T. Zhebentyayeva

Pennsylvania State University | Penn State · Schatz Center for Tree Molecular Genetics

Green ash (Fraxinus pennsylvanica) is the most widely distributed ash tree in North America. Once common, it has experienced high mortality from the non‐native invasive emerald ash borer (EAB; Agrilus planipennis). A small percentage of native green ash trees that remain healthy in long‐infested areas, termed “lingering ash,” display partial resist...

To provide a suitable seed source for the reforestation program in Cameroon, a nursery trial was set up in the Diamare Division of the Far North region of Cameroon. The aim was to assess the adaptation of 23 provenances of Faidherbia albida to the climatic conditions of Far North Cameroon. A randomized complete block design for single tree plotswas...

Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from...

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 (Prunus persica) floral buds in endodormancy, ecodormancy and bud break stages. Small RN...

Graft incompatibility (GI) between the most popular Prunus rootstocks and apricot cultivars is one of the major problems for rootstock usage and improvement. Failure in producing long-leaving healthy grafts greatly affects the range of available Prunus rootstocks for apricot cultivation. Despite recent advances related to the molecular mechanisms o...

‘HoneySweet’ plum (Prunus domestica) is resistant to Plum pox potyvirus, through an RNAi-triggered mechanism. Determining the precise nature of the transgene insertion event has been complicated due to the hexaploid genome of plum. DNA blots previously indicated an unintended hairpin arrangement of the Plum pox potyvirus coat protein gene as well a...

Forest tree species are increasingly subject to severe mortalities from exotic pests, pathogens, and invasive organisms, accelerated by climate change. Such forest health issues are threatening multiple species and ecosystem sustainability globally. One of the most extreme examples of forest ecosystem disruption is the extirpation of the American c...

Faidherbia albida (DEL.) A. Chev is widely grown in the northern region of Cameroon because of its many benefits to local communities. However, droughts and deforestation have led to decreases in the abundance of this species, increasing the need to identify improved genotypes for conservation, management, and breeding. The genetic diversity of F....

The characterization of the largest worldwide representative data set of apricot (Prunus armeniaca L.) germplasm was performed using molecular markers. Genetic diversity and structure of the cultivated apricot genetic resources were analyzed to decipher the history of diffusion of this species around the world. A common set of 25 microsatellite mar...

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 p...

Prunus domestica commonly known as European plum is a hexaploid fruit tree species cultivated around the world. Locally it is used for fresh consumption, in jams or jellies, and the production of spirits while commercially the fruit is primarily sold dried (prunes). Despite its agricultural importance and long history of cultivation, many questions...

The soilborne oomycete Phytophthora cinnamomi-which causes root rot, trunk cankers, and stem lesions on an estimated 5,000 plant species worldwide-is a lethal pathogen of American chestnut (Castanea dentata) as well as many other woody plant species. P. cinnamomi is particularly damaging to chestnut and chinquapin trees (Castanea spp.) in the south...

The genus Castanea in North America contains multiple tree and shrub taxa of conservation concern. The two species within the group, American chestnut (Castanea dentata) and chinquapin (C. pumila sensu lato), display remarkable morphological diversity across their distributions in the eastern United States and southern Ontario. Previous investigato...

Floral self-incompatibility affecting yearly yield in a weather-dependent manner and graft incompatibility affecting longevity of mature trees are two important traits for apricot production. However, genetic control of graft compatibility and relationship between these traits are unknown. Here, we analyzed its inheritance in an F1 apricot progeny...

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 wi...

Forest tree species are increasingly subject to severe mortalities from exotic pests, diseases, and invasive organisms, accelerated by climate change. Forest health issues are threatening multiple species and ecosystem sustainability globally. While sources of resistance may be available in related species, or among surviving trees, introgression o...

The objective of this study was to establish the genetic relationship among cultivars commonly used as donors for resistance to Plum pox virus (PPV) in order to identify the putative sources of resistance to PPV. The plant material tested represented the European, Central Asian and Chinese ecogeographical groups of cultivated apricots as well as th...

The Japanese chestnut (Castanea crenata) carries resistance to Phytophthora cinnamomi, the destructive and widespread oomycete causing ink disease. The European chestnut (Castanea sativa), carrying little to no disease resistance, is currently threatened by the presence of the oomycete pathogen in forests, orchards and nurseries. Determining the ge...

