Genetic dissection of stem and leaf rachis prickles in diploid rose using a pedigree-based QTL analysis.

Introduction: Prickles are often deemed undesirable traits in many crops, including roses ( sp.), and there is demand for rose cultivars with no or very few prickles. This study aims to identify new and/or validate reported quantitative trait loci (QTLs) associated with stem and leaf rachis prickle density, characterize the effects of functional haplotypes for major QTLs, and identify the sources of QTL-alleles associated with increased/decreased prickle density in roses.

Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps.

Background: Genotyping-by-sequencing (GBS) provides affordable methods for genotyping hundreds of individuals using millions of markers. However, this challenges bioinformatic procedures that must overcome possible artifacts such as the bias generated by polymerase chain reaction duplicates and sequencing errors. Genotyping errors lead to data that deviate from what is expected from regular meiosis.

Pedigree-based QTL analysis of flower size traits in two multi-parental diploid rose populations.

Rose ( spp.) is one of the most economically important ornamental species worldwide. Flower diameter, flower weight, and the number of petals and petaloids are key flower-size parameters and attractive targets for DNA-informed breeding.

QTL discovery for resistance to black spot and cercospora leaf spot, and defoliation in two interconnected F1 bi-parental tetraploid garden rose populations.

Garden roses are an economically important horticultural crop worldwide, and two major fungal pathogens, black spot ( F.A. Wolf) and cercospora leaf spot of rose ( Pass.

Physical mapping of the wheat genes in low-recombination regions: radiation hybrid mapping of the C-locus.

This work reports the physical mapping of an important gene affecting spike compactness located in a low-recombination region of hexaploid wheat. This work paves the way for the eventual isolation and characterization of the factor involved but also opens up possibilities to use this approach to precisely map other wheat genes located on proximal parts of wheat chromosomes that show highly reduced recombination. Mapping wheat genes, in the centromeric and pericentromeric regions (~ 2/3rd of a given chromosome), poses a formidable challenge due to highly suppressed recombination.

Meta-Analysis of Rose Rosette Disease-Resistant Quantitative Trait Loci and a Search for Candidate Genes.

Rose rosette disease (RRD), caused by the rose rosette emaravirus (RRV), is a major viral disease in roses ( sp.) that threatens the rose industry. Recent studies have revealed quantitative trait loci (QTL) for reduced susceptibility to RRD in the linkage groups (LGs) 1, 5, 6, and 7 in tetraploid populations and the LGs 1, 3, 5, and 6 in diploid populations.

QTL mapping and characterization of black spot disease resistance using two multi-parental diploid rose populations.

Black spot disease (BSD) () is the most common and damaging fungal disease in garden roses (.). Although qualitative resistance to BSD has been extensively investigated, the research on quantitative resistance lags behind.

Field Resistance to Rose Rosette Disease as Determined by Multi-Year Evaluations in Tennessee and Delaware.

Rose rosette disease (RRD) caused by the rose rosette emaravirus (RRV) and transmitted by the eriophyid mite , both native to North America, has caused significant damage to roses over the last several decades. As cultural and chemical control of this disease is difficult and expensive, a field trial was established to systematically screen rose germplasm for potential sources of resistance. One hundred and eight rose accessions representing the diversity of rose germplasm were planted in Tennessee and Delaware, managed to encourage disease development, and evaluated for symptom development and viral presence for three years.

Pedigree-based analysis in multi-parental diploid rose populations reveals QTLs for cercospora leaf spot disease resistance.

Cercospora leaf spot (CLS) () is a major fungal disease of roses ( sp.) in the southeastern U.S.

Rose Rosette Disease Resistance Loci Detected in Two Interconnected Tetraploid Garden Rose Populations.

Rose rosette disease (RRD), caused by the (RRV), is a major threat to the garden rose industry in the United States. There has been limited work on the genetics of host plant resistance to RRV. Two interconnected tetraploid garden rose F biparental mapping populations were created to develop high-quality tetraploid rose linkage maps that allowed the discovery of RRD resistance quantitative trait loci (QTLs) on linkage groups (LGs) 5, 6, and 7.

Identification of QTLs for Reduced Susceptibility to Rose Rosette Disease in Diploid Roses.

Resistance to rose rosette disease (RRD), a fatal disease of roses ( spp.), is a high priority for rose breeding. As RRD resistance is time-consuming to phenotype, the identification of genetic markers for resistance could expedite breeding efforts.

Application of X-ray computed tomography to analyze the structure of sorghum grain.

Background: The structural characteristics of whole sorghum kernels are known to affect end-use quality, but traditional evaluation of this structure is two-dimensional (i.e., cross section of a kernel).

High-resolution mapping of the Mov-1 locus in wheat by combining radiation hybrid (RH) and recombination-based mapping approaches.

