Association mapping in small arrays of elite germplasm – a thorough analysis of the
“Beer-Genes” varieties subset from the CAP Core
A. Cuesta-Marcos, B. Cooper, T. Filichkin, P. Szucs, TJ. Close, GJ Muehlbauer, PM
Hayes
The advent of high throughput genotyping strategies affords breeders the opportunity to
mine the large phenotype data sets generated on relatively small numbers of elite lines
that are generated in the course of a breeding program. We will perform association
mapping analyses of malting quality traits in the “Beer-Genes” subset (n = 36) of the
CAP Core. We have P-OPA 1 and 2 - and will soon have P-OPA 3 – haplotypes on all
lines. We have malting quality phenotypic data available from 11 locations and 2 two
years (a total of 21 environments). We will explore several strategies for taking
advantage of this small number of genotypes and large number of data points. While not
ideal from a genetic analysis standpoint – due to sample size and population structure
issues - this data set is typical of what a malting barley variety breeding program would
generate in the normal course of events. In order to detect all possible associations and
avoid false positives, we will use different options for modeling Genotype x Environment
Interaction (GEI) and dealing with population structure and kinship. We will devote
significant effort to determining appropriate significance thresholds for marker/phenotype
associations. We will identify genomic patterns of polymorphism distribution (e.g.
conserved haplotypes) and compare these with those detected in mapping populations in
association with known function genes and QTL related with malting and brewing
quality. Testing the hypothesis that regions of the genome appropriate for marker assisted
selection will be identified by deep analysis of small numbers of genotypes with
abundant genotype and phenotype data is an essential step in designing molecular
breeding strategies for applied breeding programs.
Zeroing in on zero degrees: comparative analysis of association mapping in
germplasm arrays and isogenic lines as tools for understanding the relationships of
vernalization sensitivity and cold hardiness
A. Cuesta-Marcos, P. Szucs, A.E. Corey, T. Filichkin, TJ. Close, GJ Muehlbauer, PM
Hayes
Germplasm arrays for association mapping and isogenic lines for finer structure analysis
represent two classes of germplasm that are typically used at the beginning and end,
respectively, of quantitative trait dissection studies. Understanding the relationship
between vernalization sensitivity and low temperature tolerance is an essential
prerequisite for systematic development of widely adapted barley varieties suitable for
fall-sowing. In this project we will use a germplasm array and a set of isogenic lines to
genotyped with B-OPA1 and phenotyped for vernalization sensitivity/ low temperature
tolerance. The isogenic lines represent all single, double and triple combinations of spring
alleles at the three Vrn loci transferred, via 11 backcrosses, to two different winter
backgrounds. The germplasm array consists of 96 winter and facultative breeding lines
form the OSU breeding program. We will compare results from analyses of the two
classes of germplasm in terms of the significance, location, and effect of main effects and
interactions. These results will have specific immediate utility for development of fallsown varieties and broader importance to the plant science community in terms of
flowering physiology and design of gene detection and characterization strategies.
Barley stripe rust resistance QTL:
allele effects and tools for marker assisted selection
A. Cuesta-Marcos, P. Kongprakhon, K. Richardson, P. Szucs, A.E. Corey, T. Filichkin,
TJ. Close, GJ Muehlbauer, PM Hayes
Quantitative resistance (QR) to plant disease is usually more durable than qualitative
resistance. Breeding for QR will be more effective when unbiased estimates of the
locations, effects, and interactions of the determinant genes - together with abundant
markers suitable for marker assisted selection (MAS) - are available. A key question in
all resistance breeding is whether there is a cost to resistance alleles per se or if yield
and/or quality traits are in repulsion linkage for an extended region of the genome or if
there is evidence for tight repulsion linkage/ or negative pleiotropic effects of the
resistance genes. For the barley: barley stripe rust (BSR; a disease incited by Puccinia
striiformis f.sp. hordei) model we used MAS to develop a set of near-isogenic lines
representing individual QR alleles and combinations of QR alleles in the high yielding,
adapted, and moderately susceptible variety Baronesse. Phase I of development of the
Barley near-ISOgeNic (BISON) lines, involved validation of QR allele effects in
intermediate near-isogenic (i-BISON) lines. We measured the response to the pathogen,
as either infection type or percent disease severity, on the i-BISON lines at the seedling
and adult plant stages, in controlled and field environments, and with various races of the
pathogen. B-OPA 1 haplotypes of the iBISON lines will be generated soon via leveraged
support from another program. An analyses of these data will confirm introgression size
and allow for accurate assignment of disease phenotype reductions to specific alleles and
allele combinations. B-OPA 1 haplotypes of the BISON will be generated via the CAP
and extensive agronomic and quality assessments will be undertaken in the summer of
2008. Disease resistance phenotypes will also be confirmed. These data will allow us to
determine if there are yield and/or quality losses associated with resistance alleles. If such
losses are identified, the haplotype resolution should allow us to estimate the relative
contributions of negative pleiotropy vs. repulsion linkage. The results will be of
immediate use to the ongoing efforts to introgress these resistance alleles into multiple
varieties. They will also assist the wider plant science community is designing disease
resistance breeding strategies.
