Genetic relationships between diploid and allotetraploid cherry species (Prunus avium, Prunus × gondouinii and Prunus cerasus)

Promising varieties of sour cherry Prunus cerasus L. with a complex of fruit quality traits for growing in the southern Russia

Southern assortment of cherries does not quite meet the modern requirements of production. Many varieties are low-productive, not resistant to cherry leaf spot ( Coccomyces hiemalis ) and moniliosis ( Monilia cinerea ), small-fruited, with low taste qualities. However, new varieties have been created that have not been studied by the complex of consumer and commodity qualities of fruits. Thus, evaluation of new varieties for these traits is relevant. The aim of the research was to evaluate cherry varieties of different origin for commodity, biochemical, and consumer qualities of fruits. The research was carried out in the Kuban horticultural zone of the Krasnodar territory. Objects of the research were 9 varieties of sour cherry trees. Field and laboratory studies were conducted according to Program and methodology of varietal study of fruit, berry and nut crops (1999), Methodological instructions on chemical and technological variety testing of vegetable, fruit and berry crops for canning industry (1993). Statistical analysis was carried out according to B.A. Dospekhov (2014) and G.F. Lakin (1990). It was found that the average fruit weight of cherry varieties varied not significantly - from 2.72 to 6.45 g, which was confirmed by the coefficient of variation (23.3 %). Indicators of maximum and minimum fruit weight varied significantly in varieties, coefficients of variation were 27.2 and 29.7 %, respectively. The following cherry varieties with large fruits were identified: Timati, Igrushka, Duk Ivanovna, Duk Khodosa, Prizvaniya and Svetlaya. were distinguished. Cherry varieties with high sugar content in fruits were as follows: Feyа, Dzhusi Frut and Igrushka. Feyа, Duk Khodosa, Prizvanie, Svetlaya and Dzhusi Frut had fruits with low acidity; Feyа, Dzhusi Frut and Igrushka fruits were characterized by high content of soluble solids in fruits. Feyа, Igrushka and Duk Khodosa fruits had the highest content of vitamin C; Igrushka, Duk Khodosa, Prizvanie, Svetlaya and Dzhusi Frut were rich in Vitamin P; Duk Khodosa, Prizvanie, Dzhusi Frut and Duk Ivanovna had the largest anthocyanin content. Therefore, Igrushka and Duk Khodosa cherry varieties are recommended for growing in the southern Russia and breeding for improvement of fruit quality.

New insights into flowering date in Prunus: fine mapping of a major QTL in sweet cherry

Flowering date is an important trait in Prunus fruit species, especially for their adaptation in a global warming context. Numerous quantitative trait loci (QTLs) have been identified and a major one was previously located on LG4. The objectives of this study were to fine-map this QTL in sweet cherry, to identify robust candidate genes by using the new sweet cherry genome sequence of the cultivar 'Regina' and to define markers usable in marker-assisted selection (MAS). We performed QTL analyses on two populations derived from crosses using cultivars 'Regina' and 'Garnet' as parents. The first one (n = 117) was phenotyped over ten years, while the second one (n = 1386) was evaluated during three years. Kompetitive allele specific PCR (KASP) markers located within the QTL region on LG4 were developed and mapped within this region, consisting in the first fine mapping in sweet cherry. The QTL interval was narrowed from 380 kb to 68 kb and candidate genes were identified by using the genome sequence of 'Regina'. Their expression was analyzed from bud dormancy period to flowering in cultivars 'Regina' and 'Garnet'. Several genes, such as PavBOI-E3, PavSR45a and PavSAUR71, were differentially expressed in these two cultivars and could be then considered as promising candidate genes. Two KASP markers were validated using a population derived from a cross between cultivars 'Regina' and 'Lapins' and two collections, including landraces and modern cultivars. Thanks to the high synteny within the Prunus genus, these results give new insights into the control of flowering date in Prunus species and pave the way for the development of molecular breeding strategies.

Nutrients, Bioactive Compounds and Bioactivity: The Health Benefits of Sweet Cherries (Prunus avium L.)

Background:

Sweet cherries are one of the most appreciated fruits worldwide as well as one of the great sources of several active substances, as phytochemical compounds (carotenoids, serotonin, melatonin and phenolic compounds) as well as in nutritive compounds (sugars and organic acids). Accumulating research demonstrate that their supplementation in our daily diet can contradict oxidative stress, mitigating or even attenuating chronic diseases, as cancerous processes, antiinflammatory- related disorders, diabetes, and neurological and cardiovascular pathologies. Therefore, the aims of this review are to present an overview on the effects of sweet cherries as health promotors, giving emphasis to the health benefits of their bioactive compounds, particularly their antimicrobial, antioxidant, antidiabetic, anticancer, anti-neurodegeneration, anti-inflammatory and cardiovascular effects.

