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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.