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1.
Phytopathology ; 113(2): 345-354, 2023 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-35972890

RESUMO

Members of the genus Luteovirus are responsible for economically destructive plant diseases worldwide. Over the past few years, three luteoviruses infecting Prunus trees have been characterized. However, the biological properties, prevalence, and genetic diversity of those viruses have not yet been studied. High-throughput sequencing of samples of various wild, cultivated, and ornamental Prunus species enabled the identification of four novel species in the genus Luteovirus for which we obtained complete or nearly complete genomes. Additionally, we identified another new putative species recovered from Sequence Read Archive data. Furthermore, we conducted a survey on peach-infecting luteoviruses in eight European countries. Analyses of 350 leaf samples collected from germplasm, production orchards, and private gardens showed that peach-associated luteovirus (PaLV), nectarine stem pitting-associated virus (NSPaV), and a novel luteovirus, peach-associated luteovirus 2 (PaLV2), are present in all countries; the most prevalent virus was NSPaV, followed by PaLV. The genetic diversity of these viruses was also analyzed. Moreover, the biological indexing on GF305 peach indicator plants demonstrated that PaLV and PaLV2, like NSPaV, are transmitted by graft at relatively low rates. No clear viral symptoms have been observed in either graft-inoculated GF305 indicators or different peach tree varieties observed in an orchard. The data generated during this study provide a broader overview of the genetic diversity, geographical distribution, and prevalence of peach-infecting luteoviruses and suggest that these viruses are likely asymptomatic in peach under most circumstances.


Assuntos
Luteovirus , Prunus , Vírus , Luteovirus/genética , Doenças das Plantas , Vírus/genética , Sequenciamento de Nucleotídeos em Larga Escala
2.
Plant J ; 2018 Jun 04.
Artigo em Inglês | MEDLINE | ID: mdl-29863810

RESUMO

Potato virus Y (PVY) is one of the most damaging viruses of tobacco. In particular, aggressive necrotic strains (PVYN ) lead to considerable losses in yield. The main source of resistance against PVY is linked to the va locus. However, va-overcoming PVY isolates inducing necrotic symptoms were observed in several countries. In this context, it is important to find va-independent protection strategies. In a previous study, the phenotyping of 162 tobacco varieties revealed 10 accessions that do not carry the va allele and do not exhibit typical PVYN -induced veinal necrosis. Despite the absence of necrotic symptoms, normal viral accumulation in these plants suggests a va-independent mechanism of tolerance to PVYN -induced systemic veinal necrosis. Fine mapping of the genetic determinant(s) was performed in a segregating F2 population. The tolerance trait is inherited as a single recessive gene, and allelism tests demonstrated that eight of the 10 tolerant varieties carry the same determinant. Anchoring the linkage map to the tobacco genome physical map allowed the identification of a RPP8-like R gene, called NtTPN1 (for Nicotiana tabacum Tolerance to PVY-induced Necrosis1), with the same single-nucleotide polymorphism in the eight tolerant accessions. Functional assays using homozygous NtTPN1 EMS mutants confirmed the role of NtTPN1 in the tolerance phenotype. PVYN -induced systemic veinal necrosis in tobacco likely represents an inefficient defense response with hypersensitive response-like characteristics. The identification of NtTPN1 opens breeding options to minimize the impact of emerging and so far uncontrolled va-breaking necrotic PVY isolates.

