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. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.

/pdf/the-high-quality-draft-genome-of-peach-prunus-persica-3z3zlpw3w6.pdf

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

In mammals, cadmium is widely considered as a non-genotoxic carcinogen acting through a methylation-dependent epigenetic mechanism. Here, the effects of Cd treatment on the DNA methylation patten are examined together with its effect on chromatin reconfiguration in Posidonia oceanica. DNA methylation level and pattern were analysed in actively growing organs, under short- (6 h) and long- (2 d or 4 d) term and low (10 mM) and high (50 mM) doses of Cd, through a Methylation-Sensitive Amplification Polymorphism technique and an immunocytological approach, respectively. The expression of one member of the CHROMOMETHYLASE (CMT) family, a DNA methyltransferase, was also assessed by qRT-PCR. Nuclear chromatin ultrastructure was investigated by transmission electron microscopy. Cd treatment induced a DNA hypermethylation, as well as an up-regulation of CMT, indicating that de novo methylation did indeed occur. Moreover, a high dose of Cd led to a progressive heterochromatinization of interphase nuclei and apoptotic figures were also observed after long-term treatment. The data demonstrate that Cd perturbs the DNA methylation status through the involvement of a specific methyltransferase. Such changes are linked to nuclear chromatin reconfiguration likely to establish a new balance of expressed/repressed chromatin. Overall, the data show an epigenetic basis to the mechanism underlying Cd toxicity in plants.

/pdf/in-posidonia-oceanica-cadmium-induces-changes-in-dna-3cu7uj83mr.pdf

In Posidonia oceanica cadmium induces changes in DNA methylation and chromatin patterning

The development of saturated linkage maps using transferable markers, restriction fragment length polymorphisms, and micro-satellites has provided a foundation for fruit tree genetics and breeding A Prunus reference map with 562 such markers is available, and a further set of 13 maps constructed with a subset of these markers has allowed genome comparison among seven Prunus diploid (x = 8) species (almond, peach, apricot, cherry, Prunus ferganensis, Prunus davidiana, and Prunus cerasifera); marker colinearity was the rule with all of them Preliminary results of the comparison between apple and Prunus maps suggest a high level of synteny between these two genera Conserved genomic regions have also been detected between Prunus and Arabidopsis By using the data from different linkage maps anchored with the reference Prunus map, it has been possible to establish, in a general map, the position of 28 major genes affecting agronomic characters found in different species Markers tightly linked to the major genes responsible for the expression of important traits (disease/pest resistances, fruit/nut quality, self-incompatibility, etc) have been developed in apple and Prunus and are currently in use for marker-assisted selection in breeding programs Quantitative character dissection using linkage maps and candidate gene approaches has already started Genomic tools such as the Prunus physical map, large EST collections in both Prunus and Malus, and the establishment of the map position of high numbers of ESTs are required for a better understanding of the Rosaceae genome and to foster additional research and applications on fruit tree genetics

https://www.pnas.org/content/pnas/101/26/9891.full.pdf

Comparative mapping and marker-assisted selection in Rosaceae fruit crops

Textural changes that lead to softening of fruits are accompanied by loss of neutral sugars, solubilisation and depolymerisation of the polysaccharides of the cell wall, and rearrangements of their associations, as the result of the combined action of several cell wall-modifying enzymes, acting in both pectic and hemicellulosic fractions. Recent studies on the structure of the plant cell wall have disclosed a large number and type of biochemical linkages between the components. Such linkages are potential targets for enzymatic action and draw attention to the putative involvement of several members of enzymes able to act and modify its structure in a developmental and coordinated way. Extensive work on fruit ripening has been done using tomato (Solanum lycopersicum [Lycopersicon esculentum Mill.]) as a plant model and the information concerning fruits other than model species is fragmented and incomplete. However, recent data from the literature had disclosed that differences exist between fruits, and even between cultivars of the same fruit species. These differences exist in the type and extent of the modification of the polysaccharides of the cell wall and in the expression and regulation of cell wall-modifying enzymes. In addition, genetic manipulation of cell wall-modifying genes re-opened the discussion about the real effect of these enzymes in the cell wall and their role in fruit softening. Moreover, the function of each enzyme has been proposed based on its homology with other annotated sequences, but, in most cases, confirmation of activity in planta and substrate specificity remains to be investigated. This aspect and recognized limitations of the in vitro enzymatic activity assays also need to be considered when discussing their role. This paper provides a critical review on the current knowledge concerning these differences and emphasises the need of using other species and more accurate methodologies to investigate general mechanisms and fruit specificities of softening among different fleshy fruits.