This work reports a quick method that integrates RH mapping and genetic mapping to map the dominant Mov-1 locus to a 1.1-Mb physical interval with a small number of candidate genes. Bread wheat is an important crop for global human population.

A whole-genome, radiation hybrid mapping resource of hexaploid wheat.

Generating a contiguous, ordered reference sequence of a complex genome such as hexaploid wheat (2n = 6x = 42; approximately 17 GB) is a challenging task due to its large, highly repetitive, and allopolyploid genome. In wheat, ordering of whole-genome or hierarchical shotgun sequencing contigs is primarily based on recombination and comparative genomics-based approaches. However, comparative genomics approaches are limited to syntenic inference and recombination is suppressed within the pericentromeric regions of wheat chromosomes, thus, precise ordering of physical maps and sequenced contigs across the whole-genome using these approaches is nearly impossible.

Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.).

Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.

Pearl millet [Pennisetum glaucum (L.) R. Br.] consensus linkage map constructed using four RIL mapping populations and newly developed EST-SSRs.

Background: Pearl millet [Pennisetum glaucum (L.) R. Br.

Population genomic and genome-wide association studies of agroclimatic traits in sorghum.

Accelerating crop improvement in sorghum, a staple food for people in semiarid regions across the developing world, is key to ensuring global food security in the context of climate change. To facilitate gene discovery and molecular breeding in sorghum, we have characterized ~265,000 single nucleotide polymorphisms (SNPs) in 971 worldwide accessions that have adapted to diverse agroclimatic conditions. Using this genome-wide SNP map, we have characterized population structure with respect to geographic origin and morphological type and identified patterns of ancient crop diffusion to diverse agroclimatic regions across Africa and Asia.

Endosperm tolerance of paternal aneuploidy allows radiation hybrid mapping of the wheat D-genome and a measure of γ ray-induced chromosome breaks.

Physical mapping and genome sequencing are underway for the ≈17 Gb wheat genome. Physical mapping methods independent of meiotic recombination, such as radiation hybrid (RH) mapping, will aid precise anchoring of BAC contigs in the large regions of suppressed recombination in Triticeae genomes. Reports of endosperm development following pollination with irradiated pollen at dosages that cause embryo abortion prompted us to investigate endosperm as a potential source of RH mapping germplasm.

Identification of genetic factors controlling kernel hardness and related traits in a recombinant inbred population derived from a soft × 'extra-soft' wheat (Triticum aestivum L.) cross.

Kernel hardness or texture, used to classify wheat (Triticum aestivum L.) into soft and hard classes, is a major determinant of milling and baking quality. Wheat genotypes in the soft class that are termed 'extra-soft' (with kernel hardness in the lower end of the spectrum) have been associated with superior end-use quality.

Quantitative trait loci analysis for resistance to Cephalosporium stripe, a vascular wilt disease of wheat.

Cephalosporium stripe, caused by Cephalosporium gramineum, can cause severe loss of wheat (Triticum aestivum L.) yield and grain quality and can be an important factor limiting adoption of conservation tillage practices. Selecting for resistance to Cephalosporium stripe is problematic; however, as optimum conditions for disease do not occur annually under natural conditions, inoculum levels can be spatially heterogeneous, and little is known about the inheritance of resistance.

Development and use of oat-maize chromosome additions and radiation hybrids.

Hybridization experiments of oat with maize require fastidious coordination of plant cultivation and flowering timing, meticulous crossing techniques, stimulation with plant growth substances, and in vitro rescue and culture of the hybrid embryos. The majority of hybrid offspring gradually lose all maize chromosomes consequently resulting in haploid oat plants. However, a minority of the offspring retain one or more maize chromosome(s) in addition to their haploid oat complements (partial hybrids).

Genetic structure of Aegilops cylindrica Host in its native range and in the United States of America.

Chloroplast and nuclear microsatellite markers were used to study genetic diversity and genetic structure of Aegilops cylindrica Host collected in its native range and in adventive sites in the USA. Our analysis suggests that Ae. cylindrica, an allotetraploid, arose from multiple hybridizations between Ae.

Maize centromere mapping: a comparison of physical and genetic strategies.

Centromere positions on 7 maize chromosomes were compared on the basis of data from 4 to 6 mapping techniques per chromosome. Centromere positions were first located relative to molecular markers by means of radiation hybrid lines and centric fission lines recovered from oat-maize chromosome addition lines. These centromere positions were then compared with new data from centric fission lines recovered from maize plants, half-tetrad mapping, and fluorescence in situ hybridizations and to data from earlier studies.

Identification of a candidate gene for the wheat endopeptidase Ep-D1 locus and two other STS markers linked to the eyespot resistance gene Pch1.

Wheat is prone to strawbreaker foot rot (eyespot), a fungal disease caused by Oculimacula yallundae and O. acuformis. The most effective source of genetic resistance is Pch1, a gene derived from Aegilops ventricosa.