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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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Okamoto M, Monden Y, Shindo A, Takeuchi T, Endo T, Shigematsu Y, Takasaki K, Fujii H, Shimada T. A target cultivar-specific identification system based on the chromatographic printed array strip method for eight prominent Japanese citrus cultivars. BREEDING SCIENCE 2023; 73:146-157. [PMID: 37404354 PMCID: PMC10316311 DOI: 10.1270/jsbbs.22065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/10/2022] [Indexed: 07/06/2023]
Abstract
Citrus is a major cultivated crop in Japan, and new cultivars are of great interest in the Japanese and global market. Recently, the infringement of breeders' rights to citrus cultivars bred in Japan has become a problem related to the agricultural product export strategy promoted by the Japanese government. Cultivar identification systems using DNA markers are an effective tool for protecting breeders' rights. Here, a novel target cultivar-specific identification system using the chromatographic printed array strip method was developed for eight prominent Japanese citrus cultivars. A polymorphic InDel fragment specific to each cultivar was explored through the screening of published citrus InDel markers and next-generation sequencing of retrotransposon libraries. The cultivar-specific DNA marker set for each cultivar comprised 1-3 polymorphic InDel fragments in combination with a PCR-positive DNA marker for the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit gene. The DNA markers were detected within 3 hours from DNA extraction to the detection by the C-PAS4 membrane stick following multiplex PCR. The developed system is superior as a convenient, rapid, and cost-effective DNA diagnostic method during inspection. The proposed target cultivar-specific identification system is expected to serve as an efficient tool for the injunction of suspicious registered cultivars, contributing to the protection of breeders' rights.
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Affiliation(s)
- Mitsutoshi Okamoto
- Ehime Research Institute of Citrus Fruits, Yoshida, Uwajima, Ehime 799-3742, Japan
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushimanaka Kitaku, Okayama, Okayama 700-8530, Japan
| | - Akiko Shindo
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushimanaka Kitaku, Okayama, Okayama 700-8530, Japan
| | | | - Tomoko Endo
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
| | - Yukinori Shigematsu
- Ehime Research Institute of Citrus Fruits, Yoshida, Uwajima, Ehime 799-3742, Japan
| | - Kazuto Takasaki
- FASMAC Co., Ltd., 3088 Okada, Atsugi, Kanagawa 243-0021, Japan
| | - Hiroshi Fujii
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
| | - Takehiko Shimada
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
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Fahmy NM, Elhady SS, Bannan DF, Malatani RT, Gad HA. Citrus reticulata Leaves Essential Oil as an Antiaging Agent: A Comparative Study between Different Cultivars and Correlation with Their Chemical Compositions. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11233335. [PMID: 36501374 PMCID: PMC9735646 DOI: 10.3390/plants11233335] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 05/27/2023]
Abstract
The mass-based metabolomic approach was implemented using GC-MS coupled with chemometric analysis to discriminate between the essential oil compositions of six cultivars of Citrus reticulata. The antiaging capability of the essential oils were investigated through measurement of their ability to inhibit the major enzymes hyaluronidase, collagenase, and amylase involved in aging. GC-MS analysis resulted in the identification of thirty-nine compounds including β-pinene, d-limonene, γ-terpinene, linalool, and dimethyl anthranilate as the main components. Multivariate analysis using principal component analysis (PCA) and hierarchal cluster analysis (HCA) successfully discriminated the cultivars into five main groups. In vitro antiaging activity showed that Kishu mandarin (Km) (2.19 ± 0.10, 465.9 ± 23.7, 0.31 ± 0.01 µg/mL), Cara mandarin (Cm) (3.22 ± 0.14, 592.1 ± 30.1, 0.66 ± 0.03 µg/mL), and Wm (8.43 ± 0.38, 695.2 ± 35.4, 0.79 ± 0.04%) had the highest inhibitory activity against hyaluronidase, collagenase, and amylase, respectively. Molecular docking studies on the major compounds validated the activities of the essential oils and suggested their possible mechanisms of action. Based on our result, certain cultivars of Citrus reticulata can be proposed as a promising candidate in antiaging skin care products.
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Affiliation(s)
- Nouran M. Fahmy
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Douha F. Bannan
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rania T. Malatani
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Haidy A. Gad
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
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Qu J, Yang J, Chen M, Zhai A. Anti-human gastric cancer study of gold nanoparticles synthesized using Alhagi maurorum. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.109859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Ahati P, Xu T, Chen L, Fang H. Biosynthesis, characterization and evaluation of anti-bone carcinoma, cytotoxicity, and antioxidant properties of gold nanoparticles mediated by Citrus reticulata seed aqueous extract: Introducing a novel chemotherapeutic drug. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.109791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Zhang YW, Wang LK, Fang-Zhou L, Yuan BH, Zou XM, Wang RT. Synthesis and characterization of silver nanoparticles green-formulated by Allium stipitatum and treat the colorectal cancer as a modern chemotherapeutic supplement. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.109781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Zhao W, Wang L, Chen H, Qi L, Yang R, Ouyang T, Ning L. Green synthesis, characterization and determination of anti-prostate cancer, cytotoxicity and antioxidant effects of gold nanoparticles synthesized using Alhagi maurorum. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.109525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Local Anesthetic, Anti-inflammatory and Analgesic Activities of Nanoparticles Green-Formulated by Plant Extract. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.109642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Fan N, Li P, Wang J, Gongsun X, Xue L, Bai J, Morovvati H, Goorani S. Novel formulation, characterization, cytotoxicity, antioxidant, and anti-lung cancer activities of silver nanoparticles green-formulated by plant extract. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.109707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Borredá C, Perez-Roman E, Talon M, Terol J. Comparative transcriptomics of wild and commercial Citrus during early ripening reveals how domestication shaped fruit gene expression. BMC PLANT BIOLOGY 2022; 22:123. [PMID: 35300613 PMCID: PMC8928680 DOI: 10.1186/s12870-022-03509-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/03/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Interspecific hybridizations and admixtures were key in Citrus domestication, but very little is known about their impact at the transcriptomic level. To determine the effects of genome introgressions on gene expression, the transcriptomes of the pulp and flavedo of three pure species (citron, pure mandarin and pummelo) and four derived domesticated genetic admixtures (sour orange, sweet orange, lemon and domesticated mandarin) have been analyzed at color break. RESULTS Many genes involved in relevant physiological processes for domestication, such sugar/acid metabolism and carotenoid/flavonoid synthesis, were differentially expressed among samples. In the low-sugar, highly acidic species lemon and citron, many genes involved in sugar metabolism, the TCA cycle and GABA shunt displayed a reduced expression, while the P-type ATPase CitPH5 and most subunits of the vacuolar ATPase were overexpressed. The red-colored species and admixtures were generally characterized by the overexpression in the flavedo of specific pivotal genes involved in the carotenoid biosynthesis, including phytoene synthase, ζ-carotene desaturase, β-lycopene cyclase and CCD4b, a carotenoid cleavage dioxygenase. The expression patterns of many genes involved in flavonoid modifications, especially the flavonoid and phenylpropanoid O-methyltransferases showed extreme diversity. However, the most noticeable differential expression was shown by a chalcone synthase gene, which catalyzes a key step in the biosynthesis of flavonoids. This chalcone synthase was exclusively expressed in mandarins and their admixed species, which only expressed the mandarin allele. In addition, comparisons between wild and domesticated mandarins revealed that the major differences between their transcriptomes concentrate in the admixed regions. CONCLUSION In this work we present a first study providing broad evidence that the genome introgressions that took place during citrus domestication largely shaped gene expression in their fruits.
