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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.06 aranzana
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05 costafruitbreedomics
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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.03 arus
03 arusfruitbreedomics
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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.04 baumgartner
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01 patocchi 1fruitbreedomics
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00 soatinfruitbreedomics
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油
The document contains data from an apple genomics study. It includes the percentages of various apple traits that can be explained by genomics, breeding, and post-harvest factors. It also contains several tables and charts showing the results of genetic mapping of apple cultivars like 'Delearly', 'Granny Smith', and 'Jazz' using molecular markers. The data identifies genetic markers associated with traits of interest and their location on apple chromosomes.Fruit breedomics workshop wp6 molecular markers technology and methods riccar...
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油
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.Fruit breedomics workshop wp6 from marker assisted breeding to genomics assis...
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油
The document discusses strategies for genotyping using single nucleotide polymorphisms (SNPs). It describes different types of molecular markers that have been used over time, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), simple sequence repeats (SSRs), amplified fragment length polymorphisms (AFLPs) and SNPs. It also provides details on different SNP genotyping techniques ranging from low to high throughput, such as gel electrophoresis, fluorescent PCR, mass spectrometry and various array-based methods. The document outlines the process of developing a high density 480K SNP array for apple, including SNP discovery by resequencing accessions and filtering SNPs for the array design.Fruit breedomics workshop wp6 a cost effective strategy for mas riccardo velasco
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油
This document summarizes the marker assisted selection (MAS) strategy used in the apple breeding program at Fondazione Edmund Mach. The program uses molecular markers to efficiently select for resistance traits and quality traits. Over 10,000 apple genotypes have been evaluated using MAS to pyramid resistance genes from different sources into new cultivars. The breeding program maintains a large germplasm collection and performs extensive crosses between sources of resistance. Offspring are rapidly screened using optimized DNA extraction and marker analysis pipelines, allowing over 10,000 plants to be analyzed in just 3 weeks. MAS is accelerating the development of new apple varieties with improved combinations of resistance to important diseases like apple scab and powdery mildew.Fruitbreedomics workshop wp6 dna extraction methods
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油
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.More from fruitbreedomics (19)
Fq haplotyper poster-eucarpia-2015-fruit-section_bologna-june_14-18
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油
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.19 van de weg
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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
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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.13 aranzana
13 aranzanafruitbreedomics
油
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.12 muranty
12 murantyfruitbreedomics
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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 breeding11 hernandez
11 hernandezfruitbreedomics
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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.10 letschka
10 letschkafruitbreedomics
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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.09 corelli
09 corellifruitbreedomics
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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 the08 mes
08 mesfruitbreedomics
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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.07 gine
07 ginefruitbreedomics
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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 to06 pacheco
06 pachecofruitbreedomics
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1. The document describes methods developed to assess brown rot resistance in peach fruits, including an orchard spray-based method and a laboratory drop-based method.
2. Phenotypic data on infection probability and rot progression was collected from multiple populations over two years using these methods. Sub-traits associated with resistance like cuticular conductance, stomatal density, and fruit size effects were also analyzed.
3. The results provide insights on factors influencing infection probability and rot progression to inform breeding for improved brown rot resistance by combining favorable sub-traits.05 di pierro
05 di pierrofruitbreedomics
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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.04 di guardo
04 di guardofruitbreedomics
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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.03 bianco
03 biancofruitbreedomics
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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.02 peil
02 peilfruitbreedomics
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This document discusses research on developing early flowering apple lines using the BpMADS4 gene. Key points:
- Several transgenic apple lines were produced containing the BpMADS4 gene from birch, which caused early flowering in vitro and in the greenhouse. Fruits and seeds were obtained.
- The early flowering trait was shown to be heritable. Crossing was used to introgress the trait into different apple genotypes and introduce disease resistance from other sources.
- Linkage analysis was performed to determine the chromosome location of the inserted BpMADS4 gene in different lines to aid future breeding.
- New early flowering lines were developed in additional apple genotypes like Gala and Santana usingAd
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- 2. FruitBreedomics MAB Services Fruit breeding programs Small sized companies (familiy owned) Limited access to expertise in genetics/genomics Limited access to laboratory facilities Soon realize that initially devised strategy (pilot studies, training sessions) was not going to be enough FruitBreedomics Services Service offered on a commercial basis Not a genotyping platform but an integrated consultancy approach (including on-site visits) Based on FruitBreedomics and other available data
- 3. FruitBreedomics MAB Services werner.howad@irta.cat massimo.pindo@fem.it fabienne.mathis@vegepolys.com