm and the inimitable efforts of historical breeders. We can now investigate how this diversity can best be exploited and refined in future breeding work, given the rich molecular toolbox now available to the rose breeding community. This paper presents possible lines of research now that rose has entered the genomics era, and attempts to partially answer the question that arises after the completion of any draft genome sequence: 'Now that we have "the" genome, what's next?'. Having access to a genome sequence will allow both (fundamental) scientific and (applied) breeding-orientated questions to be addressed. We outline possible approaches for a number of these questions.
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Affiliation(s)
- Marinus J. M. Smulders
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Paul Arens
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Peter M. Bourke
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Thomas Debener
- Faculty of Natural Sciences, Institute for Plant Genetics, Molecular Plant Breeding, Leibniz University of Hannover, Herrenhäuser Strasse 2, 30419 Hannover, Germany
| | - Marcus Linde
- Faculty of Natural Sciences, Institute for Plant Genetics, Molecular Plant Breeding, Leibniz University of Hannover, Herrenhäuser Strasse 2, 30419 Hannover, Germany
| | - Jan De Riek
- ILVO, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Caritasstraat 39, 9090 Melle, Belgium
| | - Leen Leus
- ILVO, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Caritasstraat 39, 9090 Melle, Belgium
| | - Tom Ruttink
- ILVO, Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Caritasstraat 39, 9090 Melle, Belgium
| | - Sylvie Baudino
- BVpam CNRS, FRE 3727, UJM-Saint-Étienne, Univ. Lyon, Saint-Etienne, France
| | - Laurence Hibrant Saint-Oyant
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, SFR 4207 QuaSaV, 42 rue Georges Morel BP 60057, 49 071 Beaucouzé, France
| | - Jeremy Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, SFR 4207 QuaSaV, 42 rue Georges Morel BP 60057, 49 071 Beaucouzé, France
| | - Fabrice Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, SFR 4207 QuaSaV, 42 rue Georges Morel BP 60057, 49 071 Beaucouzé, France
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20
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Li S, Zhong M, Dong X, Jiang X, Xu Y, Sun Y, Cheng F, Li DZ, Tang K, Wang S, Dai S, Hu JY. Comparative transcriptomics identifies patterns of selection in roses. BMC PLANT BIOLOGY 2018; 18:371. [PMID: 30579326 PMCID: PMC6303930 DOI: 10.1186/s12870-018-1585-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/30/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Roses are important plants for human beings with pivotal economical and biological traits like continuous flowering, flower architecture, color and scent. Due to frequent hybridization and high genome heterozygosity, classification of roses and their relatives remains a big challenge. RESULTS Here, to identify potential markers for phylogenetic reconstruction and to reveal the patterns of natural selection in roses, we generated sets of high quality and comprehensive reference transcriptomes for Rosa chinensis 'Old Blush' (OB) and R. wichuriana 'Basye's Thornless' (BT), two species exhibiting contrasted traits of high economical importance. The assembled reference transcriptomes showed transcripts N50 above 2000 bp. Two roses shared about 10,073 transcripts (N50 = 2282 bp), in which a set of 5959 transcripts was conserved within genera of Rosa. Further comparison with species in Rosaceae identified 4447 transcripts being common (Rosaceae-common) in Rosa, Malus, Prunus, Rubus, and Fragaria, while a pool of 164 transcripts being specific for roses (Rosa-specific). Among the Rosaceae-common transcripts, 409 transcripts showed a signature of positive selection and a clustered expression in different tissues. Interestingly, nine of these rapidly evolving genes were related to DNA damage repair and responses to environmental stimulus, a potential associated with genome confliction post hybridization. Coincident with this fast evolution pattern in rose genes, 24 F-box and four TMV resistant proteins were significantly enriched in the Rosa-specific genes. CONCLUSIONS We expect that these Rosaceae-common and Rosa-specific transcripts should facilitate the phylogenetic analysis of Rosaceae plants as well as investigations of Rosa-specific biology. The data reported here could provide fundamental genomic tools and knowledge critical for understanding the biology and domestication of roses and for roses breeding.
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Affiliation(s)
- Shubin Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083 China
- Flower Research Institute, Yunnan Agricultural Academy of Sciences, Kunming, 650231 China
| | - Micai Zhong
- Group of Plant Molecular Genetics and Adaptation, CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xue Dong
- Group of Plant Molecular Genetics and Adaptation, CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Xiaodong Jiang
- Group of Plant Molecular Genetics and Adaptation, CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yuxing Xu
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yibo Sun
- Group of Plant Molecular Genetics and Adaptation, CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Fang Cheng
- Group of Plant Molecular Genetics and Adaptation, CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - De-zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Kaixue Tang
- Flower Research Institute, Yunnan Agricultural Academy of Sciences, Kunming, 650231 China
| | - Siqing Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083 China
| | - Silan Dai
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083 China
| | - Jin-Yong Hu
- Group of Plant Molecular Genetics and Adaptation, CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
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21
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Bourke PM, van Geest G, Voorrips RE, Jansen J, Kranenburg T, Shahin A, Visser RGF, Arens P, Smulders MJM, Maliepaard C. polymapR-linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. BIOINFORMATICS (OXFORD, ENGLAND) 2018. [PMID: 29722786 DOI: 10.1093/bioinformatica/bty371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
MOTIVATION Polyploid species carry more than two copies of each chromosome, a condition found in many of the world's most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realize all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops. RESULTS polymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops. AVAILABILITY AND IMPLEMENTATION polymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polymapR. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Peter M Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Geert van Geest
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
- Deliflor Chrysanten B.V, Maasdijk, BS, The Netherlands
| | - Roeland E Voorrips
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Johannes Jansen
- Biometris, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Twan Kranenburg
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Arwa Shahin
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
- Van Zanten Breeding B. V, Rijsenhout, EW, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Paul Arens
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Marinus J M Smulders
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
| | - Chris Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands
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22
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Bourke PM, Gitonga VW, Voorrips RE, Visser RGF, Krens FA, Maliepaard C. Multi-environment QTL analysis of plant and flower morphological traits in tetraploid rose. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2055-2069. [PMID: 29961102 PMCID: PMC6154034 DOI: 10.1007/s00122-018-3132-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 06/20/2018] [Indexed: 05/09/2023]
Abstract
KEY MESSAGE Rose morphological traits such as prickles or petal number are influenced by a few key QTL which were detected across different growing environments-necessary for genomics-assisted selection in non-target environments. Rose, one of the world's most-loved and commercially important ornamental plants, is predominantly tetraploid, possessing four rather than two copies of each chromosome. This condition complicates genetic analysis, and so the majority of previous genetic studies in rose have been performed at the diploid level. However, there may be advantages to performing genetic analyses at the tetraploid level, not least because this is the ploidy level of most breeding germplasm. Here, we apply recently developed methods for quantitative trait loci (QTL) detection in a segregating tetraploid rose population (F1 = 151) to unravel the genetic control of a number of key morphological traits. These traits were measured both in the Netherlands and Kenya. Since ornamental plant breeding and selection are increasingly being performed at locations other than the production sites, environment-neutral QTL are required to maximise the effectiveness of breeding programmes. We detected a number of robust, multi-environment QTL for such traits as stem and petiole prickles, petal number and stem length that were localised on the recently developed high-density SNP linkage map for rose. Our work explores the complex genetic architecture of these important morphological traits at the tetraploid level, while helping to advance the methods for marker-trait exploration in polyploid species.