3.
BMC Plant Biol ; 19(1): 440, 2019 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-31640557

RESUMO

BACKGROUND: In plants, host factors encoded by susceptibility (S) genes are indispensable for viral infection. Resistance is achieved through the impairment or the absence of those susceptibility factors. Many S genes have been cloned from model and crop species and a majority of them are coding for members of the eukaryotic translation initiation complex, mainly eIF4E, eIF4G and their isoforms. The aim of this study was to investigate the role of those translation initiation factors in susceptibility of stone fruit species to sharka, a viral disease due to Plum pox virus (PPV). RESULTS: For this purpose, hairpin-inducing silencing constructs based on Prunus persica orthologs were used to generate Prunus salicina (Japanese plum) 4E and 4G silenced plants by Agrobacterium tumefaciens-mediated transformation and challenged with PPV. While down-regulated eIFiso4E transgenic Japanese plums were not regenerated in our conditions, eIFiso4G11-, but not the eIFiso4G10-, silenced plants displayed durable and stable resistance to PPV. We also investigated the alteration of the si- and mi-RNA profiles in transgenic and wild-type Japanese plums upon PPV infection and confirmed that the newly generated small interfering (si) RNAs, which are derived from the engineered inverted repeat construct, are the major contributor of resistance to sharka. CONCLUSIONS: Our results indicate that S gene function of the translation initiation complex isoform is conserved in Prunus species. We discuss the possibilities of using RNAi silencing or loss-of-function mutations of the different isoforms of proteins involved in this complex to breed for resistance to sharka in fruit trees.


Assuntos
Resistência à Doença/genética , Fatores de Iniciação em Eucariotos/metabolismo , Doenças das Plantas/imunologia , Vírus Eruptivo da Ameixa/fisiologia , Prunus/genética , Fatores de Iniciação em Eucariotos/genética , Frutas/genética , Frutas/imunologia , Frutas/virologia , Doenças das Plantas/virologia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas , Isoformas de Proteínas , Prunus/imunologia , Prunus/virologia , Interferência de RNA , RNA de Plantas/genética , RNA Interferente Pequeno/genética , Árvores
4.
Mol Ecol ; 28(24): 5299-5314, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31677192

RESUMO

Domestication is an excellent model to study diversification and this evolutionary process can be different in perennial plants, such as fruit trees, compared to annual crops. Here, we inferred the history of wild apricot species divergence and of apricot domestication history across Eurasia, with a special focus on Central and Eastern Asia, based on microsatellite markers and approximate Bayesian computation. We significantly extended our previous sampling of apricots in Europe and Central Asia towards Eastern Asia, resulting in a total sample of 271 cultivated samples and 306 wild apricots across Eurasia, mainly Prunus armeniaca and Prunus sibirica, with some Prunus mume and Prunus mandshurica. We recovered wild Chinese species as genetically differentiated clusters, with P. sibirica being divided into two clusters, one possibly resulting from hybridization with P. armeniaca. Central Asia also appeared as a diversification centre of wild apricots. We further revealed at least three domestication events, without bottlenecks, that gave rise to European, Southern Central Asian and Chinese cultivated apricots, with ancient gene flow among them. The domestication event in China possibly resulted from ancient hybridization between wild populations from Central and Eastern Asia. We also detected extensive footprints of recent admixture in all groups of cultivated apricots. Our results thus show that apricot is an excellent model for studying speciation and domestication in long-lived perennial fruit trees.


Assuntos
Domesticação , Frutas/genética , Variação Genética/genética , Prunus armeniaca/genética , China , Europa (Continente) , Evolução Molecular , Frutas/crescimento & desenvolvimento , Fluxo Gênico/genética , Hibridização Genética , Especificidade da Espécie
5.
New Phytol ; 209(2): 773-84, 2016 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-26356603

RESUMO

In fruit tree species, many important traits have been characterized genetically by using single-family descent mapping in progenies segregating for the traits. However, most mapped loci have not been sufficiently resolved to the individual genes due to insufficient progeny sizes for high resolution mapping and the previous lack of whole-genome sequence resources of the study species. To address this problem for Plum Pox Virus (PPV) candidate resistance gene identification in Prunus species, we implemented a genome-wide association (GWA) approach in apricot. This study exploited the broad genetic diversity of the apricot (Prunus armeniaca) germplasm containing resistance to PPV, next-generation sequence-based genotyping, and the high-quality peach (Prunus persica) genome reference sequence for single nucleotide polymorphism (SNP) identification. The results of this GWA study validated previously reported PPV resistance quantitative trait loci (QTL) intervals, highlighted other potential resistance loci, and resolved each to a limited set of candidate genes for further study. This work substantiates the association genetics approach for resolution of QTL to candidate genes in apricot and suggests that this approach could simplify identification of other candidate genes for other marked trait intervals in this germplasm.


