Skip to main content

Genetic Mapping and Detection of Quantitative Trait Loci

  • Chapter
  • First Online:
The Olive Tree Genome

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

  • 1137 Accesses

Abstract

Olive tree is a long-living woody species with similar genomic and phenotypic constraints to other perennial fruit crops. However, compared to apple, grape, and peach, genomic investigations for designing innovative breeding strategies are still limited to only preliminary research in this species. In this chapter, we aim to describe the studies on genetic mapping and underline the most promising investigations and initiatives to build a Mediterranean network suitable for establishing robust marker-trait associations through QTL mapping and association studies. These tools should serve to finally implement new breeding programs driven by marker-assisted breeding.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Ates D (2016) Identification of QTLs controlling genes of ripening time, flesh detachment from stone and firmness in olive (Olea europaea L.). In: XXIV plant and animal genome conference, San Diego, CA, P1163

    Google Scholar 

  • Atienza SG, De la Rosa R, Leon L et al (2014) Identification of QTL for agronomic traits of importance for olive breeding. Mol Breed 34:725–737

    Google Scholar 

  • Badenes ML, Byrne DH (eds) (2011) Fruit Breeding, vol 8. Springer Science + Business Media, New York, USA

    Google Scholar 

  • Ben Sadok I, Celton JM, Essalouh L et al (2013a) QTL mapping of flowering and fruiting traits in olive. PLoS ONE 8(5):e62831

    Article  CAS  PubMed  Google Scholar 

  • Ben Sadok I, Moutier N, Garcia G et al (2013b) Genetic determinism of the vegetative and reproductive traits in an F1 olive tree progeny evidence of tree ontogeny effect. Tree Genet Genomes 9:205–221

    Article  Google Scholar 

  • Bink MCAM, Jansen J, Madduri M et al (2014) Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple. Theor Appl Genet 127:1073–1090

    Google Scholar 

  • Cappellin L, Farneti B, Di Guardo M et al (2015) QTL analysis coupled with PTR-ToF-MS and candidate gene-based association mapping validate the role of Md-AAT1 as a major gene in the control of flavor in apple fruit. Plant Mol Biol Rep 33(2):239–252

    Article  CAS  Google Scholar 

  • Chen W, Gao Y, Xie W et al (2014) Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nat Genet 46(7):714–721

    Article  CAS  PubMed  Google Scholar 

  • Collard BC, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Phil Trans Roy Soc B 363(1491):557–572

    Article  CAS  Google Scholar 

  • Cruz F, Julca I, Gómez-Garrido J et al (2016) Genome sequence of the olive tree. Olea europaea. GigaSci 5:29

    Article  Google Scholar 

  • De la Rosa R, Angiolillo A, Guerrero C et al (2003) A first linkage map of olive (Olea europaea L.) cultivars using RAPD, AFLP, RFLP and SSR markers. Theor Appl Genet 106(7):1273–1282

    Article  PubMed  Google Scholar 

  • Di Gaspero G, Cattonaro F (2010) Application of genomics to grapevine improvement. Austr J Grape Wine Res 16(s1):122–130

    Article  Google Scholar 

  • Dirlewanger E, Graziano E, Joobeur T et al (2004) Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc Natl Acad Sci USA 101(26):9891–9896

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dominguez-Garcia MC, Belaj A, De la Rosa R et al (2012) Development of DArT markers in olive (Olea europaea L.) and usefulness in variability studies and genome mapping. Sci Hortic 136:50–60

    Article  CAS  Google Scholar 

  • Doucleff M, Jin Y, Gao F et al (2004) A genetic linkage map of grape, utilizing Vitis rupestris and Vitis arizonica. Theor Appl Genet 109(6):1178–1187

    Article  CAS  PubMed  Google Scholar 

  • Edge-Garza DA, Luby JJ, Peace C (2015) Decision support for cost-efficient and logistically feasible marker-assisted seedling selection in fruit breeding. Mol Breed 35(12):1–5

    Article  Google Scholar 

  • El Aabidine AZ, Charafi J, Grout C et al (2010) Construction of a genetic linkage map for the olive based on AFLP and SSR markers. Crop Sci 50(6):2291–2302

    Article  Google Scholar 

  • Emanuelli F, Battilana J, Costantini L et al (2010) A candidate gene association study on muscat flavor in grapevine (Vitis vinifera L.). BMC Plant Biol 10:1

    Google Scholar 

  • Essalouh L, El Aabidine AZ, Contreras S et al (2014) Genomic and EST microsatellite loci development and use in olive: molecular tools for genetic mapping and association studies. Acta Hortic 1057:543–550

    Article  Google Scholar 

  • Fernández-Martinez J, Phillips J, Sekedat MD et al (2012) Structure-function mapping of a heptameric module in the nuclear pore complex. J Cell Biol 196(4):419–434

    Article  PubMed  PubMed Central  Google Scholar 

  • González-Plaza JJ, Hulak N (2016) Olive tree in the genomic era: focus on plant architecture. Agric Consp Sci 80(4):239–246

    Google Scholar 

  • González-Plaza JJ, Ortiz-Martín I, Muñoz-Mérida A et al (2016) Transcriptomic analysis using olive varieties and breeding progenies identifies candidate genes involved in plant architecture. Front Plant Sci 7:240

