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.

1. FruitBreedomics – Technical Session
Sampling procedures:
Hands on experience and practical details
I. Baumgartner (Agroscope)
San Giuseppe di Comacchio (Italy),
June 19th 2015

2. Overview
• 96-well format – why?
• Coding systems for plant identification
• Demonstration on steps of leave sampling
procedure

3. Companies process samples in a 96-well format

4. Coding systems for individual plant identification
Individual labeling of seedlings
• combination number
• seedling number
• (parents, resistances)
Positional coding system
• 4 plates of 6 x 4 pots represent 96-well
plate
• No individual seedling labeling

5. 1 2 3 4 5 6 7 8 9 10 11 12
A
B
C
D
E
F
G
H
1 - I 1 - II
1 - III 1 - IV
Positional coding system I
Plants in 4 plates of 6 x 4 pots Leave samples in 96-well plate

6. 1 2 3 4 5 6 7 8 9 10 11 12
A
B
C
D
E
F
G
H
1 - I 1 - II
1 - III 1 - IV
1 2 3 4 5 6 7 8 9 10 11 12
A
B
C
D
E
F
G
H
2 - I 2 - II
2 - III 2 - IV
Positional coding system II

7. LGC leaf sampling I

8. LGC leaf sampling II

9. LGC leaf sampling III

11. • Plates of 6 x 4 pots allowed plant identification
without labelling
• Coding system not easy for processing of plants
• Missing plants were replaced by living plants to
fill up gaps in the plates (cost), laborious
• Puncturing the leaves and expedition of the
plates was efficient
• The whole procedure was more time-consuming
than expected
• Costs are relatively low, DNA extraction is the
most expensive, data point to low price
• Close interaction with the company
(LGC genomics) was required and successful KASP - SNP Genotyping
MAB experiences

12. Thank you for your attention
powdery mildew
Agroscope good food, healthy environment