Methods:

Research and online content about sweet cherry fruits is reviewed. The information available has been read several times to avoid inconsistencies. In addition, according what we read, original figures were done and added to facilitate understanding and to enrich the paper.

Results:

In this review, a total of 202 original reports were used. In respect to health benefits, it is possible to confirm by several studies that, in fact, the consumption of sweet cherries has positive impacts in human health, owing to their wealthy and vast constitution, particularly in phenolic compounds, vitamins and carotenoids whose health properties were already documented.

Conclusion:

The findings of this review support the evidence that sweet cherries can be applied in pharmaceutical and food formulations, since they are able to diminish free radical species and proinflammatory markers, preventing and/ or ameliorating oxidative-stress disorders.

Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear (Pyrus bretschneideri)

The INDETERMINATE DOMAIN (IDD) gene family encodes hybrid transcription factors with distinct zinc finger motifs and appears to be found in all higher plant genomes. IDD genes have been identified throughout the genomes of the model plants Arabidopsis thaliana and Oryza sativa, and the functions of many members of this gene family have been studied. However, few studies have investigated the IDD gene family in Rosaceae species (among these species, a genome-wide identification of the IDD gene family has only been completed in Malus domestica). This study focuses on a comparative genomic analysis of the IDD gene family in five Rosaceae species (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Rubus occidentalis and Prunus avium). We identified a total of 68 IDD genes: 16 genes in Chinese white pear, 14 genes in F. vesca, 13 genes in Prunus mume, 14 genes in R. occidentalis and 11 genes in Prunus avium. The evolution of the IDD genes in these five Rosaceae species was revealed by constructing a phylogenetic tree, tracking gene duplication events, and performing a sliding window analysis and a conserved microsynteny analysis. The expression analysis of different organs showed that most of the pear IDD genes are found at a very high transcription level in fruits, flowers and buds. Based on our results with those obtained in previous research, we speculated that PbIDD2 and PbIDD8 might participate in flowering induction in pear. A temporal expression analysis showed that the expression patterns of PbIDD3 and PbIDD5 were completely opposite to the accumulation pattern of fruit lignin and the stone cell content. The results of the composite phylogenetic tree and expression pattern analysis indicated that PbIDD3 and PbIDD5 might be involved in the metabolism of lignin and secondary cell wall (SCW) formation. In summary, we provide basic information about the IDD genes in five Rosaceae species and thereby provide a theoretical basis for studying the function of these IDD genes.

Crop-to-wild hybridization in cherries-Empirical evidence from Prunus fruticosa

Crop cultivation can lead to genetic swamping of indigenous species and thus pose a serious threat for biodiversity. The rare Eurasian tetraploid shrub Prunus fruticosa (ground cherry) is suspected of hybridizing with cultivated allochthonous tetraploid P. cerasus and autochthonous diploid P. avium. Three Prunus taxa (447 individuals of P. fruticosa, 43 of P. cerasus and 73 of P. avium) and their hybrids (198 individuals) were evaluated using analysis of absolute genome size/ploidy level and multivariate morphometrics. Flow cytometry revealed considerable differentiation in absolute genome size at the tetraploid level (average 2C of P. fruticosa = 1.30 pg, average 2C of P. cerasus = 1.42 pg, i.e., a 9.2% difference). The combination of methods used allowed us to ascertain the frequency of hybrids occurring under natural conditions in Central Europe. The morphological evaluation of leaves was based upon distance-based morphometrics supplemented by elliptic Fourier analysis. The results provided substantial evidence for ongoing hybridization (hybrids occurred in 39.5% of P. fruticosa populations). We detected homoploid introgressive hybridization with alien P. cerasus at the tetraploid level. We also found previously overlooked but frequent triploid hybrids resulting from heteroploid hybridization with indigenous P. avium, which, however, probably represent only the F1 generation. Although both hybrids differ in ploidy, they cannot be distinguished using morphometrics. Hybrids are frequent and may endanger wild populations of genuine P. fruticosa via direct niche competition or, alternatively or in addition, via introgression at the homoploid level (i.e., genetic swamping). The cultivation of cherries thus substantially threatens the existence of genuine P. fruticosa.