Assuntos
Doenças das Plantas/genética , Doenças das Plantas/virologia , Vírus Eruptivo da Ameixa/patogenicidade , Prunus armeniaca/genética , Prunus armeniaca/virologia , Mapeamento Cromossômico , Resistência à Doença/genética , Genética Populacional , Genoma de Planta , Estudo de Associação Genômica Ampla , Interações Hospedeiro-Patógeno/genética , Desequilíbrio de Ligação , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas
6.
Mol Ecol ; 25(19): 4712-29, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27480465

RESUMO

Studying domesticated species and their wild relatives allows understanding of the mechanisms of population divergence and adaptation, and identifying valuable genetic resources. Apricot is an important fruit in the Northern hemisphere, where it is threatened by the Plum pox virus (PPV), causing the sharka disease. The histories of apricot domestication and of its resistance to sharka are however still poorly understood. We used 18 microsatellite markers to genotype a collection of 230 wild trees from Central Asia and 142 cultivated apricots as representatives of the worldwide cultivated apricot germplasm; we also performed experimental PPV inoculation tests. The genetic markers revealed highest levels of diversity in Central Asian and Chinese wild and cultivated apricots, confirming an origin in this region. In cultivated apricots, Chinese accessions were differentiated from more Western accessions, while cultivated apricots were differentiated from wild apricots. An approximate Bayesian approach indicated that apricots likely underwent two independent domestication events, with bottlenecks, from the same wild population. Central Asian native apricots exhibited genetic subdivision and high frequency of resistance to sharka. Altogether, our results contribute to the understanding of the domestication history of cultivated apricot and point to valuable genetic diversity in the extant genetic resources of wild apricots.


Assuntos
Resistência à Doença/genética , Doenças das Plantas/genética , Vírus Eruptivo da Ameixa , Prunus armeniaca/genética , Prunus armeniaca/virologia , Ásia , Teorema de Bayes , Domesticação , Genótipo , Repetições de Microssatélites , Doenças das Plantas/virologia
7.
Plant J ; 79(5): 705-16, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-24930633

RESUMO

Arabidopsis thaliana represents a valuable and efficient model to understand mechanisms underlying plant susceptibility to viral diseases. Here, we describe the identification and molecular cloning of a new gene responsible for recessive resistance to several isolates of Watermelon mosaic virus (WMV, genus Potyvirus) in the Arabidopsis Cvi-0 accession. rwm1 acts at an early stage of infection by impairing viral accumulation in initially infected leaf tissues. Map-based cloning delimited rwm1 on chromosome 1 in a 114-kb region containing 30 annotated genes. Positional and functional candidate gene analysis suggested that rwm1 encodes cPGK2 (At1g56190), an evolutionary conserved nucleus-encoded chloroplast phosphoglycerate kinase with a key role in cell metabolism. Comparative sequence analysis indicates that a single amino acid substitution (S78G) in the N-terminal domain of cPGK2 is involved in rwm1-mediated resistance. This mutation may have functional consequences because it targets a highly conserved residue, affects a putative phosphorylation site and occurs within a predicted nuclear localization signal. Transgenic complementation in Arabidopsis together with virus-induced gene silencing in Nicotiana benthamiana confirmed that cPGK2 corresponds to rwm1 and that the protein is required for efficient WMV infection. This work uncovers new insight into natural plant resistance mechanisms that may provide interesting opportunities for the genetic control of plant virus diseases.


