A new citrus linkage map based on SRAP, SSR, ISSR, POGP, RGA and RAPD markers (original) (raw)

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.

Access this article

Log in via an institution

Subscribe and save

• Get 10 units per month
• Download Article/Chapter or eBook
• 1 Unit = 1 Article or 1 Chapter
• Cancel anytime Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

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
  Article CAS PubMed Google Scholar
• Barrett HC (1985) Hybridization of Citrus and related genera. Fruit Var J 39:11–16
  Google Scholar
• 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
  Google Scholar
• 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
  Article Google Scholar
• 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
  CAS PubMed Google Scholar
• 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
  Article CAS Google Scholar
• Dalkilic Z, Timmer LW, Gmitter FG (2005) Linkage of alternaria disease resistance gene in mandarin hybrids with RAPD fragments. JASHS 130:191–195
  CAS Google Scholar
• 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
  Google Scholar
• 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
  Article CAS Google Scholar
• 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
  Article CAS PubMed Google Scholar
• Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15
  Google Scholar
• Fang DQ, Roose ML (1997) Identification of closely related citrus cultivars with inter-simple sequence repeat markers. Theor Appl Genet 95:408–417
  Article CAS Google Scholar
• Fang DQ, Federici CT, Roose ML (1997) Development of molecular markers linked to a gene controlling fruit acidity in Citrus. Genome 40:841–849
  Article CAS PubMed Google Scholar
• 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
  CAS PubMed Google Scholar
• 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
  CAS PubMed Google Scholar
• Garcia R, Asins MJ, Carbonell EA (2000) QTL analysis of yield and seed number in Citrus. Theor Appl Genet 101:487–493
  Article CAS Google Scholar
• 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
  CAS PubMed Google Scholar
• Guerra MS (1984) Cytogenetics of Rutaceae: II. Nuclear DNA content. Caryologia 37:219–226
  CAS Google Scholar
• Gulsen O, Roose ML (2001) Lemons: diversity and relationships with selected Citrus genotypes as measured with nuclear genome markers. JASHS 126:309–317
  CAS Google Scholar
• 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
  CAS Google Scholar
• 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
  Article CAS Google Scholar
• 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
  Article CAS Google Scholar
• 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
  Article CAS Google Scholar
• 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
  Article Google Scholar
• 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
  Article CAS Google Scholar
• 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
  Article CAS Google Scholar
• Oliveira RD, Cristofani M, Machado MA (2005) Integrated genetic map of Citrus based on RAPD markers. Fruits 60:187–193
  Article CAS Google Scholar
• 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
  Google Scholar
• 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
  Chapter Google Scholar
• Ruiz C, Asins MJ (2003) Comparison between Poncirus and Citrus genetic linkage maps. Theor Appl Genet 106:826–836
  CAS PubMed Google Scholar
• 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
  Article CAS Google Scholar
• 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
  CAS PubMed Google Scholar
• Tavoletti S, Veronessi F, Osborn TC (1996) RFLP linkage map in an alfalfa diploid mutant based on F1 populations. J Hered 87:167–170
  CAS Google Scholar
• 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
  Article CAS Google Scholar
• 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
  Article CAS Google Scholar
• Van Ooijen JW (2006) JoinMap® 4.0, software for the calculation of genetic linkage maps in experimental populations. Kyazma B. V., Wageningen, Netherlands
  Google Scholar
• Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. Heredity 93:77–78
  Article CAS Google Scholar
• Yamamoto M, Tominaga S (2004) Chromosome identification in haploid clementine (Citrus clementine hort. Ex Tanaka) by fluorescent staining. Sci Hortic 101:201–206
  Article CAS Google Scholar
• 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
  CAS Google Scholar

Download references

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.

Author information

Authors and Affiliations

1. Department of Horticulture, Faculty of Agriculture, Erciyes University, Melikgazi, 38039, Kayseri, Turkey
   Osman Gulsen
2. Alata Horticultural Research Institute, Erdemli, 33740, Mersin, Turkey
   Aydin Uzun, Ihsan Canan & Ubeyit Seday
3. Plant Protection Research Institute, Seyhan, 01321, Adana, Turkey
   Ercan Canihos

Authors

1. Osman Gulsen
   You can also search for this author inPubMed Google Scholar
2. Aydin Uzun
   You can also search for this author inPubMed Google Scholar
3. Ihsan Canan
   You can also search for this author inPubMed Google Scholar
4. Ubeyit Seday
   You can also search for this author inPubMed Google Scholar
5. Ercan Canihos
   You can also search for this author inPubMed Google Scholar

Corresponding author

Correspondence toOsman Gulsen.

Electronic supplementary material

Rights and permissions

About this article

Cite this article

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

Download citation

• Received: 04 August 2009
• Accepted: 01 February 2010
• Published: 10 February 2010
• Issue Date: May 2010
• DOI: https://doi.org/10.1007/s10681-010-0146-7

Keywords