    Article  PubMed  PubMed Central  Google Scholar 

  • Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137(4):1121–1137

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hammami SB, León L, Rapoport HF et al (2011) Early growth habit and vigour parameters in olive seedlings. Sci Hortic 129(4):761–768

    Article  Google Scholar 

  • Ignatov A, Bodishevskaya A (2011) Malus. In: Kole C (ed) Wild crop relatives: genomic and breeding resources, vol Temperate., FruitsSpringer, Berlin, Heidelberg, pp 45–64

    Chapter  Google Scholar 

  • Ipek A, Yilmaz K, Sikici P et al (2016) SNP discovery by GBS in olive and the construction of a high-density genetic linkage map. Biochem Genet 54:313–325

    Article  CAS  PubMed  Google Scholar 

  • Iwata H, Hayashi T, Terakami S et al (2013) Potential assessment of genome-wide association study and genomic selection in Japanese pear Pyrus pyrifolia. Breed Sci 63(1):125–140

    Article  PubMed  PubMed Central  Google Scholar 

  • Kaya HB, Cetin O, Kaya HS et al (2016) Association mapping in Turkish olive cultivars revealed significant markers related to some important agronomic traits. Biochem Genet 54:506–533

    Article  CAS  PubMed  Google Scholar 

  • Khadari B, El Aabidine AZ, Grout C et al (2010) A genetic linkage map of olive based on amplified fragment length polymorphism, intersimple sequence repeat and simple sequence repeat markers. J Am Soc Hortic Sci 135(6):548–555

    Google Scholar 

  • Khadari B, El Bakkali A, El Aabidine A, Essalouh L, Contreras S, Ben Sadok I, Costes E, Moukhli A (2014) How can we efficiently characterize genes of agronomic interest in olive: towards the genetic association studies? Acta Hortic 1057:551–558

    Article  Google Scholar 

  • Khan MA, Korban SS (2012) Association mapping in forest trees and fruit crops. J Exp Bot 63(11):4045–4060

    Article  CAS  PubMed  Google Scholar 

  • Leon L, Rallo L, Del Rio C, Martin LM et al (2004) Variability and early selection on the seedling stage for agronomic traits in progenies from olive crosses. Plant Breed 123(1):73–78

    Article  Google Scholar 

  • Leon L, Arias-Calderon R, De la Rosa R et al (2016) Optimal spatial and temporal replications for reducing environmental variation for oil content components and fruit morphology traits in olive breeding. Euphytica 207(3):675–684

    Article  Google Scholar 

  • Li Y, Huang Y, Bergelson J et al (2010) Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana. Proc Natl Acad Sci USA 107(49):21199–21204

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lincoln SE, Daly MJ, Lander ES (1993) Constructing genetic linkage maps with MAPMAKER/EXP Version 3.0: a tutorial and reference manual. A Whitehead Institute for Biomedical Research Technical Report 78–79

    Google Scholar 

  • Mahanil S, Ramming D, Cadle-Davidson M et al (2012) Development of marker sets useful in the early selection of Ren4 powdery mildew resistance and seedlessness for table and raisin grape breeding. Theor Appl Genet 124(1):23–33

    Google Scholar 

  • Marchese A, Marra FP, Caruso T et al (2016) The first high-density sequence characterized SNP-based linkage map of olive (Olea europaea L. subsp. europaea) developed using genotyping by sequencing. Austr. J Crop Sci 10(6):857–863

    Google Scholar 

  • Martínez-García PJ, Parfitt DE, Ogundiwin EA et al (2013) High density SNP mapping and QTL analysis for fruit quality characteristics in peach (Prunus persica L.). Tree Genet Genomes 9:19–36

    Google Scholar 

  • Montanari S, Saeed M, Knäbel M et al (2013) Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids. PLoS One 8:e77022

    Google Scholar 

  • Muranty H, Troggio M, Ben Sadok I et al (2015) Accuracy and responses of genomic selection on key traits in apple breeding. Hortic Res 2:15060

    Article  PubMed  PubMed Central  Google Scholar 

  • Myles S, Peiffer J, Brown PJ et al (2009) Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21(8):2194–2202

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sauvage C, Segura V, Bauchet G et al (2014) Genome-wide association in tomato reveals 44 candidate loci for fruit metabolic traits. Plant Physiol 165(3):1120–1132

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Serra O, Donoso JM, Picañol R et al (2016) Marker-assisted introgression (MAI) of almond genes into the peach background: a fast method to mine and integrate novel variation from exotic sources in long intergeneration species. Tree Genet Genomes 12(5):96

    Google Scholar 

  • Sun R, Chang Y, Yang F et al (2015) A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality. BMC Genom 16(1):1

    Article  Google Scholar 

  • Unver T, Dorado G, Hernandez P et al (2016) Lessons from whole genome sequencing of olive tree (Olea europaea L.). In: XXIV plant and animal genome conference, W371, San Diego, CA

    Google Scholar 

  • Wu SB, Collins G, Sedgley M (2004) A molecular linkage map of olive (Olea europaea L.) based on RAPD, microsatellite, and SCAR markers. Genome 47(1):26–35

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Luciana Baldoni .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer International Publishing AG

About this chapter

Cite this chapter

Baldoni, L., Khadari, B., De La Rosa, R. (2016). Genetic Mapping and Detection of Quantitative Trait Loci. In: Rugini, E., Baldoni, L., Muleo, R., Sebastiani, L. (eds) The Olive Tree Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-48887-5_5

Download citation

Publish with us

Policies and ethics