Inheritance of resistance to Plum pox virus in apricot (Prunus armeniaca L.)

The inheritance of resistance to Plum pox virus (PPV) has been studied in 1,178 apricot hybrids. Seven hundred and eighteen F1 hybrids, obtained from controlled crosses between the susceptible Greek cultivar “Bebecou” and the resistant PPV cultivars of American origin (“Stark Early Orange,” ‘NJA2,” ‘Veecot,” “Sunglo,” “Harlayne,” and “Orangered”) were evaluated for resistance to the PPV-M (Marcus) strain, 8 years after artificial inoculation. The inheritance of resistance to PPV has been additionally studied for the first time in a BC₁ population of 95 apricot hybrids for four vegetative periods. Reaction of each hybrid to PPV-M was scored through visual symptoms, indexing onto GF-305 and double-antibody sandwich enzyme-linked immunosorbent assay tests. Segregation within the hybrids, determined by Chi-squared analysis, fits a 1:1 ratio (P ≤ 0.05) of the resistant vs susceptible, indicating that resistance to PPV is controlled by a single dominant gene locus and that the above six resistant cultivars are heterozygous for the trait. Plants carrying this gene may initially develop disease symptoms on leaves but eventually recover and no virus can be detected in leaves. Susceptible plants show similar symptoms initially but remain symptomatic. Inheritance of resistance to PPV also has been studied in 365 F1 hybrids by crossing the resistant cultivar “Stella” with the susceptible “Bebecou” and the resistant cultivars “Sunglo” and “NJA2,” for 8 years after inoculation. The segregation ratio was 1:0 (resistant/susceptible) suggesting that “Stella” is homozygous for the resistance trait. The purpose of this work was the enhancement of the knowledge of inheritance of resistance to PPV for the selection of new cultivars.     

Non-TIR-NBS-LRR resistance gene analogs in apricot (Prunus armeniaca L.)

Genes encoding for proteins with nucleotide-binding site and leucine-rich repeat motifs (NBS-LRR) have been suggested to play a general role in plant defence mechanism. In Prunus species, many TIR (Toll / Interleukin-1 Receptor), and only very few non-TIR sequences were identified, which was explained either by the unequal distribution of TIR/non-TIR sequences in the Prunus genome or by the incapability of primers in the amplification of non-TIR RGAs. The objective of this work was to check whether a new semi-nested PCR strategy can be developed for the targeted isolation of non-TIR-NBS-LRR Resistance Gene Analog (RGA) sequences from apricot. Three primers (CUB-P-loop F, CUB-Kin2 F and CUB-HD R) were designed, from which CUB-Kin2 F and CUB-HD R were constructed to anneal selectively to the non-TIR sequences. A colony Polymerase Chain Reaction (PCR) indicated that out of the 96 clones tested 28 showed amplification using the newly developed primers, while no amplification occurred when using the formerly described primers. Half of the 28 positive clones were sequenced and they turned out to represent 11 different non-TIR RGA sequences. A phylogenetic analysis was carried out based on an alignment containing 293 Rosaceae and 21 non-Rosaceaa sequences. A significantly higher ratio (91%) of non-TIR sequences were arranged in multi-genera clades than that of (57%) the TIR groups confirming that non-TIR sequences might be of more ancient origin than TIR sequences.     

Flanking the major Plum pox virus resistance locus in apricot with co-dominant markers (SSRs) derived from candidate resistance genes

