This document summarizes key management issues and deliverables for a research consortium. It outlines the addition of two new partners, reviews the deliverable submission process, and provides tables listing deliverables due in the first two years of the project including their work package, leader, nature, dissemination level, and planned delivery date. Key deliverables include descriptions of ideotypes and genetic materials, new versions of analysis software, databases of phenotypic and genotypic data, and dissemination materials like newsletters and websites.
This document provides a weekly planning schedule from February 27th to July 6th, 2012. It outlines the language skills, topics, activities, and assessments covered each week. The schedule includes listening to spoken texts, reading materials, writing descriptions and reports, discussing topics of interest, and preparing for term exams. The document organizes the curriculum into weekly blocks focusing on improving students' language proficiency, communication skills, and knowledge acquisition across various subjects.
The document contains drawings and part lists for an assembly project. It includes an assembly drawing labeled C1 with 5 numbered parts. Individual drawings show the details of each part, including dimensions. A parts list identifies the 5 parts and their quantities needed for the assembly. The student name, drawing name, date, scale, material, teacher and class are provided for each document.
The document contains engineering drawings and assembly instructions for a project consisting of 5 parts. It includes individual drawings of each part labeled Part1 through Part5 created on October 8, 2010. It also includes an assembly drawing from October 13, 2010 showing how the 5 parts fit together, labeled Assembly C2.iam. Additional information provided includes the student and teacher names, scale of the drawings, material used, and class period.
FruitBreedomics KOM 29 03-2011 5 WP3 presentationfruitbreedomics
This document outlines objectives for identifying and characterizing quantitative trait loci (QTL) for important fruit quality traits and disease resistance in apple and peach through pedigree-based analysis. The goals are to clarify the genetics underlying traits like taste, firmness, sugar and acidity levels as well as resistance to diseases. The approach involves QTL mapping in multiple breeding families using SNP genotyping data. Results will provide locations of QTL, their effects, interactions and robustness. This will support future marker-assisted breeding efforts.
FruitBreedomics KOM 29 03-2011 3 WP1 presentationfruitbreedomics
WP1 has 5 main tasks:
1. Define breeding strategies and ideotypes for pilot studies in apple and peach breeding programs.
2. Develop tightly linked SNP markers for major genes and QTLs related to important horticultural traits.
3. Conduct pilot studies applying marker-assisted breeding to test breeding strategies.
4. Optimize a genotyping pipeline for use in the pilot studies.
5. Create specifications for an interface to allow breeders to access information from a database to assist selection.
The document describes the construction and application of a high-density SNP linkage map in apple using a multi-parental population. A 20K SNP array was used to genotype over 1,600 individuals from 21 families. SNPs were organized into focal points suitable for building stable multi-allelic haplotypes. A new mapping approach called the focal point strategy was used, which analyzes haplotypes across families prior to map construction. This resulted in a very reliable genetic map for apple with correct linkage group and marker assignments.
FruitBreedomics KOM Stakeholders meeting 31-03-2011 7 WP5 presentation and fe...fruitbreedomics
This document outlines the objectives and tasks for Work Package 5 which aims to develop tools to analyze novel traits in apple and peach through 'omics approaches and phenotyping methods. The work package will select cultivars to study trait variation, develop high throughput quantification protocols, and standardize methods for research and industry use. Specific tasks include identifying factors related to disease resistance in peach, assessing fruit quality traits in apple and peach, and testing for climate change adaptation traits like chilling requirement. The work is expected to provide standardized phenotyping tools and increase knowledge of genetics underlying complex traits.
This document provides a weekly planning schedule from February 27th to July 6th, 2012. It outlines the language skills, topics, activities, and assessments covered each week. The schedule includes listening to spoken texts, reading materials, writing descriptions and reports, discussing topics of interest, and preparing for term exams. The document organizes the curriculum into weekly blocks focusing on improving students' language proficiency, communication skills, and knowledge acquisition across various subjects.
The document contains drawings and part lists for an assembly project. It includes an assembly drawing labeled C1 with 5 numbered parts. Individual drawings show the details of each part, including dimensions. A parts list identifies the 5 parts and their quantities needed for the assembly. The student name, drawing name, date, scale, material, teacher and class are provided for each document.
The document contains engineering drawings and assembly instructions for a project consisting of 5 parts. It includes individual drawings of each part labeled Part1 through Part5 created on October 8, 2010. It also includes an assembly drawing from October 13, 2010 showing how the 5 parts fit together, labeled Assembly C2.iam. Additional information provided includes the student and teacher names, scale of the drawings, material used, and class period.
FruitBreedomics KOM 29 03-2011 5 WP3 presentationfruitbreedomics
This document outlines objectives for identifying and characterizing quantitative trait loci (QTL) for important fruit quality traits and disease resistance in apple and peach through pedigree-based analysis. The goals are to clarify the genetics underlying traits like taste, firmness, sugar and acidity levels as well as resistance to diseases. The approach involves QTL mapping in multiple breeding families using SNP genotyping data. Results will provide locations of QTL, their effects, interactions and robustness. This will support future marker-assisted breeding efforts.
FruitBreedomics KOM 29 03-2011 3 WP1 presentationfruitbreedomics
WP1 has 5 main tasks:
1. Define breeding strategies and ideotypes for pilot studies in apple and peach breeding programs.
2. Develop tightly linked SNP markers for major genes and QTLs related to important horticultural traits.
3. Conduct pilot studies applying marker-assisted breeding to test breeding strategies.
4. Optimize a genotyping pipeline for use in the pilot studies.
5. Create specifications for an interface to allow breeders to access information from a database to assist selection.
The document describes the construction and application of a high-density SNP linkage map in apple using a multi-parental population. A 20K SNP array was used to genotype over 1,600 individuals from 21 families. SNPs were organized into focal points suitable for building stable multi-allelic haplotypes. A new mapping approach called the focal point strategy was used, which analyzes haplotypes across families prior to map construction. This resulted in a very reliable genetic map for apple with correct linkage group and marker assignments.
