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Li W, Fu L, Geng Z, Zhao X, Liu Q, Jiang X. Physiological Characteristic Changes and Full-Length Transcriptome of Rose (Rosa chinensis) Roots and Leaves in Response to Drought Stress. PLANT & CELL PHYSIOLOGY 2021; 61:2153-2166. [PMID: 33165546 DOI: 10.1093/pcp/pcaa137] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/14/2020] [Indexed: 06/11/2023]
Abstract
Rose (Rosa chinensis) is the most important ornamental crops worldwide. However, the physiological and molecular mechanism of rose under drought stress remains elusive. In this study, we analyzed the changes of photosynthetic and phytohormone levels in the leaves and roots of rose seedlings grown under control (no drought), mild drought (MD) and severe drought stress. The total chlorophyll content and water use efficiency were significantly enhanced under MD in rose leaves. In addition, the concentration of ABA was higher in the leaves compared to the roots, whereas the roots accumulated more IAA, methylindole-3-acetic acid and indole-3-propionic acid. We also constructed the first full-length transcriptome for rose, and identified 96,201,862 full-length reads of average length 1,149 bp that included 65,789 novel transcripts. A total of 3,657 and 4,341 differentially expressed genes (DEGs) were identified in rose leaves and roots respectively. KEGG pathway analysis showed enrichment of plant hormone, signal transduction and photosynthesis are among the DEGs. 42,544 alternatively spliced isoforms were also identified, and alternative 3' splice site was the major alternative splicing (AS) event among the DEGs. Variations in the AS patterns of three genes between leaves and roots indicated the possibility of tissue-specific posttranscriptional regulation in response to drought stress. Furthermore, 2,410 novel long non-coding RNAs were detected that may participate in regulating the drought-induced DEGs. Our findings identified previously unknown splice sites and new genes in the rose transcriptome, and elucidated the drought stress-responsive genes as well as their intricate regulatory networks.
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Affiliation(s)
- Wei Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Lufeng Fu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Ziwen Geng
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Xiaojuan Zhao
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Qinghua Liu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Xinqiang Jiang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong 266109, China
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Bai M, Liu J, Fan C, Chen Y, Chen H, Lu J, Sun J, Ning G, Wang C. KSN heterozygosity is associated with continuous flowering of Rosa rugosa Purple branch. HORTICULTURE RESEARCH 2021; 8:26. [PMID: 33518715 PMCID: PMC7848002 DOI: 10.1038/s41438-021-00464-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/10/2020] [Accepted: 11/13/2020] [Indexed: 05/02/2023]
Abstract
Rose (Rosa spp.) plants flower via two contrasting methods: once flowering (OF) and continuous flowering (CF). Purple branch is a rare continuously flowering variety of Rosa rugosa that is extensively cultivated in China. However, the genetic basis of its CF behavior is unknown. We demonstrated that Purple branch is heterozygous for the TFL1 homolog KSN. One KSN allele with a 9 kb Copia insertion was found to be identical to that from continuously flowering Rosa chinensis Old blush. The other allele was found to be a functional wild-type allele. The overall expression of KSN was closely linked to the floral transition, and it was significantly repressed in continuously flowering Purple branch compared with OF Plena. The promoter region of the normal KSN allele was hypermethylated, and histone methylation at H3H4, H3K9, and H3K27 of the KSN gene locus was modified in continuously flowering Purple branch. Silencing of the DNA methyltransferase genes MET1 and CMT3 and the histone methyltransferase gene SUVR5 in Purple branch led to enhanced KSN expression, but silencing of the histone demethylase gene JMJ12 suppressed KSN expression. Therefore, the CF habit of Purple branch may be due to reduced expression of KSN caused by the halved dose and may be associated with epigenetic modifications together with retrotransposon insertions along the chromosome. Our study revealed a novel mechanism underlying the CF behavior of rose plants.
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Affiliation(s)
- Mengjuan Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinyi Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunguo Fan
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yeqing Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Lu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jingjing Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guogui Ning
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Changquan Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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103
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Cheng QQ, Ouyang Y, Tang ZY, Lao CC, Zhang YY, Cheng CS, Zhou H. Review on the Development and Applications of Medicinal Plant Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:791219. [PMID: 35003182 PMCID: PMC8732986 DOI: 10.3389/fpls.2021.791219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/23/2021] [Indexed: 05/04/2023]
Abstract
With the development of sequencing technology, the research on medicinal plants is no longer limited to the aspects of chemistry, pharmacology, and pharmacodynamics, but reveals them from the genetic level. As the price of next-generation sequencing technology becomes affordable, and the long-read sequencing technology is established, the medicinal plant genomes with large sizes have been sequenced and assembled more easily. Although the review of plant genomes has been reported several times, there is no review giving a systematic and comprehensive introduction about the development and application of medicinal plant genomes that have been reported until now. Here, we provide a historical perspective on the current situation of genomes in medicinal plant biology, highlight the use of the rapidly developing sequencing technologies, and conduct a comprehensive summary on how the genomes apply to solve the practical problems in medicinal plants, like genomics-assisted herb breeding, evolution history revelation, herbal synthetic biology study, and geoherbal research, which are important for effective utilization, rational use and sustainable protection of medicinal plants.
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Affiliation(s)
- Qi-Qing Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yue Ouyang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Zi-Yu Tang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chi-Chou Lao
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yan-Yu Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chun-Song Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Hua Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Joint Laboratory for Translational Cancer Research of Chinese Medicine, The Ministry of Education of the People’s Republic of China, Macau University of Science and Technology, Taipa, Macao SAR, China
- *Correspondence: Hua Zhou,
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104
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Mallet J, Laufs P, Leduc N, Le Gourrierec J. Photocontrol of Axillary Bud Outgrowth by MicroRNAs: Current State-of-the-Art and Novel Perspectives Gained From the Rosebush Model. FRONTIERS IN PLANT SCIENCE 2021; 12:770363. [PMID: 35173747 PMCID: PMC8841825 DOI: 10.3389/fpls.2021.770363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/13/2021] [Indexed: 05/05/2023]
Abstract
Shoot branching is highly dependent on environmental factors. While many species show some light dependence for branching, the rosebush shows a strict requirement for light to allow branching, making this species an excellent model to further understand how light impinges on branching. Here, in the first part, we provide a review of the current understanding of how light may modulate the complex regulatory network of endogenous factors like hormones (SL, IAA, CK, GA, and ABA), nutrients (sugar and nitrogen), and ROS to control branching. We review the regulatory contribution of microRNAs (miRNAs) to branching in different species, highlighting the action of such evolutionarily conserved factors. We underline some possible pathways by which light may modulate miRNA-dependent regulation of branching. In the second part, we exploit the strict light dependence of rosebush for branching to identify putative miRNAs that could contribute to the photocontrol of branching. For this, we first performed a profiling of the miRNAs expressed in early light-induced rosebush buds and next tested whether they were predicted to target recognized regulators of branching. Thus, we identified seven miRNAs (miR156, miR159, miR164, miR166, miR399, miR477, and miR8175) that could target nine genes (CKX1/6, EXPA3, MAX4, CYCD3;1, SUSY, 6PFK, APX1, and RBOHB1). Because these genes are affecting branching through different hormonal or metabolic pathways and because expression of some of these genes is photoregulated, our bioinformatic analysis suggests that miRNAs may trigger a rearrangement of the regulatory network to modulate branching in response to light environment.
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Affiliation(s)
- Julie Mallet
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Patrick Laufs
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Nathalie Leduc
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - José Le Gourrierec
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
- *Correspondence: José Le Gourrierec,
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Abstract
A suitable pairwise relatedness estimation is key to genetic studies. Several methods are proposed to compute relatedness in autopolyploids based on molecular data. However, unlike diploids, autopolyploids still need further studies considering scenarios with many linked molecular markers with known dosage. In this study, we provide guidelines for plant geneticists and breeders to access trustworthy pairwise relatedness estimates. To this end, we simulated populations considering different ploidy levels, meiotic pairings patterns, number of loci and alleles, and inbreeding levels. Analysis were performed to access the accuracy of distinct methods and to demonstrate the usefulness of molecular marker in practical situations. Overall, our results suggest that at least 100 effective biallelic molecular markers are required to have good pairwise relatedness estimation if methods based on correlation is used. For this number of loci, current methods based on multiallelic markers show lower performance than biallelic ones. To estimate relatedness in cases of inbreeding or close relationships (as parent-offspring, full-sibs, or half-sibs) is more challenging. Methods to estimate pairwise relatedness based on molecular markers, for different ploidy levels or pedigrees were implemented in the AGHmatrix R package.
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106
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Lopez Arias DC, Chastellier A, Thouroude T, Bradeen J, Van Eck L, De Oliveira Y, Paillard S, Foucher F, Hibrand-Saint Oyant L, Soufflet-Freslon V. Characterization of black spot resistance in diploid roses with QTL detection, meta-analysis and candidate-gene identification. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3299-3321. [PMID: 32844252 DOI: 10.1007/s00122-020-03670-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/11/2020] [Indexed: 05/10/2023]
Abstract
Two environmentally stable QTLs linked to black spot disease resistance in the Rosa wichurana genetic background were detected, in different connected populations, on linkage groups 3 and 5. Co-localization between R-genes and defense response genes was revealed via meta-analysis. The widespread rose black spot disease (BSD) caused by the hemibiotrophic fungus Diplocarpon rosae Wolf. is efficiently controlled with fungicides. However, in the actual context of reducing agrochemical use, the demand for rose bushes with higher levels of resistance has increased. Qualitative resistance conferred by major genes (Rdr genes) has been widely studied but quantitative resistance to BSD requires further investigation. In this study, segregating populations connected through the BSD resistant Rosa wichurana male parent were phenotyped for disease resistance over several years and locations. A pseudo-testcross approach was used, resulting in six parental maps across three populations. A total of 45 individual QTLs with significant effect on BSD resistance were mapped on the male maps (on linkage groups (LG) B3, B4, B5 and B6), and 12 on the female maps (on LG A1, A2, A3, A4 and A5). Two major regions linked to BSD resistance were identified on LG B3 and B5 of the male maps and were integrated into a consensus map built from all three of the male maps. A meta-analysis was used to narrow down the confidence intervals of individual QTLs from three populations by generating meta-QTLs. Two 'hot spots' or meta-QTLs were found per LG, enabling reduction of the confidence interval to 10.42 cM for B3 and 11.47 cM for B5. An expert annotation of NBS-LRR encoding genes of the genome assembly of Hibrand et al. was performed and used to explore potential co-localization with R-genes. Co-localization with defense response genes was also investigated.
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Affiliation(s)
- D C Lopez Arias
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France.
| | - A Chastellier
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - T Thouroude
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - J Bradeen
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - L Van Eck
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Yannick De Oliveira
- Génétique Quantitative Et Évolution - Le Moulon, INRAE - Université Paris-Sud - CNRS - AgroParisTech, Ferme du Moulon, 91190, Gif-sur-Yvette, France
| | - S Paillard
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - F Foucher
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - L Hibrand-Saint Oyant
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - V Soufflet-Freslon
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
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107
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Zhou NN, Tang KX, Jeauffre J, Thouroude T, Arias DCL, Foucher F, Oyant LHS. Genetic determinism of prickles in rose. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3017-3035. [PMID: 32734323 DOI: 10.1007/s00122-020-03652-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 07/03/2020] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE The genetic determinism of prickle in rose is complex, with a major locus on LG3 that controls the absence/presence of prickles on the rose stem. Rose is one of the major ornamental plants. The selection of glabrous cultivars is an important breeding target but remains a difficult task due to our limited genetic knowledge. Our objective was to understand the genetic and molecular determinism of prickles. Using a segregating diploid rose F1 population, we detected two types of prickles (glandular and non-glandular) in the progeny. We scored the number of non-glandular prickles on the floral and main stems for three years. We performed QTL analysis and detected four prickle loci on LG1, 3, 4 and 6. We determined the credible interval on the reference genome. The QTL on LG3 is a major locus that controls the presence of prickles, and three QTLs (LG3, 4 and 1) may be responsible for prickle density. We further revealed that glabrous hybrids are caused by the combination of the two recessive alleles from both parents. In order to test whether rose prickles could originate from a 'trichome-like structure,' we used a candidate approach to characterize rose gene homologues known in Arabidopsis, involved in trichome initiation. Four of these homologues were located within the overlapping credible interval of the detected QTLs. Transcript accumulation analysis weakly supports the involvement of trichome homologous genes, in the molecular control of prickle initiation. Our studies provide strong evidence for a complex genetic determinism of stem prickle and could help to establish guidelines for glabrous rose breeding. New insights into the relationship between prickles and trichomes constitute valuable information for reverse genetic research on prickles.
