Association mapping of cold-induced sweetening in potato using historical phenotypic data

Polyploidy and Plant Breeding

“…The mixed-model association mapping approach using a kinship matrix, which was based on the restricted maximum likelihood estimate of the conditional probability that two genotypes carry at the same locus alleles that are identical in state but not identical by descent (T opt ), seems to be the most appropriate for association mapping. Association mapping was useful to identify QTL for host plant resistance to late blight (Malosetti et al 2007) and Verticillium wilt (Simko et al 2004), cold-induced sweetening (Baldwin et al 2011), andagro-morphological (D'hoop et al 2014) plus tuber quality traits (D'hoop et al 2008), among others. A publicly available database holding such genetic profiles of cultivars and advanced breeding lines evaluated with a common set of DNA markers will further help identifying genomic regions associated with target traits (Simko 2004).…”

Development and application of a 20K SNP array in potato

“…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.…”

“…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.…”

“…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.…”