Mapping QTLs for blight resistance and morpho-phenological traits in inter-species hybrid families of chestnut ( spp.).

Chestnut blight (caused by ), together with root rot (caused by ), has nearly extirpated American chestnut () from its native range. In contrast to the susceptibility of American chestnut, many Chinese chestnut () genotypes are resistant to blight. In this research, we performed a series of genome-wide association studies for blight resistance originating from three unrelated Chinese chestnut trees (Mahogany, Nanking and M16) and a Quantitative Trait Locus (QTL) study on a Mahogany-derived inter-species F2 family.

Genome-Wide Changes of Regulatory Non-Coding RNAs Reveal Pollen Development Initiated at Ecodormancy in Peach.

Bud dormancy is under the regulation of complex mechanisms including genetic and epigenetic factors. To study the function of regulatory non-coding RNAs in winter dormancy release, we analyzed the small RNA and long non-coding RNA (lncRNA) expression from peach () floral buds in endodormancy, ecodormancy and bud break stages. Small RNAs underwent a major shift in expression primarily between dormancy and flowering with specific pairs of microRNAs and their mRNA target genes undergoing coordinated differential expression.

Thermal-responsive genetic and epigenetic regulation of cluster controlling dormancy and chilling requirement in peach floral buds.

The () gene cluster in peach serves as a key regulatory hub on which the seasonal temperatures act and orchestrate dormancy onset and exit, chilling response and floral bud developmental pace. Yet, how different temperature regimes interact with and regulate the six linked genes remains unclear. Here, we demonstrate that chilling downregulates in dormant floral buds with distinct patterns and identify as the most abundantly expressed one.

Distinctive Gene Expression Patterns Define Endodormancy to Ecodormancy Transition in Apricot and Peach.

Dormancy is a physiological state that plants enter for winter hardiness. Environmental-induced dormancy onset and release in temperate perennials coordinate growth cessation and resumption, but how the entire process, especially chilling-dependent dormancy release and flowering, is regulated remains largely unclear. We utilized the transcriptome profiles of floral buds from fall to spring in apricot () genotypes with contrasting bloom dates and peach () genotypes with contrasting chilling requirements (CR) to explore the genetic regulation of bud dormancy.

Dissecting Resistance to in Interspecific Hybrid Chestnut Crosses Using Sequence-Based Genotyping and QTL Mapping.

The soilborne oomycete -which causes root rot, trunk cankers, and stem lesions on an estimated 5,000 plant species worldwide-is a lethal pathogen of American chestnut () as well as many other woody plant species. is particularly damaging to chestnut and chinquapin trees ( spp.) in the southern portion of its native range in the United States due to relatively mild climatic conditions that are conductive to disease development.

Association of the phenylpropanoid pathway with dormancy and adaptive trait variation in apricot (Prunus armeniaca).

Trees use many mechanisms to adapt and respond to stressful conditions. The phenylpropanoid pathway in particular is known to be associated with a diverse suite of plant stress responses. In this study, we explored the relationship between the phenylpropanoid pathway metabolite production, gene expression and adaptive trait variation associated with floral bud reactivation during and following dormancy in Prunus armeniaca L.

genetics and applications after de novo genome sequencing: achievements and prospects.

Prior to the availability of whole-genome sequences, our understanding of the structural and functional aspects of tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources. With public release of the peach genome and others that followed, significant advances in our knowledge of genomes and the genetic underpinnings of important traits ensued. In this review, we highlight key achievements in genetics and breeding driven by the availability of these whole-genome sequences.

15 years of GDR: New data and functionality in the Genome Database for Rosaceae.

The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding data and data-mining tools to facilitate basic, translational and applied research in Rosaceae.

Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes.

Background: Chinese chestnut (Castanea mollissima) has emerged as a model species for the Fagaceae family with extensive genomic resources including a physical map, a dense genetic map and quantitative trait loci (QTLs) for chestnut blight resistance. These resources enable comparative genomics analyses relative to model plants. We assessed the degree of conservation between the chestnut genome and other well annotated and assembled plant genomic sequences, focusing on the QTL regions of most interest to the chestnut breeding community.

Genotyping by Sequencing for SNP-Based Linkage Map Construction and QTL Analysis of Chilling Requirement and Bloom Date in Peach [Prunus persica (L.) Batsch].

Low-cost, high throughput genotyping methods are crucial to marker discovery and marker-assisted breeding efforts, but have not been available for many 'specialty crops' such as fruit and nut trees. Here we apply the Genotyping-By-Sequencing (GBS) method developed for cereals to the discovery of single nucleotide polymorphisms (SNPs) in a peach F2 mapping population. Peach is a genetic and genomic model within the Rosaceae and will provide a template for the use of this method with other members of this family.

The Genome Database for Rosaceae (GDR): year 10 update.

The Genome Database for Rosaceae (GDR, http:/www.rosaceae.org), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding data, and improved functionality.

PpeTAC1 promotes the horizontal growth of branches in peach trees and is a member of a functionally conserved gene family found in diverse plants species.

