Genome-enabled predictions for fruit weight and quality from repeated records in European peach progenies

Background: Highly polygenic traits such as fruit weight, sugar content and acidity strongly influence the agroeconomic value of peach varieties. Genomic Selection (GS) can accelerate peach yield and quality gain if predictions show higher levels of accuracy compared to phenotypic selection. The available IPSC 9K SNP array V1 allows standardized and highly reliable genotyping, preparing the ground for GS in peach. Results: A repeatability model (multiple records per individual plant) for genome-enabled predictions in eleven European peach populations is presented. The analysis included 1147 individuals derived from both commercial and non-commercial peach or peach-related accessions. Considered traits were average fruit weight (FW), sugar content (SC) and titratable acidity (TA). Plants were genotyped with the 9K IPSC array, grown in three countries (France, Italy, Spain) and phenotyped for 3–5 years. An analysis of imputation accuracy of missing genotypic data was conducted using the software Beagle, showing that two of the eleven populations were highly sensitive to increasing levels of missing data. The regression model produced, for each trait and each population, estimates of heritability (FW:0.35, SC:0.48, TA:0.53, on average) and repeatability (FW:0.56, SC:0.63, TA:0.62, on average). Predictive ability was estimated in a five-fold cross validation scheme within population as the correlation of true and predicted henotypes. Results differed by populations and traits, but predictive abilities were in general high (FW:0.60, SC:0.72, TA:0.65, on average). Conclusions: This study assessed the feasibility of Genomic Selection in peach for highly polygenic traits linked to yield and fruit quality. The accuracy of imputing missing genotypes was as high as 96%, and the genomic predictive ability was on average 0.65, but could be as high as 0.84 for fruit weight or 0.83 for titratable acidity. The estimated repeatability may prove very useful in the management of the typical long cycles involved in peach productions. All together, these results are very promising for the application of genomic selection to peach breeding programmes.info:eu-repo/semantics/publishedVersio

Linkage map saturation, construction, and comparison in four populations of Prunus

One of the objectives of the ISAFRUIT Project was to perform genetic analyses in four populations of Prunus, two of peach (P. persica) and two of apricot (P. armeniaca), in order to identify major genes and quantitative trait loci (QTLs) for characters related to fruit quality. This required the construction of saturated marker maps in each of these populations. Marker maps were available for an intra-specific peach × peach F2, a BC2 peach × P. davidiana (using peach as the recurrent parent), and an apricot × apricot F1. We have further saturated these maps mainly with SSR (simple sequence repeat) markers. A new map, constructed uniquely from SSRs was prepared for a fourth apricot × apricot F1 population. Using anchor markers, we compared these four maps with the reference Prunus map, constructed using an almond × peach F2 population. As previously observed, conservation of synteny and co-linearity were the general rule, providing additional evidence of the high level of similarity between all Prunus genomes. Comparisons of genetic distances between the maps suggested that those involving similar genomes had higher levels of recombination than those with more distant genomes, particularly the inter-specific crosses.The ISAFRUIT Project is funded by the European Commission under Thematic Priority 5 – Food Quality and Safety of the 6th Framework Programme of RTD (Contract No. FP6-FOOD-CT-2006-016279).Peer reviewe

The Crop Load Affects Brown Rot Progression in Fruit Orchards: High Fruit Densities Facilitate Fruit Exposure to Spores but Reduce the Infection Rate by Decreasing Fruit Growth and Cuticle Cracking

Brown rot, triggered by Monilinia spp., causes significant economic losses in fruit crop and it is mainly controlled by chemicals with inherent environmental costs. Controlling brown rot spreading by diminishing fruit susceptibility to the disease, via sustainable cultural practices, is a promising approach. In a 2 years experiment (2014–2015) on a peach (Prunus persica) orchard, we controlled fruit growth rates by varying the fruit load. Fruit thinning practices enhanced the fruit growth and laboratory analyses showed that, in both 2014 and 2015 samples, fast growing fruits were more susceptible to infection when in contact with conidia suspension of Monilinia laxa. In the field, brown rot infection took place in 2014 and not in 2015. In 2014, trees subject to moderate thinning intensities had the highest brown rot incidence. We argue that this is due to the fact that, for null thinning, slow growing fruits are less susceptible to the infection while, for intense thinning, even if faster growing fruits are more susceptible to infection, the lower fruits density reduces per-contact probability of infection. We compared meteorological data of 2014 and 2015 and we argue that brown rot did not spread in 2015 due to an absence of favorable conditions, summarized as the number of rainy days with mean temperature between 22 and 26°C, in the period of fruit susceptibility

Model assisted phenotyping and ideotype design

By formalizing traits as the result of genotypic and environmental effects and the relations among traits, ecophysiological models (or process-based models) provide a platform for integrative analyses of trait impacts on whole-plant and crop phenotypes. Over the past two decades, model development has been increasingly driven by the need to account for genotypic differences across environments, and improvements in this area have developed around well-defined traits such as leaf elongation, early vigor and flowering time. Process-based models are now increasingly used to define and characterize crop environments at various scales and help breeding programs take advantage of G × E interactions. Ecophysiological models are also used to assist plant phenotyping and could provide necessary links between controlled-conditions phenotyping and plant performance in the field. The integration of genetic controls in ecophysiological models has allowed analysis of the genetic control of phenotypic plasticity across wide ranges of environments, and the G × E × M space is now explored using efficient algorithms to find ideotypes optimizing many antagonist criteria. This later approach lies in finding combinations of values of the genetic and agronomic parameters that best satisfy the pre-defined objectives, but it is currently limited by the lack of quantitative relationships between genes and model parameters. Considerable efforts are still needed to develop robust links between genetic controls, physiological determinants and traits relevant to breeders

