Outline of Barley CAP Approach

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U.S. BARLEY COORDINATED AGRICULTURAL
PROJECT Barley CAP Consortium
Outline of Barley CAP Approach
Overall approach 96 lines from each of 10
breeding programs from each year of the project
are used for SNP genotyping (3,072 SNPs) and
phenotyping for over 40 traits. Association
mapping is used to detect QTL. MAS strategies
will be developed from the QTL information.
Visualization of Haplotype Structure
10 BREEDING PROGRAMS
NORTH DAKOTA STATE UNIVERSITY Richard
Horsley OREGON STATE UNIVERSITY Patrick Hayes
UTAH STATE UNIVERSITY Dave Hole VIRGINIA
TECH Carl Griffey WASHINGTON STATE
UNIVERSITY Steven Ullrich Denotes breeding
programs
COLORADO Blake Cooper(Busch Agricultural
Resources, Inc) USDA-ARS, IDAHO Donald
Obert UNIVERSITY OF MINNESOTA Kevin
Smith MONTANA STATE UNIVERSITY Tom Blake
Ten breeding programs each contribute 96 lines
per year to the project.
Data identifying subpopulations across 1816
breeder lines in years 1 2 show
Breeding programs are in rows populations
identified by structure are in columns. Bar
lengths proportional to lines from a program
within each population. A. No Admixture
model, k 10 lines assigned according to
posterior probability of belonging to each
population. Ten subpopulations line up fairly
well with 10 breeding programs. So subpopulations
are not explicitly named and number designations
remained. k optimal subpopulations
identified by program structure. B. Admixture
model, k 7 lines assigned by genome fraction
of line originating from each population. Gray
bars genome fraction of line originating from
population is lt 0.80. Column 8 (Admix) contains
lines for which no population contributed gt 0.50.
X-axis abbreviation for 7 subpopulations are
(i) 2- or 6-row, (ii) spring (sp) or winter (wi),
(iii) 2-letter abbreviation for breeding program
that seemed most dominant. Y-axis 2-letter
abbreviation of breeding program submitting
lines. k optimal subpopulations identified
by program structure.

• Breeding programs create separate populations
  within a crop. For example, N2 and N6 programs
  are primarily subpopulations unto themselves
  (Panel B).
• Different breeding programs align on basis of
  shared targets and germplasm exchange. For
  example, commonalities between MT, BA and AB in
  first column (Panel B).
• Programs exchange germplasm. For example, row for
  MN program has a gray bar, indicating
  introgression from N6. This means MN has used N6
  lines as breeding parents.

QTL MINER (LINKAGE DISEQUILIBRIUM MAPPING)
MAS, USDA GENOTYPING LAB
Marker-Trait Associations for Malting Quality,
and Resistance to Fusarium Head Blight DON
USDA regional genotyping centers service small
grain breeding programs by increasing efficiency
of generating marker data and by eliminating the
need for individual researchers to do genotyping.

QTL Miner software is used to identify SNP
markers associated with loci controlling traits
of interest. Traditional mapping uses populations
of progenies from two parents, whereas QTL miner
uses trait and genotype data from breeding
programs.
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CHROMOSOME 1H
Trait Affected alpha-amylase activity Grain
protein content Kernel plumpness beta glucan
(barley) Kernel plumpness Deoxynivalenol Test
weight
cM Position 12.234 22.188 35.428 77.502 77.502 88
112.049
Number 1.1. 1.2. 1.3. 1.4. 1.5. 1.6. 1.7.
1.6.
1.1.
1.2.
1.3.
1.4.
1.5.
1.7.
CHROMOSOME 2H
Trait Affected beta glucan (barley) Malt extract
Grain protein content Fusarium head blight beta
glucan (barley) Diastatic Power Deoxynivalenol Gra
in protein content
cM Position 4.405 15.397 46.469 50-56 66.181 72.75
2 125-132 173.642
Number 2.1. 2.2. 2.3. 2.4. 2.5. 2.6. 2.7. 2.8.
2.4.
2.7.
2.1.
2.2.
2.3.
2.5.
2.6.
2.8.
CHROMOSOME 3H
Trait Affected beta glucan (malt) Deoxynivalenol a
lpha-amylase activity Diastatic
Power Soluble/Total protein
cM Position 35.124 52-65 112.809 154.837 166.117
Number 3.1. 3.2. 3.3. 3.4. 3.5.
3.2.
3.1.
3.3.
3.4.
3.5.
Trait Affected Deoxynivalenol beta glucan
(malt) Diastatic Power alpha-amylase
activity Deoxynivalenol Deoxynivalenol Grain
protein content Grain protein content Kernel
plumpness beta glucanase activity Deoxynivalenol G
rain protein content
cM Position 3 6.775 23.743 25.941 21-36 24-36 43.3
99 43.399 46.734 54.441 40-61 96.363
Number 4.1. 4.2. 4.3. 4.4. 4.5. 4.6. 4.7. 4.8. 4.9
. 4.10. 4.11. 4.12.
CHROMOSOME 4H
4.1.
4.5.
4.2.
4.3.
4.4.
4.7.
4.9.
4.8.
4.12.
4.10.
4.11.
4.6.
cM Position 0 14.506 44.847 57.263 122.722 157.379
176.129 190-192 239.081
Number 5.1. 5.2. 5.3. 5.4. 5.5. 5.6. 5.7. 5.8. 5.9
.
Trait Affected Grain protein content Malt extract
alpha-amylase activity Diastatic
Power alpha-amylase activity beta glucan
(malt) Grain protein content Deoxynivalenol alpha-
amylase activity
CHROMOSOME 5H
5.1.
5.2.
5.4.
5.5.
5.6.
5.7.
5.9.
5.3.
5.8.
CHROMOSOME 6H
cM Position 30.074 30.074 42-61 42-67 67.419 86.39
3 124-127
Number 6.1. 6.2. 6.3. 6.4. 6.5. 6.6. 6.7.
Trait Affected Fine coarse difference Test
weight Fusarium head blight Deoxynivalenol alpha-a
mylase activity Diastatic Power Fusarium head
blight
6.3.
6.7.
6.1.
6.2.
6.6.
6.5.
6.4.
CHROMOSOME 7H
cM Position 31.837 60.879 61.966 74.094 122.249 16
3.886
Number 7.1. 7.2. 7.3. 7.4. 7.5. 7.6.
Trait Affected Kernel Weight alpha-amylase
activity beta glucan (malt) Extract
viscosity Grain protein content alpha-amylase
activity
7.1.
7.2.
7.4.
7.3.
7.5.
7.6.
Summary

• 2,943 SNPs were placed on the barley genetic map.
• Ten breeding programs contributed 96 lines over
  two years (1,920 lines) that were phenotyped for
  40 traits and genotyped with 3,072 SNP markers.
• Analysis of haplotype structure showed that
  breeding programs create separate populations but
  commonalities exist because of shared targets and
  germplasm exchange.
• Association mapping led to QTL identification for
  malting quality, winter hardiness, and Fusarium
  head blight and deoxynivalenol resistance
  information that is being used for MAS
  approaches.