Natural diversity of potato (Solanum tuberosum) invertases

Abstract

Background: Invertases are ubiquitous enzymes that irreversibly cleave sucrose into fructose and glucose. Plant invertases play important roles in carbohydrate metabolism, plant development, and biotic and abiotic stress responses. In potato (Solanum tuberosum), invertases are involved in 'cold-induced sweetening' of tubers, an adaptive response to cold stress, which negatively affects the quality of potato chips and French fries. Linkage and association studies have identified quantitative trait loci (QTL) for tuber sugar content and chip quality that colocalize with three independent potato invertase loci, which together encode five invertase genes. The role of natural allelic variation of these genes in controlling the variation of tuber sugar content in different genotypes is unknown.

Results: For functional studies on natural variants of five potato invertase genes we cloned and sequenced 193 full-length cDNAs from six heterozygous individuals (three tetraploid and three diploid). Eleven, thirteen, ten, twelve and nine different cDNA alleles were obtained for the genes Pain-1, InvGE, InvGF, InvCD141 and InvCD111, respectively. Allelic cDNA sequences differed from each other by 4 to 9%, and most were genotype specific. Additional variation was identified by single nucleotide polymorphism (SNP) analysis in an association-mapping population of 219 tetraploid individuals. Haplotype modeling revealed two to three major haplotypes besides a larger number of minor frequency haplotypes. cDNA alleles associated with chip quality, tuber starch content and starch yield were identified.

Conclusions: Very high natural allelic variation was uncovered in a set of five potato invertase genes. This variability is a consequence of the cultivated potato's reproductive biology. Some of the structural variation found might underlie functional variation that influences important agronomic traits such as tuber sugar content. The associations found between specific invertase alleles and chip quality, tuber starch content and starch yield will facilitate the selection of superior potato genotypes in breeding programs.

Figure 1

Structure of the Pain-1 locus on potato chromosome III (A) and the Inv-ap-a locus on chromosome X (B). Annotated open reading frames (ORFs) are numbered as in Table S1 in additional file 5. Transcriptional orientation is indicated by arrowheads. Left to right transcripts are shown in black, right to left transcripts in grey. The intron/exon structures of Pain-1 (ORF 6 on BAC BC149o15), InvCD111 and InvCD141 (ORFs 3 and 4 on BAC BC163l15) are shown as blow-ups.

Figure 2

Phylogenetic tree based on the deduced amino acid sequences of allelic variants of potato and tomato invertase genes. Forty-six alleles of Pain1, InvCD111, InvCD141, InvGE and InvGF are described in this study (Tables S2, S3, S4, S5 and S6 in additional files 6, 1, 2, 3 and 4, respectively; Figures S1, S2, S3, S4 and S5 in additional files 7, 8, 9, 10 and 11, respectively). Also included are Stpain1-a (AAA50305), Stpain1-b (AAQ17074), Stpain1-c (ACC93585), StinvCD141-d (CAA80358), StinvGF-b (CAB76674) and StinvGE-c (CAB76673) from S. tuberosum, Slpain1-a (AAB30874), SlLIN6-a (BAA33150), SlLIN8-a (AAM28822), SlLIN7-a (AAM22410), SlLIN5-a (CAB85897) and SlLIN9 (CAJ19056) from S. lycopersicum, and SpLIN5-a (CAB85898) from S. pennellii. Bootstrap values are indicated at each branchpoint.