Genetic variation, population structure and linkage disequilibrium in peach commercial varieties

11 páginas, 5 figuras, 2 tablas.[Background]: Peach [Prunus persica (L.) Batsch] is one of the most economically important fruit crops that, due to its genetic and biological characteristics (small genome size, taxonomic proximity to other important species and short juvenile period), has become a model plant in genomic studies of fruit trees. Our aim was an in-depth study of the extent, distribution and structure of peach genetic variation in North American and European commercial varieties as well as old Spanish varieties and several founders used in the early USA peach breeding programmes. For this we genotyped 224 peach cultivars using 50 SSRs evenly distributed along the 8 linkage groups of the Prunus reference map. [Results]: Genetic distance analysis based on SSRs divided the peach cultivars in three main groups based mainly on their fruit characteristics: melting flesh peaches, melting flesh nectarines and non-melting varieties. Whereas non-melting flesh peaches had a higher number of alleles than melting peaches and nectarines, they were more homozygous. With some exceptions ('Admiral Dewey', 'Early Crawford' and 'Chinese Cling'), the founder US cultivars clustered together with the commercial melting peaches, indicating that their germplasm is well represented in modern cultivars. Population structure analysis showed a similar subdivision of the sample into subpopulations. Linkage disequilibrium (LD) analysis in three unstructured, or barely structured, subpopulations revealed a high level of LD conservation in peach extending up to 13-15 cM. [Conclusions]: Using a much larger set of SSRs, our results confirm previous observations on peach variability and population structure and provide additional tools for breeding and breeders' rights enforcement. SSR data are also used for the estimation of marker mutation rates and allow pedigree inferences, particularly with founder genotypes of the currently grown cultivars, which are useful to understand the evolution of peach as a crop. Results on LD conservation can be explained by the self-pollinating nature of peach cultivated germplasm and by a bottleneck that occurred at the beginning of modern breeding practices. High LD suggests that the development of whole-genome scanning approaches is suitable for genetic studies of agronomically important traits in peach.This research was funded in part by Project AGL2006-07767/AGR and by the Consolider-Ingenio 2010 Program (CSD2007-00036), both from the Spanish Ministry of Science and Innovation.Peer reviewe

"Biographie und Geschlecht": Workshop am 04.07.2011 an der Friedrich-Schiller-Universität in Jena

"Die Herausforderung, die Lebensgeschichten von Frauen und Männern mit biographischen Methoden zu erforschen, stand im Mittelpunkt des ersten Workshops 'Biographie und Geschlecht' am 04.07.2011 in Jena. Organisiert wurde der Workshop vom Lehrstuhl für Geschlechtergeschichte der Friedrich-Schiller-Universität Jena. Sein Ziel bestand darin, über die methodologischen und konzeptionellen Erfordernisse, Problemlagen sowie Lösungsvorschläge zum Thema 'Biographie und Geschlecht' zu informieren und über die interdisziplinären Vorträge zum Austausch darüber beizutragen, wie die neuere Biographieforschung und die Geschlechterforschung miteinander zu verbinden sind. Die neun Vorträge zeigten schnell die Brisanz der Thematik und die Relevanz biographie-analytischer Zugänge zur Erforschung von historischen Geschlechterthemen in differenten Fachbereichen." (Autorenreferat)"The challenge of exploring the life stories of women and men using biographical methods was the focus of the first workshop on Biography and Gender in Jena on 4 July 2011. The workshop was organised by the Chair for Gender History at the University of Jena. The aim of the workshop was to provide information on the methodological and conceptual requirements, problems and solutions to issues raised by biography and gender, and, inspired by the interdisciplinary lectures, to contribute to sharing ideas about how recent biographical research and gender studies can be combined. The nine papers quickly showed how explosive the issue is and how relevant analytical approaches to biography are to historical gender research in different fields." (author's abstract

Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm

Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium® SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ∼75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs.The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species

Genetic analysis for physical nut traits in almond

Peer ReviewedPublishe

Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers

12 pages, 5 tables, 6 figures, additional 3 files.Background: Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable among the important crop genera within the family [e.g. Malus (apple), Fragaria (strawberry), and Prunus (peach, cherry, apricot and almond)]. The lack of molecular markers and comparative whole genome sequence analysis for this family severely hampers crop improvement efforts as well as QTL confirmation and validation studies. Results: We identified a set of 3,818 rosaceaous unigenes comprised of two or more ESTs that correspond to single copy Arabidopsis genes. From this Rosaceae Conserved Orthologous Set (RosCOS), 1039 were selected from which 857 were used for the development of intron-flanking primers and allele amplification. This led to successful amplification and subsequent mapping of 613 RosCOS onto the Prunus TxE reference map resulting in a genome-wide coverage of 0.67 to 1.06 gene-based markers per cM per linkage group. Furthermore, the RosCOS primers showed amplification success rates from 23 to 100% across the family indicating that a substantial part of the RosCOS primers can be directly employed in other less studied rosaceaous crops. Comparisons of the genetic map positions of the RosCOS with the physical locations of the orthologs in the Populus trichocarpa genome identified regions of colinearity between the genomes of Prunus-Rosaceae and Populus-Salicaceae. Conclusion: Conserved orthologous genes are extremely useful for the analysis of genome evolution among closely and distantly related species. The results presented in this study demonstrate the considerable potential of the mapped Prunus RosCOS for genome-wide marker employment and comparative whole genome studies within the Rosaceae family. Moreover, these markers will also function as useful anchor points for the genome sequencing efforts currently ongoing in this family as well as for comparative QTL analyses.This work is supported by USDA-NRI grants 2008-02259 and 2005-00743. AC was also supported by funds from the Department of Horticulture and Crop Science, The Ohio State University.Peer reviewe

