02 baumgartner

FruitBreedomics – Technical SessionSampling procedures: Hands on experience and practical detailsI. Baumgartner (Agroscope)

San Giuseppe di Comacchio (Italy), June 19th 2015

Overview

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

procedure

Companies process samples in a 96-well format

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

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

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

LGC leaf sampling I

LGC leaf sampling II

LGC leaf sampling III

• 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

Thank you for your attention

powdery mildew

Agroscope good food, healthy environment