FruitBreedomics KOM 29 03-2011 7 WP5 presentation
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WP5 aims to develop tools to determine novel traits in apple and peach, investigate complex traits using 'omics' approaches and modeling, and make trait analysis high-throughput. It will select cultivars to study trait variation, develop quantification protocols, and standardize methods for large-scale phenotyping. Specific tasks include developing tests for Monilinia resistance in peach, tools to assess texture and fiber content in apple, and tests to evaluate responses to chilling, heat, and water scarcity requirements for climate change adaptation. Results will provide knowledge of genetics underlying novel traits and validate tools on contrasting cultivars.
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This document discusses postharvest quality issues and breeding. It begins with an introduction to Jan Verschoor's background in postharvest technology research. It then discusses how 1/3 of produced food is lost due to quality issues during postharvest handling and storage. Optimizing postharvest conditions could help reduce losses and feed over 2 billion people. The document outlines several physiological and microbial quality issues like bitter pit, scald, chilling injury, and watercore. It stresses that quality starts at harvest and is influenced by cultivar selection, maturity, and growing conditions. Optimal storage conditions and tools to monitor and control disorders are described. The challenges of breeding for postharvest quality attributes are also discussed.
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FruitBreedomics KOM 303-2011 2 intellectual property issues
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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 KOM 29 03-2011 5 WP3 presentation
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.
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The seminar featured presentations from various perspectives, including industry, regulatory bodies, and academia. Topics included the history and principles of Problem Formulation, industry perspectives on Problem Formulation and how it is applied internally for microbial pesticides, regulatory approaches, and specific case studies. The seminar provided an overview of the challenges, considerations, and potential solutions in harmonising Problem Formulation for biopesticide risk assessment. It emphasised the need for collaboration and discussion to develop Problem Formulation guidance for biopesticides.
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www.fruitbreedomics.com
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WP4 aims to explore genetic diversity in European apple and peach germplasm collections using association genetics. The objectives are to improve knowledge of genetic variability, define subpopulations, identify genomic regions contributing to traits, and supply tightly linked markers to WP1. The approach involves phenotyping over 1900 apple and 1250 peach cultivars, genotyping them with SNPs, analyzing population structure and linkage disequilibrium, acquiring new phenotype data, and performing genome-wide association analysis to map quantitative trait loci. Expected results are manuscripts describing allelic diversity, population structure, linkage disequilibrium, and genomic locations of QTLs detected by association mapping in apple and peach.
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The document discusses the establishment of a seed testing laboratory. It provides information on the objectives of seed testing which are to determine seed quality, identify problems, and check if seeds meet standards. It also discusses following proper procedures for seed sampling, testing germination and purity, and storing records. The summary outlines the key steps for managing a seed testing laboratory which are receiving samples, conducting moisture tests quickly, preparing samples for germination tests, performing routine purity and germination analyses, completing other tests promptly, storing sample remains, and maintaining accessible records.
GOOD LABORATORY PRACTICES
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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.
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Abiotic Stress
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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.
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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
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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
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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.
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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
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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.
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- 1. WP5: Enhancing the knowledge of genetics underlying novel traits and providing phenotyping methods WP leader Bénédicte Quilot-Turion, INRA Avignon, FRANCE
- 5. Tasks Task T5.2: Tools to assess fruit quality - New tools for improved texture determination Instrumental tools and reference analysis to characterise the sub-traits of apple and peach texture. Apple _ non targeted approaches: microarrays (PFR-DLO) and a full genome oligo array (INRA and FEM) Peach _ gene expression of indicator genes downstream of ethylene perception - New tools to determine apple’s sensitivity to storage New storage simulation tests will be developed with the aim to develop a tool to select genotypes which are suited for prolonged storage - New tools to determine apple fibre content The use of near infra-red (NIR) analyses will be explored to make available an easy tool to determine fiber content of apple
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