Plum pox virus (PPV) is a potyvirus that causes sharka disease in infested stone fruit trees (Prunus species, peach, apricot, plum). In apricots, the resistance is controlled by a major quantitative trait locus that explains up to 70% of the phenotypic variance; it is localised in the upper part of linkage group 1. In this report, we transformed candidate genes that mapped in the region of the apricot resistance locus into polymerase chain reaction markers (SSCP and SSR) and tested for their co-localisation with the major PPV resistance locus in related and unrelated populations. Three populations of F1 and F2 individuals issued from crosses between the PPV-resistant cultivar ‘Stark Early Orange’ or ‘Goldrich’ and three susceptible parents were used in this study. Molecular-marker data were collected to determine the linkage relationship between the PPV resistance locus in apricots and markers that target candidate disease-resistance genes. In addition, SSR markers linked to resistance-gene candidates were mapped to positions flanking the PPV resistance locus in different apricot populations. Therefore, we demonstrate that this strategy helps to saturate the major genomic region controlling resistance to PPV in apricot with valuable co-dominant markers. O. Sicard and G. Marandel have contributed equally to this work.     

Quantitative trait loci meta-analysis of Plum pox virus resistance in apricot (Prunus armeniaca L.): new insights on the organization and the identification of genomic resistance factors

Plum pox virus (PPV) is responsible for sharka disease, one of the most detrimental stone fruit diseases affecting Prunus trees worldwide. Only a few apricot cultivars have been described as resistant, most originating from North American breeding programmes. Several PPV resistance quantitative trait loci (QTLs) have been mapped in various progenies, consistently highlighting the contribution to the resistance of the upper part of linkage group 1 (LG1). However, to date, no consensus has been reached on the precise number of QTLs linked to the resistance to PPV in apricot and P. davidiana or on their accurate position on the genetic linkage map. In the present study, the quantitative resistance of cultivar 'Harlayne' was analysed over five growth periods in a large F1 population. Four QTLs were identified, three mapping on LG1, explaining between 5% and 39% of the observed phenotypic variance. In an effort to further this analysis of PPV resistance in apricot, these results were merged in a single QTL meta-analysis with those of five other PPV resistance analyses available in the literature. Three consensus QTL regions were identified on LG1 and a putative fourth region on LG3. QTL meta-analysis also revealed the contribution of each resistant cultivar to metaQTLs, providing interesting comparative data on the resistance factors shared between the resistance sources used in the various studies. Finally, it was shown that one of the metaQTLs co-localizes with the eukaryotic translation initiation factor eIF4E , thus providing new hypotheses on the mechanisms of PPV resistance in apricot.     

Opportunities of marker-assisted selection for Plum pox virus resistance in apricot breeding programs

Evaluation of Plum pox virus (PPV) resistance is a laborious and expensive task, and the development of new accurate methods, including the use of molecular markers, would be very useful for breeding programs for resistance. In this work, the Plum pox virus resistance of 80 apricot genotypes of different genetic origins was evaluated in controlled greenhouse and natural field conditions. The genotypes for five simple sequence repeat (SSR) markers described as linked to PPV resistance were also determined. Depending on their behavior, cultivars were classified as resistant, susceptible, and uncertain, and the genotype was identified for each SSR linked to different phenotypes. Twenty genotypes were resistant and 37 susceptible in the greenhouse and in the field. However, 23 genotypes did not show clear behavior, probably due to the complex plant-virus interaction, so they were classified as uncertain. In general, results showed a narrow relationship between the SSRs PGS1.21 and PGS1.24, and resistance to PPV, although some genotypes did not show this relationship. Most of the susceptible genotypes did not show the alleles of resistance. Therefore, in most cases, marker-assisted selection (MAS) could be used as a means of screening new seedlings for early selection, making it possible to remove those that are susceptible. However, in certain cases, MAS using these markers has not proven to be completely effective. The origin of such discrepancies could be the presence of a second locus involved in PPV resistance. In addition, other factors affecting efficiency of MAS discussed in the work are the presence of null alleles and recombinant events. Resistant seedlings would have to be evaluated in greenhouse and natural conditions to confirm their actual behavior against PPV. From the breeding point of view, the use of homozygous resistant parents for the SSR resistance alleles, with good agronomic characteristics, would increase the efficiency of breeding programs, since all seedlings would be resistant regardless of the other parent. Finally, new molecular markers should be developed to accurately select resistant seedlings regardless of the resistant progenitors involved.     