Assuntos
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Resistência à Doença/genética , Fosfoglicerato Quinase/genética , Doenças das Plantas/imunologia , Potyvirus/fisiologia , Sequência de Aminoácidos , Substituição de Aminoácidos , Arabidopsis/enzimologia , Arabidopsis/imunologia , Arabidopsis/virologia , Proteínas de Arabidopsis/metabolismo , Cloroplastos/enzimologia , Mapeamento Cromossômico , Clonagem Molecular , DNA de Plantas/química , DNA de Plantas/genética , Dados de Sequência Molecular , Mutação de Sentido Incorreto , Fenótipo , Fosfoglicerato Quinase/metabolismo , Doenças das Plantas/virologia , Folhas de Planta/enzimologia , Folhas de Planta/genética , Folhas de Planta/imunologia , Folhas de Planta/virologia , Vírus de Plantas/fisiologia , Plantas Geneticamente Modificadas , Plântula/enzimologia , Plântula/genética , Plântula/imunologia , Plântula/virologia , Análise de Sequência de DNA
8.
Virus Genes ; 49(2): 325-38, 2014 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-24964777

RESUMO

Gene silencing and large-scale small RNA analysis can be used to develop RNA interference (RNAi)-based resistance strategies for Plum pox virus (PPV), a high impact disease of Prunus spp. In this study, a pPPViRNA hairpin-inducing vector harboring two silencing motif-rich regions of the PPV coat protein (CP) gene was evaluated in transgenic Nicotiana benthamiana (NB) plants. Wild-type NB plants infected with a chimeric PPV virus (PPV::GFP) exhibited affected leaves with mosaic chlorosis congruent to GFP fluorescence at 21 day post-inoculation; transgenic lines depicted a range of phenotypes from fully resistant to susceptible. ELISA values and GFP fluorescence intensities were used to select transgenic-resistant (TG-R) and transgenic-susceptible (TG-S) lines for further characterization of small interfering RNAs (siRNAs) by large-scale small RNA sequencing. In infected TG-S and untransformed (WT) plants, the observed siRNAs were nearly exclusively 21- and 22-nt siRNAs that targeted the whole PPV::GFP genome; 24-nt siRNAs were absent in these individuals. Challenged TG-R plants accumulated a full set of 21- to 24-nt siRNAs that were primarily associated with the selected motif-rich regions, indicating that a trans-acting siRNAs process prevented viral multiplication. BLAST analysis identified 13 common siRNA clusters targeting the CP gene. 21-nt siRNA sequences were associated with the 22-nt siRNAs and the scarce 23- and 24-nt molecules in TG-S plants and with most of the observed 22-, 23-, and 24-nt siRNAs in TG-R individuals. These results validate the use of a multi-hot spot silencing vector against PPV and elucidate the molecules by which hairpin-inducing vectors initiate RNAi in vivo.


Assuntos
Inativação Gênica , Interações Hospedeiro-Patógeno , Nicotiana/virologia , Doenças das Plantas/virologia , Vírus Eruptivo da Ameixa/crescimento & desenvolvimento , Interferência de RNA , Resistência à Doença , Perfilação da Expressão Gênica , Plantas Geneticamente Modificadas , RNA Interferente Pequeno/análise , RNA Interferente Pequeno/genética
9.
Evol Appl ; 17(5): e13691, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38707994

RESUMO

Effective population size (N e) is a pivotal evolutionary parameter with crucial implications in conservation practice and policy. Genetic methods to estimate N e have been preferred over demographic methods because they rely on genetic data rather than time-consuming ecological monitoring. Methods based on linkage disequilibrium (LD), in particular, have become popular in conservation as they require a single sampling and provide estimates that refer to recent generations. A software program based on the LD method, GONE, looks particularly promising to estimate contemporary and recent-historical N e (up to 200 generations in the past). Genomic datasets from non-model species, especially plants, may present some constraints to the use of GONE, as linkage maps and reference genomes are seldom available, and SNP genotyping is usually based on reduced-representation methods. In this study, we use empirical datasets from four plant species to explore the limitations of plant genomic datasets when estimating N e using the algorithm implemented in GONE, in addition to exploring some typical biological limitations that may affect N e estimation using the LD method, such as the occurrence of population structure. We show how accuracy and precision of N e estimates potentially change with the following factors: occurrence of missing data, limited number of SNPs/individuals sampled, and lack of information about the location of SNPs on chromosomes, with the latter producing a significant bias, previously unexplored with empirical data. We finally compare the N e estimates obtained with GONE for the last generations with the contemporary N e estimates obtained with the programs currentNe and NeEstimator.

