Open Access Methodology article

Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.)

Kevin Stoffel1, Hans van Leeuwen16, Alexander Kozik2, David Caldwell17, Hamid Ashrafi1, Xinping Cui45, Xiaoping Tan1, Theresa Hill1, Sebastian Reyes-Chin-Wo1, Maria-Jose Truco2, Richard W Michelmore23* and Allen Van Deynze13*

Author Affiliations

1 Seed Biotechnology Center, University of California, Davis, CA, 95616, USA

2 Genome Center, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA

3 Department of Plant Sciences, University of California, Davis, CA, 95616, USA

4 Department of Statistics, University of California, Riverside, CA, 92521, USA

5 Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA

6 Nunhems Netherlands B.V., P.O. Box 4005, 6080, AA, Haelen, The Netherlands

7 Monsanto, Molecular Breeding Technology, 700 Chesterfield Pkwy W, BB34, Chesterfield, MO, 63017, England

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BMC Genomics 2012, 13:185  doi:10.1186/1471-2164-13-185

Published: 14 May 2012

Additional files

Additional file 1:

Figure S1. A representation of the tiling path across a contig shows probes constructed for both sense and anti-sense strands at a 4 bp stagger deviated by 2 bp to result in final 2 bp stagger.

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Additional file 2:

Figure S2. A histogram showing the number of probes per unigene.

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Additional file 3:

Figure S3. A histogram showing the frequency of probes separated by GC bin from five to nineteen guanines or cytosines.

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Additional file 4:

Figure S4. Pair-wise scatter plots of 600,000 random RMA background corrected hybridization values comparing WGA amplified DNase I fragmented, end-labeled genomic DNA (SAL_WGA) versus untreated DNase I fragmented, endlabeled genomic DNA (SAL_30_01, SAL_30_02, SAL_30_New_1, SAL_30_New_2). Coefficient of determination (R2) values opposite their scatter plots indicates a bias in treatments.

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Additional file 5:

Figure S5. Hybridization values per GC bin of BioPrime labeled/amplified samples, two reactions combined (Bioprime_2x), WGA amplified, dUTP incorporated, APE I UDG fragmented end-labeled DNA and DNase I end labeled DNA are compared to show the effect of techniques on hybridization intensities. BioPrime labeled/amplified samples show an increased in hybridization values in probes with higher GC content compared to other methods.

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Additional file 6:

Figure S6. SPPdev values are plotted along a contig. The orange lines compared to the black lines show the effect on SPP calls when probes hybridizing below the 90th percentile of anti-genomic are removed.

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Additional file 7:

Figure S7. Enlarged view of L. sativa clade from Tree 2 phylogram. Branch lengths represent relative genetic distance.

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Additional file 8:

Table S1. An analysis of variance and least squares mean separations were performed using JMP on genotypes, separating species or classes within L. sativa when possible. Least squares means separation using Students t-test separated classes and species showing significant differences between species/classes with different letters. Left column: The three tables show the analysis of variance for all genotypes in the DP separated by species. Moving downward in the column shows the ANOVA for principle components one through three respectively. Each of the first three principle components were significant at <0.001. Right Column: The three tables show the ANOVA for each of the first three principle components separated by horticultural type. Only principle components one and three are significantly different in this analysis.

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Additional file 9:

Table S2. A table of SPP data for each of the markers used in the creation of phylogenetic trees.

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Additional file 10:

Table S3. A table of haplotype frequencies used for the principle component analysis of all individuals in the diversity panel.

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Additional file 11:

Table S4. A table of haplotype frequencies used for the principle component analysis of L. sativa.

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