Trees are capable of tremendous architectural plasticity, allowing them to maximize their light exposure under highly competitive environments. One key component of tree architecture is the branch angle, yet little is known about the molecular basis for the spatial patterning of branches in trees. Here, we report the identification of a candidate gene for the br mutation in Prunus persica (peach) associated with vertically oriented growth of branches, referred to as 'pillar' or 'broomy'.

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution.

Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype.

Genome wide identification of chilling responsive microRNAs in Prunus persica.

Background: MicroRNAs (miRNAs) are small RNAs (sRNAs) approximately 21 nucleotides in length that negatively control gene expression by cleaving or inhibiting the translation of target gene transcripts. Within this context, miRNAs and siRNAs are coming to the forefront as molecular mediators of gene regulation in plant responses to annual temperature cycling and cold stress. For this reason, we chose to identify and characterize the conserved and non-conserved miRNA component of peach (Prunus persica (L.

Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies.

Background: Rosaceae include numerous economically important and morphologically diverse species. Comparative mapping between the member species in Rosaceae have indicated some level of synteny. Recently the whole genome of three crop species, peach, apple and strawberry, which belong to different genera of the Rosaceae family, have been sequenced, allowing in-depth comparison of these genomes.

Chestnut resistance to the blight disease: insights from transcriptome analysis.

Background: A century ago, Chestnut Blight Disease (CBD) devastated the American chestnut. Backcross breeding has been underway to introgress resistance from Chinese chestnut into surviving American chestnut genotypes. Development of genomic resources for the family Fagaceae, has focused in this project on Castanea mollissima Blume (Chinese chestnut) and Castanea dentata (Marsh.

Variation of Surface Charge along the Surface of Wool Fibers Assessed by High-Resolution Force Spectroscopy.

In this study, we have mapped the surface charge of wool fibers using chemically specific high-resolution force spectroscopy in order to better understand the dispersion of amino acids in relation to fiber morphology. The inter-surface forces between standard atomic force microscopy (AFM) probe tips (tip radius ~ 50 nm) functionalized with COOH and NH(3) terminated alkanethiol self assembling monolayers and the wool surface were used to estimate the surface charge per unit area using linear Poisson-Boltzmann-based electrostatic double layer theory. The positional measurement of nano-scale surface charge showed a correlation between the surface charge and fiber morphology, indicated that basic amino acids are located near the scale edges.

Narrowing down the apricot Plum pox virus resistance locus and comparative analysis with the peach genome syntenic region.

Sharka disease, caused by the Plum pox virus (PPV), is one of the main limiting factors for stone fruit crops worldwide. Only a few resistance sources have been found in apricot (Prunus armeniaca L.), and most studies have located a major PPV resistance locus (PPVres) on linkage group 1 (LG1).

Comparative genomic sequence analysis of strawberry and other rosids reveals significant microsynteny.

Background: Fragaria belongs to the Rosaceae, an economically important family that includes a number of important fruit producing genera such as Malus and Prunus. Using genomic sequences from 50 Fragaria fosmids, we have examined the microsynteny between Fragaria and other plant models.

Results: In more than half of the strawberry fosmids, we found syntenic regions that are conserved in Populus, Vitis, Medicago and/or Arabidopsis with Populus containing the greatest number of syntenic regions with Fragaria.

Mapping quantitative trait loci associated with chilling requirement, heat requirement and bloom date in peach (Prunus persica).

*Chilling requirement, together with heat requirement, determines the bloom date, which has an impact on the climatic distribution of the genotypes of tree species. The molecular basis of floral bud chilling requirement is poorly understood, despite its importance to the adaptation and production of fruit trees. In addition, the genetic nature of heat requirement and the genetic interrelationships among chilling requirement, heat requirement and bloom date remain unclear.

Genetic linkage mapping for molecular dissection of chilling requirement and budbreak in apricot (Prunus armeniaca L.).

Commercial production of apricot is severely affected by sensitivity to climatic conditions, an adaptive feature essential for cycling between vegetative or floral growth and dormancy. Yield losses are due to late winter or early spring frosts and inhibited vegetative or floral growth caused by unfulfilled chilling requirement (CR). Two apricot cultivars, Perfection and A.

The development and characterisation of a bacterial artificial chromosome library for Fragaria vesca.

Background: The cultivated strawberry Fragaria xananassa is one of the most economically-important soft-fruit species. Few structural genomic resources have been reported for Fragaria and there exists an urgent need for the development of physical mapping resources for the genus. The first stage in the development of a physical map for Fragaria is the construction and characterisation of a high molecular weight bacterial artificial chromosome (BAC) library.

Phylogenetic analysis and molecular evolution of the dormancy associated MADS-box genes from peach.

Background: Dormancy associated MADS-box (DAM) genes are candidates for the regulation of growth cessation and terminal bud formation in peach. These genes are not expressed in the peach mutant evergrowing, which fails to cease growth and enter dormancy under dormancy-inducing conditions. We analyzed the phylogenetic relationships among and the rates and patterns of molecular evolution within DAM genes in the phylogenetic context of the MADS-box gene family.