BIOINFORMATIC METHODS AND TOOLS TO PREDICT SMALL GRAIN FIELD PERFORMANCE
Location: Plant, Soil and Nutrition Research
Title: Association genetics in barley
| Waugh, Robbie - SCRI, SCOTLAND, UK |
| Muehlbauer, Gary - UNIV. OF MINN., ST. PAUL |
| Ramsay, Luke - SCRI, SCOTLAND, UK |
Submitted to: Current Opinion in Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 7, 2008
Publication Date: April 1, 2009
Citation: Waugh, R., Muehlbauer, G.J., Jannink, J., Ramsay, L. 2009. Association genetics in barley. Current Opinion in Plant Biology. 12(2):218-222.
Interpretive Summary: Association genetics can identify and fine map genes directly in breeding populations or diversity panels, an advantage that is leading barley geneticists to use these approaches. Barley also presents an ideal system because elite cultivar populations show long-range LD, allowing whole genome scans, while wild barley populations show short-range LD, allowing fine mapping. Two large-scale efforts have been initiated leveraging the resources of applied barley breeders, who have excellent phenotypic data, and basic researchers, who have developed the necessary marker systems, to use these tools for barley improvement. Early results from these efforts are promising, including the mapping of markers with positions confirmed by comparison to the sequenced model grass genomes of rice and brachypodium, and the identification and confirmation of a candidate gene for barley two-row or six-row spike phenotype. With these successes, we believe that association genetics will rapidly take the central role in efforts to predict barley phenotype from its genotype.
Applied and basic barley geneticists have begun to use association genetics as a tool to identify and fine map polymorphisms directly in breeding populations or diversity panels. Barley presents an ideal system because its populations present different extents of LD, from long-range LD in elite cultivars through short-range LD in wild barley. High-density and throughput marker systems now exist that allow genome-wide scans in elite populations. The data and computational requirements have spurred the barley community to develop new database and visualization tools and to borrow statistical methods from human genetics. Two large-scale translational efforts have been initiated leveraging the resources of applied barley breeders and basic researchers to use these tools for barley improvement. Early results from these efforts are promising, including the mapping of SNP with positions confirmed by synteny with sequenced model grass genomes and the identification and confirmation of a candidate gene for barley spike phenotype. With these successes, we believe that association genetics will rapidly take the central role in barley genotype to phenotype mapping efforts.