[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: 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 nearM1a (LG C×
EL-2, R2=13.1–31.5 %) and EPPISF032 (LG C×EL-4, R2=
11–14 %) and the others containing QTLs for FL resistance,
near markers SNP_IGA_320761 and SNP_IGA_321601
(LG3, R2=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.
Tree Genetics & Genomes 06/2014; · 2.40 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: 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 01/2014; 9(3):e90574. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Background
Maturity date 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 cosegregated
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: 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 01/2013; · 2.40 Impact Factor
[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: 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
[Show abstract][Hide abstract] ABSTRACT: Two intraspecific peach breeding populations have been used to conduct a quantitative trait locus (QTL) analysis of fruit
quality traits: an F1 from the cross Bolero (B) x OroA (O) and an F2 from the cross Contender (C) x Ambra (A). A total of 344 Prunus simple sequence repeats (SSRs) were analyzed in B, O, C, A parents and CxA F1 hybrid. Eight SSR were mapped for the first time in peach. A multiplex-ready polymerase chain reaction (PCR) protocol has
allowed considerable time and cost saving during genotyping steps. Two maps (B map and O map) were produced for BxO population following the pseudo-test cross strategy and one for CxA. No marker could be mapped
on G6 for the B map, on G4 and G8 for the O map and on G5 for the CxA map. Both populations were phenotyped over 2years for maturity date (MD), fruit weight, external
fruit skin overcolor, juice total soluble solids (SSC, Brix degree), juice titrable acidity and juice pH. Data for blooming
time and flower type were scored only for BxO in 2007. All traits had a normal distribution, except for MD which was bimodal
in BxO and trimodal in CxA, where it was scored as a co-dominant trait. Up to two QTLs per trait were detected in each population,
and most of them were located in the same region forming clusters of QTLs, especially on G4. This is likely due to a major
pleiotropic effect of MD masking the identification of other QTLs for different traits.
Prunus persica (Batsch.) L.–SSR–Maturity date–Peach–Quality traits–Molecular maps
Tree Genetics & Genomes 01/2011; 7(2):323-335. · 2.40 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In the barley (Hordeum vulgare) Hooded (Kap) mutant, the duplication of a 305-bp intron sequence leads to the overexpression of the Barley knox3 (Bkn3) gene, resulting in the development of an extra flower in the spikelet. We used a one-hybrid screen to identify four proteins that bind the intron-located regulatory element (Kap intron-binding proteins). Three of these, Barley Ethylene Response Factor1 (BERF1), Barley Ethylene Insensitive Like1 (BEIL1), and Barley Growth Regulating Factor1 (BGRF1), were characterized and their in vitro DNA-binding capacities verified. Given the homology of BERF1 and BEIL1 to ethylene signaling proteins, we investigated if these factors might play a dual role in intron-mediated regulation and ethylene response. In transgenic rice (Oryza sativa), constitutive expression of the corresponding genes produced phenotypic alterations consistent with perturbations in ethylene levels and variations in the expression of a key gene of ethylene biosynthesis. In barley, ethylene treatment results in partial suppression of the Kap phenotype, accompanied by up-regulation of BERF1 and BEIL1 expression, followed by down-regulation of Bkn3 mRNA levels. In rice protoplasts, BEIL1 activates the expression of a reporter gene driven by the 305-bp intron element, while BERF1 can counteract this activation. Thus, BEIL1 and BERF1, likely in association with other Kap intron-binding proteins, should mediate the fine-tuning of Bkn3 expression by ethylene. We propose a hypothesis for the cross talk between the KNOX and ethylene pathways.
[Show abstract][Hide abstract] ABSTRACT: Volatile compounds, together with sugars and acids, are the main chemical species determining the characteristic aroma and flavor of food. In peach, more than 100 volatiles have been identified.
The essential oil of six peach and three nectarine accessions used in Italian breeding programs was obtained by steam distillation, and the volatiles were investigated. A total of 47 known volatiles, two unidentified compounds and nine hydrocarbons were identified, including 12 aldehydes, six alcohols, three acids, three esters, six terpenes, two phenylalanine derivates, two C(13) norisoprenoids, one ketone (C(9)) and 10 lactones. A wide variation in the number of volatiles and in their concentration was observed among the nine accessions. Twenty-one compounds presented odor activity values (OAVs) higher than 1 in at least one of the accessions and were therefore putatively considered as key odorants in the peach volatile composition.
This study reports the identification, quantification and potency, based on the OAVs, of the most important volatile compounds, along with fruit quality characteristics, of nine different peach/nectarine accessions and will help future peach volatile breeding programs for the selection of odor-rich accessions to be used in the development of new improved cultivars.
