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Jabeen S, Saif R, Haq R, Hayat A, Naz S. Whole-genome sequencing and variant discovery of Citrus reticulata "Kinnow" from Pakistan. Funct Integr Genomics 2023; 23:227. [PMID: 37422603 DOI: 10.1007/s10142-023-01153-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/10/2023]
Abstract
Citrus is a source of nutritional and medicinal advantages, cultivated worldwide with major groups of sweet oranges, mandarins, grapefruits, kumquats, lemons and limes. Pakistan produces all major citrus groups with mandarin (Citrus reticulata) being the prominent group that includes local commercial cultivars Feutral's Early, Dancy, Honey, and Kinnow. The present study designed to understand the genetic architecture of this unique variety of Citrus reticulata 'Kinnow.' The whole-genome resequencing and variant calling was performed to map the genomic variability that might be responsible for its particular characteristics like taste, seedlessness, juice content, thickness of peel, and shelf-life. A total of 139,436,350 raw sequence reads were generated with 20.9 Gb data in Fastq format having 98% effectiveness and 0.2% base call error rate. Overall, 3,503,033 SNPs, 176,949 MNPs, 323,287 INS, and 333,083 DEL were identified using the GATK4 variant calling pipeline against Citrus clementina. Furthermore, g:Profiler was applied for annotating the newly found variants, harbor genes/transcripts and their involved pathways. A total of 73,864 transcripts harbors 4,336,352 variants, most of the observed variants were predicted in non-coding regions and 1009 transcripts were found well annotated by different databases. Out of total aforementioned transcripts, 588 involved in biological processes, 234 in molecular functions and 167 transcripts in cellular components. In a nutshell, 18,153 high impact variants and 216 genic variants found in the current study, which may be used after its functional validation for marker-assisted breeding programs of "Kinnow" to propagate its valued traits for the improvement of contemporary citrus varieties in the region.
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Affiliation(s)
- Sadia Jabeen
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Rashid Saif
- Department of Biotechnology, Qarshi University, Lahore, Pakistan
- Decode Genomics, Punjab University Employees Housing Scheme, Lahore, Pakistan
| | - Rukhama Haq
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan
| | - Akbar Hayat
- Citrus Research Institute, Sargodha, Pakistan
| | - Shagufta Naz
- Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan.
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Calvez L, Dereeper A, Perdereau A, Mournet P, Miranda M, Bruyère S, Hufnagel B, Froelicher Y, Lemainque A, Morillon R, Ollitrault P. Meiotic Behaviors of Allotetraploid Citrus Drive the Interspecific Recombination Landscape, the Genetic Structures, and Traits Inheritance in Tetrazyg Progenies Aiming to Select New Rootstocks. PLANTS (BASEL, SWITZERLAND) 2023; 12:1630. [PMID: 37111854 PMCID: PMC10146282 DOI: 10.3390/plants12081630] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/29/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Sexual breeding at the tetraploid level is a promising strategy for rootstock breeding in citrus. Due to the interspecific origin of most of the conventional diploid citrus rootstocks that produced the tetraploid germplasm, the optimization of this strategy requires better knowledge of the meiotic behavior of the tetraploid parents. This work used Genotyping By Sequencing (GBS) data from 103 tetraploid hybrids to study the meiotic behavior and generate a high-density recombination landscape for their tetraploid intergenic Swingle citrumelo and interspecific Volkamer lemon progenitors. A genetic association study was performed with root architecture traits. For citrumelo, high preferential chromosome pairing was revealed and led to an intermediate inheritance with a disomic tendency. Meiosis in Volkamer lemon was more complex than that of citrumelo, with mixed segregation patterns from disomy to tetrasomy. The preferential pairing resulted in low interspecific recombination levels and high interspecific heterozygosity transmission by the diploid gametes. This meiotic behavior affected the efficiency of Quantitative Trait Loci (QTL) detection. Nevertheless, it enabled a high transmission of disease and pest resistance candidate genes from P. trifoliata that are heterozygous in the citrumelo progenitor. The tetrazyg strategy, using doubled diploids of interspecific origin as parents, appears to be efficient in transferring the dominant traits selected at the parental level to the tetraploid progenies.
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Affiliation(s)
- Lény Calvez
- UMR AGAP, CIRAD, F-97170 Petit-Bourg, France; (L.C.); (A.D.); (S.B.); (B.H.)
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
| | - Alexis Dereeper
- UMR AGAP, CIRAD, F-97170 Petit-Bourg, France; (L.C.); (A.D.); (S.B.); (B.H.)
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
| | - Aude Perdereau
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, F-91000 Evry, France; (A.P.)
| | - Pierre Mournet
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
- UMR AGAP, CIRAD, F-34398 Montpellier, France
| | - Maëva Miranda
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
- UMR AGAP, CIRAD, F-34398 Montpellier, France
| | - Saturnin Bruyère
- UMR AGAP, CIRAD, F-97170 Petit-Bourg, France; (L.C.); (A.D.); (S.B.); (B.H.)
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
| | - Barbara Hufnagel
- UMR AGAP, CIRAD, F-97170 Petit-Bourg, France; (L.C.); (A.D.); (S.B.); (B.H.)
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
| | - Yann Froelicher
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
- UMR AGAP, CIRAD, F-20230 San Giuliano, France
| | - Arnaud Lemainque
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, F-91000 Evry, France; (A.P.)
| | - Raphaël Morillon
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
- UMR AGAP, CIRAD, F-34398 Montpellier, France
| | - Patrick Ollitrault
- UMR AGAP, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France; (P.M.); (M.M.); (Y.F.); (R.M.)
- UMR AGAP, CIRAD, F-34398 Montpellier, France
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3
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Kumar K, Yu Q, Bhatia D, Honsho C, Gmitter FG. Construction of a high density genetic linkage map to define the locus conferring seedlessness from Mukaku Kishu mandarin. FRONTIERS IN PLANT SCIENCE 2023; 14:1087023. [PMID: 36875618 PMCID: PMC9976630 DOI: 10.3389/fpls.2023.1087023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Mukaku Kishu ('MK'), a small sized mandarin, is an important source of seedlessness in citrus breeding. Identification and mapping the gene(s) governing 'MK' seedlessness will expedite seedless cultivar development. In this study, two 'MK'-derived mapping populations- LB8-9 Sugar Belle® ('SB') × 'MK' (N=97) and Daisy ('D') × 'MK' (N=68) were genotyped using an Axiom_Citrus56 Array encompassing 58,433 SNP probe sets, and population specific male and female parent linkage maps were constructed. The parental maps of each population were integrated to produce sub-composite maps, which were further merged to develop a consensus linkage map. All the parental maps (except 'MK_D') had nine major linkage groups, and contained 930 ('SB'), 810 ('MK_SB'), 776 ('D') and 707 ('MK_D') SNPs. The linkage maps displayed 96.9 ('MK_D') to 98.5% ('SB') chromosomal synteny with the reference Clementine genome. The consensus map was comprised of 2588 markers including a phenotypic seedless (Fs)-locus and spanned a genetic distance of 1406.84 cM, with an average marker distance of 0.54 cM, which is substantially lower than the reference Clementine map. For the phenotypic Fs-locus, the distribution of seedy and seedless progenies in both 'SB' × 'MK' (55:42, χ2 = 1.74) and 'D' × 'MK' populations (33:35, χ2 = 0.06) followed a test cross pattern. The Fs-locus mapped on chromosome 5 with SNP marker 'AX-160417325' at 7.4 cM in 'MK_SB' map and between two SNP markers 'AX-160536283' and 'AX-160906995' at a distance of 2.4 and 4.9 cM, respectively in 'MK_D' map. The SNPs 'AX-160417325' and 'AX-160536283' correctly predicted seedlessness of 25-91.9% progenies in this study. Based on the alignment of flanking SNP markers to the Clementine reference genome, the candidate gene for seedlessness hovered in a ~ 6.0 Mb region between 3.97 Mb (AX-160906995) to 10.00 Mb (AX-160536283). This region has 131 genes of which 13 genes (belonging to seven gene families) reportedly express in seed coat or developing embryo. The findings of the study will prove helpful in directing future research for fine mapping this region and eventually underpinning the exact causative gene governing seedlessness in 'MK'.
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Affiliation(s)
- Krishan Kumar
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
- Punjab Agricultural University, Dr. JC Bakhshi Regional Research Station, Abohar, India
| | - Qibin Yu
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Chitose Honsho
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
- Laboratory of Pomology, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Frederick G. Gmitter
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
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Noda T, Daiou K, Mihara T, Nagano Y. Potential application of simple easy-to-use insertion-deletion (InDel) markers in citrus cultivar identification. BREEDING SCIENCE 2021; 71:601-608. [PMID: 35087324 PMCID: PMC8784345 DOI: 10.1270/jsbbs.21021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/09/2021] [Indexed: 05/27/2023]
Abstract
We previously developed insertion-deletion (InDel) markers that distinguish three genotypes (two homozygous and one heterozygous) of diverse citrus cultivars. These InDel markers were codominant and could be clearly detected by using simple agarose gel electrophoresis. We sought to establish a method for cultivar identification using these 28 InDel markers to genotype 31 citrus cultivars. The results revealed that a minimum of 6 markers were required to identify individuals using the three-genotype classification method. Furthermore, we found that a simple method for distinguishing between two genotypes (homozygous and heterozygous) could be used to identify individuals using a minimum of 7 markers. Our findings provide a basis for the development of simple and rapid citrus cultivar identification methods.
