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SNPs in genes functional in starch-sugar interconversion associate with natural variation of tuber starch and sugar content of potato (Solanum tuberosum L.).

Schreiber L, Nader-Nieto AC, Schönhals EM, Walkemeier B, Gebhardt C - G3 (Bethesda) (2014)

Bottom Line: Most positive or negative effects of SNPs on tuber-reducing sugar content were reproducible in two different collections of potato cultivars.An allele of the plastidic starch phosphorylase PHO1a associated with increased tuber starch content was cloned as full-length cDNA and characterized.This mutation might cause reduced enzyme activity due to impaired formation of the active dimers, thereby limiting starch breakdown.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute for Plant Breeding Research, Department of Plant Breeding and Genetics, 50829 Cologne, Germany.

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Physical map of candidate genes functional in starch-sugar interconversion. The 12 potato pseudomolecules (v4.03) (Sharma et al. 2013) are shown as solid vertical lines. The positions of 123 candidate loci specified in Table S1 are indicated to the right of the pseudomolecules (for acronyms, see also legend of Figure 1). Restriction fragment length polymorphism (GP***, CP***) (Menendez et al. 2002; Schäfer-Pregl et al. 1998) and microsatellite markers (STM****, StI***, STG****) (Feingold et al. 2005; Ghislain et al. 2009; Milbourne et al. 1998) anchoring potato genetic maps to the pseudomolecules are shown to the left. Candidate genes that have been tested for association (Fischer et al. 2013; Li et al. 2008) but are functional in pathways other than starch–sugar interconversion (Figure 1) also are shown to the left: G6PDH, glucose-6-phosphate dehydrogenase (EC 1.1.1.49); Fbp-cy, fructose-1,6-bisphosphatase (EC 3.1.3.11), cytosolic; Pha2, plasma membrane H+-ATPase 2 (EC 3.6.3.6); Rca, Ribulose bisphosphate carboxylase activase (EC 4.1.1.39); and LAP, leucine aminopeptidase (EC 3.4.11.1). Candidate genes and markers that were linked to QTL for tuber yield, starch, and/or reducing sugar content (Menendez et al. 2002; Schäfer-Pregl et al. 1998) are indicated in bold letters. Candidate genes and markers for which associations with tuber quality traits have been identified are shown in red letters, whereas candidate genes tested negatively for trait associations are shown in blue letters (Baldwin et al. 2011; Draffehn et al. 2010; Fischer et al. 2013; Kawchuk et al. 2008; Li et al. 2005, 2008, 2013; Urbany et al. 2011).
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fig4: Physical map of candidate genes functional in starch-sugar interconversion. The 12 potato pseudomolecules (v4.03) (Sharma et al. 2013) are shown as solid vertical lines. The positions of 123 candidate loci specified in Table S1 are indicated to the right of the pseudomolecules (for acronyms, see also legend of Figure 1). Restriction fragment length polymorphism (GP***, CP***) (Menendez et al. 2002; Schäfer-Pregl et al. 1998) and microsatellite markers (STM****, StI***, STG****) (Feingold et al. 2005; Ghislain et al. 2009; Milbourne et al. 1998) anchoring potato genetic maps to the pseudomolecules are shown to the left. Candidate genes that have been tested for association (Fischer et al. 2013; Li et al. 2008) but are functional in pathways other than starch–sugar interconversion (Figure 1) also are shown to the left: G6PDH, glucose-6-phosphate dehydrogenase (EC 1.1.1.49); Fbp-cy, fructose-1,6-bisphosphatase (EC 3.1.3.11), cytosolic; Pha2, plasma membrane H+-ATPase 2 (EC 3.6.3.6); Rca, Ribulose bisphosphate carboxylase activase (EC 4.1.1.39); and LAP, leucine aminopeptidase (EC 3.4.11.1). Candidate genes and markers that were linked to QTL for tuber yield, starch, and/or reducing sugar content (Menendez et al. 2002; Schäfer-Pregl et al. 1998) are indicated in bold letters. Candidate genes and markers for which associations with tuber quality traits have been identified are shown in red letters, whereas candidate genes tested negatively for trait associations are shown in blue letters (Baldwin et al. 2011; Draffehn et al. 2010; Fischer et al. 2013; Kawchuk et al. 2008; Li et al. 2005, 2008, 2013; Urbany et al. 2011).

Mentions: The annotated potato genome sequence (Potato Genome Sequencing Consortium et al. 2011) and improved physical maps of the 12 potato chromosomes (Sharma et al. 2013) allowed to estimate number and genomic positions of the genes, which function in starch-sugar interconversion according to the model shown in Figure 1. One hundred twenty-three expressed genes on all chromosomes were identified (Table S1 and Figure 4). A particularly high density of these genes was observed in distal regions of the long arms of chromosomes I, II, III, IV, and VII, where 50 genes (40%) were located. Except GWD, PWD, and SEX4, all enzymes and transporters are encoded by at least two genes, the largest family being putative invertases with 20 genes (Table S1). Approximately half of these genes have been cloned and characterized before in potato and/or tomato (Table S1). Seven of the previously characterized genes (5.7%) were not annotated in the current potato genome draft sequence. Including the results of this study, 25 loci functional in starch-sugar interconversion have been analyzed for association of DNA polymorphisms with tuber quality traits (Table S1) (Baldwin et al. 2011; Draffehn et al. 2010; Kawchuk et al. 2008; Li et al. 2005, 2008, 2013; Urbany et al. 2011), the majority of which showed associations of DNA polymorphisms with one or more tuber quality traits (Figure 4).