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Affiliation(s)
- Peter M Bourke
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Virginia W Gitonga
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
- Selecta Kenya GmbH & Co. KG, P. O. Box 64132, Nairobi, 00620, Kenya
| | - Roeland E Voorrips
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Frans A Krens
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Chris Maliepaard
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands.
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23
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A miR172 target-deficient AP2-like gene correlates with the double flower phenotype in roses. Sci Rep 2018; 8:12912. [PMID: 30150746 PMCID: PMC6110776 DOI: 10.1038/s41598-018-30918-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/06/2018] [Indexed: 01/09/2023] Open
Abstract
One of the well-known floral abnormalities in flowering plants is the double-flower phenotype, which corresponds to flowers that develop extra petals, sometimes even containing entire flowers within flowers. Because of their highly priced ornamental value, spontaneous double-flower variants have been found and selected for in a wide range of ornamental species. Previously, double flower formation in roses was associated with a restriction of AGAMOUS expression domain toward the centre of the meristem, leading to extra petals. Here, we characterized the genomic region containing the mutation associated with the switch from simple to double flowers in the rose. An APETALA2-like gene (RcAP2L), a member of the Target Of EAT-type (TOE-type) subfamily, lies within this interval. In the double flower rose, two alleles of RcAP2L are present, one of which harbours a transposable element inserted into intron 8. This insertion leads to the creation of a miR172 resistant RcAP2L variant. Analyses of the presence of this variant in a set of simple and double flower roses demonstrate a correlation between the presence of this allele and the double flower phenotype. These data suggest a role of this miR172 resistant RcAP2L variant in regulating RcAGAMOUS expression and double flower formation in Rosa sp.
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24
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Liu X, Cao X, Shi S, Zhao N, Li D, Fang P, Chen X, Qi W, Zhang Z. Comparative RNA-Seq analysis reveals a critical role for brassinosteroids in rose (Rosa hybrida) petal defense against Botrytis cinerea infection. BMC Genet 2018; 19:62. [PMID: 30126371 PMCID: PMC6102922 DOI: 10.1186/s12863-018-0668-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 08/10/2018] [Indexed: 12/31/2022] Open
Abstract
Background One of the most popular ornamental plants worldwide, roses (Rosa sp.), are very susceptible to Botrytis gray mold disease. The necrotrophic infection of rose petals by B. cinerea causes the collapse and death of these tissues in both the growth and post-harvest stages, resulting in serious economic losses. To understand the molecular basis of rose resistance against B. cinerea, we profiled the petal transcriptome using RNA-Seq technology. Results We identified differentially transcribed genes (DTGs) in petals during B. cinerea infection at 30 h post inoculation (hpi) and/or 48 hpi. Gene ontology term enrichment and pathway analyses revealed that metabolic, secondary metabolite biosynthesis, plant-pathogen interaction, and plant hormone signal transduction pathways were involved. The expression of 370 cell-surface immune receptors was upregulated during infection. In addition, 188 genes encoding transcription factors were upregulated, particularly in the ERF, WRKY, bHLH, MYB, and NAC families, implying their involvement in resistance against B. cinerea. We further identified 325 upregulated DTGs in the hormone signal transduction pathways. Among them, the brassinosteroid (BR)-related genes were the most significantly enriched. To confirm the role of BR in Botrytis resistance, exogenous BR was applied to rose flowers before the inoculation of B. cinerea, which enhanced the defense response in these petals. Conclusions Our global transcriptome profiling provides insights into the complex gene regulatory networks mediating the rose petal response to B. cinerea. We further demonstrated the role of the phytohormone BR in the resistance of petals to necrotrophic fungal pathogens. Electronic supplementary material The online version of this article (10.1186/s12863-018-0668-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xintong Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193, China
| | - Xiaoqian Cao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193, China
| | - Shaochuan Shi
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193, China
| | - Na Zhao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193, China
| | - Dandan Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193, China
| | - Peihong Fang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193, China
| | - Xi Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Weicong Qi
- Institute of Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Zhonglingjie 50, Nanjing, 210014, China.
| | - Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193, China.
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25
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Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Arens P, Voorrips RE, Maliepaard C, Neu E, Linde M, Le Paslier MC, Bérard A, Bounon R, Clotault J, Choisne N, Quesneville H, Kawamura K, Aubourg S, Sakr S, Smulders MJM, Schijlen E, Bucher E, Debener T, De Riek J, Foucher F. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. NATURE PLANTS 2018; 4:473-484. [PMID: 29892093 DOI: 10.1101/254102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/01/2018] [Indexed: 05/27/2023]
Abstract
Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.
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Affiliation(s)
- L Hibrand Saint-Oyant
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Ruttink
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - L Hamama
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - I Kirov
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
- Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - D Lakhwani
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N N Zhou
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - P M Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - N Daccord
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Leus
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - D Schulz
- Leibniz Universität, Hannover, Germany
| | - H Van de Geest
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - T Hesselink
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - K Van Laere
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - K Debray
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Balzergue
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Thouroude
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - A Chastellier
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - J Jeauffre
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Voisine
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Gaillard
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T J A Borm
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - P Arens
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - R E Voorrips
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - C Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Neu
- Leibniz Universität, Hannover, Germany
| | - M Linde
- Leibniz Universität, Hannover, Germany
| | - M C Le Paslier
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - A Bérard
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - R Bounon
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - J Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N Choisne
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - H Quesneville
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - K Kawamura
- Osaka Institute of Technology, Osaka, Japan
| | - S Aubourg
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Sakr
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - M J M Smulders
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Schijlen
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - E Bucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Debener
- Leibniz Universität, Hannover, Germany
| | - J De Riek
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - F Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France.