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Affiliation(s)
- Takahiro Noda
- Kumamoto Prefectural Agricultural Research Center, 3801 Sakae, Koshi, Kumamoto 861-1113, Japan
| | - Kaoru Daiou
- Kumamoto Prefectural Agricultural Research Center, 3801 Sakae, Koshi, Kumamoto 861-1113, Japan
| | - Takashi Mihara
- Kumamoto Prefectural Fruit Tree Research Institute, 2566 Toyofuku Matsubase-machi, Uki, Kumamoto 869-0524, Japan
| | - Yukio Nagano
- Analytical Research Center for Experimental Sciences, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
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Dou Y, Xia W, Mason AS, Huang D, Sun X, Fan H, Xiao Y. Developing functional markers for vitamin E biosynthesis in oil palm. PLoS One 2021; 16:e0259684. [PMID: 34797841 PMCID: PMC8604351 DOI: 10.1371/journal.pone.0259684] [Citation(s) in RCA: 1] [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: 07/13/2021] [Accepted: 10/24/2021] [Indexed: 11/19/2022] Open
Abstract
Vitamin E is essential for human health and plays positive roles in anti-oxidation. Previously, we detected large variation in vitamin E content among 161 oil palm accessions. In this study, twenty oil palm accessions with distinct variation in vitamin E contents (171.30 to 1 258.50 ppm) were selected for genetic variation analysis and developing functional markers associated with vitamin E contents. Thirty-seven homologous genes in oil palm belonging to vitamin E biosynthesis pathway were identified via BLASTP analysis, the lengths of which ranged from 426 to 25 717 bp (average 7 089 bp). Multiplex PCR sequencing for the 37 genes found 1 703 SNPs and 85 indels among the 20 oil palm accessions, with 226 SNPs locating in the coding regions. Clustering analysis for these polymorphic loci showed that the 20 oil palm accessions could be divided into five groups. Among these groups, group I included eight oil palm accessions whose vitamin E content (mean value: 893.50 ppm) was far higher than other groups (mean value 256.29 to 532.94 ppm). Correlation analysis between the markers and vitamin E traits showed that 134 SNP and 7 indel markers were significantly (p < 0.05) related with total vitamin E content. Among these functional markers, the indel EgTMT-1-24 was highly correlated with variation in vitamin E content, especially tocotrienol content. Our study identified a number of candidate function associated markers and provided clues for further research into molecular breeding for high vitamin E content oil palm.
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Affiliation(s)
- Yajing Dou
- College of Tropical Crops, Hainan University, Haikou, Hainan, P.R. China
- Coconut Research Institute, Chinese Academy of Tropical Agricultural sciences, Wenchang, Hainan, P.R. China
| | - Wei Xia
- College of Tropical Crops, Hainan University, Haikou, Hainan, P.R. China
| | - Annaliese S. Mason
- Plant Breeding Department, The University of Bonn, Bonn, North Rhine-Westphalia, Germany
| | - Dongyi Huang
- College of Tropical Crops, Hainan University, Haikou, Hainan, P.R. China
| | - Xiwei Sun
- Coconut Research Institute, Chinese Academy of Tropical Agricultural sciences, Wenchang, Hainan, P.R. China
| | - Haikuo Fan
- Coconut Research Institute, Chinese Academy of Tropical Agricultural sciences, Wenchang, Hainan, P.R. China
| | - Yong Xiao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural sciences, Wenchang, Hainan, P.R. China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, P.R. China
- * E-mail: ,
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6
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Dutt M, Mahmoud LM, Chamusco K, Stanton D, Chase CD, Nielsen E, Quirico M, Yu Q, Gmitter FG, Grosser JW. Utilization of somatic fusion techniques for the development of HLB tolerant breeding resources employing the Australian finger lime (Citrus australasica). PLoS One 2021; 16:e0255842. [PMID: 34375348 PMCID: PMC8354479 DOI: 10.1371/journal.pone.0255842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/23/2021] [Indexed: 11/18/2022] Open
Abstract
The Australian finger lime is a unique citrus species that has gained importance due to its unique fruit characteristics and perceived tolerance to Huanglongbing (HLB), an often-fatal disease of citrus trees. In this study, we developed allotetraploid finger lime hybrids and cybrids by utilizing somatic cell fusion techniques to fuse diploid ‘OLL8’ sweet orange or ‘Page’ tangelo callus-derived protoplasts with finger lime (FL) mesophyll-derived protoplasts. Six somatic fusions were regenerated from the ‘OLL8’ + FL fusion, while three putative cybrids were regenerated from the ‘Page’ + FL fusion. Ploidy levels and nuclear-expressed sequence tag derived simple sequence repeat (EST-SSR) markers confirmed the somatic hybrid production, and mitochondrial DNA primer sets confirmed the cybrid nature. Several trees produced by the somatic fusion remained HLB negative even after 6 years of growth in an HLB-endemic environment. Pathogenesis related (PR) and other genes that are often upregulated in HLB-tolerant trees were also upregulated in our somatic fusions. These newly developed somatic fusions and cybrids could potentially be used as breeding parents to develop the next generation of improved HLB-tolerant rootstocks and scions.
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Affiliation(s)
- Manjul Dutt
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
- * E-mail:
| | - Lamiaa M. Mahmoud
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
- Faculty of Agriculture, Pomology Department, Mansoura University, Mansoura, Egypt
| | - Karen Chamusco
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States of America
| | - Daniel Stanton
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
| | - Christine D. Chase
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States of America
| | - Ethan Nielsen
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
| | - Maria Quirico
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
| | - Qibin Yu
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
| | - Frederick G. Gmitter
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
| | - Jude W. Grosser
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
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Xu YY, Liu SR, Gan ZM, Zeng RF, Zhang JZ, Hu CG. High-Density Genetic Map Construction and Identification of QTLs Controlling Leaf Abscission Trait in Poncirus trifoliata. Int J Mol Sci 2021; 22:ijms22115723. [PMID: 34072027 PMCID: PMC8198561 DOI: 10.3390/ijms22115723] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/06/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022] Open
Abstract
A high-density genetic linkage map is essential for genetic and genomic studies including QTL mapping, genome assembly, and comparative genomic analysis. Here, we constructed a citrus high-density linkage map using SSR and SNP markers, which are evenly distributed across the citrus genome. The integrated linkage map contains 4163 markers with an average distance of 1.12 cM. The female and male linkage maps contain 1478 and 2976 markers with genetic lengths of 1093.90 cM and 1227.03 cM, respectively. Meanwhile, a genetic map comparison demonstrates that the linear order of common markers is highly conserved between the clementine mandarin and Poncirus trifoliata. Based on this high-density integrated citrus genetic map and two years of deciduous phenotypic data, two loci conferring leaf abscission phenotypic variation were detected on scaffold 1 (including 36 genes) and scaffold 8 (including 107 genes) using association analysis. Moreover, the expression patterns of 30 candidate genes were investigated under cold stress conditions because cold temperature is closely linked with the deciduous trait. The developed high-density genetic map will facilitate QTL mapping and genomic studies, and the localization of the leaf abscission deciduous trait will be valuable for understanding the mechanism of this deciduous trait and citrus breeding.
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Affiliation(s)
| | | | | | | | - Jin-Zhi Zhang
- Correspondence: (J.-Z.Z.); (C.-G.H.); Tel.: +86-27-8728-2010 (J.-Z.Z. & C.-G.H.)
| | - Chun-Gen Hu
- Correspondence: (J.-Z.Z.); (C.-G.H.); Tel.: +86-27-8728-2010 (J.-Z.Z. & C.-G.H.)
