FruitBreedomics 1st Stakeholder Day meeting 20120207 Better3fruit
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Better3fruit is a private apple and pear breeding company founded in 2000 by Annemarie Auwerkerken. They have 8 commercial apple varieties and focus on breeding for fruit quality, disease resistance, attractiveness, productivity, and storage ability. Their breeding program involves identifying parents, making crosses to generate progeny, and evaluating over 10,000 trees per year. They use markers and genetic profiling for parent selection, intellectual property, and hybrid identification. Notable commercial varieties include Nicoter, Greenstar, Zari, and Tunda. Their apple variety Apple 14 is highly productive with red skin, sour-sweet flavor, and excellent storage. Bottlenecks include space, labor, funding, and reliable markers for quantitative traits.
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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.
00 soatin
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.
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.
20 nazzicari
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.
19 van de weg
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.
18 baumgartner pascal
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.
15 pascal
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.
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.
13 aranzana
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.
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- 1. Better3fruit Annemarie Auwerkerken breeder
- 2. 1988 start apple breeding NV Johan Nicolaï Catholic University – Fruitteeltcentrum 2000 Better3fruit = Private 2005 start pear breeding 2012 8 commercial apple variaties
- 3. 9 people 1 CEO 2 Breeders 1 Intellectual Property Manager 1 Field Manager 3 Field Technical personnel 1 Administration
- 5. Mission: ‘Create new and better fruit!’ high-quality, innovative, controlled
- 6. Breeding objectives Fruit quality Texture and Taste Cold storage + Shelf life Attractivness Appeal and uniformity Durable disease resistance Scab, Powdery mildew Productivity and regular bearing
- 7. Breeding programs QUALITY Program Programs for commercial product DURABLE DISEASE RESISTANCE Program Pre-breeding programs (Recurrent back crossing) Pyramidisation programs Quality program
- 8. Breeding strategies Identification of the parents • Research projects • Test crosses • Artificial infection test • Sensory evaluations • Molecular markers • ... Origin of the parents Percentages Total Elite hybrids Better3fruit 50 Commercial cultivars 39 Elite hybrids other breeding programs 9 Germplasm collections 2 100 %
- 9. Breeding program Parents- Crosses- Progeny Average number of crosses : highly variable Average number of parents : 20-50 Average size of a progeny : 200-1000 10.000 first screeningtrees /year
- 10. Where do we use markers? Parents: major disease resistant genes, S-alleles selection, fingerprinting Genetic profile for intellectual property defence No hybrid selection !
- 11. Commercial varieties Nicoter- Kanzi/Nicogreen - Greenstar : worldwide, EFC B3F44 and B3F 45: worldwide, Univeg Zari, Zonga: Western Europe, New Zealand, Australia, Slovenia Tunda: Western-Europe apple 14: Hungary
- 12. APPLE 14 LIBERTY x GRANNY > Scab resistant, mildew tolerant, fire blight tolerant > Harvest time (Belgium): around Braeburn > Large (75/85 mm), globose-oblong fruit, very uniform in shape and size > Smooth skin with dark red blush on a green background and small white lenticels > Sour-sweet with hint of citrus > Firm and juicy > Excellent storage capacity and outstanding shelf life > Very productive! > Medium to strong vigour APPLE 14
- 13. Conclusions Bottlenecks of the program Space, labour, funding Pollen new released varieties Reliability of markers for quantitative traits General needs Markers for quantitative traits ‘Ready to use’ and ‘reliable’