Allelic variation for alpha-Glucan Water Dikinase is associated with starch phosphate content in tetraploid potato

Abstract

Key message Association analysis resulted in the identification of specific StGWD alleles causing either an increase or decrease in starch phosphate content which was verified in diploid and tetraploid potato mapping populations. Abstract Potatoes are grown for various purposes like French fries, table potatoes, crisps and for their starch. One of the most important aspects of potato starch is that it contains a high amount of phosphate ester groups which are considered to be important for providing improved functionalization after derivatization processes. Little is known about the variation in phosphate content as such in different potato varieties and thus we studied the genetic diversity for this trait. From other studies it was clear that the phosphate content is controlled by a quantitative trait locus (QTL) underlying the candidate gene α-Glucan Water Dikinase (StGWD) on chromosome 5. We performed direct amplicon sequencing of this gene by Sanger sequencing. Sequences of two StGWD amplicons from a global collection of 398 commercial cultivars and progenitor lines were used to identify 16 different haplotypes. By assigning tag SNPs to these haplotypes, each of the four alleles present in a cultivar could be deduced and linked to a phosphate content. A high value for intra-individual heterozygosity was observed (Ho = 0.765). The average number of different haplotypes per individual (Ai) was 3.1. Pedigree analysis confirmed that the haplotypes are identical-by-descent (IBD) and offered insight in the breeding history of elite potato germplasm. Haplotypes originating from introgression of wild potato accessions carrying resistance genes could be traced. Furthermore, association analysis resulted in the identification of specific StGWD alleles causing either an increase or decrease in starch phosphate content varying from 12 nmol PO4/mg starch to 38 nmol PO4/mg starch. These allele effects were verified in diploid and tetraploid mapping populations and offer possibilities to breed and select for this trait.

Peculiar properties of tuber starch in a potato mutant lacking the α-glucan water dikinase 1 gene <i>GWD1</i> created by targeted mutagenesis using the CRISPR/dMac3-Cas9 system

“…JQ388473) and Spud DB (PGSC0003DMT400019845). This gene consists of 33 exons ( Uitdewilligen et al 2022 ). For the target mutagenesis of the S. tuberosum GWD1 gene, we selected three regions, gRNA-1, gRNA-2 and gRNA-3, corresponding to the sequences within the seventh exon of the GWD1 gene ( Figure 1A ).…”

Meta-Analysis of Genetic Factors for Potato Starch Phosphorylation

“…Quite recently [20] allelic status of the GWD gene and thus the corresponding haplotypes were shown to be responsible for the variation of phosphorus content in potato tuber starch. However, in the current study, we showed that there are at least two more QTLs at chromosome 5, reliably associated with the trait.…”

“…However, in the current study, we showed that there are at least two more QTLs at chromosome 5, reliably associated with the trait. Additionally, the length of GWD does not exceed 20,000 bp (15,519 bp in [2], 19,188 bp in [20]) and solcap_snp_c2_55899 (position 5: 9,639,637) is situated far (194,454 bp) away from PotVar0091465 (position 5: 9,834,091, situated in GWD), which means that the GWD-containing QTL also contains a few more kinases-coding related genes.…”

PotatoMASH—A Low Cost, Genome-Scanning Marker System for Use in Potato Genomics and Genetics Applications

“…For example, using a targeted resequencing approach, Uitdewillegen et al were recently able to identify 16 allelic variants of the Glucan Water Di-kinase (GWD gene) by aggregating information from 81 SNPs over two regions, totalling 1 kb of the 16.5 kb. Using a variety of nucleotide windows generally under 1000 kb, it seems that gene haplotype numbers range between 5 and 20 in potato [6,[12][13][14]. Thus, whilst in terms of LD structure, the concept of surveying polymorphism at 400 × 1 Mb intervals might make sense, the actual number of relatively evenly distributed bi-allelic SNPs at which variation is surveyed is likely to have to be at least 10-fold higher in order to capture the majority of the haplotypes present in any potato germplasm collection.…”