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Affiliation(s)
- Carles Borredá
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Estela Perez-Roman
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
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Tang TX, Liu H, Deng LH, Qiu XH, Liang JF. A pattern recognition method on smartphones for planar chromatography and verification on chromatograms of four herbal medicines from citrus fruits. J LIQ CHROMATOGR R T 2021. [DOI: 10.1080/10826076.2021.1966440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tie-xin Tang
- Department of Pharmacy, Zhaoqing Medical College, Zhaoqing, China
| | - Hui Liu
- Department of Pharmacy, Zhaoqing Medical College, Zhaoqing, China
| | - Li-he Deng
- Department of Pharmacy, Zhaoqing Medical College, Zhaoqing, China
| | - Xin-hua Qiu
- Department of Pharmacy, Zhaoqing Medical College, Zhaoqing, China
| | - Jie-fei Liang
- Department of Pharmacy, Zhaoqing Medical College, Zhaoqing, China
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Fujii H, Nonaka K, Minamikawa MF, Endo T, Sugiyama A, Hamazaki K, Iwata H, Omura M, Shimada T. Allelic composition of carotenoid metabolic genes in 13 founders influences carotenoid composition in juice sac tissues of fruits among Japanese citrus breeding population. PLoS One 2021; 16:e0246468. [PMID: 33539435 PMCID: PMC7861536 DOI: 10.1371/journal.pone.0246468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/19/2021] [Indexed: 11/24/2022] Open
Abstract
To enrich carotenoids, especially β-cryptoxanthin, in juice sac tissues of fruits via molecular breeding in citrus, allele mining was utilized to dissect allelic variation of carotenoid metabolic genes and identify an optimum allele on the target loci characterized by expression quantitative trait (eQTL) analysis. SNPs of target carotenoid metabolic genes in 13 founders of the Japanese citrus breeding population were explored using the SureSelect target enrichment method. An independent allele was determined based on the presence or absence of reliable SNPs, using trio analysis to confirm inheritability between parent and offspring. Among the 13 founders, there were 7 PSY alleles, 7 HYb alleles, 11 ZEP alleles, 5 NCED alleles, and 4 alleles for the eQTL that control the transcription levels of PDS and ZDS among the ancestral species, indicating that some founders acquired those alleles from them. The carotenoid composition data of 263 breeding pedigrees in juice sac tissues revealed that the phenotypic variance of carotenoid composition was similar to that in the 13 founders, whereas the mean of total carotenoid content increased. This increase in total carotenoid content correlated with the increase in either or both β-cryptoxanthin and violaxanthin in juice sac tissues. Bayesian statistical analysis between allelic composition of target genes and carotenoid composition in 263 breeding pedigrees indicated that PSY-a and ZEP-e alleles at PSY and ZEP loci had strong positive effects on increasing the total carotenoid content, including β-cryptoxanthin and violaxanthin, in juice sac tissues. Moreover, the pyramiding of these alleles also increased the β-cryptoxanthin content. Interestingly, the offset interaction between the alleles with increasing and decreasing effects on carotenoid content and the epistatic interaction among carotenoid metabolic genes were observed and these interactions complexed carotenoid profiles in breeding population. These results revealed that allele composition would highly influence the carotenoid composition in citrus fruits. The allelic genotype information for the examined carotenoid metabolic genes in major citrus varieties and the trio-tagged SNPs to discriminate the optimum alleles (PSY-a and ZEP-e) from the rest would promise citrus breeders carotenoid enrichment in fruit via molecular breeding.
