[Show abstract][Hide abstract] ABSTRACT: Since its release the high quality peach genome sequence has fostered studies on genetic diversity, domestication and crop improvement in Prunus and related species being a central resource for comparative genomics. To improve its chromosome-scale assembly and genome annotation we performed further analyses. Extensive mapping data allowed the improvement of Peach v2.0 assembly in term of fraction of mapped (99.2%) and orientated (97.9%) sequences and correction of misassembly issues (about 12.2 Mb of wrongly located sequences). Accuracy and contiguity of Peach v2.0 were improved as well: 859 SNPs and 1,347 Indels were corrected and 212 gaps were closed. As a result the contiguity of Peach v2.0 improved of 19.5 % with a contig L50 of 255.4 kb (previously 214.2 kb) and a contig N50 of 250 (previously 294). The repeats annotation was improved as well including low copy repeats and the complete sequence and location of 1,157 non autonomous Helitrons. New gene prediction and annotation were improved using transcript assemblies obtained from 2.2 billion of peach RNA seq reads from different tissues and organs. In total 28,804 protein-coding genes were predicted in Peach v2.1 annotation, 940 more than those predicted in Peach v1.0. An increased number of transcripts (49,110 vs 28,689) were observed in Peach v2.1 with an average of 1.7 transcripts per locus. The new peach release with improved assembly and annotation will be a pivotal resource for comparative genomics in plant kingdom and will burst studies for bridging the gap between genomics and breeding in Prunus and related species.
[Show abstract][Hide abstract] ABSTRACT: Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs.
[Show abstract][Hide abstract] ABSTRACT: With the increasing affordability of SNP (single nucleotide polymorphisms) genotyping, genome-wide predictions have become popular in plant species, including fruit trees. In the framework of the Fruitbreedomics FP7 project, data on three continuous phenotypic traits (fruit weight, sugar content, and titrable acidity) for 1083 trees from 11 peach populations (size range: 43 – 131) were available. Multiple measurements (from 2 to 6) over different years were recorded on each tree. All peach populations were genotyped with the 9K peach SNP-chip. Missing SNP genotypes were imputed based on linkage disequilibrium and allele frequency as in Beagle; afterwards, SNPs with MAF < 1% were removed. Repeated phenotypic measurements were analysed in a repeatability model that included the effects of year, additive genetic and permanent environment: y = μ + year + a + pe + e. Var(a) = Gσa2, Var(pe) = Iσpe2, Var(e)=Iσe2, where G is the genomic relationship matrix and I is the identity matrix. The model was run in a 5-fold cross-validation scheme (4/5 of the data for training, 1/5 for validation) repeated 100 times. From each replicate, heritability (Var(a)/Var(y)), repeatability ((Var(a)+Var(pe))/Var(y)) and predictive ability (correlation between observed and predicted -μ + year + a + pe- phenotypes) were obtained. Initial results showed that heritability, repeatability and predictive ability ranged between 0.125 – 0.80, 0.13 – 0.83 and 0.21 – 0. 82 for fruit weight; between 0.11 – 0.66, 0.18 – 0.70 and 0.68 – 0.82 for sugar content; between 0.29 – 0.75, 0.43 – 0.86 and 0.54 – 0 .76 for titrable acidity. Genome-enabled predictions appeared to be variable both trait- and population-wise, but certainly hold the potential of being a very effective tool in peach breeding.
[Show abstract][Hide abstract] ABSTRACT: The aim of the present study was to analyse the genetic diversity and determine the population structure and the phylogenetic relationships of 123 peach accessions from the germplasm bank of the 'MAS.PES' breeding programme in order to support future research on breeding activities. Fifteen SSR markers were selected on the basis of a previous study showing a high level of allelic diversity. The population structure was analysed using the software STRUCTURE, adopting the admixture model of ancestry, and the phylogenetic analysis was performed by the DARWIN software, using the neighbour-joining method. The three clusters obtained by analysis of population structure were in accordance with the analysis performed by the software DARWIN. The fifteen studied SSRs amplified 115 alleles, with an average of 7.7 alleles per locus. The most informative markers were BPPCT001, UDP98-412 and EPPCU5176. The observed heterozygosity demonstrates an average of 0.4 alleles per locus, lower than the expected heterozygosity. The fixation index (F) values were positive in all loci, with an average of 0.3 alleles per locus. This result confirms the presence of inbreeding in the evaluated accession, as commonly found in cultivated peach.
