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Markers, Maps, and Marker-Assisted Selection

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The Kiwifruit Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

The development of molecular markers in kiwifruit followed the advances in molecular biology techniques. After occasional use of RFLP (restriction fragment length polymorphism) markers in the 1990s, most markers developed in kiwifruit were based on PCR (polymerase chain reaction). RAPD (random amplified polymorphic DNA) were followed by AFLPs (amplified fragment length polymorphisms), used mainly for the saturation of linkage maps. In the meantime, microsatellites or SSRs (simple sequence repeats) came to the fore and were extensively used for genotyping germplasm accessions and to produce linkage maps, where SSRs anchored markers for pairing parental maps of the pseudo-testcrosses and the identification of homologous linkage groups in maps produced from different cross populations. Four linkage maps for kiwifruit have been published: the first two based on SSR markers and the second two based mainly or exclusively on SNP markers identified and mapped at the same time through the approach of ‘genotyping-by-sequencing.’ These last, highly saturated, maps were produced to assist the genome-sequencing project, by anchoring and orientating scaffolds and contigs of the assembly. The linkage maps, in particular that published by the New Zealand Institute for Plant & Food Research based on 636 markers, mainly SSRs, helped in the mapping of several traits, such as gender that was mapped in the subtelomeric region of linkage group 17, corresponding to the pseudo-molecule number 25 of the genome assembly.

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References

  • Bink MCAM, Uimari P, Sillanpää MJ, Janss LG, Jansen RC (2002) Multiple QTL mapping in related plant populations via a pedigree-analysis approach. Theor Appl Genet 104:751–762

    Article  CAS  PubMed  Google Scholar 

  • Cipriani G, Di Bella R, Testolin R (1996) Screening RAPD primers for molecular taxonomy and cultivar fingerprinting in the genus Actinidia. Euphytica 90:169–174

    Article  CAS  Google Scholar 

  • Crowhurst RN, Lints R, Atkinson RG, Gardner RC (1990) Restriction fragment length-polymorphisms in the genus Actinidia (Actinidiaceae). Plant Syst Evol 172:193–203

    Article  CAS  Google Scholar 

  • Crowhurst RN, Gleave AP, MacRae EA, Ampomah-Dwamena C, Atkinson RG, Beuning LL et al (2008) Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening. BMC Genom 9:351

    Article  Google Scholar 

  • Fraser LG, Tsang GK, Datson PM, De Silva HN, Harvey CF, Gill GP et al (2009) A gene-rich linkage map in the dioecious species Actinidia chinensis (kiwifruit) reveals putative X/Y sex-determining chromosomes. BMC Genom 10:102. doi:10.1186/1471-2164-10-102

    Article  Google Scholar 

  • Gill GP, Harvey CF, Gardner RC, Fraser LG (1998) Development of sex-linked PCR markers for gender identification in Actinidia. Theor Appl Genet 97:439–445

    Article  CAS  Google Scholar 

  • Harvey CF, Gill GP, Fraser LG, McNeilage MA (1997) Sex determination in Actinidia. 1. Sex-linked markers and progeny sex ratio in diploid A. chinensis. Sexl Plant Reprod 10:149–154

    Article  Google Scholar 

  • Huang W-G, Cipriani G, Morgante M, Testolin R (1998) Microsatellite DNA in Actinidia chinensis: isolation, characterisation, and homology in related species. Theor Appl Genet 97:1269–1278

    Article  CAS  Google Scholar 

  • Huang S, Ding J, Deng D, Tang W, Sun H, Liu D et al (2013) Draft genome of the kiwifruit Actinidia chinensis. Nat. Commun 4:2640. doi:10.1038/ncomms3640

    PubMed  PubMed Central  Google Scholar 

  • Jiang C-Y, Xu X-B, Liao J, Gu Q-Q, Liu S-J, Chen J-Y (2010) Establishment of SSR markers based on EST database from Actinidia. J Fruit Sci 4

    Google Scholar 

  • Korkovelos A, Mavromatis A, Giakoundis A, Goulas C (2006) Phylogenetic relation estimation among eight Actinidia species using data from SSR molecular markers and flow cytometry. Agric Res 27(2):49–59

    Google Scholar 

  • Kwon S-J, Lee G-A, Kwack Y-B, Lee H-S, Cho G-T, Ko H-C et al (2013) Development of 34 new microsatellite markers from Actinidia arguta: intra- and interspecies genetic analysis. Plant Breed Biotechnol 1(2):137–147

    Article  Google Scholar 

  • McNeilage MA, Fraser LG, Tsang GK, Datson PM, De Silva HN, Crowhurst RN et al (2011) Molecular genetics and genomics and kiwifruit breeding. Acta Hortic 913:63–70

    Article  Google Scholar 

  • Meng M, Teng W, Liu J, Huang S, Yu J, Liu F et al (2014) Development of EST-SSR markers in Actinidia chinesis cv ‘Hongyang’ based on transcriptomic sequences. Chin J Appl Environ Biol 4:564–570

    Google Scholar 

  • Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829

    CAS  PubMed  PubMed Central  Google Scholar 

  • Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3:175–182

    Article  CAS  PubMed  Google Scholar 

  • Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7(5):e37135

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Prado MJ, Gonzalez MV, Romo S, Herrera MT (2007) Adventitious plant regeneration on leaf explants from adult male kiwifruit and AFLP analysis of genetic variation. Plant Cell Tiss Organ Culture 88:1–10