Four extra LGs obtained for C. sativa x C. crenata interspecific cross. Marker positions on LGs were assigned to reference map LGs [11], by using the common markers mapped on both genetic maps (in blue). (TIF)

EMBO Young Scientists’ Forum

Ink disease (caused by the pathogen Phytophthora cinnamomi) and chestnut blight (caused by the fungus Cryphonectria parasitica) are the two most destructive diseases affecting European chestnut (Castanea sativa) and American chestnut (C. dentata). Therefore, breeding for resistance to both pathogens is essential for the chestnut sustainability in E...

Background: Due to a relatively high level of codominant inheritance and transferability within and among taxonomic groups, simple sequence repeat (SSR) markers are important elements in comparative mapping and delineation of genomic regions associated with traits of economic importance. Expressed sequence tags (ESTs) are a source of SSRs that can...

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 degr...

Analyses of genetic diversity and phylogenetic relationships illuminate the origin and domestication of crop species and have important implications for plant breeding programs and the conservation of genetic resources. Apricot ( Prunus armeniaca L.) genetic resources in collections that are widely dispersed around the world were assessed using 25...

To exploit ecogeographical niches of the temperate zone, trees and other perennial plant species optimize the timing of floral and vegetative bud break within the dynamic nature of the annual environmental cycle. This insures successful reproduction and continued growth over their lifespan. Adapting to the annual environmental cycle as well as more...

Root rot (caused by Phytophthora cinnamomi) and chestnut blight (caused by Cryphonectria parasitica) are the two most destructive diseases affecting American chestnut, Castanea dentate. Therefore, breeding for resistance to both pathogens simultaneously is essential before the American chestnut can be restored to its full native range. Using combin...

The Forest Health Initiative (FHI) was developed and implemented to test the hypothesis that a coordinated effort in biotechnology research could lead to resistant trees capable of restoring a species in a relevant time frame. As a test case, the American chestnut (Castanea dentata) was chosen for study as it is an iconic forest tree species in the...

Introduction: The American chestnut (AC), once known as "The King of the Appalachian Forest" was destroyed in the first half of the 20 th century by chestnut blight and exotic disease inadvertently introduced from Asia. Chinese chestnut (CC), in contrast to American chestnut, is resistant to chestnut blight, and efforts are being made to transfer t...

Chilling requirement (CR) for floral bud dormancy release is one of the major limiting factors for geographical adaptation of fruiting trees. Using a whole genome sequencing approach (Illumina platform), we explored polymorphism underlying phenotypic differences among individuals in a peach F2 cross segregating for chilling requirement and bloom da...

Sharka disease, caused by Plum pox virus (PPV), is the most important viral disease affecting Prunus species. A major PPV resistance locus (PPVres) has been mapped to the upper part of apricot (Prunus armeniaca) linkage group 1. In this study, a physical map of the PPVres locus in the PPV-resistant cultivar 'Goldrich' was constructed. Bacterial art...

Trees are capable of tremendous architectural plasticity, allowing them to maximize their light exposure under highly competitive environments. One key component underlying tree architecture is the branch angle. Yet, little is known about the molecular basis for spatial patterning of branches in trees. Here, we report the identification of a candid...

The Chinese chestnut (Castanea mollissima) carries resistance to Cryphonectria parasitica, the fungal pathogen inciting chestnut blight. The pathogen, introduced from Asia, devastated the American chestnut (Castanea dentata) throughout its native range early in the twentieth century. A highly informative genetic map of Chinese chestnut was construc...

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 sequenc...

Apricot is in the Rosaceae family within the genus Prunus L., subgenus Prunophora Focke, and the section Armeniaca (Lam.) Koch. Depending on the classification system, the number of apricot species ranges from 3 to 12. Six distinct species are usually recognized: P. brigantina Vill., P. holosericeae Batal, P. armeniaca L., P. mandshurica (Maxim), P...

Three Chinese chestnut bacterial artificial chromosome (BAC) libraries were developed and used for physical map construction. Specifically, high information content fingerprinting was used to assemble 126,445 BAC clones into 1,377 contigs and 12,919 singletons. Integration of the dense Chinese chestnut genetic map with the physical map was achieved...