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Affiliation(s)
- Hiroshi Fujii
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka, Japan
| | - Keisuke Nonaka
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka, Japan
| | - Mai F. Minamikawa
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Tomoko Endo
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka, Japan
| | - Aiko Sugiyama
- Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka, Japan
| | - Kosuke Hamazaki
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hiroyoshi Iwata
- Laboratory of Biometry and Bioinformatics, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Mitsuo Omura
- Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka, Japan
| | - Takehiko Shimada
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka, Japan
- * E-mail:
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Ahmed D, Curk F, Evrard JC, Froelicher Y, Ollitrault P. Preferential Disomic Segregation and C. micrantha/C. medica Interspecific Recombination in Tetraploid 'Giant Key' Lime; Outlook for Triploid Lime Breeding. FRONTIERS IN PLANT SCIENCE 2020; 11:939. [PMID: 32670332 PMCID: PMC7330052 DOI: 10.3389/fpls.2020.00939] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 06/09/2020] [Indexed: 05/14/2023]
Abstract
The triploid 'Tahiti' lime (C. x latifolia (Yu. Tanaka) Tanaka) naturally originated from a merger between a haploid ovule of lemon (C. x limon (L.) Burm) and a diploid pollen from a 'Mexican' lime (C. x aurantiifolia (Christm.) Swing). The very limited natural inter-varietal diversity and gametic sterility of C. latifolia requires a phylogenomic based reconstruction breeding strategy to insure its diversification. We developed a strategy based on interploid hybridization between diploid lemon and the doubled diploid 'Giant Key' lime. This lime is a doubled diploid of 'Mexican' lime, itself a natural interspecific F1 hybrid between C. medica L. and C. micrantha Wester. For an optimized breeding program, we analyzed the meiotic behavior of the allotetraploid lime, the genetic structure of its diploid gametes, the interspecific recombination between C. medica and C. micrantha, and constructed its genetic map. A population of 272 triploid hybrids was generated using 'Giant Key' lime as pollinator. One hundred fifty-eight SNPs diagnostic of C. micrantha, regularly distributed throughout the citrus genome were successfully developed and applied. The genetic structure of the diploid gametes was examined based on C. micrantha doses along the genome. The diploid gametes transmitted in average 91.17% of the parental interspecific C. medica/C. micrantha heterozygosity. Three chromosomes (2, 8, and 9) showed disomic segregation with high preferential pairing values, while the remaining chromosomes showed an intermediate inheritance with a preferential disomic trend. A total of 131 SNPs were assigned to nine linkage groups to construct the genetic map. It spanned 272.8 cM with a low average recombination rate (0.99 cM Mb-1) and high synteny and colinearity with the reference clementine genome. Our results confirmed that an efficient reconstruction breeding strategy for 'Tahiti' lime is possible, based on interploid hybridization using a doubled diploid of C. aurantiifolia. The tetraploid parent should be selected for favorable agronomic traits and its genetic value should be efficiently inherited by the progeny thanks to transmission of the high level of parental heterozygosity. However, it would require developing numerous progeny to overcome the linkage drag caused by the limited interspecific recombination associated with the predominant disomic inheritance.
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Affiliation(s)
- Dalel Ahmed
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Univ Montpellier, San Giuliano, France
| | - Franck Curk
- UMR AGAP, INRA, CIRAD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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Endo T, Fujii H, Omura M, Shimada T. Fast-track breeding system to introduce CTV resistance of trifoliate orange into citrus germplasm, by integrating early flowering transgenic plants with marker-assisted selection. BMC PLANT BIOLOGY 2020; 20:224. [PMID: 32429838 PMCID: PMC7238647 DOI: 10.1186/s12870-020-02399-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 04/15/2020] [Indexed: 05/26/2023]
Abstract
BACKGROUND Global warming will expand the range of new and invasive pathogens in orchards, and subsequently increase the risk of disease epidemics and economic losses. The development of new resistant plant varieties can help to reduce the impact of pathogens, however, the breeding speed can be extremely slow, due to the growth rates of the plants, and the availability of resistance genes. Citrus trees are suffering immense damage from serious diseases such as citrus canker (XCC), huanglongbing (HLB), and citrus tristeza virus (CTV). A fast-track breeding system, that aimed at shortening the duration for disease resistance breeding by incorporating the resistance genes from related species to commercial varieties, has been developed using the integration of precocious transgenic trifoliate orange with the overexpression of CiFT and MAS. It was applied here to incorporate CTV resistance of trifoliate orange into citrus germplasm. RESULTS One generation of backcrossed breeding, that would normally take at least 5 years, was achieved in a single year by fast-track breeding system. Linkage analysis using the corresponding DNA markers revealed that CTV resistance and T-DNA integrated regions were found in different linkage groups, and they were independently segregated in the BC progenies. The CTV resistant null segregants, in which the T-DNA integrated region was removed from their genome, were feasibly obtained by MAS in each generation of the BC progenies, and their CTV resistance was confirmed by immunological analysis. Several BC3 null segregants, whose genetic backgrounds had been substituted into citrus germplasm, except for the haplotype block of CTV resistance, were successfully obtained. CGH and NGS analyses revealed that the T-DNA integrated region was safely segregated out in null segregants. CONCLUSION Fast-track breeding systems are expected to shorten the required breeding time by more than one-fifth in comparison with conventional cross breeding techniques. Using this system, we obtained BC3-8, whose genetic background was successfully substituted except for the CTV resistance locus, and could be a novel mandarin breeding material. The fast-track breeding system will be useful to introduce important traits from related species to citrus germplasm while also drastically reducing the time required for breeding.