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Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Arens P, Voorrips RE, Maliepaard C, Neu E, Linde M, Le Paslier MC, Bérard A, Bounon R, Clotault J, Choisne N, Quesneville H, Kawamura K, Aubourg S, Sakr S, Smulders MJM, Schijlen E, Bucher E, Debener T, De Riek J, Foucher F. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. NATURE PLANTS 2018; 4:473-484. [PMID: 29892093 PMCID: PMC6786968 DOI: 10.1038/s41477-018-0166-1] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/01/2018] [Indexed: 05/18/2023]
Abstract
Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.
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Affiliation(s)
- L Hibrand Saint-Oyant
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Ruttink
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - L Hamama
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - I Kirov
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
- Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - D Lakhwani
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N N Zhou
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - P M Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - N Daccord
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Leus
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - D Schulz
- Leibniz Universität, Hannover, Germany
| | - H Van de Geest
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - T Hesselink
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - K Van Laere
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - K Debray
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Balzergue
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Thouroude
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - A Chastellier
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - J Jeauffre
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Voisine
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Gaillard
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T J A Borm
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - P Arens
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - R E Voorrips
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - C Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Neu
- Leibniz Universität, Hannover, Germany
| | - M Linde
- Leibniz Universität, Hannover, Germany
| | - M C Le Paslier
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - A Bérard
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - R Bounon
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - J Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N Choisne
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - H Quesneville
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - K Kawamura
- Osaka Institute of Technology, Osaka, Japan
| | - S Aubourg
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Sakr
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - M J M Smulders
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Schijlen
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - E Bucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Debener
- Leibniz Universität, Hannover, Germany
| | - J De Riek
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - F Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France.
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Qi W, Chen X, Fang P, Shi S, Li J, Liu X, Cao X, Zhao N, Hao H, Li Y, Han Y, Zhang Z. Genomic and transcriptomic sequencing of Rosa hybrida provides microsatellite markers for breeding, flower trait improvement and taxonomy studies. BMC PLANT BIOLOGY 2018; 18:119. [PMID: 29907083 PMCID: PMC6003205 DOI: 10.1186/s12870-018-1322-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 05/24/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Rosa hybrida is a valuable ornamental, food and medicinal crop worldwide, but with relatively limited molecular marker resources, especially for flower-specific markers. In this study, we performed genomic and floral transcriptomic sequencing of modern rose. We obtained comprehensive nucleotide information, from which numerous potential simple sequence repeat (SSR) markers were identified but were found to have high rates of amplification failure and PCR product redundancy. RESULTS We applied a filtering strategy for BLAST analysis with the assembled genomic sequence and identified 124,591 genomic and 2,292 EST markers with unique annealing sites. These markers had much greater reliability than those obtained before filtering. Additional BLAST analysis against the transcriptomic sequences uncovered 5225 genomic SSRs associated with 4100 transcripts, 2138 of which were associated with functional genes that were annotated against the non-redundant database. More than 90% of these newly developed molecular markers were polymorphic, based on PCR using a subset of SSRs to analyze tetraploid modern rose accessions, diploid Rosa species and one strawberry accession. The relationships among Rosa species determined by cluster analysis (based on these results) were in agreement with modern rose breeding history, whereas strawberry was isolated in a separate cluster, as expected. CONCLUSIONS Our results provide valuable molecular-genetic tools for rose flower trait improvement, breeding and taxonomy. Importantly, we describe a reproducible organ-specific strategy for molecular marker development and selection in plants, which can be applied to other crops.
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Affiliation(s)
- Weicong Qi
- Salt-Soil Agricultural Center, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
| | - Xi Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
| | - Peihong Fang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193 China
| | - Shaochuan Shi
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193 China
| | - Jingjing Li
- Nextomics Biosciences Co., Ltd., Wuhan, 430073 China
| | - Xintong Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193 China
| | - Xiaoqian Cao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193 China
| | - Na Zhao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193 China
| | - Huiyuan Hao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193 China
| | - Yajie Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193 China
| | - Yujie Han
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193 China
| | - Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193 China
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Bourke PM, Voorrips RE, Visser RGF, Maliepaard C. Tools for Genetic Studies in Experimental Populations of Polyploids. FRONTIERS IN PLANT SCIENCE 2018; 9:513. [PMID: 29720992 PMCID: PMC5915555 DOI: 10.3389/fpls.2018.00513] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/04/2018] [Indexed: 05/19/2023]
Abstract
Polyploid organisms carry more than two copies of each chromosome, a condition rarely tolerated in animals but which occurs relatively frequently in the plant kingdom. One of the principal challenges faced by polyploid organisms is to evolve stable meiotic mechanisms to faithfully transmit genetic information to the next generation upon which the study of inheritance is based. In this review we look at the tools available to the research community to better understand polyploid inheritance, many of which have only recently been developed. Most of these tools are intended for experimental populations (rather than natural populations), facilitating genomics-assisted crop improvement and plant breeding. This is hardly surprising given that a large proportion of domesticated plant species are polyploid. We focus on three main areas: (1) polyploid genotyping; (2) genetic and physical mapping; and (3) quantitative trait analysis and genomic selection. We also briefly review some miscellaneous topics such as the mode of inheritance and the availability of polyploid simulation software. The current polyploid analytic toolbox includes software for assigning marker genotypes (and in particular, estimating the dosage of marker alleles in the heterozygous condition), establishing chromosome-scale linkage phase among marker alleles, constructing (short-range) haplotypes, generating linkage maps, performing genome-wide association studies (GWAS) and quantitative trait locus (QTL) analyses, and simulating polyploid populations. These tools can also help elucidate the mode of inheritance (disomic, polysomic or a mixture of both as in segmental allopolyploids) or reveal whether double reduction and multivalent chromosomal pairing occur. An increasing number of polyploids (or associated diploids) are being sequenced, leading to publicly available reference genome assemblies. Much work remains in order to keep pace with developments in genomic technologies. However, such technologies also offer the promise of understanding polyploid genomes at a level which hitherto has remained elusive.
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Affiliation(s)
| | | | | | - Chris Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
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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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30
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Scheben A, Batley J, Edwards D. Revolution in Genotyping Platforms for Crop Improvement. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 164:37-52. [PMID: 29356847 DOI: 10.1007/10_2017_47] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the past decade, the application of high-throughput sequencing to crop genotyping has given rise to novel platforms capable of genotyping tens of thousands of genome-wide DNA markers. Coupled with the decreasing costs of sequencing, this rapid increase in markers allows accelerated and highly accurate genotyping of entire crop populations and diversity sets using single nucleotide polymorphisms (SNPs). These revolutionary advances accelerate crop improvement by facilitating a more precise connection of phenotype to genotype through association studies, linkage mapping and diversity analysis. The platforms driving the advances in genotyping are array technologies and genotyping by sequencing (GBS) methods, which include both low-coverage whole genome resequencing (skim sequencing) and reduced representation sequencing (RRS) approaches. Here, we outline and compare these genotyping platforms and provide a perspective on the promising future of crop genotyping. While SNP arrays provide high quality, simple handling, and unchallenging analysis, the lower cost of RRS and the greater data volume produced by skim sequencing suggest that use of GBS will become more prevalent in crop genomics as sequencing costs decrease and data analysis becomes more streamlined. Graphical Abstract.
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Affiliation(s)
- Armin Scheben
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.,Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia. .,Institute of Agriculture, University of Western Australia, Crawley, WA, Australia.
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Zurn JD, Zlesak DC, Holen M, Bradeen JM, Hokanson SC, Bassil NV. Mapping a Novel Black Spot Resistance Locus in the Climbing Rose Brite Eyes™ ('RADbrite'). FRONTIERS IN PLANT SCIENCE 2018; 9:1730. [PMID: 30534133 PMCID: PMC6275305 DOI: 10.3389/fpls.2018.01730] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/07/2018] [Indexed: 05/22/2023]
Abstract
Rose black spot, caused by Diplocarpon rosae, is one of the most devastating foliar diseases of cultivated roses (Rosa spp.). The globally distributed pathogen has the potential to cause large economic losses in the outdoor cultivation of roses. Fungicides are the primary method to manage the disease, but are often viewed unfavorably by home gardeners due to potential environmental and health impacts. As such, rose cultivars with genetic resistance to black spot are highly desired. The tetraploid climbing rose Brite EyesTM ('RADbrite') is known for its resistance to black spot. To better characterize the resistance present in Brite EyesTM, phenotyping was conducted on a 94 individual F1 population developed by crossing Brite EyesTM to the susceptible tetraploid rose 'Morden Blush'. Brite EyesTM was resistant to all D. rosae races evaluated except for race 12. The progeny were either resistant or susceptible to all races (2, 3, 8, 9, 10, 11, and 13) evaluated. The segregation ratio was 1:1 (χ2 = 0.3830, P = 0.5360) suggesting resistance is conferred by a single locus. The roses were genotyped with the WagRhSNP 68K Axiom array and the 'polymapR' package was used to construct a map. A single resistance locus (Rdr4) was identified on the long arm of chromosome 5 homoeolog 4. Three resistance loci have been previously identified (Rdr1, Rdr2, and Rdr3). Both Rdr1 and Rdr2 are located on a chromosome 1 homoeolog. The chromosomal location of Rdr3 is unknown, however, races 3 and 9 are virulent on Rdr3. Rdr4 is either a novel gene or an allele of Rdr3 as it provides resistance to races 3 and 9. Due to its broad resistance, Rdr4 is an excellent gene to introgress into new rose cultivars.
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Affiliation(s)
- Jason D. Zurn
- USDA-ARS National Clonal Germplasm Repository, Corvallis, OR, United States
| | - David C. Zlesak
- Department of Plant and Earth Science, University of Wisconsin River Falls, River Falls, WI, United States
| | - Matthew Holen
- Department of Horticulture, University of Minnesota, St. Paul, MN, United States
| | - James M. Bradeen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Stan C. Hokanson
- Department of Horticulture, University of Minnesota, St. Paul, MN, United States
| | - Nahla V. Bassil
- USDA-ARS National Clonal Germplasm Repository, Corvallis, OR, United States
- *Correspondence: Nahla V. Bassil,
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Yagi M. Recent progress in whole genome sequencing, high-density linkage maps, and genomic databases of ornamental plants. BREEDING SCIENCE 2018; 68:62-70. [PMID: 29681748 PMCID: PMC5903975 DOI: 10.1270/jsbbs.17080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/19/2017] [Indexed: 05/21/2023]
Abstract
Genome information is useful for functional analysis of genes, comparative genomic analysis, breeding of new varieties by marker-assisted selection, and map-based gene isolation. Genome-related research in ornamentals plants has been relatively slow to develop because of their heterozygosity or polyploidy. Advances in analytical instruments, such as next-generation sequencers and information processing technologies have revolutionized biology, and have been applied in a large number and variety of species, including ornamental plants. Recently, high-quality whole genome sequences have been reported in plant genetics and physiology studies of model ornamentals, such as those in genus Petunia and Japanese morning glory (Ipomoea nil). In this review, whole genome sequencing and construction of high-density genetic linkage maps based on SNP markers of ornamentals will be discussed. The databases that store this information for ornamentals are also described.
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Liu J, Fu X, Dong Y, Lu J, Ren M, Zhou N, Wang C. MIKC C-type MADS-box genes in Rosa chinensis: the remarkable expansion of ABCDE model genes and their roles in floral organogenesis. HORTICULTURE RESEARCH 2018; 5:25. [PMID: 29736250 PMCID: PMC5928068 DOI: 10.1038/s41438-018-0031-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/07/2018] [Accepted: 02/27/2018] [Indexed: 05/04/2023]
Abstract
MIKCC-type MADS-box (MIKCC) genes encode transcription factors that have crucial roles in controlling floral organogenesis and flowering time in plants. Although this gene family has been well characterized in many plant species, its evolutionary and comprehensive functional analysis in rose is lacking. In this study, 58 non-redundant MIKCC uni-transcripts were extensively identified from rose transcriptomes. Phylogenetic analysis placed these genes into 12 clades with their Arabidopsis and strawberry counterparts, and revealed that ABCDE model (including AP1/FUL, AP3/PI, AG, and SEP clades), and SOC1 and AGL6 clade genes have remarkably expanded in Rosa chinensis, whereas genes from the FLC and AGL17 clades were undetectable. Sequence alignments suggest that the AP3/PI clade may contribute to more specific functions in rose due to a high variation of amino acid residues within its MADS-box domains. A comparative analysis of gene expression in specific floral organ differentiation stages and floral organs between R. chinensis cv. Old Blush and the closely related mutant genotype R. chinensis cv. Viridiflora (floral organs mutated into leaf-like structures) further revealed the roles of ABCDE model genes during floral organogenesis in rose. Analysis of co-expression networks provided an overview of the regulatory mechanisms of rose MIKCC genes and shed light on both the prominent roles of AP3/PI clade genes in floral organogenesis and the roles of RcAGL19, RcAGL24, and RcSOC1 in regulating floral transition in rose. Our analyses provide an overall insight of MIKCC genes in rose and their potential roles in floral organogenesis.
