The emergence of whole genome association scans in barley.

Barley geneticists are currently using association genetics to identify and fine map traits directly in elite plant breeding material. This has been made possible by the development of a highly parallel SNP assay platform that provides sufficient marker density for genome-wide scans and linkage disequilibrium-led gene identification. By leveraging the combined resources of the barley research and breeding sectors, marker-trait associations are being identified and a renewed interest has emerged in novel strategies for barley improvement. New database and visualization tools have been developed and statistical methods adapted from human genetics to account for complexities in the datasets. Exciting early results suggest that association genetics will assume a central role in establishing genotype-to-phenotype relationships.

[1]  M. Nordborg.  Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization. , 2000, Genetics.

[2]  P. Morrell,et al.  Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[3]  T. Komatsuda,et al.  Analysis of the barley chromosome 2 region containing the six-rowed spike gene vrs1 reveals a breakdown of rice–barley micro collinearity by a transposition , 2007, Theoretical and Applied Genetics.

[4]  A. Graner,et al.  Effects of Introgression and Recombination on Haplotype Structure and Linkage Disequilibrium Surrounding a Locus Encoding Bymovirus Resistance in Barley , 2007, Genetics.

[5]  F. V. van Eeuwijk,et al.  Linkage Disequilibrium Mapping of Yield and Yield Stability in Modern Spring Barley Cultivars , 2004, Genetics.

[6]  A Walk on the Wild Side , 2000 .

[7]  Keyan Zhao,et al.  An Arabidopsis Example of Association Mapping in Structured Samples , 2006, PLoS genetics.

[8]  D. Reich,et al.  Population Structure and Eigenanalysis , 2006, PLoS genetics.

[9]  A. Meister,et al.  Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. , 2000, Genetics.

[10]  Thomas Wiehe,et al.  Recombination and gene conversion in a 170-kb genomic region of Arabidopsis thaliana. , 2002, Genetics.

[11]  D. Reich,et al.  Principal components analysis corrects for stratification in genome-wide association studies , 2006, Nature Genetics.

[12]  P. Donnelly,et al.  Association mapping in structured populations. , 2000, American journal of human genetics.

[13]  Kevin P. Smith,et al.  A walk on the wild side : mining wild wheat and barley collections for rust resistance genes , 2007 .

[14]  Andrew J. Flavell,et al.  GERMINATE. A Generic Database for Integrating Genotypic and Phenotypic Information for Plant Genetic Resource Collections1[w] , 2005, Plant Physiology.

[15]  F. Eeuwijk,et al.  Linkage Disequilibrium Mapping of Morphological, Resistance, and Other Agronomically Relevant Traits in Modern Spring Barley Cultivars , 2005, Molecular Breeding.

[16]  M. Röder,et al.  Haplotype diversity in the endosperm specific β-amylase gene Bmy1 of cultivated barley (Hordeum vulgare L.) , 2006, Molecular Breeding.

[17]  Andrew P Morris,et al.  Linkage disequilibrium mapping via cladistic analysis of single-nucleotide polymorphism haplotypes. , 2004, American journal of human genetics.

[18]  P. Donnelly,et al.  Inference of population structure using multilocus genotype data. , 2000, Genetics.

[19]  R. Fernando,et al.  Power and Precision of Alternate Methods for Linkage Disequilibrium Mapping of Quantitative Trait Loci , 2007, Genetics.

[20]  M Quinton,et al.  Estimation of effects of single genes on quantitative traits. , 1992, Journal of animal science.

[21]  R. Waugh,et al.  Integration of microsatellite markers into the translocation-based physical RFLP map of barley chromosome 3H , 2002, Theoretical and Applied Genetics.

[22]  Paul Scheet,et al.  A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. , 2006, American journal of human genetics.

[23]  Zhaohui S. Qin,et al.  Genome-wide detection and characterization of positive selection in human populations , 2007 .

[24]  A. Jeffreys,et al.  Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex , 2001, Nature Genetics.

[25]  Virander S. Chauhan,et al.  Novel genetic mapping tools in plants , 2002 .

[26]  D. Kudrna,et al.  Diversity Arrays Technology (DArT) for whole-genome profiling of barley. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[27]  J. Rafalski.  Novel genetic mapping tools in plants: SNPs and LD-based approaches , 2002 .

[28]  D Bentley,et al.  Highly parallel SNP genotyping. , 2003, Cold Spring Harbor symposia on quantitative biology.

[29]  Montgomery Slatkin,et al.  Linkage disequilibrium — understanding the evolutionary past and mapping the medical future , 2008, Nature Reviews Genetics.

[30]  P. Donnelly,et al.  A new multipoint method for genome-wide association studies by imputation of genotypes , 2007, Nature Genetics.

[31]  Rajeev K. Varshney,et al.  Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties , 2006, Proceedings of the National Academy of Sciences.

[32]  P. Langridge,et al.  Extreme Population-Dependent Linkage Disequilibrium Detected in an Inbreeding Plant Species, Hordeum vulgare , 2006, Genetics.

[33]  P. Hayes,et al.  Validation of the VRN-H2/VRN-H1 epistatic model in barley reveals that intron length variation in VRN-H1 may account for a continuum of vernalization sensitivity , 2007, Molecular Genetics and Genomics.

[34]  M. McMullen,et al.  A unified mixed-model method for association mapping that accounts for multiple levels of relatedness , 2006, Nature Genetics.

[35]  E. Buckler,et al.  Structure of linkage disequilibrium in plants. , 2003, Annual review of plant biology.

[36]  Peter Wenzl,et al.  A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits , 2006, BMC Genomics.

[37]  D. Botstein,et al.  Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease , 2003, Nature Genetics.

[38]  G. Fischbeck.  Chapter 3 - Diversification through breeding , 2003 .