Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts.

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g.

Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts.

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g.

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.

Autopolyploid inheritance and a heterozygous reciprocal translocation shape chromosome genetic behavior in tetraploid blueberry (Vaccinium corymbosum).

Understanding chromosome recombination behavior in polyploidy species is key to advancing genetic discoveries. In blueberry, a tetraploid species, the line of evidences about its genetic behavior still remain poorly understood, owing to the inter-specific, and inter-ploidy admixture of its genome and lack of in depth genome-wide inheritance and comparative structural studies. Here we describe a new high-quality, phased, chromosome-scale genome of a diploid blueberry, clone W85.

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.

There and back again; historical perspective and future directions for breeding and research studies.

The genus L. (Ericaceae) contains a wide diversity of culturally and economically important berry crop species. Consumer demand and scientific research in blueberry ( spp.

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.

Discovery of three loci increasing resistance to charcoal rot caused by Macrophomina phaseolina in octoploid strawberry.

Charcoal rot caused by Macrophomina phaseolinais an increasing economic problem in annualized strawberry production systems around the world. Currently there are no effective postfumigation chemical controls for managing charcoal rot, and no information is available on the genetic architecture of resistance to M. phaseolina in strawberry (Fragaria ×ananassa).

Crop Wild Relatives as Germplasm Resource for Cultivar Improvement in Mint ( L.).

is a strongly scented herb of the (formerly ) and includes about 30 species and hybrid species that are distributed or introduced throughout the globe. These fragrant plants have been selected throughout millennia for use by humans as herbs, spices, and pharmaceutical needs. The distilling of essential oils from mint began in Japan and England but has become a significant industrial product for the US, China, India, and other countries.

Reconstruction of the Largest Pedigree Network for Pear Cultivars and Evaluation of the Genetic Diversity of the USDA-ARS National Collection.

The USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, maintains one of the world's largest and most diverse living collection. A thorough genetic characterization of this germplasm will provide relevant information to optimize the conservation strategy of pear biodiversity, support the use of this germplasm in breeding, and increase our knowledge of taxonomy, evolution, and domestication. In the last two decades simple sequence repeat (SSR) markers have been used at the NCGR for cultivar identification and small population structure analysis.

A roadmap for research in octoploid strawberry.

The cultivated strawberry ( × ) is an allo-octoploid species, originating nearly 300 years ago from wild progenitors from the Americas. Since that time the strawberry has become the most widely cultivated fruit crop in the world, universally appealing due to its sensory qualities and health benefits. The recent publication of the first high-quality chromosome-scale octoploid strawberry genome (cv.

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.

Target Capture Sequencing Unravels Evolution.

(Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of challenging.

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.

Genetic and genomic resources for breeding: a roadmap for the future.

fruits are high-value crops that are sought after by consumers for their flavor, visual appeal, and health benefits. To meet this demand, production of red and black raspberries ( L. and L.

Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization.

Background: Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are equally important to enable faster progress in plant breeding. Pear (Pyrus spp.) lags far behind other fruit and nut crops in terms of employment of available genetic resources for new cultivar development.

Development of a reliable Corylus sp. reference database through the implementation of a DNA fingerprinting test.

This DNA fingerprinting test confirmed 195 unique Corylus sp. accessions that were used to build a reference database for identity verification of unknown hazelnut trees from three locations in Ontario. Hazelnut is one of the most profitable tree nuts worldwide.

Validation of SNP markers for fruit quality and disease resistance loci in apple ( × Borkh.) using the OpenArray® platform.

Genome mapping has promised much to tree fruit breeding during the last 10 years. Nevertheless, one of the greatest challenges remaining to tree fruit geneticists is the translation of trait loci and whole genome sequences into diagnostic genetic markers that are efficient and cost-effective for use by breeders, who must select genetically optimal parents and subsequently select genetically superior individuals among their progeny. To take this translational step, we designed the apple International RosBREED SNP Consortium OpenArray v1.

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.

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.

A High-Density Linkage Map of the Ancestral Diploid Strawberry, , Constructed with Single Nucleotide Polymorphism Markers from the IStraw90 Array and Genotyping by Sequencing.

Makino is recognized as an ancestor of the octoploid strawberry species, which includes the cultivated strawberry, × Duchesne ex Rozier. Here we report the construction of the first high-density linkage map for . The linkage map (Fii map) is based on two high-throughput techniques of single nucleotide polymorphism (SNP) genotyping: the IStraw90 Array (hereafter "Array"), and genotyping by sequencing (GBS).

Public Availability of a Genotyped Segregating Population May Foster Marker Assisted Breeding (MAB) and Quantitative Trait Loci (QTL) Discovery: An Example Using Strawberry.

Much of the cost associated with marker discovery for marker assisted breeding (MAB) can be eliminated if a diverse, segregating population is generated, genotyped, and made available to the global breeding community. Herein, we present an example of a hybrid, wild-derived family of the octoploid strawberry that can be used by other breeding programs to economically find and tag useful genes for MAB. A pseudo test cross population between two wild species of Fragaria virginiana and F.