Characterization of hemizygous deletions in Citrus using array-Comparative Genomic Hybridization and microsynteny comparisons with the poplar genome

Ríos, Gabino; Naranjo, Miguel A.; Iglesias, Domingo J.; Ruiz-Rivero, Omar; Geraud, Marion; Usach, Antonio; Talón, Manuel
January 2008
BMC Genomics;2008, Vol. 9, Special section p1
Academic Journal
Background: Many fruit-tree species, including relevant Citrus spp varieties exhibit a reproductive biology that impairs breeding and strongly constrains genetic improvements. In citrus, juvenility increases the generation time while sexual sterility, inbreeding depression and self-incompatibility prevent the production of homozygous cultivars. Genomic technology may provide citrus researchers with a new set of tools to address these various restrictions. In this work, we report a valuable genomics-based protocol for the structural analysis of deletion mutations on an heterozygous background. Results: Two independent fast neutron mutants of self-incompatible clementine (Citrus clementina Hort. Ex Tan. cv. Clemenules) were the subject of the study. Both mutants, named 39B3 and 39E7, were expected to carry DNA deletions in hemizygous dosage. Array-based Comparative Genomic Hybridization (array-CGH) using a Citrus cDNA microarray allowed the identification of underrepresented genes in these two mutants. Subsequent comparison of citrus deleted genes with annotated plant genomes, especially poplar, made possible to predict the presence of a large deletion in 39B3 of about 700 kb and at least two deletions of approximately 100 and 500 kb in 39E7. The deletion in 39B3 was further characterized by PCR on available Citrus BACs, which helped us to build a partial physical map of the deletion. Among the deleted genes, ClpC-like gene coding for a putative subunit of a multifunctional chloroplastic protease involved in the regulation of chlorophyll b synthesis was directly related to the mutated phenotype since the mutant showed a reduced chlorophyll a/b ratio in green tissues. Conclusion: In this work, we report the use of array-CGH for the successful identification of genes included in a hemizygous deletion induced by fast neutron irradiation on Citrus clementina. The study of gene content and order into the 39B3 deletion also led to the unexpected conclusion that microsynteny and local gene colinearity in this species were higher with Populus trichocarpa than with the phylogenetically closer Arabidopsis thaliana. This work corroborates the potential of Citrus genomic resources to assist mutagenesis-based approaches for functional genetics, structural studies and comparative genomics, and hence to facilitate citrus variety improvement.


Related Articles

  • TILLING for allergen reduction and improvement of quality traits in peanut (Arachis hypogaea L.). Knoll, Joseph E.; Ramos, M. Laura; Zeng, Yajuan; Holbrook, C. Corley; Chow, Marjorie; Chen, Sixue; Maleki, Soheila; Bhattacharya, Anjanabha; Ozias-Akins, Peggy // BMC Plant Biology;2011, Vol. 11 Issue 1, p81 

    Background: Allergic reactions to peanuts (Arachis hypogaea L.) can cause severe symptoms and in some cases can be fatal, but avoidance is difficult due to the prevalence of peanut-derived products in processed foods. One strategy of reducing the allergenicity of peanuts is to alter or eliminate...

  • Towards a mutation in every gene in Caenorhabditis elegans. Moerman, Donald G.; Barstead, Robert J. // Briefings in Functional Genomics & Proteomics;May2008, Vol. 7 Issue 3, p195 

    The combined efforts of the Caenorhabditis elegans Knockout Consortium and individuals within the worm community are moving us closer to the goal of identifying mutations in every gene in the nematode C. elegans. At present, we count about 7000 deletion alleles that fall within 5500 genes. The...

  • Genomic profiling of malignant melanoma using tiling-resolution arrayCGH. Jönsson, G.; Dahl, C.; Staaf, J.; Sandberg, T.; Bendahl, P.-O.; Ringnér, M.; Guldberg, P.; Borg, Å. // Oncogene;7/12/2007, Vol. 26 Issue 32, p4738 

    Malignant melanoma is an aggressive, heterogeneous disease where new biomarkers for diagnosis and clinical outcome are needed. We searched for chromosomal aberrations that characterize its pathogenesis using 47 different melanoma cell lines and tiling-resolution bacterial artificial...

  • Array CGH Change Genetic Diagnostics. Shaffer, Catherine // Drug Discovery & Development;Dec2006, Vol. 9 Issue 12, pG12 

    The article presents information on the importance of comparative genomic hybridization (CGH) in genetics. The CGH has brought major critical changes in genetic diagnostics. The technology was first described in 1992 for the study of mutations in cancer cells. With the array CGH, it is possible...

  • Genetic analysis of multifocal superficial urothelial cancers by array-based comparative genomic hybridisation. Kawanishi, H.; Takahashi, T.; Ito, M.; Matsui, Y.; Watanabe, J.; Ito, N.; Kamoto, T.; Kadowaki, T.; Tsujimoto, G.; Imoto, I.; Inazawa, J.; Nishiyama, H.; Ogawa, O. // British Journal of Cancer;7/16/2007, Vol. 97 Issue 2, p260 

    The purpose of this study was to investigate the accumulation of genetic alterations during metachronous and/or synchronous development of multifocal low-grade superficial urothelial tumours in the same patient, by using array-based comparative genomic hybridisation (array-CGH) and FGFR mutation...

  • Generation and application of dynamic standard reference intervals for analyzing results of comparative genomic hybridization. Min'zhenkova, M.; Shilova, N.; Markova, Zh.; Antonenko, V.; Lebedev, I.; Kozlova, Yu.; Zemlyakova, V.; Zolotukhina, T. // Russian Journal of Genetics;Oct2013, Vol. 49 Issue 10, p1072 

    The present work was aimed at generating the dynamic standard reference intervals (DSRI) and their application for chromosomal-aberration (CA) analysis. The evaluation of the generated DSRI was performed using the DNA samples from four patients with already known CA. High-resolution comparative...

  • Implications of gene copy-number variation in health and diseases. Almal, Suhani H; Padh, Harish // Journal of Human Genetics;Jan2012, Vol. 57 Issue 1, p6 

    Inter-individual genomic variations have recently become evident with advances in sequencing techniques and genome-wide array comparative genomic hybridization. Among such variations single nucleotide polymorphisms (SNPs) are widely studied and better defined because of availability of...

  • Leveraging the rice genome sequence for monocot comparative and translational genomics. Lohithaswa, H. C.; Feltus, F. A.; Singh, H. P.; Bacon, C. D.; Bailey, C. D.; Paterson, A. H. // Theoretical & Applied Genetics;Jul2007, Vol. 115 Issue 2, p237 

    Common genome anchor points across many taxa greatly facilitate translational and comparative genomics and will improve our understanding of the Tree of Life. To add to the repertoire of genomic tools applicable to the study of monocotyledonous plants in general, we aligned Allium and Musa ESTs...

  • Erratum.  // Journal of Heredity;Sep/Oct2007, Vol. 98 Issue 6, p635 

    A correction to the article "A Cytogenetically Chracterized, Genome-Anchored 10-Mb BAC Set and CGH Array for the Domestic Dog," that was published in the 2007 Symposium issue is presented.


Read the Article


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

Try another library?
Sign out of this library

Other Topics