Mapping QTLs controlling fruit quality 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 F₂ 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, glucose, fructose, sorbitol) contents. QTLs were detected for all fruit components analysed, except for fruit colour. 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 effect as the parental phenotypes. By contrast, for maturity date, titratable acidity, malic and citric acids and fructose, some QTLs displayed the same effect as the parental phenotypes while others displayed the opposite effect. 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 of the characters analysed, epistasis was observed between QTLs. Received: 10 October 1997 / Accepted: 18 August 1998     

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

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. Received: 18 June 1999 / Accepted: 6 December 1999     

In vitro callus induction from adult tissues of peach (Prunus persica L. Batsch)

We describe an efficient protocol for callus induction from adult tissues of Prunus persica (L.) Batsch. Three different commercial peach genotypes, Early May®, Zise May®, and UFO-3®, plus three other genotypes from hybrid crosses performed in February 2006, PS108, PS208, and PS708, were used in the study. Thirteen explant treatments were tested using nine different plant parts. Murashige and Skoog and woody plant medium salts were assayed with several concentrations of 2,4-dichlorophenoxyacetic acid (2,4-D), kinetin (KN), and thidiazuron, and two different photoperiods were tested, a 16-h photoperiod or continuous darkness. In terms of the quantitative response, two parameters were assessed: the number of d to callus induction and relative callus growth recorded after 30 d. Woody plant medium supplemented with 2,4-D and KN significantly increased the rates of callus induction in the majority of treatments. And no significant differences among the P. persica genotypes were found. The explants derived from stem and calyx produced up to 85 and 96% callus induction, respectively. The protocol described here could be used for efficient callus induction in a range of Prunus spp.     

Genetic mapping of the evergrowing gene in peach [Prunus persica (L.) Batsch

In temperate locations, terminal apices on evergrowing (also called evergreen) peach trees keep growing in winter until killed by low temperatures, while the lateral buds go into dormancy. A recessive allele of a single gene (evergrowing or evg) controls this trait in peach. The amplified fragment length polymorphism (AFLP) technique and bulked segregant analysis were applied to construct a local genetic linkage map for the evg gene from the cross Empress op op dwarf x Evergrowing (P.I. 442380). This map, comprising nine AFLP markers and the evg locus, covers a total genetic distance of 79.3 cM. Four dominant AFLP markers (EAT/MCAC, ETT/MCCA2, EAT/MCTA, and ETT/MACC) were linked to the evg locus at distances of 1, 5.3, 6.7, and 11.7 cM, respectively. EAT/MCAC and EAT/MCTA were converted into polymorphic sequence-tagged sites. Microsatellite markers in the evg region were developed from peach bacterial artificial chromosome (BAC) clones that hybridized to the AFLP marker fragments. Using three microsatellite anchor markers (pchgms12, pchgms17, and pchgms19), the local genetic linkage map was integrated into one minor linkage group of a previously constructed peach rootstock genetic linkage map. Three AFLP markers from the rootstock genetic linkage map were found linked to the evg locus.     

A first insight into peach [Prunus persica (L.) Batsch] SNP variability

Three factors may have reduced the diversity at both individual gene and whole genome levels in cultivated peach: its self-compatible mating system, the narrow genetic basis of most commercial cultivars, and the recent strong selection towards agronomically interesting traits. Previous diversity analyses with markers such as simple sequence repeats (SSRs) have revealed low levels of genetic variability. Here, we sequenced 23 genome-wide distributed DNA fragments in 47 occidental peach varieties, also observing reduced variability levels. On average, there was one single nucleotide polymorphism (SNP) every 598 bp and one indel every 4,189 bp. As expected, variability was higher in non-coding than in coding regions (one SNP every 390 non-coding bp versus one in 1,850 bp in coding DNA). In general, SNPs were observed at relatively high frequency, mean minor allele frequency?=?0.225, meaning that a large proportion of the SNPs discovered by sequencing similar germplasm will be useful for other purposes, such as association mapping. The average heterozygosity of the varieties was 0.28, with a low correlation between SSR and SNP heterozygosity. The whole sequence of two candidate genes, a pectate lyase 1 candidate for fruit firmness (CGPAA2668) and a sucrose synthase 1 candidate for sugar content (CGPPB6189), in the 47 varieties revealed that they both may have suffered a process of balancing selection.     