Reference
Cuesta-Marcos et al. (2008) Barley Stripe Rust Resistance QTL: Allele effects and tools
for marker assisted selection. Plant & Animal Genome XVI, Abstracts 328.
(http://www.intl-pag.org/16/abstracts/PAG16_P05c_328.html)
Re-sequencing winter-hardiness and domestication-related loci emphasizes the
importance of using haplotype information in association mapping
P. Szucs, A. Cuesta-Marcos, T. Filichkin, TJ. Close, GJ Muehlbauer, PM Hayes
BMC Genetics by September 30, 2008
The power of association mapping in barley, and by extension in self-pollinated cereals,
lies in long distance LD decay. Via the Barley CAP, this assumption will be testable in
breeding germplasm arrays that meet more closely the criteria of inter-mating than
collections of accessions assembled based on criteria other than an absence of population
structure. Nonetheless, there is an intuitive appeal to use structured germplasm arrays for
gene detection. The CAP Core is a structured set of 102 cultivated barley accessions
representing key cultivars and accessions of interest to the 10 U.S. Barley CAP breeding
programs. We have previously found that allele type of the P-OPA2 marker
corresponding to VRN-H1 –one of the primary determinants of growth habit– shows no
relationship with growth habit in this germplasm set. The lack of the association between
the VRN-H1 SNP and growth habit could be due to a number of factors – epistasis; the
complexity of the functional allelic differences; rapid LD decay within the gene; or
stratified sampling. In order to better understand the basis of this inability to detect the
major gene responsible adaptation to fall-sown vs. spring-sown environments, we will
compare the power of association mapping using SNP data from large set of genes vs.
haplotype information from candidate genes determining the growth habit and
inflorescence type. The core set was genotyped for 3,072 EST-based P-OPA markers and
map location for 1,022 of these markers was determined using the OWB population. In
this report, we will present the new OWB marker map harboring a total of 1,933 P-OPA,
DArT and conventional markers. We will then proceed to compare the results of
association mapping of flowering time and inflorescence type using these markers with
the results of analyzing haplotypes based on the known determinants of growth habit
(VRN-H1, VRN-H2 and VRN-H3), photoperiod response (PPD-H1 and PPD-H2), low
temperature tolerance (FR-H1, FR-H2), and inflorescence type (VRS1). The reference
phenotypes will be vernalization sensitivity under long-day greenhouse conditions and
inflorescence type. The genotype data, in addition to P-OPA1, 2, and 3 will be resequenced and/or genotyped alleles at the VRN-H1, VRN-H2, VRN-H3, PPD-H1, PPDH2, FR-H2 and VRS1 loci. The results of this investigation should reveal haplotypes
useful for growth habit MAS and be of broader utility to the plant science community in
terms of assessing the power of association mapping to detect determinants of key traits
in structured germplasm arrays.
Reference:
Szűcs et al. (2008) Allele structure of the vernalization and photoperiod loci in the barley
CAP core germplasm array. Plant & Animal Genome XVI, Abstracts 198.