FruitBreedomics KOM Stakeholders meeting 31-03-2011 7 WP5 presentation and fe...fruitbreedomics
This document outlines the objectives and tasks for Work Package 5 which aims to develop tools to analyze novel traits in apple and peach through 'omics approaches and phenotyping methods. The work package will select cultivars to study trait variation, develop high throughput quantification protocols, and standardize methods for research and industry use. Specific tasks include identifying factors related to disease resistance in peach, assessing fruit quality traits in apple and peach, and testing for climate change adaptation traits like chilling requirement. The work is expected to provide standardized phenotyping tools and increase knowledge of genetics underlying complex traits.
This document summarizes the development and use of high density genotyping tools to improve the apple genome. It describes the creation of an Affymetrix Axiom Apple480K chip containing 487,249 SNPs identified from resequencing 67 apple cultivars. The chip was used to genotype over 1,400 samples and validated SNPs from previous studies. Mapping populations genotyped with the new chip validated over 30,000 contigs containing 485 Mb of the apple genome sequence. Future plans include using the chip and additional sequencing to further improve scaffolding and validation of the apple genome.
The document describes an automatic SNP scoring tool called ASSIsT that analyzes SNP data. It summarizes the key functions of ASSIsT, which includes filtering SNPs, classifying markers as informative, not robust, or needing further elaboration, and exporting data for various downstream analyses. The tool aims to improve over standard GenomeStudio outputs by reducing errors and missing data in SNP scoring.
This document summarizes pilot studies on peach conducted for the FruitBreedomics project. The objective was to verify the efficiency of MAS selection by screening 1500 trees from public and private partners for quality and resistance traits using SNP markers. Traits like flesh color, shape, acidity level, and resistance to aphids and powdery mildew were studied. Genotyping was performed using KASP technology. Results showed good prediction efficiency for resistance to green peach aphid and several quality traits, demonstrating the effectiveness of MAS. Further analysis of data and development of additional markers is needed to finalize the approach.
FruitBreedomics 1st Stakeholder Day meeting 20120207 The use of markers in Wä...fruitbreedomics
This document discusses the use of marker-assisted selection (MAS) in the apple breeding program at Agroscope Changins-Wädenswil Research Station (ACW) in Switzerland. The goals of the ACW breeding program are to develop apple varieties with resistance to multiple diseases like apple scab, powdery mildew and fire blight, as well as high fruit quality. MAS is used to select seedlings with desired disease resistance genes and phenotypes at various stages of the breeding process, from initial crosses to field trials, to increase selection efficiency. Marker analyses are outsourced to different laboratories. The costs of MAS per seedling or tree are estimated to range from 1 euro for initial scab screening to
FruitBreedomics KOM Stakeholders meeting 31-03-2011 5 WP3 presentation and fe...fruitbreedomics
This document outlines objectives and approaches for identifying and characterizing quantitative trait loci (QTL) for fruit quality traits and disease resistance in apple and peach through a pedigree-based approach. The goals are to clarify the genetics underlying important traits, identify linked molecular markers, discover new QTLs, fine-map known QTLs, and establish a basis for marker-assisted breeding. The project will analyze multiple breeding families using statistical genetics software and SNP genotyping arrays to map QTLs for traits like taste, firmness, sugar content, and resistance to diseases. Results will provide insights into the genetics of these traits and identify molecular markers for use in breeding programs.
FruitBreedomics 1st Stakeholder Day meeting WP8 presentationfruitbreedomics
The document discusses dissemination and outreach activities for the WP8 annual meeting, including preparing posters and templates, communicating scientific papers, and coordinating conferences. It provides statistics on the project website and social media presence. It also describes building a network of 64 stakeholders in fruit breeding programs and administering questionnaires. Finally, it outlines plans for 6 training sessions on topics like PBA software and tools, genetic resources, and MAB protocols.
This document summarizes a genome wide association study (GWAS) of two phenology traits, flowering period and picking date, in apple. The study used 1168 apple cultivars genotyped with an Affymetrix Axiom_Apple480k SNP array. Heritability estimates for the phenology traits were moderate to high. GWAS models accounting for population structure and kinship identified several significant SNPs associated with flowering period on chromosomes 9, 11, and 12. For picking date, significant SNPs were identified on chromosome 3. Some of the identified genomic regions overlapped with previous QTL mapping studies of the same traits, validating the GWAS approach. The study provides new markers that can be used for apple breeding
Fruit breedomics workshop wp6 molecular markers technology and methods riccar...fruitbreedomics
The document discusses the development of molecular marker technologies from the 1980s to the present. It describes early techniques like restriction fragment length polymorphisms (RFLPs) and advances to polymerase chain reaction (PCR)-based methods. More recently, technologies have focused on high-throughput single nucleotide polymorphism (SNP) detection and genotyping using techniques like SNPlex genotyping, sequencing, and KASP assays. The document also compares different marker types and methods based on cost, throughput, and applications.
The document discusses marker-assisted breeding and the services provided by the Sequencing and Genotyping Platform. It outlines the steps in marker-assisted selection, from laying out seedlings and collecting samples to running analyses. It also lists the facilities and equipment available, including robotic platforms for liquid handling and DNA/RNA extraction, real-time PCR systems, capillary sequencers, and Illumina platforms for high-throughput genotyping. The platform provides support for marker-assisted breeding programs through services like whole genome sequencing, targeted resequencing, and protocol development for next-generation sequencing applications.
The document summarizes a technical session on fruit tree sampling procedures for genomic analysis. It describes using a 96-well format for efficiency and two coding systems for identifying individual plants without labeling - positional coding using the layout of pots in plates and a combination number system. The demonstration showed efficient procedures for puncturing leaves and expediting plates for analysis, though the whole process took more time than expected. Costs are relatively low compared to DNA extraction and analysis, requiring close work with partner companies.