10.
Sci Rep ; 13(1): 15247, 2023 09 14.
Artigo em Inglês | MEDLINE | ID: mdl-37709842

RESUMO

Members of the eukaryotic translation initiation complex are co-opted in viral infection, leading to susceptibility in many crop species, including stone fruit trees (Prunus spp.). Therefore, modification of one of those eukaryotic translation initiation factors or changes in their gene expression may result in resistance. We searched the crop and wild Prunus germplasm from the Armeniaca and Amygdalus taxonomic sections for allelic variants in the eIF4E and eIFiso4E genes, to identify alleles potentially linked to resistance to Plum pox virus (PPV). Over one thousand stone fruit accessions (1397) were screened for variation in eIF4E and eIFiso4E transcript sequences which are in single copy within the diploid Prunus genome. We identified new alleles for both genes differing from haplotypes associated with PPV susceptible accessions. Overall, analyses showed that eIFiso4E is genetically more constrained since it displayed less polymorphism than eIF4E. We also demonstrated more variations at both loci in the related wild species than in crop species. As the eIFiso4E translation initiation factor was identified as indispensable for PPV infection, a selection of ten different eIFiso4E haplotypes along 13 accessions were tested by infection with PPV and eight of them displayed a range of reduced susceptibility to resistance, indicating new potential sources of resistance to sharka.


Assuntos
Fator de Iniciação 4E em Eucariotos , Prunus , Alelos , Fator de Iniciação 4E em Eucariotos/genética , Fatores de Iniciação em Eucariotos/genética , Citoplasma , Prunus/genética
11.
New Phytol ; 196(3): 873-886, 2012 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-22943366

RESUMO

Sharka is a devastating viral disease caused by the Plum pox virus (PPV) in stone fruit trees and few sources of resistance are known in its natural hosts. Since any knowledge gained from Arabidopsis on plant virus susceptibility factors is likely to be transferable to crop species, Arabidopsis's natural variation was searched for host factors essential for PPV infection. To locate regions of the genome associated with susceptibility to PPV, linkage analysis was performed on six biparental populations as well as on multiparental lines. To refine quantitative trait locus (QTL) mapping, a genome-wide association analysis was carried out using 147 Arabidopsis accessions. Evidence was found for linkage on chromosomes 1, 3 and 5 with restriction of PPV long-distance movement. The most relevant signals occurred within a region at the bottom of chromosome 3, which comprises seven RTM3-like TRAF domain-containing genes. Since the resistance mechanism analyzed here is recessive and the rtm3 knockout mutant is susceptible to PPV infection, it suggests that other gene(s) present in the small identified region encompassing RTM3 are necessary for PPV long-distance movement. In consequence, we report here the occurrence of host factor(s) that are indispensable for virus long-distance movement.


Assuntos
Arabidopsis/genética , Mapeamento Cromossômico/métodos , Ligação Genética , Genoma de Planta , Vírus Eruptivo da Ameixa/patogenicidade , Agrobacterium tumefaciens/genética , Agrobacterium tumefaciens/metabolismo , Alelos , Arabidopsis/imunologia , Arabidopsis/metabolismo , Arabidopsis/virologia , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Cromossomos de Plantas/genética , Cromossomos de Plantas/metabolismo , Cruzamentos Genéticos , Resistência à Doença , Técnicas de Inativação de Genes , Genes de Plantas , Estudos de Associação Genética/métodos , Repetições de Microssatélites , Doenças das Plantas/genética , Doenças das Plantas/imunologia , Doenças das Plantas/virologia , Vírus Eruptivo da Ameixa/imunologia , Vírus Eruptivo da Ameixa/metabolismo , Polinização , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas
12.
Viruses ; 14(11)2022 10 23.
Artigo em Inglês | MEDLINE | ID: mdl-36366423

