FruitBreedomics KOM Stakeholders meeting 31-03-2011 3 WP1 presentation and feedback session
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WP1 aims to increase the efficiency of marker-assisted breeding in apple and peach. It has 5 tasks: 1) Define breeding strategies and test them in pilot studies 2) Develop molecular markers linked to horticultural traits 3) Conduct pilot studies to validate MAB predictions 4) Optimize a genotyping pipeline for use in the pilot studies 5) Specify a breeder interface to access trait/marker data The work will be carried out over 54 months with partners taking leadership roles in different tasks and countries. Stakeholder input will help determine breeding objectives and evaluate results.
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Application of Molecular Markers SNP and DArT in Plant Breeding: A Review Paper
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Molecular markers (DNA markers) have entered the scene of genetic improvement in a wide range of horticultural crops. Among the major traits targeted for improvement in horticultural breeding programmes are disease and pest resistance, fruit yield and quality, tree shape, floral morphology, drought tolerance and dormancy. The development of molecular techniques for genetic analysis has led to a great increase in the knowledge of horticultural genetics and understanding and behavior of their genomes. These molecular techniques in particular, molecular markers, have been used to monitor DNA sequence variation in and among the species and create new sources of genetic variation by introducing new and favorable traits from landraces, wild relatives and related species and to fasten the time taken in conventional breeding. Today, markers are also being used for, genetic mapping, gene tagging and gene introgression from exotic and wild species.07 wp6 progresses&results-20130221
WP6 aims to develop genomic tools for apple and peach breeding. It has created a 384-SNP array and 20K-SNP array for apple. It validated the IPSC peach 9K-SNP array. Future plans include resequencing 48 apple genotypes for SNP discovery, developing a 400K-600K apple SNP chip, and testing GBS for genome-wide association studies in apple. Protocols for marker-assisted selection are being updated. The workplan interacts with other RosBREED work packages on mapping populations, germplasm, and bioinformatics.
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11 nazzicari
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Fq haplotyper poster-eucarpia-2015-fruit-section_bologna-june_14-18
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:
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01 patocchi 1
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.
17 biscarini
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.
16 bink
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.
14 kellerhals
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.
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12 muranty
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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- 1. WP1: Increase efficiency of (marker assisted) breeding Andrea Patocchi ACW (EVD), Switzerland
- 8. Structure of WP1 and interaction with other WPs T1.3 PILOT STUDIES T1.1. Definition of breeding aims (ideotypes) and strategies to reach this aims Needs of the stakeholders T1.5 Breeder interface allows selection of best parents for cross Test in pilot studies T1.2, WP3 and 4 Identification of SNP markers associated with traits/loci segregating in the populations of the pilot studies WP6 MAS genotyping protocols to be used for the genotyping of the populations of the pilot studies (T1.4) and later in commercial Breeding programs (fully outsourced) WP8 Presentation of the results of the pilot studies results to the stakeholders (8.4)