Characterization and mapping of NBS-LRR resistance gene analogs in apricot (Prunus armeniaca L.)

Genomic DNA sequences sharing homology with the NBS-LRR (nucleotide binding site-leucine-rich repeat) resistance genes were isolated and cloned from apricot (Prunus armeniaca L.) using a PCR approach with degenerate primers designed from conserved regions of the NBS domain. Restriction digestion and sequence analyses of the amplified fragments led to the identification of 43 unique amino acid sequences grouped into six families of resistance gene analogs (RGAs). All of the RGAs identified belong to the Toll-Interleukin receptor (TIR) group of the plant disease resistance genes (R-genes). RGA-specific primers based on non-conserved regions of the NBS domain were developed from the consensus sequences of each RGA family. These primers were used to develop amplified fragment length polymorphism (AFLP)-RGA markers by means of an AFLP-modified procedure where one standard primer is substituted by an RGA-specific primer. Using this method, 27 polymorphic markers, six of which shared homology with the TIR class of the NBS-LRR R-genes, were obtained from 17 different primer combinations. Of these 27 markers, 16 mapped in an apricot genetic map previously constructed from the self-pollination of the cultivar Lito. The development of AFLP-RGA markers may prove to be useful for marker-assisted selection and map-based cloning of R-genes in apricot.     

Transgenic plums (Prunus domestica L.) express the plum pox virus coat protein gene

Summary Plum hypocotyl slices were transformed with the coat protein (CP) gene of plum pox virus (PPV-CP) following cocultivation with Agrobacterium tumefaciens containing the plasmid pGA482GG/PPVCP-33. This binary vector carries the PPV-CP gene construct, as well as the chimeric neomycin phosphotransferase and -glucuronidase genes. Integration and expression of the transferred genes into regenerated plum plants was verified through kan resistance, GUS assays, and PCR amplification of the PPV-CP gene. Twenty-two transgenic clones were identified from approximately 1800 hypocotyl slices. DNA, mRNA, and protein analyses of five transgenic plants confirmed the integration of the engineered CP gene, the accumulation of CP mRNA and of PPV-CP-immunoreactive protein. CP mRNA levels ranged from high to undetectable levels, apparently correlated with gene structure, as indicated by DNA blot analysis. Western analysis showed that transgenic plants produced amounts of CP which generally correlated with amounts of detected mRNA.     

Genetic linkage maps of two apricot cultivars ( Prunus armeniaca L.), and mapping of PPV (sharka) resistance

Genetic linkage maps for two apricot cultivars have been constructed using AFLP, RAPD, RFLP and SSR markers in 81 F1 individuals from the cross 'Goldrich' x 'Valenciano'. This family segregated for resistance to 'plum pox virus' (PPV), the most-important virus affecting Prunus species. Of the 160 RAPD arbitrary primers screened a total of 44 were selected. Sixty one polymorphic RAPD markers were scored on the mapping population: 30 heterozygous in 'Goldrich', 19 heterozygous in 'Valenciano', segregating 1:1, and 12 markers heterozygous in both parents, segregating 3:1. A total of 33 and 19 RAPD markers were mapped on the 'Goldrich' and 'Valenciano' maps respectively. Forteen primer combinations were used for AFLPs and all of them detected polymorphism. Ninety five markers segregating 1:1 were identified, of which 62 were heterozygous in the female parent 'Goldrich' and 33 in the male parent 'Valenciano'. Forty five markers were present in both parents and segregated 3:1. A total of 82 and 48 AFLP markers were mapped on the 'Goldrich' and 'Valenciano' maps. Twelve RFLPs probes were screened in the population, resulting in five loci segregating in the family, one locus heterozygous for 'Valenciano' and four heterozygous for both, segregating 1:2:1. Of the 45 SSRs screened 17 segregated in the mapping family, resulting in seven loci heterozygous for the maternal parent and ten heterozygous for both, segregating 1:2:1 or 1:1:1:1. A total of 16 and 13 co-dominant markers were mapped in the female and male parent maps respectively. A total of 132 markers were placed into eight linkage groups on the 'Goldrich' map, defining 511 cM of the total map-length. The average distance between adjacent markers was 3.9 cM. A total of 80 markers were placed into seven linkage groups on the 'Valenciano' map, defining 467.2 cM of the total map-distance, with an average interval of 5.8 cM between adjacent markers. Thirty six marker loci heterozygous in both parents revealed straightforward homologies between five linkage groups in both maps. The sharka resistance trait mapped on linkage group 2. The region containing sharka resistance is flanked by two co-dominant markers that will be used for targeted SSR development employing a recently constructed complete apricot BAC library. SSRs tightly linked to sharka resistance will facilitate MAS in breeding for resistance in apricot.     