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Curtolo M, Granato LM, Soratto TAT, Curtolo M, Gazaffi R, Takita MA, Cristofani-Yaly M, Machado MA. Expression Quantitative Trait Loci (eQTL) mapping for callose synthases in intergeneric hybrids of Citrus challenged with the bacteria Candidatus Liberibacter asiaticus. Genet Mol Biol 2020; 43:e20190133. [PMID: 32568357 PMCID: PMC7295156 DOI: 10.1590/1678-4685-gmb-2019-0133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 01/07/2020] [Indexed: 11/21/2022] Open
Abstract
Citrus plants have been extremely affected by Huanglongbing (HLB) worldwide, causing
economic losses. HLB disease causes disorders in citrus plants, leading to callose
deposition in the phloem vessel sieve plates. Callose is synthesized by callose
synthases, which are encoded by 12 genes (calS1–
calS12)in Arabidopsis thaliana. We evaluated the
expression of eight callose synthase genes from Citrus in hybrids between
Citrus sunki and Poncirus trifoliata infected
with HLB. The objective of this work was to identify possible tolerance loci
combining the expression quantitative trait loci (eQTL) of different callose
synthases and genetic Single-Nucleotide Polymorphism (SNP) maps of C.
sunki and P. trifoliata. The expression data from all
CscalS ranged widely among the hybrids. Furthermore, the data
allowed the detection of 18 eQTL in the C. sunki map and 34 eQTL in
the P. trifoliata map. In both maps, some eQTL for different
CscalS were overlapped; thus, a single region could be associated
with the regulation of more than one CscalS. The regions identified
in this work can be interesting targets for future studies of Citrus
breeding programs to manipulate callose synthesis during HLB infection.
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Affiliation(s)
- Maiara Curtolo
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil.,Universidade Estadual de Campinas, Programa de Pós-Graduação em Genética e Biologia Molecular, Campinas, SP, Brazil
| | - Laís Moreira Granato
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil
| | | | - Maisa Curtolo
- Universidade de São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Programa de Pós-Graduação em Genética e Melhoramento de Plantas, Piracicaba, SP, Brazil
| | - Rodrigo Gazaffi
- Universidade Federal de São Carlos, Centro de Ciências Agrárias, Departamento de Biotecnologia e Produção Vegetal e Animal, Araras, SP, Brazil
| | - Marco Aurélio Takita
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil
| | | | - Marcos Antonio Machado
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil
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Garavello M, Cuenca J, Dreissig S, Fuchs J, Navarro L, Houben A, Aleza P. Analysis of Crossover Events and Allele Segregation Distortion in Interspecific Citrus Hybrids by Single Pollen Genotyping. FRONTIERS IN PLANT SCIENCE 2020; 11:615. [PMID: 32523591 PMCID: PMC7261893 DOI: 10.3389/fpls.2020.00615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/21/2020] [Indexed: 05/17/2023]
Abstract
In citrus, a classical method of studying crossovers and segregation distortion (SD) is the genetic analysis of progenies. A new strategy combining fluorescence-activated cell sorting and whole genome amplification of haploid pollen nuclei with a large set of molecular markers, offers the opportunity to efficiently determine the frequency of crossovers and the identification of SD without the need to generate segregating populations. Here we have analyzed meiotic crossover events in a pollen nuclei population from "Eureka" lemon and the allelic SD was evaluated in a pollen nuclei population from a clementine × sweet orange hybrid ("CSO"). Data obtained from the "CSO" pollen nuclei population were compared to those obtained from genotyping of a segregating population ("RTSO") arising from a hand-made sexual hybridization between diploid non apomictic selected tangor (mandarin × sweet orange; "RTO" tangor) as female parent pollinated with "CSO" tangor as male parent. The analysis of crossovers rates on chromosome 1 revealed the presence of up to five crossovers events on one arm and four on the corresponding other arm, with an average of 1.97 crossovers per chromosome while no crossover events were observed in five "Eureka" lemon pollen nuclei. The rate of SD observed in "CSO" pollen nuclei (13.8%) was slightly lower than that recovered in the "RTSO" population (20.7%). In the pollen nuclei population, SD was found on linkage group (LG) 2, while the "RTSO" population showed SD on LGs 2 and 7. Potential male gametic selection mechanisms were distinguished in pollen grains, while in the population, mechanisms of gametophytic selection and/or zygotic selection were observed. This methodology is a very useful tool to facilitate research focused on the reproductive biology of citrus and study the mechanisms that affect crossovers and SD.
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Affiliation(s)
- Miguel Garavello
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
- Concordia Agricultural Experiment Station, National Agricultural Technology Institute, Entre Ríos, Argentina
| | - José Cuenca
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Steven Dreissig
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Jörg Fuchs
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Luis Navarro
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Andreas Houben
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Pablo Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
- *Correspondence: Pablo Aleza,
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Zheng X, Tang Y, Ye J, Pan Z, Tan M, Xie Z, Chai L, Xu Q, Fraser PD, Deng X. SLAF-Based Construction of a High-Density Genetic Map and Its Application in QTL Mapping of Carotenoids Content in Citrus Fruit. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:994-1002. [PMID: 30589260 DOI: 10.1021/acs.jafc.8b05176] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Carotenoids are important antioxidant components in the human diet. To develop carotenoid-rich agricultural products by genetic intervention, understanding the genetic basis of carotenoids variation is essential. In this study, we constructed a high-density integrated genetic map with 3817 molecular markers using specific locus amplified fragment (SLAF) sequencing from a C. reticulata × P. trifoliata F1 pseudotestcross population. A total of 17 significant quantitative trait loci (QTLs) distributed on Chromosomes (Chr) 2, 3, 5, 6, and 9 were detected to determine the carotenoid variation in the population. In particular, three QTL colocalizations for multiple carotenoid constituents were observed on Chr 2, 3, and 9, one of which was located on Chr2:34,654,608-35430715 accounted for 20.1-25.4% of the variation of luteoxanthin, auroxanthin, lutein, violaxanthin, and total carotenoid content. Overall, this study provides a genetic foundation for marker-assisted selection (MAS) breeding of nutritionally enhanced citrus fruit.
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Affiliation(s)
- Xiongjie Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Yuqing Tang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Junli Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Zhiyong Pan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Meilian Tan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Zongzhou Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Lijun Chai
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
| | - Paul D Fraser
- School of Biological Sciences, Royal Holloway , University of London , Egham, Surrey TW20 0EX , United Kingdom
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education) , Huazhong Agricultural University , Wuhan , China
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11
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Huang M, Roose ML, Yu Q, Du D, Yu Y, Zhang Y, Deng Z, Stover E, Gmitter FG. Construction of High-Density Genetic Maps and Detection of QTLs Associated With Huanglongbing Tolerance in Citrus. FRONTIERS IN PLANT SCIENCE 2018; 9:1694. [PMID: 30542355 PMCID: PMC6278636 DOI: 10.3389/fpls.2018.01694] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/31/2018] [Indexed: 05/29/2023]
Abstract
Huanglongbing (HLB), or citrus greening, is the most devastating disease in citrus worldwide. Commercial citrus varieties including sweet orange (Citrus sinensis) are highly susceptible to HLB, and trifoliate orange (Poncirus trifoliata, a close Citrus relative) is widely considered resistant or highly tolerant to HLB. In this study, an intergeneric F1 population of sweet orange and trifoliate orange was genotyped by Genotyping-by-Sequencing, and high-density SNP-based genetic maps were constructed separately for trifoliate orange and sweet orange. The two genetic maps exhibited high synteny and high coverage of the citrus genome. Progenies of the F1 population and their parents were planted in a replicated field trial, exposed to intense HLB pressure for 3 years, and then evaluated for susceptibility to HLB over 2 years. The F1 population exhibited a wide range in severity of HLB foliar symptom and canopy damage. Genome-wide QTL analysis based on the phenotypic data of foliar symptom and canopy damage in 2 years identified three clusters of repeatable QTLs in trifoliate orange linkage groups LG-t6, LG-t8 and LG-t9. Co-localization of QTLs for two traits was observed within all three regions. Additionally, one cluster of QTLs in sweet orange (linkage group LG-s7) was also detected. The majority of the identified QTLs each explained 18-30% of the phenotypic variation, indicating their major role in determining HLB responses. These results show, for the first time, a quantitative genetic nature yet the presence of major loci for the HLB tolerance in trifoliate orange. The results suggest that sweet orange also contains useful genetic factor(s) for improving HLB tolerance in commercial citrus varieties. Findings from this study should be very valuable and timely to researchers worldwide as they are hastily searching for genetic solutions to the devastating HLB crisis through breeding, genetic engineering, or genome editing.