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Affiliation(s)
- N N Zhou
- INRAE, GDO-IRHS (Genetics and Diversity of Ornamental Plants, Institut de Recherche en Horticulture Et Semences), Université D'Angers, Agrocampus-Ouest, SFR 4207 QUASAV, 49071, Angers, France.
- National Engineering Research Center for Ornamental Horticulture; Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650231, China.
| | - K X Tang
- National Engineering Research Center for Ornamental Horticulture; Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650231, China
| | - J Jeauffre
- INRAE, GDO-IRHS (Genetics and Diversity of Ornamental Plants, Institut de Recherche en Horticulture Et Semences), Université D'Angers, Agrocampus-Ouest, SFR 4207 QUASAV, 49071, Angers, France
| | - T Thouroude
- INRAE, GDO-IRHS (Genetics and Diversity of Ornamental Plants, Institut de Recherche en Horticulture Et Semences), Université D'Angers, Agrocampus-Ouest, SFR 4207 QUASAV, 49071, Angers, France
| | - D C Lopez Arias
- INRAE, GDO-IRHS (Genetics and Diversity of Ornamental Plants, Institut de Recherche en Horticulture Et Semences), Université D'Angers, Agrocampus-Ouest, SFR 4207 QUASAV, 49071, Angers, France
| | - F Foucher
- INRAE, GDO-IRHS (Genetics and Diversity of Ornamental Plants, Institut de Recherche en Horticulture Et Semences), Université D'Angers, Agrocampus-Ouest, SFR 4207 QUASAV, 49071, Angers, France
| | - L Hibrand-Saint Oyant
- INRAE, GDO-IRHS (Genetics and Diversity of Ornamental Plants, Institut de Recherche en Horticulture Et Semences), Université D'Angers, Agrocampus-Ouest, SFR 4207 QUASAV, 49071, Angers, France
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108
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Song Z, Lin C, Xing P, Fen Y, Jin H, Zhou C, Gu YQ, Wang J, Li X. A high-quality reference genome sequence of Salvia miltiorrhiza provides insights into tanshinone synthesis in its red rhizomes. THE PLANT GENOME 2020; 13:e20041. [PMID: 33217202 DOI: 10.1002/tpg2.20041] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 05/02/2020] [Accepted: 05/26/2020] [Indexed: 05/21/2023]
Abstract
Salvia miltiorrhiza Bunge, also known as red sage or Danshen, is an important traditional Chinese medicine (TCM) that has been used for thousands of years to treat cardiovascular and other diseases. It is also considered an important model TCM plant. Here, a high-quality reference genome of S. miltiorrhiza was generated by combining PacBio long-read sequencing and chromatin interaction mapping (Hi-C) technologies, resulting in the chromosome-scale assembly of a 594.75-Mb genome sequence with a contig N50 of 2.70 Mb. This assembly shows the highest level of continuity for a Danshen genome generated thus far. The S. miltiorrhiza genome contained 32,483 protein-coding genes, with a repetitive DNA content of approximately 64.84%. The high percentage of young LTRs suggests that multiple TE transposition bursts occurred recently in S. miltiorrhiza. Genes unique to secondary metabolism pathways were expanded in the S. miltiorrhiza genome. A new CYP450 gene cluster was identified in the phloem of red roots where active components were synthesized. This reference genome sequence will facilitate future studies aimed at the elucidation of the secondary metabolism synthesis pathway and the genetic improvement of S. miltiorrhiza.
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Affiliation(s)
- Zhenqiao Song
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271028, China
| | - Caicai Lin
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
| | - Piyi Xing
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
| | - Yuanyuan Fen
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
| | - Hua Jin
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
| | - Changhao Zhou
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
| | - Yong Q Gu
- Crop Improvement & Genetics Research, Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA
| | - Jianhua Wang
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271028, China
| | - Xingfeng Li
- Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271028, China
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, 271028, China
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109
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Porcher A, Guérin V, Montrichard F, Lebrec A, Lothier J, Vian A. Ascorbate glutathione-dependent H2O2 scavenging is an important process in axillary bud outgrowth in rosebush. ANNALS OF BOTANY 2020; 126:1049-1062. [PMID: 32639526 PMCID: PMC7596375 DOI: 10.1093/aob/mcaa130] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/04/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS Branching is an important mechanism of plant shape establishment and the direct consequence of axillary bud outgrowth. Recently, hydrogen peroxide (H2O2) metabolism, known to be involved in plant growth and development, has been proposed to contribute to axillary bud outgrowth. However, the involvement of H2O2 in this process remains unclear. METHODS We analysed the content of H2O2 during bud outgrowth and characterized its catabolism, both at the transcriptional level and in terms of its enzymatic activities, using RT-qPCR and spectrophotometric methods, respectively. In addition, we used in vitro culture to characterize the effects of H2O2 application and the reduced glutathione (GSH) synthesis inhibitor l-buthionine sulfoximine (BSO) on bud outgrowth in relation to known molecular markers involved in this process. KEY RESULTS Quiescent buds displayed a high content of H2O2 that declined when bud outgrowth was initiated, as the consequence of an increase in the scavenging activity that is associated with glutathione pathways (ascorbate-glutathione cycle and glutathione biosynthesis); catalase did not appear to be implicated. Modification of bud redox state after the application of H2O2 or BSO prevented axillary bud outgrowth by repressing organogenesis and newly formed axis elongation. Hydrogen peroxide also repressed bud outgrowth-associated marker gene expression. CONCLUSIONS These results show that high levels of H2O2 in buds that are in a quiescent state prevents bud outgrowth. Induction of ascorbate-glutathione pathway scavenging activities results in a strong decrease in H2O2 content in buds, which finally allows bud outgrowth.
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Affiliation(s)
- Alexis Porcher
- Université d’Angers, Agrocampus Ouest, INRAE, UMR IRHS, SFR QuaSaV, Beaucouzé, France
| | - Vincent Guérin
- Université d’Angers, Agrocampus Ouest, INRAE, UMR IRHS, SFR QuaSaV, Beaucouzé, France
| | - Françoise Montrichard
- Université d’Angers, Agrocampus Ouest, INRAE, UMR IRHS, SFR QuaSaV, Beaucouzé, France
| | - Anita Lebrec
- Université d’Angers, Agrocampus Ouest, INRAE, UMR IRHS, SFR QuaSaV, Beaucouzé, France
| | - Jérémy Lothier
- Université d’Angers, Agrocampus Ouest, INRAE, UMR IRHS, SFR QuaSaV, Beaucouzé, France
| | - Alain Vian
- Université d’Angers, Agrocampus Ouest, INRAE, UMR IRHS, SFR QuaSaV, Beaucouzé, France
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110
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Singh P, Bharti N, Singh AP, Tripathi SK, Pandey SP, Chauhan AS, Kulkarni A, Sane AP. Petal abscission in fragrant roses is associated with large scale differential regulation of the abscission zone transcriptome. Sci Rep 2020; 10:17196. [PMID: 33057097 PMCID: PMC7566604 DOI: 10.1038/s41598-020-74144-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/08/2020] [Indexed: 12/03/2022] Open
Abstract
Flowers of fragrant roses such as Rosa bourboniana are ethylene-sensitive and undergo rapid petal abscission while hybrid roses show reduced ethylene sensitivity and delayed abscission. To understand the molecular mechanism underlying these differences, a comparative transcriptome of petal abscission zones (AZ) of 0 h and 8 h ethylene-treated flowers from R. bourboniana was performed. Differential regulation of 3700 genes (1518 up, 2182 down) representing 8.5% of the AZ transcriptome was observed between 0 and 8 h ethylene-treated R. bourboniana petal AZ. Abscission was associated with large scale up-regulation of the ethylene pathway but prominent suppression of the JA, auxin and light-regulated pathways. Regulatory genes encoding kinases/phosphatases/F-box proteins and transcription factors formed the major group undergoing differential regulation besides genes for transporters, wall modification, defense and phenylpropanoid pathways. Further comparisons with ethylene-treated petals of R. bourboniana and 8 h ethylene-treated AZ (R. hybrida) identified a core set of 255 genes uniquely regulated by ethylene in R. bourboniana AZ. Almost 23% of these encoded regulatory proteins largely conserved with Arabidopsis AZ components. Most of these were up-regulated while an entire set of photosystem genes was prominently down-regulated. The studies provide important information on regulation of petal abscission in roses.
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Affiliation(s)
- Priya Singh
- Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Neeraj Bharti
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, 411007, India.,High Performance Computing-Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, 411008, India
| | - Amar Pal Singh
- Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001, India.,National Institute for Plant Genome Research, New Delhi, 110067, India
| | - Siddharth Kaushal Tripathi
- Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001, India.,National Centre for Natural Products Research, School of Pharmacy, University of Mississippi, Oxford, MS, 38677, USA
| | - Saurabh Prakash Pandey
- Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Abhishek Singh Chauhan
- Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Abhijeet Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, 411007, India
| | - Aniruddha P Sane
- Molecular Biology and Biotechnology, CSIR-National Botanical Research Institute, Lucknow, 226001, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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111
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A Rosaceae Family-Level Approach To Identify Loci Influencing Soluble Solids Content in Blackberry for DNA-Informed Breeding. G3-GENES GENOMES GENETICS 2020; 10:3729-3740. [PMID: 32769135 PMCID: PMC7534445 DOI: 10.1534/g3.120.401449] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A Rosaceae family-level candidate gene approach was used to identify genes associated with sugar content in blackberry (Rubus subgenus Rubus). Three regions conserved among apple (Malus × domestica), peach (Prunus persica), and alpine strawberry (Fragaria vesca) were identified that contained previously detected sweetness-related quantitative trait loci (QTL) in at least two of the crops. Sugar related genes from these conserved regions and 789 sugar-associated apple genes were used to identify 279 Rubus candidate transcripts. A Hyb-Seq approach was used in conjunction with PacBio sequencing to generate haplotype level sequence information of sugar-related genes for 40 cultivars with high and low soluble solids content from the University of Arkansas and USDA blackberry breeding programs. Polymorphisms were identified relative to the ‘Hillquist’ blackberry (R. argutus) and ORUS 4115-3 black raspberry (R. occidentalis) genomes and tested for their association with soluble solids content (SSC). A total of 173 alleles were identified that were significantly (α = 0.05) associated with SSC. KASP genotyping was conducted for 92 of these alleles on a validation set of blackberries from each breeding program and 48 markers were identified that were significantly associated with SSC. One QTL, qSSC-Ruh-ch1.1, identified in both breeding programs accounted for an increase of 1.5 °Brix and the polymorphisms were detected in the intron space of a sucrose synthase gene. This discovery represents the first environmentally stable sweetness QTL identified in blackberry. The approach demonstrated in this study can be used to develop breeding tools for other crops that have not yet benefited directly from the genomics revolution.
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112
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Park J, Xi H, Kim Y, Nam S, Heo KI. The complete mitochondrial genome of new species candidate of Rosa rugosa (Rosaceae). Mitochondrial DNA B Resour 2020; 5:3435-3437. [PMID: 33458196 PMCID: PMC7782103 DOI: 10.1080/23802359.2020.1821820] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/04/2020] [Indexed: 01/13/2023] Open
Abstract
Completed mitochondrial genome of a new species candidate of Rosa rugosa, named as Rosa angusta, is 303,484 bp long. The overall GC content of this mitochondrial genome is 45.2%. It contains 52 genes covering 31 protein-coding genes, 17 tRNAs, and 3 rRNAs. In comparison to R. rugosa mitochondrial genome assembled from the public NGS raw reads, 124 SNPs and 769 INDELs were identified. Phylogenetic trees suggest that more Rosa mitochondrial genomes will be needed to understand phylogenetic relationship of the two Rosa species.