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 a...

Table S2. Conserved microRNA (miRNA) distribution in plant lineages. miRNA data are a compilation from miRBase 17 and this study. Divergence dates for land plant clades is from Leebens-Mack et al. (2005).

Table S4. Expression of conserved miRNAs in leaf and bud samples. Number of reads in leaf (L18 to L23) and bud (B18 to B23) dataset corresponding the different length variants (18 to 23 nt) of conserved miRNAs identified in peach. The number of reads of miRNA variants and the total count are indicated.

Table S5. Expression of non-conserved miRNAs in leaf and bud samples. Number of reads in leaf (L18 to L23) and bud (B18 to B23) dataset corresponding the different length variants (18 to 23 nt) of non-conserved miRNAs identified in peach. The number of reads of miRNA variants and the total count are indicated.

Table S6. List of conserved and non-conserved miRNAs up-regulated or down-regulated in winter buds and leaves.

Table S9. List of targets of peach non-conserved miRNAs with the best scores. The name, the target score, peach CDS name, the Arabidopsis homolog to peach CDS and its annotation are indicated.

Table S10. List of all peach genes targeted by non-conserved miRNAs with a score less than 4. The name, the target score, peach CDS name, the Arabidopsis homolog to peach CDS and its annotation are indicated.

Table S1. Conserved miRNAs identified in peach. The length (len) of each miRNA, the chromosome location (Chr), the start (start) and the end (stop) position on the chromosome of each miRNA and miRNA*sequences, the miRNA orientation (Dir), whether or not a miRNA* was observed are indicated, miRNA and miRNA* sequences, and sequence coordinates on the...

Table S7. List of targets of peach conserved miRNAs with the best scores. The name, the target score, peach CDS name, the Arabidopsis homolog to peach CDS and its annotation are indicated.

Table S3. Non-conserved miRNAs identified in peach. The length (len) of each miRNA, the chromosome location (Chr), the start (start) and the end (stop) position on the chromosome of each miRNA and miRNA*sequences, the miRNA orientation (Dir), whether or not a miRNA was observed are indicated, and miRNA and miRNA* sequences.

Table S8. List of all peach genes targeted by conserved miRNAs with a score less than 4. The name, the target score, peach CDS name, the Arabidopsis homolog to peach CDS and its annotation are indicated.

Cinnamate 4-hydroxylase (C4H) is the second enzyme in the phenylpropanoid pathway which participates in the synthesis of numerous phenylpropanoid compounds such as flavonoids, lignins, suberins and others. We identified a gene putatively coding for Class I C4H in apricot and plum and we analyzed the expression pattern of this gene under different a...

Sharka disease, caused by the plum pox virus (PPV), is one of the major limiting factors for stone fruit production in Europe and America. Attempts to stop the disease through the eradication of infected trees have been unsuccessful. Introgression of PPV resistance for crop improvement is therefore the most important goal in Prunus breeding program...

The peach [Prunus persica (L.) Batsch] genome sequence has been recently made available to the scientific community. This represents the culmination of a long process that started less than two decades ago with the release of the first marker-based linkage maps. The process has advanced rapidly with the studies of molecular diversity, detection of...

With 5 figures and 3 tables AbstractIn peach [Prunus persica (L.) Batsch], trees showing columnar (also termed pillar or broomy) growth habit are of interest for high‐density production systems. While the selection of the pillar homozygous phenotype (brbr) can be carried out prior to field planting, the intermediate heterozygous upright phenotype i...

Perennial fruiting trees require sustained exposure to low, near freezing, temperatures before vigorous floral and vegetative bud break is possible after the resumption of warm temperatures in the spring. The depth of dormancy, duration of chilling required (the chilling requirement, CR) blooming date (BD) and heat requirement to break buds (HR) ar...

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). However, the mapping accuracy was not sufficiently reli...

The TERMINAL FLOWER 1 (TFL1) plays crucial roles in regulating the vegetative to reproductive phase transition and maintaining the inflorescence meristem. We characterized one apricot (Pa_GBa141J23) and one peach (Pp_NBa103A15) BAC clone harboring a TFL1 gene. Sequence analysis revealed that the apricot and peach TFL1 (PaTFL1 and PpTFL1) genes disp...