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Affiliation(s)
- Ming Huang
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Mikeal L. Roose
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Qibin Yu
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Dongliang Du
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Yuan Yu
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Yi Zhang
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Zhanao Deng
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Ed Stover
- United States Horticultural Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Fort Pierce, FL, United States
| | - Frederick G. Gmitter
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
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12
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Kamiri M, Stift M, Costantino G, Dambier D, Kabbage T, Ollitrault P, Froelicher Y. Preferential Homologous Chromosome Pairing in a Tetraploid Intergeneric Somatic Hybrid ( Citrus reticulata + Poncirus trifoliata) Revealed by Molecular Marker Inheritance. FRONTIERS IN PLANT SCIENCE 2018; 9:1557. [PMID: 30450106 PMCID: PMC6224360 DOI: 10.3389/fpls.2018.01557] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/04/2018] [Indexed: 05/23/2023]
Abstract
The creation of intergeneric somatic hybrids between Citrus and Poncirus is an efficient approach for citrus rootstock breeding, offering the possibility of combining beneficial traits from both genera into novel rootstock lineages. These somatic hybrids are also used as parents for further tetraploid sexual breeding. In order to optimize these latter breeding schemes, it is essential to develop knowledge on the mode of inheritance in the intergeneric tetraploid hybrids. We assessed the meiotic behavior of an intergeneric tetraploid somatic hybrid resulting from symmetric protoplast fusion of diploid Citrus reticulata and diploid Poncirus trifoliata. The analysis was based on the segregation patterns of 16 SSR markers and 9 newly developed centromeric/pericentromeric SNP markers, representing all nine linkage groups of the Citrus genetic map. We found strong but incomplete preferential pairing between homologues of the same ancestral genome. The proportion of gametes that can be explained by random meiotic chromosome associations (τ) varied significantly between chromosomes, from 0.09 ± 0.02 to 0.47 ± 0.09, respectively, in chromosome 2 and 1. This intermediate inheritance between strict disomy and tetrasomy, with global preferential disomic tendency, resulted in a high level of intergeneric heterozygosity of the diploid gametes. Although limited, intergeneric recombinations occurred, whose observed rates, ranging from 0.09 to 0.29, respectively, in chromosome 2 and 1, were significantly correlated with τ. Such inheritance is of particular interest for rootstock breeding because a large part of the multi-trait value selected at the teraploid parent level is transmitted to the progeny, while the potential for some intergeneric recombination offers opportunities for generating plants with novel allelic combinations that can be targeted by selection.
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Affiliation(s)
| | - Marc Stift
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
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13
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Goto S, Yoshioka T, Ohta S, Kita M, Hamada H, Shimizu T. QTL mapping of male sterility and transmission pattern in progeny of Satsuma mandarin. PLoS One 2018; 13:e0200844. [PMID: 30016346 PMCID: PMC6049952 DOI: 10.1371/journal.pone.0200844] [Citation(s) in RCA: 14] [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: 03/29/2018] [Accepted: 07/02/2018] [Indexed: 11/19/2022] Open
Abstract
Seedlessness is one of the important traits in citrus breeding. Male sterility derived from Satsuma mandarin (Citrus unshiu) has been used in Japanese citrus breeding programs to obtain seedless cultivars. The efficiency of seedless cultivar breeding would be improved by developing a selection marker linked to seedlessness. In this study, we performed QTL mapping in ‘Okitsu No. 46’ × ‘Okitsu No. 56’ (O46-O56) crosses for the number of pollen grains per anther (NPG) and apparent pollen fertility (APF), two traits used as an index of male sterility, and detected a candidate QTL for NPG (MS-P1) on linkage group 8 with a significant LOD score (7.31) and 47% of variance explained. The QTL for APF (MS-F1) was detected on linkage group 6 with a significant LOD score (5.71) and 63.6% of variance explained. The role of both MS-P1 in reducing NPG and MS-F1 in decreasing APF were confirmed with the ‘Okitsu No.46’ × ‘Kara’ (O46-K) cross. Pedigree analysis inferred that both MS-P1 and MS-F1 in ‘Okitsu No. 46’ were derived from kunenbo (Citrus nobilis) through hassaku (C. hassaku) and ‘Sweet Spring’. Cytoplasm analysis revealed that both male-sterile ‘Sweet Spring’ and ‘Okitsu No. 46’ have cytoplasm derived from Kishu (C. kinokuni hort. ex Tanaka), but the cytoplasm of male-sterile kunenbo and hassaku were derived from other varieties rather than Kishu. These results suggest that MS-P1 and MS-F1 primarily reduce the NPG and decrease APF, but their expression requires a cytoplasm derived from Kishu. These findings will improve our understanding of the molecular mechanism of male sterility in citrus and help to develop a DNA marker for seedless breeding in citrus.
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Affiliation(s)
- Shingo Goto
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shizuoka, Japan
| | - Terutaka Yoshioka
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shizuoka, Japan
| | - Satoshi Ohta
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shizuoka, Japan
| | - Masayuki Kita
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shizuoka, Japan
| | - Hiroko Hamada
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shizuoka, Japan
| | - Tokurou Shimizu
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shizuoka, Japan
- * E-mail:
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14
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Huang M, Roose ML, Yu Q, Du D, Yu Y, Zhang Y, Deng Z, Stover E, Gmitter FG. Construction of High-Density Genetic Maps and Detection of QTLs Associated With Huanglongbing Tolerance in Citrus. FRONTIERS IN PLANT SCIENCE 2018. [PMID: 30542355 DOI: 10.1101/330753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Huanglongbing (HLB), or citrus greening, is the most devastating disease in citrus worldwide. Commercial citrus varieties including sweet orange (Citrus sinensis) are highly susceptible to HLB, and trifoliate orange (Poncirus trifoliata, a close Citrus relative) is widely considered resistant or highly tolerant to HLB. In this study, an intergeneric F1 population of sweet orange and trifoliate orange was genotyped by Genotyping-by-Sequencing, and high-density SNP-based genetic maps were constructed separately for trifoliate orange and sweet orange. The two genetic maps exhibited high synteny and high coverage of the citrus genome. Progenies of the F1 population and their parents were planted in a replicated field trial, exposed to intense HLB pressure for 3 years, and then evaluated for susceptibility to HLB over 2 years. The F1 population exhibited a wide range in severity of HLB foliar symptom and canopy damage. Genome-wide QTL analysis based on the phenotypic data of foliar symptom and canopy damage in 2 years identified three clusters of repeatable QTLs in trifoliate orange linkage groups LG-t6, LG-t8 and LG-t9. Co-localization of QTLs for two traits was observed within all three regions. Additionally, one cluster of QTLs in sweet orange (linkage group LG-s7) was also detected. The majority of the identified QTLs each explained 18-30% of the phenotypic variation, indicating their major role in determining HLB responses. These results show, for the first time, a quantitative genetic nature yet the presence of major loci for the HLB tolerance in trifoliate orange. The results suggest that sweet orange also contains useful genetic factor(s) for improving HLB tolerance in commercial citrus varieties. Findings from this study should be very valuable and timely to researchers worldwide as they are hastily searching for genetic solutions to the devastating HLB crisis through breeding, genetic engineering, or genome editing.
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Affiliation(s)
- Ming Huang
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Mikeal L Roose
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Qibin Yu
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Dongliang Du
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Yuan Yu
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Yi Zhang
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Zhanao Deng
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Ed Stover
- United States Horticultural Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Fort Pierce, FL, United States
| | - Frederick G Gmitter
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
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15
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Curtolo M, Cristofani-Yaly M, Gazaffi R, Takita MA, Figueira A, Machado MA. QTL mapping for fruit quality in Citrus using DArTseq markers. BMC Genomics 2017; 18:289. [PMID: 28403819 PMCID: PMC5389163 DOI: 10.1186/s12864-017-3629-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/14/2017] [Indexed: 11/24/2022] Open
Abstract
Background Citrus breeding programs have many limitations associated with the species biology and physiology, requiring the incorporation of new biotechnological tools to provide new breeding possibilities. Diversity Arrays Technology (DArT) markers, combined with next-generation sequencing, have wide applicability in the construction of high-resolution genetic maps and in quantitative trait locus (QTL) mapping. This study aimed to construct an integrated genetic map using full-sib progeny derived from Murcott tangor and Pera sweet orange and DArTseq™ molecular markers and to perform QTL mapping of twelve fruit quality traits. A controlled Murcott x Pera crossing was conducted at the Citrus Germplasm Repository at the Sylvio Moreira Citrus Centre of the Agronomic Institute (IAC) located in Cordeirópolis, SP, in 1997. In 2012, 278 F1 individuals out of a family of 312 confirmed hybrid individuals were analyzed for fruit traits and genotyped using the DArTseq markers. Using OneMap software to obtain the integrated genetic map, we considered only the DArT loci that showed no segregation deviation. The likelihood ratio and the genomic information from the available Citrus sinensis L. Osbeck genome were used to determine the linkage groups (LGs). Results The resulting integrated map contained 661 markers in 13 LGs, with a genomic coverage of 2,774 cM and a mean density of 0.23 markers/cM. The groups were assigned to the nine Citrus haploid chromosomes; however, some of the chromosomes were represented by two LGs due the lack of information for a single integration, as in cases where markers segregated in a 3:1 fashion. A total of 19 QTLs were identified through composite interval mapping (CIM) of the 12 analyzed fruit characteristics: fruit diameter (cm), height (cm), height/diameter ratio, weight (g), rind thickness (cm), segments per fruit, total soluble solids (TSS, %), total titratable acidity (TTA, %), juice content (%), number of seeds, TSS/TTA ratio and number of fruits per box. The genomic sequence (pseudochromosomes) of C. sinensis was compared to the genetic map, and synteny was clearly identified. Further analysis of the map regions with the highest LOD scores enabled the identification of putative genes that could be associated with the fruit quality characteristics. Conclusion An integrated linkage map of Murcott tangor and Pera sweet orange using DArTseq™ molecular markers was established and it was useful to perform QTL mapping of twelve fruit quality traits. The next generation sequences data allowed the comparison between the linkage map and the genomic sequence (pseudochromosomes) of C. sinensis and the identification of genes that may be responsible for phenotypic traits in Citrus. The obtained linkage map was used to assign sequences that had not been previously assigned to a position in the reference genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3629-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maiara Curtolo
- Centro de Energia Nuclear na Agricultura - Universidade de São Paulo (USP), 13400-970, Piracicaba, SP, Brazil.,Centro APTA Citros Sylvio Moreira - Instituto Agronômico (IAC), CP 04, 13490-970, Cordeirópolis, SP, Brazil
| | - Mariângela Cristofani-Yaly
- Centro APTA Citros Sylvio Moreira - Instituto Agronômico (IAC), CP 04, 13490-970, Cordeirópolis, SP, Brazil.
