The lack of a gene marker directly affecting starch biosynthesis in the potato tuber is documented. The absence of a 454 bp amplified fragment length polymorphism (AFLP) Solanum tuberosum fragment was identified in the wild potato species Solanum sandemanii and its absence results in a combined increased-amylose/high-sugar tuber chemotype. The trait is recessive, termed IAm (Increased Amylose) and was transferred to modern tetraploid S. tuberosum potato cultivars by marker-assisted crossing. Compared to controls, IAm plants had a larger number of stems and air exposed stolons, their tubers were smaller, elongated, and they were irregularly shaped. IAm starch had 28-59% higher amylose content than control starch, the starch granules were small and grossly misshaped, they had reduced crystallinity, swelling, and viscosity, reduced in vitro digestion rates with increased resistant starch fraction. The primary gene(s) responsible for the IAm phenotype is not known, but increased granule-associated phosphorylase (Pho1) and reduced starch synthase (SS) protein and enzyme activity in the IAm plants might explain the effects on starch structure. The data support the establishment of non-genetically modified crops with health-related slowly digestible carbohydrate.

In this study we introduce the starch-recognising carbohydrate binding module family 20 (CBM20) from Aspergillus niger for screening biological variations in starch molecular structure using high throughput carbohydrate microarray technology. Defined linear, branched and phosphorylated maltooligosaccharides, pure starch samples including a variety of different structures with variations in the amylopectin branching pattern, amylose content and phosphate content, enzymatically modified starches and glycogen were included. Using this technique, different important structures, including amylose content and branching degrees could be differentiated in a high throughput fashion. The screening method was validated using transgenic barley grain analysed during development and subjected to germination. Typically, extreme branching or linearity were detected less than normal starch structures. The method offers the potential for rapidly analysing resistant and slowly digested dietary starches.

Summary Solanum tuberosum potato lines with high amylose content were generated by crossing with the wild potato species Solanum sandemanii followed by repeated backcrossing to Solanum tuberosum lines. The trait, termed increased amylose (IAm), was recessive and present after three generations of backcrossing into S. tuberosum lines (6.25% S. sandemanii genes). The tubers of these lines were small, elongated and irregular with small and misshaped starch granules and high sugar content. Additional backcrossing resulted in less irregular tuber morphology, increased starch content (4.3%–9.5%) and increased amylose content (29%–37.9%) but indifferent sugar content. The amylose in the IAm starch granules was mainly located in peripheral spots, and large cavities were found in the granules. Starch pasting was suppressed, and the digestion‐resistant starch (RS) content was increased. Comprehensive microarray polymer profiling (CoMPP) analysis revealed specific alterations of major pectic and glycoprotein cell wall components. This complex phenotype led us to search for candidate IAm genes exploiting its recessive trait. Hence, we sequenced genomic DNA of a pool of IAm lines, identified SNPs genome wide against the draft genome sequence of potato and searched for regions of decreased heterozygosity. Three regions, located on chromosomes 3, 7 and 10, respectively, displayed markedly less heterozygosity than average. The only credible starch metabolism‐related gene found in these regions encoded the isoamylase‐type debranching enzyme Stisa1. Decreased expression of mRNA (>500 fold) and reduced enzyme activity (virtually absent from IAm lines) supported Stisa1 as a candidate gene for IAm.