RESUMO

As part of a virome characterization of Prunus species, a novel cheravirus was discovered in two wild species, Prunus brigantina and P. mahaleb, and in an apricot (P. armeniaca) accession. The sequence of the two genomic RNAs was completed for two isolates. The Pro-Pol conserved region showed 86% amino acid (aa) identity with the corresponding region of trillium govanianum cheravirus (TgCV), a tentative Cheravirus member, whereas the combined coat proteins (CPs) shared only 40% aa identity with TgCV CPs, well below the species demarcation threshold for the genus. This suggests that the new virus should be considered a new species for which the name alpine wild prunus virus (AWPV) is proposed. In parallel, the complete genome sequence of stocky prune virus (StPV), a poorly known cheravirus for which only partial sequences were available, was determined. A phylogenetic analysis showed that AWPV, TgCV and StPV form a distinct cluster, away from other cheraviruses.


Assuntos
Prunus , Secoviridae , Vírus , Filogenia , Genoma Viral , RNA Viral/genética , Doenças das Plantas , Secoviridae/genética , Vírus/genética
13.
Nat Commun ; 12(1): 3956, 2021 06 25.
Artigo em Inglês | MEDLINE | ID: mdl-34172741

RESUMO

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 independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding.


Assuntos
Domesticação , Genoma de Planta/genética , Prunus armeniaca/genética , Cromossomos de Plantas/genética , Resistência à Doença/genética , Evolução Molecular , Frutas/classificação , Frutas/genética , Frutas/crescimento & desenvolvimento , Fluxo Gênico , Variação Genética , Estágios do Ciclo de Vida/genética , Metagenômica , Fenótipo , Filogenia , Prunus armeniaca/classificação , Prunus armeniaca/crescimento & desenvolvimento , Seleção Genética
14.
Front Plant Sci ; 11: 180, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32180783

RESUMO

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 (Prunus armeniaca) genotypes with contrasting bloom dates and peach (Prunus persica) genotypes with contrasting chilling requirements (CR) to explore the genetic regulation of bud dormancy. We identified distinct gene expression programming patterns in endodormancy and ecodormancy that reproducibly occur between different genotypes and species. During the transition from endo- to eco-dormancy, 1,367 and 2,102 genes changed in expression in apricot and peach, respectively. Over 600 differentially expressed genes were shared in peach and apricot, including three DORMANCY ASSOCIATED MADS-box (DAM) genes (DAM4, DAM5, and DAM6). Of the shared genes, 99 are located within peach CR quantitative trait loci, suggesting these genes as candidates for dormancy regulation. Co-expression and functional analyses revealed that distinctive metabolic processes distinguish dormancy stages, with genes expressed during endodormancy involved in chromatin remodeling and reproduction, while the genes induced at ecodormancy were mainly related to pollen development and cell wall biosynthesis. Gene expression analyses between two Prunus species highlighted the conserved transcriptional control of physiological activities in endodormancy and ecodormancy and revealed genes that may be involved in the transition between the two stages.

15.
Hortic Res ; 6: 58, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30962943

RESUMO

Prior to the availability of whole-genome sequences, our understanding of the structural and functional aspects of Prunus 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 Prunus genomes and the genetic underpinnings of important traits ensued. In this review, we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome sequences. Within the structural and evolutionary contexts, we summarize: (1) the current status of Prunus whole-genome sequences; (2) preliminary and ongoing work on the sequence structure and diversity of the genomes; (3) the analyses of Prunus genome evolution driven by natural and man-made selection; and (4) provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs worldwide. Functionally, we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus traits. These include phenology, fruit quality, allergens, disease resistance, tree architecture, and self-incompatibility. Translationally, we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop improvement. Finally, we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae (GDR) and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry.