Brown Rot Strikes Prunus Fruit: An Ancient Fight Almost Always Lost

Brown rot (BR) caused by Monilinia spp., has been an economic problem for the stone fruit market due to dramatic losses, mainly during the postharvest period. There is much literature about basic aspects of Monilinia spp. infection, which indicates that environment significantly influences its occurrence in the orchard. However, progress is needed to sustainably limit this disease: the pathogen is able to develop resistance to pesticides, and most of BR resistance research programs in plant models perish. Solving this problem becomes important due to the need to decrease chemical treatments and reduce residues on fruit. Thus, research has recently increased, exploring a wide range of disease control strategies (e.g., genetic, chemical, physical). Summarizing this information is difficult, as studies evaluate different Monilinia and Prunus model species, with diverse strategies and protocols. Thus, the purpose of this review is to present the diversity and distribution of agents causing BR, focusing on the biochemical mechanisms of Monilinia spp. infection both of the fungi and of the fruit, and report on the resistance sources in Prunus germplasm. This review comprehensively compiles the information currently available to better understand mechanisms related to BR resistance."FruitBreedomics" European Project (Seventh Frame Program) FP7-265582 CONICYT, Chile (Post-Doctoral Fellowship) 74130043 CONICYT, Chile (Academy Insertion Grant) 79140020 CAPES foundation Brazilian Ministry of Educatio

Genome-enabled predictions for fruit weight and quality from repeated records in European peach progenies

Background: Highly polygenic traits such as fruit weight, sugar content and acidity strongly influence the agroeconomic value of peach varieties. Genomic Selection (GS) can accelerate peach yield and quality gain if predictions show higher levels of accuracy compared to phenotypic selection. The available IPSC 9K SNP array V1 allows standardized and highly reliable genotyping, preparing the ground for GS in peach. Results: A repeatability model (multiple records per individual plant) for genome-enabled predictions in eleven European peach populations is presented. The analysis included 1147 individuals derived from both commercial and non-commercial peach or peach-related accessions. Considered traits were average fruit weight (FW), sugar content (SC) and titratable acidity (TA). Plants were genotyped with the 9K IPSC array, grown in three countries (France, Italy, Spain) and phenotyped for 3–5 years. An analysis of imputation accuracy of missing genotypic data was conducted using the software Beagle, showing that two of the eleven populations were highly sensitive to increasing levels of missing data. The regression model produced, for each trait and each population, estimates of heritability (FW:0.35, SC:0.48, TA:0.53, on average) and repeatability (FW:0.56, SC:0.63, TA:0.62, on average). Predictive ability was estimated in a five-fold cross validation scheme within population as the correlation of true and predicted henotypes. Results differed by populations and traits, but predictive abilities were in general high (FW:0.60, SC:0.72, TA:0.65, on average). Conclusions: This study assessed the feasibility of Genomic Selection in peach for highly polygenic traits linked to yield and fruit quality. The accuracy of imputing missing genotypes was as high as 96%, and the genomic predictive ability was on average 0.65, but could be as high as 0.84 for fruit weight or 0.83 for titratable acidity. The estimated repeatability may prove very useful in the management of the typical long cycles involved in peach productions. All together, these results are very promising for the application of genomic selection to peach breeding programmes.info:eu-repo/semantics/publishedVersio

Additional file 1 of Genome-enabled predictions for fruit weight and quality from repeated records in European peach progenies

Detailed phenotypic data. Phenotypic data per year, cross and trait, comprising descriptive statistics. (CSV 3 kb

The multi-site PeachRefPop collection: a true cultural heritage and international scientific tool for fruit trees

Plants have evolved a range of adaptive mechanisms that adjust their development and physiology to variable external conditions, particularly in perennial species subjected to long-term interplay with the environment. Exploiting the allelic diversity within available germplasm and leveraging the knowledge of the mechanisms regulating genotype interaction with the environment are crucial to address climatic challenges and assist the breeding of novel cultivars with improved resilience. The development of multisite collections is of utmost importance for the conservation and utilization of genetic materials and will greatly facilitate the dissection of genotype-by-environment interaction. Such resources are still lacking for perennial trees, especially with the intrinsic difficulties of successful propagation, material exchange and living collection maintenance. This work describes the concept, design and realization of the first multi-site peach [Prunus persica (L.) Batsch] reference collection (PeachRefPop: PRP) located across different European countries and sharing the same experimental design. Other than an invaluable tool for scientific studies in perennial species, the PRP provides a milestone in an international collaborative project for the conservation and exploitation of European peach germplasm resources and, ultimately, as a true heritage for future generations.info:eu-repo/semantics/acceptedVersio