EST contig-based SSR linkage maps for Malus × domestica cv Royal Gala and an apple scab resistant accession of M. sieversii , the progenitor species of domestic apple

Malus sieversii is a progenitor species of domestic apple M.×domestica. Using population "GMAL 4595” of 188 individuals derived from a cross of Royal Gala×PI 613988 (apple scab resistant, M. sieversii), 287 SSR (simple sequence repeats) loci were mapped. Of these SSRs, 80 are published anchors and 207 are newly developed EST (expressed sequence tag) contig-based SSRs, representing 1,630 Malus EST accessions in GenBank. Putative gene functions of these EST contigs are diverse, including regulating plant growth, development and response to environmental stresses. Among the 80 published SSRs, 18 are PI 613988 specific, 38 are common and 24 are Royal Gala specific. Out of the 207 newly developed EST contig-based SSRs, 79 are PI 613988 specific, 45 are common and 83 are Royal Gala specific. These results led to the construction of a M. sieversii map (1,387.0cM) of 180 SSR markers and a Royal Gala map (1,283.4cM) of 190 SSR markers. Mapping of scab resistance was independently conducted in two subsets of population "GMAL 4595” that were inoculated with Ventura inaequalis races (1) and (2), respectively. In combination with the two major resistance reactions Chl (chlorotic lesions) and SN (stellate necrosis) to each race, four subsets of resistance data, i.e., Chl/race (1), SN/race (1), Chl/race (2) and SN/race (2), were constituted and analyzed, leading to four resistance loci mapped to the linkage group 2 of PI 613988; SNR1 (stellate necrosis resistance to race (1)) and SNR2 are tightly linked in a region of known scab resistance genes, and ChlR1 (Chlorotic lesion resistance to race (1)) and ChlR2 are also linked tightly but in a region without known scab resistance genes. The utility of the two linkage maps, the new EST contig-based markers and M. sieversii as sources of apple scab resistance are discusse

Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum L.)

Linkage map. This file contains the details of the linkage map. (XLSX 38 kb

A roadmap for research in octoploid strawberry

The cultivated strawberry (Fragaria × ananassa) 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. Camarosa) is enabling rapid advances in genetics, stimulating scientific debate and provoking new research questions. In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture. Among these are the origins of the genome, characterization of genetic variants, and big data approaches to breeding. Key areas of research in molecular biology will include the control of flowering, fruit development, fruit quality, and plant–pathogen interactions. In order to realize this potential as a global community, investments in genome resources must be continually augmented.Peer reviewe

A framework physical map for peach, a model Rosaceae species

A genome-wide framework physical map of peach was constructed using high-information content fingerprinting (HICF) and FPC software. The resulting HICF assembly contained 2,138 contigs composed of 15,655 clones (4.3× peach genome equivalents) from two complementary bacterial artificial chromosome libraries. The total physical length of all contigs is estimated at 303 Mb or 104.5% of the peach genome. The framework physical map is anchored on the Prunus genetic reference map and integrated with the peach transcriptome map. The physical length of anchored contigs is estimated at 45.0 Mb or 15.5% of the genome. Altogether, 2,636 markers, i.e., genetic markers, peach unigene expressed sequence tags, and gene-specific and overgo probes, were incorporated into the physical framework and supported the accuracy of contig assembly.This project was supported by the United States Department of Agriculture NRI Award # 2005-35300-15452.Peer reviewe

There and back again: historical perspective and future directions for Vaccinium breeding and research studies

The genus Vaccinium L. (Ericaceae) contains a wide diversity of culturally and economically important berry crop species. Consumer demand and scientific research in blueberry (Vaccinium spp.) and cranberry (Vaccinium macrocarpon) have increased worldwide over the crops' relatively short domestication history (~100 years). Other species, including bilberry (Vaccinium myrtillus), lingonberry (Vaccinium vitis-idaea), and ohelo berry (Vaccinium reticulatum) are largely still harvested from the wild but with crop improvement efforts underway. Here, we present a review article on these Vaccinium berry crops on topics that span taxonomy to genetics and genomics to breeding. We highlight the accomplishments made thus far for each of these crops, along their journey from the wild, and propose research areas and questions that will require investments by the community over the coming decades to guide future crop improvement efforts. New tools and resources are needed to underpin the development of superior cultivars that are not only more resilient to various environmental stresses and higher yielding, but also produce fruit that continue to meet a variety of consumer preferences, including fruit quality and health related trait

Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm

Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium® SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ∼75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs.The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species

Genomics and bioinformatics resources for translational science in Rosaceae

Recent technological advances in biology promise unprecedented opportunities for rapid and sustainable advancement of crop quality. Following this trend, the Rosaceae research community continues to generate large amounts of genomic, genetic and breeding data. These include annotated whole genome sequences, transcriptome and expression data, proteomic and metabolomic data, genotypic and phenotypic data, and genetic and physical maps. Analysis, storage, integration and dissemination of these data using bioinformatics tools and databases are essential to provide utility of the data for basic, translational and applied research. This review discusses the currently available genomics and bioinformatics resources for the Rosaceae family