Supplemental Table 1. Carbohydrate, photosynthesis and developmental metabolic genes located close to QTL identified for seven agronomic traits in the DRH diploid population of potato†

Gene / Gene ID / Chr / Mb / Metabolism associated and reference‡ / Genbank accession
AGPaseS gene / PGSC0003DMG400009026 / I / 62.1 / Starch synthesis, gene characterized byLa Cognata et al. (1995) associated with sugar content (Menendez et al., 2002) / NM_001288466
Anesinn / PGSC0003DMG400019446
PGSC0003DMG402019427 / I / 75.2 / Stress response associated gene (Urbany et al., 2012)
Calreticulinholologues of Calcium binding peptide CBPgene / PGSC0003DMG400002776 / I / 78.1 / Stress response associated (McCord et al., 2009)
Protein kinase family protein / PGSC0003DMG400000724 / I / 85.9 / Stress response associated gene (McCord, 2009)
Large unit S of Glucose-1-phosphate adenylyltransferaseAGPaseS / PGSC0003DMG400000735 / I / 86.1 / Starch synthesis, candidate gene for tuber starch content(Chen et al., 2001) / X61187
The chloroplasticRibulosebisphosphate carboxylase small chain C / PGSC0003DMG400024182 / II / 21.9 / Photosynthesis, candidate gene for tuber starch content(Chen et al., 2001)
Acclimationof photosynthesis to the environment APE1 / PGSC0003DMG400019582 / III / 4.7 / Plant growth metabolism associated gene (Walters et al., 2003)
Heat shock protein / PGSC0003DMG400009509 / III / 44.1 / Stress response
Heat shock protein / PGSC0003DMG400009110 / III / 45 / Stress response
Kunitz-type tuber invertase inhibitor / PGSC0003DMG400010146 / III / 50 / Sugar metabolism (Fischer et al., 2013)
Pyruvate kinasePK / PGSC0003DMG400025298 / IV / 3.9 / Sucrose and starch metabolism, candidate gene for tuber starch content(Chen et al., 2001) / S53332
Phosphoenolpyruvate carboxylase PPC1 / PGSC0003DMG400011502 / IV / 6.1 / Photosynthesis / AF453448
α-glucosidaseAgl / PGSC0003DMG400005353 / IV / 30.7 / Sucrose and starch metabolism, candidate gene for tuber starch content (Chen et al., 2001) / AJ001374
4-α-glucanotransferase / PGSC0003DMG400016589 / IV / 54 / Sucrose and starch metabolism / X68664
Fructose-1,6-bisphosphatase FBPase-cy / PGSC0003DMG400024109 / IV / 60 / Sucrose and starch metabolism, candidate gene for tuber starch content (Chen et al., 2001) / X76946
Glucose-1-phosphate adenylyltransferaseAGPaseS / No annotated / IV / 61 / Sucrose and starch metabolism
L-type starch phosphorylaseStpL / PGSC0003DMG400028382 / V / 0.3 / Starch synthesis, associated with higher starch content and low yield(Li et al., 2008) / X73684
Rubisco subunit binding-protein beta subunit / PGSC0003DMG400025122 / V / 1.5 / Photosynthesis
Phytochrome and flowering time 1 protein / PGSC0003DMG401000817 / V / 2.1 / Plant growth metabolism
Heat shock protein binding protein / PGSC0003DMG400030542 / V / 4.2 / Stress response
DNA-binding transcription factor CDF1 / PGSC0003DMG400018408 / V / 4.5 / Maturity locus characterized byKloosterman et al. (2013)
Phytochrome kinase substrate 1 / PGSC0003DMG400031263 / V / 5.1 / Plant growth metabolism
Sucrose transporter SUT2 / PGSC0003DMG400025610 / V / 5.7 / Sucrose metabolism, associated with sugar content (Menendez et al., 2002) / AY291289
Isoamylase isoform 3 Stisa3 / PGSC0003DMG402007274 / VI / 0.4 / Starch biosynthesis / AY132998
Heat shock protein / PGSC0003DMG400030426 / VI / 57 / Stress response
InvertasesInvGE and InvGF / PGSC0003DMG400008942 PGSC0003DMG400008943
PGSC0003DMG400008974 / IX / 2.5 / Starch metabolism associated with sugar content (Menendez et al., 2002) / AJ33765
Enolase / PGSC0003DMG402002721 / IX / 3.9 / Starch metabolism(Werij et al., 2012) / X58108
Ribulosebisphosphate carboxylase/oxygenaseactivase 1 / PGSC0003DMG400011072 / X / 54.3 / Photosynthesis
Sucrose synthase / PGSC0003DMG400002895 / XII / 0.3 / Sucrose metabolism, associated with sugar content (Menendez et al., 2002)