Molecular characterisation of sweet cherry (Prunus avium L.) genotypes using peach [Prunus persica (L.) Batsch] SSR sequences

A total of 76 sweet cherry genotypes were screened with 34 microsatellite primer pairs previously developed in peach. Amplification of SSR loci was obtained for 24 of the microsatellite primer pairs, and 14 of them produced polymorphic amplification patterns. On the basis of polymorphism and quality of amplification, a set of nine primer pairs and the resulting 27 informative alleles were used to identify 72 genotype profiles. Of these, 68 correspond to unique cultivar genotypes, and the remaining four correspond to three cultivars that could not be differentiated from the two original genotypes of which they are mutants, and two very closely related cultivars. The mean number of alleles per locus was 3.7 while the mean heterozygosity over the nine polymorphic loci averaged 0.49. The results demonstrate the usefulness of cross-species transferability of microsatellite sequences allowing the discrimination of different genotypes of a fruit tree species with sequences developed in other species of the same genus. UPGMA cluster analysis of the similarity data divided the ancient genotypes studied into two fairly well-defined groups that reflect their geographic origin, one with genotypes originating in southern Europe and the other with the genotypes from northern Europe and North America.     

Dormancy in peach (Prunus persica L.) flower buds

Morphological studies were carried out with peach flower buds collected monthly in 1989 and 1990, from two months before leaf fall (7 March) until two to three weeks before bloom (7/8 August). Chilled (2–4°C for 30 days) and unchilled buds were exposed to 20 to 25°C, 100% RH and continuous light. Gibberellin A₃ (3 ng or 30 ng) was applied to some of the non-chilled cuttings at three days intervals. Then, 12, 19, and 26 days after they were planted, the buds were sampled and processed for histological studies. Cultured flower buds (chilled or unchilled) had accelerated anther and gynoecium morphogenesis after 12 days under controlled conditions, compared to buds processed immediately after collection from the field. Chilling treatment augmented the bud culture effect, while Gibberellin A₃ applications to the excised buds retarded bud morphogenesis to a stage comparable to that of buds collected directly from the field. This, suggests that the comparatively high levels of Gibberellin A_1/3 we previously found in mid winter [15, 18] could be at least one of the factors that controls floral bud dormancy by retarding anther and gynoecium development.     

Vascular flows and transpiration affect peach (Prunus persica Batsch.) fruit daily growth

The relative contributions of xylem, phloem, and transpiration to fruit growth and the daily patterns of their flows have been determined in peach, during the two stages of rapid diameter increase, by precise and continuous monitoring of fruit diameter variations. Xylem, phloem, and transpiration contributions to growth were quantified by comparing the diurnal patterns of diameter change of fruits, which were then girdled and subsequently detached. Xylem supports peach growth by 70%, and phloem 30%, while transpiration accounts for approximately 60% of daily total inflows. These figures and their diurnal patterns were comparable among years, stages, and cultivars. Xylem was functional at both stage I and III, while fruit transpiration was high and strictly dependent on environmental conditions, causing periods of fruit shrinkage. Phloem imports were correlated to fruit shrinkage and appear to facilitate subsequent fruit enlargement. Peach displays a growth mechanism which can be explained on the basis of passive unloading of photoassimilates from the phloem. A pivotal role is played by the large amount of water flowing from the tree to the fruit and from the fruit to the atmosphere.     