| | - Rodrigo Gazaffi
- Universidade Federal de São Carlos (UFSCar) - Centro de Ciências Agrárias, Rodovia Anhanguera, km 174, 13600-970, Araras, SP, Brazil
| | - Marco Aurélio Takita
- Centro APTA Citros Sylvio Moreira - Instituto Agronômico (IAC), CP 04, 13490-970, Cordeirópolis, SP, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura - Universidade de São Paulo (USP), 13400-970, Piracicaba, SP, Brazil
| | - Marcos Antonio Machado
- Centro APTA Citros Sylvio Moreira - Instituto Agronômico (IAC), CP 04, 13490-970, Cordeirópolis, SP, Brazil
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16
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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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17
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Patterns of genetic structure and evidence of gene flow among Tunisian Citrus species based on informative nSSR markers. C R Biol 2016; 339:371-7. [PMID: 27522638 DOI: 10.1016/j.crvi.2016.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 11/22/2022]
Abstract
This study investigates the extent of genetic diversity, phylogenetic relationships and the amount of gene flow among Tunisian Citrus species based on a set of 15 informative nuclear SSR molecular markers. Genotyping data highlighted an allelic richness among Tunisian Citrus species and has allowed the detection of 168 alleles among them 104.19 were effective. The partition of the total genetic diversity (HT=0.832) showed that the highest amount of variation within the Citrus species is HS=0.550, while the relative amount of the between-species genetic diversity GST does not exceed 0.338. This pattern of genetic structure was supported by low-to-moderate FST pairwise values and the presence of a gene flow (Nm) among the eight Citrus species. The lowest genetic differentiation was revealed between the species C. sinensis and C. insitorum (FST=0.111, Nm=1.99), while the highest genetic differentiation was recorded between the species C. aurantifolia and C. paradisi (FST=0.367, Nm=0.43). The established Neighbor Joining analysis showed that all genotypes were widely discriminated and clearly pooled according to their species of origin, with minor exceptions.
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18
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Honsho C, Sakata A, Tanaka H, Ishimura S, Tetsumura T. Single-pollen genotyping to estimate mode of unreduced pollen formation in Citrus tamurana cv. Nishiuchi Konatsu. PLANT REPRODUCTION 2016; 29:189-97. [PMID: 26968168 DOI: 10.1007/s00497-016-0277-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/22/2016] [Indexed: 05/23/2023]
Abstract
2n pollen formed by FDR in citrus. The Japanese local citrus cultivar, Nishiuchi Konatsu (Citrus tamurana hort. ex Tanaka; NK hereafter), has the ability to produce unreduced 2n pollen grains, allowing generation of polyploid progenies via sexual polyploidization. In this study, we developed a method of single-pollen genotyping for citrus and applied it to the analysis of transmission of heterozygosity in NK 2n pollen grains. Heterozygosity transmission was expressed as the percentage inheritance of a set of heterozygous alleles from the parent to the 2n gamete. The pathway of 2n pollen development was investigated by applying the observed heterozygosity transmission and genetic distance to two different map functions, for first division restitution (FDR) and second division restitution (SDR). The fit of the values observed for both functions was calculated, while virtually moving the centromere position. We screened for six heterozygous SSR (codominant microsatellite marker loci) in NK, all of which were expected to lie within the same linkage group. Pollen germination prior to DNA extraction was essential for this work, and 6-h incubation proved to be optimal for subsequent PCR amplification. Single-pollen genotyping unreduced NK 2n pollen grains revealed that heterozygosity transmission exceeded 50 % in all six alleles, and fitness tests indicated that the FDR map function better fitted the heterozygosity transmission observed rather than the SDR function. Our data thus strongly indicate that 2n pollen in NK is a result of first division restitution.
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Affiliation(s)
- Chitose Honsho
- Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan.
| | - Aisa Sakata
- Graduate School of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Hikaru Tanaka
- Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Shuji Ishimura
- Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Takuya Tetsumura
- Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
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19
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Wang G, Guo Y, Zhao Y, Su K, Zhang J. Construction of a molecular genetic map for hawthorn based on SRAP markers. BIOTECHNOL BIOTEC EQ 2015. [DOI: 10.1080/13102818.2015.1018322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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20
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Ranade SS, Lin YC, Zuccolo A, Van de Peer Y, García-Gil MDR. Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera. BMC PLANT BIOLOGY 2014; 14:220. [PMID: 25143005 PMCID: PMC4160553 DOI: 10.1186/s12870-014-0220-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 08/05/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5'UTR, ORF and 3'UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera). RESULTS Our analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera. CONCLUSIONS Our analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.
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Affiliation(s)
- Sonali Sachin Ranade
- />Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden
| | - Yao-Cheng Lin
- />Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Andrea Zuccolo
- />Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy
- />Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy
| | - Yves Van de Peer
- />Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- />Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, 0028 South Africa
| | - María del Rosario García-Gil
- />Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden
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21
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Sequence analysis reveals genomic factors affecting EST-SSR primer performance and polymorphism. Mol Genet Genomics 2014; 289:1147-56. [PMID: 24948352 DOI: 10.1007/s00438-014-0875-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 05/30/2014] [Indexed: 10/25/2022]
Abstract
This study was to explore genomic factors affecting the performance and polymorphism of 340 randomly selected EST-SSR (expressed sequence tag-simple sequence repeat) primers through BLAST of primer sequences to a reference genome. Genotyping showed 111 failed and 229 succeeded. The failed types included "no peaks" (NP, 69 primers), "weak peaks" (WP, 30), and "multiple peaks" (MP, 12). The successful types were divided into HM (homozygous between two selected parents, 78 primers) and HT (heterozygous at least in one parent, 151 primers). The BLAST revealed primer alignment status, genomic amplicon size (GAS), and genomic and expressed amplicon size difference (ASD). The alignment status was categorized as: "no hits found" (NHF); "multiple partial alignments" (MPA); "single partial alignment" (SPA); "multiple full alignments" (MFA); and "single full alignment" (SFA). NHF and partial alignment (PA) mainly resulted from discrepant nucleotides in contig-derived primers. The ASD separated 247 non-NHF primers into: "deletion", "same size", "insertion", "intron (GAS ≤500)", "intron (GAS >500)", and "error" categories. Most SFA primers were successful. About 88 % "error", 53 % NHF primers, and 47 % "intron (GAS >500)" failed. The "deletion" and "insertion" primers had the higher HT rates, and the "same size" had the highest HM rate. Optimized primer selection criteria are discussed.
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22
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Hvarleva T, Kapari-Isaia T, Papayiannis L, Atanassov A, Hadjinicoli A, Kyriakou A. Characterization of Citrus Cultivars and Clones in Cyprus Through Microsatellite and RAPD Analysis. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2008.10817554] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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23
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Nageswara-Rao M, Irey M, Garnsey SM, Gowda S. Candidate gene markers for Candidatus Liberibacter asiaticus for detecting citrus greening disease. J Biosci 2013; 38:229-37. [PMID: 23660656 DOI: 10.1007/s12038-013-9315-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Citrus Huanglongbing (HLB) also known as citrus greening is one of the most devastating diseases of citrus worldwide. The disease is caused by Candidatus Liberibacter bacterium, vectored by the psyllid Diaphorina citri Kuwayama and Trioza erytreae Del Guercio. Citrus plants infected by the HLB bacterium may not show visible symptoms sometimes for years following infection. The aim of this study was to develop effective gene-specific primer pairs for polymerase chain reaction based method for quick screening of HLB disease. Thirty-two different gene-specific primer pairs, across the Ca. Liberibacter asiaticus genome, were successfully developed. The possibility of these primer pairs for cross-genome amplification across 'Ca. Liberibacter africanus' and 'Ca. Liberibacter americanus' were tested. The applicability of these primer pairs for detection and differentiation of Ca Liberibacter spp. is discussed.
