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Huang Y, He J, Xu Y, Zheng W, Wang S, Chen P, Zeng B, Yang S, Jiang X, Liu Z, Wang L, Wang X, Liu S, Lu Z, Liu Z, Yu H, Yue J, Gao J, Zhou X, Long C, Zeng X, Guo YJ, Zhang WF, Xie Z, Li C, Ma Z, Jiao W, Zhang F, Larkin RM, Krueger RR, Smith MW, Ming R, Deng X, Xu Q. Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits. Nat Genet 2023; 55:1964-1975. [PMID: 37783780 DOI: 10.1038/s41588-023-01516-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/28/2023] [Indexed: 10/04/2023]
Abstract
The orange subfamily (Aurantioideae) contains several Citrus species cultivated worldwide, such as sweet orange and lemon. The origin of Citrus species has long been debated and less is known about the Aurantioideae. Here, we compiled the genome sequences of 314 accessions, de novo assembled the genomes of 12 species and constructed a graph-based pangenome for Aurantioideae. Our analysis indicates that the ancient Indian Plate is the ancestral area for Citrus-related genera and that South Central China is the primary center of origin of the Citrus genus. We found substantial variations in the sequence and expression of the PH4 gene in Citrus relative to Citrus-related genera. Gene editing and biochemical experiments demonstrate a central role for PH4 in the accumulation of citric acid in citrus fruits. This study provides insights into the origin and evolution of the orange subfamily and a regulatory mechanism underpinning the evolution of fruit taste.
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Affiliation(s)
- Yue Huang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Hongshan Laboratory, Wuhan, People's Republic of China
| | - Jiaxian He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yuantao Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Hongshan Laboratory, Wuhan, People's Republic of China
| | - Weikang Zheng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shaohua Wang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, People's Republic of China
| | - Peng Chen
- Horticulture Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Bin Zeng
- Horticulture Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Shuizhi Yang
- Horticulture Institute, Hunan Academy of Agricultural Sciences, Changsha, People's Republic of China
| | - Xiaolin Jiang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Zishuang Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Lun Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xia Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shengjun Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Zhihao Lu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Ziang Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Huiwen Yu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jianqiang Yue
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, People's Republic of China
| | - Junyan Gao
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, People's Republic of China
| | - Xianyan Zhou
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, People's Republic of China
| | - Chunrui Long
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, People's Republic of China
| | - Xiuli Zeng
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station, Ministry of Agriculture and Rural Affairs, Lhasa, People's Republic of China
| | - Yong-Jie Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Wen-Fu Zhang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, People's Republic of China
| | - Zongzhou Xie
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Chunlong Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Zhaocheng Ma
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Wenbiao Jiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Fei Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Robert M Larkin
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Robert R Krueger
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA, USA
| | - Malcolm W Smith
- Department of Agriculture and Fisheries, Bundaberg, Queensland, Australia
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Qiang Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, People's Republic of China.
- Hubei Hongshan Laboratory, Wuhan, People's Republic of China.
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Jabeen S, Saif R, Haq R, Hayat A, Naz S. Whole-genome sequencing and variant discovery of Citrus reticulata "Kinnow" from Pakistan. Funct Integr Genomics 2023; 23:227. [PMID: 37422603 DOI: 10.1007/s10142-023-01153-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/10/2023]
Abstract
Citrus is a source of nutritional and medicinal advantages, cultivated worldwide with major groups of sweet oranges, mandarins, grapefruits, kumquats, lemons and limes. Pakistan produces all major citrus groups with mandarin (Citrus reticulata) being the prominent group that includes local commercial cultivars Feutral's Early, Dancy, Honey, and Kinnow. The present study designed to understand the genetic architecture of this unique variety of Citrus reticulata 'Kinnow.' The whole-genome resequencing and variant calling was performed to map the genomic variability that might be responsible for its particular characteristics like taste, seedlessness, juice content, thickness of peel, and shelf-life. A total of 139,436,350 raw sequence reads were generated with 20.9 Gb data in Fastq format having 98% effectiveness and 0.2% base call error rate. Overall, 3,503,033 SNPs, 176,949 MNPs, 323,287 INS, and 333,083 DEL were identified using the GATK4 variant calling pipeline against Citrus clementina. Furthermore, g:Profiler was applied for annotating the newly found variants, harbor genes/transcripts and their involved pathways. A total of 73,864 transcripts harbors 4,336,352 variants, most of the observed variants were predicted in non-coding regions and 1009 transcripts were found well annotated by different databases. Out of total aforementioned transcripts, 588 involved in biological processes, 234 in molecular functions and 167 transcripts in cellular components. In a nutshell, 18,153 high impact variants and 216 genic variants found in the current study, which may be used after its functional validation for marker-assisted breeding programs of "Kinnow" to propagate its valued traits for the improvement of contemporary citrus varieties in the region.
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Affiliation(s)
- Sadia Jabeen
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Rashid Saif
- Department of Biotechnology, Qarshi University, Lahore, Pakistan
- Decode Genomics, Punjab University Employees Housing Scheme, Lahore, Pakistan
| | - Rukhama Haq
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Akbar Hayat
- Citrus Research Institute, Sargodha, Pakistan
| | - Shagufta Naz
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan.
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Singh J, Sharma A, Sharma V, Gaikwad PN, Sidhu GS, Kaur G, Kaur N, Jindal T, Chhuneja P, Rattanpal HS. Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species. Sci Rep 2023; 13:10919. [PMID: 37407627 DOI: 10.1038/s41598-023-37024-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 06/14/2023] [Indexed: 07/07/2023] Open
Abstract
Citrus species among the most important and widely consumed fruit in the world due to Vitamin C, essential oil glands, and flavonoids. Highly variable simple sequence repeats (SSR) markers are one of the most informative and versatile molecular markers used in perennial tree genetic research. SSR survey of Citrus sinensis and Citrus maxima were identified perfect SSRs spanning nine chromosomes. Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. We designed and validated a class I SSRs in the C. sinensis and C. maxima genome through electronic polymerase chain reaction (ePCR) and found 83.89% in C. sinensis and 78.52% in C. maxima SSRs producing a single amplicon. Then, we selected extremely variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across seven draft genomes of citrus, which provided us a subset of 84.74% in C. sinensis and 77.53% in C. maxima highly polymorphic SSRs. Out of these, 129 primers were validated on 24 citrus genotypes through wet-lab experiment. We found 127 (98.45%) polymorphic HvSSRs on 24 genotypes. The utility of the developed HvSSRs was demonstrated by analysing genetic diversity of 181 citrus genotypes using 17 HvSSRs spanning nine citrus chromosomes and were divided into 11 main groups through 17 HvSSRs. These chromosome-specific SSRs will serve as a powerful genomic tool used for future QTL mapping, molecular breeding, investigation of population genetic diversity, comparative mapping, and evolutionary studies among citrus and other relative genera/species.
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Affiliation(s)
- Jagveer Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
- Department of Fruit Science, College of Horticulture & Forestry, Acharya Narendra Deva University of Agricultural & Technology, Kumarganj, 224229, India
| | - Ankush Sharma
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Vishal Sharma
- National Agri-Food Biotechnology Institute, Sector-81, SAS Nagar, Mohali, Punjab, 140308, India
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, 173229, India
| | - Popat Nanaso Gaikwad
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Gurupkar Singh Sidhu
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Gurwinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Nimarpreet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Taveena Jindal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - H S Rattanpal
- Department of Fruit Science, Punjab Agricultural University, Ludhiana, 141004, India
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Reuse of Food Waste: The Chemical Composition and Health Properties of Pomelo ( Citrus maxima) Cultivar Essential Oils. Molecules 2022; 27:molecules27103273. [PMID: 35630750 PMCID: PMC9146573 DOI: 10.3390/molecules27103273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022] Open
Abstract
The aim of the present study is to investigate the chemical profile, antioxidant activity, carbohydrate-hydrolysing enzyme inhibition, and hypolipidemic effect of essential oils (EOs) extracted from Sicilian Citrus maxima (pomelo) flavedo. Using gas-chromatography-mass spectrometry analysis (GC-MS) we analysed the Eos of five cultivars of C. maxima, namely, ‘Chadock’, ‘Maxima’, ‘Pyriformis’, ‘Terracciani’, and ‘Todarii’, and their blends. The antioxidant activity was performed by using a multi-target approach using 2,2′-Azino-Bis-3-Ethylbenzothiazoline-6-Sulfonic acid (ABTS), 2,2-Diphenyl-1-picrylhydrazyl (DPPH), ferric reducing ability power (FRAP), and β-carotene bleaching tests. The α-amylase, α-glucosidase, and lipase-inhibitory activities were also assessed. GC-MS analyses revealed D-limonene as the main monoterpene hydrocarbon in all cultivars, albeit with different percentages in the range of 21.72–71.13%. A good content of oxygenated monoterpenes was detected for all cultivars, especially for ‘Todarii’. The analysis of the principal components (PCA), and related clusters (HCA), was performed to find chemo-diversity among the analysed samples. EOs from ‘Chadock’ and ‘Maxima’ were statistically similar to each other, and they differed from P3 in the smaller amount of sesquiterpene hydrocarbons, while the oils from ‘Terracciani’ and ‘Todarii’ were found to be chemically and statistically different. ‘Chadock’ EO was the most active to scavenge radicals (IC50 values of 22.24 and 27.23 µg/mL in ABTS and DPPH tests, respectively). ‘Terracciani’ EO was the most active against both lipase and α-amylase, whereas the blends obtained by the combination (1:1 v/v) of C. maxima ‘Maxima’ + ‘Todarii’ were the most active against α-glucosidase. Generally, the blends did not exert a unique behaviour in potentiating or reducing the bioactivity of the pomelo EOs.
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Clery RA, Armendi A, Franco V, Furrer S, Genereux JC, Kahn TL, Koshiro K. Chemical Diversity of Citrus Leaf Essential Oils. Chem Biodivers 2022; 19:e202100963. [DOI: 10.1002/cbdv.202100963] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/20/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Robin A Clery
- Givaudan Schweiz AG: Givaudan Suisse SA Science & Technology Kemptpark 50 8310 Kemptthal SWITZERLAND
| | - Anjo Armendi
- University of California Riverside Chemistry 501 Big Springs Road 92521 Riverside UNITED STATES
| | - Veronica Franco
- University of California Riverside Chemistry 501 Big Springs Road 92521 Riverside UNITED STATES
| | - Stefan Furrer
- Givaudan Flavors Corp Cincinnati Science & Technology 1199 Edison Drive 45216 Cincinnati UNITED STATES
| | - Joseph C. Genereux
- University of California Riverside Chemistry 501 Big Springs Road 92521 Riverside UNITED STATES
| | - Tracy L. Kahn
- University of California Riverside Department of Botany and Plant Sciences Department of Botany and Plant SciencesUniversity of California at Riverside 92521 Riverside UNITED STATES
| | - Kevin Koshiro
- University of California Riverside Chemistry 501 Big Springs Road 92521 Riverside UNITED STATES
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Noda T, Daiou K, Mihara T, Nagano Y. Potential application of simple easy-to-use insertion-deletion (InDel) markers in citrus cultivar identification. BREEDING SCIENCE 2021; 71:601-608. [PMID: 35087324 PMCID: PMC8784345 DOI: 10.1270/jsbbs.21021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/09/2021] [Indexed: 05/27/2023]
Abstract
We previously developed insertion-deletion (InDel) markers that distinguish three genotypes (two homozygous and one heterozygous) of diverse citrus cultivars. These InDel markers were codominant and could be clearly detected by using simple agarose gel electrophoresis. We sought to establish a method for cultivar identification using these 28 InDel markers to genotype 31 citrus cultivars. The results revealed that a minimum of 6 markers were required to identify individuals using the three-genotype classification method. Furthermore, we found that a simple method for distinguishing between two genotypes (homozygous and heterozygous) could be used to identify individuals using a minimum of 7 markers. Our findings provide a basis for the development of simple and rapid citrus cultivar identification methods.
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Affiliation(s)
- Takahiro Noda
- Kumamoto Prefectural Agricultural Research Center, 3801 Sakae, Koshi, Kumamoto 861-1113, Japan
| | - Kaoru Daiou
- Kumamoto Prefectural Agricultural Research Center, 3801 Sakae, Koshi, Kumamoto 861-1113, Japan
| | - Takashi Mihara
- Kumamoto Prefectural Fruit Tree Research Institute, 2566 Toyofuku Matsubase-machi, Uki, Kumamoto 869-0524, Japan
| | - Yukio Nagano
- Analytical Research Center for Experimental Sciences, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
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Chemical Variability of Peel and Leaf Essential Oils in the Citrus Subgenus Papeda (Swingle) and Few Relatives. PLANTS 2021; 10:plants10061117. [PMID: 34073135 PMCID: PMC8227882 DOI: 10.3390/plants10061117] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 12/03/2022]
Abstract
The Papeda Citrus subgenus includes several species belonging to two genetically distinct groups, containing mostly little-exploited wild forms of citrus. However, little is known about the potentially large and novel aromatic diversity contained in these wild citruses. In this study, we characterized and compared the essential oils obtained from peels and leaves from representatives of both Papeda groups, and three related hybrids. Using a combination of GC, GC-MS, and 13C-NMR spectrometry, we identified a total of 60 compounds in peel oils (PO), and 76 compounds in leaf oils (LO). Limonene was the major component in almost all citrus PO, except for C. micrantha and C. hystrix, where β-pinene dominated (around 35%). LO composition was more variable, with different major compounds among almost all samples, except for two citrus pairs: C. micrantha/C. hystrix and two accessions of C. ichangensis. In hybrid relatives, the profiles were largely consistent with their Citrus/Papeda parental lineage. This high chemical diversity, not only among the sections of the subgenus Papeda, but also between species and even at the intraspecific level, suggests that Papeda may be an important source of aroma diversity for future experimental crosses with field crop species.