No preview · Article · May 2015 · Acta horticulturae
[Show abstract][Hide abstract] ABSTRACT: Plant responses to herbivore insects involve direct and indirect defense with the production of signal molecules including jasmonic acid (JA) and its derivatives (e.g. methyl jasmonate, MeJA). In maize (Zea mays), root feeding by Diabrotica virgifera larvae activates an indirect defense mechanism, through enthomopathogenic nematodes that are recruited after Terpene Synthase 23 (tps23) upregulation and (E)-β-caryophyllene root emission. In order to gain insight into the correlation between JA signaling and response to Diabrotica attack, we analyzed tps23 expression and protein profiles in maize roots in response to MeJA treatment and insect infestation. Similar to herbivore feeding, MeJA treatment was found to increase tps23 transcript accumulation, with consistent variations for both treatments in maize lines differing in (E)-β-caryophyllene production. Analysis of root protein profiles showed specific alterations leading to the identification of three proteins that were induced by MeJA treatment. We focused on a peroxidase-like protein (Px-like) showing that the corresponding transcripts accumulated in all tested lines.Results show that exogenous application of MeJA upregulates tps23 expression and specifically alters protein patterns in maize roots. Parallel effects on tps23 transcript accumulation were observed upon hormone exposure and insect infestation in different maize lines. In contrast, Px-like transcript profiling showed differences between treatments. These results support the possible involvement of MeJA in mediating the upregulation of tps23 in response to Diabrotica attack.
Full-text · Article · Mar 2015 · Journal of Plant Physiology
[Show abstract][Hide abstract] ABSTRACT: Fruit weight is a quantitative trait influenced by the combined action of several genes and environmental factors. Knowledge of the quantitative trait loci (QTLs) associated with fruit weight and size is a priority to support breeding programmes in peach (Prunus persica (L.) Batsch) because of commercial interest in larger fruits. To this end, we built a genetic map of an F2 progeny of 117 individuals from the cross PI91459 (‘NJ Weeping’) 9 ‘Bounty’ using a single nucleotide polymorphism (SNP) genotyping array for peach (9K SNP array v1). Data for fruit weight, height, width, and depth were recorded for the progeny and both parents over 2 years (2011, 2012). Correlations between the traits fruit weight and size were positive and significant for both years. A SNP map was constructed comprising 1,148 markers distributed over eight linkage groups. The map spans 536.6 cM with an average distance between markers of 0.52 cM, covering 93.6 % of the physical length of the peach genome, thus representing an ideal basis for QTL mapping. QTL analysis led to the identification of a total of 28 QTLs for the considered traits, eleven of which remained stable in both years. We also observed clusters of QTLs, some of which were mapped for the first time, while others correspond to loci previously identified in different progenies and following different approaches.
Full-text · Article · Feb 2015 · Molecular Breeding
[Show abstract][Hide abstract] ABSTRACT: Triticum monococcum (genome A(m)) and Triticum urartu (genome A(u)) are diploid wheats with the first having been domesticated in the Neolithic Era and the second being a wild species. In a germplasm collection rare wild T. urartu lines with the presence of T. monococcum alleles were found. This stimulated our interest to develop interspecific introgression lines of T. urartu in T. monococcum, a breeding tool currently implemented in several crop species. Moreover the experiments reported were designed to reveal the existence in nature of A(m)/A(u) intermediate forms and to clarify if the two species are at least marginally sexually compatible. From hand-made interspecific crosses, almost sterile F1 plants were obtained when the seed bearing parent was T. monococcum. A high degree of fertility was however evident in some advanced generations, particularly when T. urartu donors were molecularly more related to T. monococcum. Analysis of the marker populations demonstrated chromosome pairing and recombination in F1 hybrid plants. Forty-six introgression lines were developed using a line of T. monococcum with several positive agronomic traits as a recurrent parent. Microsatellite markers were tested on A(u) and A(m) genomes, ordered in a T. monococcum molecular map and used to characterize the exotic DNA fragments present in each introgression line. In a test based on 28 interspecific introgression lines, the existence of genetic variation associated with T. urartu chromosome fragments was proven for the seed content of carotenoids, lutein, β-cryptoxanthin and zinc. The molecular state of available introgression lines is summarized.
Full-text · Article · Aug 2014 · G3-Genes Genomes Genetics
[Show abstract][Hide abstract] ABSTRACT: Drought is one of the most important abiotic stresses, constraining crop production seriously. The Dehydration Responsive Element Binding proteins (DREBs) are important plant- specific transcription factors that respond to various abiotic stresses and consequently induce abiotic stress-related genes that impart stress endurance in plants. Wild species are naturally exposed to various abiotic stresses and potentially harbor suitable alleles through natural selection. In this study we isolated and characterized Dreb2 from T. urartu (GenBank: KF731664), Ae. spletoides (GenBank: KF731665) and Ae. tauschii (GenBank: KF731663), the A, B and D genome ancestors of bread wheat, respectively. Analysis of over 1.3kb upstream region of the gene revealed the presence of several conserved cis-acting regulatory elements including ABA-responsive elements, low temperature responsive elements, and several light and environmental signaling related motifs potentially vindicate Dreb2 responses to environmental signals. Moreover, the gene exhibited an alternative splicing, conserved among orthologous genes in grasses, producing a non-functional isoform due to splicing in an exon resulted a frame-shift creating an early stop codon before the functional domain. The expression analysis of Dreb2 under normal and different levels of dehydration stress conditions indicated that the two active spliced isoforms are upregulated when the plant exposed to drought stress whereas the non-functional isoform is downregulated in severe drought.
[Show abstract][Hide abstract] ABSTRACT: Brown rot (BR) caused by Monilinia spp. leads to significant post-harvest losses in stone fruit production, especially peach. Previous genetic analyses in peach progenies suggested that BR resistance segregates as a quantitative trait. In order to uncover genomic regions associated with this trait and identify molecular markers for assisted selection (MAS) in peach, an F1 progeny from the cross “Contender” (C, resistant) × “Elegant Lady” (EL, susceptible) was chosen for quantitative trait loci (QTL) analysis. Over two phenotyping seasons, skin (SK) and flesh (FL) artificial infections were performed on fruits using a Monilinia fructigena isolate. For each treatment, infection frequency (if) and average rot diameter (rd) were scored. Significant seasonal and intertrait correlations were found. Maturity date (MD) was significantly correlated with disease impact. Sixty-three simple sequence repeats (SSRs) plus 26 single-nucleotide polymorphism (SNP) markers were used to genotype the C × EL population and to construct a linkage map. C × EL map included the eight Prunus linkage groups (LG), spanning 572.92 cM, with an average interval distance of 6.9 cM, covering 78.73 % of the peach genome (V1.0). Multiple QTL mapping analysis including MD trait as covariate uncovered three genomic regions associated with BR resistance in the two phenotyping seasons: one containing QTLs for SK resistance traits near M1a (LG C × EL-2, R
2 = 13.1–31.5 %) and EPPISF032 (LG C × EL-4, R
2 = 11–14 %) and the others containing QTLs for FL resistance, near markers SNP_IGA_320761 and SNP_IGA_321601 (LG3, R
2 = 3.0–11.0 %). These results suggest that in the C × EL F1 progeny, skin resistance to fungal penetration and flesh resistance to rot spread are distinguishable mechanisms constituting BR resistance trait, associated with different genomic regions. Discovered QTLs and their associated markers could assist selection of new cultivars with enhanced resistance to Monilinia spp. in fruit.
Full-text · Article · Jun 2014 · Tree Genetics & Genomes
[Show abstract][Hide abstract] ABSTRACT: Nectarines play a key role in peach industry; the fuzzless skin has implications for consumer acceptance. The peach/nectarine (G/g) trait was described as monogenic and previously mapped on chromosome 5. Here, the position of the G locus was delimited within a 1.1 cM interval (635 kb) based on linkage analysis of an F2 progeny from the cross 'Contender' (C, peach) x 'Ambra' (A, nectarine). Careful inspection of the genes annotated in the corresponding genomic sequence (Peach v1.0), coupled with variant discovery, led to the identification of MYB gene PpeMYB25 as a candidate for trichome formation on fruit skin. Analysis of genomic re-sequencing data from five peach/nectarine accessions pointed to the insertion of a LTR retroelement in exon 3 of the PpeMYB25 gene as the cause of the recessive glabrous phenotype. A functional marker (indelG) developed on the LTR insertion cosegregated with the trait in the CxA F2 progeny and was validated on a broad panel of genotypes, including all known putative donors of the nectarine trait. This marker was shown to efficiently discriminate between peach and nectarine plants, indicating that a unique mutational event gave rise to the nectarine trait and providing a useful diagnostic tool for early seedling selection in peach breeding programs.
[Show abstract][Hide abstract] ABSTRACT: Tillering, or the production of lateral branches (i.e., culms), is an important agronomic trait that determines shoot architecture and grain production in grasses. Shoot architecture is based on the actions of the apical and axillary meristems (AXMs). The shoot apical meristem (SAM) produces all aboveground organs, including AXMs, leaves, stems, and inflorescences. In grasses like rice (Oryza sativa L.) and barley (Hordeum vulgare L.), vegetative AXMs form in the leaf axil of lower leaves of the plant and produce tillers (branches). Tiller development is characterized by three stages, including (i) AXM initiation, (ii) bud development,
and (iii) outgrowth of the axillary bud into a tiller. Each tiller has the potential to produce a seed-bearing inflorescence and, hence, increase yield. However, a balance between number and vigor of tillers is required, as unproductive tillers consume nutrients and can lead to a decreased grain production. Because
of its agronomic and biological importance, tillering has been widely studied, and numerous works demonstrate that the control of AXM initiation, bud development, and tillering in the grasses is via a suite of genes, hormones, and environmental conditions. In this review, we describe the genes and hormones that control tillering in two key cereal crops, rice and barley. In addition, we discuss how the development of new genomics tools and approaches, coupled with the synteny between the rice and barley genomes, are accelerating the isolation of barley genes underlying tillering phenotypes.
[Show abstract][Hide abstract] ABSTRACT: KNOX genes are important regulators of meristem function and a complex network of transcription factors ensures tight control of their expression. Here we show that members of the GROWTH-REGULATING FACTOR (GRF) family act as players in this network. A yeast one-hybrid screen with the upstream sequence of the KNOX gene Oskn2 from rice (Oryza sativa) resulted in isolation of OsGRF3 and OsGRF10. Specific binding to a region in the untranslated leader sequence of Oskn2 was confirmed by yeast and in vitro binding assays. ProOskn2:GUS reporter expression was downregulated by OsGRF3 and OsGRF10 in vivo, suggesting that these proteins function as transcriptional repressors. Likewise, we found that the GRF protein BGRF1 from barley could act as a repressor on an intron sequence in the KNOX gene Hooded/Bkn3 and that AtGRF4, -5 and -6 from Arabidopsis thaliana could repress KNAT2 promoter activity. OsGRF overexpression phenotypes in rice were consistent with aberrant meristematic activity, showing reduced formation of tillers and internodes and extensive adventitious root/shoot formation on nodes. These effects were associated with downregulation of endogenous Oskn2 expression by OsGRF3. Conversely, RNAi silencing of OsGRF3, -4 and -5 resulted in dwarfism, delayed growth and inflorescence formation, and upregulation of Oskn2. These data demonstrate conserved interactions between the GRF and KNOX families of transcription factors in both monocot and dicot plants.
