8 fem fruit breedomics mab services pindo massimo

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  • Marker assisted selection (MAS) permits the selection of plants carrying alleles conferring superior phenotypes through the screening of markers tightly linked to those traits. In practice, it is possible to select plants at the seedling stage to enable the breeders to retain only germplasm conferring desirable traits from an early stage. Usually MAS involves the screening of hundreds or thousands of seedlings: the main challenge faced is thus developing a pipeline that begins with a “lab friendly” and unambiguous seedling configuration in greenhouse, which then allows the rapid collection of samples avoiding cross contamination, implements a fast, cost-effective, high-throughput method of DNA extraction to be used for a small number of PCRs, and utilizes robust, reliable, and easy to interpret molecular markers. In this work we report on the development of a pipeline at the Fondazione Edmund Mach (FEM) to enable the implementation of a time and cost effective MAS program for apple (Malus pumila Mill.).
    We screened 6.471 seedlings sown in a greenhouse from 24 apple crosses in order to select seedlings conferring resistance traits, fruit quality traits or both.
    CONCLUSIONS
    MAS involves a large numbers of seedlings, that have to be screened in a relatively short time so only superior genotypes can be transplanted.
    We have demonstrated that marker assisted selection for apple fruit quality and disease resistance at FEM is reliable and in future years will improve in time and cost effectiveness.
  • 8 fem fruit breedomics mab services pindo massimo

    1. 1. Sequencing and Genotyping Platform Applications Facilities & Services Massimo Pindo, PhD massimo.pindo@fmach.it Sequencing & Genotyping Platform Edmund Mach Foundation
    2. 2. Edmund Mach Foundation (since 2007) Inheritance of Ist. Agrario San Michele a/A since 1874 A non for profit organization with private legal status and over 750 staff operating in several sites in the Trentino province It provides Research, Education,Technology Transfer and Advisory Service in the Agri-Food and Environmental sectors.
    3. 3. FEM Research and Innovation Centre
    4. 4. Mission: The Sequencing and Genotyping Platform takes part in the research and development activity of the CRI by offering support at the researchers activity and with the development of new methods of experimental investigation. The first purpose of the Platform is the development of new investigative methods, with the acquisition of new knowledge in the green biotechnology field and the continuous improvement of present and future instruments. Platform facilities Platform Services Platform Equipment
    5. 5. Genomics and Biology of Fruit Crops Germplasm platform Apple: - 13.4 ha for apple breeding + germplasm collection - 1,200 accessions (wild and cultivated spp.) - 54,000 genotypes under evaluation /several mapping population (quality and pyramidation of resistances) - 8,000 genotypes in greenhouse Grape: - 4.5 ha for grapevine breeding + germplasm collection - 1,900 accessions (wild, hybrids and cultivated) - 12,000 new crosses (crosses, selected individuals or large mapping populations) resistances with high quality standards Softfruits: - 2.5 ha for raspberry & blueberry breeding + germplasm - 104 strawbeery accessions - 140 blueberry accessions (20,000 seedlings/48 crosses) - 240 raspberry accessions (14,300 seedlings/110 crosses)
    6. 6. MAS 2013 AT FEM 24 APPLE CROSSES 6.471 PLANTS - 8.068 GENOTYPING ASSAY CROSS SELECTED FOR: 12.1 12.3 12.4 12.5 12.6 12.8 12.9 12.10 12.11 12.12 12.14 12.15 12.16 12.17 12.18 12.19 12.20 12.21 12.24 12.27 12.28 12.29 12.30 12.31 disesase resistance texture texture and ethylene disesase resistance disesase resistance disesase resistance ethylene disesase resistance texture ethylene disesase resistance disesase resistance disesase resistance and texture disesase resistance texture disesase resistance disesase resistance disesase resistance and ethylene disesase resistance ethylene disesase resistance and texture disesase resistance ethylene ethylene GENE Vf Pl1 Md-PG1   Md-PG1 Md-ACO1 Vf   Vf   Vf   Md-ACO1   Vf   Md-PG1   Md-ACO1   Vh4   Vh2   Vf Md-PG1 Vf Vr2 Md-PG1   Vf SAMPLES TESTED   Vf Pl1 Vf Md-ACO1 Vf Vr2 Md-ACO1   Vf Md-PG1 Vf   Md-ACS1   Md-ACO1   69,51% Plants with desiderable traits
    7. 7. Marker Assisted Breeding at FEM MASTER TRAITS (ie: Resistance, Texture, Storage) - MAB consultant (management system) - gold standard markers - well optimazed flowthrough
    8. 8. Marker Assisted Breeding at FEM STEP 1 Seedling layout STEP 2 Sample collection STEP 3 Run Analysis
    9. 9. People: Sequencing and Genotyping Platform Erika Stefani Daniela Nicolini Next Gen. Sequencing Next Gen. Sequencing Next Gen. Sequencing and Next Gen. Sequencing and Protocol Setting Protocol Setting Whole Genome Seq. Whole Genome Seq. Target Reseq. Target Reseq. Metagenomics Metagenomics Transcriptome Seq. Transcriptome Seq. Shot gun & PE gDNA library Shot gun & PE gDNA library Amplicon Library Amplicon Library Next Gen. Sequencing Next Gen. Sequencing Application Application Massimo Pindo Simone Larger Elisa Banchi Genotyping & Genotyping & Robotic Platform Robotic Platform DNA & RNA extraction DNA & RNA extraction Capillary Sequencing Capillary Sequencing Mid- to High-plex Genotyping Mid- to High-plex Genotyping Lara Poles
    10. 10. People: Sequencing and Genotyping Platform Erika Stefani Daniela Nicolini Next Gen. Sequencing Next Gen. Sequencing Next Gen. Sequencing and Next Gen. Sequencing and Protocol Setting Protocol Setting Whole Genome Seq. Whole Genome Seq. Target Reseq. Target Reseq. Metagenomics Metagenomics Transcriptome Seq. Transcriptome Seq. Shot gun & PE gDNA library Shot gun & PE gDNA library Amplicon Library Amplicon Library Next Gen. Sequencing Next Gen. Sequencing Application Application Massimo Pindo Simone Larger Elisa Banchi Genotyping & Genotyping & Robotic Platform Robotic Platform DNA & RNA extraction DNA & RNA extraction Capillary Sequencing Capillary Sequencing Mid- to High-plex Genotyping Mid- to High-plex Genotyping Lara Poles

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