The document discusses selection for sub-acid taste and flat shape in peaches. It identifies single nucleotide polymorphisms (SNPs) associated with these traits: sub-acid taste is associated with one SNP; flat shape is associated with a haplotype of three highly linked SNPs. The SNPs could be used for marker-assisted breeding to more efficiently select for sub-acid taste and flat fruit shape, which are desirable traits for consumers.
Phenotyping texture and aroma wp5 unravel the complexity of apple aroma by pt...fruitbreedomics
The document discusses research using PTR-ToF-MS (Proton Transfer Reaction-Time of Flight-Mass Spectrometry) to analyze the volatile organic compound (VOC) profiles of apples. Key points include:
- PTR-ToF-MS provides a non-invasive way to monitor VOCs, which are important for sensory qualities like aroma and flavor.
- Research aims to understand the genetic, physiological and metabolic traits related to apple quality, ripening, and storage through VOC fingerprinting and analysis.
- Studies found 1-MCP post-harvest treatment reduces certain VOCs and may help prevent superficial scald disorder by altering VOC profiles in the skin versus flesh.
- A genome-
Fruitbreedomics workshop wp6 dna extraction methodsfruitbreedomics
The document summarizes methods for DNA extraction that were tested for use in marker-assisted breeding of fruit trees. Four extraction methods were evaluated: 1) "quick and dirty" commercial kits, 2) "direct PCR" kits, 3) magnetic particle-based kits, and 4) a homemade CTAB method. The homemade CTAB method was found to provide high quality DNA at the lowest cost and was well-suited for marker-assisted breeding work requiring analysis of hundreds of samples. The document also provides details on optimization of the KAPA 3G Plant PCR kit for short DNA fragments and highlights CTAB and KAPA 3G PCR as good extraction methods.
FQ-haplotyper is an R script that analyzes haplotype data from FlexQTL and assigns haplotype alleles. It considers each haploblock separately in half-sibling families, imputing missing SNP data or removing conflicting data based on Mendelian inheritance. The output includes files for further analysis and visualization of original and imputed haplotype alleles in pedigrees.
This document discusses the costs of using marker-assisted selection (MAS) in a peach breeding program run by IRTA-FruitFutur-ASF. It notes that MAS has been used routinely since 2012 to select for traits like flat fruit shape and acidity. The costs of MAS are about 3.5 euros per tree for DNA extraction, marker genotyping, and analysis. In comparison, traditional phenotypic selection costs about 6.7 euros per tree when considering costs of planting, maintaining trees in the orchard, evaluation, and elimination of trees from the orchard. An example is provided showing that for genotyping 1,000 trees using MAS, the total cost is around 7,272 euros, lower than the
FruitBreedomics MAB Services offers integrated consulting services to small fruit breeding companies to help overcome limitations in genetics expertise and laboratory facilities. The initial strategy of pilot studies and training was deemed insufficient, so FruitBreedomics now provides commercial consultancy services using their own data and expertise, with an approach that includes on-site visits to help clients.
This document summarizes apple and peach traits that have genetic markers available or in development for marker-assisted breeding. For apples, markers are available for resistances to scab, mildew, fire blight, and woolly apple aphid. Markers are also available or being developed for traits like fruit texture, acidity, sweetness, and color. For peaches, markers have been applied for resistance to green peach aphid and powdery mildew, as well as traits like flesh color, pubescence, and melting/non-melting flesh. Additional traits are still in development for both crops.
This document summarizes a technical session on pyramiding scab and mildew resistance genes in apple breeding at Agroscope. The objective is to cross parent lines with different resistance genes to combine two or more genes against the same pathogen. Two crosses were made between parent lines containing different resistance genes for apple scab (Rvi6 and Rvi2) and powdery mildew (Pl2). SNP markers were used to analyze the crosses and determine which resistance genes were passed to the progeny. The document demonstrates using Excel to interpret the results of the marker analysis and determine which resistance genes were combined in the progeny for future disease resistance.
This document discusses the use of markers for parent selection in peach breeding and production. It covers 1) using markers to characterize relationships between parents and for cross planning to maximize genetic distance and heterozygosity, 2) using markers for seedling selection, and 3) using markers to assist in introgressing traits. It also discusses using markers for breeder's rights protection by creating molecular fingerprints of varieties.
This document provides information about Centro Innovazione Varietale (CIV), including:
- CIV is an Italian company founded in 1983 aiming to develop new plant varieties through breeding and produce certified propagation materials.
- CIV operates on 52 hectares of land for variety trials, production of certified buds and seedlings, and strawberry nurseries.
- In addition to its own breeding programs, CIV participates in variety development programs with organizations around the world.
- CIV's portfolio includes over 30 strawberry, 12 apple, and 6 peach/nectarine varieties it has developed and licensed in over 27 countries.
This document provides a summary of a training seminar on the use of molecular markers in apple and peach breeding. The one-day seminar will cover topics including sampling procedures, utilizing markers for parental selection and hybrid selection in various breeding programs, markers available for different traits, and cost comparisons. Speakers will discuss examples from breeding programs at IRTA, Agroscope, FEM, and INRA. The afternoon will focus on the FruitBreedomics molecular breeding services and interface. The seminar aims to demonstrate how molecular markers can help breeders in tasks such as selecting for disease resistance, fruit quality traits, and verifying pedigrees.
This document summarizes the development and use of high density genotyping tools to improve the apple genome. It describes the creation of an Affymetrix Axiom Apple480K chip containing 487,249 SNPs identified from resequencing 67 apple cultivars. The chip was used to genotype over 1,400 samples and validated SNPs from previous studies. Mapping populations genotyped with the new chip validated over 30,000 contigs containing 485 Mb of the apple genome sequence. Future plans include using the chip and additional sequencing to further improve scaffolding and validation of the apple genome.
The document describes an automatic SNP scoring tool called ASSIsT that analyzes SNP data. It summarizes the key functions of ASSIsT, which includes filtering SNPs, classifying markers as informative, not robust, or needing further elaboration, and exporting data for various downstream analyses. The tool aims to improve over standard GenomeStudio outputs by reducing errors and missing data in SNP scoring.
