Characterization of red-fleshed pear accessions from Emilia-Romagna region

Germplasm collections represent a reservoir of traits and genes that might be used in breeding programs to cope with the evolving market demand. Some old pear accessions still cultivated in the Apennine Mountains in Italy possess a red flesh fruit. This paper reports the molecular analysis of 33 red-fleshed pear accessions, collected in different areas of the Emilia-Romagna region and genotyped with 18 simple sequence repeat (SSR) markers with the aim of improving germplasm conservation strategies for old red-fleshed pears and for supporting ongoing breeding programs. The molecular profiles revealed both cases of synonymy and homonymy and only 6 unique genotypes were identified. S-genotypes were also established in order to highlight the genetic relationships among these landraces. Four of the unique genotypes have been clustered based on pomological data

Identification of QTLs linked to fruit quality traits in apricot (Prunus armeniaca L.) and biological validation through gene expression analysis using qPCR

Nine important fruit quality traits\u2014including fruit weight, stone weight, fruit diameter, skin ground colour, flesh colour, blush colour, firmness, soluble solids content and acidity content\u2014were studied for two consecutive years in two F 1 apricot progeny derived from the crosses \u2018Bergeron\u2019 7 \u2018Currot\u2019 (B 7C) and \u2018Goldrich\u2019 7 \u2018Currot\u2019 (G 7C). Results showed great segregation variability between populations, which was expected because of the polygenic nature and quantitative inheritance of all the studied traits. In addition, some correlations were observed among the fruit quality traits studied. QTL (quantitative trait loci) analysis was carried out using the phenotypic data and genetic linkages maps of \u2018B 7C\u2019 and \u2018G 7C\u2019 obtained with SSR and SNP markers. The most significant QTLs were localised in LG4 for soluble solids content and in LG3 for skin and flesh colour. In LG4, we can highlight the presence of candidate genes involved in D-glucose and D-mannose binding, while in LG3, we identified MYB genes previously linked to skin colour by other authors. In order to clearly identify the candidate genes responsible for the analysed traits, we converted the QTLs into expression QTLs and analysed the abundance of transcripts in the segregating genotypes \u2018GC 2\u201311\u2019 and \u2018GC 3\u20137\u2019 from the G 7C population. Using qPCR, we analysed the gene expression of nine candidate genes associated with the QTLs identified, including transcription factors (MYB 10), carotenoid biosynthesis genes (LOX 2, CCD1 and CCD4), anthocyanin biosynthesis genes (ANS, UFGT and F3\u20195\u2019H), organic acid biosynthesis genes (NAD ME) and ripening date genes (NAC). Results showed variable expression patterns throughout fruit development and between contrasted genotypes, with a correlation between validated genes and linked QTLs. The MYB10 gene was the best candidate gene for skin colour. In addition, we found that monitoring NAC expression is a good RNA marker for evaluating ripening progression

Simulation of greenhouse gases following land-use change to bioenergy crops using the ECOSSE model. A comparison between site measurements and model predictions

This article evaluates the suitability of the ECOSSE model to estimate soil greenhouse gas (GHG) fluxes from short rotation coppice willow (SRC-Willow), short rotation forestry (SRF-Scots Pine) and Miscanthus after landuse change from conventional systems (grassland and arable). We simulate heterotrophic respiration (Rh), nitrous oxide (N2O) and methane (CH4) fluxes at four paired sites in the UK and compare them to estimates of Rh derived from the ecosystem respiration estimated from eddy covariance (EC) and Rh estimated from chamber (IRGA) measurements, as well as direct measurements of N2O and CH4 fluxes. Significant association between modelled and EC-derived Rh was found under Miscanthus, with correlation coefficient (r) ranging between 0.54 and 0.70. Association between IRGA-derived Rh and modelled outputs was statistically significant at the Aberystwyth site (r = 0.64), but not significant at the Lincolnshire site (r = 0.29). At all SRC-Willow sites, significant association was found between modelled and measurement-derived Rh (0.44 ≤ r ≤ 0.77); significant error was found only for the EC-derived Rh at the Lincolnshire site. Significant association and no significant error were also found for SRF-Scots Pine and perennial grass. For the arable fields, the modelled CO2 correlated well just with the IRGA-derived Rh at one site (r = 0.75). No bias in the model was found at any site, regardless of the measurement type used for the model evaluation. Across all land uses, fluxes of CH4 and N2O were shown to represent a small proportion of the total GHG balance; these fluxes have been modelled adequately on a monthly time-step. This study provides confidence in using ECOSSE for predicting the impacts of future land use on GHG balance, at site level as well as at national level