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Affiliation(s)
- Tomoko Endo
- National Agriculture and Food Research Organization, Institute of Fruit and Tea Tree Science (NIFTS), Shizuoka, Shimizu 424-0292 Japan
| | - Hiroshi Fujii
- National Agriculture and Food Research Organization, Institute of Fruit and Tea Tree Science (NIFTS), Shizuoka, Shimizu 424-0292 Japan
| | - Mitsuo Omura
- Faculty of Agriculture, Shizuoka University, Shizuoka, Suruga 422-8529 Japan
| | - Takehiko Shimada
- National Agriculture and Food Research Organization, Institute of Fruit and Tea Tree Science (NIFTS), Shizuoka, Shimizu 424-0292 Japan
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Kawahara Y, Endo T, Omura M, Teramoto Y, Itoh T, Fujii H, Shimada T. Mikan Genome Database (MiGD): integrated database of genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding. BREEDING SCIENCE 2020; 70:200-211. [PMID: 32523402 PMCID: PMC7272249 DOI: 10.1270/jsbbs.19097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/16/2019] [Indexed: 06/11/2023]
Abstract
Citrus species are some of the most valuable and widely consumed fruits globally. The genome sequences of representative citrus (e.g., Citrus clementina, C. sinensis, C. grandis) species have been released but the research base for mandarin molecular breeding is still poor. We assembled the genomes of Citrus unshiu and Poncirus trifoliata, two important species for citrus industry in Japan, using hybrid de novo assembly of Illumina and PacBio sequence data, and developed the Mikan Genome Database (MiGD). The assembled genome sizes of C. unshiu and P. trifoliata are 346 and 292 Mb, respectively, similar to those of citrus species in public databases; they are predicted to possess 41,489 and 34,333 protein-coding genes in their draft genome sequences, with 9,642 and 8,377 specific genes when compared to C. clementina, respectively. MiGD is an integrated database of genome annotation, genetic diversity, and Cleaved Amplified Polymorphic Sequence (CAPS) marker information, with these contents being mutually linked by genes. MiGD facilitates access to genome sequences of interest from previously reported linkage maps through CAPS markers and obtains polymorphism information through the multiple genome browser TASUKE. The genomic resources in MiGD (https://mikan.dna.affrc.go.jp) could provide valuable information for mandarin molecular breeding in Japan.
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Affiliation(s)
- Yoshihiro Kawahara
- National Agriculture and Food Research Organization Advanced Analysis Center, Tsukuba, Ibaraki 305-8602, Japan
- National Agriculture and Food Research Organization Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan
| | - Tomoko Endo
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
| | - Mitsuo Omura
- Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka 422-8529, Japan
| | - Yumiko Teramoto
- IMSBIO Co., Ltd., Owl Tower 6F, 4-21-1, Higashi-ikebukuro, Toshima-ku, Tokyo 170-0013, Japan
| | - Takeshi Itoh
- National Agriculture and Food Research Organization Advanced Analysis Center, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroshi Fujii
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
| | - Takehiko Shimada
- National Agriculture and Food Research Organization Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka 424-0292, Japan
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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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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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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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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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20
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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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21
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McKain MR, Johnson MG, Uribe‐Convers S, Eaton D, Yang Y. Practical considerations for plant phylogenomics. APPLICATIONS IN PLANT SCIENCES 2018; 6:e1038. [PMID: 29732268 PMCID: PMC5895195 DOI: 10.1002/aps3.1038] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/13/2018] [Indexed: 05/10/2023]
Abstract
The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome-scale data from diverse lineages. The development of high-throughput sequencing and long-read technologies has ushered in the era of phylogenomics, where hundreds to thousands of nuclear genes and whole organellar genomes are routinely used to reconstruct evolutionary relationships. As a result, understanding which options are best suited for a particular set of questions can be difficult, especially for those just starting in the field. Here, we review the most recent advances in plant phylogenomic methods and make recommendations for project-dependent best practices and considerations. We focus on the costs and benefits of different approaches in regard to the information they provide researchers and the questions they can address. We also highlight unique challenges and opportunities in plant systems, such as polyploidy, reticulate evolution, and the use of herbarium materials, identifying optimal methodologies for each. Finally, we draw attention to lingering challenges in the field of plant phylogenomics, such as reusability of data sets, and look at some up-and-coming technologies that may help propel the field even further.
