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Table 5 Identical genes detected by two genome wide genotyping methods in the QUEST case-control and PIN184 populations

From: Physical mapping of QTL for tuber yield, starch content and starch yield in tetraploid potato (Solanum tuberosum L.) by means of genome wide genotyping by sequencing and the 8.3 K SolCAP SNP array

Locus PGSC0003 Chromosome: Mbp (v4.03) Annotation QUEST cases/controls SolCAP SNPs QUEST cases/controls RADseq SNPs PIN184 GWAS SolCAP SNPs Function category
DMG400006283 I:60.5 ABC-transporter - TSC TSC Transport [64]
DMG400006766 I:64.6 Conserved gene of unknown function TSC, TSY - TSC Unknown
DMG400000010 I:71.4 Glycosyltransferase - TY TSC Cell wall biosynthesis [74]
DMG400025878 I:84.2 Phenylpropanoid:glycosyltransferase 1 TSC - TSC Phenylpropanoid metabolism [75]
DMG400030954 I:86.4 Beta-galactosidase - TSC, TY, TSY TSC Carbohydrate metabolism (uniprot/P48980)
DMG400003324 II:22.6 Squalene epoxidase - TY, TSY TSC Cyclic triterpenoid biosynthesis [76]
DMG400006975 II:26.7 Chloride channel/carrier, CLC-Nt2 - TSC, TY, TSY TSC Transport [77]
DMG400001369 II:45.4 Kinase - TSC, TY, TSY TSC Phosphorylation of specific substrates (proteins, lipids, carbohydrates and others)
Solyc03g065340 3 III:? Starch phosphorylase PHO1a TSC - TSC Starch degradation [17]
DMG400025328 III:53.3 Plasma membrane ATPase 3 - TY, TSY TSC Providing energy for transport [78]
DMG400024596 III:54.1 Protein kinase ATMRK1 - TSC TSC Posttranslational regulation [79]
DMG401024510 III:54.6 Enolase TSC - TSC Glycolysis, central metabolism
DMG400014223 III:57.6 4-coumarate-CoA ligase 2 - TSC, TY TSC Phenylpropanoid biosynthesis (uniprot/O24146)
DMG400029505 IV:3.0 NB-LRR protein required for HR- associated cell death 1 (NRC1) - TSC, TY TSC Biotic stress [80]
DMG400011479 IV:6.2 Glycogenin-like starch initiation protein 6 - TSC, TY TSC Carbohydrate metabolism (AT5G18480)
DMG400027236 IV:9.8 Transcriptional factor B3 TSC - TSC Transcription regulation (IPR003340)
DMG400003751 IV:70.2 Bel1 homeotic protein - TSC, TY, TSY TSC Development [81]
DMG400028325 V:0.32 Heparanase, family-79 endo-β-glucuronidase - TSC, TY, TSY TSC Carbohydrate metabolism https://www.cazypedia.org/index.php/Glycoside_Hydrolase_Family_79
Solyc05g010320 3 V:1.4 Chalcone-flavonone isomerase TSC - TSC Anthocyanin biosynthesis [82]
DMG400000810 V:2.0 Di-glucose binding protein with Leucine-rich repeat domain, serine-threonine protein kinase - TSC, TY, TSY TSC Posttranslational regulation [79]
DMG401012961 V:2.1 Aspartic proteinase nepenthesin-1 - TY, TSY TSC Protein degradation [83]
DMG400031262 V:5.0 Methyltransferase TSC, TSY TSC, TY, TSY TSC Methylation of specific substrates
Solyc05g007070 3 V:5.9 Alpha amylase 2 TSC - TSC Starch degradation
Solyc05g007030 3 V:6.0 AT3g17900/MEB5_12 TSC - TSC Unknown
DMG400018605 V:10.3 Binding protein - TY, TSY TSC Unknown
DMG400023508 V:50.6 Kinase - TSC, TY, TSY TSC Phosphorylation of specific substrates (proteins, lipids, carbohydrates and others)
DMG400004062 VI:51.2 DOF domain class transcription factor - TSC, TSY TSC Transcription regulation [84]
DMG400033051 VI:51.5 Conserved gene of unknown function - TSC TSC Unknown
DMG400033034 VI:51.9 Plasma membrane H+-ATPase - TSC, TY, TSY TSC Providing energy for transport [78]
DMG402026985 VI:52.6 Kinase - TSC TSC Phosphorylation of specific substrates (proteins, lipids, carbohydrates and others)
DMG400012129 VIII:56.4 Beta-amylase 8 - TSC, TY TSC Starch degradation
DMG400003874 IX: 4.8 Splicing factor 3A subunit - TY, TSY TSC mRNA processing
DMG400023084 IX:8.5 LMBR1 integral membrane family protein - TSC TSC Lysosomal membrane
DMG400004415 IX:15.6 Kinase - TSC TSC Phosphorylation of specific substrates (proteins, lipids, carbohydrates and others)
DMG400029885 IX:19.2 Kinase TSC TSC, TY TSC Phosphorylation of specific substrates (proteins, lipids, carbohydrates and others)
DMG400027986 IX: 33.7 Copper ion binding protein TSC TSC, TY TSC Copper ion transport (IPR000428)
DMG402017675 IX:40.4 Binding protein - TSC, TY TSC Unknown
DMG400019363 IX:47.7 Ribosome-recycling factor, chloroplastic - TSC, TY, TSY TSC Chloroplast biogenesis [85]
DMG400026430 IX:59.3 Beta-galactosidase - TSC, TY TSC Cell wall metabolism [86]
DMG400019131 X:50.6 Tubulin beta-1 chain - TSC, TY, TSY TSC Cytoskeleton structure (uniprot/P12411)
DMG403008663 XI:32.9 L-lactate dehydrogenase - TSC, TY TSC Anaeorbic glycolysis (IPR011304)
DMG400004642 XII:60.3 Lipoyl synthase, chloroplastic - TSC TSC Protein modification by lipoylation (uniprot/Q8LEE8)
  1. 1Entry in the InterPro database (http://www.ebi.ac.uk/interpro/)
  2. 2Entry in the uniprot database (http://www.uniprot.org/)
  3. 3The gene is not annotated in the potato genome. Solyc**g****** corresponds to the annotated orthologous gene in the tomato genome (https://solgenomics.net/)
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BMC Genomics

ISSN: 1471-2164

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