This document summarizes pilot studies on peach conducted for the FruitBreedomics project. The objective was to verify the efficiency of MAS selection by screening 1500 trees from public and private partners for quality and resistance traits using SNP markers. Traits like flesh color, shape, acidity level, and resistance to aphids and powdery mildew were studied. Genotyping was performed using KASP technology. Results showed good prediction efficiency for resistance to green peach aphid and several quality traits, demonstrating the effectiveness of MAS. Further analysis of data and development of additional markers is needed to finalize the approach.
FruitBreedomics 1st Stakeholder Day meeting 20120207 The use of markers in Wä...fruitbreedomics
This document discusses the use of marker-assisted selection (MAS) in the apple breeding program at Agroscope Changins-Wädenswil Research Station (ACW) in Switzerland. The goals of the ACW breeding program are to develop apple varieties with resistance to multiple diseases like apple scab, powdery mildew and fire blight, as well as high fruit quality. MAS is used to select seedlings with desired disease resistance genes and phenotypes at various stages of the breeding process, from initial crosses to field trials, to increase selection efficiency. Marker analyses are outsourced to different laboratories. The costs of MAS per seedling or tree are estimated to range from 1 euro for initial scab screening to
FruitBreedomics KOM Stakeholders meeting 31-03-2011 5 WP3 presentation and fe...fruitbreedomics
This document outlines objectives and approaches for identifying and characterizing quantitative trait loci (QTL) for fruit quality traits and disease resistance in apple and peach through a pedigree-based approach. The goals are to clarify the genetics underlying important traits, identify linked molecular markers, discover new QTLs, fine-map known QTLs, and establish a basis for marker-assisted breeding. The project will analyze multiple breeding families using statistical genetics software and SNP genotyping arrays to map QTLs for traits like taste, firmness, sugar content, and resistance to diseases. Results will provide insights into the genetics of these traits and identify molecular markers for use in breeding programs.
FruitBreedomics 1st Stakeholder Day meeting WP8 presentationfruitbreedomics
The document discusses dissemination and outreach activities for the WP8 annual meeting, including preparing posters and templates, communicating scientific papers, and coordinating conferences. It provides statistics on the project website and social media presence. It also describes building a network of 64 stakeholders in fruit breeding programs and administering questionnaires. Finally, it outlines plans for 6 training sessions on topics like PBA software and tools, genetic resources, and MAB protocols.
This document summarizes a genome wide association study (GWAS) of two phenology traits, flowering period and picking date, in apple. The study used 1168 apple cultivars genotyped with an Affymetrix Axiom_Apple480k SNP array. Heritability estimates for the phenology traits were moderate to high. GWAS models accounting for population structure and kinship identified several significant SNPs associated with flowering period on chromosomes 9, 11, and 12. For picking date, significant SNPs were identified on chromosome 3. Some of the identified genomic regions overlapped with previous QTL mapping studies of the same traits, validating the GWAS approach. The study provides new markers that can be used for apple breeding
Fruit breedomics workshop wp6 molecular markers technology and methods riccar...fruitbreedomics
The document discusses the development of molecular marker technologies from the 1980s to the present. It describes early techniques like restriction fragment length polymorphisms (RFLPs) and advances to polymerase chain reaction (PCR)-based methods. More recently, technologies have focused on high-throughput single nucleotide polymorphism (SNP) detection and genotyping using techniques like SNPlex genotyping, sequencing, and KASP assays. The document also compares different marker types and methods based on cost, throughput, and applications.
The document discusses marker-assisted breeding and the services provided by the Sequencing and Genotyping Platform. It outlines the steps in marker-assisted selection, from laying out seedlings and collecting samples to running analyses. It also lists the facilities and equipment available, including robotic platforms for liquid handling and DNA/RNA extraction, real-time PCR systems, capillary sequencers, and Illumina platforms for high-throughput genotyping. The platform provides support for marker-assisted breeding programs through services like whole genome sequencing, targeted resequencing, and protocol development for next-generation sequencing applications.
The document summarizes a technical session on fruit tree sampling procedures for genomic analysis. It describes using a 96-well format for efficiency and two coding systems for identifying individual plants without labeling - positional coding using the layout of pots in plates and a combination number system. The demonstration showed efficient procedures for puncturing leaves and expediting plates for analysis, though the whole process took more time than expected. Costs are relatively low compared to DNA extraction and analysis, requiring close work with partner companies.
The document discusses selection for sub-acid taste and flat shape in peaches. It identifies single nucleotide polymorphisms (SNPs) associated with these traits: sub-acid taste is associated with one SNP; flat shape is associated with a haplotype of three highly linked SNPs. The SNPs could be used for marker-assisted breeding to more efficiently select for sub-acid taste and flat fruit shape, which are desirable traits for consumers.
Phenotyping texture and aroma wp5 unravel the complexity of apple aroma by pt...fruitbreedomics
The document discusses research using PTR-ToF-MS (Proton Transfer Reaction-Time of Flight-Mass Spectrometry) to analyze the volatile organic compound (VOC) profiles of apples. Key points include:
- PTR-ToF-MS provides a non-invasive way to monitor VOCs, which are important for sensory qualities like aroma and flavor.
- Research aims to understand the genetic, physiological and metabolic traits related to apple quality, ripening, and storage through VOC fingerprinting and analysis.
- Studies found 1-MCP post-harvest treatment reduces certain VOCs and may help prevent superficial scald disorder by altering VOC profiles in the skin versus flesh.
- A genome-
Fruitbreedomics workshop wp6 dna extraction methodsfruitbreedomics
The document summarizes methods for DNA extraction that were tested for use in marker-assisted breeding of fruit trees. Four extraction methods were evaluated: 1) "quick and dirty" commercial kits, 2) "direct PCR" kits, 3) magnetic particle-based kits, and 4) a homemade CTAB method. The homemade CTAB method was found to provide high quality DNA at the lowest cost and was well-suited for marker-assisted breeding work requiring analysis of hundreds of samples. The document also provides details on optimization of the KAPA 3G Plant PCR kit for short DNA fragments and highlights CTAB and KAPA 3G PCR as good extraction methods.
FQ-haplotyper is an R script that analyzes haplotype data from FlexQTL and assigns haplotype alleles. It considers each haploblock separately in half-sibling families, imputing missing SNP data or removing conflicting data based on Mendelian inheritance. The output includes files for further analysis and visualization of original and imputed haplotype alleles in pedigrees.
This document discusses the costs of using marker-assisted selection (MAS) in a peach breeding program run by IRTA-FruitFutur-ASF. It notes that MAS has been used routinely since 2012 to select for traits like flat fruit shape and acidity. The costs of MAS are about 3.5 euros per tree for DNA extraction, marker genotyping, and analysis. In comparison, traditional phenotypic selection costs about 6.7 euros per tree when considering costs of planting, maintaining trees in the orchard, evaluation, and elimination of trees from the orchard. An example is provided showing that for genotyping 1,000 trees using MAS, the total cost is around 7,272 euros, lower than the
FruitBreedomics MAB Services offers integrated consulting services to small fruit breeding companies to help overcome limitations in genetics expertise and laboratory facilities. The initial strategy of pilot studies and training was deemed insufficient, so FruitBreedomics now provides commercial consultancy services using their own data and expertise, with an approach that includes on-site visits to help clients.
This document summarizes apple and peach traits that have genetic markers available or in development for marker-assisted breeding. For apples, markers are available for resistances to scab, mildew, fire blight, and woolly apple aphid. Markers are also available or being developed for traits like fruit texture, acidity, sweetness, and color. For peaches, markers have been applied for resistance to green peach aphid and powdery mildew, as well as traits like flesh color, pubescence, and melting/non-melting flesh. Additional traits are still in development for both crops.
This document summarizes a technical session on pyramiding scab and mildew resistance genes in apple breeding at Agroscope. The objective is to cross parent lines with different resistance genes to combine two or more genes against the same pathogen. Two crosses were made between parent lines containing different resistance genes for apple scab (Rvi6 and Rvi2) and powdery mildew (Pl2). SNP markers were used to analyze the crosses and determine which resistance genes were passed to the progeny. The document demonstrates using Excel to interpret the results of the marker analysis and determine which resistance genes were combined in the progeny for future disease resistance.
This document discusses the use of markers for parent selection in peach breeding and production. It covers 1) using markers to characterize relationships between parents and for cross planning to maximize genetic distance and heterozygosity, 2) using markers for seedling selection, and 3) using markers to assist in introgressing traits. It also discusses using markers for breeder's rights protection by creating molecular fingerprints of varieties.
This document provides information about Centro Innovazione Varietale (CIV), including:
- CIV is an Italian company founded in 1983 aiming to develop new plant varieties through breeding and produce certified propagation materials.
- CIV operates on 52 hectares of land for variety trials, production of certified buds and seedlings, and strawberry nurseries.
- In addition to its own breeding programs, CIV participates in variety development programs with organizations around the world.
- CIV's portfolio includes over 30 strawberry, 12 apple, and 6 peach/nectarine varieties it has developed and licensed in over 27 countries.
This document provides a summary of a training seminar on the use of molecular markers in apple and peach breeding. The one-day seminar will cover topics including sampling procedures, utilizing markers for parental selection and hybrid selection in various breeding programs, markers available for different traits, and cost comparisons. Speakers will discuss examples from breeding programs at IRTA, Agroscope, FEM, and INRA. The afternoon will focus on the FruitBreedomics molecular breeding services and interface. The seminar aims to demonstrate how molecular markers can help breeders in tasks such as selecting for disease resistance, fruit quality traits, and verifying pedigrees.
The document describes Fruitbreedomics, a project that developed a database and breeding interface to improve fruit breeding programs. It collected large amounts of phenotype and genotype data from apple and peach varieties, including traits, markers, and resequencing data. It provides online tools for users to explore the data, including a JBrowse genome browser, breeder's interface to design crosses, and LDExplorer for linkage disequilibrium analysis. The goal is to bridge the gap between genetic research and breeding applications.
The document describes Pedimap software, which is a tool for visually presenting pedigree relationships. It can be used to clarify genetic structures in breeding germplasm and inheritance patterns. The software allows input of pedigree data along with optional phenotypic trait or marker genotype data. It provides different view types, including overviews, names only, names with phenotypic values, and names with marker genotypes. Pedimap is freely available and helps breeding programs validate parentage, true-to-type status of germplasm, and understand the origin and introgression of chromosome segments.
This document summarizes the work of the FruitBreedomics project WP2 on developing apple and peach pre-breeding material. For apples, the objectives were to introduce resistance to scab, mildew and fire blight through marker-assisted breeding in Switzerland and Germany. Selected progenies combined multiple resistance genes. For peaches, the focus was on resistance to powdery mildew and brown rot through conventional breeding in Italy, with some progenies combining both resistances. Marker-assisted breeding in France targeted resistance to multiple pests and diseases. The availability of pre-breeding material from different populations was also outlined.
This document summarizes initial results from modeling genome-wide predictions in peach. Eleven peach populations from four sites were genotyped and phenotyped for traits like fruit weight, sugar content, and acidity. Genotypes were imputed and a repeatability model was used to estimate heritability and predict trait values based on genomic relationships. Preliminary results showed variable predictive ability across populations and traits. Next steps include standardizing the data analysis and interpreting the results to draft a paper on genomic predictions in peach breeding.
This document summarizes a two-year pilot study on genomic selection in apple breeding. The study involved genotyping and phenotyping a training population of 20 full-sib families and 5 application families. Genomic prediction models were developed and used to calculate genomic estimated breeding values (GEBV) for traits like fruit quality, size, and disease resistance. The accuracy of genomic prediction varied among traits from poor to moderate, and selection differentials based on GEBV were significant for several traits. The study provides a proof of concept for genomic selection in apple breeding but highlights the need for further research on prediction accuracy across multiple years and environments.