Multiple Events of Allopolyploidy in the Evolution of the Racemose Lineages in Prunus (Rosaceae) Based on Integrated Evidence from Nuclear and Plastid Data

Prunus is an economically important genus well-known for cherries, plums, almonds, and peaches. The genus can be divided into three major groups based on inflorescence structure and ploidy levels: (1) the diploid solitary-flower group (subg. Prunus, Amygdalus and Emplectocladus); (2) the diploid corymbose group (subg. Cerasus); and (3) the polyploid racemose group (subg. Padus, subg. Laurocerasus, and the Maddenia group). The plastid phylogeny suggests three major clades within Prunus: Prunus-Amygdalus-Emplectocladus, Cerasus, and Laurocerasus-Padus-Maddenia, while nuclear ITS trees resolve Laurocerasus-Padus-Maddenia as a paraphyletic group. In this study, we employed sequences of the nuclear loci At103, ITS and s6pdh to explore the origins and evolution of the racemose group. Two copies of the At103 gene were identified in Prunus. One copy is found in Prunus species with solitary and corymbose inflorescences as well as those with racemose inflorescences, while the second copy (II) is present only in taxa with racemose inflorescences. The copy I sequences suggest that all racemose species form a paraphyletic group composed of four clades, each of which is definable by morphology and geography. The tree from the combined At103 and ITS sequences and the tree based on the single gene s6pdh had similar general topologies to the tree based on the copy I sequences of At103, with the combined At103-ITS tree showing stronger support in most clades. The nuclear At103, ITS and s6pdh data in conjunction with the plastid data are consistent with the hypothesis that multiple independent allopolyploidy events contributed to the origins of the racemose group. A widespread species or lineage may have served as the maternal parent for multiple hybridizations involving several paternal lineages. This hypothesis of the complex evolutionary history of the racemose group in Prunus reflects a major step forward in our understanding of diversification of the genus and has important implications for the interpretation of its phylogeny, evolution, and classification.

Genetic diversity, linkage disequilibrium, population structure and construction of a core collection of Prunus avium L. landraces and bred cultivars

BACKGROUND

Depiction of the genetic diversity, linkage disequilibrium (LD) and population structure is essential for the efficient organization and exploitation of genetic resources. The objectives of this study were to (i) to evaluate the genetic diversity and to detect the patterns of LD, (ii) to estimate the levels of population structure and (iii) to identify a 'core collection' suitable for association genetic studies in sweet cherry.

RESULTS

A total of 210 genotypes including modern cultivars and landraces from 16 countries were genotyped using the RosBREED cherry 6 K SNP array v1. Two groups, mainly bred cultivars and landraces, respectively, were first detected using STRUCTURE software and confirmed by Principal Coordinate Analysis (PCoA). Further analyses identified nine subgroups using STRUCTURE and Discriminant Analysis of Principal Components (DAPC). Several sub-groups correspond to different eco-geographic regions of landraces distribution. Linkage disequilibrium was evaluated showing lower values than in peach, the reference Prunus species. A 'core collection' containing 156 accessions was selected using the maximum length sub tree method.

CONCLUSION

The present study constitutes the first population genetics analysis in cultivated sweet cherry using a medium-density SNP (single nucleotide polymorphism) marker array. We provided estimations of linkage disequilibrium, genetic structure and the definition of a first INRA's Sweet Cherry core collection useful for breeding programs, germplasm management and association genetics studies.

Genetic relationships among cherry species with transferability of simple sequence repeat loci

Sweet and sour cherries are two economically important species in the world. The capability to distinguish among cherry genotypes in breeding, cultivation and germplasm collection is extremely important for scientific as well as economic reasons. In the present research, sixteen simple sequences repeat (SSR) loci were used to estimate the relationships among sweet, sour, duke and wild cherries. All of the SSR markers showed high transferability across the studied species that allowed us to study genetic diversity in them. Totally 96 alleles were generated with SSR loci, of which 93 were found polymorphic with 97.57 % polymorphism. Values of genetic similarity between genotypes varied from 0.16 to 0.97 which indicated high level of genetic diversity. On the basis of their genetic similarities, SSR analysis allowed to group the genotypes into three main clusters according to their species. These results have an important implication for cherry germplasm characterization, improvement, and conservation.

Quality evaluation of sour and duke cherries cultivated in south-west Europe

BACKGROUND

The results of many studies describing sour cherry polyphenols and their positive effects on human health have been reported. However, there are no detailed studies concerning the physical quality of fresh fruits of sour and duke cherry.

RESULTS

Several physical, chemical and colour fruit-characteristics of 10 sour and duke cherry cultivars cultivated for industrial use in south-west Europe were investigated during a 3-year (2008-2010) period. Some of the cultivars showed distinctive and interesting agronomical characters, such as low susceptibility to fruit cracking and high soluble solids and total polyphenol levels. This was the case with the duke cherry cultivar Guindo Garrafal Negro. Its fruits were quite sweet (18.49°Brix), resistant to cracking (6.34%) and rich in polyphenols (17.16 g gallic acid kg(-1) dry weight). Other relevant cherry cultivars were Guindo Tomatillo and Seixas, which had large and fleshy fruits (4.71 and 3.69 cm(3), respectively) and Guindo Silvestre, for which the lowest fruit cracking values (3.12%) were recorded.

CONCLUSIONS

Sour and duke cherries are rich in healthy compounds such as polyphenols. Studies including the physical, chemical and colour properties of sour and duke cherry fruits are very interesting to engineers in the design of equipment for harvesting and post-harvest technology.

Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry

High-throughput genome scans are important tools for genetic studies and breeding applications. Here, a 6K SNP array for use with the Illumina Infinium® system was developed for diploid sweet cherry (Prunus avium) and allotetraploid sour cherry (P. cerasus). This effort was led by RosBREED, a community initiative to enable marker-assisted breeding for rosaceous crops. Next-generation sequencing in diverse breeding germplasm provided 25 billion basepairs (Gb) of cherry DNA sequence from which were identified genome-wide SNPs for sweet cherry and for the two sour cherry subgenomes derived from sweet cherry (avium subgenome) and P. fruticosa (fruticosa subgenome). Anchoring to the peach genome sequence, recently released by the International Peach Genome Initiative, predicted relative physical locations of the 1.9 million putative SNPs detected, preliminarily filtered to 368,943 SNPs. Further filtering was guided by results of a 144-SNP subset examined with the Illumina GoldenGate® assay on 160 accessions. A 6K Infinium® II array was designed with SNPs evenly spaced genetically across the sweet and sour cherry genomes. SNPs were developed for each sour cherry subgenome by using minor allele frequency in the sour cherry detection panel to enrich for subgenome-specific SNPs followed by targeting to either subgenome according to alleles observed in sweet cherry. The array was evaluated using panels of sweet (n = 269) and sour (n = 330) cherry breeding germplasm. Approximately one third of array SNPs were informative for each crop. A total of 1825 polymorphic SNPs were verified in sweet cherry, 13% of these originally developed for sour cherry. Allele dosage was resolved for 2058 polymorphic SNPs in sour cherry, one third of these being originally developed for sweet cherry. This publicly available genomics resource represents a significant advance in cherry genome-scanning capability that will accelerate marker-locus-trait association discovery, genome structure investigation, and genetic diversity assessment in this diploid-tetraploid crop group.

From forest to field: perennial fruit crop domestication

PREMISE OF THE STUDY

Archaeological and genetic analyses of seed-propagated annual crops have greatly advanced our understanding of plant domestication and evolution. Comparatively little is known about perennial plant domestication, a relevant topic for understanding how genes and genomes evolve in long-lived species, and how perennials respond to selection pressures operating on a relatively short time scale. Here, we focus on long-lived perennial crops (mainly trees and other woody plants) grown for their fruits.

KEY RESULTS

We reviewed (1) the basic biology of long-lived perennials, setting the stage for perennial domestication by considering how these species evolve in nature; (2) the suite of morphological features associated with perennial fruit crops undergoing domestication; (3) the origins and evolution of domesticated perennials grown for their fruits; and (4) the genetic basis of domestication in perennial fruit crops.

CONCLUSIONS

Long-lived perennials have lengthy juvenile phases, extensive outcrossing, widespread hybridization, and limited population structure. Under domestication, these features, combined with clonal propagation, multiple origins, and ongoing crop-wild gene flow, contribute to mild domestication bottlenecks in perennial fruit crops. Morphological changes under domestication have many parallels to annual crops, but with key differences for mating system evolution and mode of reproduction. Quantitative trait loci associated with domestication traits in perennials are mainly of minor effect and may not be stable across years. Future studies that take advantage of genomic approaches and consider demographic history will elucidate the genetics of agriculturally and ecologically important traits in perennial fruit crops and their wild relatives.