Association genetics in Solanum tuberosum provides new insights into potato tuber bruising and enzymatic tissue discoloration

Abstract

BackgroundMost agronomic plant traits result from complex molecular networks involving multiple genes and from environmental factors. One such trait is the enzymatic discoloration of fruit and tuber tissues initiated by mechanical impact (bruising). Tuber susceptibility to bruising is a complex trait of the cultivated potato (Solanum tuberosum) that is crucial for crop quality. As phenotypic evaluation of bruising is cumbersome, the application of diagnostic molecular markers would empower the selection of low bruising potato varieties. The genetic factors and molecular networks underlying enzymatic tissue discoloration are sparsely known. Hitherto there is no association study dealing with tuber bruising and diagnostic markers for enzymatic discoloration are rare.ResultsThe natural genetic diversity for bruising susceptibility was evaluated in elite middle European potato germplasm in order to elucidate its molecular basis. Association genetics using a candidate gene approach identified allelic variants in genes that function in tuber bruising and enzymatic browning. Two hundred and five tetraploid potato varieties and breeding clones related by descent were evaluated for two years in six environments for tuber bruising susceptibility, specific gravity, yield, shape and plant maturity. Correlations were found between different traits. In total 362 polymorphic DNA fragments, derived from 33 candidate genes and 29 SSR loci, were scored in the population and tested for association with the traits using a mixed model approach, which takes into account population structure and kinship. Twenty one highly significant (p < 0.001) and robust marker-trait associations were identified.ConclusionsThe observed trait correlations and associated marker fragments provide new insight in the molecular basis of bruising susceptibility and its natural variation. The markers diagnostic for increased or decreased bruising susceptibility will facilitate the combination of superior alleles in breeding programs. In addition, this study presents novel candidates that might control enzymatic tissue discoloration and tuber bruising. Their validation and characterization will increase the knowledge about the underlying biological processes.

Development and application of a 20K SNP array in potato

“…In Chapter 2 we report on a total of 6.7% explained by the two first principal coordinates, comparable to the value of 8% reported for US material (Rosyara et al 2016). A substantial 12.7% was reported by Urbany et al (2011), whereas only 2.1% was reported by Schönhals et al (2016). In other studies no significant subpopulation structure was detected (Li et al 2008;Li et al 2010;Schreiber et al 2014).…”

“…Firstly, more genetic variation can be analysed simultaneously, and the mapping resolution is increased because all historical recombination can be exploited. Initial association mapping had a targeted approach on several candidate genes (Li et al 2008;Li et al 2010;Baldwin et al 2011;Urbany et al 2011;Schreiber et al 2014). Later the studies of (D'hoop et al 2008; D'hoop et al 2014) used an untargeted approach with AFLP markers.…”

“…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.…”

“…Despite these disadvantages, association studies still offer the potential to dissect the genetics of complex traits, with the ultimate goal to improve breeding efficiency through the use of molecular markers. In the last decade several association studies have been conducted in potato (Baldwin et al 2011;D'hoop et al 2014;D'hoop et al 2008;Li et al 2010;Lindqvist-Kreuze et al 2014;Malosetti et al 2007;Rosyara et al 2016;Schönhals et al 2016;Urbany et al 2011). All of these studies found significant markertrait associations, but differ in number of markers and marker types used.…”

“…For example, in the studies of D'hoop et al (2008, 2014) a relatively high number of markers were used, however the multi-locus AFLP marker system is not easily simplified into a single locus assay for follow-up studies or breeding. Other studies (Baldwin et al 2011;Li et al 2010;Schönhals et al 2016;Urbany et al 2011) focused on a fixed number of several candidate genes, and as a consequence only a relatively small portion of the genome is taken into account. These studies can therefore technically not be considered as true genome-wide.…”