High-density mapping suggests cytoplasmic male sterility with two restorer genes in almond x peach progenies

Peach (Prunus persica) and almond (Prunus dulcis) are two sexually compatible species that produce fertile offspring. Almond, a highly polymorphic species, is a potential source of new genes for peach that has a strongly eroded gene pool. Here we describe the genetics of a male sterile phenotype that segregated in two almond (‘Texas’) 3 peach (‘Earlygold’) progenies: an F2 (T3E) and a backcross one (T1E) to the ‘Earlygold’ parent. High-density maps were developed using a 9k peach SNP chip and 135 simple-sequence repeats. Three highly syntenic and collinear maps were obtained: one for the F2 (T3E) and two for the backcross, T1E (for the hybrid) and E (for ‘Earlygold’). A major reduction of recombination was observed in the interspecific maps (T3E and T1E) compared to the intraspecific parent (E). The E map also had extensive monomorphic genomic regions suggesting the presence of large DNA fragments identical by descent. Our data for the male sterility character were consistent with the existence of cytoplasmic male sterility, where individuals having the almond cytoplasm required the almond allele in at least one of two independent restorer genes, Rf1 and Rf2, to be fertile. The restorer genes were located in a 3.4 Mbp fragment of linkage group 2 (Rf1) and 1.4 Mbp of linkage group 6 (Rf2). Both fragments contained several genes coding for pentatricopeptide proteins, demonstrated to be responsible for restoring fertility in other species. The implications of these results for using almond as a source of novel variability in peach are discussed.info:eu-repo/semantics/publishedVersio

Characterization of Japanese Plum (Prunus salicina) PsMYB10 Alleles Reveals Structural Variation and Polymorphisms Correlating With Fruit Skin Color

The red to blue hue of plant organs is caused due to anthocyanins, which are water-soluble flavonoid pigments. The accumulation of these pigments is regulated by a complex of R2R3-MYB transcription factors (TFs), basic-helix-loop-helix (bHLH), and WD-repeat (WDR) proteins (MBW complex). In Rosaceae species, R2R3-MYBs, particularly MYB10 genes, are responsible for part of the natural variation in anthocyanin colors. Japanese plum cultivars, which are hybrids of Prunus salicina, have high variability in the color hue and pattern, going from yellow-green to red and purple-blue, probably as a result of the interspecific hybridization origin of the crop. Because of such variability, Japanese plum can be considered as an excellent model to study the color determination in Rosaceae fruit tree species. Here, we cloned and characterized the alleles of the PsMYB10 genes in the linkage group LG3 region where quantitative trait loci (QTLs) for the organ color have been mapped to other Prunus species. Allele segregation in biparental populations as well as in a panel of varieties, combined with the whole-genome sequence of two varieties with contrasting fruit color, allowed the organization of the MYB10 alleles into haplotypes. With the help of this strategy, alleles were assigned to genes and at least three copies of PsMYB10.1 were identified in some varieties. In total, we observed six haplotypes, which were able to characterize 91.36% of the cultivars. In addition, two alleles of PsMYB10.1 were found to be highly associated with anthocyanin and anthocyanin-less skin. Their expression during the fruit development confirms their role in the fruit skin coloration. Here, we provide a highly efficient molecular marker for the early selection of colored or non-colored fruits in Japanese plum breeding programs.info:eu-repo/semantics/publishedVersio

Survey of over 4, 500 monumental olive trees preserved on-farm in the northeast Iberian Peninsula, their genotyping and characterization

Inventorying, characterising and conserving on-farm ancient olive trees is a priority for safeguarding their genetic, natural and agricultural value and for protecting ancient genotypes threatened with extinction. In the “Taula del Sénia” (M-TdS) area (northeast Iberian Peninsula) a highly important cultural landscape has been preserved, in which the olive groves play an outstanding social and economic role: the ancient olive trees, sustained by many local farmers, constitute a living heritage and provide a clear example of High Nature Value (HNV). A total of 4526 ancient productive olive trees, with a trunk circumference (PBH) larger than 3.5 m, were inventoried and their spatial localization and biometric measurements were collected. 41 olive trees have shown the highest category in monumentality (PBH >8.1 m). The outstanding trees might be 634–1082 years old. The endocarp morphology of a representative sample of the most ancient trees from this settlement resulted in 14 different profiles. The ancient trees genotyped, through eight simple sequence repeat (SSR) markers, revealed 43 SSR profiles. The use of SSR enabled us to verify that most of the trees (98%) belong to the local cv. ‘Farga’, a male sterile variety with a rare chlorotype, only a few trees corresponded with other local varieties, ‘Morrut’, ‘Canetera’ and ‘Sevillenca’, and ten hitherto unidentified genotypes were distinguished, some with chloroplast lineages different from the ‘Farga’ type. The M-TdS area holds a unique living and exploitable heritage with the highest concentration of ancient olive trees worldwide. On-farm conservation of this germplasm by the community of local growers is enabling preservation of this important source of genetic variation, potentially holding traits of resilience and adaptation to adverse soil and climatic conditions, demonstrated by the survival of these trees over the centuries. Farmers have undertaken initiatives to valorize the olive oil deriving from these M-TdS trees.info:eu-repo/semantics/acceptedVersio

Identification of a major QTL for Xanthomonas arboricola pv. pruni resistance in apricot

Xanthomonas arboricola pv. pruni causes bacterial spot of stone fruit resulting in severe yield losses in apricot production systems. Present on all continents, the pathogen is regulated in Europe as a quarantine organism. Host resistance is an important component of integrated pest management; however, little work has been done describing resistance against X. arboricola pv. pruni. In this study, an apricot population derived from the cross “Harostar” × “Rouge de Mauves” was used to construct two parental genetic maps and to perform a quantitative trait locus analysis of resistance to X. arboricola pv. pruni. A population of 101 F1 individuals was inoculated twice for two consecutive years in a quarantine greenhouse with a mixture of bacterial strains, and disease incidence and resistance index data were collected. A major QTL for disease incidence and resistance index accounting respectively for 53 % (LOD score of 15.43) and 46 % (LOD score of 12.26) of the phenotypic variation was identified at the same position on linkage group 5 of “Rouge de Mauves.” Microsatellite marker UDAp-452 co-segregated with the resistance, and two flanking microsatellites, namely BPPCT037 and BPPCT038A, were identified. When dividing the population according to the alleles of UDAp-452, the subgroup with unfavorable allele had a disease incidence of 32.6 % whereas the group with favorable allele had a disease incidence of 21 %, leading to a reduction of 35.6 % in disease incidence. This study is a first step towards the marker-assisted breeding of new apricot varieties with an increased tolerance to X. arboricola pv. pruni

Genomic characterization of putative allergen genes in peach/almond and their synteny with apple

<p>Abstract</p> <p>Background</p> <p>Fruits from several species of the Rosaceae family are reported to cause allergic reactions in certain populations. The allergens identified belong to mainly four protein families: pathogenesis related 10 proteins, thaumatin-like proteins, lipid transfer proteins and profilins. These families of putative allergen genes in apple (<it>Mal d 1 </it>to <it>4</it>) have been mapped on linkage maps and subsequent genetic study on allelic diversity and hypoallergenic traits has been carried out recently. In peach (<it>Prunus persica</it>), these allergen gene families are denoted as <it>Pru p 1 </it>to <it>4 </it>and for almond (<it>Prunus dulcis</it>)<it>Pru du 1 </it>to <it>4</it>. Genetic analysis using current molecular tools may be helpful to establish the cause of allergenicity differences observed among different peach cultivars. This study was to characterize putative peach allergen genes for their genomic sequences and linkage map positions, and to compare them with previously characterized homologous genes in apple (<it>Malus domestica</it>).</p> <p>Results</p> <p>Eight <it>Pru p/du 1 </it>genes were identified, four of which were new. All the <it>Pru p/du 1 </it>genes were mapped in a single bin on the top of linkage group 1 (G1). Five <it>Pru p/du 2 </it>genes were mapped on four different linkage groups, two very similar <it>Pru p/du 2.01 </it>genes (<it>A </it>and <it>B</it>) were on G3, <it>Pru p/du 2.02 </it>on G7,<it>Pru p/du 2.03 </it>on G8 and <it>Pru p/du 2.04 </it>on G1. There were differences in the intron and exon structure in these <it>Pru p/du 2 </it>genes and in their amino acid composition. Three <it>Pru p/du 3 </it>genes (3.01–3.03) containing an intron and a mini exon of 10 nt were mapped in a cluster on G6. Two <it>Pru p/du 4 </it>genes (<it>Pru p/du 4.01 </it>and <it>4.02</it>) were located on G1 and G7, respectively. The <it>Pru p/du 1 </it>cluster on G1 aligned to the <it>Mal d 1 </it>clusters on LG16; <it>Pru p/du 2.01A </it>and <it>B </it>on G3 to <it>Mal d 2.01A </it>and <it>B </it>on LG9; the <it>Pru p/du 3 </it>cluster on G6 to <it>Mal d 3.01 </it>on LG12; <it>Pru p/du 4.01 </it>on G1 to <it>Mal d 4.03 </it>on LG2; and <it>Pru p/du 4.02 </it>on G7 to <it>Mal d 4.02 </it>on LG2.</p> <p>Conclusion</p> <p>A total of 18 putative peach/almond allergen genes have been mapped on five linkage groups. Their positions confirm the high macro-synteny between peach/almond and apple. The insight gained will help to identify key genes causing differences in allergenicity among different cultivars of peach and other <it>Prunus </it>species.</p