TITLE

High-throughput marker discovery in melon using a self-designed oligo microarray

AUTHOR(S)
Ophir, Ron; Eshed, Ravit; Harel-Beja, Rotem; Tzuri, Galil; Portnoy, Vitaly; Burger, Yoseph; Uliel, Shai; Katzir, Nurit; Sherman, Amir
PUB. DATE
January 2010
SOURCE
BMC Genomics;2010, Vol. 11, p269
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Genetic maps constitute the basis of breeding programs for many agricultural organisms. The creation of these maps is dependent on marker discovery. Melon, among other crops, is still lagging in genomic resources, limiting the ability to discover new markers in a high-throughput fashion. One of the methods used to search for molecular markers is DNA hybridization to microarrays. Microarray hybridization of DNA from different accessions can reveal differences between them--single-feature polymorphisms (SFPs). These SFPs can be used as markers for breeding purposes, or they can be converted to conventional markers by sequencing. This method has been utilized in a few different plants to discover genetic variation, using Affymetrix arrays that exist for only a few organisms. We applied this approach with some modifications for marker discovery in melon. Results: Using a custom-designed oligonucleotide microarray based on a partial EST collection of melon, we discovered 6184 putative SFPs between the parents of our mapping population. Validation by sequencing of 245 SFPs from the two parents showed a sensitivity of around 79%. Most SFPs (81%) contained single-nucleotide polymorphisms. Testing the SFPs on another mapping population of melon confirmed that many of them are conserved. Conclusion: Thousands of new SFPs that can be used for genetic mapping and molecular-assisted breeding in melon were discovered using a custom-designed oligo microarray. A portion of these SFPs are conserved and can be used in different breeding populations. Although improvement of the discovery rate is still needed, this approach is applicable to many agricultural systems with limited genomic resources.
ACCESSION #
51167857

 

Related Articles

  • Segregation distortion in Lolium: evidence for genetic effects. Anhalt, U. C. M.; Heslop-Harrison, P. (J. S.); Byrne, S.; Guillard, A.; Barth, S. // Theoretical & Applied Genetics;Jul2008, Vol. 117 Issue 2, p297 

    Segregation distortion (SD) is the deviation of genetic segregation ratios from their expected Mendelian fraction and is a common phenomenon found in most genetic mapping studies. In this study two segregating Lolium perenne populations were used to construct two genetic maps: an ‘F2...

  • Karyotyping in Melon (Cucumis melo L.) by Cross-Species Fosmid Fluorescence in situ Hybridization. Liu, C.; Liu, J.; Li, H.; Zhang, Z.; Han, Y.; Huang, S.; Jin, W. // Cytogenetic & Genome Research;2010, Vol. 129 Issue 1-3, p241 

    Chromosome identification is critical for cytogenetic research and will accelerate studies on genetic variation and breeding, especially for those species with relatively little sequence information. So far, no reliable cytological landmarks have been developed to distinguish individual...

  • Single-copy gene fluorescence in situ hybridization and genome analysis: Acc-2 loci mark evolutionary chromosomal rearrangements in wheat. Danilova, Tatiana; Friebe, Bernd; Gill, Bikram // Chromosoma;Dec2012, Vol. 121 Issue 6, p597 

    Fluorescence in situ hybridization (FISH) is a useful tool for physical mapping of chromosomes and studying evolutionary chromosome rearrangements. Here we report a robust method for single-copy gene FISH for wheat. FISH probes were developed from cDNA of cytosolic acetyl-CoA carboxylase...

  • Single nucleotide polymorphism genotyping by heteroduplex analysis in sunflower ( Helianthus annuus L.). Fusari, Corina; Lia, Verónica; Nishinakamasu, Verónica; Zubrzycki, Jeremías; Puebla, Andrea; Maligne, Alberto; Hopp, H.; Heinz, Ruth; Paniego, Norma // Molecular Breeding;Jun2011, Vol. 28 Issue 1, p73 

    Single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) are increasingly used for cultivar identification, construction of genetic maps, genetic diversity assessment, association mapping and marker-assisted breeding. Although there are several highly sensitive methods for the...

  • High-resolution tyramide-FISH mapping of markers tightly linked to the male-fertility restoration ( Ms) locus of onion. Khrustaleva, Ludmila; Jiang, Jiming; Havey, Michael // Theoretical & Applied Genetics;Mar2016, Vol. 129 Issue 3, p535 

    Key message: Tyramide FISH was used to locate relatively small genomic amplicons from molecular markers linked to Ms locus onto onion chromosome 2 near the centromere, a region of relatively low recombination. Abstract: Fluorescence in situ hybridization (FISH) has not been readily exploited for...

  • Chromosomal Localization of ESTs Obtained from Human Fetal Liver via BAC-mediated FISH Mapping. Sun Shim Choi; Yoon Sung Kang; Ung-Jin Kim; Kwang-Ho Lee; Hee-Sup Shin // Molecules & Cells (Springer Science & Business Media B.V.);1999, Vol. 9 Issue 4, p403 

    Presents information on a study which screened an arrayed human bacterial artificial chromosome (BAC) library to generate fluorescence in situ hybridization (FISH) mapping probes. FISH analysis; Regional mapping of expressed sequence tags (EST) via FISH using BAC intermediates; Detailed...

  • Genetic and physical mapping of flowering time loci in canola ( Brassica napus L.). Raman, Harsh; Raman, Rosy; Eckermann, Paul; Coombes, Neil; Manoli, Sahana; Zou, Xiaoxiao; Edwards, David; Meng, Jinling; Prangnell, Roslyn; Stiller, Jiri; Batley, Jacqueline; Luckett, David; Wratten, Neil; Dennis, Elizabeth // Theoretical & Applied Genetics;Jan2013, Vol. 126 Issue 1, p119 

    We identified quantitative trait loci (QTL) underlying variation for flowering time in a doubled haploid (DH) population of vernalisation-responsive canola ( Brassica napus L.) cultivars Skipton and Ag-Spectrum and aligned them with physical map positions of predicted flowering genes from the...

  • SSCP analysis of cDNA Markers Provides a Dense Linkage Map of the Aedes aegypti Genome. Fulton, Ruth E.; Salasek, Michael L.; DuTeau, Nancy M.; Black IV, William C. // Genetics;Jun2001, Vol. 158 Issue 2, p715 

    Reports on the single-strand conformation polymorphism analysis of cDNA markers to develop an intensive linkage map of the yellow fever mosquito, Aedes aegypti. Detection of single nucleotide polymorphisms in cDNA loci; Comparative linkage analysis between A. zegypti and Drosophila melanogaster...

  • Dense Genetic Linkage Maps of Three Populus Species (Populus deltoides, P. nigra and P... Cervera, Maria-Teresa; Storme, Veronique; ivens, Bart; Gusmao, Jaqueline; Liu, Ben H.; Hostyn, Vanessa; Van Slycken, Jos; Van Montagu, Marc; Boerjan, Wout // Genetics;Jun2001, Vol. 158 Issue 2, p787 

    Analyzes the dense genetic linkage mapping of Populus deltoides, P. nigra and P. trichocarpa based on amplified fragment length polymorphism and microsatellite markers. Segregation distortion; Alignment of homologous groups; Analysis of sequence-tagged sites.

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics