From QTLs for enzyme activity to candidate genes in maize

In order to facilitate the search for genes underlying QTLs (Quantitative Trait Loci), the activities of key enzymes of the carbohydrate metabolism in maize, and the concentration of their substrates or products were used as quantitative traits. For each of the chosen enzyme, i.e. ADPglucose pyrophosphorylase, sucrose-phosphate-synthase and invertases, the corresponding cDNA was available. Since biochemical traits are more closely related to gene expression than agronomic traits, cc-locations could be expected between an enzyme structural gene and a QTL for its enzyme activity, and/or the corresponding product or substrate content. This approach was applied using recombinant inbred lines on leaves at 3- or 4-leaf stage, under control and water stress conditions and on grain, at maturity. Several QTLs were detected for each trait, particularly for two enzyme activities measured in mature leaves. Apparent cc-locations between QTL for activity and structural locus were observed for sucrose-phosphate-synthase (chromosome 8) and acid-soluble invertase (chromosomes 2 and 5). Leaf acid-soluble (vacuolar) invertase provided an interesting case since a QTL, on chromosome 5, explaining 17% of variability was apparently cc-located with the Ivr2 gene encoding a vacuolar invertase protein which was strongly water-stress inducible. Similarly, in grain, an amylose QTL co-located with the Sh2 gene of ADPglucose pyrophosphorylase. The reliability of this candidate was further tested through the examination of Sh2 DNA polymorphism in 46 genetically unrelated lines. A correlation was obtained between this polymorphism and kernel starch content, which further validated Sh2 as a candidate. Some improvements or alternatives to this strategy are briefly discussed.