Download Comparative mapping of the Oregon Wolfe Barley

Comparative mapping of the
Oregon Wolfe Barley using
doubled haploid lines derived
from female and male gametes
L. Cistue, A. Cuesta-Marcos, S. Chao, B. Echavarri, Y. Chutimanitsakun, A. Corey,
T. Filichkina, N. Garchia-Marino, I. Romagosa, P. M. Hayes
Rationale/Goals
• Aimed to increase the Oregon Wolfe Barley population size to create
a more useful linkage map
• Great resource, particularly for Barley research
• Barley is an economically important plant
• Aimed to study differences in creating linkage maps from doubled
haploid populations with different sources (female vs male gametes)
• Increased population size better for QTL mapping
Introduction
• Previous population doubled haploids from female gametes (H.b.) – 82 unique
individuals
• A number of different types of molecular data were used on linkage map for this
population
• RFLP, AFLP, SSR, DArTs, SNPS, RADs
• Created population of doubled haploids from male gametes (A.C.) – 93
individuals
• Combined population – 82+93 = 175
Doubled Haploids
Parent 1
Parent 2
OWB Dominant Parent
OWB Recessive Parent
F1
Gametes
Materials and Methods
• Create linkage map using molecular markers
• SNP markers (total of 1,328 polymorphic markers)
• Created linkage maps for the A.C. population, the H.b. population, and the
combined data set
• Phenotypes
• Grew plants in greenhouse and measured a number of characters important
to barley growers
• QTL Mapping
• QTL = quantitative trait locus
• Links phenotype with genotype
• Finding the locus (or loci) that control a phenotypic trait
Results
• All the loci are in the
same order!
Results
• Why would we see
different numbers of
crossovers between
these two populations?
Because male and female gametes may have
different rates of recombination (one reason
that this study was done with male gametes
– to see if this was true)
Because the two populations were derived from
different meiotic events, and one would
expect some level of variability
Recombination rate is 1.78 in
A.C., 1.72 for H.b.
So, pretty darn close
Results
• What is the expected
dominant allele
frequency in this
population?
Female Gamete
Male Gamete
0.5 – same for
recessive
• What are the different
dashed lines?
Different confidence levels
Way to avoid calling false positives
• What does it mean if
the peak is over the
dashed lines?
Segregation distortion – genotype
frequencies NOT what expected
Combined
Results
• Main takeaway:
• Segregation distortion was higher in
the A.C. population
• Regions on 3H and 5H correspond with
areas found to control phenotypes that
could have affected a plant’s ability to
survive the A.C. process
• Region on 2H corresponds with ZEO-1, a
dominant dwarfing allele.
• Perhaps when ZEO-1 was dominant, the
plants did not survive, so the study did not
see their alleles in the population.
QTL mapping = connecting phenotype to genotype
Shows positions on the chromosome (in cM) where QTLs, or the region controlling traits, are found. The peaks
also map to the same place as known genes VRS1 and ZEO1
The peaks are not straight lines at a single position because of linkage
These genes are pleiotropic – seen in multiple peaks aligned with each gene
Conclusions
• Some differences between populations from male and female
gametes, but both would be suitable for linkage map studies
• Recombination rate slightly higher in A.C. population
• Higher segregation distortion in A.C. population, but not due to production
method
• Gained further insight into relationships between genotype and
phenotype and what loci control which phenotypes
• Successfully created a larger population of OWB doubled haploids for
future studies
Generate F1
progeny
B
B
b Bb Bb
b Bb Bb
Make
doubled
haploids
from pollen
of progeny
BB or bb
genotype
Plant grows and
produces seed
Plant two seeds per
individual to phenotype in
greenhouse