A multiplexed plant-animal SNP array for selective breeding and species conservation applications.

Reliable and high-throughput genotyping platforms are of immense importance for identifying and dissecting genomic regions controlling important phenotypes, supporting selection processes in breeding programs, and managing wild populations and germplasm collections. Amongst available genotyping tools, single nucleotide polymorphism arrays have been shown to be comparatively easy to use and generate highly accurate genotypic data. Single-species arrays are the most commonly used type so far; however, some multi-species arrays have been developed for closely related species that share single nucleotide polymorphism markers, exploiting inter-species cross-amplification.

Exploring the diversity and genetic structure of the U.S. National Cultivated Strawberry Collection.

The cultivated strawberry ( ×) arose through a hybridization of two wild American octoploid strawberry species in a French garden in the 1750s. Since then, breeders have developed improved cultivars adapted to different growing regions. Diverse germplasm is crucial to meet the challenges strawberry breeders will continue to address.

Two fingerprinting sets for Humulus lupulus based on KASP and microsatellite markers.

Verification of clonal identity of hop (Humulus lupulus L.) cultivars within breeding programs and germplasm collections is vital to conserving genetic resources. Accurate and economic DNA-based tools are needed in dioecious hop to confirm identity and parentage, neither of which can be reliably determined from morphological observations.

Genomic Analysis and Delineation of the Tan Spot Susceptibility Locus in Wheat.

The necrotrophic fungal pathogen () causes the foliar disease tan spot in both bread wheat and durum wheat. Wheat lines carrying the tan spot susceptibility gene are sensitive to the -produced necrotrophic effector (NE) Ptr ToxC. A compatible interaction results in leaf chlorosis, reducing yield by decreasing the photosynthetic area of leaves.

RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops.

The Rosaceae crop family (including almond, apple, apricot, blackberry, peach, pear, plum, raspberry, rose, strawberry, sweet cherry, and sour cherry) provides vital contributions to human well-being and is economically significant across the U.S. In 2003, industry stakeholder initiatives prioritized the utilization of genomics, genetics, and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural quality.

A Rosaceae Family-Level Approach To Identify Loci Influencing Soluble Solids Content in Blackberry for DNA-Informed Breeding.

A Rosaceae family-level candidate gene approach was used to identify genes associated with sugar content in blackberry ( subgenus ). Three regions conserved among apple (), peach (), and alpine strawberry () were identified that contained previously detected sweetness-related quantitative trait loci (QTL) in at least two of the crops. Sugar related genes from these conserved regions and 789 sugar-associated apple genes were used to identify 279 candidate transcripts.

Dissecting Genetic Resistance to Fire Blight in Three Pear Populations.

Fire blight, caused by the bacterial pathogen , is a persistent problem for pear ( spp.) growers in the United States. Growing resistant cultivars is one of the best options for managing fire blight.

Mapping the black spot resistance locus Rdr3 in the shrub rose 'George Vancouver' allows for the development of improved diagnostic markers for DNA-informed breeding.

Rdr3 is a novel resistance gene of black spot in roses that maps to a chromosome 6 homolog. A new DNA test was developed and can be used to pyramid black spot resistance in roses. Diplocarpon rosae, the cause of rose black spot, is one of the most devastating foliar pathogens of cultivated roses (Rosa spp.

Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.).

Background: We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping.

Mapping a Resistance Gene to f. sp. in the Bread Wheat Cultivar 'Matlabas'.

f. sp. race TTKSF+ was collected from the South African wheat cultivar 'Matlabas' in 2010.

Mapping a Novel Black Spot Resistance Locus in the Climbing Rose Brite Eyes™ ('RADbrite').

Rose black spot, caused by , is one of the most devastating foliar diseases of cultivated roses ( spp.). The globally distributed pathogen has the potential to cause large economic losses in the outdoor cultivation of roses.

Dissection of the multigenic wheat stem rust resistance present in the Montenegrin spring wheat accession PI 362698.

Background: Research to identify and characterize stem rust resistance genes in common wheat, Triticum aestivum, has been stimulated by the emergence of Ug99-lineage races of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici (Pgt), in Eastern Africa.

Clarifying sub-genomic positions of QTLs for flowering habit and fruit quality in U.S. strawberry (×) breeding populations using pedigree-based QTL analysis.

The cultivated strawberry (×) is consumed worldwide for its flavor and nutritional benefits. Genetic analysis of commercially important traits in strawberry are important for the development of breeding methods and tools for this species. Although several quantitative trait loci (QTL) have been previously detected for fruit quality and flowering traits using low-density genetic maps, clarity on the sub-genomic locations of these QTLs was missing.

Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families.

Genotyping-by-sequencing (GBS) was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry ( × ) populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence data were aligned to the '' reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190.

Inverse gene-for-gene interactions contribute additively to tan spot susceptibility in wheat.

Tan spot susceptibility is conferred by multiple interactions of necrotrophic effector and host sensitivity genes. Tan spot of wheat, caused by Pyrenophora tritici-repentis, is an important disease in almost all wheat-growing areas of the world. The disease system is known to involve at least three fungal-produced necrotrophic effectors (NEs) that interact with the corresponding host sensitivity (S) genes in an inverse gene-for-gene manner to induce disease.