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Table 2 Candidate gene prioritization: comparison with QTL fine-mapping a

From: Prioritization of candidate genes in QTL regions based on associations between traits and biological processes

Trait and fine-mapped candidate gene #genes #sel Overrepresented biological processes involved
Leaf size: 214 21 regulation of flower development
LOC_Os01g11940 [47] lysine biosynthetic process via diaminopimelate
Leaf size: 214 21 organic acid catabolic process
LOC_Os01g11946 [47]
Number of spikelets per panicle: LOC_Os01g12160 [48] 246 8 systemic acquired resistance
Gel consistency: 167 14 monosaccharide metabolic process
LOC_Os06g04200 [49] glycolipid biosynthetic process
membrane lipid biosynthetic process
glucose metabolic process
Gelatinization temperature: 53 3 monosaccharide metabolic process
LOC_Os06g12450 [50] glycolipid biosynthetic process
membrane lipid biosynthetic process
Heading date: 330 13 positive regulation of RNA metabolic process
LOC_Os08g07740 [51]b positive regulation of nucleobase-containing compound metabolic process
positive regulation of (macromolecule/cellular) metabolic process
Yield, plant height: 188 8 positive regulation of macromolecule/cellular/nitrogen compound biosynthetic process
LOC_Os08g07740 [52]b positive regulation of gene expression
Grain size and quality: 300 29 regulation of post-embryonic development
LOC_Os08g41940 [53]
Viscosity parameter: 120 4 monosaccharide/glucose meta-/catabolic process
LOC_Os08g42410 [54] glycolysis
hexose catabolic process
alcohol catabolic process
  1. aFor each trait found in literature with a fine-mapped candidate gene, QTL traits in our dataset were obtained which were similar/related to the literature trait, and for which the fine-mapped gene occurred in one of the QTL regions. Only cases for which the candidate gene was correctly prioritized by our approach are shown, in combination with the biological processes involved. #genes, number of genes in the input QTL region. #sel, total number of genes prioritized in the QTL region. For complete overview of comparison with fine-mapped candidate genes, see Additional file 3: Table S3.
  2. bLOC_Os08g07740 is found as fine-mapped candidate gene for two different traits.