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Affiliation(s)
- Jongsun Park
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Yongsung Kim
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Suhwan Nam
- Baekdudaegan National Arboretum, Gyeongsangbuk-do, Korea
| | - Kyeong-In Heo
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
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113
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Zhang J, Lei Y, Wang B, Li S, Yu S, Wang Y, Li H, Liu Y, Ma Y, Dai H, Wang J, Zhang Z. The high-quality genome of diploid strawberry (Fragaria nilgerrensis) provides new insights into anthocyanin accumulation. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1908-1924. [PMID: 32003918 PMCID: PMC7415782 DOI: 10.1111/pbi.13351] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 05/11/2023]
Abstract
Fragaria nilgerrensis is a wild diploid strawberry species endemic to east and southeast region in Asia and provides a rich source of genetic variations for strawberry improvement. Here, we present a chromosome-scale assembly of F. nilgerrensis using single-molecule real-time (SMRT) Pacific Biosciences sequencing and chromosome conformation capture (Hi-C) genome scaffolding. The genome assembly size was 270.3 Mb, with a contig N50 of ∼8.5 Mb. A total of 28 780 genes and 117.2 Mb of transposable elements were annotated for this genome. Next, detailed comparative genomics with the high-quality F. vesca reference genome was conducted to obtain the difference among transposable elements, SNPs, Indels, and so on. The genome size of F. nilgerrensis was enhanced by around 50 Mb relatively to F. vesca, which is mainly due to expansion of transposable elements. In comparison with the F. vesca genome, we identified 4 561 825 SNPs, 846 301 Indels, 4243 inversions, 35 498 translocations and 10 099 relocations. We also found a marked expansion of genes involved in phenylpropanoid biosynthesis, starch and sucrose metabolism, cyanoamino acid metabolism, plant-pathogen interaction, brassinosteroid biosynthesis and plant hormone signal transduction in F. nilgerrensis, which may account for its specific phenotypes and considerable environmental adaptability. Interestingly, we found sequence variations in the upstream regulatory region of FnMYB10, a core transcriptional activator of anthocyanin biosynthesis, resulted in the low expression level of the FnMYB10 gene, which is likely responsible for white fruit phenotype of F. nilgerrensis. The high-quality F. nilgerrensis genome will be a valuable resource for biological research and comparative genomics research.
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Affiliation(s)
- Junxiang Zhang
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Yingying Lei
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Baotian Wang
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Song Li
- Biomarker Technologies CorporationBeijingChina
| | - Shuang Yu
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Yan Wang
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - He Li
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Yuexue Liu
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Yue Ma
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Hongyan Dai
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | | | - Zhihong Zhang
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
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114
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Sun P, Dégut C, Réty S, Caissard JC, Hibrand-Saint Oyant L, Bony A, Paramita SN, Conart C, Magnard JL, Jeauffre J, Abd-El-Haliem AM, Marie-Magdelaine J, Thouroude T, Baltenweck R, Tisné C, Foucher F, Haring M, Hugueney P, Schuurink RC, Baudino S. Functional diversification in the Nudix hydrolase gene family drives sesquiterpene biosynthesis in Rosa × wichurana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:185-199. [PMID: 32639596 DOI: 10.1111/tpj.14916] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/03/2020] [Accepted: 06/24/2020] [Indexed: 05/25/2023]
Abstract
Roses use a non-canonical pathway involving a Nudix hydrolase, RhNUDX1, to synthesize their monoterpenes, especially geraniol. Here we report the characterization of another expressed NUDX1 gene from the rose cultivar Rosa x wichurana, RwNUDX1-2. In order to study the function of the RwNUDX1-2 protein, we analyzed the volatile profiles of an F1 progeny generated by crossing R. chinensis cv. 'Old Blush' with R. x wichurana. A correlation test of the volatilomes with gene expression data revealed that RwNUDX1-2 is involved in the biosynthesis of a group of sesquiterpenoids, especially E,E-farnesol, in addition to other sesquiterpenes. In vitro enzyme assays and heterologous in planta functional characterization of the RwNUDX1-2 gene corroborated this result. A quantitative trait locus (QTL) analysis was performed using the data of E,E-farnesol contents in the progeny and a genetic map was constructed based on gene markers. The RwNUDX1-2 gene co-localized with the QTL for E,E-farnesol content, thereby confirming its function in sesquiterpenoid biosynthesis in R. x wichurana. Finally, in order to understand the structural bases for the substrate specificity of rose NUDX proteins, the RhNUDX1 protein was crystallized, and its structure was refined to 1.7 Å. By molecular modeling of different rose NUDX1 protein complexes with their respective substrates, a structural basis for substrate discrimination by rose NUDX1 proteins is proposed.
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Affiliation(s)
- Pulu Sun
- Univ Lyon, UJM-Saint-Etienne, CNRS, BVpam FRE 3727, Saint-Etienne, F-42023, France
- Green Life Sciences Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Clément Dégut
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), Paris, 75005, France
| | - Stéphane Réty
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, LBMC, 46 Allée d'Italie Site Jacques Monod, Lyon, F-69007, France
| | - Jean-Claude Caissard
- Univ Lyon, UJM-Saint-Etienne, CNRS, BVpam FRE 3727, Saint-Etienne, F-42023, France
| | | | - Aurélie Bony
- Univ Lyon, UJM-Saint-Etienne, CNRS, BVpam FRE 3727, Saint-Etienne, F-42023, France
| | - Saretta N Paramita
- Univ Lyon, UJM-Saint-Etienne, CNRS, BVpam FRE 3727, Saint-Etienne, F-42023, France
| | - Corentin Conart
- Univ Lyon, UJM-Saint-Etienne, CNRS, BVpam FRE 3727, Saint-Etienne, F-42023, France
| | - Jean-Louis Magnard
- Univ Lyon, UJM-Saint-Etienne, CNRS, BVpam FRE 3727, Saint-Etienne, F-42023, France
| | - Julien Jeauffre
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, 49071, France
| | - Ahmed M Abd-El-Haliem
- Green Life Sciences Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Jordan Marie-Magdelaine
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, 49071, France
| | - Tatiana Thouroude
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, 49071, France
| | | | - Carine Tisné
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), Paris, 75005, France
| | - Fabrice Foucher
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, 49071, France
| | - Michel Haring
- Green Life Sciences Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Philippe Hugueney
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, Colmar, F-68000, France
| | - Robert C Schuurink
- Green Life Sciences Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Sylvie Baudino
- Univ Lyon, UJM-Saint-Etienne, CNRS, BVpam FRE 3727, Saint-Etienne, F-42023, France
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115
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Sun YB, Zhang XJ, Zhong MC, Dong X, Yu DM, Jiang XD, Wang D, Cui WH, Chen JH, Hu JY. Genome-wide identification of WD40 genes reveals a functional diversification of COP1-like genes in Rosaceae. PLANT MOLECULAR BIOLOGY 2020; 104:81-95. [PMID: 32621166 DOI: 10.1007/s11103-020-01026-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
Genome-wide identification of WD40-like genes reveals a duplication of COP1-like genes, one of the key players involved in regulation of flowering time and photomorphogenesis, with strong functional diversification in Rosaceae. WD40 proteins play crucial roles in a broad spectrum of developmental and physiological processes. Here, we conducted a systematic characterization of this family of genes in Rosa chinensis 'Old Blush' (OB), a founder genotype for modern rose domestication. We identified 187 rose WD40 genes and classified them into 5 clusters and 15 subfamilies with 11 of RcWD40s presumably generated via tandem duplication. We found RcWD40 genes were expressed differentially following stages of vegetative and reproductive development. We detected a duplication of CONSTITUTIVE PHOTOMORPHOGENIC1-like genes in rose (RcCOP1 and RcCOP1L) and other Rosaceae plants. Featuring a distinct expression pattern and a different profile of cis-regulatory-elements in the transcriptional regulatory regions, RcCOP1 seemed being evolutionarily conserved while RcCOP1L did not dimerize with RcHY5 and RcSPA4. Our data thus reveals a functional diversification of COP1-like genes in Rosacaeae plants, and provides a valuable resource to explore the potential function and evolution of WD40-like genes in Rosaceae plants.
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Affiliation(s)
- Yi-Bo Sun
- 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
| | - Xiao-Jia Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Science, Kunming, 650223, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mi-Cai Zhong
- 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
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Dong-Mei Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiao-Dong Jiang
- 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
| | - Dan Wang
- 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
| | - Wei-Hua Cui
- 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
| | - Jiang-Hua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Science, Kunming, 650223, Yunnan, China
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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116
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Yang C, Ma Y, Cheng B, Zhou L, Yu C, Luo L, Pan H, Zhang Q. Molecular Evidence for Hybrid Origin and Phenotypic Variation of Rosa Section Chinenses. Genes (Basel) 2020; 11:genes11090996. [PMID: 32854427 PMCID: PMC7564265 DOI: 10.3390/genes11090996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/01/2020] [Accepted: 08/18/2020] [Indexed: 11/18/2022] Open
Abstract
Rosa sect. Chinenses (Rosaceae) is an important parent of modern rose that is widely distributed throughout China and plays an important role in breeding and molecular biological research. R. sect. Chinenses has variable morphological traits and mixed germplasm. However, the taxonomic status and genetic background of sect. Chinenses varieties remain unclear. In this study, we collected germplasm resources from sect. Chinenses varieties with different morphological traits. Simple sequence repeat (SSR) markers, chloroplast markers, and single copy nuclear markers were used to explore the genetic background of these germplasm resources. We described the origin of hybridization of rose germplasm resources by combining different molecular markers. The results showed that the flower and hip traits of different species in R. sect. Chinenses were significantly different. The SSR analysis showed that the two wild type varieties have different genetic backgrounds. The double petal varieties of R. sect. Chinenses could be hybrids of two wild type varieties. A phylogenetic analysis showed that the maternal inheritance of sect. Chinenses varieties had two different origins. To some extent, variation in the morphological traits of double petal species of R. sect. Chinenses reflects the influence of cultivation process. This study emphasizes that different genetic markers vary in their characteristics. Therefore, analyzing different genetic markers in could provide an insight into highly heterozygous species.
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117
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Ren H, Bai M, Sun J, Liu J, Ren M, Dong Y, Wang N, Ning G, Wang C. RcMYB84 and RcMYB123 mediate jasmonate-induced defense responses against Botrytis cinerea in rose (Rosa chinensis). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1839-1849. [PMID: 32524706 DOI: 10.1111/tpj.14871] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 05/02/2023]
Abstract
Jasmonates (JAs) are important for pathogen resistance in many plants, but the role of these phytohormones in fungal pathogen resistance in rose is unclear. Here, we determined that exogenous application of methyl jasmonate increased resistance to the important fungal pathogen Botrytis cinerea in Rosa chinensis 'Old blush', whereas silencing the JA biosynthetic pathway gene Allene Oxide Synthase (AOS) and JA co-receptor gene CORONATINE INSENSITIVE 1 (COI1) suppressed this response. Transcriptome profiling identified various MYB transcription factor genes that responded to both JA and B. cinerea treatment. Silencing Ri-RcMYB84/Ri-RcMYB123 increased the susceptibility of rose plants to B. cinerea and inhibited the protective effects of JA treatment, confirming the crucial roles of these genes in JA-induced responses to B. cinerea. JAZ1, a key repressor of JA signaling, directly interacts with RcMYB84 and RcMYB123 to deplete their free pools. The JAZ1-RcMYB84 complex binds to the RcMYB123 promoter via the CAACTG motifs to block its transcription. Upon JA treatment, the expression of RcMYB123 is de-repressed, and free forms of RcMYB84 and RcMYB123 are released due to JAZ1 degradation, thereby activating the defense responses of plants to B. cinerea. These findings shed light on the molecular mechanisms underlying JA-induced pathogen resistance in roses.
