Validation of candidate gene markers for marker-assisted selection of potato cultivars with improved tuber quality

Abstract

Tuber yield, starch content, starch yield and chip color are complex traits that are important for industrial uses and food processing of potato. Chip color depends on the quantity of reducing sugars glucose and fructose in the tubers, which are generated by starch degradation. Reducing sugars accumulate when tubers are stored at low temperatures. Early and efficient selection of cultivars with superior yield, starch yield and chip color is hampered by the fact that reliable phenotypic selection requires multiple year and location trials. Application of DNA-based markers early in the breeding cycle, which are diagnostic for superior alleles of genes that control natural variation of tuber quality, will reduce the number of clones to be evaluated in field trials. Association mapping using genes functional in carbohydrate metabolism as markers has discovered alleles of invertases and starch phosphorylases that are associated with tuber quality traits. Here, we report on new DNA variants at loci encoding ADP-glucose pyrophosphorylase and the invertase Pain-1, which are associated with positive or negative effect with chip color, tuber starch content and starch yield. Marker-assisted selection (MAS) and marker validation were performed in tetraploid breeding populations, using various combinations of 11 allele-specific markers associated with tuber quality traits. To facilitate MAS, user-friendly PCR assays were developed for specific candidate gene alleles. In a multi-parental population of advanced breeding clones, genotypes were selected for having different combinations of five positive and the corresponding negative marker alleles. Genotypes combining five positive marker alleles performed on average better than genotypes with four negative alleles and one positive allele. When tested individually, seven of eight markers showed an effect on at least one quality trait. The direction of effect was as expected. Combinations of two to three marker alleles were identified that significantly improved average chip quality after cold storage and tuber starch content. In F1 progeny of a single-cross combination, MAS with six markers did not give the expected result. Reasons and implications for MAS in potato are discussed.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-012-2035-z) contains supplementary material, which is available to authorized users.

Overview and Breeding Strategies of Table Potato Production in Sweden and the Fennoscandian Region

“…for cyst nematode and Potato virus Y (Ortega and Lopez-Vizcon 2012;Whitworth et al 2009). It also looks promising for tuber quality features (Li et al, 2013). MAS along with the estimation of breeding values for simple and complex traits may improve the efficiency in future potato breeding since it will likely reduce significantly the time for identifying superior germplasm (Slater et al 2013;Slater et al 2014).…”

Development and application of a 20K SNP array in potato

“…Studies on North American material also show a separation of subgroups based on market segments (Hirsch et al 2013;Rosyara et al 2016). In contrast, in several German studies with undisclosed material from German breeders hardly any structure was observed (Li et al 2008;Li et al 2010;Li et al 2013;Schreiber et al 2014;Schönhals et al 2016). Because the German contributions are contradictory with the US and NL papers, the issue of population structure should be reviewed at greater depth.…”

“…In literature a range of association studies in potato have used different thresholds to define a marker as significant. Ranging from α = 0.05 (Li et al 2008;Li et al 2010;Baldwin et al 2011;Li et al 2013;Schönhals et al 2016) to α = 0.001 (-10 log(p) = 3) (Urbany et al 2011;D'hoop et al 2014) to -10 log(p) = 4.3 (Rosyara et al 2016). In Chapter 4 we used a threshold of -10 log(p) = 4, which is relative conservative as compared to the majority of the studies mentioned above.…”

Application of sequence specific amplified polymorphism (SSAP) and simple sequence repeat (SSR) markers for variability and molecular assisted selection (MAS) studies of the Mexican guava

“…Other crops of commercial importance in which the SSR markers were shown to be associated to quantitative features of interest include papaya (Blas et al, 2011), potato (Li et al, 2013), and apple (Longhi et al, 2013), crops in which the use of these markers in improvement programs has been successful.…”

“…Furthermore, early selection would allow for obtaining pure lines with desired fruit characteristics in less time for satisfying the needs of producers, consumers, and the industry (Darwin-Robbins and Staub-Jack, 2009;Li et al, 2013). Currently desired guava phenotypes are white pulp, thick external and internal pulp, and high soluble solid content.…”