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Garcia-Lor A, Bermejo A, Morales J, Hernández M, Medina A, Cuenca J, Navarro L, Aleza P. Strategies to Produce Grapefruit-Like Citrus Varieties With a Low Furanocoumarin Content and Distinctive Flavonoid Profiles. FRONTIERS IN PLANT SCIENCE 2021; 12:640512. [PMID: 33719319 PMCID: PMC7943927 DOI: 10.3389/fpls.2021.640512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Pummelos and hybrids, such as grapefruits, have high furanocoumarin and low flavonoid contents. Furanocoumarins interact negatively with certain drugs, while flavonoids are antioxidant compounds with health benefits. To obtain new grapefruit-like varieties with low furanocoumarin and high flavonoid contents, diploid and triploid hybrid populations from crosses between diploid and tetraploid "Clemenules" clementine and diploid "Pink" pummelo were recovered and analyzed. With regard to furanocoumarins, triploids produce less bergapten, bergamottin and 6,7-DHB than diploids. Regarding flavonoids, triploids yielded more eriocitrin, narirutin, hesperidin and neohesperidin than diploids, whereas no differences were observed in neoeriocitrin and naringin. These results indicate that, the strategy to recover triploid hybrids by 4x × 2x crosses is more appropriate than the recovery of diploid hybrids by 2x × 2x crosses for obtaining grapefruit-like varieties of citrus with lower furanocoumarin and higher flavonoid contents.
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Rao MJ, Zuo H, Xu Q. Genomic insights into citrus domestication and its important agronomic traits. PLANT COMMUNICATIONS 2021; 2:100138. [PMID: 33511347 PMCID: PMC7816076 DOI: 10.1016/j.xplc.2020.100138] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/04/2020] [Accepted: 12/25/2020] [Indexed: 05/12/2023]
Abstract
Citrus originated in Southeast Asia, and it has become one of the most important fruit crops worldwide. Citrus has a long and obscure domestication history due to its clonal propagation, long life cycle, wide sexual compatibility, and complex genetic background. As the genomic information of both wild and cultivated citrus becomes available, their domestication history and underlying traits or genes are becoming clear. This review outlines the genomic features of wild and cultivated species. We propose that the reduction of citric acid is a critical trait for citrus domestication. The genetic model representing the change during domestication may be associated with a regulatory complex known as WD-repeat-MYB-bHLH-WRKY (WMBW), which is involved in acidification and anthocyanin accumulation. The reduction in or loss of anthocyanins may be due to a hitchhiking effect of fruit acidity selection, in which mutation occurs in the common regulator of these two pathways in some domesticated types. Moreover, we have summarized the domestication traits and candidate genes for breeding purposes. This review represents a comprehensive summary of the genes controlling key traits of interest, such as acidity, metabolism, and disease resistance. It also sheds light on recent advances in early flowering from transgenic studies and provides a new perspective for fast breeding of citrus. Our review lays a foundation for future research on fruit acidity, flavor, and disease resistance in citrus.
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Affiliation(s)
- Muhammad Junaid Rao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Key Laboratory of Horticultural Plant Biology (Ministry of Education) Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Hao Zuo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Key Laboratory of Horticultural Plant Biology (Ministry of Education) Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Qiang Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Key Laboratory of Horticultural Plant Biology (Ministry of Education) Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
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Mendes S, Régis T, Terol J, Soares Filho WDS, Talon M, Pedrosa-Harand A. Integration of mandarin ( Citrus reticulata) cytogenetic map with its genome sequence. Genome 2020; 63:437-444. [PMID: 32758104 DOI: 10.1139/gen-2020-0046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Citrus is an extremely important genus in terms of world fruit production. Despite its economic importance and the small genome sizes of its species (2n = 18, 1C = 430 ± 68 Mbp), entire genomic assemblies have only recently become available for some of its representatives. Together with the previous CMA/DAPI banding and fluorescence in situ hybridization (FISH) in the group, these data are important for understanding the complex relationships between its species and for assisting breeding programs. To anchor genomic data with the cytogenetic map of mandarin (Citrus reticulata), the parental species of several economically important hybrids such as sweet orange and clementine, 18 BAC (bacterial artificial chromosome) clones were used. Eleven clementine BACs were positioned by BAC-FISH, doubling the number of chromosome markers so far available for BAC-FISH in citrus. Additionally, six previously mapped BACs were end-sequenced, allowing, together with one BAC previously sequenced, their assignment to scaffolds and the subsequent integration of chromosomes and the genome assembly. This study therefore established correlations between mandarin scaffolds and chromosomes, allowing further structural genomic and comparative study with the sweet orange genome, as well as insights into the chromosomal evolution of the group.
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Affiliation(s)
- Sandra Mendes
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil
| | - Thallita Régis
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | | | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Andrea Pedrosa-Harand
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, Recife, PE, Brazil
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Garavello M, Cuenca J, Garcia-Lor A, Ortega N, Navarro L, Ollitrault P, Aleza P. Male and female inheritance patterns in tetraploid 'Moncada' mandarin. PLANT CELL REPORTS 2020; 39:335-349. [PMID: 31781856 PMCID: PMC7018676 DOI: 10.1007/s00299-019-02494-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/20/2019] [Indexed: 05/11/2023]
Abstract
KEY MESSAGE Tetraploid `Moncada´ mandarin, used as male and female in interploidy hybridizations, displays mainly tetrasomic inheritance for most LGs, with slight variations according to the direction of the crossing. Triploid-breeding programs in citrus are key tool to develop seedless cultivars. Obtaining triploid citrus hybrids may be achieved through different strategies, such as the exploitation of female unreduced gamete in crosses between diploid parents and diploid by tetraploid sexual hybridizations, in which tetraploid genotypes can be used as male or female parents. Genetic configuration of triploid populations from interploid crosses greatly depends on the chromosomic segregation mode of the tetraploid parent used. Here, we have analyzed the inheritance of the tetraploid 'Moncada' mandarin and compared the genetic structures of the resulting gametes when used as male and as female parent. The preferential chromosome pairing rate is calculated from the parental heterozygosity restitution (PHR) of codominant molecular markers, indicating the proportion between disomic and tetrasomic segregation. Tetraploid 'Moncada' both as female and male parent largely exhibited tetrasomic segregation. However, as female parent, one linkage group (LG8) showed intermediate segregation with tendency towards tetrasomic inheritance, while another linkage group (LG4) evidenced a clear intermediate segregation. On the other hand, when used as male parent two linkage groups (LG5 and LG6) showed values that fit an intermediate inheritance model with tetrasomic tendency. Significant doubled reduction (DR) rates were observed in five linkage groups as female parent, and in six linkage groups as male parent. The new knowledge generated here will serve to define crossing strategies in citrus improvement programs to efficiently obtain new varieties of interest in the global fresh consumption market.
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Affiliation(s)
- Miguel Garavello
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315, km 10.7, Moncada, 46113, Valencia, Spain
- INTA, Concordia Agricultural Experiment Station, 3200, Concordia, CC 34, Entre Ríos, Argentina
| | - José Cuenca
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315, km 10.7, Moncada, 46113, Valencia, Spain
| | - Andrés Garcia-Lor
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315, km 10.7, Moncada, 46113, Valencia, Spain
| | - Neus Ortega
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315, km 10.7, Moncada, 46113, Valencia, Spain
| | - Luis Navarro
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315, km 10.7, Moncada, 46113, Valencia, Spain
| | - Patrick Ollitrault
- Unité Mixte de Recherche, Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Corse, 20230, San Giuliano, France.
| | - Pablo Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera CV-315, km 10.7, Moncada, 46113, Valencia, Spain.
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12
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Alves MN, Lopes SA, Raiol-Junior LL, Wulff NA, Girardi EA, Ollitrault P, Peña L. Resistance to ' Candidatus Liberibacter asiaticus,' the Huanglongbing Associated Bacterium, in Sexually and/or Graft-Compatible Citrus Relatives. FRONTIERS IN PLANT SCIENCE 2020; 11:617664. [PMID: 33488659 PMCID: PMC7820388 DOI: 10.3389/fpls.2020.617664] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/10/2020] [Indexed: 05/14/2023]
Abstract
Huanglongbing (HLB) is the most destructive, yet incurable disease of citrus. Finding sources of genetic resistance to HLB-associated 'Candidatus Liberibacter asiaticus' (Las) becomes strategic to warrant crop sustainability, but no resistant Citrus genotypes exist. Some Citrus relatives of the family Rutaceae, subfamily Aurantioideae, were described as full-resistant to Las, but they are phylogenetically far, thus incompatible with Citrus. Partial resistance was indicated for certain cross-compatible types. Moreover, other genotypes from subtribe Citrinae, sexually incompatible but graft-compatible with Citrus, may provide new rootstocks able to restrict bacterial titer in the canopy. Use of seedlings from monoembryonic species and inconsistencies in previous reports likely due to Las recalcitrance encouraged us to evaluate more accurately these Citrus relatives. We tested for Las resistance a diverse collection of graft-compatible Citrinae species using an aggressive and consistent challenge-inoculation and evaluation procedure. Most Citrinae species examined were either susceptible or partially resistant to Las. However, Eremocitrus glauca and Papua/New Guinea Microcitrus species as well as their hybrids and those with Citrus arose here for the first time as full-resistant, opening the way for using these underutilized genotypes as Las resistance sources in breeding programs or attempting using them directly as possible new Las-resistant Citrus rootstocks or interstocks.
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Affiliation(s)
| | | | | | | | | | - Patrick Ollitrault
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, BIOS Department, UPR amélioration génétique des espèces à multiplication végétative, Montpellier, France
| | - Leandro Peña
- Fundo de Defesa da Citricultura, Araraquara, Brazil
- Instituto de Biologia Molecular y Celular de Plantas – Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, Spain
- *Correspondence: Leandro Peña, ;
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13
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Garavello M, Cuenca J, Dreissig S, Fuchs J, Navarro L, Houben A, Aleza P. Analysis of Crossover Events and Allele Segregation Distortion in Interspecific Citrus Hybrids by Single Pollen Genotyping. FRONTIERS IN PLANT SCIENCE 2020; 11:615. [PMID: 32523591 PMCID: PMC7261893 DOI: 10.3389/fpls.2020.00615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/21/2020] [Indexed: 05/17/2023]
Abstract
In citrus, a classical method of studying crossovers and segregation distortion (SD) is the genetic analysis of progenies. A new strategy combining fluorescence-activated cell sorting and whole genome amplification of haploid pollen nuclei with a large set of molecular markers, offers the opportunity to efficiently determine the frequency of crossovers and the identification of SD without the need to generate segregating populations. Here we have analyzed meiotic crossover events in a pollen nuclei population from "Eureka" lemon and the allelic SD was evaluated in a pollen nuclei population from a clementine × sweet orange hybrid ("CSO"). Data obtained from the "CSO" pollen nuclei population were compared to those obtained from genotyping of a segregating population ("RTSO") arising from a hand-made sexual hybridization between diploid non apomictic selected tangor (mandarin × sweet orange; "RTO" tangor) as female parent pollinated with "CSO" tangor as male parent. The analysis of crossovers rates on chromosome 1 revealed the presence of up to five crossovers events on one arm and four on the corresponding other arm, with an average of 1.97 crossovers per chromosome while no crossover events were observed in five "Eureka" lemon pollen nuclei. The rate of SD observed in "CSO" pollen nuclei (13.8%) was slightly lower than that recovered in the "RTSO" population (20.7%). In the pollen nuclei population, SD was found on linkage group (LG) 2, while the "RTSO" population showed SD on LGs 2 and 7. Potential male gametic selection mechanisms were distinguished in pollen grains, while in the population, mechanisms of gametophytic selection and/or zygotic selection were observed. This methodology is a very useful tool to facilitate research focused on the reproductive biology of citrus and study the mechanisms that affect crossovers and SD.
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Affiliation(s)
- Miguel Garavello
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
- Concordia Agricultural Experiment Station, National Agricultural Technology Institute, Entre Ríos, Argentina
| | - José Cuenca
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Steven Dreissig
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Jörg Fuchs
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Luis Navarro
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Andreas Houben
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Pablo Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
- *Correspondence: Pablo Aleza,
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14
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Luro F, Viglietti G, Marchi E, Costantino G, Scarpa GM, Tomi F, Paoli M, Curk F, Ollitrault P. Genetic, morphological and chemical investigations reveal the genetic origin of Pompia (C. medica tuberosa Risso & Poiteau) - An old endemic Sardinian citrus fruit. PHYTOCHEMISTRY 2019; 168:112083. [PMID: 31521382 DOI: 10.1016/j.phytochem.2019.112083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/30/2019] [Accepted: 08/03/2019] [Indexed: 06/10/2023]
Abstract
Citrus fruits have been introduced to the Mediterranean area from Asia for centuries and spontaneous crosses have generated several hybrid forms, some of which have had agricultural or industrial success while others have remained niche food or ornamental products, or have disappeared. Pompia (C. medica tuberosa Risso & Poiteau) is an old endemic citrus fruit from Sardinia of unknown genetic origin. Initial phenotypic and molecular characterizations revealed a high degree of similarity with lemon (C. limon (L.) Burm.) and citron (C. medica L.). To identify the ancestors of Pompia, 70 citrus species of the Citrus genus were genotyped with 36 codominant molecular markers (SSR and InDel) of nuclear and cytoplasmic genomes. Diversity analysis and allelic comparisons between each citrus species at each locus indicated that Pompia resembles lemon and limonette of Marrakech, i.e. the result of a cross between sour orange (C. aurantium L.) and citron, where citron was the pollinator. Two Italian citron varieties were identified as potential male parents, i.e. Diamante and Common Poncire. However, we were unable to differentiate varieties of sour oranges because varietal diversification in this horticultural group resulted from DNA sequence variations that SSR or InDel markers could not reveal. Rhob el Arsa and Poncire de Collioure were found to be two synonyms of Pompia. Pompia appeared to be equally distinct from citron, lemon and sour orange based on the overall analysis of the fruit, leaf and seed phenotype, and juice chemical composition. At the leaf level, the Pompia essential oil (EO) composition is close to that of citron whereas the zest is much closer to that of sour orange.