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Affiliation(s)
- Michael R. McKain
- Department of Biological SciencesThe University of AlabamaBox 870344TuscaloosaAlabama35487USA
| | - Matthew G. Johnson
- Department of Biological SciencesTexas Tech University2901 Main Street, Box 43131LubbockTexas79409USA
| | - Simon Uribe‐Convers
- Department of Ecology and Evolutionary BiologyUniversity of Michigan830 North UniversityAnn ArborMichigan48109USA
| | - Deren Eaton
- Department of Ecology, Evolution, and Environmental BiologyColumbia University1200 Amsterdam AvenueNew YorkNew York10027USA
| | - Ya Yang
- Department of Plant and Microbial BiologyUniversity of Minnesota–Twin Cities1445 Gortner AvenueSt. PaulMinnesota55108USA
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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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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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Mochizuki T, Tanizawa Y, Fujisawa T, Ohta T, Nikoh N, Shimizu T, Toyoda A, Fujiyama A, Kurata N, Nagasaki H, Kaminuma E, Nakamura Y. DNApod: DNA polymorphism annotation database from next-generation sequence read archives. PLoS One 2017; 12:e0172269. [PMID: 28234924 PMCID: PMC5325239 DOI: 10.1371/journal.pone.0172269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/02/2017] [Indexed: 01/18/2023] Open
Abstract
With the rapid advances in next-generation sequencing (NGS), datasets for DNA polymorphisms among various species and strains have been produced, stored, and distributed. However, reliability varies among these datasets because the experimental and analytical conditions used differ among assays. Furthermore, such datasets have been frequently distributed from the websites of individual sequencing projects. It is desirable to integrate DNA polymorphism data into one database featuring uniform quality control that is distributed from a single platform at a single place. DNA polymorphism annotation database (DNApod; http://tga.nig.ac.jp/dnapod/) is an integrated database that stores genome-wide DNA polymorphism datasets acquired under uniform analytical conditions, and this includes uniformity in the quality of the raw data, the reference genome version, and evaluation algorithms. DNApod genotypic data are re-analyzed whole-genome shotgun datasets extracted from sequence read archives, and DNApod distributes genome-wide DNA polymorphism datasets and known-gene annotations for each DNA polymorphism. This new database was developed for storing genome-wide DNA polymorphism datasets of plants, with crops being the first priority. Here, we describe our analyzed data for 679, 404, and 66 strains of rice, maize, and sorghum, respectively. The analytical methods are available as a DNApod workflow in an NGS annotation system of the DNA Data Bank of Japan and a virtual machine image. Furthermore, DNApod provides tables of links of identifiers between DNApod genotypic data and public phenotypic data. To advance the sharing of organism knowledge, DNApod offers basic and ubiquitous functions for multiple alignment and phylogenetic tree construction by using orthologous gene information.