Dormancy in peach (Prunus persica L.) flower buds

Summary Peach buds (floral and vegetative) were periodically collected from midsummer until the spring flowering and sprouted under continuous light, 100% relative humidity and 20–25°C. Treatments with 200 ppm gibberellin A₃ (GA₃) or chilling (2–4°C for 30 days before planting) were applied. Vegetative buds showed well-defined phenological stages: pre-dormancy, true dormancy, and end of dormancy. Both GA₃ and chilling treatments shortened the sprouting times of vegetative dormant buds close to those in predormancy. Isolated floral buds were irresponsive under all conditions and did not sprout even with the GA₃ or chilling treatments. In a comparative study with buds immediately after collection anatomical analysis demonstrated that vegetative buds were almost completely developed by midsummer/early automn and remained in a resting state until the end of winter. Floral buds developed continuously over the same period. Both types of verticils began to differentiate in midsummer. Sepals and petals developed mainly in late summer, androecious floral parts developed throughout the resting period, while gynoecious floral parts showed differentiation in late winter. The flower was completely formed a few days prior to blossoming. Thus, in isolated peach buds fertile verticils are not sufficiently developed during the resting time to allow sprouting.     

Mapping quantitative trait loci associated with blush in peach [Prunus persica (L.) Batsch]

Blush is an important trait for marketing peaches. The red skin pigmentation develops through the flavonoid and anthocyanin pathways, and both genetic and environmental stimuli, and their interaction, control the regulation of these pathways. The molecular basis of blush development in peach is yet to be understood. An F₂ blush population (ZC²) derived from a cross between two peach cultivars with contrasting phenotypes for blush, “Zin Dai” (～30 % red) and “Crimson Lady” (～100 % red), was used for linkage map construction and quantitative trait loci (QTLs) mapping. The segregating population was phenotyped for blush for 4 years using a visual rating scale and quantified using a colorimeter (L*, a*, and b*) 1 year. The ZC² population was genotyped with the IPSC 9 K peach single-nucleotide polymorphism (SNP) array v1, and a high-density ZC² genetic linkage map was constructed. The map covers genetic a distance of ～452.51 cM with an average marker spacing of 2.38 cM/marker. Four QTLs were detected: one major QTL on LG3 (Blush.Pp.ZC-3.1) and three minor QTLs on LG 4 and 7 (Blush.Pp.ZC-4.1; Blush.Pp.ZC-4.2; Blush.Pp.ZC-7.1), indicating the presence of major and minor genes involved in blush development. Candidate genes involved in skin and flesh coloration of peach (PprMYB10), cherry (PavMYB10), and apple (MdMYB1/MdMYBA/MdMYB10) are located within the interval of the major QTL on LG3, suggesting the same genetic control for color development in the Rosaceae family. Marker-assisted selection (MAS) for blush is discussed.     

Development of microsatellite markers in peach [ Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry ( Prunus avium L.)

We report the sequence of 41 primer pairs of microsatellites from a CT-enriched genomic library of the peach cultivar 'Merrill O'Henry'. Ten microsatellite-containing clones had sequences similar to plant coding sequences in databases and could be used as markers for known functions. For microsatellites segregating at least in one of the two Prunus F(2) progenies analyzed, it was possible to demonstrate Mendelian inheritance. Microsatellite polymorphism was evaluated in 27 peach and 21 sweet cherry cultivars. All primer pairs gave PCR-amplification products on peach and 33 on cherry (80.5%). Six PCR-amplifications revealed several loci (14.6%) in peach and eight (19.5%) in sweet cherry. Among the 33 single-locus microsatellites amplified in peach and sweet cherry, 13 revealed polymorphism both in peach and cherry, 19 were polymorphic only on peach and one was polymorphic only on cherry. The number of alleles per locus ranged from 1 to 9 for peach and from 1 to 6 on sweet cherry with an average of 4.2 and 2.8 in peach and sweet cherry, respectively. Cross-species amplification was tested within the Prunus species: Prunus avium L. (sweet cherry and mazzard), Prunus cerasus L. (sour cherry), Prunus domestica L. (European plum), Prunus amygdalus Batsch. (almond), Prunus armeniaca L. (apricot), Prunus cerasifera Ehrh. (Myrobalan plum). Plants from other genera of the Rosaceae were also tested: Malus (apple) and Fragaria (strawberry), as well as species not belonging to the Rosaceae: Castanea (chestnut tree), Juglans (walnut tree) and Vitis (grapevine). Six microsatellites gave amplification on all the tested species. Among them, one had an amplified region homologous to sequences encoding a MADS-box protein in Malus x domestica. Twelve microsatellites (29.3%) were amplified in all the Rosaceae species tested and 31 (75.6%) were amplified in all the six Prunus species tested. Thirty three (80.5%), 18 (43.9%) and 13 (31.7%) gave amplification on chestnut tree, grapevine and walnut tree, respectively.     

