Ultrahigh-density linkage map for cultivated cucumber (Cucumis sativus L.) using a single-nucleotide polymorphism genotyping array.

Genotyping arrays are tools for high-throughput genotyping, which is beneficial in constructing saturated genetic maps and therefore high-resolution mapping of complex traits. Since the report of the first cucumber genome draft, genetic maps have been constructed mainly based on simple-sequence repeats (SSRs) or on combinations of SSRs and sequence-related amplified polymorphism (SRAP). In this study, we developed the first cucumber genotyping array consisting of 32,864 single-nucleotide polymorphisms (SNPs). These markers cover the cucumber genome with a median interval of ~2 Kb and have expected genotype calls in parents/F1 hybridizations as a training set. The training set was validated with Fluidigm technology and showed 96% concordance with the genotype calls in the parents/F1 hybridizations. Application of the genotyping array was illustrated by constructing a 598.7 cM genetic map based on a '9930' × 'Gy14' recombinant inbred line (RIL) population comprised of 11,156 SNPs. Marker collinearity between the genetic map and reference genomes of the two parents was estimated at R2 = 0.97. We also used the array-derived genetic map to investigate chromosomal rearrangements, regional recombination rate, and specific regions with segregation distortions. Finally, 82% of the linkage-map bins were polymorphic in other cucumber variants, suggesting that the array can be applied for genotyping in other lines. The genotyping array presented here, together with the genotype calls of the parents/F1 hybridizations as a training set, should be a powerful tool in future studies with high-throughput cucumber genotyping. An ultrahigh-density linkage map constructed by this genotyping array on RIL population may be invaluable for assembly improvement, and for mapping important cucumber QTLs

Additional file 1: Table S1. of Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome

Mango transcriptome annotation. (XLSX 16205 kb

Summary of marker properties on the array and in the 'good training set' subset.

<p>Summary of marker properties on the array and in the 'good training set' subset.</p

Illustration of genotype call refinement.

<p>Genotype call refinement was performed to improve the genotype call for stretches or blocks. Inconsistencies within a block were corrected to either the genotype block (AA—red; BB—green; AB—blue) or to no call (light gray). (A) An example of specific locus refinement by flanking loci according to the following criteria. First, six or more flanking loci from both sides of the locus were called other than the locus call, but consecutively. This locus was modified to the call of the flanking loci. Otherwise, if the flanking loci did not contain uniformly consecutive calls, the locus call was set to ‘no call’. (B) If a region was stretched out over 12 or more different consecutive calls, the whole region was set to ‘no call’. (C) A heatmap plot of the genotype calls, before and after refinement. To illuminate the improvement, a zoom into a subset of SNPs and RILs of 20 x 20 (left bottom corner) was plotted.</p

Genetic and physical map comparison for chromosome 5.

<p>Scatter plots of marker positions on the genetic map against the positions of the genome reference of both (A) ‘9930’ and (B) ‘Gy14’. These maps were drawn to their relative axis in a dot plot (C) of the two genomes for comparison.</p

Application of cucumber genotyping array to four cucumber accessions.

<p>Genomic DNA of four cucumber accessions—H19, TL, G421, and WI 2757—was hybridized on the cucumber array. The genotype calls of the array were plotted as heatmap per chromosome where A is the ‘9930’ allele and B is the ‘Gy14’ allele. The mixed color blocks illustrate the polymorphic property of the SNPs on the array.</p

Regional recombination rate.

<p>For each chromosome, a sliding window was run over 5 SNP markers on the genetic map. Within that window, the slope of the genetic distance (cM) vs. physical genomic distance (Mb) was calculated and plotted on a log scale. Markers whose order on the genetic map was inconsistent with their order on the genome were removed. The recombination rate was calculated for the 'Gy14' genome.</p

Example of three types of training sets.

<p>Hybridization signals of ‘GY14’ (green X), ‘9930’ (red circles), and their F₁ (blue triangles) were plotted as scatter plots of allele X signals against allele Y signals. (A) Three distinct clusters were generated. This was considered a probe set for a SNP with a good training set. (B) Three distinct clusters were generated, one of which was clustered incorrectly. This was also considered a good training set. (C) No distinct cluster was generated. These SNP probe sets were not included in the genotype call analysis.</p

Identification of a Novel Hypoxia-Inducible Factor 1-Responsive Gene, RTP801, Involved in Apoptosis

Hypoxia is an important factor that elicits numerous physiological and pathological responses. One of the major gene expression programs triggered by hypoxia is mediated through hypoxia-responsive transcription factor hypoxia-inducible factor 1 (HIF-1). Here, we report the identification and cloning of a novel HIF-1-responsive gene, designated RTP801. Its strong up-regulation by hypoxia was detected both in vitro and in vivo in an animal model of ischemic stroke. When induced from a tetracycline-repressible promoter, RTP801 protected MCF7 and PC12 cells from hypoxia in glucose-free medium and from H(2)O(2)-triggered apoptosis via a dramatic reduction in the generation of reactive oxygen species. However, expression of RTP801 appeared toxic for nondividing neuron-like PC12 cells and increased their sensitivity to ischemic injury and oxidative stress. Liposomal delivery of RTP801 cDNA to mouse lungs also resulted in massive cell death. Thus, the biological effect of RTP801 overexpression depends on the cell context and may be either protecting or detrimental for cells under conditions of oxidative or ischemic stresses. Altogether, the data suggest a complex type of involvement of RTP801 in the pathogenesis of ischemic diseases