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Affiliation(s)
- Takako Mochizuki
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yasuhiro Tanizawa
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takatomo Fujisawa
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tazro Ohta
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Naruo Nikoh
- Department of Liberal Arts, The Open University of Japan, Chiba, Chiba, Japan
| | - Tokurou Shimizu
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Nori Kurata
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hideki Nagasaki
- Genome Informatics Group, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Eli Kaminuma
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- * E-mail:
| | - Yasukazu Nakamura
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
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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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Shimizu T, Kitajima A, Nonaka K, Yoshioka T, Ohta S, Goto S, Toyoda A, Fujiyama A, Mochizuki T, Nagasaki H, Kaminuma E, Nakamura Y. Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes. PLoS One 2016; 11:e0166969. [PMID: 27902727 PMCID: PMC5130255 DOI: 10.1371/journal.pone.0166969] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 11/07/2016] [Indexed: 01/07/2023] Open
Abstract
Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins. Structure analysis with DNA markers that are in Hardy-Weinberg equilibrium deduce three basic taxa coinciding with the current understanding of citrus ancestors. Genotyping analysis of 101 indigenous citrus varieties with 123 selected DNA markers infers the parentages of 22 indigenous citrus varieties including Satsuma, Temple, and iyo, and single parents of 45 indigenous citrus varieties, including kunenbo, C. ichangensis, and Ichang lemon by allele-sharing and parentage tests. Genotyping analysis of chloroplast and mitochondrial genomes using 11 DNA markers classifies their cytoplasmic genotypes into 18 categories and deduces the combination of seed and pollen parents. Likelihood ratio analysis verifies the inferred parentages with significant scores. The reconstructed genealogy identifies 12 types of varieties consisting of Kishu, kunenbo, yuzu, koji, sour orange, dancy, kobeni mikan, sweet orange, tachibana, Cleopatra, willowleaf mandarin, and pummelo, which have played pivotal roles in the occurrence of these indigenous varieties. The inferred parentage of the indigenous varieties confirms their hybrid origins, as found by recent studies.
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Affiliation(s)
- Tokurou Shimizu
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
- * E-mail:
| | - Akira Kitajima
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kizugawa, Kyoto, Japan
| | - Keisuke Nonaka
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
| | - Terutaka Yoshioka
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
| | - Satoshi Ohta
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
| | - Shingo Goto
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
| | - Atsushi Toyoda
- National Institute of Genetics, Comparative Genomics laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- National Institute of Genetics, Comparative Genomics laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takako Mochizuki
- National Institute of Genetics, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hideki Nagasaki
- National Institute of Genetics, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Eli Kaminuma
- National Institute of Genetics, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yasukazu Nakamura
- National Institute of Genetics, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
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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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Aleza P, Cuenca J, Juárez J, Navarro L, Ollitrault P. Inheritance in doubled-diploid clementine and comparative study with SDR unreduced gametes of diploid clementine. PLANT CELL REPORTS 2016; 35:1573-86. [PMID: 27038940 DOI: 10.1007/s00299-016-1972-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/21/2016] [Indexed: 05/23/2023]
Abstract
Tetraploid clementine displays mainly tetrasomic inheritance. Genetic structures of 2n SDR and 2 × gametes from DD clementine are complementary and will guides triploids citrus breeding strategies. Triploid breeding is developed worldwide to create new seedless cultivars. Citrus triploid hybrids can be recovered from 2x × 2x sexual hybridizations as a consequence of the formation of unreduced gametes (2n), or from 4x × 2x interploid hybridizations in which tetraploid parents used are most often doubled-diploid (DD). Here we have analyzed the inheritance in doubled-diploid clementine and compared the genetic structures of gametes of DD clementine with SDR unreduced gametes of diploid clementine. Parental heterozygosity restitution (PHR) with DD parents depends on the rate of preferential chromosome pairing and thus the proportion of disomic versus tetrasomic segregations. Doubled-diploid clementine largely exhibited tetrasomic segregation. However, three linkage groups had intermediate segregation and one had a tendency for disomy. Significant doubled reduction rates (DR) rates were observed in six of the nine LGs. Differences of PHR between 2n SDR and 2x DD gametes were highest in the centromeric region and progressively decreased toward the distal regions where they were not significant. Over all markers, PHR was lower (two-thirds) in SDR 2n gametes than in DD-derived diploid gametes. The two strategies appear complementary in terms of genotypic variability. Interploid 4x × 2x hybridization is potentially more efficient for developing new cultivars that are phenotypically closer to the diploid parent of the DD than sexual hybridization through SDR 2n gametes. Conversely, 2x × 2x triploidisation has the potential to produce novel products with characteristics for market segmentation strategies.