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Affiliation(s)
- Haoran Ren
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Mengjuan Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jingjing Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinyi Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Min Ren
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuwei Dong
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Na Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Guogui Ning
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Changquan Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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118
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Abstract
Virus-induced gene silencing (VIGS) is a favorable method to study gene function by posttranscriptional gene silencing in plants. Here we describe a methodology of graft-accelerated VIGS in rose aimed at obtaining posttranscriptional gene silencing in the flower. The resulting phenotype can be observed within 5-6 weeks post infiltration. By using this method, we successfully silenced the expression of several genes involved in processes such as scent production, petal coloration, or flower architecture. We showed that graft-accelerated VIGS was faster, more efficient, and more convenient than conventional methods previously developed in rose such as agroinfiltration of young plantlets and in vitro cultured tissues or seeds.
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119
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Lunerová J, Herklotz V, Laudien M, Vozárová R, Groth M, Kovařík A, Ritz CM. Asymmetrical canina meiosis is accompanied by the expansion of a pericentromeric satellite in non-recombining univalent chromosomes in the genus Rosa. ANNALS OF BOTANY 2020; 125:1025-1038. [PMID: 32095807 PMCID: PMC7262465 DOI: 10.1093/aob/mcaa028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 02/24/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Despite their abundant odd-ploidy (2n = 5x = 35), dogroses (Rosa sect. Caninae) are capable of sexual reproduction due to their unique meiosis. During canina meiosis, two sets of chromosomes form bivalents and are transmitted by male and female gametes, whereas the remaining chromosomes form univalents and are exclusively transmitted by the egg cells. Thus, the evolution of chromosomes is expected to be driven by their behaviour during meiosis. METHODS To gain insight into differential chromosome evolution, fluorescence in situ hybridization was conducted for mitotic and meiotic chromosomes in four dogroses (two subsections) using satellite and ribosomal DNA probes. By exploiting high-throughput sequencing data, we determined the abundance and diversity of the satellite repeats in the genus Rosa by analysing 20 pentaploid, tetraploid and diploid species in total. KEY RESULTS A pericentromeric satellite repeat, CANR4, was found in all members of the genus Rosa, including the basal subgenera Hulthemia and Hesperhodos. The satellite was distributed across multiple chromosomes (5-20 sites per mitotic cell), and its genomic abundance was higher in pentaploid dogroses (2.3 %) than in non-dogrose species (1.3 %). In dogrose meiosis, univalent chromosomes were markedly enriched in CANR4 repeats based on both the number and the intensity of the signals compared to bivalent-forming chromosomes. Single-nucleotide polymorphisms and cluster analysis revealed high intragenomic homogeneity of the satellite in dogrose genomes. CONCLUSIONS The CANR4 satellite arose early in the evolution of the genus Rosa. Its high content and extraordinary homogeneity in dogrose genomes is explained by its recent amplification in non-recombining chromosomes. We hypothesize that satellite DNA expansion may contribute to the divergence of univalent chromosomes in Rosa species with non-symmetrical meiosis.
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Affiliation(s)
- Jana Lunerová
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Melanie Laudien
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Technical University Dresden, International Institute Zittau (IHI), Chair of Biodiversity of Higher Plants, Zittau, Germany
| | - Radka Vozárová
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
- Masaryk University, Faculty of Science, Brno, Czech Republic
| | - Marco Groth
- Leibniz Institute on Ageing – Fritz Lipmann Institute, Jena, Germany
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Christiane M Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
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120
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High density SNP and SSR linkage map and QTL analysis for resistance to black spot in segregating rose population. ACTA ACUST UNITED AC 2020. [DOI: 10.17660/actahortic.2020.1283.26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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121
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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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Ahn CH, Ramya M, An HR, Park PM, Kim YJ, Lee SY, Jang S. Progress and Challenges in the Improvement of Ornamental Plants by Genome Editing. PLANTS 2020; 9:plants9060687. [PMID: 32481726 PMCID: PMC7356337 DOI: 10.3390/plants9060687] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/18/2020] [Accepted: 05/27/2020] [Indexed: 01/08/2023]
Abstract
Biotechnological approaches have been used to modify the floral color, size, and fragrance of ornamental plants, as well as to increase disease resistance and vase life. Together with the advancement of whole genome sequencing technologies, new plant breeding techniques have rapidly emerged in recent years. Compared to the early versions of gene editing tools, such as meganucleases (MNs), zinc fingers (ZFNs), and transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeat (CRISPR) is capable of altering a genome more efficiently and with higher accuracy. Most recently, new CRISPR systems, including base editors and prime editors, confer reduced off-target activity with improved DNA specificity and an expanded targeting scope. However, there are still controversial issues worldwide for the recognition of genome-edited plants, including whether genome-edited plants are genetically modified organisms and require a safety evaluation process. In the current review, we briefly summarize the current progress in gene editing systems and also introduce successful/representative cases of the CRISPR system application for the improvement of ornamental plants with desirable traits. Furthermore, potential challenges and future prospects in the use of genome-editing tools for ornamental plants are also discussed.
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Affiliation(s)
- Chang Ho Ahn
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
| | - Mummadireddy Ramya
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
| | - Hye Ryun An
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
| | - Pil Man Park
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
| | - Yae-Jin Kim
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
| | - Su Young Lee
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
- Correspondence: (S.Y.L.); (S.J.); Tel.: +82-238-6840 (S.Y.L.); +82-63-238-6677 (S.J.)
| | - Seonghoe Jang
- World Vegetable Center Korea Office (WKO), Wanju-gun, Jellabuk-do 55365, Korea
- Correspondence: (S.Y.L.); (S.J.); Tel.: +82-238-6840 (S.Y.L.); +82-63-238-6677 (S.J.)
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123
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Gattolin S, Cirilli M, Chessa S, Stella A, Bassi D, Rossini L. Mutations in orthologous PETALOSA TOE-type genes cause a dominant double-flower phenotype in phylogenetically distant eudicots. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2585-2595. [PMID: 31960023 PMCID: PMC7210751 DOI: 10.1093/jxb/eraa032] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/17/2020] [Indexed: 05/04/2023]
Abstract
The double-flower phenotype has been selected by humans for its attractiveness in various plant species and it is of great commercial value for the ornamental market. In this study we investigated the genetic determinant of the dominant double-flower trait in carnation, petunia, and Rosa rugosa, and identified mutant alleles of TARGET OF EAT (TOE)-type genes characterized by a disruption of the miR172 target sequence and of the C-terminal portion of the encoded protein. Despite the phylogenetic distance between these eudicots, which diverged in the early Cretaceous, the orthologous genes carrying these mutations all belong to a single TOE-type subgroup, which we name as PETALOSA (PET). Homology searches allowed us to identify PET sequences in various other species. To confirm the results from naturally occurring mutations, we used CrispR-Cas9 to induce lesions within the miR172 target site of Nicotiana tabacum PET genes, and this resulted in the development of supernumerary petaloid structures. This study describes pet alleles in economically important ornamental species and provides evidence about the possibility of identifying and engineering PET genes to obtain the desirable double-flower trait in different plants.
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Affiliation(s)
- Stefano Gattolin
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biologia e Biotecnologia Agraria (IBBA), Milano, Italy
- PTP Science Park, Lodi, Italy
- Correspondence: or
| | - Marco Cirilli
- Università degli Studi di Milano – DiSAA, Milano, Italy
| | - Stefania Chessa
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biologia e Biotecnologia Agraria (IBBA), Milano, Italy
| | - Alessandra Stella
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biologia e Biotecnologia Agraria (IBBA), Milano, Italy
| | - Daniele Bassi
- Università degli Studi di Milano – DiSAA, Milano, Italy
| | - Laura Rossini
- Università degli Studi di Milano – DiSAA, Milano, Italy
- Correspondence: or
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Gattolin S, Cirilli M, Chessa S, Stella A, Bassi D, Rossini L. Mutations in orthologous PETALOSA TOE-type genes cause a dominant double-flower phenotype in phylogenetically distant eudicots. JOURNAL OF EXPERIMENTAL BOTANY 2020. [PMID: 31960023 DOI: 10.1093/jxb/eraa032/5710789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The double-flower phenotype has been selected by humans for its attractiveness in various plant species and it is of great commercial value for the ornamental market. In this study we investigated the genetic determinant of the dominant double-flower trait in carnation, petunia, and Rosa rugosa, and identified mutant alleles of TARGET OF EAT (TOE)-type genes characterized by a disruption of the miR172 target sequence and of the C-terminal portion of the encoded protein. Despite the phylogenetic distance between these eudicots, which diverged in the early Cretaceous, the orthologous genes carrying these mutations all belong to a single TOE-type subgroup, which we name as PETALOSA (PET). Homology searches allowed us to identify PET sequences in various other species. To confirm the results from naturally occurring mutations, we used CrispR-Cas9 to induce lesions within the miR172 target site of Nicotiana tabacum PET genes, and this resulted in the development of supernumerary petaloid structures. This study describes pet alleles in economically important ornamental species and provides evidence about the possibility of identifying and engineering PET genes to obtain the desirable double-flower trait in different plants.
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Affiliation(s)
- Stefano Gattolin
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biologia e Biotecnologia Agraria (IBBA), Milano, Italy
- PTP Science Park, Lodi, Italy
| | - Marco Cirilli
- Università degli Studi di Milano - DiSAA, Milano, Italy
| | - Stefania Chessa
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biologia e Biotecnologia Agraria (IBBA), Milano, Italy
| | - Alessandra Stella
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biologia e Biotecnologia Agraria (IBBA), Milano, Italy
| | - Daniele Bassi
- Università degli Studi di Milano - DiSAA, Milano, Italy
| | - Laura Rossini
- Università degli Studi di Milano - DiSAA, Milano, Italy
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125
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Fan Y, Liu J, Zou J, Zhang X, Jiang L, Liu K, Lü P, Gao J, Zhang C. The RhHB1/ RhLOX4 module affects the dehydration tolerance of rose flowers ( Rosa hybrida) by fine-tuning jasmonic acid levels. HORTICULTURE RESEARCH 2020; 7:74. [PMID: 32377364 PMCID: PMC7195446 DOI: 10.1038/s41438-020-0299-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/11/2020] [Accepted: 03/16/2020] [Indexed: 05/14/2023]
Abstract
Phytohormones are key factors in plant responsiveness to abiotic and biotic stresses, and maintaining hormone homeostasis is critically important during stress responses. Cut rose (Rosa hybrida) flowers experience dehydration stress during postharvest handling, and jasmonic acid (JA) levels change as a result of this stress. However, how JA is involved in dehydration tolerance remains unclear. We investigated the functions of the JA- and dehydration-induced RhHB1 gene, which encodes a homeodomain-leucine zipper I γ-clade transcription factor, in rose flowers. Silencing RhHB1 decreased petal dehydration tolerance and resulted in a persistent increase in JA-Ile content and reduced dehydration tolerance. An elevated JA-Ile level had a detrimental effect on rose petal dehydration tolerance. RhHB1 was shown to lower the transient induction of JA-Ile accumulation in response to dehydration. In addition to transcriptomic data, we obtained evidence that RhHB1 suppresses the expression of the lipoxygenase 4 (RhLOX4) gene by directly binding to its promoter both in vivo and in vitro. We propose that increased JA-Ile levels weaken the capacity for osmotic adjustment in petal cells, resulting in reduced dehydration tolerance. In conclusion, a JA feedback loop mediated by an RhHB1/RhLOX4 regulatory module provides dehydration tolerance by fine-tuning bioactive JA levels in dehydrated flowers.