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Affiliation(s)
- Madhugiri Nageswara-Rao
- University of Florida, IFAS, Citrus Research and Education Center, Lake Alfred, FL 33850, USA
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24
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Liu SR, Li WY, Long D, Hu CG, Zhang JZ. Development and characterization of genomic and expressed SSRs in citrus by genome-wide analysis. PLoS One 2013; 8:e75149. [PMID: 24204572 PMCID: PMC3810390 DOI: 10.1371/journal.pone.0075149] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 08/10/2013] [Indexed: 12/26/2022] Open
Abstract
Microsatellites or simple sequence repeats (SSRs) are one of the most popular sources of genetic markers and play a significant role in plant genetics and breeding. In this study, we identified citrus SSRs in the genome of Clementine mandarin and analyzed their frequency and distribution in different genomic regions. A total of 80,708 SSRs were detected in the genome with an overall density of 268 SSRs/Mb. While di-nucleotide repeats were the most frequent microsatellites in genomic DNA sequence, tetra-nucleotides, which had more repeat units than any other SSR types, had the highest cumulative sequence length. We identified 6,834 transcripts as containing 8,989 SSRs in 33,929 Clementine mandarin transcripts, among which, tri-nucleotide motifs (36.0%) were the most common, followed by di-nucleotide (26.9%) and hexa-nucleotide motifs (15.1%). The motif AG (16.7%) was most abundant among these SSRs, while motifs AAG (6.6%), AAT (5.0%), and TAG (2.2%) were most common among tri-nucleotides. Functional categorization of transcripts containing SSRs revealed that 5,879 (86.0%) of such transcripts had homology with known proteins, GO and KEGG annotation revealed that transcripts containing SSRs were those implicated in diverse biological processes in plants, including binding, development, transcription, and protein degradation. When 27 genomic and 78 randomly selected SSRs were tested on Clementine mandarin, 95 SSRs revealed polymorphism. These 95 SSRs were further deployed on 18 genotypes of the three generas of Rutaceae for the genetic diversity assessment, genomic SSRs generally show low transferability in comparison to SSRs developed from expressed sequences. These transcript-markers identified in our study may provide a valuable genetic and genomic tool for further genetic research and varietal development in citrus, such as diversity study, QTL mapping, molecular breeding, comparative mapping and other genetic analyses.
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Affiliation(s)
- Sheng-Rui Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Wen-Yang Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Dang Long
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Chun-Gen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Jin-Zhi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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25
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Germana MA, Aleza P, Carrera E, Chen C, Chiancone B, Costantino G, Dambier D, Deng X, Federici CT, Froelicher Y, Guo W, Ibáñez V, Juárez J, Kwok K, Luro F, Machado MA, Naranjo MA, Navarro L, Ollitrault P, Ríos G, Roose ML, Talon M, Xu Q, Gmitter FG. Cytological and molecular characterization of three gametoclones of Citrus clementina. BMC PLANT BIOLOGY 2013; 13:129. [PMID: 24020638 PMCID: PMC3847870 DOI: 10.1186/1471-2229-13-129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 08/24/2013] [Indexed: 05/08/2023]
Abstract
BACKGROUND Three gametoclonal plants of Citrus clementina Hort. ex Tan., cv. Nules, designated ESP, FRA, and ITA (derived from three labs in Spain, France, and Italy, respectively), were selected for cytological and molecular characterization in order to elucidate genomic rearrangements provoked by haploidization. The study included comparisons of their ploidy, homozygosity, genome integrity, and gene dosage, using chromosome counting, flow cytometry, SSR marker genotyping, and array-Comparative Genomic Hybridization (array-CGH). RESULTS Chromosome counting and flow cytometry revealed that ESP and FRA were haploid, but ITA was tri-haploid. Homozygous patterns, represented by a single peak (allele), were observed among the three plants at almost all SSR loci distributed across the entire diploid donor genome. Those few loci with extra peaks visualized as output from automated sequencing runs, generally low or ambiguous, might result from amplicons of paralogous members at the locus, non-specific sites, or unexpected recombinant alleles. No new alleles were found, suggesting the genomes remained stable and intact during gametogenesis and regeneration. The integrity of the haploid genome also was supported by array-CGH studies, in which genomic profiles were comparable to the diploid control. CONCLUSIONS The presence of few gene hybridization abnormalities, corroborated by gene dosage measurements, were hypothetically due to the segregation of hemizygous alleles and minor genomic rearrangements occurring during the haploidization procedure. In conclusion, these plants that are valuable genetic and breeding materials contain completely homozygous and essentially intact genomes.
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Affiliation(s)
- Maria Antonietta Germana
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie e Forestali, Viale delle Scienze, 11, Palermo 90128, Italy
| | - Pablo Aleza
- IVIA, Centro de Proteccion Vegetal y Biotecnologia, Moncada, Valencia, Spain
| | | | - Chunxian Chen
- University of Florida, Citrus Research and Education Center, Lake Alfred, FL, USA
- USDA-ARS, Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA, USA
| | - Benedetta Chiancone
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie e Forestali, Viale delle Scienze, 11, Palermo 90128, Italy
| | | | - Dominique Dambier
- CIRAD, Département “Systèmes Biologiques” Unité de Recherche ‘Multiplication Végétative’ Montpellier, Paris, France
| | - Xiuxin Deng
- Huazhong Agricultural University, Wuhan, Hubei, China
| | - Claire T Federici
- University of California, Department of Botany and Plant Sciences, Riverside, CA, USA
| | - Yann Froelicher
- CIRAD, Département “Systèmes Biologiques” Unité de Recherche ‘Multiplication Végétative’ Montpellier, Paris, France
| | - Wenwu Guo
- Huazhong Agricultural University, Wuhan, Hubei, China
| | | | - José Juárez
- IVIA, Centro de Proteccion Vegetal y Biotecnologia, Moncada, Valencia, Spain
| | - Kevin Kwok
- University of California, Department of Botany and Plant Sciences, Riverside, CA, USA
| | | | - Marcos A Machado
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil
| | | | - Luis Navarro
- IVIA, Centro de Proteccion Vegetal y Biotecnologia, Moncada, Valencia, Spain
| | - Patrick Ollitrault
- CIRAD, Département “Systèmes Biologiques” Unité de Recherche ‘Multiplication Végétative’ Montpellier, Paris, France
| | - Gabino Ríos
- IVIA, Centro de Genómica, Moncada, Valencia, Spain
| | - Mikeal L Roose
- University of California, Department of Botany and Plant Sciences, Riverside, CA, USA
| | - Manuel Talon
- IVIA, Centro de Genómica, Moncada, Valencia, Spain
| | - Qiang Xu
- Huazhong Agricultural University, Wuhan, Hubei, China
| | - Fred G Gmitter
- University of Florida, Citrus Research and Education Center, Lake Alfred, FL, USA
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26
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Kim NH, Choi HI, Ahn IO, Yang TJ. EST-SSR Marker Sets for Practical Authentication of All Nine Registered Ginseng Cultivars in Korea. J Ginseng Res 2013; 36:298-307. [PMID: 23717131 PMCID: PMC3659598 DOI: 10.5142/jgr.2012.36.3.298] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 04/04/2012] [Accepted: 04/04/2012] [Indexed: 11/30/2022] Open
Abstract
Panax ginseng has been cultivated for centuries, and nine commercial cultivars have been registered in Korea. However, these nine elite cultivars are grown in less than 10% of ginseng fields, and there is no clear authentication system for each cultivar even though their values are higher than those of local landraces. Here, we have developed 19 microsatellite markers using expressed gene sequences and established an authentication system for all nine cultivars. Five cultivars, ‘Chunpoong’, ‘Sunpoong’, ‘Gumpoong’, ‘Sunun’, and ‘Sunone’, can each be identified by one cultivar-unique allele, gm47n-a, gm47n-c, gm104-a, gm184-a (or gm129-a), and gm175-c, respectively. ‘Yunpoong’ can be identified by the co-appearance of gm47n-b and gm129-c. ‘Sunhyang’ can be distinguished from the other eight cultivars by the co-appearance of gm47n-b, gm129-b, and gm175-a. The two other cultivars, ‘Gopoong’ and ‘Cheongsun’, can be identified by their specific combinations of five marker alleles. This marker set was successfully utilized to identify the cultivars among 70 ginseng individuals and to select true F1 hybrid plants between two cultivars. We further analyzed the homogeneity of each cultivar and phylogenetic relationships among cultivars using these markers. This marker system will be useful to the seed industry and for breeding of ginseng.