This document summarizes pilot studies on using molecular markers to assist breeding of new apple cultivars with improved disease resistance and fruit quality traits. Two crosses were made in 2011 and progeny were screened using SNP markers for scab, mildew resistance and fruit quality. Over 1000 seedlings were analyzed, and the best 176 for cross 1 and 100 for cross 2 were selected for further evaluation based on their molecular profiles. The studies demonstrated both benefits and challenges of marker-assisted breeding in apple.
This document summarizes research exploring phenotypic and genetic diversity in peach. Over 1580 accessions were studied across multiple locations in Europe and China. Phenotypic data was collected over several years and correlated between locations. Genetic analysis using a 9K SNP chip identified 473 clones and grouped accessions into occidental breeding, occidental non-breeding, oriental, and admixed categories. Genome-wide association studies identified major genes and QTLs associated with traits like acidity, melting behavior, and fruit flesh color.
This document summarizes research that used pedigree-based analysis (PBA) to identify quantitative trait loci (QTLs) in peach using data from multiple research centers. PBA was applied to 1,472 offspring from 18 crossing populations genotyped with 9K SNP markers and phenotyped for 24 traits. Several significant QTLs were detected for ripening date, sugar content, blush percentage, and acidity. The QTLs identified new alleles and genomic regions associated with these economically important traits. Integrating data from diverse populations allowed for discovery of more QTLs than previous studies using single progenies.
The researchers conducted QTL mapping in apple using a large pedigree with over 1,500 individuals from 7 countries. They phenotyped over 30 traits related to fruit quality and identified several QTLs associated with titratable acidity, including major QTLs on linkage groups 1, 8, and 16. The QTLs explained 55% of the phenotypic variance. They were able to fine map positions of known genes like Ma1 and Ma2. Additional QTLs were found to cluster on linkage group 1, suggesting potential pleiotropic effects or trait correlations in this region linked to scab resistance. The results provide reliable markers that can be used to accelerate apple breeding for fruit quality and storage traits.
This document discusses methods for detecting water stress tolerance in apple plants. It presents a water stress protocol that maintains plants at 37% of available water to induce stress without visible symptoms. Six physiological parameters were tested as potential indicators of stress, but multiple regression analysis identified three parameters - chlorophyll fluorescence, leaf temperature, and stomatal conductance - measured in 30 seconds that best discriminated genotypes' stress tolerance when compiled into a single index called IPL. A cluster analysis of IPL scores grouped genotypes as susceptible, intermediate, or tolerant of water stress with 53% consistency over two years. While IPL shows promise, replicating the water stress protocol across years and genotypes remains challenging. Reliable, quick measurements may help improve the
This document discusses strategies to select apple varieties that are optimal for long-term storage. It describes testing various apple varieties under different storage conditions to assess traits like chilling injury, texture, and disorder sensitivity. Gene expression analysis is proposed as a way to potentially identify indicator genes that could help select good varieties earlier in breeding. A storage stress test is developed applying extreme short-term storage conditions followed by analysis of responses and symptoms. This may help select lines with better long-term storage potential while using fewer fruits than longer storage tests.
1. Researchers assessed various instrumental, biochemical, and sensory techniques to evaluate texture phenotypes in peaches from different cultivars grown over multiple seasons.
2. Instrumental measurements of firmness loss during storage revealed differences between cultivars that maintain firmness for longer, like Big Top, versus those that soften more quickly.
3. Computerized tomography, fruit fluorescence, and monitoring firmness changes over time showed potential for distinguishing slow melting from regular melting cultivars. However, other tests did not consistently capture differences between cultivars.
4. Preliminary results identified a major QTL on chromosome 5 that could explain up to 30% of the slow melting trait, though the trait is also linked to
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4. Deliverable review process
• Deliverables are contractual elements to be
provided at a specific delivery date to the EC.
• In case a delay is foreseen, please inform me
as soon as possible.
Ask for revisions if
needed
Due date
WP Coordinator
Author
Leader Project Manager EC
Write the
deliverable Check & approve Check & validate
5. Deliverables due during the first 2
years of the project
Due Date
2011 2012
2012
Initial
Year 1 Year 2
Year 2
WP Del. Description
Ma. Ap. May Ju. Ju. Au. Se. Oc. No. De. Ja. Fe.
Ma. Ap. May Ju. Ju. Au. Se. Oc. No. De. Ja. Fe. Ma. Ap. May Ju. Ju. Au. Se. Oc. No. De. Ja. Fe.
1 2 3 4 5 6 7 8 13 14 15 16 17 18 19 20 21 22 23 24
9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
1 D1.1 Description of ideotypes and breeding schemes M12 I P
2 D2.1 Detailed description of available genetic material carrying the chosen traits M23 useful for breeding
and II
D3.1 List of EU-founders and indications on their level of exploitation in breeding.M10 I P
3 D3.2 New version of the FlexQTLTM with several new capacities and functionalities. M24 II
D4.1 I collections.
Description of phenotypic and genotypic variability using available data in (i) in 4 peach germplasm collections and (ii) in 5 apple germplasm collections.
M12
4 D4.2 Database uploaded with already-available phenotypic characterisation of the 600 peach cultivars of the selected core collections (4 CC of 150 cultivars each) and the 1500 app
M24 II
each) and the 1500 app
D5.1 List of the tools and protocols developed for phenotyping new (sub)-traits. M12 I
5 D5.2 Identification of effective tools or protocols to characterise (sub)-traits. M24 II
D6.1 Low density apple genotyping array (384 SNP array) is made available. M4 I, 0
D6.2 Medium density apple genotyping array (3-9K SNP array) is made available M12 I
6
D6.3 The peach GWA genotyping array (9K SNP) is made available M12 I
D6.4 Apple GWA genotyping array (ca. 50K SNP array, final density to be decided based on LD extension (see milestone year 1.5) is made available.
M24 II
D7.1 Fruit Breedomics database frame M12 I
7 D7.2 Complete collections of trait phenotypic data from genetic material available and complete list of identified genomic variation.