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Affiliation(s)
- Youwei Fan
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Jitao Liu
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
- Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, Guangdong 510642 China
| | - Jing Zou
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Xiangyu Zhang
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Liwei Jiang
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Kun Liu
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Peitao Lü
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Junping Gao
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Changqing Zhang
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
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126
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Liu Z, Ma H, Jung S, Main D, Guo L. Developmental Mechanisms of Fleshy Fruit Diversity in Rosaceae. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:547-573. [PMID: 32442388 DOI: 10.1146/annurev-arplant-111119-021700] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Rosaceae (the rose family) is an economically important family that includes species prized for high-value fruits and ornamentals. The family also exhibits diverse fruit types, including drupe (peach), pome (apple), drupetum (raspberry), and achenetum (strawberry). Phylogenetic analysis and ancestral fruit-type reconstruction suggest independent evolutionary paths of multiple fleshy fruit types from dry fruits. A recent whole genome duplication in the Maleae/Pyreae tribe (with apple, pear, hawthorn, and close relatives; referred to as Maleae here) may have contributed to the evolution of pome fruit. MADS-box genes, known to regulate floral organ identity, are emerging as important regulators of fruit development. The differential competence of floral organs to respond to fertilization signals may explain the different abilities of floral organs to form fleshy fruit. Future comparative genomics and functional studies in closely related Rosaceae species with distinct fruit types will test hypotheses and provide insights into mechanisms of fleshy fruit diversity. These efforts will be facilitated by the wealth of genome data and resources in Rosaceae.
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Affiliation(s)
- Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA; ,
| | - Hong Ma
- Department of Biology, Eberly College of Science, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, Washington 99164, USA; ,
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, Washington 99164, USA; ,
| | - Lei Guo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA; ,
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Martínez MC, Santiago JL, Boso S, Gago P, Álvarez-Acero I, De Vega ME, Martínez-Bartolomé M, Álvarez-Nogal R, Molíst P, Caser M, Scariot V, Gómez-García D. Narcea-an unknown, ancient cultivated rose variety from northern Spain. HORTICULTURE RESEARCH 2020; 7:44. [PMID: 32257230 PMCID: PMC7109042 DOI: 10.1038/s41438-020-0266-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 02/06/2020] [Accepted: 02/12/2020] [Indexed: 05/18/2023]
Abstract
The present work reports the discovery and the complete characterisation of an ancient cultivated rose variety found growing in a private garden in the southwest of the Principality of Asturias (northern Spain). The variety is here given the name Narcea. The majority of roses currently cultivated belong to the so-called group of 'Modern Roses', all of which were obtained after 1867 via artificial crosses and improvement programmes. All are destined for ornamental use. Until the 19th century, the great majority of the many ancient cultivated roses in Europe were used in perfumery and cosmetics, or had medicinal uses. Rosa damascena and Rosa centifollia are still grown and used by the French and Bulgarian perfume industries. The Asturian Massif of the Cantabrian Mountain Range provides a natural habitat for some 75% of the wild members of the genus Rosa, but until now there was no evidence that this area was home to ancient cultivated roses. A complete botanical description is here provided for a discovered ancient rose. It is also characterised according to a series of sequence tagged microsatellite sites, and its agronomic features are reported. In addition, a histological description (optical and scanning electronic microscope studies) of the petals is offered, along with an analysis of the volatile compounds present in these organs as determined by solid phase microextraction and gas chromatography-mass spectroscopy. The results reveal the uniqueness of this ancient type of rose and suggest it may be of interest to the perfume industry.
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Affiliation(s)
| | - José-Luis Santiago
- Misión Biológica de Galicia (CSIC), Carballeira 8, Salcedo, 36143 Pontevedra Spain
| | - Susana Boso
- Misión Biológica de Galicia (CSIC), Carballeira 8, Salcedo, 36143 Pontevedra Spain
| | - Pilar Gago
- Misión Biológica de Galicia (CSIC), Carballeira 8, Salcedo, 36143 Pontevedra Spain
| | - Inmaculada Álvarez-Acero
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición (CSIC) (Spain), C/José Antonio Novais 10, 28040 Madrid, Spain
| | - María-Estela De Vega
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición (CSIC) (Spain), C/José Antonio Novais 10, 28040 Madrid, Spain
| | - Miguel Martínez-Bartolomé
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición (CSIC) (Spain), C/José Antonio Novais 10, 28040 Madrid, Spain
| | - Rafael Álvarez-Nogal
- Departamento de Biología Molecular-Área de Biología Celular, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Pilar Molíst
- Grupo Neurolamb, Biología funcional y Ciencias de la Salud, Universidad de Vigo (Spain), 36310 As Lagoas-Marcosende, Spain
| | - Matteo Caser
- Department of Agricultural, Forest and Food Sciences, University of Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Turin Italy
| | - Valentina Scariot
- Department of Agricultural, Forest and Food Sciences, University of Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Turin Italy
| | - Daniel Gómez-García
- Instituto Pirenaico de Ecología (CSIC), Dpto. Conservación de Ecosistemas Naturales, Avda. Montaña S/N, Zaragoza, 50016 Zaragoza, Spain
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128
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Wu X, Alexander LW. Genome-wide association studies for inflorescence type and remontancy in Hydrangea macrophylla. HORTICULTURE RESEARCH 2020; 7:27. [PMID: 32140236 PMCID: PMC7049302 DOI: 10.1038/s41438-020-0255-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/31/2019] [Accepted: 01/04/2020] [Indexed: 05/28/2023]
Abstract
Inflorescence type and remontancy are two valuable traits in bigleaf hydrangea (Hydrangea macrophylla L.) and both are recessively inherited. Molecular marker-assisted selection (MAS) can greatly reduce the time necessary to breed cultivars with desired traits. In this study, a genome-wide association study (GWAS) using 5803 single-nucleotide polymorphisms (SNPs) was performed using a panel of 82 bigleaf hydrangea cultivars. One SNP locus (Hy_CAPS_Inflo) associated with inflorescence type was identified with general linear model (GLM) and mixed linear model (MLM) methods that explained 65.5% and 36.1% of the phenotypic variations, respectively. Twenty-three SNPs associated with remontancy were detected in GLM whereas no SNP was detected in MLM. The SNP locus (Hy_CAPS_Inflo) was converted to a cleaved amplified polymorphic sequence (CAPS) marker that showed absolute identification accuracy (100%) of inflorescence type in a validation panel consisting of eighteen H. macrophylla cultivars. The SNP was investigated in 341 F1 progenies using genotyping by sequencing (GBS) and co-segregated with inflorescence type (χ 2 = 0.12; P = 0.73). The SNP was subsequently used for breeding selection using kompetitive allele specific PCR (KASP) technology. Future directions for the use of genomics and MAS in hydrangea breeding improvement are discussed. The results presented in this study provide insights for further research on understanding genetic mechanisms behind inflorescence type and remontancy in H. macrophylla. The CAPS and KASP markers developed here will be immediately useful for applying MAS to accelerate breeding improvement in hydrangea.
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Affiliation(s)
- Xingbo Wu
- Oak Ridge Institute of Science and Technology, Otis L. Floyd Nursery Research Center, 472 Cadillac Lane, McMinnville, TN USA
| | - Lisa W. Alexander
- U.S. Department of Agriculture, Agricultural Research Service, U.S. National Arboretum, Floral and Nursery Plants Research Unit, Otis L. Floyd Nursery Research Center, 472 Cadillac Lane, McMinnville, TN USA
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129
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Menz I, Lakhwani D, Clotault J, Linde M, Foucher F, Debener T. Analysis of the Rdr1 gene family in different Rosaceae genomes reveals an origin of an R-gene cluster after the split of Rubeae within the Rosoideae subfamily. PLoS One 2020; 15:e0227428. [PMID: 31971947 PMCID: PMC6977733 DOI: 10.1371/journal.pone.0227428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/18/2019] [Indexed: 11/20/2022] Open
Abstract
The Rdr1 gene confers resistance to black spot in roses and belongs to a large TNL gene family, which is organized in two major clusters at the distal end of chromosome 1. We used the recently available chromosome scale assemblies for the R. chinensis 'Old Blush' genome, re-sequencing data for nine rose species and genome data for Fragaria, Rubus, Malus and Prunus to identify Rdr1 homologs from different taxa within Rosaceae. Members of the Rdr1 gene family are organized into two major clusters in R. chinensis and at a syntenic location in the Fragaria genome. Phylogenetic analysis indicates that the two clusters existed prior to the split of Rosa and Fragaria and that one cluster has a more recent origin than the other. Genes belonging to cluster 2, such as the functional Rdr1 gene muRdr1A, were subject to a faster evolution than genes from cluster 1. As no Rdr1 homologs were found in syntenic positions for Prunus persica, Malus x domestica and Rubus occidentalis, a translocation of the Rdr1 clusters to the current positions probably happened after the Rubeae split from other groups within the Rosoideae approximately 70-80 million years ago during the Cretaceous period.
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Affiliation(s)
- Ina Menz
- Institute for Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Deepika Lakhwani
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, Beaucouzé, France
| | - Jérémy Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, Beaucouzé, France
| | - Marcus Linde
- Institute for Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Fabrice Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, Beaucouzé, France
| | - Thomas Debener
- Institute for Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
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130
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Kirov I, Odintsov S, Omarov M, Gvaramiya S, Merkulov P, Dudnikov M, Ermolaev A, Van Laere K, Soloviev A, Khrustaleva L. Functional Allium fistulosum Centromeres Comprise Arrays of a Long Satellite Repeat, Insertions of Retrotransposons and Chloroplast DNA. FRONTIERS IN PLANT SCIENCE 2020; 11:562001. [PMID: 33193489 PMCID: PMC7644871 DOI: 10.3389/fpls.2020.562001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/07/2020] [Indexed: 05/08/2023]
Abstract
The centromere is a unique part of the chromosome combining a conserved function with an extreme variability in its DNA sequence. Most of our knowledge about the functional centromere organization is obtained from species with small and medium genome/chromosome sizes while the progress in plants with big genomes and large chromosomes is lagging behind. Here, we studied the genomic organization of the functional centromere in Allium fistulosum and A. cepa, both species with a large genome (13 Gb and 16 Gb/1C, 2n = 2x = 16) and large-sized chromosomes. Using low-depth DNA sequencing for these two species and previously obtained CENH3 immunoprecipitation data we identified two long (1.2 Kb) and high-copy repeats, AfCen1K and AcCen1K. FISH experiments showed that AfCen1K is located in all centromeres of A. fistulosum chromosomes while no AcCen1K FISH signals were identified on A. cepa chromosomes. Our molecular cytogenetic and bioinformatics survey demonstrated that these repeats are partially similar but differ in chromosomal location, sequence structure and genomic organization. In addition, we could conclude that the repeats are transcribed and their RNAs are not polyadenylated. We also observed that these repeats are associated with insertions of retrotransposons and plastidic DNA and the landscape of A. cepa and A. fistulosum centromeric regions possess insertions of plastidic DNA. Finally, we carried out detailed comparative satellitome analysis of A. cepa and A. fistulosum genomes and identified a new chromosome- and A. cepa-specific tandem repeat, TR2CL137, located in the centromeric region. Our results shed light on the Allium centromere organization and provide unique data for future application in Allium genome annotation.
