Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato

Abstract

BackgroundGenome-wide single nucleotide polymorphism (SNP) markers coupled with allele dosage information has emerged as a powerful tool for studying complex traits in cultivated autotetraploid potato (Solanum tuberosum L., 2n = 4× = 48). To date, this approach has been effectively applied to the identification of quantitative trait loci (QTLs) underlying highly heritable traits such as disease resistance, but largely unexplored for traits with complex patterns of inheritance.ResultsIn this study, an F1 tetraploid russet mapping population (162 individuals) was evaluated for multiple quantitative traits over two years and two locations to identify QTLs associated with tuber sugar concentration, processing quality, vine maturity, and other high-value agronomic traits. We report the linkage maps for the 12 potato chromosomes and the QTL location with corresponding genetic models and candidate SNPs explaining the highest phenotypic variation for tuber quality and maturity related traits. Significant QTLs for tuber glucose concentration and tuber fry color were detected on chromosomes 4, 5, 6, 10, and 11. Collectively, these QTLs explained between 24 and 46% of the total phenotypic variation for tuber glucose and fry color, respectively. The QTL on chromosome 10 was associated with apoplastic invertases, with ‘Premier Russet’ contributing the favorable allele for fry processing quality. On chromosome 5, minor-effect QTLs for tuber glucose concentration and fry color co-localized with various major-effect QTLs, including vine maturity, growth habit, tuber shape, early blight (Altenaria tenuis), and Verticillium wilt (Verticillium spp.).ConclusionsLinkage analysis and QTL mapping in a russet mapping population (A05141) using SNP dosage information successfully identified favorable alleles and candidate SNPs for resistance to the accumulation of tuber reducing sugars. These novel markers have a high potential for the improvement of tuber processing quality. Moreover, the discovery of different genetic models for traits with overlapping QTLs at the maturity locus clearly suggests an independent genetic control.Electronic supplementary materialThe online version of this article (10.1186/s12863-018-0672-1) contains supplementary material, which is available to authorized users.

Multiple QTL Mapping in Autopolyploids: A Random-Effect Model Approach with Application in a Hexaploid Sweetpotato Full-Sib Population

“…In order to declare a QTL, empirical LOD thresholds are computed for each trait using permutations (Churchill and Doerge 1994). This approach has been used widely so far (e.g., Schumann et al 2017;van Geest et al 2017;Massa et al 2018). However, limitations in fitting multiple-QTL models have been presented, due mostly to the possibility of over-parameterization or the lack of optimized algorithms for model selection (Mengist et al 2018;Klaassen et al 2019).…”

Insight into the bZIP Gene Family in Solanum tuberosum: Genome and Transcriptome Analysis to Understand the Roles of Gene Diversification in Spatiotemporal Gene Expression and Function

“…The identification of the bZIP gene family in potato will act as the first step towards structural and functional characterization of the bZIP family. Together with the recent reports describing quantitative trait loci associated with the key developmental and stress-related traits [ 82 , 83 , 84 , 85 , 86 ], these findings will help breeders to develop future-proof potato varieties with enhanced yield potential.…”

Quantitative trait loci for starch-corrected chip color after harvest, cold storage and after reconditioning mapped in diploid potato

“…Chromosome I was previously described as important for AH and RC in another chipping population 11-40; the main QTLs spanned 44.7-50.7 cM and 66.0-72.9 cM, respectively, and corresponded with the regions of the QTLs for AH and RC in population 12-3 (Sołtys-Kalina et al 2015). The significance of the QTLs on chromosome IV for reducing sugar content and tuber fry color after CS was previously detected in diploid and tetraploid potatoes (Menendez et al 2002;Massa et al 2018). Chromosomes I and IV harbor genes encoding enzymes influencing starch content and involved in direct carbohydrate metabolism, e.g., β-galactosidase and β-amylase (chromosome I) and maltose content as phosphoglucoisomerase (chromosome IV); carbohydrate transport, e.g., triose-phosphate/phosphate translocator (chromosome I) or genes regulating cell wall biosynthesis, such as glycosyltransferase (chromosome I); transcription regulation, e.g., transcriptional factor B3 (Schönhals et al 2017;Van Harsselaar et al 2017).…”