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Affiliation(s)
| | - Grazia Viglietti
- Dipartimento di Agraria Research Unit SACEG, University of Sassari, 07100, Sassari, Italy
| | | | | | - Grazia Maria Scarpa
- Dipartimento di Agraria Research Unit SACEG, University of Sassari, 07100, Sassari, Italy
| | - Felix Tomi
- Université de Corse - CNRS, Equipe Chimie et Biomasse, UMR SPE 6134, 20000 Ajaccio, France
| | - Mathieu Paoli
- Université de Corse - CNRS, Equipe Chimie et Biomasse, UMR SPE 6134, 20000 Ajaccio, France
| | - Franck Curk
- UMR AGAP INRA, Avenue Agropolis 34 398 Montpellier cedex 5, France
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15
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Zhu C, Zheng X, Huang Y, Ye J, Chen P, Zhang C, Zhao F, Xie Z, Zhang S, Wang N, Li H, Wang L, Tang X, Chai L, Xu Q, Deng X. Genome sequencing and CRISPR/Cas9 gene editing of an early flowering Mini-Citrus (Fortunella hindsii). PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2199-2210. [PMID: 31004551 PMCID: PMC6790359 DOI: 10.1111/pbi.13132] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 03/22/2019] [Accepted: 04/14/2019] [Indexed: 05/19/2023]
Abstract
Hongkong kumquat (Fortunella hindsii) is a wild citrus species characterized by dwarf plant height and early flowering. Here, we identified the monoembryonic F. hindsii (designated as 'Mini-Citrus') for the first time and constructed its selfing lines. This germplasm constitutes an ideal model for the genetic and functional genomics studies of citrus, which have been severely hindered by the long juvenility and inherent apomixes of citrus. F. hindsii showed a very short juvenile period (~8 months) and stable monoembryonic phenotype under cultivation. We report the first de novo assembled 373.6 Mb genome sequences (Contig-N50 2.2 Mb and Scaffold-N50 5.2 Mb) for F. hindsii. In total, 32 257 protein-coding genes were annotated, 96.9% of which had homologues in other eight Citrinae species. The phylogenomic analysis revealed a close relationship of F. hindsii with cultivated citrus varieties, especially with mandarin. Furthermore, the CRISPR/Cas9 system was demonstrated to be an efficient strategy to generate target mutagenesis on F. hindsii. The modifications of target genes in the CRISPR-modified F. hindsii were predominantly 1-bp insertions or small deletions. This genetic transformation system based on F. hindsii could shorten the whole process from explant to T1 mutant to about 15 months. Overall, due to its short juvenility, monoembryony, close genetic background to cultivated citrus and applicability of CRISPR, F. hindsii shows unprecedented potentials to be used as a model species for citrus research.
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Affiliation(s)
- Chenqiao Zhu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)Huazhong Agricultural UniversityWuhanChina
| | - Xiongjie Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)Huazhong Agricultural UniversityWuhanChina
| | - Yue Huang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)Huazhong Agricultural UniversityWuhanChina
| | - Junli Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)Huazhong Agricultural UniversityWuhanChina
| | - Peng Chen
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)Huazhong Agricultural UniversityWuhanChina
| | - Chenglei Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)Huazhong Agricultural UniversityWuhanChina
| | - Fei Zhao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)Huazhong Agricultural UniversityWuhanChina
| | - Zongzhou Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)Huazhong Agricultural UniversityWuhanChina
| | - Siqi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)Huazhong Agricultural UniversityWuhanChina
| | - Nan Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)Huazhong Agricultural UniversityWuhanChina
| | - Hang Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)Huazhong Agricultural UniversityWuhanChina
| | - Lun Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)Huazhong Agricultural UniversityWuhanChina
| | - Xiaomei Tang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)Huazhong Agricultural UniversityWuhanChina
| | - Lijun Chai
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)Huazhong Agricultural UniversityWuhanChina
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)Huazhong Agricultural UniversityWuhanChina
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education)Huazhong Agricultural UniversityWuhanChina
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16
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do Amaral M, Barbosa de Paula MF, Ollitrault F, Rivallan R, de Andrade Silva EM, da Silva Gesteira A, Luro F, Garcia D, Ollitrault P, Micheli F. Phylogenetic Origin of Primary and Secondary Metabolic Pathway Genes Revealed by C. maxima and C. reticulata Diagnostic SNPs. FRONTIERS IN PLANT SCIENCE 2019; 10:1128. [PMID: 31608086 PMCID: PMC6771394 DOI: 10.3389/fpls.2019.01128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/15/2019] [Indexed: 06/10/2023]
Abstract
Modern cultivated Citrus species and varieties result from interspecific hybridization between four ancestral taxa. Among them, Citrus maxima and Citrus reticulata, closely associated with the pummelo and mandarin horticultural groups, respectively, were particularly important as the progenitors of sour and sweet oranges (Citrus aurantium and Citrus sinensis), grapefruits (Citrus paradisi), and hybrid types resulting from modern breeding programs (tangors, tangelos, and orangelos). The differentiation between the four ancestral taxa and the phylogenomic structure of modern varieties widely drive the phenotypic diversity's organization. In particular, strong phenotypic differences exist in the coloration and sweetness and represent important criteria for breeders. In this context, focusing on the genes of the sugar, carotenoid, and chlorophyll biosynthesis pathways, the aim of this work was to develop a set of diagnostic single-nucleotide polymorphism (SNP) markers to distinguish the ancestral haplotypes of C. maxima and C. reticulata and to provide information at the intraspecific diversity level (within C. reticulata or C. maxima). In silico analysis allowed the identification of 3,347 SNPs from selected genes. Among them, 1,024 were detected as potential differentiation markers between C. reticulata and C. maxima. A total of 115 SNPs were successfully developed using a competitive PCR technology. Their transferability among all Citrus species and the true citrus genera was very good, with only 0.87% of missing data. The ancestral alleles of the SNPs were identified, and we validated the usefulness of the developed markers for tracing the ancestral haplotype in large germplasm collections and sexually recombined progeny issued from the C. reticulata/C. maxima admixture gene pool. These markers will pave the way for targeted association studies based on ancestral haplotypes.
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Affiliation(s)
- Milena do Amaral
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas (DCB), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
| | - Marcia Fabiana Barbosa de Paula
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas (DCB), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
| | | | | | - Edson Mario de Andrade Silva
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas (DCB), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
| | | | | | | | | | - Fabienne Micheli
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas (DCB), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
- CIRAD, UMR AGAP, Montpellier, France
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17
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Ahmed D, Comte A, Curk F, Costantino G, Luro F, Dereeper A, Mournet P, Froelicher Y, Ollitrault P. Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus. ANNALS OF BOTANY 2019; 123:1231-1251. [PMID: 30924905 PMCID: PMC6612944 DOI: 10.1093/aob/mcz029] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/17/2019] [Accepted: 02/18/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS Reticulate evolution, coupled with reproductive features limiting further interspecific recombinations, results in admixed mosaics of large genomic fragments from the ancestral taxa. Whole-genome sequencing (WGS) data are powerful tools to decipher such complex genomes but still too costly to be used for large populations. The aim of this work was to develop an approach to infer phylogenomic structures in diploid, triploid and tetraploid individuals from sequencing data in reduced genome complexity libraries. The approach was applied to the cultivated Citrus gene pool resulting from reticulate evolution involving four ancestral taxa, C. maxima, C. medica, C. micrantha and C. reticulata. METHODS A genotyping by sequencing library was established with the restriction enzyme ApeKI applying one base (A) selection. Diagnostic single nucleotide polymorphisms (DSNPs) for the four ancestral taxa were mined in 29 representative varieties. A generic pipeline based on a maximum likelihood analysis of the number of read data was established to infer ancestral contributions along the genome of diploid, triploid and tetraploid individuals. The pipeline was applied to 48 diploid, four triploid and one tetraploid citrus accessions. KEY RESULTS Among 43 598 mined SNPs, we identified a set of 15 946 DSNPs covering the whole genome with a distribution similar to that of gene sequences. The set efficiently inferred the phylogenomic karyotype of the 53 analysed accessions, providing patterns for common accessions very close to that previously established using WGS data. The complex phylogenomic karyotypes of 21 cultivated citrus, including bergamot, triploid and tetraploid limes, were revealed for the first time. CONCLUSIONS The pipeline, available online, efficiently inferred the phylogenomic structures of diploid, triploid and tetraploid citrus. It will be useful for any species whose reproductive behaviour resulted in an interspecific mosaic of large genomic fragments. It can also be used for the first generations of interspecific breeding schemes.
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Affiliation(s)
- Dalel Ahmed
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, San Giuliano, France
| | - Aurore Comte
- IRD, CIRAD, Université de Montpellier, IPME, Montpellier, France
- South Green Bioinformatics Platform, Bioversity, CIRAD, INRA, IRD, Montpellier, France
| | - Franck Curk
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Gilles Costantino
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, San Giuliano, France
| | - François Luro
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, San Giuliano, France
| | - Alexis Dereeper
- IRD, CIRAD, Université de Montpellier, IPME, Montpellier, France
- South Green Bioinformatics Platform, Bioversity, CIRAD, INRA, IRD, Montpellier, France
| | - Pierre Mournet
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
- CIRAD, UMR AGAP, Montpellier, France
| | - Yann Froelicher
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
- CIRAD, UMR AGAP, San Giuliano, France
| | - Patrick Ollitrault
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
- CIRAD, UMR AGAP, San Giuliano, France
- For correspondence. E-mail
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18
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De Ollas C, Morillón R, Fotopoulos V, Puértolas J, Ollitrault P, Gómez-Cadenas A, Arbona V. Facing Climate Change: Biotechnology of Iconic Mediterranean Woody Crops. FRONTIERS IN PLANT SCIENCE 2019; 10:427. [PMID: 31057569 PMCID: PMC6477659 DOI: 10.3389/fpls.2019.00427] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 03/21/2019] [Indexed: 05/03/2023]
Abstract
The Mediterranean basin is especially sensitive to the adverse outcomes of climate change and especially to variations in rainfall patterns and the incidence of extremely high temperatures. These two concurring adverse environmental conditions will surely have a detrimental effect on crop performance and productivity that will be particularly severe on woody crops such as citrus, olive and grapevine that define the backbone of traditional Mediterranean agriculture. These woody species have been traditionally selected for traits such as improved fruit yield and quality or alteration in harvesting periods, leaving out traits related to plant field performance. This is currently a crucial aspect due to the progressive and imminent effects of global climate change. Although complete genome sequence exists for sweet orange (Citrus sinensis) and clementine (Citrus clementina), olive tree (Olea europaea) and grapevine (Vitis vinifera), the development of biotechnological tools to improve stress tolerance still relies on the study of the available genetic resources including interspecific hybrids, naturally occurring (or induced) polyploids and wild relatives under field conditions. To this respect, post-genomic era studies including transcriptomics, metabolomics and proteomics provide a wide and unbiased view of plant physiology and biochemistry under adverse environmental conditions that, along with high-throughput phenotyping, could contribute to the characterization of plant genotypes exhibiting physiological and/or genetic traits that are correlated to abiotic stress tolerance. The ultimate goal of precision agriculture is to improve crop productivity, in terms of yield and quality, making a sustainable use of land and water resources under adverse environmental conditions using all available biotechnological tools and high-throughput phenotyping. This review focuses on the current state-of-the-art of biotechnological tools such as high throughput -omics and phenotyping on grapevine, citrus and olive and their contribution to plant breeding programs.
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Affiliation(s)
- Carlos De Ollas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
| | - Raphaël Morillón
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Petit-Bourg, France
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Jaime Puértolas
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Patrick Ollitrault
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), San-Giuliano, France
| | - Aurelio Gómez-Cadenas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Castellón de la Plana, Spain
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19
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Garavello M, Cuenca J, Dreissig S, Fuchs J, Houben A, Aleza P. Assessing Ploidy Level Analysis and Single Pollen Genotyping of Diploid and Euploid Citrus Genotypes by Fluorescence-Activated Cell Sorting and Whole-Genome Amplification. FRONTIERS IN PLANT SCIENCE 2019; 10:1174. [PMID: 31611896 PMCID: PMC6769063 DOI: 10.3389/fpls.2019.01174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 08/27/2019] [Indexed: 05/06/2023]
Abstract
Flow cytometry is widely used to determine genome size and ploidy level in plants. This technique, when coupled with fluorescence-activated cell sorting (FACS), whole genome amplification and genotyping (WGA), opens up new opportunities for genetic studies of individualized nuclei. This strategy was used to analyze the genetic composition of single pollen nuclei of different citrus species. The flow cytometry and microscope observations allowed us to differentiate the populations of pollen nuclei present in the diploid and euploid genotypes analyzed, showing that citrus has binuclear pollen. We have identified in the "CSO" tangor an additional nuclei population composed by the vegetative plus generative nuclei. Genotyping of this nuclei population revealed that vegetative and generative nuclei show the same genetic configuration. In addition, we have demonstrated the presence of unreduced gametes in the diploid genotype "Mexican lime." Genomic amplification is a robust method for haploid nuclei genotyping with several molecular markers, whereas in diploid nuclei using heterozygous markers showed a bias towards one of the two alleles, limiting the use of this tool in this type of nuclei. We further discuss the importance and applications of single pollen genotyping in citrus genetic studies.
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Affiliation(s)
- Miguel Garavello
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
- INTA, Concordia Agricultural Experiment Station, Concordia, Argentina
| | - José Cuenca
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Steven Dreissig
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jörg Fuchs
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Andreas Houben
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Pablo Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
- *Correspondence: Pablo Aleza,
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20
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Ruiz M, Pensabene-Bellavia G, Quiñones A, García-Lor A, Morillon R, Ollitrault P, Primo-Millo E, Navarro L, Aleza P. Molecular Characterization and Stress Tolerance Evaluation of New Allotetraploid Somatic Hybrids Between Carrizo Citrange and Citrus macrophylla W. rootstocks. FRONTIERS IN PLANT SCIENCE 2018; 9:901. [PMID: 30123223 PMCID: PMC6085489 DOI: 10.3389/fpls.2018.00901] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/07/2018] [Indexed: 05/18/2023]
Abstract
Polyploidy is one of the main forces that drives the evolution of plants and provides great advantages for breeding. Somatic hybridization by protoplast fusion is used in citrus breeding programs. This method allows combining the whole parental genomes in a single genotype, adding complementary dominant characters, regardless of parental heterozygosity. It also contributes to surpass limitations imposed by reproductive biology and quickly generates progenies that combine the required traits. Two allotetraploid somatic hybrids recovered from the citrus rootstocks-Citrus macrophylla (CM) and Carrizo citrange (CC)-were characterized for morphology, genome composition using molecular markers (SNP, SSR, and InDel), and their tolerance to iron chlorosis, salinity, and Citrus tristeza virus (CTV). Both hybrids combine the whole parental genomes even though the loss of parental alleles was detected in most linkage groups. Mitochondrial genome was inherited from CM in both the hybrids, whereas recombination was observed for chloroplastic genome. Thus, somatic hybrids differ from each other in their genome composition, indicating that losses and rearrangements occurred during the fusion process. Both inherited the tolerance to stem pitting caused by CTV from CC, are tolerant to iron chlorosis such as CM, and have a higher tolerance to salinity than the sensitive CC. These hybrids have potential as improved rootstocks to grow citrus in areas with calcareous and saline soils where CTV is present, such as the Mediterranean region. The provided knowledge on the effects of somatic hybridization on the genome composition, anatomy, and physiology of citrus rootstocks will be key for breeding programs that aim to address current and future needs of the citrus industry.
