# Presentation: 017577

## Use of breeding populations to detect and use QTL

- Jean-Luc Jannink
- Iowa State University
- 2006 American Oat Workers Conference
- Fargo, ND	24 July 2006

## Translation

- ExperimentalPopulations

## Bi-parental cross

- From Schön et al., yield, plant height, and grain moisture all over here

## Community Effort Needed

- The number of “effective factors” influencing a “highly quantitative” trait (e.g., grain yield): probably >50.
- Number of individuals needed to identify such small-effect QTL: probably ~ 1000.

## http://www.barleycap.org

- Objective: Capitalize on phenotyping in breeding programs

## Barley CAP

## QTL Detection in Breeding Populations

- P = E + G
- P = E + M + u

## Requirement of Linkage Disequilibrium

- A specific typed marker allele always comes together with the same causal QTL allele
- This is *Linkage Disequilibrium*
- Under what conditions does this occur?

## Mutation

- Original Population State

- AB

- aB_x0003_

- aB_x0003_

- aB_x0003_

- aB_x0003_

- AB

- AB

- AB

- The **b** allele now always occurs in the presence of the **A** allele

## Subpopulation structure / admixture

- Population 1

- B
-   A

-  a
- B

-   a
- B_x0003_

- a
-    B

-    B
- a

- B
-  A

- A   B

- A
-   B

## Structure

## Analysis Given Structure

- Each individual has a probability of belonging to each subpopulation: Q
- Each subpopulation has its own mean, *v**k*
- But only one effect is associated with each allele, 

## QTL x E?

- Dry

- Wet

- QTL x  E x Structure?

## Barley CAP

## Possible Use

## Key Question

- What level of LD exists in the “American Oat Population?”
- To detect causal polymorphisms, they need to be in high LD (r2 > 0.5) with typed polymorphisms.
- If (r2 > 0.5) extends over several cM, we will need fewer markers

## LD in European barley

- “There were in total 53 marker pairs with distance < 1 cM, of which 32 had a significant correlation (P < 0.01), while 19 pairs were not significantly correlated (P > 0.01) and thus in LE.”

*N.B.* r2>0.06 => P < 0.01, whereas r2>0.50 needed...

## Linkage Disequilibrium

## LD in North American Oat

- O’Donoughue et al. 1994 “Relationships among North American Oat Cultivars Based on Restriction Fragment Length Polymorphisms”
- 83 cultivars (both spring and winter)
- 48 probes
- 205 polymorphic bands

## Extended data from Sorrells

- 56 Probes
- 239 Polymorphic bands (alleles)
- 28441 allele pairs

## Distribution of r2

## Linkage Disequilibrium

## Extended data from Sorrells

- 56 Probes
- 40 Probes with position on KxO (Wight 2003)
- 21 Probes with a *single* position on KxO
- 8 Probe pairs with single location on same linkage group

## LD in North American Oat

## Questions for DArT markers

- Likely to be biased toward transcribed / untranscribed genomic regions?
- What minor allele frequencies does the discovery process allow?
- Will they mark only a single location in the hexaploid genome?
- We should probably be able to use the discovery / diversity panel for an LD study

## Conclusion

- I think LD-based MAS has promise
- integrated discovery and use of QTL
- capitalizes on phenotyping by breeders
- I think we are already setting up the DArT marker discovery process so as to get a first estimate of feasibility in oat.

## LD decay over time