† Gene ID, gene identification number on potato genome pseudomoleculeassembly 4.03; Chr, chromosome; Mb, megabase pair position on potato genome pseudomoleculeassembly 4.03.

‡ Metabolism associated with the gene function and reference if the gene was reported as candidate gene for an agronomic trait.

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References

Chen, X., F. Salamini and C. Gebhardt. 2001. A potato molecular-function map for carbohydrate metabolism and transport. Theor Appl Genet 102: 284-295. Doi 10.1007/S001220051645

Fischer, M., L. Schreiber, T. Colby, M. Kuckenberg, E. Tacke, H.R. Hofferbert, et al. 2013. Novel candidate genes influencing natural variation in potato tuber cold sweetening identified by comparative proteomics and association mapping. BMC Plant Biol 13: 15. Doi 10.1186/1471-2229-13-113

Kloosterman, B., J.A. Abelenda, M.D.C. Gomez, M. Oortwijn, J.M. de Boer, K. Kowitwanich, et al. 2013. Naturally occurring allele diversity allows potato cultivation in northern latitudes. Nature 495: 246-250. Doi 10.1038/Nature11912

La Cognata, U., L. Willmitzer and B. Mullerrober. 1995. Molecular cloning and characterization of novel isoforms of potato ADP-Glucose pyrophosphorylase. Mol Gen Genet 246: 538-548.

Li, L., M.J. Paulo, J. Strahwald, J. Lubeck, H.R. Hofferbert, E. Tacke, et al. 2008. Natural DNA variation at candidate loci is associated with potato chip color, tuber starch content, yield and starch yield. Theor Appl Genet 116: 1167-1181. Doi 10.1007/S00122-008-0746-Y

McCord, P.H. 2009. Genetic, genomic, and transgenic approaches to understand internal heat necrosis in potato. Ph D, North Carolina State University, Raleigh, North Carolina.

McCord, P.H., G.C. Yencho, B.R. Sosinski and J.A. Osborne. 2009. A microarray approach to identify candidate genes for internal heat necrosis in potato. Hortscience 44: 558-558.

Menendez, C.M., E. Ritter, R. Schafer-Pregl, B. Walkemeier, A. Kalde, F. Salamini, et al. 2002. Cold sweetening in diploid potato: Mapping quantitative trait loci and candidate genes. Genetics 162: 1423-1434.

Urbany, C., T. Colby, B. Stich, L. Schmidt, J. Schmidt and C. Gebhardt. 2012. Analysis of natural variation of the potato tuber proteome reveals novel candidate genes for tuber bruising. J Proteome Res 11: 703-716. Doi 10.1021/Pr2006186

Walters, R.G., F. Shephard, J.J.M. Rogers, S.A. Rolfe and P. Horton. 2003. Identification of mutants of Arabidopsis defective in acclimation of photosynthesis to the light environment. Plant Physiol 131: 472-481. Doi 10.1104/Pp.015479

Werij, J.S., H. Furrer, H.J. van Eck, R.G.F. Visser and C.W.B. Bachem. 2012. A limited set of starch related genes explain several interrelated traits in potato. Euphytica 186: 501-516. Doi 10.1007/S10681-012-0651-Y

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