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Affiliation(s)
- Marta Ruiz
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Giovanni Pensabene-Bellavia
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Ana Quiñones
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Andrés García-Lor
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Raphaël Morillon
- UMR AGAP, Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Montpellier, France
| | - Patrick Ollitrault
- UMR AGAP, Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Montpellier, France
| | - Eduardo Primo-Millo
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Luis Navarro
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Pablo Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
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Yu H, Wang X, Lu Z, Xu Y, Deng X, Xu Q. Endogenous pararetrovirus sequences are widely present in Citrinae genomes. Virus Res 2018; 262:48-53. [PMID: 29792903 DOI: 10.1016/j.virusres.2018.05.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 05/20/2018] [Accepted: 05/20/2018] [Indexed: 01/04/2023]
Abstract
Endogenous pararetroviruses (EPRVs) are characterized in several plant genomes and their biological effects have been reported. In this study, hundreds of EPRV segments were identified in six Citrinae genomes. A total of 1034 EPRV segments were identified in the genomes of sweet orange, 2036 in pummelo, 598 in clementine mandarin, 752 in Ichang papeda, 2060 in citron and 245 in atalantia. Genomic analysis indicated that EPRV segments tend to cluster as hot spots in the genomes, particularly on chromosome 2 and 5. Large numbers of simple repeats and transposable elements were identified in the 2-kb flanking regions of the EPRV segments. Comparative genomic analysis and PCR experiments showed that there are highly conserved EPRV segments and species-specific EPRV segments between the Citrinae genomes. Phylogenetic analysis suggested that the integration events of EPRVs could initiate in a common progenitor of Citrinae species and repeatedly occur during the Citrinae divergence.
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Affiliation(s)
- Huiwen Yu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Xia Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Zhihao Lu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Yuantao Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China.
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22
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Rouiss H, Bakry F, Froelicher Y, Navarro L, Aleza P, Ollitrault P. Origin of C. latifolia and C. aurantiifolia triploid limes: the preferential disomic inheritance of doubled-diploid 'Mexican' lime is consistent with an interploid hybridization hypothesis. ANNALS OF BOTANY 2018; 121:571-585. [PMID: 29293884 PMCID: PMC5838810 DOI: 10.1093/aob/mcx179] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/14/2017] [Indexed: 05/23/2023]
Abstract
Background and Aims Two main types of triploid limes are produced worldwide. The 'Tahiti' lime type (Citrus latifolia) is predominant, while the 'Tanepao' type (C. aurantiifolia) is produced to a lesser extent. Both types result from natural interspecific hybridization involving a diploid gamete of C. aurantiifolia 'Mexican' lime type (itself a direct interspecific C. micrantha × C. medica hybrid). The meiotic behaviour of a doubled-diploid 'Mexican' lime, the interspecific micrantha/medica recombination and the resulting diploid gamete structures were analysed to investigate the possibility that 'Tahiti' and 'Tanepao' varieties are derived from natural interploid hybridization. Methods A population of 85 tetraploid hybrids was established between a doubled-diploid clementine and a doubled-diploid 'Mexican' lime and used to infer the genotypes of 'Mexican' lime diploid gametes. Meiotic behaviour was studied through combined segregation analysis of 35 simple sequenbce repeat (SSR) and single nucleotide polymorphismn (SNP) markers covering the nine citrus chromosomes and cytogenetic studies. It was supplemented by pollen viability assessment. Key Results Pollen viability of the doubled-diploid Mexican lime (64 %) was much higher than that of the diploid. On average, 65 % of the chromosomes paired as bivalents and 31.4 % as tetravalents. Parental heterozygosity restitution ranged from 83 to 99 %. Disomic inheritance with high preferential pairing values was deduced for three chromosomes. Intermediate inheritances, with disomic trend, were found for five chromosomes, and an intermediate inheritance was observed for one chromosome. The average effective interspecific recombination rate was low (1.2 cM Mb-1). Conclusion The doubled-diploid 'Mexican' lime had predominantly disomic segregation, producing interspecific diploid gamete structures with high C. medica/C. micrantha heterozygosity, compatible with the phylogenomic structures of triploid C. latifolia and C. aurantiifolia varieties. This disomic trend limits effective interspecific recombination and diversity of the diploid gamete population. Interploid reconstruction breeding using doubled-diploid lime as one parent is a promising approach for triploid lime diversification.
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Affiliation(s)
- H Rouiss
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Petit-Bourg, Guadeloupe, France
| | - F Bakry
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
| | - Y Froelicher
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), San Giuliano, Corse, France
| | - L Navarro
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - P Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - P Ollitrault
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Petit-Bourg, Guadeloupe, France
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23
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Oueslati A, Salhi-Hannachi A, Luro F, Vignes H, Mournet P, Ollitrault P. Genotyping by sequencing reveals the interspecific C. maxima / C. reticulata admixture along the genomes of modern citrus varieties of mandarins, tangors, tangelos, orangelos and grapefruits. PLoS One 2017; 12:e0185618. [PMID: 28982157 PMCID: PMC5628881 DOI: 10.1371/journal.pone.0185618] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 09/15/2017] [Indexed: 11/19/2022] Open
Abstract
The mandarin horticultural group is an important component of world citrus production for the fresh fruit market. This group formerly classified as C. reticulata is highly polymorphic and recent molecular studies have suggested that numerous cultivated mandarins were introgressed by C. maxima (the pummelos). C. maxima and C. reticulata are also the ancestors of sweet and sour oranges, grapefruit, and therefore of all the "small citrus" modern varieties (mandarins, tangors, tangelos) derived from sexual hybridization between these horticultural groups. Recently, NGS technologies have greatly modified how plant evolution and genomic structure are analyzed, moving from phylogenetics to phylogenomics. The objective of this work was to develop a workflow for phylogenomic inference from Genotyping By Sequencing (GBS) data and to analyze the interspecific admixture along the nine citrus chromosomes for horticultural groups and recent varieties resulting from the combination of the C. reticulata and C. maxima gene pools. A GBS library was established from 55 citrus varieties, using the ApekI restriction enzyme and selective PCR to improve the read depth. Diagnostic polymorphisms (DPs) of C. reticulata/C. maxima differentiation were identified and used to decipher the phylogenomic structure of the 55 varieties. The GBS approach was powerful and revealed 30,289 SNPs and 8,794 Indels with 12.6% of missing data. 11,133 DPs were selected covering the nine chromosomes with a higher density in genic regions. GBS combined with the detection of DPs was powerful for deciphering the "phylogenomic karyotypes" of cultivars derived from admixture of the two ancestral species after a limited number of interspecific recombinations. All the mandarins, mandarin hybrids, tangelos and tangors analyzed displayed introgression of C. maxima in different parts of the genome. C. reticulata/C. maxima admixture should be a major component of the high phenotypic variability of this germplasm opening up the way for association studies based on phylogenomics.
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Affiliation(s)
- Amel Oueslati
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis (FST), Université de Tunis El Manar, Tunis, Tunisia
- AGAP Research Unit, Centre de coopération Internationale en Recherche Agronomique pour le Développement Petit-Bourg, Guadeloupe, France
| | - Amel Salhi-Hannachi
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis (FST), Université de Tunis El Manar, Tunis, Tunisia
| | - François Luro
- AGAPResearch Unit, Institut National de la Recherche Agronomique, San Giuliano, France
| | - Hélène Vignes
- AGAP Research Unit, Centre de coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - Pierre Mournet
- AGAP Research Unit, Centre de coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - Patrick Ollitrault
- AGAP Research Unit, Centre de coopération Internationale en Recherche Agronomique pour le Développement Petit-Bourg, Guadeloupe, France
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24
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Rouiss H, Cuenca J, Navarro L, Ollitrault P, Aleza P. Unreduced Megagametophyte Production in Lemon Occurs via Three Meiotic Mechanisms, Predominantly Second-Division Restitution. FRONTIERS IN PLANT SCIENCE 2017; 8:1211. [PMID: 28747921 PMCID: PMC5506204 DOI: 10.3389/fpls.2017.01211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 06/27/2017] [Indexed: 05/23/2023]
Abstract
Unreduced (2n) gametes have played a pivotal role in polyploid plant evolution and are useful for sexual polyploid breeding in various species, particularly for developing new seedless citrus varieties. The underlying mechanisms of 2n gamete formation were recently revealed for Citrus reticulata but remain poorly understood for other citrus species, including lemon (C. limon [L.] Burm. f.). Here, we investigated the frequency and causal meiotic mechanisms of 2n megagametophyte production in lemon. We genotyped 48progeny plants of two lemon genotypes, "Eureka Frost" and "Fino", using 16 Simple Sequence Repeat (SSR) and 18 Single Nucleotide Polymorphism (SNP) markers to determine the genetic origin of the progenies and the underlying mechanisms for 2n gamete formation. We utilized a maximum-likelihood method based on parental heterozygosity restitution (PHR) of centromeric markers and analysis of PHR patterns along the chromosome. The frequency of 2n gamete production was 4.9% for "Eureka Frost" and 8.3% for "Fino", with three meiotic mechanisms leading to 2n gamete formation. We performed the maximum-likelihood method at the individual level via centromeric marker analysis, finding that 88% of the hybrids arose from second-division restitution (SDR), 7% from first-division restitution (FDR) or pre-meiotic doubling (PRD), and 5% from post-meiotic genome doubling (PMD). The pattern of PHR along LG1 confirmed that SDR is the main mechanism for 2n gamete production. Recombination analysis between markers in this LG revealed partial chiasma interference on both arms. We discuss the implications of these restitution mechanisms for citrus breeding and lemon genetics.
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Affiliation(s)
- Houssem Rouiss
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones AgrariasMoncada, Valencia, Spain
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Station de RoujolPetit-Bourg, Guadeloupe, France
| | - José Cuenca
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones AgrariasMoncada, Valencia, Spain
| | - Luis Navarro
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones AgrariasMoncada, Valencia, Spain
| | - Patrick Ollitrault
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Station de RoujolPetit-Bourg, Guadeloupe, France
| | - Pablo Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones AgrariasMoncada, Valencia, Spain
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Rivera MJ, Pelz‐Stelinski KS, Martini X, Stelinski LL. Bacterial phytopathogen infection disrupts belowground plant indirect defense mediated by tritrophic cascade. Ecol Evol 2017; 7:4844-4854. [PMID: 28690813 PMCID: PMC5496533 DOI: 10.1002/ece3.3052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 04/16/2017] [Indexed: 12/13/2022] Open
Abstract
Plants can defend themselves against herbivores through activation of defensive pathways and attraction of third-trophic-level predators and parasites. Trophic cascades that mediate interactions in the phytobiome are part of a larger dynamic including the pathogens of the plant itself, which are known to greatly influence plant defenses. As such, we investigated the impact of a phloem-limited bacterial pathogen, Candidatus Liberibacter asiaticus (CLas), in cultivated citrus rootstock on a well-studied belowground tritrophic interaction involving the attraction of an entomopathogenic nematode (EPN), Steinernema diaprepesi, to their root-feeding insect hosts, Diaprepes abbreviatus larvae. Using belowground olfactometers, we show how CLas infection interferes with this belowground interaction by similarly inducing the release of a C12 terpene, pregeijerene, and disconnecting the association of the terpene with insect presence. D. abbreviatus larvae that were not feeding but in the presence of a CLas-infected plant were more likely to be infected by EPN than those near uninfected plants. Furthermore, nonfeeding larvae associated with CLas-infected plants were just as likely to be infected by EPN as those near noninfected plants with D. abbreviatus larval damage. Larvae of two weevil species, D. abbreviatus and Pachnaeus litus, were also more attracted to plants with infection than to uninfected plants. D. abbreviatus larvae were most active when exposed to pregeijerene at a concentration of 0.1 μg/μl. We attribute this attraction to CLas-infected plants to the same signal previously thought to be a herbivore-induced plant volatile specifically induced by root-feeding insects, pregeijerene, by assessing volatiles collected from the roots of infected plants and uninfected plants with and without feeding D. abbreviatus. Synthesis. Phytopathogens can influence the structuring of soil communities extending to the third trophic level. Field populations of EPN may be less effective at host-finding using pregeijerene as a cue in citrus grove agroecosystems with high presence of CLas infection.
