Quantitative trait loci for tuber blackspot bruise and enzymatic discoloration susceptibility in diploid potato

Abstract

Tuber tissue discolorations caused by impact (blackspot bruising) and enzymatic discoloration (ED) after tuber cutting are crucial quality traits of the cultivated potato. To understand the complex genetics of the traits, quantitative trait locus (QTL) analysis using diploid mapping population and diversity array technology (DArT) markers was performed. The phenotypic assessment included the complex evaluation of blackspot bruising susceptibility through two methods: rotating drum (B RD) and falling bolt (B FB) in combination with the evaluation of enzymatic discoloration. Because of observed in-practice relationship between bruising susceptibility and tuber starch content (TSC), analysis of starch content-corrected bruising susceptibility (SCB) was performed. QTLs for bruising were detected on chromosomes I, V with both test methods. The rotating drum method enabled the detection of additional QTLs on chromosomes VIII and XII. Analysis of SCB enabled the identification of the major QTL on chromosome V and two weaker QTLs on chromosomes VIII and XII, independently of starch content. The QTL for bruising detected on chromosome I overlapped with the most significant QTL for tuber starch content. This QTL was not significant for starch content-corrected bruising susceptibility, and the effect of the QTL on chromosome V was enhanced for this trait. The QTL analysis of ED revealed the contribution of seven QTLs for the trait, located on six chromosomes, including these detected for the first time: a major locus on chromosome V and minor QTLs on chromosomes VII and X, which were specific for the trait. The QTL for ED on chromosome VIII was co-localized with the marker for polyphenol oxidase (POT32). The phenotypic correlation between bruising and ED was confirmed in QTL analyses of both traits, and the QTLs detected for these traits overlapped on chromosomes I, V, and VIII. Our results should provide a basis for further studies on candidate genes affecting blackspot bruise susceptibility and enzymatic discoloration.Electronic supplementary materialThe online version of this article (doi:10.1007/s00438-017-1387-0) contains supplementary material, which is available to authorized users.

Quantitative trait loci analysis of potato tuber greening

“…The SEN 12-01 genetic map is the first genetic map of the full potato genome constructed with DArTseq™ markers. Its length and density are comparable with earlier DArT maps for which the markers were generated by hybridization methods [18,19]. A main advantage of DArTseq™ markers was the possibility of comparison of the marker order on our genetic map to the physical map of the reference genome, by a BLAST search of the obtained sequences.…”

“…DNA isolation and DArTseq™ genotyping were performed as described by Plich et al [14]. Total genomic DNA was Table 1 Mean scores of three year evaluations for tuber greening and tuber greening depth (± SD) of the parents and standards and in the mapping population SEN 12-01 a Where 0-lack of greening and 5-very intensive greening (for tuber greening) or greening deeper that 10 mm (for tuber greening depth) b Values marked with the same letter within column do not differ significantly according to Duncan's test at p = 0.05 c Pearson's correlation coefficients between the results of assessment from particular years for the tested traits were all significant at p < 0.001 [18,19] using interval mapping with MapQTL®6 software [20]. QTLs were detected using an LOD threshold ≥ 3.0, estimated from cumulative distribution function of the maximum LOD on a chromosome for QTL analysis based on four QTL genotypes [21].…”

QTLs for potato tuber resistance to Dickeya solani are located on chromosomes II and IV

“…The DArTseq markers mapped to chromosomes other than those in the reference potato genome (PGSC DM1‐3 v. 6.1) were removed manually from the maps. QTL analysis was performed as described previously (Hara‐Skrzypiec et al, 2018; Śliwka et al, 2016) using interval mapping with MapQTL 6 software (Van Ooijen, 2009). QTLs were detected using an LOD threshold ≥3.0 estimated from the cumulative distribution function of the maximum LOD on a chromosome for QTL analysis based on four QTL genotypes (Van Ooijen, 1999).…”

QTLs for potato tuber resistance toDickeya solaniare located on chromosomes II and IV

“…The DArTseq™ markers mapped to chromosomes other than those in the reference potato genome (PGSC DM1 −3 v 6.1) were removed manually from the maps. QTL analysis was performed as described previously (Śliwka et al 2016, Hara-Skrzypiec et al 2018) using interval mapping with MapQTL®6 software (Van Ooijen 2009). QTLs were detected using an LOD threshold ≥ 3.0 estimated from the cumulative distribution function of the maximum LOD on a chromosome for QTL analysis based on four QTL genotypes (van Ooijen 1999).…”