    Article  Google Scholar 

  • Scaglione D, Fornasiero A, Pinto C, Cattonaro F, Spadotto A, Infante R et al (2015) A RAD-based linkage map of kiwifruit (Actinidia chinensis Pl.) as a tool to improve the genome assembly and to scan the genomic region of the gender-determinant for the marker-assisted breeding. Tree Genet Genomes 11:115

    Google Scholar 

  • Schlötterer C (2004) The evolution of molecular markers—just a matter of fashion? Nat Rev Genet 5:63–69

    Article  PubMed  Google Scholar 

  • Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 3:739–744

    Article  CAS  Google Scholar 

  • Testolin R (2011) Kiwifruit breeding: from the phenotypic analysis of parents to the genomic estimation of their breeding value (GEBV). Acta Hort 913:123–130

    Article  CAS  Google Scholar 

  • Testolin R, Cipriani G, Costa G (1995) Sex segregation ratio and gender expression in the genus Actinidia. Sexual Plant Reprod 8:129–132

    Article  Google Scholar 

  • Testolin R, Morisset C, Chat J, Goulas C, Huang H-W, Xiao X-G (2000) Collection, evaluation and cryo-preservation of germplasm of the genus Actinidia and breeding for a novel kiwifruit fruit. EU INCO-DC contract no. ERBIC18-CT97-0183. Final report

    Google Scholar 

  • Testolin R, Huang WG, Lain O, Messina R, Vecchione A, Cipriani G (2001). A kiwifruit (Actinidia spp.) linkage map based on microsatellites and integrated with AFLP markers. Theor Appl Genet 103:30–36

    Google Scholar 

  • Testolin R, Di Gaspero G, Huang WG, Lain O, Messina R, Cipriani G (2003) Linkage map in kiwifruit: the choice of mapping populations. Acta Hort 610:517–523

    Article  Google Scholar 

  • Van Ooijen JW (2006) JoinMap® 4, Software for the mapping of quantitative trait loci in experimental populations. Kyazma B.V., Wageningen, Netherlands

    Google Scholar 

  • Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23(1):48–55

    Article  CAS  PubMed  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M et al (1995) AFLP: a new concept for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang TC, Gleave AP (2012) Applications of biotechnology in kiwifruit (Actinidia). In: Agbo EC (ed) Innovations in biotechnology. InTech. ISBN: 978-953-51-0096-6. e-book available from http://www.intechopen.com/books/innovations-in-biotechnology/application-of-biotechnology-in-kiwifruit-actinidia

    Google Scholar 

  • Wang Y-C, Zhang L, Man Y-P, Li Z-Z, Qin R (2012) Phenotypic characterization and simple sequence repeat identification of red-fleshed kiwifruit germplasm accessions. HortSci 47(8):992–999

    CAS  Google Scholar 

  • Weising K, Fung RWM, Keeling DJ, Atkinson RG, Gardner RC (1996) Characterisation of microsatellites from Actinidia chinensis. Mol Breed 2:117–131

    Article  CAS  Google Scholar 

  • Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl Acid Res 18:6531–6535

    Article  CAS  Google Scholar 

  • Xiao X, Zhang L, Li S, Testolin R, Cipriani G (2003) Molecular markers for early sex determination in Actinidia. Acta Hor 610:533–538

    Article  CAS  Google Scholar 

  • Xu X-B, Liao J, Huang C-H, Gu Q-Q, Qu X-Y, Liu S-J et al (2012) Genetic relationships from Kiwifruit germplasms based on EST-SSR markers. J Fruit Sci 2

    Google Scholar 

  • Zhang Q, Liu C-Y, Liu Y-F, VanBuren R, Yao X-H, Zhong C-H et al (2015) High-density interspecific genetic maps of kiwifruit and the identification of sex-specific markers. DNA Res 22(5):367–375. doi:10.1093/dnares/dsv019

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhen Y-Q, Li Z-Z, Huang H-W, Wang Y (2004) Molecular characterization of kiwifruit (Actinidia) cultivars and selections using SSR markers. J Am Soc Hort Sci 129(3):374–382

    CAS  Google Scholar 

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Acknowledgments

Authors thank R. Ferguson, L. Fraser, and M.A. McNeilage for revising manuscript and helpful comments.

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Authors and Affiliations

  1. Department of Agriculture and Environmental Sciences, University of Udine, Via delle Scienze 208, 33100, Udine, Italy

    Raffaele Testolin & Guido Cipriani

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  1. Raffaele Testolin
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  2. Guido Cipriani
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Correspondence to Raffaele Testolin .

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Editors and Affiliations

  1. Department of Agriculture, University of Udine, Udine, Italy

    Raffaele Testolin

  2. Chinese Academy of Sciences, South China Botanical Garden, Guangzhou, China

    Hong-Wen Huang

  3. for Plant & Food Research, The New Zealand Institute, Auckland, New Zealand

    Allan Ross Ferguson

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Testolin, R., Cipriani, G. (2016). Markers, Maps, and Marker-Assisted Selection. In: Testolin, R., Huang, HW., Ferguson, A. (eds) The Kiwifruit Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-32274-2_7

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