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Affiliation(s)
- P Aleza
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain
| | - J Cuenca
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain
| | - J Juárez
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain
| | - L Navarro
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain.
| | - P Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113, Moncada, Valencia, Spain.
- UMR AGAP, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Station de Roujol, 97170, Petit-Bourg, Guadeloupe.
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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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Uribe-Convers S, Settles ML, Tank DC. A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae). PLoS One 2016; 11:e0148203. [PMID: 26828929 PMCID: PMC4734709 DOI: 10.1371/journal.pone.0148203] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/14/2016] [Indexed: 11/30/2022] Open
Abstract
Advances in high-throughput sequencing (HTS) have allowed researchers to obtain large amounts of biological sequence information at speeds and costs unimaginable only a decade ago. Phylogenetics, and the study of evolution in general, is quickly migrating towards using HTS to generate larger and more complex molecular datasets. In this paper, we present a method that utilizes microfluidic PCR and HTS to generate large amounts of sequence data suitable for phylogenetic analyses. The approach uses the Fluidigm Access Array System (Fluidigm, San Francisco, CA, USA) and two sets of PCR primers to simultaneously amplify 48 target regions across 48 samples, incorporating sample-specific barcodes and HTS adapters (2,304 unique amplicons per Access Array). The final product is a pooled set of amplicons ready to be sequenced, and thus, there is no need to construct separate, costly genomic libraries for each sample. Further, we present a bioinformatics pipeline to process the raw HTS reads to either generate consensus sequences (with or without ambiguities) for every locus in every sample or—more importantly—recover the separate alleles from heterozygous target regions in each sample. This is important because it adds allelic information that is well suited for coalescent-based phylogenetic analyses that are becoming very common in conservation and evolutionary biology. To test our approach and bioinformatics pipeline, we sequenced 576 samples across 96 target regions belonging to the South American clade of the genus Bartsia L. in the plant family Orobanchaceae. After sequencing cleanup and alignment, the experiment resulted in ~25,300bp across 486 samples for a set of 48 primer pairs targeting the plastome, and ~13,500bp for 363 samples for a set of primers targeting regions in the nuclear genome. Finally, we constructed a combined concatenated matrix from all 96 primer combinations, resulting in a combined aligned length of ~40,500bp for 349 samples.
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Affiliation(s)
- Simon Uribe-Convers
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Stillinger Herbarium, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
| | - Matthew L. Settles
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - David C. Tank
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Stillinger Herbarium, University of Idaho, Moscow, Idaho, United States of America
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Mason AS, Batley J. Creating new interspecific hybrid and polyploid crops. Trends Biotechnol 2015; 33:436-41. [PMID: 26164645 DOI: 10.1016/j.tibtech.2015.06.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/19/2015] [Accepted: 06/01/2015] [Indexed: 12/16/2022]
Abstract
Agricultural selection of desirable traits in domesticated plant and animal species mimics natural evolutionary selection for ability of species to survive, thrive, and reproduce in the wild. However, one evolutionary process is currently underutilised for human agricultural purposes: speciation through interspecific hybridisation and polyploid formation. Despite promising successes in creation of new hybrid and or polyploid species in many genera, few geneticists and breeders deliberately take advantage of polyploidy and interspecific hybridisation for crop improvement. We outline the possible benefits as well as potential problems and criticisms with this approach, and address how modern advances in technology and knowledge can help to create new crop species for agriculture.
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Affiliation(s)
- Annaliese S Mason
- Plant Breeding Department, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
| | - Jacqueline Batley
- School of Plant Biology, The University of Western Australia, 35 Stirling Hwy, Crawley 6009, Australia
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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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