Journal: PLoS ONE

Article Title: Quantitative Assessment of Common Genetic Variants on Chromosome 5p12 and Hormone Receptor Status with Breast Cancer Risk

doi: 10.1371/journal.pone.0072154

Figure Lengend Snippet: Characteristics of the studies included in the meta-analysis.

Article Snippet: Fletcher , 2011 , British , SNP Array, GoldenGate , 7643/7443 , GP.

Techniques:

Journal: BMC Genomics

Article Title: A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy

doi: 10.1186/1471-2164-13-142

Figure Lengend Snippet: Genotype calling using the Miscanthus GoldenGate™ array . The graphs in panels A-F plot normalized theta (ratio of signal intensities assayed for A and B SNP alleles) against normalized R (signal intensity) for each individual represented as a colored square. Panels A, C, and E illustrate markers that cluster as predicted for a biallelic SNP, which segregate as AA (red), AB (yellow), or BB (blue). Panels B, D, and F illustrate markers that cluster as predicted for a SNP distinguishing alleles for one of two duplicated and unlinked loci, where theta is skewed by the relative dosage of A and B SNPs. In all panels, clusters are defined as sharing alleles with either the Grosse Fontaine (green circles) or Undine (pink circles) parents, individuals that fall outside the cluster are marked as "no calls" (NC, grey), and the doubled haploid genotype is indicated by the black arrow. Panel G reports the relative fraction of genotyped segregating SNPs within each clustering type among the Grosse Fontaine and Undine parents, the population of their F1 progeny, as well as the two doubled haploids and their respective parents. Single cluster markers (fixed differences between paralogs) behave similarly in diploids and doubled haploids. In contrast, while diploid accessions show extensive heterozygosity at segregating loci (two- and three-cluster markers), doubled haploids show no heterozygosity.

Article Snippet: Out of 1,536 putative markers on the Miscanthus GoldenGate array (Additional file : Table S3), 1,243 showed one or more clusters in GoldenGate signal space (Figure ), indicating consistent genotyping across individuals.

Techniques:

Journal: BMC Genomics

Article Title: A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy

doi: 10.1186/1471-2164-13-142

Figure Lengend Snippet: Tetraploidy of Miscanthus relative to sorghum, with extensive colinearity and a single chromosome fusion . Panel A . Horizontal axis shows genetic map position of markers on the 19 Miscanthus linkage groups, in centiMorgans; vertical axis shows physical map position of markers aligned to the 10 sorghum chromosomes in megabases. Each dot corresponds to a single marker. Markers that could not be uniquely mapped to sorghum are shown along the horizontal axis as black dots. Duplication and colinearity of nearly all chromosomes is evident (markers in magenta). A copy of sorghum chromosome 7 (markers in sky blue) has been inserted into a copy of sorghum chromosome 4 (markers in green) to produce Miscanthus linkage group 7. Markers on Miscanthus linkage group 13, which are also syntenic with sorghum chromosome 7, are shown in a darker blue. Panel B . Circos plot showing centromeric insertion of sorghum chromosome 7 into sorghum chromosome 4 to form Miscanthus linkage group 7 (approximate boundaries indicated by arrows). Each line represents an orthologous relationship between a mapped Miscanthus marker and its unique counterpart on the Sorghum bicolor genome. Both Miscanthus linkage groups 7 and 8 have a region corresponding to sorghum chromosome 4, which is inverted with respect to the other markers (dark green arrow and lines). As also shown, Miscanthus linkage group 8 is an intact copy of sorghum chromosome 4, and Miscanthus linkage group 13 is an intact copy of sorghum chromosome 7.

Article Snippet: Out of 1,536 putative markers on the Miscanthus GoldenGate array (Additional file : Table S3), 1,243 showed one or more clusters in GoldenGate signal space (Figure ), indicating consistent genotyping across individuals.

Techniques: Marker

Journal: Molecular Breeding

Article Title: Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties

doi: 10.1007/s11032-015-0335-0

Figure Lengend Snippet: MaizeSNP3072 cluster file constructed to improve the genotyping efficiency of the 3072 loci. Samples with reproducibility errors appear as squares . a , c Automatic SNP calling using GenomeStudio software and b , d corrected SNP calling using a maizeSNP3072 cluster file

Article Snippet: The probe pool was developed according to the flanking sequences of the 3072 SNPs, and the maizeSNP3072 array chip was ordered based on GoldenGate technology.

Techniques: Construct, Software

Journal: Molecular Breeding

Article Title: Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties

doi: 10.1007/s11032-015-0335-0

Figure Lengend Snippet: Design of the maizeSNP3072 array. a Numbers of single nucleotide polymorphisms (SNPs) with their corresponding designability scores for 3072 SNPs evaluated by Illumina, b MAF values of the 3072 SNPs based on data from 96 samples, c MAF values of the 3072 SNPs based on data from 309 inbred lines and d distribution of the 3072 SNPs on 10 chromosomes. The window size is 1000 kbp, the x -axis represents the order of the widows, and the y -axis corresponds to the number of SNP loci

Article Snippet: The probe pool was developed according to the flanking sequences of the 3072 SNPs, and the maizeSNP3072 array chip was ordered based on GoldenGate technology.

Techniques:

Journal: Molecular Breeding

Article Title: Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties

doi: 10.1007/s11032-015-0335-0

Figure Lengend Snippet: Comparative analysis of maizeSNP3072 and maizeSNP50K chips based on data from 3072 and 56,110 single nucleotide polymorphisms in 96 evaluated maize samples

Article Snippet: The probe pool was developed according to the flanking sequences of the 3072 SNPs, and the maizeSNP3072 array chip was ordered based on GoldenGate technology.

Techniques: Marker