Abstract
BackgroundAssociation studies are of great interest to identify genes explaining trait variation since they deal with more than just a few alleles like classical QTL analyses. They are usually performed using collections representing a wide range of variability but which could present a genetic substructure. The aim of this paper is to demonstrate that association studies can be performed using synthetic varieties obtained after several panmictic generations. This demonstration is based on an example of association between the gibberellic acid insensitive gene (GAI) polymorphism and leaf length polymorphism in 'Herbie', a synthetic variety of perennial ryegrass.MethodsLeaf growth parameters, consisted of leaf length, maximum leaf elongation rate (LERmax) and leaf elongation duration (LED), were evaluated in spring and autumn on 216 plants of Herbie with three replicates. For each plant, a sequence of 370 bp in GAI was analysed for polymorphism.ResultsGenetic effect was highly significant for all traits. Broad sense heritabilities were higher for leaf length and LERmax with about 0.7 in each period and 0.5 considering both periods than for LED with about 0.4 in each period and 0.3 considering both periods. GAI was highly polymorphic with an average of 12 bp between two consecutive SNPs and 39 haplotypes in which 9 were more frequent. Linkage disequilibrium declined rapidly with distance with r 2 values lower than 0.2 beyond 150 bp. Sequence polymorphism of GAI explained 8-14% of leaf growth parameter variation. A single SNP explained 4% of the phenotypic variance of leaf length in both periods which represents a difference of 33 mm on an average of 300 mm.ConclusionsSynthetic varieties in which linkage disequilibrium declines rapidly with distance are suitable for association studies using the "candidate gene" approach. GAI polymorphism was found to be associated with leaf length polymorphism which was more correlated to LERmax than to LED in Herbie. It is a good candidate to explain leaf length variation in other plant material.
Highlights
Association studies are of great interest to identify genes explaining trait variation since they deal with more than just a few alleles like classical Quantitative trait locus (QTL) analyses
This demonstration is based on an example of association between the gibberellic acid insensitive gene (GAI) polymorphism and leaf length polymorphism in ‘Herbie’, a synthetic variety of perennial ryegrass (Lolium perenne L.) which presents no substructure and a short linkage disequilibrium (LD) decline [8]
Phenotypic analysis leaf length (Llength), LERmax and leaf elongation duration (LED) were determined for 216 plants of ‘Herbie’ in spring and autumn and on 100 plants of a perennial ryegrass core-collection (Cc) in autumn
Summary
Association studies are of great interest to identify genes explaining trait variation since they deal with more than just a few alleles like classical QTL analyses. They are usually performed using collections representing a wide range of variability but which could present a genetic substructure. The second one is the whole genome scan approach used for populations showing a slow LD decline [4] These two approaches have been mainly used for analysing the genetic variability of a species through core collections. The best plant material for association studies should be multi-allelic and without any substructure This is the case in synthetic varieties, obtained after several panmictic multiplication generations, as shown by Auzanneau [8]. To our knowledge, there are no previous reports concerning association studies on synthetic plant varieties
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