Abstract
Sequence-related amplified polymorphism (SRAP), simple sequence repeats (SSR), inter-simple sequence repeat (ISSR), peroxidase gene polymorphism (POGP), resistant gene analog (RGA), randomly amplified polymorphic DNA (RAPD), and a morphological marker, Alternaria brown spot resistance gene of citrus named as Cabsr caused by (Alternaria alternata f. sp. Citri) were used to establish genetic linkage map of citrus using a population of 164 F1 individuals derived between ‘Clementine’ mandarin (Citrus reticulata Blanco ‘Clementine) and ‘Orlando’ tangelo’ (C. paradisi Macf. ‘Duncan’ × C. reticulata Blanco ‘Dancy’). A total of 609 markers, including 385 SRAP, 97 RAPD, 95 SSR, 18 ISSR, 12 POGP, and 2 RGA markers were used in linkage analysis. The ‘Clementine’ linkage map has 215 markers, comprising 144 testcross and 71 intercross markers placed in nine linkage groups. The ‘Clementine’ linkage map covered 858 cM with and average map distance of 3.5 cM between adjacent markers. The ‘Orlando’ linkage map has 189 markers, comprising 126 testcross and 61 intercross markers placed in nine linkage groups. The ‘Orlando’ linkage map covered 886 cM with an average map distance of 3.9 cM between adjacent markers. Segregation ratios for Cabsr were not significantly different from 1:1, suggesting that this trait is controlled by a single locus. This locus was placed in ‘Orlando’ linkage group 1. The new map has an improved distribution of markers along the linkage groups with fewer gaps. Combining different marker systems in linkage mapping studies may give better genome coverage due to their chromosomal target site differences, therefore fewer gaps in linkage groups.
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References
Barkley NA, Roose ML, Krueger RR, Federici CT (2006) Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theor Appl Genet 112:1519–1531
Barrett HC (1985) Hybridization of Citrus and related genera. Fruit Var J 39:11–16
Bradshaw HD, Stettles RF (1994) Molecular genetics of growth and development in Populus. II. Segregation distortion due to genetic load. Theor Appl Genet 139:963–973
Canihos Y, Peewer TL, Timmer LW (1998) Temperature, leaf wetness, and isolate effects on infection of Minneola tangelo leaves by Alternaria sp. Plant Dis 83:429–433
Cervera MT, Storme V, Ivens B, Gusmao J, Liu BH, Hostyn V, Slycken JV, Montagu MW, Boerjan W (2001) Dense genetic linkage maps of three Populus species (Populus deltoids, P. nigra and P. trichocarpa) based on AFLP and microsatellite markers. Genetics 158:787–809
Chen C, Bowman KD, Choi YA, Dang PM, Rao MN, Huang S, Soneji JR, McCollum TG, Gmitter FG Jr (2007) EST-SSR genetic maps for Citrus sinensis and Poncirus trifoliate. Tree Genet Genomes 4:1–10
Dalkilic Z, Timmer LW, Gmitter FG (2005) Linkage of alternaria disease resistance gene in mandarin hybrids with RAPD fragments. JASHS 130:191–195
de Simone M, Russo MP, Puelo G, Marsan PA, Lorenzoni C, Marocco A, Recupero GR (1998) Construction genetic linkage maps for Citrus aurantium and C. latipes based on RFLP, RAPD RFLP markers. Fruits 53:383–390
Deng Z, Huang S, Ling P, Chen C, Yu C, Weber CA, Moore GA, Gmitter FG Jr (2000) Cloning and characterization of NBS-LRR class resistance-gene candidate sequences in citrus. Theor Appl Genet 101:814–822
Doucleff M, Yin Y, Gao F, Riaz S, Krivanek AF, Walker MA (2004) A genetic linkage map of grape, utilizing Vitis rupestris and Vitis arizonica. Theor Appl Genet 109:1178–1187
Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15
Fang DQ, Roose ML (1997) Identification of closely related citrus cultivars with inter-simple sequence repeat markers. Theor Appl Genet 95:408–417
Fang DQ, Federici CT, Roose ML (1997) Development of molecular markers linked to a gene controlling fruit acidity in Citrus. Genome 40:841–849
Fang DQ, Federici CT, Roose ML (1998) A high resolution linkage map of the citrus tristeza virus resistance gene region in Poncirus trifoliate (L.) Raf. Genetics 150:883–890
Fishman L, Kelly AJ, Morgan E, Willis JH (2001) A genetic map in the Mimulus guttatus species complex reveals transmission ratio distortion due to heterospecific interactions. Genetics 159:1701–1716
Garcia R, Asins MJ, Carbonell EA (2000) QTL analysis of yield and seed number in Citrus. Theor Appl Genet 101:487–493
Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudotestcross: mapping strategy and RAPD markers. Genetics 137:1121–1137
Guerra MS (1984) Cytogenetics of Rutaceae: II. Nuclear DNA content. Caryologia 37:219–226