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Affiliation(s)
- Nam-Hoon Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
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27
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Zhao Y, Williams R, Prakash CS, He G. Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.). BMC PLANT BIOLOGY 2012; 12:237. [PMID: 23241238 PMCID: PMC3568718 DOI: 10.1186/1471-2229-12-237] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 12/12/2012] [Indexed: 05/23/2023]
Abstract
BACKGROUND Date palm (Phoenix dactylifera L.) is an important tree in the Middle East and North Africa due to the nutritional value of its fruit. Molecular Breeding would accelerate genetic improvement of fruit tree through marker assisted selection. However, the lack of molecular markers in date palm restricts the application of molecular breeding. RESULTS In this study, we analyzed 28,889 EST sequences from the date palm genome database to identify simple-sequence repeats (SSRs) and to develop gene-based markers, i.e. expressed sequence tag-SSRs (EST-SSRs). We identified 4,609 ESTs as containing SSRs, among which, trinucleotide motifs (69.7%) were the most common, followed by tetranucleotide (10.4%) and dinucleotide motifs (9.6%). The motif AG (85.7%) was most abundant in dinucleotides, while motifs AGG (26.8%), AAG (19.3%), and AGC (16.1%) were most common among trinucleotides. A total of 4,967 primer pairs were designed for EST-SSR markers from the computational data. In a follow up laboratory study, we tested a sample of 20 random selected primer pairs for amplification and polymorphism detection using genomic DNA from date palm cultivars. Nearly one-third of these primer pairs detected DNA polymorphism to differentiate the twelve date palm cultivars used. Functional categorization of EST sequences containing SSRs revealed that 3,108 (67.4%) of such ESTs had homology with known proteins. CONCLUSION Date palm EST sequences exhibits a good resource for developing gene-based markers. These genic markers identified in our study may provide a valuable genetic and genomic tool for further genetic research and varietal development in date palm, such as diversity study, QTL mapping, and molecular breeding.
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Affiliation(s)
- Yongli Zhao
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088, USA
| | - Roxanne Williams
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088, USA
| | - C S Prakash
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088, USA
| | - Guohao He
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, 36088, USA
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28
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Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen J, Gao S, Xing F, Lan H, Chang JW, Ge X, Lei Y, Hu Q, Miao Y, Wang L, Xiao S, Biswas MK, Zeng W, Guo F, Cao H, Yang X, Xu XW, Cheng YJ, Xu J, Liu JH, Luo OJ, Tang Z, Guo WW, Kuang H, Zhang HY, Roose ML, Nagarajan N, Deng XX, Ruan Y. The draft genome of sweet orange (Citrus sinensis). Nat Genet 2012. [PMID: 23179022 DOI: 10.1038/ng.2472] [Citation(s) in RCA: 500] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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29
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Ai XY, Lin G, Sun LM, Hu CG, Guo WW, Deng XX, Zhang JZ. A global view of gene activity at the flowering transition phase in precocious trifoliate orange and its wild-type [Poncirus trifoliata (L.) Raf.] by transcriptome and proteome analysis. Gene 2012; 510:47-58. [DOI: 10.1016/j.gene.2012.07.090] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 07/30/2012] [Indexed: 10/28/2022]
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30
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Pastina MM, Malosetti M, Gazaffi R, Mollinari M, Margarido GRA, Oliveira KM, Pinto LR, Souza AP, van Eeuwijk FA, Garcia AAF. A mixed model QTL analysis for sugarcane multiple-harvest-location trial data. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:835-49. [PMID: 22159754 PMCID: PMC3284670 DOI: 10.1007/s00122-011-1748-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 10/28/2011] [Indexed: 05/05/2023]
Abstract
Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane.
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Affiliation(s)
- M. M. Pastina
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, 13400-970 Piracicaba, SP Brazil
| | - M. Malosetti
- Biometris, Wageningen University, P.O. Box 100, 6700 AC Wageningen, The Netherlands
| | - R. Gazaffi
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, 13400-970 Piracicaba, SP Brazil
| | - M. Mollinari
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, 13400-970 Piracicaba, SP Brazil
| | - G. R. A. Margarido
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, 13400-970 Piracicaba, SP Brazil
| | - K. M. Oliveira
- Centro de Tecnologia Canavieira (CTC), CP 162, 13400-970 Piracicaba-SP, Brazil
| | - L. R. Pinto
- Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana, IAC/Apta, CP 206, 14001-970 Ribeirão Preto, SP Brazil
| | - A. P. Souza
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Departamento de Genética e Evolução, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, 13083-875 Campinas, SP Brazil
| | - F. A. van Eeuwijk
- Biometris, Wageningen University, P.O. Box 100, 6700 AC Wageningen, The Netherlands
| | - A. A. F. Garcia
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, 13400-970 Piracicaba, SP Brazil
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31
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Wang XC, Guo L, Shangguan LF, Wang C, Yang G, Qu SC, Fang JG. Analysis of expressed sequence tags from grapevine flower and fruit and development of simple sequence repeat markers. Mol Biol Rep 2012; 39:6825-34. [DOI: 10.1007/s11033-012-1507-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 01/24/2012] [Indexed: 10/14/2022]
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32
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Belknap WR, Wang Y, Huo N, Wu J, Rockhold DR, Gu YQ, Stover E. Characterizing the citrus cultivar Carrizo genome through 454 shotgun sequencing. Genome 2011; 54:1005-15. [DOI: 10.1139/g11-070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The citrus cultivar Carrizo is the single most important rootstock to the US citrus industry and has resistance or tolerance to a number of major citrus diseases, including citrus tristeza virus, foot rot, and Huanglongbing (HLB, citrus greening). A Carrizo genomic sequence database providing approximately 3.5× genome coverage (haploid genome size approximately 367 Mb) was populated through 454 GS FLX shotgun sequencing. Analysis of the repetitive DNA fraction indicated a total interspersed repeat fraction of 36.5%. Assembly and characterization of abundant citrus Ty3/gypsy elements revealed a novel type of element containing open reading frames encoding a viral RNA-silencing suppressor protein (RNA binding protein, rbp) and a plant cytokinin riboside 5′-monophosphate phosphoribohydrolase-related protein (LONELY GUY, log). Similar gypsy elements were identified in the Populus trichocarpa genome. Gene-coding region analysis indicated that 24.4% of the nonrepetitive reads contained genic regions. The depth of genome coverage was sufficient to allow accurate assembly of constituent genes, including a putative phloem-expressed gene. The development of the Carrizo database ( http://citrus.pw.usda.gov/ ) will contribute to characterization of agronomically significant loci and provide a publicly available genomic resource to the citrus research community.
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Affiliation(s)
| | - Yi Wang
- USDA-ARS, Western Regional Research Center, Albany, CA 94710, USA
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Naxin Huo
- USDA-ARS, Western Regional Research Center, Albany, CA 94710, USA
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Jiajie Wu
- USDA-ARS, Western Regional Research Center, Albany, CA 94710, USA
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | | | - Yong Q. Gu
- USDA-ARS, Western Regional Research Center, Albany, CA 94710, USA
| | - Ed Stover
- USDA-ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL 34945, USA
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Multilocus half-tetrad analysis and centromere mapping in citrus: evidence of SDR mechanism for 2n megagametophyte production and partial chiasma interference in mandarin cv 'Fortune'. Heredity (Edinb) 2011; 107:462-70. [PMID: 21587302 DOI: 10.1038/hdy.2011.33] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The genetic structure of 2n gametes and, particularly, the parental heterozygosity restitution at each locus depends on the meiotic process by which they originated, with first-division restitution and second-division restitution (SDR) being the two major mechanisms. The origin of 2n gametes in citrus is still controversial, although sexual polyploidisation is widely used for triploid seedless cultivar development. In this study, we report the analysis of 2n gametes of mandarin cv 'Fortune' by genotyping 171 triploid hybrids with 35 simple sequence repeat markers. The microsatellite DNA allele counting-peak ratios method for allele-dosage evaluation proved highly efficient in segregating triploid progenies and allowed half-tetrad analysis (HTA) by inferring the 2n gamete allelic configuration. All 2n gametes arose from the female genitor. The observed maternal heterozygosity restitution varied between 10 and 82%, depending on the locus, thus SDR appears to be the mechanism underlying 2n gamete production in mandarin cv 'Fortune'. A new method to locate the centromere, based on the best fit between observed heterozygosity restitution within a linkage group and theoretical functions under either partial or no chiasmata interference hypotheses was successfully applied to linkage group II. The maximum value of heterozygosity restitution and the pattern of restitution along this linkage group would suggest there is partial chiasma interference. The implications of such a restitution mechanism for citrus breeding are discussed.
