Technical note: Generation of a Cerenkov scatter function convolution kernel for a primary proton beam.

PURPOSE: To generate a Cerenkov scatter function (CSF) for a primary proton beam and to study the dependence of the CSF on the irradiated medium. MATERIALS AND METHODS: The MCNP 6.2 code was used to generate the CSF. The CSF was calculated for light-pigmented, medium-pigmented, and dark-pigmented stratified skin, as well as for a homogeneous optical phantom, which mimics the optical properties of human tissue. CSFs were generated by binning all of the Cerenkov photons which escape the back end (end opposite beam incidence) of a 20 × 20 × 20 cm phantom. A 4 × 4 cm, 500 × 500 bin grid was used to create a histogram of the Cerenkov photon flux on the simulated medium's back surface (surface opposite beam incidence). A triple Gaussian was then used to fit the data. RESULTS: From the triple Gaussian fit, the coefficients of the CSF for the four phantom materials was generated. The individual CSF fit coefficient errors, with respect to the Gaussian representation, were found to be between 0.92% and 4.11%. The R2 value for the fit was calculated to be 0.99. The phantom material was found to have a significant effect (63% difference between materials) on the CSF amplitude and full width at half maximum (195% difference between materials). The difference in these parameters for the three skin pigments was found to be small. CONCLUSIONS: The CSF was obtained for a proton beam using the MCNP 6.2 code for a phantom constructed of light, medium, and dark stratified human skin, as well as for an optical phantom. The CSFs were then fit with a triple-Gaussian function. The coefficients can be used to generate a radially symmetric CSF, which can then be used to deconvolve a measured Cerenkov image to obtain the dose distribution.

Development of highly polymorphic SNP markers from the complexity reduced portion of maize [Zea mays L.] genome for use in marker-assisted breeding.

The duplicated and the highly repetitive nature of the maize genome has historically impeded the development of true single nucleotide polymorphism (SNP) markers in this crop. Recent advances in genome complexity reduction methods coupled with sequencing-by-synthesis technologies permit the implementation of efficient genome-wide SNP discovery in maize. In this study, we have applied Complexity Reduction of Polymorphic Sequences technology (Keygene N.V., Wageningen, The Netherlands) for the identification of informative SNPs between two genetically distinct maize inbred lines of North and South American origins. This approach resulted in the discovery of 1,123 putative SNPs representing low and single copy loci. In silico and experimental (Illumina GoldenGate (GG) assay) validation of putative SNPs resulted in mapping of 604 markers, out of which 188 SNPs represented 43 haplotype blocks distributed across all ten chromosomes. We have determined and clearly stated a specific combination of stringent criteria (>0.3 minor allele frequency, >0.8 GenTrainScore and >0.5 Chi_test100 score) necessary for the identification of highly polymorphic and genetically stable SNP markers. Due to these criteria, we identified a subset of 120 high-quality SNP markers to leverage in GG assay-based marker-assisted selection projects. A total of 32 high-quality SNPs represented 21 haplotypes out of 43 identified in this study. The information on the selection criteria of highly polymorphic SNPs in a complex genome such as maize and the public availability of these SNP assays will be of great value for the maize molecular genetics and breeding community.

Mapping of the loci controlling oleic and linolenic acid contents and development of fad2 and fad3 allele-specific markers in canola (Brassica napus L.).

The quality of canola oil is determined by its constituent fatty acids such as oleic acid (C18:1), linoleic acid (C18:2) and linolenic acid (C18:3). Most canola cultivars normally produce oil with about 55-65% oleic acid and 8-12% linolenic acid. High concentrations of linolenic acid lead to oil instability and off-type flavor, while high levels of oleic acid increase oxidative stability and nutritional value of oil. Therefore, development of canola cultivars with increased oleic acid and reduced linolenic acid is highly desirable for canola oil quality. In this study, we have mapped one locus that has a major effect and one locus that has a minor effect for high oleic acid and two loci that have major effects for low linolenic acid in a doubled haploid population. The major locus for high C18:1 was proven to be the fatty acid desaturase-2 (fad2) gene and it is located on the linkage group N5; the minor locus is located on N1. One major QTL for C18:3 is the fatty acid desaturase-3 gene of the genome C (fad3c) and it is located on N14. The second major QTL resides on N4 and is the fad3a gene of the A genome. We have sequenced genomic clones of the fad2 and fad3c genes amplified from an EMS-induced mutant and a wild-type canola cultivar. A comparison of the mutant and wild-type allele sequences of the fad2 and fad3c genes revealed single nucleotide mutations in each of the genes. Detailed sequence analyses suggested mechanisms by which both the mutations can cause altered fatty acid content. Based on the sequence differences between the mutant and wild-type alleles, two single nucleotide polymorphism (SNP) markers, corresponding to the fad2 and fad3c gene mutations, were developed. These markers will be highly useful for direct selection of desirable fad2 and fad3c alleles during marker-assisted trait introgression and breeding of canola with high oleic and low linolenic acid.