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Affiliation(s)
- Monique J. Rivera
- Entomology and Nematology DepartmentCitrus Research and Education CenterUniversity of FloridaLake AlfredFLUSA
| | - Kirsten S. Pelz‐Stelinski
- Entomology and Nematology DepartmentCitrus Research and Education CenterUniversity of FloridaLake AlfredFLUSA
| | - Xavier Martini
- Entomology and Nematology DepartmentCitrus Research and Education CenterUniversity of FloridaLake AlfredFLUSA
- Entomology and Nematology DepartmentNorth Florida Research and Education CenterUniversity of FloridaQuincyFLUSA
| | - Lukasz L. Stelinski
- Entomology and Nematology DepartmentCitrus Research and Education CenterUniversity of FloridaLake AlfredFLUSA
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26
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Cirmi S, Maugeri A, Ferlazzo N, Gangemi S, Calapai G, Schumacher U, Navarra M. Anticancer Potential of Citrus Juices and Their Extracts: A Systematic Review of Both Preclinical and Clinical Studies. Front Pharmacol 2017; 8:420. [PMID: 28713272 PMCID: PMC5491624 DOI: 10.3389/fphar.2017.00420] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 06/14/2017] [Indexed: 01/16/2023] Open
Abstract
Background: During the last decades, a huge body of evidence has been accumulated suggesting that Citrus fruits and their juices might have a role in preventing many diseases including cancer. Objective: To summarize the numerous evidences on the potential of Citrus juices and their extracts as anticancer agents. Data sources: A systematic review of articles written in English using MEDLINE (1946-present), EMBASE (1974-present) and Web of Sciences (1970-present) was performed independently by two reviewers. Search terms included Citrus, Citrus aurantifolia, Citrus sinensis, Citrus paradisi, Citrus fruits, Citrus fruits extract, cancer, neoplasm, neoplasia, tumor, metastasis, carcinogenesis, proliferation. The last search was performed on March 16th, 2017. Study selection: Study selection and systematic review were carried out in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. Prior to the beginning of the review, Authors defined a checklist for inclusion criteria, thus including articles which meet the following: (i) published on peer-reviewed scientific journals; (ii) Citrus juice used alone; (iii) extracts derived from Citrus juice; (iii) for preclinical studies, an exposure time to Citrus juices and their extracts more than 24 h. Reviews, meta-analyses, conference abstracts and book chapters were excluded. Data extraction: Three reviewers independently performed the extraction of articles. Data synthesis: 22 papers met our inclusion criteria and were eligible for inclusion in the final review. According to the kind of study, the selected ones were further divided in preclinical (n = 20) and observational (n = 2) studies. Conclusion: The studies discussed in this review strongly corroborate the role of Citrus juices and their derivatives as potential resource against cancer.
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Affiliation(s)
- Santa Cirmi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of MessinaMessina, Italy.,Prof. Antonio Imbesi FoundationMessina, Italy
| | - Alessandro Maugeri
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of MessinaMessina, Italy.,Prof. Antonio Imbesi FoundationMessina, Italy
| | - Nadia Ferlazzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of MessinaMessina, Italy
| | - Sebastiano Gangemi
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy and Institute of Applied Sciences and Intelligent Systems, National Research CouncilPozzuoli, Italy
| | - Gioacchino Calapai
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of MessinaMessina, Italy
| | - Udo Schumacher
- Department of Anatomy and Experimental Morphology, University Medical Center Hamburg-EppendorfHamburg, Germany
| | - Michele Navarra
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of MessinaMessina, Italy
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27
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Butelli E, Garcia-Lor A, Licciardello C, Las Casas G, Hill L, Recupero GR, Keremane ML, Ramadugu C, Krueger R, Xu Q, Deng X, Fanciullino AL, Froelicher Y, Navarro L, Martin C. Changes in Anthocyanin Production during Domestication of Citrus. PLANT PHYSIOLOGY 2017; 173:2225-2242. [PMID: 28196843 PMCID: PMC5373055 DOI: 10.1104/pp.16.01701] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 02/10/2017] [Indexed: 05/17/2023]
Abstract
Mandarin (Citrus reticulata), citron (Citrus medica), and pummelo (Citrus maxima) are important species of the genus Citrus and parents of the interspecific hybrids that constitute the most familiar commercial varieties of Citrus: sweet orange, sour orange, clementine, lemon, lime, and grapefruit. Citron produces anthocyanins in its young leaves and flowers, as do species in genera closely related to Citrus, but mandarins do not, and pummelo varieties that produce anthocyanins have not been reported. We investigated the activity of the Ruby gene, which encodes a MYB transcription factor controlling anthocyanin biosynthesis, in different accessions of a range of Citrus species and in domesticated cultivars. A white mutant of lemon lacks functional alleles of Ruby, demonstrating that Ruby plays an essential role in anthocyanin production in Citrus Almost all the natural variation in pigmentation by anthocyanins in Citrus species can be explained by differences in activity of the Ruby gene, caused by point mutations and deletions and insertions of transposable elements. Comparison of the allelic constitution of Ruby in different species and cultivars also helps to clarify many of the taxonomic relationships in different species of Citrus, confirms the derivation of commercial varieties during domestication, elucidates the relationships within the subgenus Papeda, and allows a new genetic classification of mandarins.
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Affiliation(s)
- Eugenio Butelli
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.);
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.);
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.);
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.);
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.);
- University of California, Riverside, California 92521 (C.R.);
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.);
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Andrés Garcia-Lor
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Concetta Licciardello
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Giuseppina Las Casas
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Lionel Hill
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Giuseppe Reforgiato Recupero
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Manjunath L Keremane
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Chandrika Ramadugu
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Robert Krueger
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Qiang Xu
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Xiuxin Deng
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Anne-Laure Fanciullino
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Yann Froelicher
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Luis Navarro
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
| | - Cathie Martin
- John Innes Centre, Norwich NR4 7UH, United Kingdom (E.B., L.H., C.M.)
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain (A.G.-L., L.N.)
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, 95024 Acireale, Italy (C.L., G.R.-R.)
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy (G.L.C.)
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507-5437 (M.L.K., R.K.)
- University of California, Riverside, California 92521 (C.R.)
- Key Laboratory of Horticultural Plant Biology of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China (Q.X., X.D.)
- Institut National de la Recherche Agronomique, UR1115 PSH, F-84914 Avignon, France (A.-L.F.); and
- CIRAD, Unité Mixte de Recherche AGAP, Station Institut National de la Recherche Agronomique, F-20230 San Giuliano, France (Y.F.)
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Theile D, Hohmann N, Kiemel D, Gattuso G, Barreca D, Mikus G, Haefeli WE, Schwenger V, Weiss J. Clementine juice has the potential for drug interactions – In vitro comparison with grapefruit and mandarin juice. Eur J Pharm Sci 2017; 97:247-256. [DOI: 10.1016/j.ejps.2016.11.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 11/07/2016] [Accepted: 11/19/2016] [Indexed: 02/07/2023]
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Alquézar B, Rodríguez A, de la Peña M, Peña L. Genomic Analysis of Terpene Synthase Family and Functional Characterization of Seven Sesquiterpene Synthases from Citrus sinensis. FRONTIERS IN PLANT SCIENCE 2017; 8:1481. [PMID: 28883829 PMCID: PMC5573811 DOI: 10.3389/fpls.2017.01481] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/09/2017] [Indexed: 05/17/2023]
Abstract
Citrus aroma and flavor, chief traits of fruit quality, are derived from their high content in essential oils of most plant tissues, including leaves, stems, flowers, and fruits. Accumulated in secretory cavities, most components of these oils are volatile terpenes. They contribute to defense against herbivores and pathogens, and perhaps also protect tissues against abiotic stress. In spite of their importance, our understanding of the physiological, biochemical, and genetic regulation of citrus terpene volatiles is still limited. The availability of the sweet orange (Citrus sinensis L. Osbeck) genome sequence allowed us to characterize for the first time the terpene synthase (TPS) family in a citrus type. CsTPS is one of the largest angiosperm TPS families characterized so far, formed by 95 loci from which just 55 encode for putative functional TPSs. All TPS angiosperm families, TPS-a, TPS-b, TPS-c, TPS-e/f, and TPS-g were represented in the sweet orange genome, with 28, 18, 2, 2, and 5 putative full length genes each. Additionally, sweet orange β-farnesene synthase, (Z)-β-cubebene/α-copaene synthase, two β-caryophyllene synthases, and three multiproduct enzymes yielding β-cadinene/α-copaene, β-elemene, and β-cadinene/ledene/allo-aromandendrene as major products were identified, and functionally characterized via in vivo recombinant Escherichia coli assays.
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Affiliation(s)
- Berta Alquézar
- Laboratório de Biotecnologia Vegetal, Pesquisa y Desenvolvimento, Fundo de Defesa da CitriculturaAraraquara, Brazil
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas and Universidad Politécnica de ValenciaValencia, Spain
| | - Ana Rodríguez
- Laboratório de Biotecnologia Vegetal, Pesquisa y Desenvolvimento, Fundo de Defesa da CitriculturaAraraquara, Brazil
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas and Universidad Politécnica de ValenciaValencia, Spain
| | - Marcos de la Peña
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas and Universidad Politécnica de ValenciaValencia, Spain
| | - Leandro Peña
- Laboratório de Biotecnologia Vegetal, Pesquisa y Desenvolvimento, Fundo de Defesa da CitriculturaAraraquara, Brazil
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas and Universidad Politécnica de ValenciaValencia, Spain
- *Correspondence: Leandro Peña
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Penjor T, Mimura T, Kotoda N, Matsumoto R, Nagano AJ, Honjo MN, Kudoh H, Yamamoto M, Nagano Y. RAD-Seq analysis of typical and minor Citrus accessions, including Bhutanese varieties. BREEDING SCIENCE 2016; 66:797-807. [PMID: 28163596 PMCID: PMC5282754 DOI: 10.1270/jsbbs.16059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 10/11/2016] [Indexed: 05/30/2023]
Abstract
We analyzed the reduced-representation genome sequences of Citrus species by double-digest restriction site-associated DNA sequencing (ddRAD-Seq) using 44 accessions, including typical and minor accessions, such as Bhutanese varieties. The results of this analysis using typical accessions were consistent with previous reports that citron, papeda, pummelo, and mandarin are ancestral species, and that most Citrus species are derivatives or hybrids of these four species. Citrus varieties often reproduce asexually and heterozygosity is highly conserved within each variety. Because this approach could readily detect conservation of heterozygosity, it was able to discriminate citrus varieties such as satsuma mandarin from closely related species. Thus, this method provides an inexpensive way to protect citrus varieties from unintended introduction and to prevent the provision of incorrect nursery stocks to customers. One Citrus variety in Bhutan was morphologically similar to Mexican lime and was designated as Himalayan lime. The current analysis confirmed the previous proposition that Mexican lime is a hybrid between papeda and citron, and also suggested that Himalayan lime is a probable hybrid between mandarin and citron. In addition to Himalayan lime, current analysis suggested that several accessions were formed by previously undescribed combinations.
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Affiliation(s)
- Tshering Penjor
- Faculty of Agriculture, Saga University,
1 Honjo-machi, Saga 840-8502,
Japan
- Renewable Natural Resources Research Centre Wengkhar,
Mongar,
Bhutan
| | - Takashi Mimura
- Faculty of Agriculture, Saga University,
1 Honjo-machi, Saga 840-8502,
Japan
| | - Nobuhiro Kotoda
- Faculty of Agriculture, Saga University,
1 Honjo-machi, Saga 840-8502,
Japan
| | - Ryoji Matsumoto
- Faculty of Agriculture, Saga University,
1 Honjo-machi, Saga 840-8502,
Japan
| | - Atsushi J. Nagano
- Center for Ecological Research, Kyoto University,
509-3 2-chome, Hirano, Otsu, Shiga 520-2113,
Japan
- JST PRESTO,
4-1-8, Honcho, Kawaguchi, Saitama 332-0012,
Japan
- Faculty of Agriculture, Ryukoku University,
1-5 Yokotani, Seta Oe-cho, Otsu, Shiga 520-2194,
Japan
| | - Mie N. Honjo
- Center for Ecological Research, Kyoto University,
509-3 2-chome, Hirano, Otsu, Shiga 520-2113,
Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University,
509-3 2-chome, Hirano, Otsu, Shiga 520-2113,
Japan
| | - Masashi Yamamoto
- Faculty of Agriculture, Kagoshima University,
1-21-35 Korimoto, Kagoshima 890-0065,
Japan
| | - Yukio Nagano
- Analytical Research Center for Experimental Sciences, Saga University,
1 Honjo-machi, Saga 840-8502,
Japan
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Long JM, Liu Z, Wu XM, Fang YN, Jia HH, Xie ZZ, Deng XX, Guo WW. Genome-scale mRNA and small RNA transcriptomic insights into initiation of citrus apomixis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5743-5756. [PMID: 27619233 PMCID: PMC5066493 DOI: 10.1093/jxb/erw338] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Nucellar embryony (NE) is an adventitious form of apomixis common in citrus, wherein asexual embryos initiate directly from nucellar cells surrounding the embryo sac. NE enables the fixation of desirable agronomic traits and the production of clonal offspring of virus-free rootstock, but impedes progress in hybrid breeding. In spite of the great importance of NE in citrus breeding and commercial production, little is understood about the underlying molecular mechanisms. In this study, the stages of nucellar embryo initiation (NEI) were determined for two polyembryonic citrus cultivars via histological observation. To explore the genes and regulatory pathways involved in NEI, we performed mRNA-seq and sRNA-seq analyses of ovules immediately prior to and at stages during NEI in the two pairs of cultivars. A total of 305 differentially expressed genes (DEGs) were identified between the poly- and monoembryonic ovules. Gene ontology (GO) analysis revealed that several processes are significantly enriched based on DEGs. In particular, response to stress, and especially response to oxidative stress, was over-represented in polyembryonic ovules. Nearly 150 miRNAs, comprising ~90 conserved and ~60 novel miRNAs, were identified in the ovules of either cultivar pair. Only two differentially expressed miRNAs (DEMs) were identified, of which the novel miRN23-5p was repressed whereas the targets accumulated in the polyembryonic ovules. This integrated study on the transcriptional and post-transcriptional regulatory profiles between poly- and monoembryonic citrus ovules provides new insights into the mechanism of NE, which should contribute to revealing the regulatory mechanisms of plant apomixis.
