Use of breeding populations to detect and use QTL Jean-Luc Jannink Iowa State University 2006 American Oat Workers Conference Fargo, ND24 July 2006

Translation Experimental Populations Breeding Populations

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.

Total: 960 Lines / Year 3000 SNP / Line Objective: Capitalize on phenotyping in breeding programs 96 Lines

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? usually

Mutation Original Population State AB aB AB aB AB Ab A mutation arises The b allele now always occurs in the presence of the A allele

Subpopulation structure / admixture Population 1 B A a B a B a B a B A A B A B Population 2 A b A b AbAb A b A b A b A b If the populations come together, the b allele again always occurs in the presence of the A allele

Structure Spring barley & 2 vs. 6 row Winter barley

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 Make Crosses F2F3F3F4F2F3F3F4 F1F2F1F2 F 4 Spc Plt Head Row PLT ALT Yr1 Yr2 Yr3 Yr4 Yr5 Make Crosses F2F3F3F4F2F3F3F4 F1F2F1F2 F 4 Spc PltALT Yr1 Yr2Yr3 Genotype Select on m Increase in NZ Contribute phenotype genotype data to THT

Key Question What level of LD exists in the “American Oat Population?” To detect causal polymorphisms, they need to be in high LD (r 2 > 0.5) with typed polymorphisms. If (r 2 > 0.5) extends over several cM, we will need fewer markers

LD in European barley “ There were in total 53 marker pairs with distance 0.01) and thus in LE. ” N.B. r 2 >0.06 => P 0.50 needed…

Linkage Disequilibrium

LD in North American Oat O’Donoughue et al “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) allele pairs

Distribution of r 2

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