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Affiliation(s)
- Ilya Kirov
- Laboratory of Marker-assisted and genomic selection of plants, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
- *Correspondence: Ilya Kirov,
| | - Sergey Odintsov
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - Murad Omarov
- Laboratory of Marker-assisted and genomic selection of plants, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
- National Research University Higher School of Economics, Moscow, Russia
| | - Sofya Gvaramiya
- Laboratory of Marker-assisted and genomic selection of plants, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Pavel Merkulov
- Laboratory of Marker-assisted and genomic selection of plants, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Maxim Dudnikov
- Laboratory of Marker-assisted and genomic selection of plants, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Alexey Ermolaev
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - Katrijn Van Laere
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
| | - Alexander Soloviev
- Laboratory of Marker-assisted and genomic selection of plants, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Ludmila Khrustaleva
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
- Plant Cell Engineering Laboratory, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
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131
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Wilson AE, Tian L. Phylogenomic analysis of UDP-dependent glycosyltransferases provides insights into the evolutionary landscape of glycosylation in plant metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1273-1288. [PMID: 31446648 DOI: 10.1111/tpj.14514] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/09/2019] [Accepted: 08/19/2019] [Indexed: 05/05/2023]
Abstract
Glycosylated metabolites generated by UDP-dependent glycosyltransferases (UGTs) play critical roles in plant interactions with the environment as well as human and animal nutrition. The evolution of plant UGTs has previously been explored, but with a limited taxon sampling. In this study, 65 fully sequenced plant genomes were analyzed, and stringent criteria for selection of candidate UGTs were applied to ensure a more comprehensive taxon sampling and reliable sequence inclusion. In addition to revealing the overall evolutionary landscape of plant UGTs, the phylogenomic analysis also resolved the phylogenetic association of UGTs from free-sporing plants and gymnosperms, and identified an additional UGT group (group R) in seed plants. Furthermore, lineage-specific expansions and contractions of UGT groups were detected in angiosperms, with the total number of UGTs per genome remaining constant generally. The loss of group Q UGTs in Poales and Brassicales, rather than functional convergence in the group Q containing species, was supported by a gene tree of group Q UGTs sampled from many species, and further corroborated by the absence of group Q homologs on the syntenic chromosomal regions in Arabidopsis thaliana (Brassicales). Branch-site analyses of the group Q UGT gene tree allowed for identification of branches and amino acid sites that experienced episodic positive selection. The positively selected sites are located on the surface of a representative group Q UGT (PgUGT95B2), away from the active site, suggesting their role in protein folding/stability or protein-protein interactions.
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Affiliation(s)
- Alexander E Wilson
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Li Tian
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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132
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Desta ZA, Kolano B, Shamim Z, Armstrong SJ, Rewers M, Sliwinska E, Kushwaha SK, Parkin IAP, Ortiz R, de Koning DJ. Field cress genome mapping: Integrating linkage and comparative maps with cytogenetic analysis for rDNA carrying chromosomes. Sci Rep 2019; 9:17028. [PMID: 31745130 PMCID: PMC6863836 DOI: 10.1038/s41598-019-53320-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/30/2019] [Indexed: 11/09/2022] Open
Abstract
Field cress (Lepidium campestre L.), despite its potential as a sustainable alternative oilseed plant, has been underutilized, and no prior attempts to characterize the genome at the genetic or molecular cytogenetic level have been conducted. Genetic maps are the foundation for anchoring and orienting annotated genome assemblies and positional cloning of candidate genes. Our principal goal was to construct a genetic map using integrated approaches of genetic, comparative and cytogenetic map analyses. In total, 503 F2 interspecific hybrid individuals were genotyped using 7,624 single nucleotide polymorphism markers. Comparative analysis demonstrated that ~57% of the sequenced loci in L. campestre were congruent with Arabidopsis thaliana (L.) genome and suggested a novel karyotype, which predates the ancestral crucifer karyotype. Aceto-orcein chromosome staining and fluorescence in situ hybridization (FISH) analyses confirmed that L. campestre, L. heterophyllum Benth. and their hybrids had a chromosome number of 2n = 2x = 16. Flow cytometric analysis revealed that both species possess 2C roughly 0.4 picogram DNA. Integrating linkage and comparative maps with cytogenetic map analyses assigned two linkage groups to their particular chromosomes. Future work could incorporate FISH utilizing A. thaliana mapped BAC clones to allow the chromosomes of field cress to be identified reliably.
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Affiliation(s)
- Zeratsion Abera Desta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundesvagen 10, Box 101, SE-23053, Alnarp, Sweden.
| | - Bozena Kolano
- Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28, 40-032, Katowice, Poland
| | - Zeeshan Shamim
- Mirpur University of Science and Technology (MUST), Mirpur AJK, Pakistan
- School of Biosciences, University of Birmingham, Birmingham, B 15 2TT, United Kingdom
| | - Susan J Armstrong
- School of Biosciences, University of Birmingham, Birmingham, B 15 2TT, United Kingdom
| | - Monika Rewers
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Science and Technology, Kaliskiego Ave. 7, 85-789, Bydgoszcz, Poland
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Science and Technology, Kaliskiego Ave. 7, 85-789, Bydgoszcz, Poland
| | - Sandeep Kumar Kushwaha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundesvagen 10, Box 101, SE-23053, Alnarp, Sweden
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N0X2, Canada
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundesvagen 10, Box 101, SE-23053, Alnarp, Sweden
| | - Dirk-Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE 75007, Uppsala, Sweden
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133
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Genome-Wide Identification and Characterization of ABC Transporters in Nine Rosaceae Species Identifying MdABCG28 as a Possible Cytokinin Transporter linked to Dwarfing. Int J Mol Sci 2019; 20:ijms20225783. [PMID: 31744249 PMCID: PMC6887749 DOI: 10.3390/ijms20225783] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/08/2019] [Accepted: 11/15/2019] [Indexed: 01/04/2023] Open
Abstract
ATP-binding cassette (ABC) transporters constitute a large, diverse, and ubiquitous superfamily that is involved in a broad range of processes. The completion of genome sequencing provides an opportunity to understand the phylogenetic history of the ABC transporter superfamily among Rosaceae species. This study identified a total of 1323 ABC transporter genes from nine Rosaceae genomes: 191 from Malus domestica, 174 from Pyrus communis, 138 from Prunus persica, 118 from Prunus avium, 141 from Prunus dulcis, 122 from Fragaria vesca, 98 from Rubus occidentalis, 162 from Prunus mume, and 179 from Rosa chinensis. Their chemical characterization, phylogenetic analysis, chromosomal localization, gene structure, gene duplication, and tissue-specific expression were studied. Their subcellular localization, transmembrane structures, and protein motifs were predicted. All the ABC transporter genes were grouped into eight subfamilies on the basis of their phylogenetic relationships and structural features. Furthermore, cis-element and expression analysis of 10 potential phytohormone transporters in MdABCG subfamily genes were also performed. Loss of the W-box in the promoter region of MdABCG28 was found to reduce the gene expression level and was linked to the dwarfing phenotype in apple rootstocks. MdABCG28 overexpression promoted shoot growth of atabcg14 mutants in Arabidopsis.
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134
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Su J, Jiang J, Zhang F, Liu Y, Ding L, Chen S, Chen F. Current achievements and future prospects in the genetic breeding of chrysanthemum: a review. HORTICULTURE RESEARCH 2019; 6:109. [PMID: 31666962 PMCID: PMC6804895 DOI: 10.1038/s41438-019-0193-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/11/2019] [Accepted: 08/14/2019] [Indexed: 05/05/2023]
Abstract
Chrysanthemum (Chrysanthemum morifolium Ramat.) is a leading flower with applied value worldwide. Developing new chrysanthemum cultivars with novel characteristics such as new flower colors and shapes, plant architectures, flowering times, postharvest quality, and biotic and abiotic stress tolerance in a time- and cost-efficient manner is the ultimate goal for breeders. Various breeding strategies have been employed to improve the aforementioned traits, ranging from conventional techniques, including crossbreeding and mutation breeding, to a series of molecular breeding methods, including transgenic technology, genome editing, and marker-assisted selection (MAS). In addition, the recent extensive advances in high-throughput technologies, especially genomics, transcriptomics, proteomics, metabolomics, and microbiomics, which are collectively referred to as omics platforms, have led to the collection of substantial amounts of data. Integration of these omics data with phenotypic information will enable the identification of genes/pathways responsible for important traits. Several attempts have been made to use emerging molecular and omics methods with the aim of accelerating the breeding of chrysanthemum. However, applying the findings of such studies to practical chrysanthemum breeding remains a considerable challenge, primarily due to the high heterozygosity and polyploidy of the species. This review summarizes the recent achievements in conventional and modern molecular breeding methods and emerging omics technologies and discusses their future applications for improving the agronomic and horticultural characteristics of chrysanthemum.
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Affiliation(s)
- Jiangshuo Su
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Fei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Ye Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Lian Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
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135
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Hirakawa H, Sumitomo K, Hisamatsu T, Nagano S, Shirasawa K, Higuchi Y, Kusaba M, Koshioka M, Nakano Y, Yagi M, Yamaguchi H, Taniguchi K, Nakano M, Isobe SN. De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis. DNA Res 2019; 26:195-203. [PMID: 30689773 PMCID: PMC6589549 DOI: 10.1093/dnares/dsy048] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 01/02/2019] [Indexed: 11/13/2022] Open
Abstract
Cultivated chrysanthemum (Chrysanthemum morifolium Ramat.) is one of the most economically important ornamental crops grown worldwide. It has a complex hexaploid genome (2n = 6x = 54) and large genome size. The diploid Chrysanthemum seticuspe is often used as a model of cultivated chrysanthemum, since the two species are closely related. To expand our knowledge of the cultivated chrysanthemum, we here performed de novo whole-genome assembly in C. seticuspe using the Illumina sequencing platform. XMRS10, a C. seticuspe accession developed by five generations of self-crossing from a self-compatible strain, AEV2, was used for genome sequencing. The 2.72 Gb of assembled sequences (CSE_r1.0), consisting of 354,212 scaffolds, covered 89.0% of the 3.06 Gb C. seticuspe genome estimated by k-mer analysis. The N50 length of scaffolds was 44,741 bp. For protein-encoding genes, 71,057 annotated genes were deduced (CSE_r1.1_cds). Next, based on the assembled genome sequences, we performed linkage map construction, gene discovery and comparative analyses for C. seticuspe and cultivated chrysanthemum. The generated C. seticuspe linkage map revealed skewed regions in segregation on the AEV2 genome. In gene discovery analysis, candidate flowering-related genes were newly found in CSE_r1.1_cds. Moreover, single nucleotide polymorphism identification and annotation on the C. × morifolium genome showed that the C. seticuspe genome was applicable to genetic analysis in cultivated chrysanthemums. The genome sequences assembled herein are expected to contribute to future chrysanthemum studies. In addition, our approach demonstrated the usefulness of short-read genome assembly and the importance of choosing an appropriate next genome sequencing technology based on the purpose of the post-genome analysis.
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Affiliation(s)
| | - Katsuhiko Sumitomo
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, Japan
| | - Tamotsu Hisamatsu
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, Japan
| | - Soichiro Nagano
- Kazusa DNA Research Institute, Kisarazu, Chiba, Japan.,Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Juo, Hitachi, Ibaraki, Japan
| | | | - Yohei Higuchi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Makoto Kusaba
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Masaji Koshioka
- College of Bioresource Sciences, Nihon University, Kameino, Fujisawa, Kanagawa, Japan
| | - Yoshihiro Nakano
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, Japan
| | - Masafumi Yagi
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, Japan
| | - Hiroyasu Yamaguchi
- Institute of Vegetable and Floriculture Sciences, NARO, Tsukuba, Ibaraki, Japan
| | - Kenji Taniguchi
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Michiharu Nakano
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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136
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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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137
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Wang M, Ogé L, Voisine L, Perez-Garcia MD, Jeauffre J, Hibrand Saint-Oyant L, Grappin P, Hamama L, Sakr S. Posttranscriptional Regulation of RhBRC1 ( Rosa hybrida BRANCHED1) in Response to Sugars is Mediated via its Own 3' Untranslated Region, with a Potential Role of RhPUF4 (Pumilio RNA-Binding Protein Family). Int J Mol Sci 2019; 20:ijms20153808. [PMID: 31382685 PMCID: PMC6695800 DOI: 10.3390/ijms20153808] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/24/2019] [Accepted: 07/27/2019] [Indexed: 01/07/2023] Open
Abstract
The shoot branching pattern is a determining phenotypic trait throughout plant development. During shoot branching, BRANCHED1 (BRC1) plays a master regulator role in bud outgrowth, and its transcript levels are regulated by various exogenous and endogenous factors. RhBRC1 (the homologous gene of BRC1 in Rosa hybrida) is a main branching regulator whose posttranscriptional regulation in response to sugar was investigated through its 3'UTR. Transformed Rosa calluses containing a construction composed of the CaMV35S promoter, the green fluorescent protein (GFP) reporter gene, and the 3'UTR of RhBRC1 (P35S:GFP::3'UTRRhBRC1) were obtained and treated with various combinations of sugars and with sugar metabolism effectors. The results showed a major role of the 3'UTR of RhBRC1 in response to sugars, involving glycolysis/the tricarboxylic acid cycle (TCA) and the oxidative pentose phosphate pathway (OPPP). In Rosa vegetative buds, sequence analysis of the RhBRC1 3'UTR identified six binding motifs specific to the Pumilio/FBF RNA-binding protein family (PUF) and probably involved in posttranscriptional regulation. RhPUF4 was highly expressed in the buds of decapitated plants and in response to sugar availability in in-vitro-cultured buds. RhPUF4 was found to be close to AtPUM2, which encodes an Arabidopsis PUF protein. In addition, sugar-dependent upregulation of RhPUF4 was also found in Rosa calluses. RhPUF4 expression was especially dependent on the OPPP, supporting its role in OPPP-dependent posttranscriptional regulation of RhBRC1. These findings indicate that the 3'UTR sequence could be an important target in the molecular regulatory network of RhBRC1 and pave the way for investigating new aspects of RhBRC1 regulation.