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). However, the mapping accuracy was not sufficiently reliable and PPVres was predicted within a low confidence interval. In this study, we have constructed two high-density simple sequence repeat (SSR) improved maps with 0.70 and 0.68 markers/cm, corresponding to LG1 of 'Lito' and 'Goldrich' PPV-resistant cultivars, respectively. Using these maps, and excluding genotype-phenotype incongruent individuals, a new binary trait locus (BTL) analysis for PPV resistance was performed, narrowing down the PPVres support intervals to 7.3 and 5.9 cm in 'Lito' and 'Goldrich', respectively. Subsequently, 71 overlapping oligonucleotides (overgo) probes were hybridized against an apricot bacterial artificial chromosome (BAC) library, identifying 870 single BACs from which 340 were anchored onto a map region of approximately 30-40 cm encompassing PPVres. Partial BAC contigs assigned to the two allelic haplotypes (resistant/susceptible) of the PPVres locus were built by high-information content fingerprinting (HICF). In addition, a total of 300 BAC-derived sequences were obtained, and 257 showed significant homology with the peach genome scaffold_1 corresponding to LG1. According to the peach syntenic genome sequence, PPVres was predicted within a region of 2.16 Mb in which a few candidate resistance genes were identified.     

High resistance to plum pox virus (PPV) in transgenic plants containing modified and truncated forms of PPV coat protein gene

Two modified plum pox virus (PPV) coat protein (CP) gene constructs, designed to reduce putative biological risks associated with heteroen capsidation, were integrated into Nicotiana benthamiana plants. The first one contained a deletion of the nucleotides encoding for the DAG amino acid triplet involved in virus aphid-transmission. In the second one, the first 420 nucleotides of the PPV CP gene were removed. We present here the analysis and the selection throughout the generations of PPV-resistant transgenic lines containing these constructs. In most of the lines, a recovery phenotype was observed and was associated with a down-regulation of the transgene products (RNA or protein). We also describe two lines that were highly resistant to PPV. This immunity was correlated with a high number of transgene copies (at least three) and with low or undetectable transgene RNA levels. No heterologous protection was observed against other potyviruses. These characteristics indicate that the described resistance against PPV was RNA-mediated and can be classified as a 'sense suppression' or homology-dependent resistance. Moreover, the production of a highly resistant line containing the PPV CP gene with one third of its 5 end deleted indicated that this region is not necessary to trigger the plant resistance mechanism(s)     

An apricot (Prunus armeniaca L.) F2 progeny linkage map based on SSR and AFLP markers,mapping plum pox virus resistance and self-incompatibility traits

A genetic linkage map of apricot ( Prunus armeniaca L.) was constructed using AFLP and SSR markers. The map is based on an F(2) population (76 individuals) derived from self-pollination of an F(1) individual ('Lito') originated from a cross between 'Stark Early Orange' and 'Tyrinthos'. This family, designated as 'Lito' x 'Lito', segregated for two important agronomical traits: plum pox virus resistance (PPV) and self-incompatibility. A total of 211 markers (180 AFLPs, 29 SSRs and two agronomic traits) were assigned to 11 linkage groups covering 602 cM of the apricot genome. The average distance (cM/marker) between adjacent markers is 3.84 cM. The PPV resistance trait was mapped on linkage group G1 and the self-incompatibility trait was mapped on linkage group G6. Twenty two loci held in common with other Prunus maps allowed us to compare and establish homologies among the respective linkage groups.     