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Affiliation(s)
- Jinyi Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Xiaodong Fu
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Yuwei Dong
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Jun Lu
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Min Ren
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Ningning Zhou
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan 650200 China
| | - Changquan Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
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Nguyen THN, Schulz D, Winkelmann T, Debener T. Genetic dissection of adventitious shoot regeneration in roses by employing genome-wide association studies. PLANT CELL REPORTS 2017. [PMID: 28647832 DOI: 10.1007/s00299-017-2170-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We analysed the capacity to regenerate adventitious shoots in 96 rose genotypes and found 88 SNP markers associated with QTLs, some of which are derived from candidate genes for shoot regeneration. In an association panel of 96 rose genotypes previously analysed for petal colour, we conducted a genome-wide association study on the capacity of leaf petioles for direct shoot regeneration. Shoot regeneration rate and shoot ratio (number of shoots/total number of explants) were used as phenotypic descriptors for regeneration capacity. Two independent experiments were carried out with six replicates of ten explants each. We found significant variation between the genotypes ranging from 0.88 to 88.33% for the regeneration rate and from 0.008 to 1.2 for the shoot ratio, which exceeded the rates reported so far. Furthermore, we found 88 SNP markers associated with either the shoot regeneration rate or the shoot ratio. In this association analysis, we found 12 SNP markers from ESTs (expressed sequence tags) matching known candidate genes that are involved in shoot morphogenesis. The best markers explained more than 51% of the variance in the shoot regeneration rate and more than 0.65 of the variance in the shoot regeneration ratio between the homozygote marker classes. The genes underlying some of the best markers such as a GT-transcription factor or an LRR receptor-like protein kinase are novel candidate genes putatively involved in the observed phenotypic differences. The associated markers were mapped to the closely related genome of Fragaria vesca and revealed many distinct clusters, which also comprised the known candidate genes that functioned in the organogenesis of plant shoots. However, the validation of candidate genes and their functional relationship to shoot regeneration require further analysis in independent rose populations and functional analyses.
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Affiliation(s)
- Thi Hong Nhung Nguyen
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
- Institute of Agricultural Genetics, Hanoi, Vietnam
| | - Dietmar Schulz
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Woody Plant and Propagation Physiology, Leibniz Universität Hannover, Hannover, Germany
| | - Thomas Debener
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany.
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Rasheed A, Hao Y, Xia X, Khan A, Xu Y, Varshney RK, He Z. Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives. MOLECULAR PLANT 2017; 10:1047-1064. [PMID: 28669791 DOI: 10.1016/j.molp.2017.06.008] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/29/2017] [Accepted: 06/19/2017] [Indexed: 05/18/2023]
Abstract
There is a rapidly rising trend in the development and application of molecular marker assays for gene mapping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop molecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype-phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of (a) rapid development in gene discovery of important traits, (b) deepened understanding of quantitative traits through new analytical models and population designs, (c) integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and (d) improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.
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Affiliation(s)
- Awais Rasheed
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Awais Khan
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY, USA
| | - Yunbi Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing 100081, China.
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van Geest G, Voorrips RE, Esselink D, Post A, Visser RG, Arens P. Conclusive evidence for hexasomic inheritance in chrysanthemum based on analysis of a 183 k SNP array. BMC Genomics 2017; 18:585. [PMID: 28784083 PMCID: PMC5547472 DOI: 10.1186/s12864-017-4003-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 08/02/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Cultivated chrysanthemum is an outcrossing hexaploid (2n = 6× = 54) with a disputed mode of inheritance. In this paper, we present a single nucleotide polymorphism (SNP) selection pipeline that was used to design an Affymetrix Axiom array with 183 k SNPs from RNA sequencing data (1). With this array, we genotyped four bi-parental populations (with sizes of 405, 53, 76 and 37 offspring plants respectively), and a cultivar panel of 63 genotypes. Further, we present a method for dosage scoring in hexaploids from signal intensities of the array based on mixture models (2) and validation of selection steps in the SNP selection pipeline (3). The resulting genotypic data is used to draw conclusions on the mode of inheritance in chrysanthemum (4), and to make an inference on allelic expression bias (5). RESULTS With use of the mixture model approach, we successfully called the dosage of 73,936 out of 183,130 SNPs (40.4%) that segregated in any of the bi-parental populations. To investigate the mode of inheritance, we analysed markers that segregated in the large bi-parental population (n = 405). Analysis of segregation of duplex x nulliplex SNPs resulted in evidence for genome-wide hexasomic inheritance. This evidence was substantiated by the absence of strong linkage between markers in repulsion, which indicated absence of full disomic inheritance. We present the success rate of SNP discovery out of RNA sequencing data as affected by different selection steps, among which SNP coverage over genotypes and use of different types of sequence read mapping software. Genomic dosage highly correlated with relative allele coverage from the RNA sequencing data, indicating that most alleles are expressed according to their genomic dosage. CONCLUSIONS The large population, genotyped with a very large number of markers, is a unique framework for extensive genetic analyses in hexaploid chrysanthemum. As starting point, we show conclusive evidence for genome-wide hexasomic inheritance.
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Affiliation(s)
- Geert van Geest
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6708 PB, Wageningen, the Netherlands. .,Deliflor Chrysanten B.V, Korte Kruisweg 163, 2676 BS, Maasdijk, the Netherlands.
