Association studies using synthetic varieties: case study of GAI gene and leaf length in perennial ryegrass
2007
Barre, Philippe, | Auzanneau, Jerome | Julier, Bernadette | Huyghe, Christian,
Identification of genome regions controlling quantitative trait variations is generally obtained from QTL analyses on mapping populations exhibiting a low allelic diversity. An alternative approach would be association studies using collections of individuals. Any structure of these collections would hinder detection of associations. An ideal plant material for association studies would be multi-allelic and unstructured populations. The objective of this study was to test whether synthetic varieties could be used for association studies. In a first experiment, three perennial ryegrass varieties with contrasting numbers of parental plants were studied for their structuration, variability and linkage disequilibrium (LD) decline. This decline defines which association study approach has to be envisaged: "candidate gene" when LD rapidly decreases or "genome scan" when LD slowly decreases. The varieties were not structured. LD decreased more rapidly when the number of parents increased. LD is low beyond 150 bp for Herbie, a variety built from 336 parents whose molecular and morphological diversity was similar to a core collection. In a second experiment, an association study was performed between the Gibberellic Acid Insensitive gene and leaf length in the variety Herbie. One specific SNP explained 4% of leaf length variation. Differences between genotypic classes of this SNP reach 30 mm for a mean value of 303 mm.
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