Effective pollination period in apricot (Prunus armeniaca L.) varieties

A study of the effective pollination period (E.P.P.) of six varieties of apricot has shown that in the warm climate of the South Mediterranean this parameter is extremely short. The percentage of fruit set of emasculated flowers diminishes rapidly with time. Temperature plays an important role in this process and is responsible for the rapid degradation of the stigma, which hinders pollen germination.     

Influence of intraovular reserves on ovule fate in apricot (Prunus armeniaca L.)

 In many plant species with multiovulate ovaries, a considerable reduction in the number of ovules takes place. However, the underlying physiological causes are not clear. In Prunus spp., although flowers present two ovules, usually only one seed is produced. We have followed the development and degeneration of the two ovules in apricot (Prunus armeniaca L.) and examined the extent to which carbohydrates within the ovule might be involved in determining the fate of the ovule. While the primary ovule grows in the days following anthesis, growth of the secondary ovule is arrested. Starch distribution along the different ovular tissues exhibits several changes that are different in the two ovules. Primary ovule growth is inversely related to starch content and this growth takes place independently of pollination since it occurs in the same way in pollinated and unpollinated flowers. In the secondary ovule, starch disappears simultaneously from all ovular structures and callose is layered at the chalazal end of the nucellus. The size of the secondary ovule does not change significantly from anthesis to degeneration, and callose starts to accumulate 5 days after anthesis. Likewise, this process occurs independently of pollination. These results are discussed in terms of the implications of the starch content of ovules in fertilization success and ovule fate. Received: 26 August 1997 / Revision accepted: 17 December 1997     

An efficient viral vector for functional genomic studies of Prunus fruit trees and its induced resistance to Plum pox virus via silencing of a host factor gene

RNA silencing is a powerful technology for molecular characterization of gene functions in plants. A commonly used approach to the induction of RNA silencing is through genetic transformation. A potent alternative is to use a modified viral vector for virus‐induced gene silencing (VIGS) to degrade RNA molecules sharing similar nucleotide sequence. Unfortunately, genomic studies in many allogamous woody perennials such as peach are severely hindered because they have a long juvenile period and are recalcitrant to genetic transformation. Here, we report the development of a viral vector derived from Prunus necrotic ringspot virus (PNRSV), a widespread fruit tree virus that is endemic in all Prunus fruit production countries and regions in the world. We show that the modified PNRSV vector, harbouring the sense‐orientated target gene sequence of 100‐200 bp in length in genomic RNA3, could efficiently trigger the silencing of a transgene or an endogenous gene in the model plant Nicotiana benthamiana. We further demonstrate that the PNRSV‐based vector could be manipulated to silence endogenous genes in peach such as eukaryotic translation initiation factor 4E isoform (eIF(iso)4E), a host factor of many potyviruses including Plum pox virus (PPV). Moreover, the eIF(iso)4E‐knocked down peach plants were resistant to PPV. This work opens a potential avenue for the control of virus diseases in perennial trees via viral vector‐mediated silencing of host factors, and the PNRSV vector may serve as a powerful molecular tool for functional genomic studies of Prunus fruit trees.     