Gulsen O, Roose ML (2001) Lemons: diversity and relationships with selected Citrus genotypes as measured with nuclear genome markers. JASHS 126:309–317
Gulsen O, Shearman RC, Vogel KP, Lee DJ, Baenziger PS, Heng-Moss TM, Budak H (2005) Nuclear genome diversity and relationships among naturally occurring buffalograss genotypes determined by sequence-related amplified polymorphism. HortScience 40:537–541
Gulsen O, Shearman RC, Heng-Moss TM, Mutlu N, Lee DJ, Sarath G (2007) Peroxidase gene polymorphism in buffalograss and other grasses. Crop Sci 47:767–772
Jarrell DC, Roose ML, Traugh SN, Kupper RS (1992) A genetic map of citrus based on the segregation of isozymes and RFLPs in an intergeneric cross. Theor Appl Genet 84:49–56
Kijas JMH, Thomas MR, Fowler JCS, Roose ML (1997) Integration of trinucleotide microsatellites into a linkage map of Citrus. Theor Appl Genet 94:701–706
Kohmoto K, Akimitsu K, Otani H (1991) Correlation of resistance and susceptibility of citrus to Alternaria alternata with sensitivity to host specific toxins. Phytopathology 81:719–722
Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP) a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet 103:455–461
Nicolosi E, Deng ZN, Gentile A, La Malfa S, Continella G, Tribulato E (2000) Citrus phylogeny and genetic origin of important species as investigated by molecular markers. Theor Appl Genet 100:1155–1166
Oliveira RD, Cristofani M, Machado MA (2005) Integrated genetic map of Citrus based on RAPD markers. Fruits 60:187–193
Oliveira AC, Bastianel M, Cristofani-Yaly M, Amaral AM, Machado MA (2007) Development of genetic maps of the citrus varieties ‘Murcott’ tangor and Pera’ sweet orange by using fluorescent AFLP markers. J Appl Genet 48:219–231
Roose ML (2000) Linkage mapping and marker-assisted selection in Citrus. Proceedings of the international society of citriculture. IX congress, Florida, USA, pp 69–70
Roose ML (2007) Mapping and marker assisted selection in Citrus. In: Khan IA (ed) Citrus genetics, breeding and biotechnology. CAB International, Wallingford, UK, pp 275–286
Ruiz C, Asins MJ (2003) Comparison between Poncirus and Citrus genetic linkage maps. Theor Appl Genet 106:826–836
Sankar AA, Moore GA (2001) Evaluation of inter-simple sequence repeat analysis for mapping in Citrus and extension of the genetic linkage map. Theor Appl Genet 102:206–214
Soost RK, Roose ML (1996) Citrus. In: Janick J, Moore JN (eds) Fruit breeding, vol 1, pp 256–323
Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB, Messeguer R, Miller JC, Miller L, Paterson AH, Pineda O, Röder MS, Wing RA, Wu W, Young ND (1992) High density molecular linkage maps for tomato and potato genomes. Genetics 132:1141–1160
Tavoletti S, Veronessi F, Osborn TC (1996) RFLP linkage map in an alfalfa diploid mutant based on F1 populations. J Hered 87:167–170
Tozlu I, Guy CL, Moore GA (1999) QTL analysis of morphological traits in an intergeneric BC1 progeny of Citrus and Poncirus under saline and non-saline environments. Genome 42:1020–1029
Uzun A, Yesiloglu T, Aka-Kacar Y, Tuzcu O, Gulsen O (2009) Genetic diversity and population structure within Citrus and related genera based on sequence related amplified polymorphism markers (SRAPs). Sci Hortic 121:306–312
Van Ooijen JW (2006) JoinMap® 4.0, software for the calculation of genetic linkage maps in experimental populations. Kyazma B. V., Wageningen, Netherlands
Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. Heredity 93:77–78
Yamamoto M, Tominaga S (2004) Chromosome identification in haploid clementine (Citrus clementine hort. Ex Tanaka) by fluorescent staining. Sci Hortic 101:201–206
Zhang L, Pond SK, Gaut BS (2001) A survey of the molecular evolutionary dynamics of twenty-five multigene families from four taxa. Mol Evol 52:144–156
Acknowledgements
We thank Dr. Mikeal L. Roose for technical help and providing SSR primers. This study was funded by the Scientific and Technological Research Council (TUBITAK) with the project code TOVAG-105 O 628 and the General Directorate of Agricultural Research of Ministry of Agriculture and Rural Affairs, Turkey.
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Gulsen, O., Uzun, A., Canan, I. et al. A new citrus linkage map based on SRAP, SSR, ISSR, POGP, RGA and RAPD markers. Euphytica 173, 265–277 (2010). https://doi.org/10.1007/s10681-010-0146-7
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DOI: https://doi.org/10.1007/s10681-010-0146-7