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Affiliation(s)
- Ming Wang
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49000 Angers, France
| | - Laurent Ogé
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49000 Angers, France
| | - Linda Voisine
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49000 Angers, France
| | | | - Julien Jeauffre
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49000 Angers, France
| | | | - Philippe Grappin
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49000 Angers, France
| | - Latifa Hamama
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49000 Angers, France
| | - Soulaiman Sakr
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, 49000 Angers, France.
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138
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Debray K, Marie-Magdelaine J, Ruttink T, Clotault J, Foucher F, Malécot V. Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae). BMC Evol Biol 2019; 19:152. [PMID: 31340752 PMCID: PMC6657147 DOI: 10.1186/s12862-019-1479-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/16/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND With an ever-growing number of published genomes, many low levels of the Tree of Life now contain several species with enough molecular data to perform shallow-scale phylogenomic studies. Moving away from using just a few universal phylogenetic markers, we can now target thousands of other loci to decipher taxa relationships. Making the best possible selection of informative sequences regarding the taxa studied has emerged as a new issue. Here, we developed a general procedure to mine genomic data, looking for orthologous single-copy loci capable of deciphering phylogenetic relationships below the generic rank. To develop our strategy, we chose the genus Rosa, a rapid-evolving lineage of the Rosaceae family in which several species genomes have recently been sequenced. We also compared our loci to conventional plastid markers, commonly used for phylogenetic inference in this genus. RESULTS We generated 1856 sequence tags in putative single-copy orthologous nuclear loci. Associated in silico primer pairs can potentially amplify fragments able to resolve a wide range of speciation events within the genus Rosa. Analysis of parsimony-informative site content showed the value of non-coding genomic regions to obtain variable sequences despite the fact that they may be more difficult to target in less related species. Dozens of nuclear loci outperform the conventional plastid phylogenetic markers in terms of phylogenetic informativeness, for both recent and ancient evolutionary divergences. However, conflicting phylogenetic signals were found between nuclear gene tree topologies and the species-tree topology, shedding light on the many patterns of hybridization and/or incomplete lineage sorting that occur in the genus Rosa. CONCLUSIONS With recently published genome sequence data, we developed a set of single-copy orthologous nuclear loci to resolve species-level phylogenomics in the genus Rosa. This genome-wide scale dataset contains hundreds of highly variable loci which phylogenetic interest was assessed in terms of phylogenetic informativeness and topological conflict. Our target identification procedure can easily be reproduced to identify new highly informative loci for other taxonomic groups and ranks.
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Affiliation(s)
- Kevin Debray
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France.
| | | | - Tom Ruttink
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - Jérémy Clotault
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Fabrice Foucher
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Valéry Malécot
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France.
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139
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Li S, Yang G, Yang S, Just J, Yan H, Zhou N, Jian H, Wang Q, Chen M, Qiu X, Zhang H, Dong X, Jiang X, Sun Y, Zhong M, Bendahmane M, Ning G, Ge H, Hu JY, Tang K. The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose. Sci Rep 2019; 9:5985. [PMID: 30979937 PMCID: PMC6461668 DOI: 10.1038/s41598-019-42428-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 03/07/2019] [Indexed: 01/11/2023] Open
Abstract
Roses are important woody plants featuring a set of important traits that cannot be investigated in traditional model plants. Here, we used the restriction-site associated DNA sequencing (RAD-seq) technology to develop a high-density linkage map of the backcross progeny (BC1F1) between Rosa chinensis 'Old Blush' (OB) and R. wichuraiana 'Basyes' Thornless' (BT). We obtained 643.63 million pair-end reads and identified 139,834 polymorphic tags that were distributed uniformly in the rose genome. 2,213 reliable markers were assigned to seven linkage groups (LGs). The length of the genetic map was 1,027.425 cM in total with a mean distance of 0.96 cM per marker locus. This new linkage map allowed anchoring an extra of 1.21/23.14 Mb (12.18/44.52%) of the unassembled OB scaffolds to the seven reference pseudo-chromosomes, thus significantly improved the quality of assembly of OB reference genome. We demonstrate that, while this new linkage map shares high collinearity level with strawberry genome, it also features two chromosomal rearrangements, indicating its usefulness as a resource for understanding the evolutionary scenario among Rosaceae genomes. Together with the newly released genome sequences for OB, this linkage map will facilitate the identification of genetic components underpinning key agricultural and biological traits, hence should greatly advance the studies and breeding efforts of rose.
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Affiliation(s)
- Shubin Li
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Guoqian Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan Province, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Shuhua Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jeremy Just
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69364, Lyon, France
| | - Huijun Yan
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Ningning Zhou
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Hongying Jian
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Qigang Wang
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Min Chen
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Xianqin Qiu
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Hao Zhang
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China
| | - Xue Dong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiaodong Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan Province, China
| | - Yibo Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan Province, China
| | - Micai Zhong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan Province, China
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69364, Lyon, France
| | - Guogui Ning
- Key laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Ge
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Kaixue Tang
- National Engineering Research Center For Ornamental Horticulture, Flower Research Institute, Yunnan Academy of Agricultural Sciences; Yunnan Flower Breeding Key Lab, Kunming, 650231, China.
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140
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Rusanov K, Kovacheva N, Rusanova M, Linde M, Debener T, Atanassov I. Genetic control of flower petal number in Rosa x Damascena Mill f. trigintipetala. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1599731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Krasimir Rusanov
- Molecular Genetics Group, AgroBioInstitute Agricultural Academy, Sofia, Bulgaria
| | | | - Mila Rusanova
- Molecular Genetics Group, AgroBioInstitute Agricultural Academy, Sofia, Bulgaria
| | - Marcus Linde
- Department of Molecular Plant Breeding, Institute of Plant Genetics Leibniz Universität Hannover, Hannover, Germany
| | - Thomas Debener
- Department of Molecular Plant Breeding, Institute of Plant Genetics Leibniz Universität Hannover, Hannover, Germany
| | - Ivan Atanassov
- Molecular Genetics Group, AgroBioInstitute Agricultural Academy, Sofia, Bulgaria
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141
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Zhang L, Hu J, Han X, Li J, Gao Y, Richards CM, Zhang C, Tian Y, Liu G, Gul H, Wang D, Tian Y, Yang C, Meng M, Yuan G, Kang G, Wu Y, Wang K, Zhang H, Wang D, Cong P. A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. Nat Commun 2019; 10:1494. [PMID: 30940818 PMCID: PMC6445120 DOI: 10.1038/s41467-019-09518-x] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 03/13/2019] [Indexed: 01/14/2023] Open
Abstract
A complete and accurate genome sequence provides a fundamental tool for functional genomics and DNA-informed breeding. Here, we assemble a high-quality genome (contig N50 of 6.99 Mb) of the apple anther-derived homozygous line HFTH1, including 22 telomere sequences, using a combination of PacBio single-molecule real-time (SMRT) sequencing, chromosome conformation capture (Hi-C) sequencing, and optical mapping. In comparison to the Golden Delicious reference genome, we identify 18,047 deletions, 12,101 insertions and 14 large inversions. We reveal that these extensive genomic variations are largely attributable to activity of transposable elements. Interestingly, we find that a long terminal repeat (LTR) retrotransposon insertion upstream of MdMYB1, a core transcriptional activator of anthocyanin biosynthesis, is associated with red-skinned phenotype. This finding provides insights into the molecular mechanisms underlying red fruit coloration, and highlights the utility of this high-quality genome assembly in deciphering agriculturally important trait in apple.
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Affiliation(s)
- Liyi Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Research Institute of Pomology, Chinese Academy of Agricultural Science, 125100, Xingcheng, Liaoning, China
| | - Jiang Hu
- Nextomics Biosciences Institute, 430000, Wuhan, Hubei, China
| | - Xiaolei Han
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Research Institute of Pomology, Chinese Academy of Agricultural Science, 125100, Xingcheng, Liaoning, China
| | - Jingjing Li
- Nextomics Biosciences Institute, 430000, Wuhan, Hubei, China
| | - Yuan Gao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Research Institute of Pomology, Chinese Academy of Agricultural Science, 125100, Xingcheng, Liaoning, China
| | - Christopher M Richards
- USDA-ARS National Center for Genetic Resources Preservation, Fort Collins, CO, 80521, USA
| | - Caixia Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Research Institute of Pomology, Chinese Academy of Agricultural Science, 125100, Xingcheng, Liaoning, China
| | - Yi Tian
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Research Institute of Pomology, Chinese Academy of Agricultural Science, 125100, Xingcheng, Liaoning, China
| | - Guiming Liu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China
| | - Hera Gul
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Research Institute of Pomology, Chinese Academy of Agricultural Science, 125100, Xingcheng, Liaoning, China
| | - Dajiang Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Research Institute of Pomology, Chinese Academy of Agricultural Science, 125100, Xingcheng, Liaoning, China
| | - Yu Tian
- Nextomics Biosciences Institute, 430000, Wuhan, Hubei, China
| | - Chuanxin Yang
- Nextomics Biosciences Institute, 430000, Wuhan, Hubei, China
| | - Minghui Meng
- Nextomics Biosciences Institute, 430000, Wuhan, Hubei, China
| | - Gaopeng Yuan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Research Institute of Pomology, Chinese Academy of Agricultural Science, 125100, Xingcheng, Liaoning, China
| | - Guodong Kang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Research Institute of Pomology, Chinese Academy of Agricultural Science, 125100, Xingcheng, Liaoning, China
| | - Yonglong Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Research Institute of Pomology, Chinese Academy of Agricultural Science, 125100, Xingcheng, Liaoning, China
| | - Kun Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Research Institute of Pomology, Chinese Academy of Agricultural Science, 125100, Xingcheng, Liaoning, China
| | - Hengtao Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, 450009, Zhengzhou, Henan, China
| | - Depeng Wang
- Nextomics Biosciences Institute, 430000, Wuhan, Hubei, China.
| | - Peihua Cong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Research Institute of Pomology, Chinese Academy of Agricultural Science, 125100, Xingcheng, Liaoning, China.
