Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Single feature polymorphism array 16K Unigenes: marker discovery in melon

ABSTRACT: One of the methods used to search for molecular markers is DNA hybridization to microarrays. Microarray hybridization of DNA from different individuals 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. For marker discovery, we used DNA from the parents of our mapping population, developed by Katzir's group from a cross between representatives of two subspecies of Cucumis melo L.: PI414723 (subspecies agrestis) and 'Dulce' (subspecies melo). Two biological replicates from PI414723 and two from 'Dulce' were used. Each biological replicate contained gDNAs pooled from 10 different plants. gDNA samples were labeled and hybridized using standard Agilent procedures for comparative genomic hybridization (CGH). The inter-population genetic variation was detected using two arrays, with one of the biological replicates of 'Dulce' against one of the PI414723 replicates on each array. The intra-population variation was detected by hybridizing the PI414723 replicates against each other and the 'Dulce' replicates against each other. Intra-population variation was estimated to ensure that the genetic variation between these populations is based on alleles that are fixed in the population and not due to intra-population variation.

ORGANISM(S): Cucumis melo subsp. melo

SUBMITTER: Ron Ophir

PROVIDER: E-GEOD-17673 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

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

Ophir Ron R Eshed Ravit R Harel-Beja Rotem R Tzuri Galil G Portnoy Vitaly V Burger Yoseph Y Uliel Shai S Katzir Nurit N Sherman Amir A

BMC genomics 20100428

<h4>Background</h4>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--sing ...[more]

PMID: 20426811

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Project description:Background: Differences in levels of gene expression among individuals are an important source of phenotypic variation within populations. Recent microarray studies have revealed that expression variation is abundant in many species, including Drosophila melanogaster. However, previous expression surveys in this species generally focused on a small number of laboratory strains established from derived populations. Thus, these studies were not ideal for population genetic analyses. Results: We surveyed gene expression variation in adult males of 16 D. melanogaster strains from two natural populations, including an ancestral African population and a derived European population. Levels of expression polymorphism were nearly equal in the two populations, but a higher number of differences was detected when comparing strains between populations. Expression variation was greatest for genes associated with few molecular functions or biological processes, as well as those expressed predominantly in males. Our analysis also identified genes that differed in expression level between the European and African populations, which may be candidates for adaptive regulatory evolution. Genes involved in flight musculature and fatty acid metabolism were over-represented in the list of candidates. Conclusions: Overall, stabilizing selection appears to be the major force governing gene expression variation within populations. However, positive selection may be responsible for much of the between-population expression divergence. The nature of the genes identified to differ in expression between populations may reveal which traits were important for local adaptation to the European and African environments. We used dual channel microarrays to compare genome-wide expression profiles in adult males from 16 inbred strains derived from two natural populations. In total 80 hybidizations were performed including dye-swaps. The hybridization scheme consisted of a balanced loop design, which allowed an unbiased comparison of relative expression levels within and between populations.

Project description:Advances in genomic technologies are rapidly filling the gap in genomic information available from non-model species that are economically and ecologically important. Reduction in costs and higher throughput of data acquisition will progressively increase the application of genomics in population and quantitative genetics. In molecular breeding, the ability to rapidly develop large numbers of genetic markers and generate high-density genetic maps at low cost is critical because they provide the framework for identification of elements that regulate trait variation, connecting genetics and genomics to phenotype. To generate the first high-density, gene-based genetic map for Eucalyptus, we genotyped a hybrid segregating population with microarray-based markers. The genus Eucalyptus includes the most economically important species used for bioenergy pulp and paper production worldwide. A custom 25-mers oligonucleotide array was designed based on 20,726 expressed sequence tags consensus, and RNA from 28 biologically-replicated individuals allowed clear-cut detection of putative single feature polymorphisms (SFPs) segregating 1:1 and 3:1. A genotyping array confirmed the segregation in a larger portion of the family and a genetic map with 1064 gene-related markers is made available with an average of one marker every 1.2 cM. Interestingly, reanalyzing the data from the 28 genotypes using a mixed-model approach resulted in most of the mapped genes among the significant probesets. We also demonstrate that designing more probes per gene increases the chance of mapping those genes. Finally, in silico validatation shows that 87% of the markers map to expected location on the draft genome, an important characteristic of SFP markers. Simultaneously detecting and genotyping SFP markers in a subset of the mapping population instead of only the genitors was more efficient for mapping genes in outcrossing species than previously reported approaches. Mapping SFP markers require low genomic resources and can be done at relatively low cost. We demonstrate the possibility of mapping hundreds to thousands of genes that can ultimately be used in generating further genomic resources, such as genome assembly, or for more direct applications, such as QTL analysis. Two biological replication of 28 genotypes were hybridized to the custom microarray, labeled with Cy3 and Cy5. Genotypes are fullsib progenies of the cross E. urophylla X E. grandis. A loop design was employed for the hybridization using xylem tissue. In total the microarray comprised 103,000 probes representing 20,726 unigenes with an average of five probes per unigene. Twenty-six negative control probes were also included in the microarray.

Dataset Information

Single feature polymorphism array 16K Unigenes: marker discovery in melon

Publications

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

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