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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/)