Selection of candidate genes from QTL mapping
In order to select and prioritize positional candidate genes from the
QTL confidence intervals, we conducted a literature screen and anin silico analysis (explained in more detail in the Materials and
Methods section) that were based on functional annotations, gene
expression data and tissue distribution of the selected genes. We
analyzed loci from the Dol-associated QTL (DOL1) and from the three
Pren-associated QTLs (PRE1, PRE2, PRE3). We selected the intervals that
were characterized by the highest percentage of phenotypic variance
related to each QTL and the highest LOD score values linked with the
lowest number of loci (Table S1). As a result of the above-described
procedure of selection and prioritization, we generated four sets of
genes ‒ three for Prens (Table S2) and one for Dol (Table S3).
Within a set of potential candidate genes for Pren (Table S2), there was
the AT5G45940 gene encoding the Nudix hydrolase 11 (Kupke,
Caparrós-Martín, Malquichagua Salazar, & Culiáñez-Macià, 2009) with
putative IPP isomerase activity. For Dol biosynthesis, we identified
three loci that might be directly implicated in the process: AT2G17570,
encoding a cis -prenyltransferase 3 (CPT3), AT2G17370, encoding
HMGR2 (hydroxymethylglutaryl Coenzyme-A reductase 2, also called HMG2, a
highly regulated enzyme that constitutes a rate-limiting step in the MVA
pathway), and AT2G18620, encoding a putative GGPPS2 (geranylgeranyl
diphosphate synthase 2). A brief comment on the putative role of the two
latter genes in the Dol pathway is presented in Table S3, while an
in-depth characteristic of AT2G17570 (CPT3) is presented below.