| | - Roeland E Voorrips
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6708 PB, Wageningen, the Netherlands
| | - Danny Esselink
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6708 PB, Wageningen, the Netherlands
| | - Aike Post
- Deliflor Chrysanten B.V, Korte Kruisweg 163, 2676 BS, Maasdijk, the Netherlands
| | - Richard Gf Visser
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6708 PB, Wageningen, the Netherlands
| | - Paul Arens
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6708 PB, Wageningen, the Netherlands
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Schmitz Carley CA, Coombs JJ, Douches DS, Bethke PC, Palta JP, Novy RG, Endelman JB. Automated tetraploid genotype calling by hierarchical clustering. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:717-726. [PMID: 28070610 DOI: 10.1007/s00122-016-2845-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/22/2016] [Indexed: 05/24/2023]
Abstract
New software to make tetraploid genotype calls from SNP array data was developed, which uses hierarchical clustering and multiple F1 populations to calibrate the relationship between signal intensity and allele dosage. SNP arrays are transforming breeding and genetics research for autotetraploids. To fully utilize these arrays, the relationship between signal intensity and allele dosage must be calibrated for each marker. We developed an improved computational method to automate this process, which is provided as the R package ClusterCall. In the training phase of the algorithm, hierarchical clustering within an F1 population is used to group samples with similar intensity values, and allele dosages are assigned to clusters based on expected segregation ratios. In the prediction phase, multiple F1 populations and the prediction set are clustered together, and the genotype for each cluster is the mode of the training set samples. A concordance metric, defined as the proportion of training set samples equal to the mode, can be used to eliminate unreliable markers and compare different algorithms. Across three potato families genotyped with an 8K SNP array, ClusterCall scored 5729 markers with at least 0.95 concordance (94.6% of its total), compared to 5325 with the software fitTetra (82.5% of its total). The three families were used to predict genotypes for 5218 SNPs in the SolCAP diversity panel, compared with 3521 SNPs in a previous study in which genotypes were called manually. One of the additional markers produced a significant association for vine maturity near a well-known causal locus on chromosome 5. In conclusion, when multiple F1 populations are available, ClusterCall is an efficient method for accurate, autotetraploid genotype calling that enables the use of SNP data for research and plant breeding.
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Affiliation(s)
| | - Joseph J Coombs
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - David S Douches
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Paul C Bethke
- Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA
- USDA Agricultural Research Service, Madison, WI, 53706, USA
| | - Jiwan P Palta
- Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA
| | - Richard G Novy
- USDA-ARS Small Grains and Potato Germplasm Research Unit, Aberdeen, ID, 83210, USA
| | - Jeffrey B Endelman
- Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA.
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Bourke PM, Arens P, Voorrips RE, Esselink GD, Koning-Boucoiran CFS, Van't Westende WPC, Santos Leonardo T, Wissink P, Zheng C, van Geest G, Visser RGF, Krens FA, Smulders MJM, Maliepaard C. Partial preferential chromosome pairing is genotype dependent in tetraploid rose. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:330-343. [PMID: 28142191 DOI: 10.1111/tpj.13496] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 05/18/2023]
Abstract
It has long been recognised that polyploid species do not always neatly fall into the categories of auto- or allopolyploid, leading to the term 'segmental allopolyploid' to describe everything in between. The meiotic behaviour of such intermediate species is not fully understood, nor is there consensus as to how to model their inheritance patterns. In this study we used a tetraploid cut rose (Rosa hybrida) population, genotyped using the 68K WagRhSNP array, to construct an ultra-high-density linkage map of all homologous chromosomes using methods previously developed for autotetraploids. Using the predicted bivalent configurations in this population we quantified differences in pairing behaviour among and along homologous chromosomes, leading us to correct our estimates of recombination frequency to account for this behaviour. This resulted in the re-mapping of 25 695 SNP markers across all homologues of the seven rose chromosomes, tailored to the pairing behaviour of each chromosome in each parent. We confirmed the inferred differences in pairing behaviour among chromosomes by examining repulsion-phase linkage estimates, which also carry information about preferential pairing and recombination. Currently, the closest sequenced relative to rose is Fragaria vesca. Aligning the integrated ultra-dense rose map with the strawberry genome sequence provided a detailed picture of the synteny, confirming overall co-linearity but also revealing new genomic rearrangements. Our results suggest that pairing affinities may vary along chromosome arms, which broadens our current understanding of segmental allopolyploidy.
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Affiliation(s)
- Peter M Bourke
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Paul Arens
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Roeland E Voorrips
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - G Danny Esselink
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | | | - Wendy P C Van't Westende
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Tiago Santos Leonardo
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Patrick Wissink
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Chaozhi Zheng
- Biometris, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Geert van Geest
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Horticulture and Product Physiology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Frans A Krens
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Marinus J M Smulders
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Chris Maliepaard
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Peace CP. DNA-informed breeding of rosaceous crops: promises, progress and prospects. HORTICULTURE RESEARCH 2017; 4:17006. [PMID: 28326185 PMCID: PMC5350264 DOI: 10.1038/hortres.2017.6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/02/2017] [Accepted: 02/03/2017] [Indexed: 05/18/2023]
Abstract
Crops of the Rosaceae family provide valuable contributions to rural economies and human health and enjoyment. Sustained solutions to production challenges and market demands can be met with genetically improved new cultivars. Traditional rosaceous crop breeding is expensive and time-consuming and would benefit from improvements in efficiency and accuracy. Use of DNA information is becoming conventional in rosaceous crop breeding, contributing to many decisions and operations, but only after past decades of solved challenges and generation of sufficient resources. Successes in deployment of DNA-based knowledge and tools have arisen when the 'chasm' between genomics discoveries and practical application is bridged systematically. Key steps are establishing breeder desire for use of DNA information, adapting tools to local breeding utility, identifying efficient application schemes, accessing effective services in DNA-based diagnostics and gaining experience in integrating DNA information into breeding operations and decisions. DNA-informed germplasm characterization for revealing identity and relatedness has benefitted many programs and provides a compelling entry point to reaping benefits of genomics research. DNA-informed germplasm evaluation for predicting trait performance has enabled effective reallocation of breeding resources when applied in pioneering programs. DNA-based diagnostics is now expanding from specific loci to genome-wide considerations. Realizing the full potential of this expansion will require improved accuracy of predictions, multi-trait DNA profiling capabilities, streamlined breeding information management systems, strategies that overcome plant-based features that limit breeding progress and widespread training of current and future breeding personnel and allied scientists.