Journal of the Science of Food and Agriculture 05/2010; 90(7):1146-54. · 1.76 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Two quantitative trait loci (Fr-H1 and Fr-H2) for frost tolerance (FT) have been discovered on the long arm of chromosome 5H in barley. Two tightly linked groups of CBF genes, known to play a key role in the FT regulatory network in A. thaliana, have been found to co- segregate with Fr-H2. Here, we investigate the allelic variations of four barley CBF genes (HvCbf3, HvCbf6, HvCbf9 and HvCbf14) in a panel of European cultivars, landraces and H. spontaneum accessions. In the cultivars a reduction of nucleotide and haplotype diversities in CBFs compared with the landraces and the wild ancestor H. spontaneum, was evident. In particular, in cultivars the loss of HvCbf9 genetic variants was higher compared to other sequences. In order to verify if the pattern of CBF genetic variants correlated with the level of FT, an association procedure was adopted. The pairwise analysis of linkage disequilibrium (LD) among the genetic variants in four CBF genes was computed to evaluate the resolution of the association procedure. The pairwise plotting revealed a low level of LD in cultivated varieties, despite the tight physical linkage of CBF genes analysed. A structured association procedure based on a general liner model was implemented, including the variants in CBFs,of Vrn-H1, and of two reference genes not involved in FT (alpha-Amy1 and Gapdh) and considering the phenotypic data for FT. Association analysis recovered two nucleotide variants of HvCbf14 and one nucleotide variant of Vrn-H1 as statistically associated to FT.
Theoretical and Applied Genetics 09/2009; 119(7):1335-48. · 3.66 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: To individuate candidate genes (CGs) for a set of barley developmental mutants, a synteny approach comparing the genomes of barley and rice has been introduced. Based on map positions of mutants, sequenced RFLP markers linked to the target loci were selected. The markers were mapped in silico by BLAST searches against the rice genome sequence and chromosomal regions syntenous to barley target intervals were identified. Rice syntenous regions were defined for 15 barley chromosomal intervals hosting 23 mutant loci affecting plant height (brh1; brh2; sld4), shoot and inflorescence branching (als; brc1; cul-2, -3, -5, -15, -16; dub1; mnd6; vrs1), development of leaves (lig) and leaf-like organs (cal-b19, -C15, -d4; lks5; suKD-25; suKE-74; suKF-76; trd; trp). Annotation of 110 Mb of rice genomic sequence made it possible to screen for putative CGs which are listed together with the reasons supporting mutant-gene associations. For two loci, CGs were identified with a clear probability to represent the locus considered. These include FRIZZY PANICLE, a candidate for the brc1 barley mutant, and the rice ortholog of maize Liguleless1 (Lg1), a candidate for the barley lig locus on chromosome 2H. For this locus, the validity of the approach was supported by the PCR-amplification of a genomic fragment of the orthologous barley sequence. SNP mapping located this fragment on chromosome 2H in the region hosting the lig genetic locus.
Theoretical and Applied Genetics 05/2006; 112(6):1073-85. · 3.66 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The molecular basis of the barley dominant Hooded (K) mutant is a duplication of 305 bp in intron IV of the homeobox gene Bkn3. A chemical mutagenesis screen was carried out to identify genetical factors that participate in Bkn3 intron-mediated gene regulation. Plants from recurrently mutagenized KK seeds were examined for the suppression of the hooded awn phenotype induced by the K allele and, in total, 41 suK (suppressor of K) recessive mutants were identified. Complementation tests established the existence of five suK loci, and alleles suKB-4, suKC-33, suKD-25, suKE-74, and suKF-76 were studied in detail. All K-suppressed mutants showed a short-awn phenotype. The suK loci have been mapped by bulked segregant analysis nested in a standard mapping procedure based on AFLP markers. K suppressor loci suKB, B, E, and F all map in a short interval of chromosome 7H, while the locus suKD is assigned to chromosome 5H. A complementation test between the four suK mutants mapping on chromosome 7H and the short-awn mutant lks2, located nearby, excluded the allelism between suK loci and lks2. The last experiment made clear that the short-awn phenotype of suK mutants is due to a specific dominant function of the K allele, a function that is independent from the control on hood formation. The suK loci are discussed as candidate participants in the regulation of Bkn3 expression.
[Show abstract][Hide abstract] ABSTRACT: The leaf is a coordinated mosaic of developmental domains, which are evident from leaf inception on the flanks of the apical meristem. The subdivision of the meristem into molecularly defined domains is regulated by the interactions of a number of gene products and by receptor kinase-mediated signals. The acquisition of symmetry axes in the emerging leaf is a process coordinated by hormones (such as auxin and cytokinins) and the expression of classes of genes (such as the knox and the ARP, as1/rs2/phan, genes). As with simple leaves, the architecture of compound leaves is defined by spatial/temporal gradients of regulatory gene functions: complexity results from the interplay between leaf differentiation processes and genes maintaining a partial level of indeterminacy in the developing primordium. Boundaries between regions with different molecular 'addresses' are considered, in plants as in Drosophila, as organizing centres for lateral organ development.
Seminars in Cell and Developmental Biology 11/2001; 12(5):363-72. · 6.20 Impact Factor