M24 II
D8.1 Project website and brochure. M6 I X 0
D8.2 Detailed stakeholder requirements compiled from the seminars. M9 I P I
8 D8.3 Publication of annual newsletters M12 I II
D8.4 Printing the Booklets M24 II
D8.5 Mapping of the connections established with other project and initiatives. M20 I
D9.1 Kick-off meeting (including ExCom meeting). M1 I 0
D9.2 Project Collaborative workspace. M3 I,0
9 D9.3 Management Guidelines. M3 I X,0
D9.4 I
Organisation of Annual Project Meetings (including meetings of the ExCom, the General Assembly, and the Stakeholder Advisory Board) and preparation of minutes.
M12 preparation of minutes. II
D9.5 1st Reporting Period consolidated technical and financial reports M20 I
6. Deliverables due during the second
year of the project
Dissem Delivery
N° Deliverable title WP N° Leader Nature ination date
level (planned)
Description of ideotypes and breeding M12
D1.1 schemes WP1 INRA R RE
(M15)
Detailed description of available genetic
D2.1 material carrying the chosen traits and WP2 CRA R RE M23
useful for breeding
List of EU-founders and indications on M10
D3.1 their level of exploitation in breeding. WP3 DLO R RE
(M18)
New version of the FlexQTLTM with
D3.2 several new capacities and WP3 DLO P CO M24
functionalities.
Description of phenotypic and genotypic
variability using available data in (i) in 4 M12
D4.1 WP4 CRA-W R RE
peach germplasm collections and (ii) in 5 (M17)
apple germplasm collections.
Database uploaded with already-
available phenotypic characterisation of
the 600 peach cultivars of the selected
D4.2 WP4 CRA O RE M24
core collections (4 CC of 150 cultivars
each) and the 1500 apple cultivars from 5
European CC.
List of the tools and protocols developed
D5.1 WP5 INRA R PU M12
for phenotyping new (sub)-traits.
Identification of effective ols or procols
D5.2 WP5 INRA R PU M24
characterise (sub)-traits.
7. Deliverables due during the second
year of the project
Medium density apple genotyping array (3- M12
D6.2 WP6 FEM P Co
9K SNP array) is made available (M15)
The peach GWA genotyping array (9K
D6.3 WP6 FEM P Co M12
SNP) is made available
Apple GWA genotyping array (ca. 50K SNP
array, final density be decided based on LD
D6.4 WP6 FEM P Co M24
extension (see milesne year 1.5) is made
available.
D7.1 Fruit Breedomics database frame WP7 PTP P RE M12
Complete collections of trait phenotypic
data from genetic material available and
D7.2 complete list of identified genomic variation. WP7 PTP R RE M24
D8.2 Detailed stakeholder requirements compiled
WP8 INRA R RE M9 & M21
from the seminars.
D8.3 Publication of annual newsletters M12 &
WP8 IRTA O PU
M24
D8.4 Printing the Booklets WP8 IRTA R PU M24
D8.5 Mapping of the connections established
WP8 IRTA R RE M20
with other project and initiatives.
D9.4 Organisation of Annual Project Meetings
(including meetings of the ExCom, the
General Assembly, and the Stakeholder M12 &
WP9 IT O RE
Advisory Board) and preparation of minutes. M24
D9.5 1st Reporting Period consolidated technical
WP9 IT R RE M20
and financial reports
8. Milestones
• Milestones are significant points or events in
the project to follow-up the project
progresses.
• No official report is necessary.
• Each milestone must at least lead to a short
description of the result that must be
uploaded on the workspace for internal
purpose: even if they are only working
document and not beautiful reports.
9. Overall planning
2nd Pre-financing = Kick-off, Annual Meetings and Final Conference
M13
= Lead to
March 2012
Evaluation 1st Interim Payment 2nd Interim Payment
Procedure M22 M42
M12 Dec. 2012 Aug. 2014
Final Payment
EC Review EC Review M60
M21 M39 Feb. 2016
1st Pre-
financing Periodic Periodic
M3 Report Report Final Report
May 2011 M20 M38 M56
First Reporting period Second Reporting period Third Reporting period
M1 M18 M36 M54
March 2011 Aug. 2012 Feb. 2014 Aug. 2015
10. M12-Evaluation procedure
– In addition to the 3 reports due to the EC, an
Evaluation Procedure is taking place to check
the good start of the project.
• It will lead to the payment of the second part of
the pre-financing to the partners (“Conditional
Pre-Financing” outlined in Article 7.3 of the
Consortium Agreement).
• It will be done on the basis of scientific and
technical indicators in order to check the
adherence of each Partner contribution with that
outlined in the DoW (tasks, milestones,
deliverables).
11. FruitBreedomics
M12-Evaluation procedure
M12-Evaluation Procedure
29
Annual
Meeting February
24 March
9 January 1 February 5 March 21 March 10 April
M11 M12 M13 M14
Missing partners’ reports:
IT
Partners Coord.
Provides WP Leaders
•ASF Fill in the report
report Analyze and IT
Makes the
template
•Novadi
templates synthesize Compiles the
payment to
the validated
their reports report for the
•DLO whole project
partners
•ARC
ExCom
•PFR Checks and Coord. + IT
validates Analyze
reports IT
Informs the
partners for
which payment
is retained if
any
• The payment will be made after approval by the ExCom.
• More details can be found in the Reference Sheet N°7 of the
Researchers’ Guide.
12. M18-Periodic report
• Covers the period from 1st March 2011 to 31st August 2012
• This report includes:
• A scientific report of the tasks the partner contributed to (including
the Use of foreground and dissemination activities). This report should
include a description of the work progress towards the objectives of
the project compared to the planned objectives of the DoW.
• Cost declaration (Financial Statement = Form C) to be filled in online
and signed after validation of the form by the project manager
• Detailed justification of costs and resources deployed by each
contractor during the reporting period (Detailed Form C)
• Templates will be made available after the end of the M12-
Evaluation
• The EC asks for a technical report restricted to the description of
the work done in order to justify the costs declared by the partners.