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

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.     

Candidate genes and QTLs for sugar and organic acid content in peach [ Prunus persica (L.) Batsch

The identification of genes involved in variation of peach fruit quality would assist breeders in creating new cultivars with improved fruit quality. Major genes and quantitative trait loci (QTLs) for physical and chemical components of fruit quality have already been detected, based on the peach [Prunus persica (L.) Batsch] cv. Ferjalou Jalousia^® (low-acid peach) 2 cv. Fantasia (normally-acid nectarine) F₂ intraspecific cross. Our aim was to associate these QTLs to structural genes using a candidate gene/QTL approach. Eighteen cDNAs encoding key proteins in soluble sugar and organic acid metabolic pathways as well as in cell expansion were isolated from peach fruit. A single-strand conformation polymorphism strategy based on specific cDNA-based primers was used to map the corresponding genes. Since no polymorphism could be detected in the Ferjalou Jalousia^® 2 Fantasia population, gene mapping was performed on the almond [Prunus amygdalus (P. dulcis)] cv. Texas 2 peach cv. Earlygold F₂ interspecific cross from which a saturated map was available. Twelve candidate genes were assigned to four linkage groups of the peach genome. In a second step, the previous QTL detection was enhanced by integrating anchor loci between the Ferjalou Jalousia^® 2 Fantasia and Texas 2 Earlygold maps and data from a third year of trait assessment on the Ferjalou Jalousia^® 2 Fantasia population. Comparative mapping allowed us to detect a candidate gene/QTL co-location. It involved a cDNA encoding a vacuolar H⁺-pyrophosphatase (PRUpe;Vp2) that energises solute accumulation, and QTLs for sucrose and soluble solid content. This preliminary result may be the first step in the future development of marker-assisted selection for peach fruit sucrose and soluble solid content.     

The potential of Prunus davidiana for introgression into peach [Prunus persica (L.) Batsch] assessed by comparative mapping

The potential for introgression of Prunus davidiana, a wild species related to peach, was evaluated with respect to problems of non-Mendelian segregation or suppressed recombination which often hamper breeding processes based on interspecific crosses. Three connected (F1, F2 and BC2) populations, derived from a cross between P. davidiana clone P1908 and the peach cultivar Summergrand were used. The intraspecific map of P. davidiana already established using the F1 progeny was complemented, and two interspecific maps, for the F2 and BC2 progenies, were built with a set of markers selected from the Prunus reference map. With the molecular data collected for the F2 map construction, regions with distorted marker segregation were detected on the genome; one third of all loci deviated significantly from the expected Mendelian ratios. However, some of these distorted segregations were probably not due to the interspecific cross. On linkage group 6, a skewed area under gametic selection was most likely influenced by the self-incompatibility gene of P. davidiana. Using anchor loci, a good colinearity between the three maps built and the Prunus reference map was demonstrated. Comparative mapping also revealed that homologous recombination occurred normally between P. davidiana and the Prunus persica genome. This confirmed the closeness of the two species. Higher recombination rates were generally observed between P. davidiana and P. persica than between Prunus amygdalus and P. persica. The consequences for plant breeding strategy are discussed. The three maps of the F1, F2 and BC2 progenies provide useful tools for QTL detection and marker-assisted selection, as well as for assessing the efficiency of the peach breeding scheme applied to introgress P. davidiana genes into peach cultivated varieties.     