[Show abstract][Hide abstract] ABSTRACT: Background
Maturity date (MD) is a crucial factor for marketing of fresh fruit, especially those with limited shelf-life such as peach (Prunus persica L. Batsch): selection of several cultivars with differing MD would be advantageous to cover and extend the marketing season. Aims of this work were the fine mapping and identification of candidate genes for the major maturity date locus previously identified on peach linkage group 4. To improve genetic resolution of the target locus two F2 populations derived from the crosses Contender x Ambra (CxA, 306 individuals) and PI91459 (NJ Weeping) x Bounty (WxBy, 103 individuals) were genotyped with the Sequenom and 9K Illumina Peach Chip SNP platforms, respectively.
Recombinant individuals from the WxBy F2 population allowed the localisation of maturity date locus to a 220 kb region of the peach genome. Among the 25 annotated genes within this interval, functional classification identified ppa007577m and ppa008301m as the most likely candidates, both encoding transcription factors of the NAC (NAM/ATAF1, 2/CUC2) family. Re-sequencing of the four parents and comparison with the reference genome sequence uncovered a deletion of 232 bp in the upstream region of ppa007577m that is homozygous in NJ Weeping and heterozygous in Ambra, Bounty and the WxBy F1 parent. However, this variation did not segregate in the CxA F2 population being the CxA F1 parent homozygous for the reference allele. The second gene was thus examined as a candidate for maturity date. Re-sequencing of ppa008301m, showed an in-frame insertion of 9 bp in the last exon that co-segregated with the maturity date locus in both CxA and WxBy F2 populations.
Using two different segregating populations, the map position of the maturity date locus was refined from 3.56 Mb to 220 kb. A sequence variant in the NAC gene ppa008301m was shown to co-segregate with the maturity date locus, suggesting this gene as a candidate controlling ripening time in peach. If confirmed on other genetic materials, this variant may be used for marker-assisted breeding of new cultivars with differing maturity date.
Full-text · Article · Oct 2013 · BMC Plant Biology
[Show abstract][Hide abstract] ABSTRACT: In this study, we used 83 winter and spring barley (Hordeum vulgare L.) cultivars representing European diversity for drought tolerance to carryout a Genome Wide Association Study (GWAS) for agronomic traits under different water regimes. Genotyping with an iSELECT Infinium® Illumina 9K SNP panel and filtering out of monomorphic and failed markers resulted in the identification of a total of 5135 SNPs distributed over the whole genome. Population stratification was investigated with a subset of 260 SNPs selected as highly informative using admixture model implemented in STRUCTURE v2.3.3 software. Accordingly, two or three main subgroups were identified corresponding to winter and spring barleys, respectively. Genome wide association analyses of agronomical traits such as grain yield (GY), flowering date (FD), and plant height (PH) are presented
[Show abstract][Hide abstract] ABSTRACT: The expression profile of flavour-related genes during ripening was investigated in two peach genotypes, Bolero and OroA, which have been selected for their contrasting aroma/ripening behaviour. A new peach microarray containing 4776 oligonucleotide probes corresponding to a set of ESTs specifically enriched in secondary metabolism (μPEACH2.0) was designed to investigate transcriptome changes during three fruit ripening stages, revealing 1807 transcripts differentially expressed within and between the two genotypes. Differences in the expression of genes involved in the biosynthesis of aroma compounds were detected during the ripening process within and between the two genotypes. In particular, a subset of 12 transcripts involved in metabolism of esters, norisoprenoids, phenylpropanoids and lactones, varied in expression during ripening and between Bolero and OroA.