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Affiliation(s)
- Jian-Mei Long
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Zheng Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao-Meng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Yan-Ni Fang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Hui-Hui Jia
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Zong-Zhou Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Xiu-Xin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
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Oueslati A, Ollitrault F, Baraket G, Salhi-Hannachi A, Navarro L, Ollitrault P. Towards a molecular taxonomic key of the Aurantioideae subfamily using chloroplastic SNP diagnostic markers of the main clades genotyped by competitive allele-specific PCR. BMC Genet 2016; 17:118. [PMID: 27539067 PMCID: PMC4991024 DOI: 10.1186/s12863-016-0426-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/11/2016] [Indexed: 11/28/2022] Open
Abstract
Background Chloroplast DNA is a primary source of molecular variations for phylogenetic analysis of photosynthetic eukaryotes. However, the sequencing and analysis of multiple chloroplastic regions is difficult to apply to large collections or large samples of natural populations. The objective of our work was to demonstrate that a molecular taxonomic key based on easy, scalable and low-cost genotyping method should be developed from a set of Single Nucleotide Polymorphisms (SNPs) diagnostic of well-established clades. It was applied to the Aurantioideae subfamily, the largest group of the Rutaceae family that includes the cultivated citrus species. Results The publicly available nucleotide sequences of eight plastid genomic regions were compared for 79 accessions of the Aurantioideae subfamily to search for SNPs revealing taxonomic differentiation at the inter-tribe, inter-subtribe, inter-genus and interspecific levels. Diagnostic SNPs (DSNPs) were found for 46 of the 54 clade levels analysed. Forty DSNPs were selected to develop KASPar markers and their taxonomic value was tested by genotyping 108 accessions of the Aurantioideae subfamily. Twenty-seven markers diagnostic of 24 clades were validated and they displayed a very high rate of transferability in the Aurantioideae subfamily (only 1.2 % of missing data on average). The UPGMA from the validated markers produced a cladistic organisation that was highly coherent with the previous phylogenetic analysis based on the sequence data of the eight plasmid regions. In particular, the monophyletic origin of the “true citrus” genera plus Oxanthera was validated. However, some clarification remains necessary regarding the organisation of the other wild species of the Citreae tribe. Conclusions We validated the concept that with well-established clades, DSNPs can be selected and efficiently transformed into competitive allele-specific PCR markers (KASPar method) allowing cost-effective highly efficient cladistic analysis in large collections at subfamily level. The robustness of this genotyping method is an additional decisive advantage for network collaborative research. The availability of WGS data for the main “true citrus” species should soon make it possible to develop a set of DSNP markers allowing very fine resolution of this very important horticultural group. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0426-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amel Oueslati
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie LR99ES12, Faculté des Sciences de Tunis (FST), Université de Tunis El Manar, Campus Universitaire, El Manar-Tunis, 2092, Tunisia.,UMR Agap, CIRAD, Petit-Bourg, F-97170, Guadeloupe, France
| | - Frederique Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain
| | - Ghada Baraket
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie LR99ES12, Faculté des Sciences de Tunis (FST), Université de Tunis El Manar, Campus Universitaire, El Manar-Tunis, 2092, Tunisia
| | - Amel Salhi-Hannachi
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie LR99ES12, Faculté des Sciences de Tunis (FST), Université de Tunis El Manar, Campus Universitaire, El Manar-Tunis, 2092, Tunisia
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain
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Patterns of genetic structure and evidence of gene flow among Tunisian Citrus species based on informative nSSR markers. C R Biol 2016; 339:371-7. [PMID: 27522638 DOI: 10.1016/j.crvi.2016.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 11/22/2022]
Abstract
This study investigates the extent of genetic diversity, phylogenetic relationships and the amount of gene flow among Tunisian Citrus species based on a set of 15 informative nuclear SSR molecular markers. Genotyping data highlighted an allelic richness among Tunisian Citrus species and has allowed the detection of 168 alleles among them 104.19 were effective. The partition of the total genetic diversity (HT=0.832) showed that the highest amount of variation within the Citrus species is HS=0.550, while the relative amount of the between-species genetic diversity GST does not exceed 0.338. This pattern of genetic structure was supported by low-to-moderate FST pairwise values and the presence of a gene flow (Nm) among the eight Citrus species. The lowest genetic differentiation was revealed between the species C. sinensis and C. insitorum (FST=0.111, Nm=1.99), while the highest genetic differentiation was recorded between the species C. aurantifolia and C. paradisi (FST=0.367, Nm=0.43). The established Neighbor Joining analysis showed that all genotypes were widely discriminated and clearly pooled according to their species of origin, with minor exceptions.
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Curk F, Ollitrault F, Garcia-Lor A, Luro F, Navarro L, Ollitrault P. Phylogenetic origin of limes and lemons revealed by cytoplasmic and nuclear markers. ANNALS OF BOTANY 2016; 117:565-83. [PMID: 26944784 PMCID: PMC4817432 DOI: 10.1093/aob/mcw005] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/21/2015] [Accepted: 12/08/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS The origin of limes and lemons has been a source of conflicting taxonomic opinions. Biochemical studies, numerical taxonomy and recent molecular studies suggested that cultivated Citrus species result from interspecific hybridization between four basic taxa (C. reticulata,C. maxima,C. medica and C. micrantha). However, the origin of most lemons and limes remains controversial or unknown. The aim of this study was to perform extended analyses of the diversity, genetic structure and origin of limes and lemons. METHODS The study was based on 133 Citrus accessions. It combined maternal phylogeny studies based on mitochondrial and chloroplastic markers, and nuclear structure analysis based on the evaluation of ploidy level and the use of 123 markers, including 73 basic taxa diagnostic single nucleotide polymorphism (SNP) and indel markers. KEY RESULTS The lime and lemon horticultural group appears to be highly polymorphic, with diploid, triploid and tetraploid varieties, and to result from many independent reticulation events which defined the sub-groups. Maternal phylogeny involves four cytoplasmic types out of the six encountered in the Citrus genus. All lime and lemon accessions were highly heterozygous, with interspecific admixture of two, three and even the four ancestral taxa genomes. Molecular polymorphism between varieties of the same sub-group was very low. CONCLUSIONS Citrus medica contributed to all limes and lemons and was the direct male parent for the main sub-groups in combination with C. micrantha or close papeda species (for C. aurata, C. excelsa, C. macrophylla and C. aurantifolia--'Mexican' lime types of Tanaka's taxa), C. reticulata(for C. limonia, C. karna and C. jambhiri varieties of Tanaka's taxa, including popular citrus rootstocks such as 'Rangpur' lime, 'Volkamer' and 'Rough' lemons), C. aurantium (for C. limetta and C. limon--yellow lemon types--varieties of Tanaka's taxa) or the C. maxima × C. reticulate hybrid (for C. limettioides--'Palestine sweet' lime types--and C. meyeri). Among triploid limes, C. latifolia accessions ('Tahiti' and 'Persian' lime types) result from the fertilization of a haploid ovule of C. limon by a diploid gamete of C. aurantifolia, while C. aurantifolia triploid accessions ('Tanepao' lime types and 'Madagascar' lemon) probably result from an interspecific backcross (a diploid ovule of C. aurantifolia fertilized by C. medica). As limes and lemons were vegetatively propagated (apomixis, horticultural practices) the intra-sub-group phenotypic diversity results from asexual variations.
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Affiliation(s)
- Franck Curk
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Institut National de la Recherche Agronomique (INRA), F-20230 San Giuliano, France, Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain and
| | - Frédérique Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain and
| | - Andres Garcia-Lor
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain and
| | - François Luro
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Institut National de la Recherche Agronomique (INRA), F-20230 San Giuliano, France
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain and
| | - Patrick Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain and Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (UMR Agap), Centre de coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Station de Roujol, F-97170, Petit-Bourg, Guadeloupe, France
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Lu S, Zhang Y, Zheng X, Zhu K, Xu Q, Deng X. Isolation and Functional Characterization of a Lycopene β-cyclase Gene Promoter from Citrus. FRONTIERS IN PLANT SCIENCE 2016; 7:1367. [PMID: 27679644 PMCID: PMC5020073 DOI: 10.3389/fpls.2016.01367] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 08/29/2016] [Indexed: 05/19/2023]
Abstract
Lycopene β-cyclases are key enzymes located at the branch point of the carotenoid biosynthesis pathway. However, the transcriptional regulatory mechanisms of LCYb1 in citrus with abundant carotenoid accumulation are still unclear. To understand the molecular basis of CsLCYb1 expression, we isolated and functionally characterized the 5' upstream sequences of CsLCYb1 from citrus. The full-length CsLCYb1 promoter and a series of its 5' deletions were fused to the β-glucuronidase (GUS) reporter gene and transferred into different plants (tomato, Arabidopsis and citrus callus) to test the promoter activities. The results of all transgenic species showed that the 1584 bp upstream region from the translational start site displayed maximal promoter activity, and the minimal promoter containing 746 bp upstream sequences was sufficient for strong basal promoter activity. Furthermore, the CsLCYb1 promoter activity was developmentally and tissue-specially regulated in transgenic Arabidopsis, and it was affected by multiple hormones and environmental cues in transgenic citrus callus under various treatments. Finer deletion analysis identified an enhancer element existing as a tandem repeat in the promoter region between -574 to -513 bp and conferring strong promoter activity. The copy numbers of the enhancer element differed among various citrus species, leading to the development of a derived simple sequence repeat marker to distinguish different species. In conclusion, this study elucidates the expression characteristics of the LCYb1 promoter from citrus and further identifies a novel enhancer element required for the promoter activity. The characterized promoter fragment would be an ideal candidate for genetic engineering and seeking of upstream trans-acting elements.
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Dugrand-Judek A, Olry A, Hehn A, Costantino G, Ollitrault P, Froelicher Y, Bourgaud F. The Distribution of Coumarins and Furanocoumarins in Citrus Species Closely Matches Citrus Phylogeny and Reflects the Organization of Biosynthetic Pathways. PLoS One 2015; 10:e0142757. [PMID: 26558757 PMCID: PMC4641707 DOI: 10.1371/journal.pone.0142757] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/23/2015] [Indexed: 11/18/2022] Open
Abstract
Citrus plants are able to produce defense compounds such as coumarins and furanocoumarins to cope with herbivorous insects and pathogens. In humans, these chemical compounds are strong photosensitizers and can interact with medications, leading to the "grapefruit juice effect". Removing coumarins and furanocoumarins from food and cosmetics imply additional costs and might alter product quality. Thus, the selection of Citrus cultivars displaying low coumarin and furanocoumarin contents constitutes a valuable alternative. In this study, we performed ultra-performance liquid chromatography coupled with mass spectrometry analyses to determine the contents of these compounds within the peel and the pulp of 61 Citrus species representative of the genetic diversity all Citrus. Generally, Citrus peel contains larger diversity and higher concentrations of coumarin/furanocoumarin than the pulp of the same fruits. According to the chemotypes found in the peel, Citrus species can be separated into 4 groups that correspond to the 4 ancestral taxa (pummelos, mandarins, citrons and papedas) and extended with their respective secondary species descendants. Three of the 4 ancestral taxa (pummelos, citrons and papedas) synthesize high amounts of these compounds, whereas mandarins appear practically devoid of them. Additionally, all ancestral taxa and their hybrids are logically organized according to the coumarin and furanocoumarin pathways described in the literature. This organization allows hypotheses to be drawn regarding the biosynthetic origin of compounds for which the biogenesis remains unresolved. Determining coumarin and furanocoumarin contents is also helpful for hypothesizing the origin of Citrus species for which the phylogeny is presently not firmly established. Finally, this work also notes favorable hybridization schemes that will lead to low coumarin and furanocoumarin contents, and we propose to select mandarins and Ichang papeda as Citrus varieties for use in creating species devoid of these toxic compounds in future breeding programs.
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Affiliation(s)
- Audray Dugrand-Judek
- Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- INRA, UMR 1121 Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | - Alexandre Olry
- Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- INRA, UMR 1121 Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | - Alain Hehn
- Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- INRA, UMR 1121 Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, 54518, Vandœuvre-lès-Nancy, France
| | | | - Patrick Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (Ivia), 46113 Moncada, Valencia, Spain
- CIRAD, UMR AGAP, Station de Roujol, 97170 Petit-Bourg, Guadeloupe, France
| | - Yann Froelicher
- CIRAD, UMR AGAP, Station INRA, F-20230, San Giuliano, France
| | - Frédéric Bourgaud
- Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, 54518, Vandœuvre-lès-Nancy, France
- INRA, UMR 1121 Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, 54518, Vandœuvre-lès-Nancy, France
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Lado J, Zacarías L, Gurrea A, Page A, Stead A, Rodrigo MJ. Exploring the diversity in Citrus fruit colouration to decipher the relationship between plastid ultrastructure and carotenoid composition. PLANTA 2015. [PMID: 26202736 DOI: 10.1007/s00425-015-2370-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Differentiation of new and characteristic plastid ultrastructures during ripening of citrus fruits in both peel and pulp appears to be strongly correlated with the content and complement of carotenoids. Most of the species of the Citrus genus display a wide range in fruit colouration due to differences in carotenoids; however, how this diversity is related and may contribute to plastid differentiation and ultrastructure is currently unknown. To that end, carotenoid profile and plastid ultrastructure were compared in peel and pulp of three sweet oranges: the ordinary orange-coloured Navel, rich in β,β-xanthophylls, the yellow Pinalate mutant with an elevated content of colourless carotenes and reduced β,β-xanthophylls, and the red-fleshed Cara Cara with high concentration of colourless carotenes and lycopene in the pulp; and two grapefruits: the white Marsh, with low carotenoid content, and the red Star Ruby, accumulating upstream carotenes and lycopene. The most remarkable differences in plastid ultrastructure among varieties were detected in the pulp at full colour, coinciding with major differences in carotenoid composition. Accumulation of lycopene in Cara Cara and Star Ruby pulp was associated with the presence of needle-like crystals in the plastids, while high content of upstream carotenes in Pinalate pulp was related to the development of a novel plastid type with numerous even and round vesicles. The presence of plastoglobuli was linked to phytoene and xanthophyll accumulation, suggesting these structures as the main sites for the accumulation of these pigments. Peel chromoplasts were richer in membranes compared to pulp chromoplasts, reflecting their different biogenesis. In summary, differences in carotenoid composition and accumulation of unusual carotenoids are mirrored by the development of diverse and novel chromoplast types, revealing the plasticity of these organelles to rearrange carotenoids inside different structures to allow massive accumulation and thus contributing to the chemical stability of the carotenoids.