Contribution of vegetative storage proteins to seasonal nitrogen variations in the young shoots of peach trees (Prunus persica L. Batsch)

Qualitative and quantitative variations in the level of two low molecular weight vegetative storage proteins (VSP 19 kDa and 16.5 kDa) in peach shoots were compared with annual variations in total nitrogen and total soluble proteins. Protein patterns were obtained by SDS-PAGE and silver staining on each of the 12 kinetic samples collected between October 1995 and November 1996. VSP 16.5 kDa and 19 kDa exhibited typical annual VSP variations in both parenchyma and phloem. In wood, VSP 16.5 kDa was only present in November. All N compounds tested were stored in the autumn and their levels fell in the spring. Parenchyma was the principal stem storage tissue for all N compounds tested, even if proteins were more often highly concentrated in phloem and even if wood was the major shoot constituent. In winter, the two VSP accounted for 13% of bark proteins and 11% of wood proteins. Their storage yield, given by the winter/summer (W/S) ratio was higher (18.5) than that of total proteins (4). Between August to March, i.e. during the storage phase, N fractions obtained from VSP (N3) and total soluble proteins minus VSP (N2) accounted, respectively, for only 3% and 21% of total N accumulation in the bark, the remainder being due to the fraction not extracted (N1). A marked drop in all N compound levels characterized the mobilization phase (March to April), particularly for N3 (-84% between March and April) which were mobilized slightly before other N compounds. Although N3 exhibited the best mobilization yield, it represented only 5% of the total N mobilized. So, in spite of a similarity between VSP and N annual variation patterns, there was no tight correlation between their contents in bark. N2 supplied a high proportion of the N used for spring regrowth (40%), but the larger share (55%) came from N1 which was probably made up of free amino acids. Very tight positive correlations have been observed between these two N fractions and the N status. The lower bark total N content measured in August (6.4 mg N g(-1 )DW) during the assimilation phase (April to August) was equal to the unavailable N fraction, and the bark N mobilization potential (between March and August) was estimated at 6.35 mg N g(-1) DW. VSP did not quantitatively represent the main stored N pool. But, because of their high W/S ratio and their early remobilization, they seemed to play an important role in spring regrowth initiation.     

Influence of nitrogen availability on shoot development in young peach trees [Prunus persica (L.) Batsch]

It is commonly stated that nitrogen (N) influences biomass accumulation in plants. For trees, however, a precise characterisation of shoot response to N and its impact on architecture is lacking. We attempted to study on the phytomer scale the effects of N limitation on shoot growth components, i.e. leaf emergence rate, final internode length and branching on the main and secondary axes of 1-year-old peach trees [Prunus persica (L.) Batsch]. Trees were grown on recycled nutrient solutions in which N concentration was restored once a week. We used two hydroponic set-ups in which weekly N availability, i.e. amount of N per tree, differed being either low (N1) or high (N2). Net N availability was defined weekly as the relative amount of N remaining in each set-up before solution replenishment. It declined with time and three periods of contrasting net N availability were identified. During these periods, leaf emergence rate and final internode length were similar on the main axis of N1 and N2 trees, so too was the distribution of secondary axes along the main axis. Secondary axes responded to N limitation by decreasing their growth components according to their position along the main axis. Differences were most important for basal secondary axes. Leaf emergence rate and final internode length responded similarly to N availability depending on axis order and position in the tree. It was concluded that N availability, particularly during the period of maximum growth of axes, influenced the shoot growth components and thus tree architecture.