[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: 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.
[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.
[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.
[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.
PLoS ONE 03/2014; 9(3):e90574. DOI:10.1371/journal.pone.0090574 · 3.23 Impact Factor
[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.
The Plant Genome 03/2014; 7(1). DOI:10.3835/plantgenome2013.10.0032 · 3.88 Impact Factor
[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.
[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
XI National Congress of Biotechnology, Insubria University, Varese, Italy.; 06/2013
[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.
[Show abstract][Hide abstract] ABSTRACT: 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 1 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.
[Show abstract][Hide abstract] ABSTRACT: Genome analysis based on next generation sequencing (NGS) technologies provides a novel approach for surveying molecular diversity among individuals, which in turn can generate tools for linkage and association mapping, gene cloning, molecular breeding, population genetics, germplasm management, and crop systematics and evolution. 'De novo' assembly of short reads is challenging in general and even more so as the size and complexity of genomes increase. A high quality and well annotated reference genome sequence can help solve most of the conflicts. Yet, the identification of several structural variants, such as the movement of transposable elements, large insertions/deletions, segmental duplications, inversions and other genomic features is still a challenge to algorithms and automatic procedures. We sequenced 14 Prunus accessions that include ten peach cultivars, two wild peach-related species, one almond and one apricot accession using the NGS Illumina platform. We produced 64 to 109 bp long single reads as well as paired ends from approx. 300-500 bp long fragments. The coverage varied from approximately 16 to 75 genome equivalents. Individual genomes were aligned using the reference sequence of the doubled haploid peach cultivar 'Lovell', recently released by the International Peach Genome Initiative (IPGI) (http://www.rosaceae. org/peach/genome). In this paper we present a repertoire of molecular variants that can be mined, namely SNPs (Single Nucleotide Polymorphisms), DIPs (Deletion/Insertion Polymorphisms), larger structural variations, which include movement of transposable elements, the so called copy-number variations, segmental duplications and others. Some of these variants, such as SNPs, are easily detectable and much commercial and open-access software can perform the search. Others variants, such as the large structural variations, still need analytical approaches to be implemented or improved. For several variants, theoretical and methodological approaches are presented and discussed and, when available, preliminary results are reported. INTRODUCTION Genome analysis based on next generation sequencing (NGS) technologies provides a novel approach for exploring molecular diversity among individuals, which in turn can generate tools for linkage and association mapping, gene cloning, molecular breeding, population genetics, germplasm management, and crop systematics and evolution (Varshney et al., 2009). De novo assembly of short reads produced by NGS technologies is challenging in
Eucarpia Symposium on Fruit Breeding and Genetics; 02/2013
[Show abstract][Hide abstract] ABSTRACT: Volatile organic compounds (VOCs) in plants are involved in aroma and pest resistance. These compounds form a complex mixture whose composition is specific to species and often to varieties. Despite their importance as essential factors that determine peach fruit quality, understanding of molecular, genetic, and physiological mechanisms underlying aroma formation is limited. The aim of this study was the identification in peach of quantitative trait loci (QTLs) for fruit VOCs to understand their genetic basis using an F1 population of 126 seedlings deriving from the cross between “Bolero” (B) and “OroA” (O), two peach cultivars differing in their aroma profile. Dense single nucleotide polymorphism (SNP) and SSR maps covering the eight linkage groups of the peach genome were constructed by genotyping with the International Peach SNP Consortium peach SNP array v1, and data for 23 VOCs with high or unknown “odor activity value” were obtained by gas chromatography–mass spectrometry analysis of fruit essential oil in the years 2007 and 2008. A total of 72 QTLs were identified, most consistent in both years. QTLs were identified for the 23 VOCs studied, including three major QTLs for nonanal, linalool, and for p -menth-1-en-9-al stable in both years. Collocations between candidate genes and major QTLs were identified taking advantage of the peach genome sequence: genes encoding two putative terpene synthases and one lipoxygenase ( Lox ) might be involved in the biosynthesis of linalool and p -menth-1-en-9-al, and nonanal, respectively. Implications for marker-assisted selection and future research on the subject are discussed
Tree Genetics & Genomes 02/2013; DOI:10.1007/s11295-012-0546-z · 2.44 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The genomic resources of small grain cereals that include some of the most important crop species such as wheat, barley, and rye are attaining a level of completion that now is contributing to new structural and functional studies as well as refining molecular marker development and mapping strategies for increasing the efficiency of breeding processes. The integration of new efforts to obtain reference sequences in bread wheat and barley, in particular, is accelerating the acquisition and interpretation of genome-level analyses in both of these major crops.
[Show abstract][Hide abstract] ABSTRACT: To identify genes involved in the expression of a trait using the candidate gene (CG) approach, the genome positions of the
maximum number of genes which potentially cause the observed phenotypic variability needs to be known. This position is compared
with that of major genes or quantitative trait loci (QTL) for this character, with the co-location of the CG and major gene
or QTL indicating a possible cause and effect relationship. In the present study we selected 273 sequences from expressed
sequence tag collections, corresponding to CGs from metabolic pathways affecting fruit growth and maturity, texture, sugar
and organic acid content, aroma and color, and mapped them in the Prunus reference map (T×E) based on an interspecific almond×peach F2 population. We used the bin-mapping approach, where only eight plants, six
of the T×E progeny plus one of the parents and the F1 hybrid, are used to determine the position of a marker. This strategy was very
efficient, with 206 CGs mapped, based mainly on the segregation of one or more single-nucleotide polymorphisms. These CGs
were located throughout the Prunus genome and are a resource for genetic analysis in stone fruit (peach, plum, apricot and cherry) and almond. Co-locations
between CGs and major genes or QTL responsible for natural variability of fruit quality characters in Prunus were identified using the available information on their positions.
KeywordsCandidate genes–Bin mapping–Prunus–Fruit quality–SNP variability