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Affiliation(s)
- Cameron P Peace
- Department of Horticulture, Washington State University, PO Box 646414, Pullman, WA 99164-6414, USA
- ()
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40
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Carvalho DRA, Vasconcelos MW, Lee S, Koning-Boucoiran CFS, Vreugdenhil D, Krens FA, Heuvelink E, Carvalho SMP. Gene expression and physiological responses associated to stomatal functioning in Rosa×hybrida grown at high relative air humidity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 253:154-163. [PMID: 27968984 DOI: 10.1016/j.plantsci.2016.09.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 09/02/2016] [Accepted: 09/30/2016] [Indexed: 06/06/2023]
Abstract
High relative air humidity (RH≥85%) during growth disturbs stomatal functioning, resulting in excessive water loss in conditions of high evaporative demand. We investigated the expression of nine abscisic acid (ABA)-related genes (involved in ABA biosynthesis, oxidation and conjugation) and two non-ABA related genes (involved in the water stress response) aiming to better understand the mechanisms underlying contrasting stomatal functioning in plants grown at high RH. Four rose genotypes with contrasting sensitivity to high RH (one sensitive, one tolerant and two intermediate) were grown at moderate (62±3%) or high (89±4%) RH. The sensitive genotype grown at high RH showed a significantly higher stomatal conductance (gs) and water loss in response to closing stimuli as compared to the other genotypes. Moreover, high RH reduced the leaf ABA concentration and its metabolites to a greater extent in the sensitive genotype as compared to the tolerant one. The large majority of the studied genes had a relevant role on stomatal functioning (NCED1, UGT75B2, BG2, OST1, ABF3 and Rh-APX) while two others showed a minor contribution (CYP707A3 and BG1) and AAO3, CYP707A1 and DREB1B did not contribute to the tolerance trait. These results show that multiple genes form a highly complex regulatory network acting together towards the genotypic tolerance to high RH.
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Affiliation(s)
- Dália R A Carvalho
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal.
| | - Marta W Vasconcelos
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal
| | - Sangseok Lee
- Plant Sciences Group, Wageningen University, Plant Physiology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Gyeongsangbuk-Do Agricultural Research & Extension Services, 136 Gil-14, Chilgokiungang-Daero, Daegu, South Korea
| | - Carole F S Koning-Boucoiran
- Plant Sciences Group, Wageningen University, Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Dick Vreugdenhil
- Plant Sciences Group, Wageningen University, Plant Physiology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Frans A Krens
- Plant Sciences Group, Wageningen University, Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ep Heuvelink
- Plant Sciences Group, Wageningen University, Horticulture and Product Physiology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Susana M P Carvalho
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal; Plant Sciences Group, Wageningen University, Horticulture and Product Physiology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; GreenUP/CITAB-UP & DGAOT, Faculty of Sciences, University of Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 7. 4485-661 Vairão, Portugal.
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41
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Azadi P, Bagheri H, Nalousi AM, Nazari F, Chandler SF. Current status and biotechnological advances in genetic engineering of ornamental plants. Biotechnol Adv 2016; 34:1073-1090. [PMID: 27396521 DOI: 10.1016/j.biotechadv.2016.06.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 06/22/2016] [Accepted: 06/28/2016] [Indexed: 01/15/2023]
Abstract
Cut flower markets are developing in many countries as the international demand for cut flowers is rapidly growing. Developing new varieties with modified characteristics is an important aim in floriculture. Production of transgenic ornamental plants can shorten the time required in the conventional breeding of a cultivar. Biotechnology tools in combination with conventional breeding methods have been used by cut flower breeders to change flower color, plant architecture, post-harvest traits, and disease resistance. In this review, we describe advances in genetic engineering that have led to the development of new cut flower varieties.
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Affiliation(s)
- Pejman Azadi
- Department of Genetic Engineering, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Hedayat Bagheri
- Department of Plant Biotechnology, Faculty of Agriculture Science, Buali Sina University, Hamedan, Iran
| | - Ayoub Molaahmad Nalousi
- Department of Horticultural Science, Faculty of Agriculture Science, University of Guilan, Rasht, Iran
| | - Farzad Nazari
- Department of Horticultural Science, College of Agriculture, University of Kurdistan, Sanandaj, Iran
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42
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Bianco L, Cestaro A, Linsmith G, Muranty H, Denancé C, Théron A, Poncet C, Micheletti D, Kerschbamer E, Di Pierro EA, Larger S, Pindo M, Van de Weg E, Davassi A, Laurens F, Velasco R, Durel CE, Troggio M. Development and validation of the Axiom(®) Apple480K SNP genotyping array. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:62-74. [PMID: 26919684 DOI: 10.1111/tpj.13145] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/03/2016] [Accepted: 02/05/2016] [Indexed: 05/18/2023]
Abstract
Cultivated apple (Malus × domestica Borkh.) is one of the most important fruit crops in temperate regions, and has great economic and cultural value. The apple genome is highly heterozygous and has undergone a recent duplication which, combined with a rapid linkage disequilibrium decay, makes it difficult to perform genome-wide association (GWA) studies. Single nucleotide polymorphism arrays offer highly multiplexed assays at a relatively low cost per data point and can be a valid tool for the identification of the markers associated with traits of interest. Here, we describe the development and validation of a 487K SNP Affymetrix Axiom(®) genotyping array for apple and discuss its potential applications. The array has been built from the high-depth resequencing of 63 different cultivars covering most of the genetic diversity in cultivated apple. The SNPs were chosen by applying a focal points approach to enrich genic regions, but also to reach a uniform coverage of non-genic regions. A total of 1324 apple accessions, including the 92 progenies of two mapping populations, have been genotyped with the Axiom(®) Apple480K to assess the effectiveness of the array. A large majority of SNPs (359 994 or 74%) fell in the stringent class of poly high resolution polymorphisms. We also devised a filtering procedure to identify a subset of 275K very robust markers that can be safely used for germplasm surveys in apple. The Axiom(®) Apple480K has now been commercially released both for public and proprietary use and will likely be a reference tool for GWA studies in apple.