• The actual results of the project should be described in more
details in the Deliverables which are the actual outcomes of the
project and can be added as Attachments to the report.
13. M18-Periodic report
• Note the dates in your agenda
FruitBreedomics
• Forward these deadlines to your financial and administrative
services (check that these contacts are Process contact list)
M18-Reporting correct in the
31 August 31
October
10 September 20 September 15 October
1 August 28 September 10 October 24 October
M18 M19 M20
Scientific Report
IT
Partners
Provides WP Leaders
Fill in the report IT
report Analyze and synthesize ExCom
template Checks and Checks and Coord. + IT
templates their reports
Compiles validates Write the
the report final report
IT EC
Financial Report
Partners
Provides Fill in the report templates: IT
report Checks & Partners
1. Annex I “FormC” Sign the FormC IT
templates 2. Annex II “Detailed FormC” Compiles Checks and
validated by the
3. A Word file with partner Project Manager Compiles
information
15. Financial issues
• Refer to the Reference Sheet N°9 of the Researchers’ Guide
for general principles
• Temporary and permanent staff must declare their working
time on timesheets (no FruitBreedomics standards)
• Reimbursement of congress costs:
– The EC recently reminded the rules to ask reimbursement of
the participation to a scientific congress under the frame of an
EU project:
• there must be an action of dissemination (poster minimum in Europe;
oral communication minimum outside of Europe) by the person
asking reimbursement of his/her travel,
• it is limited to one person per institute (or per research units for large
institutes like INRA).
– To have more researchers attending a congress, you have to
provide justifications that will be forwarded to the Project
Officer for validation. If you don’t do so before attending a
congress, the EC might refuse to reimburse your costs.
16. EC Financial contribution per
activity
MAXIMUM EC CONTRIBUTION
Non-profit public bodies,
secondary and higher
ACTIVITIES education establishments, Others
research organisations
and SMEs
Research: WPs 1 to 7 75 % 50 %
Dissemination of results:
articles, presentation in
conferences, news for the
website, etc. WP8 100 % 100 %
Management: WP9 (only for
INRA and INRA Transfert) 100 % 100 %
17. Payments
European
Commission
• Pre-financing : contract signature + 45
days
• Interim or Final payments: 105 days after
receipt of the validated report
INRA Transfert INRA
Preparation of No more than 15 days after receiving the
payments EC payments
PARTNER 1 PARTNER 2 PARTNER n
18. Next Payments
• On the basis of M12-Evaluation and following the
validation by the ExCom, the Coordinator will
distribute the second part of the pre-financing to the
partners at the end of April 2012:
– A subsequent pre-financing of 30% of (160 % of the
average EC funding per period, minus the contribution to
the Guarantee Fund - 5% of the total EC contribution for
the project).
• Following approval by the EC of the first M18-periodic
report, the Coordinator will distribute:
– a payment which settles the amounts justified and
accepted by the EC during the first reporting period. This
payment will be limited to 75% of the EC contribution to
be received during the whole project duration and might
be distributed around December 2012
20. Researcher’s Guide
• The FruitBreedomics Researcher’s Guide
is intended to help all the persons
involved in the project.
• It sets up common rules to be applied by
all.
• Please print it and have it available at all
time on your desk. It will answer most of
your questions about your participation to
the project and the EC rules in EU-funded
projects.
21. Collaborative workspace
• The collaborative workspace has been designed to help
you to achieve your tasks in the project.
• It is not a web-site but a place where you can exchange
ideas, information and documents with other
FruitBreedomics participants, plan meetings, etc.
• This tool is the core of the project so do not hesitate to
use it.
• All the minutes of the workshops organised by your
tasks should be available on the workspace so that
other members of the project can see what is going on
in your task.
• The Internal Newsletter displays links to the workspace
22. External communication
• Every partner must be actor of external communication
by:
– adding a link on the website of your organization to the
FruitBreedomics website,
– providing input to the FruitBreedomics website if you have
some items to disseminate to the outside world,
– representing FruitBreedomics at national or International
events,
– spreading information about FruitBreedomics in your country
and to your usual contacts (national projects, press, etc.).
23. Communication tools
• Dedicated communication tools to present the project
have been developed by WP8. You can find them on the
workspace:
– A PowerPoint template
– A Poster template
– A general PowerPoint presentation of the project
– A general Poster presentation of the project
– The logo of the project
• The brochure of the project is now available. Each
partner organization will receive some copies. Do not
hesitate to use it when you present FruitBreedomics in
your country or when you go to a conference. If you
need some additional copies, contact Joan Bonany
(Joan.Bonany@irta.cat).
24. Stakeholder Platform
• The objectives of the Stakeholder Platform are:
– to provide preferential contact for the dissemination of the
project’s outcomes to society,
– to discuss the most promising results and how they should be
transferred.
• The Stakeholder Platform gathers representatives of all
players intervening in the supply chain from
scientists, breeders, germplasm collection
curators, nurserymen, to cooperatives, and growers.
• Do not hesitate to propose additional contacts in order
to enlarge the platform and ensure the efficient uptake
of FruitBreedomics results. Send your propositions of
contacts to Joan Bonany (Joan.Bonany@irta.cat).
25. Publication
• Publications and communications are an important part
of the evaluation of the success of a project by the EC.
We therefore remind you that:
– Any project of publication must be submitted through the workspace
30 days before publication (or 30 days before submission in the case
of a scientific paper) following the process described in the
FruitBreedomics Researcher’s Guide (Reference Sheet N°5). This
concerns all publications linked to FruitBreedomics funding which are
not necessarily 100% financed by FruitBreedomics but for which some
funding have been received.
– It is mandatory acknowledge EC funding in every publication or
communication.
26. Next meetings organisation
• Next ExCom meeting by Phone beginning
of March 2012
• 2013 Annual Meeting in IRTA
– Dates and location will be chosen in the
coming weeks/months