/pdf/cell-wall-modifications-during-fruit-ripening-when-a-fruit-20d7rtnw85.pdf

Cell wall modifications during fruit ripening: when a fruit is not the fruit

Microsatellites have emerged as an important system of molecular markers. We evaluated the potential of microsatellites for use in genetic studies of peach [Prunus persica (L.) Batsch]. Microsatellite loci in peach were identified by screening a pUC8 genomic library, a λZAPII leaf cDNA library, as well as through database searches. Primer sequences for the microsatellite loci were tested from the related Rosaceae species apple (Malus×domestica) and sour cherry (Prunus cerasus L.). The genomic library was screened for CT, CA and AGG repeats, while the cDNA library was screened for (CT)n- and (CA)n-containing clones. Estimates of microsatellite frequencies were determined from the genomic library screening, and indicate that CT repeats occur every 100 kb, CA repeats every 420 kb, and AGG repeats every 700 kb in the peach genome. Microsatellite- containing clones were sequenced, and specific PCR primers were designed to amplify the microsatellite- containing regions from genomic DNA. The level of microsatellite polymorphism was evaluated among 28 scion peach cultivars which displayed one to four alleles per primer pair. Five microsatellites were found to segregate in intraspecific peach-mapping crosses. In addition, these microsatellite markers were tested for their utility in cross-species amplification for use in comparative mapping both within the Rosaceae, and with the un- related species Arabidopsis thaliana L.

Characterization of microsatellite markers in peach (Prunus persica (L.) Batsch)

The organoleptic quality of fleshy fruits is in a large part defined by their composition of soluble sugars and organic acids. An F 2 population issuing from a cross between two peach varieties, 'Ferjalou Jalousia', a non-acid peach, and 'Fantasia', an acid nectarine, was analysed over 2 successive years for agronomic characters and for molecular-marker (isoenzymes, RFLPs, RAPDs, IMAs and AFLPs) segregations. Blooming and maturity dates, as well as productivity, were noted for each tree. Four fruits per tree were analysed at maturity for fresh weight, colour, pH, titratable acidity, soluble-solids content (SSC), acid (malic, citric and quinic acids) and sugar (sucrose, glu- cose, fructose, sorbitol) contents. QTLs were detected for all fruit components analysed, except for fruit col- our. The QTLs for nearly all components were present on two linkage groups. For productivity, fresh weight, pH, quinic acid, sucrose and sorbitol content, all the detected QTLs displayed the same e⁄ect as the parental phenotypes. By contrast, for maturity date, titratable acidity, malic and citric acids and fructose, some QTLs displayed the same e⁄ect as the parental phenotypes while others displayed the opposite e⁄ect. The fraction of the total variation in each trait throughout the population explained by the QTLs was very high and reached more than 90% for some characters. For most

Mapping QTLs controlling fruit quality in peach (Prunus persica (L.) Batsch)

Detection of qtls controlling peach fruit acidity and sweetness

A genetic linkage map of peach [Prunus persica (L.) Batch] was constructed in order to identify molecular markers linked to economically important agronomic traits that would be particularly useful for long-lived perennial species. An intraspecific F2 population was generated from self-pollinating a single F1 plant from a cross between a flat non-acid peach, ‘Ferjalou Jalousia®’ and an acid round nectarine ‘Fantasia’. Mendelian segregations were observed for 270 markers including four agronomic characters (peach/nectarine, flat/round fruit, acid/non-acid fruit, and pollen sterility) and 1 isoenzyme, 50 RFLP, 92 RAPD, 8 inter-microsatellite amplification (IMA), and 115 amplified fragment length polymorphism (AFLP) markers. Two hundred and forty-nine markers were mapped to 11 linkage groups covering 712 centiMorgans (cM). The average density between pairs of markers is 4.5 cM. For the four agronomic characters studied, molecular markers were identified. This map will be used for the detection of QTL controlling fruit quality in peach and, particularly, the acid and sugar content.

Genetic linkage map of peach [Prunus persica (L.) Batsch] using morphological and molecular markers

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Mapping QTLs controlling fruit quality in peach (Prunus persica (L.) Batsch)

Detection of qtls controlling peach fruit acidity and sweetness

Genetic linkage map of peach [Prunus persica (L.) Batsch] using morphological and molecular markers