Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome.
Although commonplace in human disease genetics, genome-wide association (GWA) studies have only relatively recently been applied to plants. Using 32 phenotypes in the inbreeding crop barley, we report GWA mapping of 15 morphological traits across ∼500 cultivars genotyped with 1,536 SNPs. In contrast to the majority of human GWA studies, we observe high levels of linkage disequilibrium within and between chromosomes. Despite this, GWA analysis readily detected common alleles of high penetrance. To investigate the potential of combining GWA mapping with comparative analysis to resolve traits to candidate polymorphism level in unsequenced genomes, we fine-mapped a selected phenotype (anthocyanin pigmentation) within a 140-kb interval containing three genes. Of these, resequencing the putative anthocyanin pathway gene HvbHLH1 identified a deletion resulting in a premature stop codon upstream of the basic helix-loop-helix domain, which was diagnostic for lack of anthocyanin in our association and biparental mapping populations. The methodology described here is transferable to species with limited genomic resources, providing a paradigm for reducing the threshold of map-based cloning in unsequenced crops.
Brewing Research International, Surrey, United Kingdom.
James
J
Cockram
Jon
J
White
Diana L
DL
Zuluaga
David
D
Smith
Jordi
J
Comadran
Malcolm
M
Macaulay
Zewei
Z
Luo
Mike J
MJ
Kearsey
Peter
P
Werner
David
D
Harrap
Chris
C
Tapsell
Hui
H
Liu
Peter E
PE
Hedley
Nils
N
Stein
Daniela
D
Schulte
Burkhard
B
Steuernagel
David F
DF
Marshall
William T B
WT
Thomas
Luke
L
Ramsay
Ian
I
Mackay
David J
DJ
Balding
Robbie
R
Waugh
Donal M
DM
O'Sullivan
D029681:Arabidopsis Proteins / Q000235:genetics; D002874:Chromosome Mapping; D005819:Genetic Markers; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D018398:Homeodomain Proteins / Q000235:genetics; D001467:Hordeum / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D010641:Phenotype; D011110:Polymorphism, Genetic; D025341:Principal Component Analysis
C121063:ANL2 protein, Arabidopsis; D029681:Arabidopsis Proteins; D005819:Genetic Markers; D018398:Homeodomain Proteins