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Affiliation(s)
- Joanna Lado
- Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Avenida Agustín Escardino 7, 46980, Paterna, Valencia, Spain
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Telfer EJ, Stovold GT, Li Y, Silva-Junior OB, Grattapaglia DG, Dungey HS. Parentage Reconstruction in Eucalyptus nitens Using SNPs and Microsatellite Markers: A Comparative Analysis of Marker Data Power and Robustness. PLoS One 2015; 10:e0130601. [PMID: 26158446 PMCID: PMC4497620 DOI: 10.1371/journal.pone.0130601] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 05/21/2015] [Indexed: 12/28/2022] Open
Abstract
Pedigree reconstruction using molecular markers enables efficient management of inbreeding in open-pollinated breeding strategies, replacing expensive and time-consuming controlled pollination. This is particularly useful in preferentially outcrossed, insect pollinated Eucalypts known to suffer considerable inbreeding depression from related matings. A single nucleotide polymorphism (SNP) marker panel consisting of 106 markers was selected for pedigree reconstruction from the recently developed high-density Eucalyptus Infinium SNP chip (EuCHIP60K). The performance of this SNP panel for pedigree reconstruction in open-pollinated progenies of two Eucalyptus nitens seed orchards was compared with that of two microsatellite panels with 13 and 16 markers respectively. The SNP marker panel out-performed one of the microsatellite panels in the resolution power to reconstruct pedigrees and out-performed both panels with respect to data quality. Parentage of all but one offspring in each clonal seed orchard was correctly matched to the expected seed parent using the SNP marker panel, whereas parentage assignment to less than a third of the expected seed parents were supported using the 13-microsatellite panel. The 16-microsatellite panel supported all but one of the recorded seed parents, one better than the SNP panel, although there was still a considerable level of missing and inconsistent data. SNP marker data was considerably superior to microsatellite data in accuracy, reproducibility and robustness. Although microsatellites and SNPs data provide equivalent resolution for pedigree reconstruction, microsatellite analysis requires more time and experience to deal with the uncertainties of allele calling and faces challenges for data transferability across labs and over time. While microsatellite analysis will continue to be useful for some breeding tasks due to the high information content, existing infrastructure and low operating costs, the multi-species SNP resource available with the EuCHIP60k, opens a whole new array of opportunities for high-throughput, genome-wide or targeted genotyping in species of Eucalyptus.
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Affiliation(s)
- Emily J. Telfer
- Scion (New Zealand Forest Research Institute Ltd.), Whakarewarewa, Rotorua, New Zealand
| | - Grahame T. Stovold
- Scion (New Zealand Forest Research Institute Ltd.), Whakarewarewa, Rotorua, New Zealand
| | - Yongjun Li
- Scion (New Zealand Forest Research Institute Ltd.), Whakarewarewa, Rotorua, New Zealand
| | - Orzenil B. Silva-Junior
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Programa de Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasilia, Brazil
| | - Dario G. Grattapaglia
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Programa de Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasilia, Brazil
| | - Heidi S. Dungey
- Scion (New Zealand Forest Research Institute Ltd.), Whakarewarewa, Rotorua, New Zealand
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Nuclear species-diagnostic SNP markers mined from 454 amplicon sequencing reveal admixture genomic structure of modern citrus varieties. PLoS One 2015; 10:e0125628. [PMID: 25973611 PMCID: PMC4431842 DOI: 10.1371/journal.pone.0125628] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/16/2015] [Indexed: 11/19/2022] Open
Abstract
Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP marker set will be useful for systematic estimation of admixture structure of citrus germplasm and for diverse genetic studies.
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Ding Y, Chang J, Ma Q, Chen L, Liu S, Jin S, Han J, Xu R, Zhu A, Guo J, Luo Y, Xu J, Xu Q, Zeng Y, Deng X, Cheng Y. Network analysis of postharvest senescence process in citrus fruits revealed by transcriptomic and metabolomic profiling. PLANT PHYSIOLOGY 2015; 168:357-76. [PMID: 25802366 PMCID: PMC4424016 DOI: 10.1104/pp.114.255711] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/19/2015] [Indexed: 05/04/2023]
Abstract
Citrus (Citrus spp.), a nonclimacteric fruit, is one of the most important fruit crops in global fruit industry. However, the biological behavior of citrus fruit ripening and postharvest senescence remains unclear. To better understand the senescence process of citrus fruit, we analyzed data sets from commercial microarrays, gas chromatography-mass spectrometry, and liquid chromatography-mass spectrometry and validated physiological quality detection of four main varieties in the genus Citrus. Network-based approaches of data mining and modeling were used to investigate complex molecular processes in citrus. The Citrus Metabolic Pathway Network and correlation networks were constructed to explore the modules and relationships of the functional genes/metabolites. We found that the different flesh-rind transport of nutrients and water due to the anatomic structural differences among citrus varieties might be an important factor that influences fruit senescence behavior. We then modeled and verified the citrus senescence process. As fruit rind is exposed directly to the environment, which results in energy expenditure in response to biotic and abiotic stresses, nutrients are exported from flesh to rind to maintain the activity of the whole fruit. The depletion of internal substances causes abiotic stresses, which further induces phytohormone reactions, transcription factor regulation, and a series of physiological and biochemical reactions.
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Affiliation(s)
- Yuduan Ding
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Jiwei Chang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Qiaoli Ma
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Lingling Chen
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Shuzhen Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Shuai Jin
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Jingwen Han
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Rangwei Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Andan Zhu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Jing Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Yi Luo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Juan Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - YunLiu Zeng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
| | - Yunjiang Cheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) and Key Laboratory of Horticultural Crop Biology and Genetic Improvement, Central Region (Ministry of Agriculture), Wuhan 430070, China (Y.D., Q.M., S.L., S.J., J.H., R.X., A.Z., Y.L., J.X., Q.X., Y.Z., X.D., Y.C.); andAgricultural Bioinformatics Key Laboratory of Hubei Province, College of Information, Huazhong Agricultural University, Wuhan 430070, China (J.C., L.C., J.G.)
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Cuenca J, Aleza P, Juárez J, García-Lor A, Froelicher Y, Navarro L, Ollitrault P. Maximum-likelihood method identifies meiotic restitution mechanism from heterozygosity transmission of centromeric loci: application in citrus. Sci Rep 2015; 5:9897. [PMID: 25894579 PMCID: PMC4403285 DOI: 10.1038/srep09897] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/13/2015] [Indexed: 11/09/2022] Open
Abstract
Polyploidisation is a key source of diversification and speciation in plants. Most researchers consider sexual polyploidisation leading to unreduced gamete as its main origin. Unreduced gametes are useful in several crop breeding schemes. Their formation mechanism, i.e., First-Division Restitution (FDR) or Second-Division Restitution (SDR), greatly impacts the gametic and population structures and, therefore, the breeding efficiency. Previous methods to identify the underlying mechanism required the analysis of a large set of markers over large progeny. This work develops a new maximum-likelihood method to identify the unreduced gamete formation mechanism both at the population and individual levels using independent centromeric markers. Knowledge of marker-centromere distances greatly improves the statistical power of the comparison between the SDR and FDR hypotheses. Simulating data demonstrated the importance of selecting markers very close to the centromere to obtain significant conclusions at individual level. This new method was used to identify the meiotic restitution mechanism in nineteen mandarin genotypes used as female parents in triploid citrus breeding. SDR was identified for 85.3% of 543 triploid hybrids and FDR for 0.6%. No significant conclusions were obtained for 14.1% of the hybrids. At population level SDR was the predominant mechanisms for the 19 parental mandarins.
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Affiliation(s)
- José Cuenca
- Crop Protection and Biotechnology Center. Instituto Valenciano de Investigaciones Agrarias (IVIA)
| | - Pablo Aleza
- Crop Protection and Biotechnology Center. Instituto Valenciano de Investigaciones Agrarias (IVIA)
| | - José Juárez
- Crop Protection and Biotechnology Center. Instituto Valenciano de Investigaciones Agrarias (IVIA)
| | - Andrés García-Lor
- Crop Protection and Biotechnology Center. Instituto Valenciano de Investigaciones Agrarias (IVIA)
| | - Yann Froelicher
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)
| | - Luis Navarro
- Crop Protection and Biotechnology Center. Instituto Valenciano de Investigaciones Agrarias (IVIA)
| | - Patrick Ollitrault
- Crop Protection and Biotechnology Center. Instituto Valenciano de Investigaciones Agrarias (IVIA)
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)
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Carbonell-Caballero J, Alonso R, Ibañez V, Terol J, Talon M, Dopazo J. A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus. Mol Biol Evol 2015; 32:2015-35. [PMID: 25873589 PMCID: PMC4833069 DOI: 10.1093/molbev/msv082] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Citrus genus includes some of the most important cultivated fruit trees worldwide. Despite being extensively studied because of its commercial relevance, the origin of cultivated citrus species and the history of its domestication still remain an open question. Here, we present a phylogenetic analysis of the chloroplast genomes of 34 citrus genotypes which constitutes the most comprehensive and detailed study to date on the evolution and variability of the genus Citrus. A statistical model was used to estimate divergence times between the major citrus groups. Additionally, a complete map of the variability across the genome of different citrus species was produced, including single nucleotide variants, heteroplasmic positions, indels (insertions and deletions), and large structural variants. The distribution of all these variants provided further independent support to the phylogeny obtained. An unexpected finding was the high level of heteroplasmy found in several of the analyzed genomes. The use of the complete chloroplast DNA not only paves the way for a better understanding of the phylogenetic relationships within the Citrus genus but also provides original insights into other elusive evolutionary processes, such as chloroplast inheritance, heteroplasmy, and gene selection.
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Affiliation(s)
- Jose Carbonell-Caballero
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Roberto Alonso
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Victoria Ibañez
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Joaquin Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain Functional Genomics Node, Spanish National Institute of Bioinformatics at CIPF, Valencia, Spain
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Durand-Hulak M, Dugrand A, Duval T, Bidel LPR, Jay-Allemand C, Froelicher Y, Bourgaud F, Fanciullino AL. Mapping the genetic and tissular diversity of 64 phenolic compounds in Citrus species using a UPLC-MS approach. ANNALS OF BOTANY 2015; 115:861-77. [PMID: 25757470 PMCID: PMC4373293 DOI: 10.1093/aob/mcv012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/10/2014] [Accepted: 01/13/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS Phenolic compounds contribute to food quality and have potential health benefits. Consequently, they are an important target of selection for Citrus species. Numerous studies on this subject have revealed new molecules, potential biosynthetic pathways and linkage between species. Although polyphenol profiles are correlated with gene expression, which is responsive to developmental and environmental cues, these factors are not monitored in most studies. A better understanding of the biosynthetic pathway and its regulation requires more information about environmental conditions, tissue specificity and connections between competing sub-pathways. This study proposes a rapid method, from sampling to analysis, that allows the quantitation of multiclass phenolic compounds across contrasting tissues and cultivars. METHODS Leaves and fruits of 11 cultivated citrus of commercial interest were collected from adult trees grown in an experimental orchard. Sixty-four phenolic compounds were simultaneously quantified by ultra-high-performance liquid chromatography coupled with mass spectrometry. KEY RESULTS Combining data from vegetative tissues with data from fruit tissues improved cultivar classification based on polyphenols. The analysis of metabolite distribution highlighted the massive accumulation of specific phenolic compounds in leaves and the external part of the fruit pericarp, which reflects their involvement in plant defence. The overview of the biosynthetic pathway obtained confirmed some regulatory steps, for example those catalysed by rhamnosyltransferases. The results suggest that three other steps are responsible for the different metabolite profiles in 'Clementine' and 'Star Ruby' grapefruit. CONCLUSIONS The method described provides a high-throughput method to study the distribution of phenolic compounds across contrasting tissues and cultivars in Citrus, and offers the opportunity to investigate their regulation and physiological roles. The method was validated in four different tissues and allowed the identification and quantitation of 64 phenolic compounds in 20 min, which represents an improvement over existing methods of analysing multiclass polyphenols.