High resolution spatial modelling of greenhouse gas emissions from land use change to energy crops in the UK

We implemented a spatial application of a previously evaluated model of soil GHG emissions, ECOSSE, in the United Kingdom to examine the impacts to 2050 of land-use transitions from existing land use, rotational cropland, permanent grassland or woodland, to six bioenergy crops; three ‘first-generation’ energy crops: oilseed rape, wheat and sugar beet, and three ‘second-generation’ energy crops: Miscanthus, short rotation coppice willow (SRC) and short rotation forestry poplar (SRF). Conversion of rotational crops to Miscanthus, SRC and SRF and conversion of permanent grass to SRF show beneficial changes in soil GHG balance over a significant area. Conversion of permanent grass to Miscanthus, permanent grass to SRF and forest to SRF shows detrimental changes in soil GHG balance over a significant area. Conversion of permanent grass to wheat, oilseed rape, sugar beet and SRC and all conversions from forest show large detrimental changes in soil GHG balance over most of the United Kingdom, largely due to moving from uncultivated soil to regular cultivation. Differences in net GHG emissions between climate scenarios to 2050 were not significant. Overall, SRF offers the greatest beneficial impact on soil GHG balance. These results provide one criterion for selection of bioenergy crops and do not consider GHG emission increases/decreases resulting from displaced food production, bio-physical factors (e.g. the energy density of the crop) and socio-economic factors (e.g. expenditure on harvesting equipment). Given that the soil GHG balance is dominated by change in soil organic carbon (SOC) with the difference among Miscanthus, SRC and SRF largely determined by yield, a target for management of perennial energy crops is to achieve the best possible yield using the most appropriate energy crop and cultivar for the local situation

A Unique Mutation in a MYB Gene Cosegregates with the Nectarine Phenotype in Peach

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 \u2018Contender\u2019 (C, peach) x \u2018Ambra\u2019 (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

The Peach v2.0 Release : An Improved Genome Sequence for Bridging the Gap Between Genomics and Breeding in Prunus

Since its release the high quality peach genome sequence (Peach v1.0) has fostered studies on comparative genomics as well as on genetic diversity, domestication and crop improvement in Prunus and related species. To improve the chromosome-scale assembly and genome annotation we performed further analyses. Extensive mapping data allowed the improvement of Peach v2.0 assembly in terms of fraction of mapped (99.2%) and orientated (97.9%) sequences and correction of misassembly issues (about 12.2 Mb of incorrectly positioned sequences). Assembled resequencing data (42x) improved base accuracy and contiguity: 859 SNPs and 1,347 Indels were corrected and 212 gaps were closed. As a result the contiguity of Peach v2.0 improved with a contig L50 of 255.4 kb (previously 214.2 kb) and a contig N50 of 250 (previously 294). Repeat annotation was enhanced including low copy repeats and the complete sequence and location of 1,157 non autonomous Helitrons. Gene prediction and annotation were improved using transcript assemblies obtained from 2.2 billion of RNA seq reads from different peach tissues and organs. In total, after masking with the improved repeat annotation, 26,873 protein-coding genes were predicted in Peach v2.1 annotation, 991 less than those predicted in Peach v1.0. Gene annotation was highly enhanced with the prediction of almost 20,000 new isoforms. The new peach release with improved assembly and annotation will be a pivotal resource for comparative genomics in the plant kingdom and will serve as a foundation for studies bridging the gap between genomics and breeding in Prunus and related species

Bats' Conquest of a Formidable Foraging Niche: The Myriads of Nocturnally Migrating Songbirds

Along food chains, i.e., at different trophic levels, the most abundant taxa often represent exceptional food reservoirs, and are hence the main target of consumers and predators. The capacity of an individual consumer to opportunistically switch towards an abundant food source, for instance, a prey that suddenly becomes available in its environment, may offer such strong selective advantages that ecological innovations may appear and spread rapidly. New predator-prey relationships are likely to evolve even faster when a diet switch involves the exploitation of an unsaturated resource for which few or no other species compete. Using stable isotopes of carbon and nitrogen as dietary tracers, we provide here strong support to the controversial hypothesis that the giant noctule bat Nyctalus lasiopterus feeds on the wing upon the multitude of flying passerines during their nocturnal migratory journeys, a resource which, while showing a predictable distribution in space and time, is only seasonally available. So far, no predator had been reported to exploit this extraordinarily diverse and abundant food reservoir represented by nocturnally migrating passerines

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