Selecting with markers linked to the PPVres major QTL is not sufficient to predict resistance to Plum Pox Virus (PPV) in apricot

Sharka is one of the most serious viral diseases affecting stone fruit species and, in apricot, resistance to its viral agent, the Plum Pox Virus (PPV), is conferred by one major quantitative trait locus (QTL), named PPVres for PPV resistance. Previous studies indicated that PPV-resistant cultivars and breeding progenies can be selected by using a set of SSR markers (named PGS) targeting the PPVres locus. However, before these markers can be employed for marker-assisted selection, they were validated in a wide range of genetic backgrounds and environments. We used a total of 11 mapping populations issued from three distinct environments to confirm that this marker set located within the QTL adequately predicted PPV resistance. In this study, we show that selection of PPV-resistant material based only on markers co-localizing with the PPVres major locus is not fully reliable. Indeed, genotype-phenotype discrepancies were observed depending on the progeny and the PPV-resistant/susceptible parents. While most of the PPV-resistant individuals displayed the resistant alleles, a significant number of PPV-susceptible individuals showed the same resistant haplotype. An effect of the PPV strain used for phenotyping was also demonstrated. We thus hypothesize that the presence of other factors or genes involved in the mechanism of resistance to sharka in apricot could explain these unexpected results. Our work indicates that the current PGS marker set is not broadly applicable for MAS and that marker-assisted breeding based on the sole PPVres locus is not sufficient to unambiguously select PPV-resistant apricot cultivars.     

New gene(s) involved in the resistance of Poncirus trifoliata (L.) Raf. to citrus tristeza virus

 Citrus tristeza virus (CTV) causes important economic losses in the citrus industry worldwide. Resistance to CTV is present in Poncirus trifoliata and is known to be controlled by a dominant gene at the Ctr locus. Short-distance movement of CTV around the inoculum, as well as passive movement through the phloem vessels, were studied in segregant plants derived by self-pollination from P. trifoliata var. “Flying Dragon” in order to genetically analyze the mechanism of CTV resistance. Accumulation of CTV in the vicinity of the inoculum and in new flushes was studied by means of a direct tissue-blot immunoassay (DTBIA). CTV is able to passively move with the phloematic flux from inoculated resistant genotypes Ctr-Rr and Ctr-RR up to a susceptible scion cultivar (Ctr-rr). Differences regarding CTV accumulation around the inoculum were found among Ctr-Rr individuals of the progeny. Bulked segregant analysis identified five RAPD markers linked to a locus (Ctm), or a genomic region, involved in short-distance accumulation of CTV but located in a different linkage group from Ctr. This result indicates that Ctr is not the only locus responsible for resistance to CTV in P. trifoliata, and that at least one other gene is involved. Given that citrus is a perennial crop, breeding for durable disease resistance should take into account selection at both the Ctr and Ctm loci. Received : 13 March 1996 / Accepted : 18 April 1997     

The effect of summer shading on flower bud morphogenesis in apricot (Prunus armeniaca L.)

The aim of this investigation was to assess whether imposed summer shading treatments in apricot (Prunus armeniaca L.) can affect the main phenological phases related to the floral morphogenesis (floral differentiation, xylogenesis), flower bud growth and quality in terms of bud capacity to set fruit. Experimental trials were carried out on fully-grown trees of ‘San Castrese’ and ‘Stark Early Orange’ cultivars characterized by different biological and agronomical traits to which shadings were imposed in July and August. Histological analysis was carried out from summer onwards in order to determine the evolution of floral bud differentiation, and the acropetal progression of primary xylem differentiation along the flower bud axis. Periodical recordings to evaluate the bud drop, blooming time, flowering and fruit set rates were performed also. These shade treatments determined a temporary shutdown of floral differentiation, slowed xylem progression up to the resumption of flower bud growth and a reduced entity of flowering and fruit set. These events were particularly marked in ‘San Castrese’ cultivar, which is well known for its adaptability to different climatic conditions. These findings suggest that adequate light penetration within the canopy during the summer season could be the determining factor when defining the qualitative traits of flower buds and their regular growth, and ultimately to obtain good and constant crops.