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142
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Neu E, Domes HS, Menz I, Kaufmann H, Linde M, Debener T. Interaction of roses with a biotrophic and a hemibiotrophic leaf pathogen leads to differences in defense transcriptome activation. PLANT MOLECULAR BIOLOGY 2019; 99:299-316. [PMID: 30706286 DOI: 10.1007/s11103-018-00818-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 12/22/2018] [Indexed: 05/09/2023]
Abstract
Transcriptomic analysis resulted in the upregulation of the genes related to common defense mechanisms for black spot and the downregulation of the genes related to photosynthesis and cell wall modification for powdery mildew. Plant pathogenic fungi successfully colonize their hosts by manipulating the host defense mechanisms, which is accompanied by major transcriptome changes in the host. To characterize compatible plant pathogen interactions at early stages of infection by the obligate biotrophic fungus Podosphaera pannosa, which causes powdery mildew, and the hemibiotrophic fungus Diplocarpon rosae, which causes black spot, we analyzed changes in the leaf transcriptome after the inoculation of detached rose leaves with each pathogen. In addition, we analyzed differences in the transcriptomic changes inflicted by both pathogens as a first step to characterize specific infection strategies. Transcriptomic changes were analyzed using next-generation sequencing based on the massive analysis of cDNA ends approach, which was validated using high-throughput qPCR. We identified a large number of differentially regulated genes. A common set of the differentially regulated genes comprised of pathogenesis-related (PR) genes, such as of PR10 homologs, chitinases and defense-related transcription factors, such as various WRKY genes, indicating a conserved but insufficient PTI [pathogen associated molecular pattern (PAMP) triggered immunity] reaction. Surprisingly, most of the differentially regulated genes were specific to the interactions with either P. pannosa or D. rosae. Specific regulation in response to D. rosae was detected for genes from the phenylpropanoid and flavonoid pathways and for individual PR genes, such as paralogs of PR1 and PR5, and other factors of the salicylic acid signaling pathway. Differently, inoculation with P. pannosa leads in addition to the general pathogen response to a downregulation of genes related to photosynthesis and cell wall modification.
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Affiliation(s)
- Enzo Neu
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany
- KWS SAAT SE, 37574, Einbeck, Germany
| | - Helena Sophia Domes
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany
| | - Ina Menz
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany
| | - Helgard Kaufmann
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany
| | - Marcus Linde
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany
| | - Thomas Debener
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany.
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143
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Roccia A, Hibrand-Saint Oyant L, Cavel E, Caissard JC, Machenaud J, Thouroude T, Jeauffre J, Bony A, Dubois A, Vergne P, Szécsi J, Foucher F, Bendahmane M, Baudino S. Biosynthesis of 2-Phenylethanol in Rose Petals Is Linked to the Expression of One Allele of RhPAAS. PLANT PHYSIOLOGY 2019; 179:1064-1079. [PMID: 30622153 PMCID: PMC6393788 DOI: 10.1104/pp.18.01468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 12/20/2018] [Indexed: 05/23/2023]
Abstract
Floral scent is one of the most important characters in horticultural plants. Roses (Rosa spp.) have been cultivated for their scent since antiquity. However, probably by selecting for cultivars with long vase life, breeders have lost the fragrant character in many modern roses, especially the ones bred for the cut flower market. The genetic inheritance of scent characters has remained elusive so far. In-depth knowledge of this quantitative trait is thus very much needed to breed more fragrant commercial cultivars. Furthermore, rose hybrids harbor a composite genomic structure, which complexifies quantitative trait studies. To understand rose scent inheritance, we characterized a segregating population from two diploid cultivars, Rosa × hybrida cv H190 and Rosa wichurana, which have contrasting scent profiles. Several quantitative trait loci for the major volatile compounds in this progeny were identified. One among these loci contributing to the production of 2-phenylethanol, responsible for the characteristic odor of rose, was found to be colocalized with a candidate gene belonging to the 2-phenylethanol biosynthesis pathway: the PHENYLACETALDEHYDE SYNTHASE gene RhPAAS An in-depth allele-specific expression analysis in the progeny demonstrated that only one allele was highly expressed and was responsible for the production of 2-phenylethanol. Unexpectedly, its expression was found to start early during flower development, before the production of the volatile 2-phenylethanol, leading to the accumulation of glycosylated compounds in petals.
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Affiliation(s)
- Aymeric Roccia
- Université Lyon, Université Saint-Etienne, Centre National de la Recherche Scientifique, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, FRE 3727, F-42023 Saint-Etienne, France
- Laboratoire Reproduction et Développement des Plantes, Université Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, F-69342 Lyon, France
| | - Laurence Hibrand-Saint Oyant
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, Institut National de la Recherche Agronomique, Université d'Angers, Structure Fédérative de Recherche 4207 Qualité et Santé du végétal, 49071 Beaucouzé, France
| | - Emilie Cavel
- Université Lyon, Université Saint-Etienne, Centre National de la Recherche Scientifique, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, FRE 3727, F-42023 Saint-Etienne, France
| | - Jean-Claude Caissard
- Université Lyon, Université Saint-Etienne, Centre National de la Recherche Scientifique, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, FRE 3727, F-42023 Saint-Etienne, France
| | - Jana Machenaud
- Université Lyon, Université Saint-Etienne, Centre National de la Recherche Scientifique, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, FRE 3727, F-42023 Saint-Etienne, France
| | - Tatiana Thouroude
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, Institut National de la Recherche Agronomique, Université d'Angers, Structure Fédérative de Recherche 4207 Qualité et Santé du végétal, 49071 Beaucouzé, France
| | - Julien Jeauffre
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, Institut National de la Recherche Agronomique, Université d'Angers, Structure Fédérative de Recherche 4207 Qualité et Santé du végétal, 49071 Beaucouzé, France
| | - Aurélie Bony
- Université Lyon, Université Saint-Etienne, Centre National de la Recherche Scientifique, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, FRE 3727, F-42023 Saint-Etienne, France
| | - Annick Dubois
- Laboratoire Reproduction et Développement des Plantes, Université Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, F-69342 Lyon, France
| | - Philippe Vergne
- Laboratoire Reproduction et Développement des Plantes, Université Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, F-69342 Lyon, France
| | - Judit Szécsi
- Laboratoire Reproduction et Développement des Plantes, Université Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, F-69342 Lyon, France
| | - Fabrice Foucher
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, Institut National de la Recherche Agronomique, Université d'Angers, Structure Fédérative de Recherche 4207 Qualité et Santé du végétal, 49071 Beaucouzé, France
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, Université Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, F-69342 Lyon, France
| | - Sylvie Baudino
- Université Lyon, Université Saint-Etienne, Centre National de la Recherche Scientifique, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, FRE 3727, F-42023 Saint-Etienne, France
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144
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Soundararajan P, Won SY, Kim JS. Insight on Rosaceae Family with Genome Sequencing and Functional Genomics Perspective. BIOMED RESEARCH INTERNATIONAL 2019; 2019:7519687. [PMID: 30911547 PMCID: PMC6399558 DOI: 10.1155/2019/7519687] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 01/02/2019] [Accepted: 01/23/2019] [Indexed: 11/26/2022]
Abstract
Rosaceae is one of the important families possessing a variety of diversified plant species. It includes many economically valuable crops that provide nutritional and health benefits for the human. Whole genome sequences of valuable crop plants were released in recent years. Understanding of genomics helps to decipher the plant physiology and developmental process. With the information of cultivating species and its wild relative genomes, genome sequence-based molecular markers and mapping loci for economically important traits can be used to accelerate the genome assisted breeding. Identification and characterization of disease resistant capacities and abiotic stress tolerance related genes are feasible to study across species with genome information. Further breeding studies based on the identification of gene loci for aesthetic values, flowering molecular circuit controls, fruit firmness, nonacid fruits, etc. is required for producing new cultivars with valuable traits. This review discusses the whole genome sequencing reports of Malus, Pyrus, Fragaria, Prunus, and Rosa and status of functional genomics of representative traits in individual crops.
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Affiliation(s)
- Prabhakaran Soundararajan
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Republic of Korea
| | - So Youn Won
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Republic of Korea
| | - Jung Sun Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Republic of Korea
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145
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Huang X, Yan H, Zhai L, Yi Y. GLABROUS1 from Rosa roxburghii Tratt regulates trichome formation by interacting with the GL3/EGL3 protein. Gene 2019; 692:60-67. [PMID: 30641212 DOI: 10.1016/j.gene.2018.12.071] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/08/2018] [Accepted: 12/20/2018] [Indexed: 11/26/2022]
Abstract
GLABROUS1 is an R2R3 MYB homolog that is essential for the initiation of trichome development. In this study, we used RACE to clone a full-length cDNA from Rosa roxburghii Tratt, termed RrGL1, which was 1013 bp, including an open reading frame of 792 bp that encoded 263 amino acids. In situ hybridization, corresponding with qRT-PCR results, revealed that RrGL1 transcripts were mainly expressed in petiole, leaf, and stem. RrGL1 expression levels at various fruit developmental stages in R. roxburghii were also evaluated. RrGL1 was highly expressed in young fruit, and the expression level decreased with fruit maturation. The overexpression of RrGL1 was able to functionally complemented the Arabidopsis thaliana gl1-/- mutant in trichome formation. RrGL1 was located in the cell nucleus with analysis of subcellular localization and physically interacted with A. thaliana GL3/EGL3 in the yeast two-hybrid assay, implying that RrGL1 might exert functions by forming a MYB-basic helix-loop-helix complex in trichome initiation. The formation of prickles in R. roxburghii is similar to that of Arabidopsis trichome. These results provided a foundation for further research on the molecular mechanisms underlying the formation and development of prickles that could assist and cultivate in the genetic engineering of prickle-free fruits.
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Affiliation(s)
- Xiaolong Huang
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China /Key Laboratory of Plant Physiology and Developmental Regulation/ School of Life Sciences, Guizhou Normal University, Guiyang 550001, China
| | - Huiqing Yan
- School of Life Sciences, Guizhou Normal University, Guiyang 550001, China.
| | - Lisheng Zhai
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China /Key Laboratory of Plant Physiology and Developmental Regulation/ School of Life Sciences, Guizhou Normal University, Guiyang 550001, China
| | - Yin Yi
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China /Key Laboratory of Plant Physiology and Developmental Regulation/ School of Life Sciences, Guizhou Normal University, Guiyang 550001, China.
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146
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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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147
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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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148
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Wan H, Yu C, Han Y, Guo X, Luo L, Pan H, Zheng T, Wang J, Cheng T, Zhang Q. Determination of Flavonoids and Carotenoids and Their Contributions to Various Colors of Rose Cultivars ( Rosa spp.). FRONTIERS IN PLANT SCIENCE 2019; 10:123. [PMID: 30809238 PMCID: PMC6379320 DOI: 10.3389/fpls.2019.00123] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/24/2019] [Indexed: 05/22/2023]
Abstract
Rose is one of the most valuable ornamental crops worldwide. In this study, the composition of hydrophilic and lipophilic pigments in petals of six rose cultivars at seven developing stages was investigated using high performance liquid chromatography and mass spectrometry. Four anthocyanins, 20 flavonols, and 10 carotenoids were detected in petals of tested cultivars. Major individual anthocyanin, flavonol, and carotenoid were cyanidin/pelargonidin 3,5-diglucoside, kaempferol 3-O-rhamnoside, and (9Z)-violaxanthin, respectively. Significant differences were observed in pigments content in petals of different rose cultivars. The yellow petals of YI and GC exhibited no to very small amounts of anthocyanins, moderate amount of total flavonols, and highest content of total carotenoids. Similarly, pink petals of PF, WQ, and YX showed average concentration of total anthocyanins, highest concentration of total flavonols, and small amount of carotenoids. Further, orange petals of CH showed highest content of total anthocyanins, lowest content of total flavonols, and average content of total carotenoids. Correlation analysis demonstrated that there were many pigments influencing petal colors. Moreover, multiple linear regression indicated that pelargonidin 3,5-diglucoside, total anthocyanins and (9Z)-violaxanthin were the major factors. In addition, this study showed that orange cultivar CH, pink cultivar PF and yellow cultivar YI can have great potential as a natural source for the extraction of pelargonidin 3-O-glucoside, kaempferol 3-O-rhamnoside, and (9Z)-violaxanthin, respectively. These investigations would contribute toward understanding the mechanism on the development of flower colors and provide a theoretical basis for the breeding of rose with specific color.
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Affiliation(s)
- Huihua Wan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Chao Yu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Yu Han
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Xuelian Guo
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Le Luo
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangchun Zheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- *Correspondence: Qixiang Zhang,
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149
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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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150
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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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