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Affiliation(s)
- Marie Durand-Hulak
- CIRAD, UMR AGAP, F-20230 San Giuliano, France, INRA, UMR AGAP, F-20230 San Giuliano, France, Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, F-54518 Vandœuvre-lès-Nancy, France, INRA, UMR AGAP, Place P. Viala, F-34060 Montpellier, France, Université Montpellier II, UMR DIADE, F-34394 Montpellier, France and INRA, UR 1115, Plantes et Systèmes de Culture Horticoles, Domaine St-Paul - Site Agroparc, F-84914 Avignon, France CIRAD, UMR AGAP, F-20230 San Giuliano, France, INRA, UMR AGAP, F-20230 San Giuliano, France, Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, F-54518 Vandœuvre-lès-Nancy, France, INRA, UMR AGAP, Place P. Viala, F-34060 Montpellier, France, Université Montpellier II, UMR DIADE, F-34394 Montpellier, France and INRA, UR 1115, Plantes et Systèmes de Culture Horticoles, Domaine St-Paul - Site Agroparc, F-84914 Avignon, France
| | - Audray Dugrand
- CIRAD, UMR AGAP, F-20230 San Giuliano, France, INRA, UMR AGAP, F-20230 San Giuliano, France, Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, F-54518 Vandœuvre-lès-Nancy, France, INRA, UMR AGAP, Place P. Viala, F-34060 Montpellier, France, Université Montpellier II, UMR DIADE, F-34394 Montpellier, France and INRA, UR 1115, Plantes et Systèmes de Culture Horticoles, Domaine St-Paul - Site Agroparc, F-84914 Avignon, France
| | - Thibault Duval
- CIRAD, UMR AGAP, F-20230 San Giuliano, France, INRA, UMR AGAP, F-20230 San Giuliano, France, Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, F-54518 Vandœuvre-lès-Nancy, France, INRA, UMR AGAP, Place P. Viala, F-34060 Montpellier, France, Université Montpellier II, UMR DIADE, F-34394 Montpellier, France and INRA, UR 1115, Plantes et Systèmes de Culture Horticoles, Domaine St-Paul - Site Agroparc, F-84914 Avignon, France
| | - Luc P R Bidel
- CIRAD, UMR AGAP, F-20230 San Giuliano, France, INRA, UMR AGAP, F-20230 San Giuliano, France, Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, F-54518 Vandœuvre-lès-Nancy, France, INRA, UMR AGAP, Place P. Viala, F-34060 Montpellier, France, Université Montpellier II, UMR DIADE, F-34394 Montpellier, France and INRA, UR 1115, Plantes et Systèmes de Culture Horticoles, Domaine St-Paul - Site Agroparc, F-84914 Avignon, France
| | - Christian Jay-Allemand
- CIRAD, UMR AGAP, F-20230 San Giuliano, France, INRA, UMR AGAP, F-20230 San Giuliano, France, Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, F-54518 Vandœuvre-lès-Nancy, France, INRA, UMR AGAP, Place P. Viala, F-34060 Montpellier, France, Université Montpellier II, UMR DIADE, F-34394 Montpellier, France and INRA, UR 1115, Plantes et Systèmes de Culture Horticoles, Domaine St-Paul - Site Agroparc, F-84914 Avignon, France
| | - Yann Froelicher
- CIRAD, UMR AGAP, F-20230 San Giuliano, France, INRA, UMR AGAP, F-20230 San Giuliano, France, Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, F-54518 Vandœuvre-lès-Nancy, France, INRA, UMR AGAP, Place P. Viala, F-34060 Montpellier, France, Université Montpellier II, UMR DIADE, F-34394 Montpellier, France and INRA, UR 1115, Plantes et Systèmes de Culture Horticoles, Domaine St-Paul - Site Agroparc, F-84914 Avignon, France
| | - Frédéric Bourgaud
- CIRAD, UMR AGAP, F-20230 San Giuliano, France, INRA, UMR AGAP, F-20230 San Giuliano, France, Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, F-54518 Vandœuvre-lès-Nancy, France, INRA, UMR AGAP, Place P. Viala, F-34060 Montpellier, France, Université Montpellier II, UMR DIADE, F-34394 Montpellier, France and INRA, UR 1115, Plantes et Systèmes de Culture Horticoles, Domaine St-Paul - Site Agroparc, F-84914 Avignon, France
| | - Anne-Laure Fanciullino
- CIRAD, UMR AGAP, F-20230 San Giuliano, France, INRA, UMR AGAP, F-20230 San Giuliano, France, Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, F-54518 Vandœuvre-lès-Nancy, France, INRA, UMR AGAP, Place P. Viala, F-34060 Montpellier, France, Université Montpellier II, UMR DIADE, F-34394 Montpellier, France and INRA, UR 1115, Plantes et Systèmes de Culture Horticoles, Domaine St-Paul - Site Agroparc, F-84914 Avignon, France CIRAD, UMR AGAP, F-20230 San Giuliano, France, INRA, UMR AGAP, F-20230 San Giuliano, France, Université de Lorraine, UMR 1121 Laboratoire Agronomie et Environnement Nancy-Colmar, 2 avenue de la forêt de Haye, TSA 40602, F-54518 Vandœuvre-lès-Nancy, France, INRA, UMR AGAP, Place P. Viala, F-34060 Montpellier, France, Université Montpellier II, UMR DIADE, F-34394 Montpellier, France and INRA, UR 1115, Plantes et Systèmes de Culture Horticoles, Domaine St-Paul - Site Agroparc, F-84914 Avignon, France
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Liang M, Yang X, Li H, Su S, Yi H, Chai L, Deng X. De novo transcriptome assembly of pummelo and molecular marker development. PLoS One 2015; 10:e0120615. [PMID: 25799271 PMCID: PMC4370633 DOI: 10.1371/journal.pone.0120615] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/24/2015] [Indexed: 11/19/2022] Open
Abstract
Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtained a 12-Gb transcriptome dataset of pummelo through a mixture of RNA from seven tissues using Illumina pair-end sequencing, assembled into 57,212 unigenes with an average length of 1010 bp. The annotation and classification results showed that a total of 39,584 unigenes had similar hits to the known proteins of four public databases, and 31,501 were classified into 55 Gene Ontology (GO) functional sub-categories. The search for putative molecular markers among 57,212 unigenes identified 10,276 simple sequence repeats (SSRs) and 64,720 single nucleotide polymorphisms (SNPs). High-quality primers of 1174 SSR loci were designed, of which 88.16% were localized to nine chromosomes of sweet orange. Of 100 SSR primers that were randomly selected for testing, 87 successfully amplified clear banding patterns. Of these primers, 29 with a mean PIC (polymorphic information content) value of 0.52 were effectively applied for phylogenetic analysis. Of the 20 SNP primers, 14 primers, including 54 potential SNPs, yielded target amplifications, and 46 loci were verified via Sanger sequencing. This new dataset will be a valuable resource for molecular biology studies of pummelo and provides reliable information regarding SNP and SSR marker development, thus expediting the breeding program of pummelo.
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Affiliation(s)
- Mei Liang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xiaoming Yang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hang Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Shiying Su
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hualin Yi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Lijun Chai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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Zheng X, Xie Z, Zhu K, Xu Q, Deng X, Pan Z. Isolation and characterization of carotenoid cleavage dioxygenase 4 genes from different citrus species. Mol Genet Genomics 2015; 290:1589-603. [DOI: 10.1007/s00438-015-1016-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 02/16/2015] [Indexed: 01/03/2023]
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Curk F, Ancillo G, Garcia-Lor A, Luro F, Perrier X, Jacquemoud-Collet JP, Navarro L, Ollitrault P. Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrus species: analysis of chromosome 2. BMC Genet 2014; 15:152. [PMID: 25544367 PMCID: PMC4302129 DOI: 10.1186/s12863-014-0152-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The most economically important Citrus species originated by natural interspecific hybridization between four ancestral taxa (Citrus reticulata, Citrus maxima, Citrus medica, and Citrus micrantha) and from limited subsequent interspecific recombination as a result of apomixis and vegetative propagation. Such reticulate evolution coupled with vegetative propagation results in mosaic genomes with large chromosome fragments from the basic taxa in frequent interspecific heterozygosity. Modern breeding of these species is hampered by their complex heterozygous genomic structures that determine species phenotype and are broken by sexual hybridisation. Nevertheless, a large amount of diversity is present in the citrus gene pool, and breeding to allow inclusion of desirable traits is of paramount importance. However, the efficient mobilization of citrus biodiversity in innovative breeding schemes requires previous understanding of Citrus origins and genomic structures. Haplotyping of multiple gene fragments along the whole genome is a powerful approach to reveal the admixture genomic structure of current species and to resolve the evolutionary history of the gene pools. In this study, the efficiency of parallel sequencing with 454 methodology to decipher the hybrid structure of modern citrus species was assessed by analysis of 16 gene fragments on chromosome 2. RESULTS 454 amplicon libraries were established using the Fluidigm array system for 48 genotypes and 16 gene fragments from chromosome 2. Haplotypes were established from the reads of each accession and phylogenetic analyses were performed using the haplotypic data for each gene fragment. The length of 454 reads and the level of differentiation between the ancestral taxa of modern citrus allowed efficient haplotype phylogenetic assignations for 12 of the 16 gene fragments. The analysis of the mixed genomic structure of modern species and cultivars (i) revealed C. maxima introgressions in modern mandarins, (ii) was consistent with previous hypotheses regarding the origin of secondary species, and (iii) provided a new picture of the evolution of chromosome 2. CONCLUSIONS 454 sequencing was an efficient strategy to establish haplotypes with significant phylogenetic assignations in Citrus, providing a new picture of the mixed structure on chromosome 2 in 48 citrus genotypes.
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Affiliation(s)
- Franck Curk
- UMR AGAP, Institut National de la Recherche Agronomique (Inra), Centre Inra de Corse, F-20230, San Giuliano, France.
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
| | - Gema Ancillo
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
| | - Andres Garcia-Lor
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
| | - François Luro
- UMR AGAP, Institut National de la Recherche Agronomique (Inra), Centre Inra de Corse, F-20230, San Giuliano, France.
| | - Xavier Perrier
- UMR AGAP, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), TA A-108/02, 34398, Montpellier, Cedex 5, France.
| | - Jean-Pierre Jacquemoud-Collet
- UMR AGAP, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), TA A-108/02, 34398, Montpellier, Cedex 5, France.
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
| | - Patrick Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
- UMR AGAP, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), TA A-108/02, 34398, Montpellier, Cedex 5, France.
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Utility of indels for species-level identification of a biologically complex plant group: a study with intergenic spacer in Citrus. Mol Biol Rep 2014; 41:7217-22. [PMID: 25048292 DOI: 10.1007/s11033-014-3606-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 07/10/2014] [Indexed: 11/27/2022]
Abstract
The Consortium of Barcode of Life plant working group proposed to use the defined portion of plastid genes rbcL and matK either singly or in combination as the standard DNA barcode for plants. But DNA barcode based identification of biologically complex plant groups are always a challenging task due to the occurrence of natural hybridization. Here, we examined the use of indels polymorphism in trnH-psbA and trnL-trnF sequences for rapid species identification of citrus. DNA from young leaves of selected citrus species were isolated and matK gene (~800 bp) and trnH-psbA spacer (~450 bp) of Chloroplast DNA was amplified for species level identification. The sequences within the group taxa of Citrus were aligned using the ClustalX program. With few obvious misalignments were corrected manually using the similarity criterion. We identified a 54 bp inverted repeat or palindrome sequence (27-80 regions) and 6 multi residues indel coding regions. Large inverted repeats in cpDNA provided authentication at the higher taxonomic levels. These diagnostics indel marker from trnH-psbA were successful in identifying different species (5 out of 7) within the studied Citrus except Citrus limon and Citrus medica. These two closely related species are distinguished through the 6 bp deletion in trnL-trnF. This study demonstrated that the indel polymorphism based approach easily characterizes the Citrus species and the same may be applied in other complex groups. Likewise other indels occurring intergenic spacer of chloroplast regions may be tested for rapid identification of other secondary citrus species.
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Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, Perrier X, Ruiz M, Scalabrin S, Terol J, Takita MA, Labadie K, Poulain J, Couloux A, Jabbari K, Cattonaro F, Del Fabbro C, Pinosio S, Zuccolo A, Chapman J, Grimwood J, Tadeo FR, Estornell LH, Muñoz-Sanz JV, Ibanez V, Herrero-Ortega A, Aleza P, Pérez-Pérez J, Ramón D, Brunel D, Luro F, Chen C, Farmerie WG, Desany B, Kodira C, Mohiuddin M, Harkins T, Fredrikson K, Burns P, Lomsadze A, Borodovsky M, Reforgiato G, Freitas-Astúa J, Quetier F, Navarro L, Roose M, Wincker P, Schmutz J, Morgante M, Machado MA, Talon M, Jaillon O, Ollitrault P, Gmitter F, Rokhsar D. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol 2014; 32:656-62. [PMID: 24908277 PMCID: PMC4113729 DOI: 10.1038/nbt.2906] [Citation(s) in RCA: 333] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 04/14/2014] [Indexed: 01/21/2023]
Abstract
Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes--a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes--and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement.
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Affiliation(s)
- G. Albert Wu
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Simon Prochnik
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jerry Jenkins
- HudsonAlpha Biotechnology Institute, Huntsville, AL, USA
| | - Jerome Salse
- INRA/UBP UMR 1095 GDEC, Clermont Ferrand, France
| | - Uffe Hellsten
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | | | | | - Javier Terol
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | | | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Julie Poulain
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Arnaud Couloux
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Kamel Jabbari
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | | | | | | | - Andrea Zuccolo
- Istituto di Genomica Applicata, Udine, Italy
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Jarrod Chapman
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jane Grimwood
- HudsonAlpha Biotechnology Institute, Huntsville, AL, USA
| | - Francisco R. Tadeo
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Leandro H. Estornell
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Juan V. Muñoz-Sanz
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Victoria Ibanez
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Amparo Herrero-Ortega
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Pablo Aleza
- Centro de Protección Vegetal y Biotecnología-IVIA, Moncada, Valencia, Spain
| | | | | | - Dominique Brunel
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- INRA, US EPGV_1279, Evry, France
| | | | - Chunxian Chen
- Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, USA
| | - William G. Farmerie
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Brian Desany
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Chinnappa Kodira
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Mohammed Mohiuddin
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Tim Harkins
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Karin Fredrikson
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Paul Burns
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Alexandre Lomsadze
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mark Borodovsky
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Giuseppe Reforgiato
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA-ACM), Acireale, Italy
| | - Juliana Freitas-Astúa
- Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis, SP, Brazil
- Embrapa Cassava and Fruits, Cruz das Almas, BA, Brazil
| | - Francis Quetier
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Département de Biologie, Université d’Evry, Evry, France
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología-IVIA, Moncada, Valencia, Spain
| | - Mikeal Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Département de Biologie, Université d’Evry, Evry, France
- Centre National de Recherche Scientifique (CNRS), Evry, France
| | - Jeremy Schmutz
- HudsonAlpha Biotechnology Institute, Huntsville, AL, USA
| | - Michele Morgante
- Istituto di Genomica Applicata, Udine, Italy
- Department of Agriculture and Environmental Sciences, University of Udine, Udine, Italy
| | | | - Manuel Talon
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Olivier Jaillon
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Département de Biologie, Université d’Evry, Evry, France
- Centre National de Recherche Scientifique (CNRS), Evry, France
| | | | - Frederick Gmitter
- Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, USA
| | - Daniel Rokhsar
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
- Division of Genetics, Genomics, and Development, University of California, Berkeley, CA, USA
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Shen D, Bo W, Xu F, Wu R. Genetic diversity and population structure of the Tibetan poplar (Populus szechuanica var. tibetica) along an altitude gradient. BMC Genet 2014; 15 Suppl 1:S11. [PMID: 25079034 PMCID: PMC4118629 DOI: 10.1186/1471-2156-15-s1-s11] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background The Tibetan poplar (Populus szechuanica var. tibetica Schneid), which is distributed at altitudes of 2,000-4,500 m above sea level, is an ecologically important species of the Qinghai-Tibet Plateau and adjacent areas. However, the genetic adaptations responsible for its ability to cope with the harsh environment remain unknown. Results In this study, a total of 24 expressed sequence tag microsatellite (EST-SSR) markers were used to evaluate the genetic diversity and population structure of Tibetan poplars along an altitude gradient. The 172 individuals were of genotypes from low-, medium- and high-altitude populations, and 126 alleles were identified. The expected heterozygosity (HE) value ranged from 0.475 to 0.488 with the highest value found in low-altitude populations and the lowest in high-altitude populations. Genetic variation was low among populations, indicating a limited influence of altitude on microsatellite variation. Low genetic differentiation and high levels of gene flow were detected both between and within the populations along the altitude gradient. An analysis of molecular variance (AMOVA) showed that 6.38% of the total molecular variance was attributed to diversity between populations, while 93.62% variance was associated with differences within populations. There was no clear correlation between genetic variation and altitude, and a Mantel test between genetic distance and altitude resulted in a coefficient of association of r = 0.001, indicating virtually no correlation. Conclusion Microsatellite genotyping results showing genetic diversity and low differentiation suggest that extensive gene flow may have counteracted local adaptations imposed by differences in altitude. The genetic analyses carried out in this study provide new insight for conservation and optimization of future arboriculture.
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