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Affiliation(s)
- Luca Bianco
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Alessandro Cestaro
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Gareth Linsmith
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Hélène Muranty
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 QUASAV, 42 Rue Georges Morel, F-49071, Beaucouzé, France
| | - Caroline Denancé
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 QUASAV, 42 Rue Georges Morel, F-49071, Beaucouzé, France
| | - Anthony Théron
- Plateforme Gentyane, INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039, Clermont-Ferrand, France
| | - Charles Poncet
- Plateforme Gentyane, INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039, Clermont-Ferrand, France
| | - Diego Micheletti
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Emanuela Kerschbamer
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Erica A Di Pierro
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milano, Italy
| | - Simone Larger
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Eric Van de Weg
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Alessandro Davassi
- Affymetrix UK Ltd, Mercury Park, Wycombe Lane, Wooburn Green, High Wycombe, HP10 0HH, UK
| | - François Laurens
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 QUASAV, 42 Rue Georges Morel, F-49071, Beaucouzé, France
| | - Riccardo Velasco
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Charles-Eric Durel
- Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 QUASAV, 42 Rue Georges Morel, F-49071, Beaucouzé, France
| | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
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Fu Y, Esselink GD, Visser RGF, van Tuyl JM, Arens P. Transcriptome Analysis of Gerbera hybrida Including in silico Confirmation of Defense Genes Found. FRONTIERS IN PLANT SCIENCE 2016; 7:247. [PMID: 26973688 PMCID: PMC4771743 DOI: 10.3389/fpls.2016.00247] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 02/14/2016] [Indexed: 05/21/2023]
Abstract
For the ornamental crop Gerbera hybrida, breeding at the moment is done using conventional methods. As this has drawbacks in breeding speed and efficiency, especially for complex traits like disease resistance, we set out to develop genomic resources. The leaf and flower bud transcriptomes of four parents, used to generate two gerbera populations, were sequenced using Illumina paired-end sequencing. In total, 36,770 contigs with an average length of 1397 bp were generated and these have been the starting point for SNP identification and annotation. The consensus contig sequences were used to map reads of individual parents, to identify genotype specific SNPs, and to assess the presence of common SNPs between genotypes. Comparison with the non-redundant protein database (nr) showed that 29,146 contigs gave BLAST hits. Of sequences with blast results, 73.3% obtained a clear gene ontology (GO) annotation. EST contigs coding for enzymes were found in Kyoto Encyclopedia of Genes and Genomes maps (KEGG). Through, these annotated data and KEGG molecular interaction network, transcripts associated with the phenylpropanoid metabolism, other secondary metabolite biosynthesis pathways, phytohormone biosynthesis and signal transduction were analyzed in more detail. Identifying genes involved in these processes could provide genetic and genomic resources for studying the mechanism of disease resistance in gerbera.
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44
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Gitonga VW, Stolker R, Koning-Boucoiran CFS, Aelaei M, Visser RGF, Maliepaard C, Krens FA. Inheritance and QTL analysis of the determinants of flower color in tetraploid cut roses. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2016; 36:143. [PMID: 27795693 PMCID: PMC5055553 DOI: 10.1007/s11032-016-0565-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 10/03/2016] [Indexed: 05/09/2023]
Abstract
The success of cut rose cultivars is a direct result of their aesthetic value. The rose industry thrives on novelty, and the production of novel flower color has been extensively studied. The most popular color is red, and it is, therefore, important for breeders to produce a good red cultivar. The final visible color of the flower is a combination of a number of factors including the type of anthocyanin accumulating, modifications to the anthocyanidin molecule, co-pigmentation and vacuolar pH. Here, we analyze the quantitative variation of the biochemical constituents of flower color in a tetraploid rose population and combine this with marker information in the segregating rose population to map the chromosomal locations of putative QTLs for flower color traits. Within our tetraploid population, we found a number of QTLs that were mapped on ICM 1, 2, 6 and 7. We were able to show the effect of the different QTLs on the final visible color of the flower from salmon to dark red.
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Affiliation(s)
- Virginia W. Gitonga
- Wageningen UR Plant Breeding, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
- Selecta Kenya GmbH & Co. KG, P.O. Box 64132, Nairobi, 00620 Kenya
| | - Robert Stolker
- Wageningen UR Plant Breeding, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
- Deliflor Chrysanten b.v., P.O. Box 77, 2676 ZH Maasdijk, The Netherlands
| | - Carole F. S. Koning-Boucoiran
- Wageningen UR Plant Breeding, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
- HAN University of Applied Sciences, P.O. Box 6960, 6503 GL Nijmegen, The Netherlands
| | - Mitra Aelaei
- Department of Horticulture, Tehran University, Karaj, 31587-77871 Iran
- Department of Horticultural Sciences, University of Zanjan, Zanjan, 45371-38791 Iran
| | | | - Chris Maliepaard
- Wageningen UR Plant Breeding, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Frans A. Krens
- Wageningen UR Plant Breeding, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
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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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Schulz DF, Schott RT, Voorrips RE, Smulders MJM, Linde M, Debener T. Genome-Wide Association Analysis of the Anthocyanin and Carotenoid Contents of Rose Petals. FRONTIERS IN PLANT SCIENCE 2016; 7:1798. [PMID: 27999579 PMCID: PMC5138216 DOI: 10.3389/fpls.2016.01798] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/15/2016] [Indexed: 05/18/2023]
Abstract
Petal color is one of the key characteristics determining the attractiveness and therefore the commercial value of an ornamental crop. Here, we present the first genome-wide association study for the important ornamental crop rose, focusing on the anthocyanin and carotenoid contents in petals of 96 diverse tetraploid garden rose genotypes. Cultivated roses display a vast phenotypic and genetic diversity and are therefore ideal targets for association genetics. For marker analysis, we used a recently designed Axiom SNP chip comprising 68,000 SNPs with additionally 281 SSRs, 400 AFLPs and 246 markers from candidate genes. An analysis of the structure of the rose population revealed three subpopulations with most of the genetic variation between individual genotypes rather than between clusters and with a high average proportion of heterozygous loci. The mapping of markers significantly associated with anthocyanin and carotenoid content to the related Fragaria and Prunus genomes revealed clusters of associated markers indicating five genomic regions associated with the total anthocyanin content and two large clusters associated with the carotenoid content. Among the marker clusters associated with the phenotypes, we found several candidate genes with known functions in either the anthocyanin or the carotenoid biosynthesis pathways. Among others, we identified a glutathione-S-transferase, 4CL, an auxin response factor and F3'H as candidate genes affecting anthocyanin concentration, and CCD4 and Zeaxanthine epoxidase as candidates affecting the concentration of carotenoids. These markers are starting points for future validation experiments in independent populations as well as for functional genomic studies to identify the causal factors for the observed color phenotypes. Furthermore, validated markers may be interesting tools for marker-assisted selection in commercial breeding programmes in that they provide the tools to identify superior parental combinations that combine several associated markers in higher dosages.
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Affiliation(s)
- Dietmar F. Schulz
- Abteilung Molekulare Pflanzenzüchtung, Institute for Plant Genetics, Leibnitz University HannoverHannover, Germany
| | - Rena T. Schott
- Abteilung Molekulare Pflanzenzüchtung, Institute for Plant Genetics, Leibnitz University HannoverHannover, Germany
| | - Roeland E. Voorrips
- Wageningen University and Research Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Marinus J. M. Smulders
- Wageningen University and Research Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Marcus Linde
- Abteilung Molekulare Pflanzenzüchtung, Institute for Plant Genetics, Leibnitz University HannoverHannover, Germany
| | - Thomas Debener
- Abteilung Molekulare Pflanzenzüchtung, Institute for Plant Genetics, Leibnitz University HannoverHannover, Germany
- *Correspondence: Thomas Debener
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