SNPs in genes functional in starch-sugar interconversion associate with natural variation of tuber starch and sugar content of potato (Solanum tuberosum L.).

Schreiber L, Nader-Nieto AC, Schönhals EM, Walkemeier B, Gebhardt C - G3 (Bethesda) (2014)

Physical map of candidate genes functional in starch-sugar interconversion. The 12 potato pseudomolecules (v4.03) (Sharma et al. 2013) are shown as solid vertical lines. The positions of 123 candidate loci specified in Table S1 are indicated to the right of the pseudomolecules (for acronyms, see also legend of Figure 1). Restriction fragment length polymorphism (GP***, CP***) (Menendez et al. 2002; Schäfer-Pregl et al. 1998) and microsatellite markers (STM****, StI***, STG****) (Feingold et al. 2005; Ghislain et al. 2009; Milbourne et al. 1998) anchoring potato genetic maps to the pseudomolecules are shown to the left. Candidate genes that have been tested for association (Fischer et al. 2013; Li et al. 2008) but are functional in pathways other than starch–sugar interconversion (Figure 1) also are shown to the left: G6PDH, glucose-6-phosphate dehydrogenase (EC 1.1.1.49); Fbp-cy, fructose-1,6-bisphosphatase (EC 3.1.3.11), cytosolic; Pha2, plasma membrane H+-ATPase 2 (EC 3.6.3.6); Rca, Ribulose bisphosphate carboxylase activase (EC 4.1.1.39); and LAP, leucine aminopeptidase (EC 3.4.11.1). Candidate genes and markers that were linked to QTL for tuber yield, starch, and/or reducing sugar content (Menendez et al. 2002; Schäfer-Pregl et al. 1998) are indicated in bold letters. Candidate genes and markers for which associations with tuber quality traits have been identified are shown in red letters, whereas candidate genes tested negatively for trait associations are shown in blue letters (Baldwin et al. 2011; Draffehn et al. 2010; Fischer et al. 2013; Kawchuk et al. 2008; Li et al. 2005, 2008, 2013; Urbany et al. 2011).
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fig4: Physical map of candidate genes functional in starch-sugar interconversion. The 12 potato pseudomolecules (v4.03) (Sharma et al. 2013) are shown as solid vertical lines. The positions of 123 candidate loci specified in Table S1 are indicated to the right of the pseudomolecules (for acronyms, see also legend of Figure 1). Restriction fragment length polymorphism (GP***, CP***) (Menendez et al. 2002; Schäfer-Pregl et al. 1998) and microsatellite markers (STM****, StI***, STG****) (Feingold et al. 2005; Ghislain et al. 2009; Milbourne et al. 1998) anchoring potato genetic maps to the pseudomolecules are shown to the left. Candidate genes that have been tested for association (Fischer et al. 2013; Li et al. 2008) but are functional in pathways other than starch–sugar interconversion (Figure 1) also are shown to the left: G6PDH, glucose-6-phosphate dehydrogenase (EC 1.1.1.49); Fbp-cy, fructose-1,6-bisphosphatase (EC 3.1.3.11), cytosolic; Pha2, plasma membrane H+-ATPase 2 (EC 3.6.3.6); Rca, Ribulose bisphosphate carboxylase activase (EC 4.1.1.39); and LAP, leucine aminopeptidase (EC 3.4.11.1). Candidate genes and markers that were linked to QTL for tuber yield, starch, and/or reducing sugar content (Menendez et al. 2002; Schäfer-Pregl et al. 1998) are indicated in bold letters. Candidate genes and markers for which associations with tuber quality traits have been identified are shown in red letters, whereas candidate genes tested negatively for trait associations are shown in blue letters (Baldwin et al. 2011; Draffehn et al. 2010; Fischer et al. 2013; Kawchuk et al. 2008; Li et al. 2005, 2008, 2013; Urbany et al. 2011).
Mentions: The annotated potato genome sequence (Potato Genome Sequencing Consortium et al. 2011) and improved physical maps of the 12 potato chromosomes (Sharma et al. 2013) allowed to estimate number and genomic positions of the genes, which function in starch-sugar interconversion according to the model shown in Figure 1. One hundred twenty-three expressed genes on all chromosomes were identified (Table S1 and Figure 4). A particularly high density of these genes was observed in distal regions of the long arms of chromosomes I, II, III, IV, and VII, where 50 genes (40%) were located. Except GWD, PWD, and SEX4, all enzymes and transporters are encoded by at least two genes, the largest family being putative invertases with 20 genes (Table S1). Approximately half of these genes have been cloned and characterized before in potato and/or tomato (Table S1). Seven of the previously characterized genes (5.7%) were not annotated in the current potato genome draft sequence. Including the results of this study, 25 loci functional in starch-sugar interconversion have been analyzed for association of DNA polymorphisms with tuber quality traits (Table S1) (Baldwin et al. 2011; Draffehn et al. 2010; Kawchuk et al. 2008; Li et al. 2005, 2008, 2013; Urbany et al. 2011), the majority of which showed associations of DNA polymorphisms with one or more tuber quality traits (Figure 4).

Bottom Line: Most positive or negative effects of SNPs on tuber-reducing sugar content were reproducible in two different collections of potato cultivars.An allele of the plastidic starch phosphorylase PHO1a associated with increased tuber starch content was cloned as full-length cDNA and characterized.This mutation might cause reduced enzyme activity due to impaired formation of the active dimers, thereby limiting starch breakdown.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute for Plant Breeding Research, Department of Plant Breeding and Genetics, 50829 Cologne, Germany.

Show MeSH
Related in: MedlinePlus