16.
Mol Plant Pathol ; 20(8): 1051-1066, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31115167

RESUMO

Many recessive resistances against potyviruses are mediated by eukaryotic translation initiation factor 4E (eIF4E). In tobacco, the va resistance gene commonly used to control Potato virus Y (PVY) corresponds to a large deletion affecting the eIF4E-1 gene on chromosome 21. Here, we compared the resistance durability conferred by various types of mutations affecting eIF4E-1 (deletions of various sizes, frameshift or nonsense mutations). The 'large deletion' genotypes displayed the broadest and most durable resistance, whereas frameshift and nonsense mutants displayed a less durable resistance, with rapid and frequent apparition of resistance-breaking variants. In addition, genetic and transcriptomic analyses revealed that resistance durability is strongly impacted by a complex genetic locus on chromosome 14, which contains three other eIF4E genes. One of these, eIF4E-3, is rearranged as a hybrid gene between eIF4E-2 and eIF4E-3 (eIF4E-2-3 ) in the genotypes showing the most durable resistance, while eIF4E-2 is differentially expressed between the tested varieties. RNA-seq and quantitative reverse transcriptase-polymerase chain reaction experiments demonstrated that eIF4E-2 expression level is positively correlated with resistance durability. These results suggest that besides the nature of the mutation affecting eIF4E-1, three factors linked with a complex locus may potentially impact va durability: loss of an integral eIF4E-3, presence of eIF4E-2-3 and overexpression of eIF4E-2. This latter gene might act as a decoy in a non-productive virus-plant interaction, limiting the ability of PVY to evolve towards resistance breaking. Taken together, these results show that va resistance durability can in large part be explained by complex redundancy effects in the eIF4E gene family.


Assuntos
Resistência à Doença , Fator de Iniciação 4E em Eucariotos/genética , Genes de Plantas , Loci Gênicos , Nicotiana/imunologia , Nicotiana/virologia , Doenças das Plantas/imunologia , Doenças das Plantas/virologia , Potyvirus/fisiologia , Substituição de Aminoácidos/genética , Cromossomos de Plantas/genética , Ecótipo , Dosagem de Genes , Regulação da Expressão Gênica de Plantas , Genótipo , Modelos Biológicos , Mutação/genética , Fenótipo , Filogenia , Doenças das Plantas/genética , Deleção de Sequência , Nicotiana/genética
17.
Tree Physiol ; 39(7): 1136-1148, 2019 07 18.
Artigo em Inglês | MEDLINE | ID: mdl-31070767

RESUMO

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. (apricot). Concentrations of eight phenylpropanoid metabolites were measured during chill accumulation and at developmental stages corresponding to the emergence of sepals and petals in floral buds of varieties that differ phenotypically in bloom date (BD). A significant interaction effect of chill hours and BD phenotype on the concentration of each of the compounds was observed (mixed analysis of variance, P < 0.05), with the concentration of most phenylpropanoid metabolites dropping precipitously when sepals and petals emerged. While phenylpropanoid biosynthetic gene expression patterns were more variable in general, expression changed over time and was impacted, although to a lesser degree, by BD phenotype. Furthermore, separation of BD phenotypic groups was most pronounced when early and late BD varieties were at different developmental stages, i.e., 800 chill hours. Taken together, these results suggest that the phenylpropanoid pathway is associated with floral bud reactivation in apricot. Furthermore, we show that the phenylpropanoid pathway is also impacted by phenological trait variation associated with dormancy. A better understanding of how apricot and other perennial tree species respond and adapt to environmental perturbations will be critical for improvement programs aimed at identifying and breeding trees more suitable for rapidly changing environments.


Assuntos
Prunus armeniaca , Flores , Fenótipo
18.
Mol Plant Microbe Interact ; 21(2): 198-207, 2008 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-18184064