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Mendes S, Moraes AP, Mirkov TE, Pedrosa-Harand A. Chromosome homeologies and high variation in heterochromatin distribution between Citrus L. and Poncirus Raf. as evidenced by comparative cytogenetic mapping. Chromosome Res 2011; 19:521-30. [DOI: 10.1007/s10577-011-9203-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 03/15/2011] [Accepted: 03/15/2011] [Indexed: 10/18/2022]
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Genomic resources in horticultural crops: Status, utility and challenges. Biotechnol Adv 2011; 29:199-209. [DOI: 10.1016/j.biotechadv.2010.11.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2010] [Revised: 09/04/2010] [Accepted: 09/26/2010] [Indexed: 01/02/2023]
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Boava LP, Cristofani-Yaly M, Mafra VS, Kubo K, Kishi LT, Takita MA, Ribeiro-Alves M, Machado MA. Global gene expression of Poncirus trifoliata, Citrus sunki and their hybrids under infection of Phytophthora parasitica. BMC Genomics 2011; 12:39. [PMID: 21241495 PMCID: PMC3033816 DOI: 10.1186/1471-2164-12-39] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 01/17/2011] [Indexed: 11/14/2022] Open
Abstract
Background Gummosis and root rot caused by Phytophthora are among the most economically important diseases in citrus. Four F1 resistant hybrids (Pool R), and four F1 susceptible hybrids (Pool S) to P. parasitica, were selected from a cross between susceptible Citrus sunki and resistant Poncirus trifoliata cv. Rubidoux. We investigated gene expression in pools of four resistant and four susceptible hybrids in comparison with their parents 48 hours after P. parasitica inoculation. We proposed that genes differentially expressed between resistant and susceptible parents and between their resistant and susceptible hybrids provide promising candidates for identifying transcripts involved in disease resistance. A microarray containing 62,876 UniGene transcripts selected from the CitEST database and prepared by NimbleGen Systems was used for analyzing global gene expression 48 hours after infection with P. parasitica. Results Three pairs of data comparisons (P. trifoliata/C. sunki, Pool R/C. sunki and Pool R/Pool S) were performed. With a filter of false-discovery rate less than 0.05 and fold change greater than 3.0, 21 UniGene transcripts common to the three pairwise comparative were found to be up-regulated, and 3 UniGene transcripts were down-regulated. Among them, our results indicated that the selected transcripts were probably involved in the whole process of plant defense responses to pathogen attack, including transcriptional regulation, signaling, activation of defense genes participating in HR, single dominant genes (R gene) such as TIR-NBS-LRR and RPS4 and switch of defense-related metabolism pathway. Differentially expressed genes were validated by RT-qPCR in susceptible and resistant plants and between inoculated and uninoculated control plants Conclusions Twenty four UniGene transcripts were identified as candidate genes for Citrus response to P. parasitica. UniGene transcripts were likely to be involved in disease resistance, such as genes potentially involved in secondary metabolite synthesis, intracellular osmotic adjustment, signal transduction pathways of cell death, oxidative burst and defense gene expression. Furthermore, our microarray data suggest another type of resistance in Citrus-Phytophthora interaction conferred by single dominant genes (R gene) since we encountered two previously reported R genes (TIR-NBS-LRR and RPS4) upregulated in the resistant genotypes relative to susceptible. We identified 7 transcripts with homology in other plants but yet unclear functional characterization which are an interesting pool for further analyses and 3 transcripts where no significant similarity was found. This is the first microarray study addressing an evaluation of transcriptional changes in response to P. parasitica in Citrus.
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Affiliation(s)
- Leonardo P Boava
- Centro APTA Citros Sylvio Moreira, CP4, 13490-970, Cordeirópolis-SP, Brazil.
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Zhao Y, Guo Y, Fu J, Huang S, Lu B, Zhou J, Hu G, iu C. Molecular Genetic Map Construction and QTL Analysis for Fruit Maturation Period in Litchi. BIOTECHNOL BIOTEC EQ 2011. [DOI: 10.5504/bbeq.2011.0046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Hartung JS, Halbert SE, Pelz-Stelinski K, Brlansky RH, Chen C, Gmitter FG. Lack of Evidence for Transmission of 'Candidatus Liberibacter asiaticus' Through Citrus Seed Taken from Affected Fruit. PLANT DISEASE 2010; 94:1200-1205. [PMID: 30743616 DOI: 10.1094/pdis-09-09-0595] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Citrus huanglongbing, putatively caused by the associated bacterium 'Candidatus Liberibacter asiaticus', is the greatest threat to the world citrus industry today. The bacterium is spread locally and regionally by the citrus psyllid Diaphorina citri, and also can be disseminated by propagation of contaminated scion budwood that is grafted to the appropriate rootstock. The planting of 'Ca. Liberibacter asiaticus'-free trees is a component of a comprehensive strategy to manage huanglongbing. In contrast to the scion budwood, the rootstocks used to produce these trees are grown from seed. This research was undertaken to provide evidence as to whether or not 'Ca. L. asiaticus' can be transmitted through seed. Two groups of 360 or more seedlings each of various citrus species were grown from seed removed from fruit on trees that were symptomatic for huanglongbing and confirmed to be infected with 'Ca. L. asiaticus' by polymerase chain reaction (PCR) tests. These seedlings were tested multiple times over periods of up to 3 years. No symptoms typical of huanglongbing, such as blotchy leaf mottle, chlorotic shoots, or dieback of branches, were observed in these seedlings, and none of these 723 seedlings tested positive for the presence of 'Ca. L. asiaticus' even after repeated testing by sensitive quantitative PCR assays. Some sour orange seedlings did have quite pronounced and atypical growth, including stunting and mild to severe leaf malformation. These atypical growth habits were limited to seedlings that arose from zygotic embryos as determined by expressed-sequence tag simple-sequence repeat analyses. Thus, no evidence of transmission of 'Ca. L. asiaticus' via seed was obtained, and an earlier report of transmission of the pathogen through seed was not confirmed.
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Affiliation(s)
- John S Hartung
- United States Department of Agriculture, Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville, MD 20705
| | - Susan E Halbert
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Gainesville, FL 32608
| | | | - Ronald H Brlansky
- University of Florida, Citrus Research and Education Center, Lake Alfred, FL 33850
| | - Chunxian Chen
- University of Florida, Citrus Research and Education Center, Lake Alfred, FL 33850
| | - Fred G Gmitter
- University of Florida, Citrus Research and Education Center, Lake Alfred, FL 33850
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Li X, Shangguan L, Song C, Wang C, Gao Z, Yu H, Fang J. Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers. BMC Genet 2010; 11:66. [PMID: 20626882 PMCID: PMC2920227 DOI: 10.1186/1471-2156-11-66] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 07/13/2010] [Indexed: 12/05/2022] Open
Abstract
Background Expressed Sequence Tag (EST) has been a cost-effective tool in molecular biology and represents an abundant valuable resource for genome annotation, gene expression, and comparative genomics in plants. Results In this study, we constructed a cDNA library of Prunus mume flower and fruit, sequenced 10,123 clones of the library, and obtained 8,656 expressed sequence tag (EST) sequences with high quality. The ESTs were assembled into 4,473 unigenes composed of 1,492 contigs and 2,981 singletons and that have been deposited in NCBI (accession IDs: GW868575 - GW873047), among which 1,294 unique ESTs were with known or putative functions. Furthermore, we found 1,233 putative simple sequence repeats (SSRs) in the P. mume unigene dataset. We randomly tested 42 pairs of PCR primers flanking potential SSRs, and 14 pairs were identified as true-to-type SSR loci and could amplify polymorphic bands from 20 individual plants of P. mume. We further used the 14 EST-SSR primer pairs to test the transferability on peach and plum. The result showed that nearly 89% of the primer pairs produced target PCR bands in the two species. A high level of marker polymorphism was observed in the plum species (65%) and low in the peach (46%), and the clustering analysis of the three species indicated that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the Prunus species. Conclusions We have constructed the first cDNA library of P. mume flower and fruit, and our data provide sets of molecular biology resources for P. mume and other Prunus species. These resources will be useful for further study such as genome annotation, new gene discovery, gene functional analysis, molecular breeding, evolution and comparative genomics between Prunus species.
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Affiliation(s)
- Xiaoying Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
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Talon M, Gmitter Jr. FG. Citrus genomics. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2008; 2008:528361. [PMID: 18509486 PMCID: PMC2396216 DOI: 10.1155/2008/528361] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Accepted: 03/15/2008] [Indexed: 05/18/2023]
Abstract
Citrus is one of the most widespread fruit crops globally, with great economic and health value. It is among the most difficult plants to improve through traditional breeding approaches. Currently, there is risk of devastation by diseases threatening to limit production and future availability to the human population. As technologies rapidly advance in genomic science, they are quickly adapted to address the biological challenges of the citrus plant system and the world's industries. The historical developments of linkage mapping, markers and breeding, EST projects, physical mapping, an international citrus genome sequencing project, and critical functional analysis are described. Despite the challenges of working with citrus, there has been substantial progress. Citrus researchers engaged in international collaborations provide optimism about future productivity and contributions to the benefit of citrus industries worldwide and to the human population who can rely on future widespread availability of this health-promoting and aesthetically pleasing fruit crop.
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Affiliation(s)
- Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia, Spain
| | - Fred G. Gmitter Jr.
- Citrus Research and Education Center (CREC), University of Florida, IFAS, Lake Alfred, FL 33850, USA
- *Fred G. Gmitter Jr.:
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