RESUMO

In compatible interactions between plants and viruses that result in systemic infection, symptom development is a major phenotypic trait. However, host determinants governing this trait are mostly unknown, and the mechanisms underlying it are still poorly understood. In a previous study on the Arabidopsis thaliana-Plum pox virus (PPV) pathosystem, we showed a large degree of variation in symptom development among susceptible accessions. In particular, Cvi-1 (Cape Verde islands) accumulates viral particules but remains symptomless, Col-0 (Columbia) sometimes shows weak symptoms compared with Ler (Landsberg erecta), which always shows severe symptoms. Genetic analyses of Col x Ler and Cvi x Ler F2 and recombinant inbred line (RIL) populations suggested that symptom development as well as viral accumulation traits are polygenic and quantitative. Three of the symptom quantitative trait loci (QTL) identified could be confirmed in near-isogenic lines, including PSI1 (PPV symptom induction 1), which was identified on the distal part of chromosome 1 in both RIL populations. With respect to viral accumulation, several factors have been detected and, interestingly, in the Col x Ler population, two out of three viral accumulation QTL colocalized with loci controlling symptom development, although correlation analysis showed weak linearity between symptom severity and virus accumulation. In addition, in the Cvi x Ler RIL population, a digenic recessive determinant controlling PPV infection was identified.


Assuntos
Arabidopsis/genética , Arabidopsis/virologia , Doenças das Plantas/genética , Doenças das Plantas/virologia , Vírus de Plantas/fisiologia , Locos de Características Quantitativas/genética , Mapeamento Cromossômico , Cromossomos de Plantas , Imunidade Inata/imunologia , Endogamia , Padrões de Herança , Fenótipo , Doenças das Plantas/imunologia
19.
Pest Manag Sci ; 74(6): 1219-1227, 2018 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-29205815

RESUMO

Currently, European farmers do not have access to sufficient numbers and diversity of crop species/varieties. This prevents them from designing cropping systems more resilient to abiotic and biotic stresses. Crop diversification is a key lever to reduce pest (pathogens, animal pests and weeds) pressures at all spatial levels from fields to landscapes. In this context, plant breeding should consist of: (1) increased efforts in the development of new or minor crop varieties to foster diversity in cropping systems, and (2) focus on more resilient varieties showing local adaptation. This new breeding paradigm, called here 'breeding for integrated pest management (IPM)', may boost IPM through the development of cultivars with tolerance or resistance to key pests, with the goal of reducing reliance on conventional pesticides. At the same time, this paradigm has legal and practical implications for future breeding programs, including those targeting sustainable agricultural systems. By putting these issues into the context, this article presents the key outcomes of a questionnaire survey and experts' views expressed during an EU workshop entitled 'Breeding for IPM in sustainable agricultural systems'. © 2017 Society of Chemical Industry.


Assuntos
Produtos Agrícolas/genética , Controle de Pragas/métodos , Melhoramento Vegetal , Europa (Continente)
20.
Gene ; 374: 96-103, 2006 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-16564142

RESUMO

We investigated the changes in the expression profiles of the partially resistant apricot (Prunus armeniaca L.) cultivar Goldrich following inoculation with Plum pox virus (PPV) using cDNA-amplification fragment length polymorphism (AFLP). Altered expression patterns were detected and twenty-one differentially expressed cDNA had homologies with genes in databases coding for proteins involved in metabolism, signal transduction, defense, stress and intra/intercellular connections. Seven of the modified expressed patterns were further investigated by semi-quantitative RT-PCR or Northern blotting. The expression patterns of five of these genes were confirmed in the partially resistant P. armeniaca cv. 'Goldrich' and assessed in a susceptible genotype. One of these cDNAs, coding for a putative class III chitinase, appeared to be repressed in infected plants of the partially resistant genotype and expressed in the susceptible one which could be related to the partially resistant phenotype. On the contrary, the expression patterns of the genes coding for a transketolase, a kinesin-like and an ankyrin-like protein, were clearly linked to the susceptible interaction. These candidate genes could play a role either in the compatible interaction leading to virus invasion or to the quantitative resistance of apricot to PPV.


Assuntos
Expressão Gênica/fisiologia , Genes de Plantas , Doenças das Plantas/virologia , Vírus Eruptivo da Ameixa/fisiologia , Prunus/virologia , Frutas/virologia , Perfilação da Expressão Gênica , Vírus Eruptivo da Ameixa/genética , Vírus Eruptivo da Ameixa/patogenicidade , Prunus/genética
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