Interval Mapping of Quantitative Trait Loci for Resistance to Late Blight [Phytophthora infestans (Mont.) de Bary], Height and Maturity in a Tetraploid Population of Potato (Solanum tuberosum subsp. tuberosum)

Abstract

Interval mapping of quantitative trait loci (QTL) for resistance to late blight, height, and maturity was performed on a tetraploid full-sib family of potato comprising 227 clones from a cross between a susceptible parent, 12601ab1, and a resistant cultivar, Stirling, which were of similar height and main crop maturity. Thirty-eight AFLP primer combinations provided 585 informative markers, and 23 SSRs proved useful for identifying linkage groups (LGs). A simplex QTL allele was found on LGV of Stirling close to marker STM3179, which was associated with early maturity, short plants, and susceptibility to blight and explained 54.7, 26.5, 26.3, and 17.5% of the variation for maturity, height, tuber blight, and foliage blight. When the residuals from the regressions of foliage and tuber blight on maturity were analyzed, there was no significant effect of a QTL on LGV, but a duplex QTL allele for resistance was found on LGIV of Stirling, which explained 30.7 and 13.6% of the variation for foliage and tuber blight on an additive model. Partial dominance for resistance explained even more of the variation, up to 37.2% for foliage blight. A major gene for blight resistance in Stirling was also mapped to LGXI. I N recent years, advances in computer technology which marker placings are fixed and to identify the have led to an increasing interest in extending linkmarkers whose positions are less certain. The method age analysis and quantitative trait locus (QTL) mapping was tested by computer simulation and application to methods from diploid to polyploid plant species, which 30 AFLP and SSR markers on linkage group IV of potato. display complex polysomic inheritance (Doerge and Once a reliable linkage map is available, the method of Craig 2000; Luo et al. 2001; Gallais 2003). This is Hackett et al. (2001) can be used for QTL interval not surprising, given the occurrence and evolutionary mapping in a full-sib family of an autotetraploid species significance of autopolyploidy in wild plants and the derived by crossing two parents. The success of the economic importance of several autopolyploid crop spemethod was demonstrated in a simulation study but not cies such as tetraploid alfalfa and potato, hexaploid on real data. The theory in these articles (Hackett et sweet potato, and octaploid strawberry and sugarcane al. 2001, 2003; Luo et al. 2001) was based on the simplest (Gallais 2003).situation that can give tetrasomic inheritance, namely Luo et al. (2001) presented a methodology for the random pairing of four homologous chromosomes to construction of a linkage map in an autotetraploid spegive two pairs of bivalents at meiosis and an orderly cies using either codominant or dominant molecular meiosis in which all possible diploid gametes are equally markers scored on two parents and their full-sib proglikely and viable. eny. The methods were applied to a simulated data set In practice, many departures from this simple situaand to a small set of SSR (microsatellite) and amplified tion could occur, in particular: m...

The Double-Reduction Landscape in Tetraploid Potato as Revealed by a High-Density Linkage Map

“…This is partly due to the lack of software to perform linkage mapping and QTL analysis in polyploids but is also due to the complicated nature of autopolyploid genomes and genetics. The software program TetraploidMap (Hackett and Luo 2003) is a notable exception to this but is constrained by the relatively low numbers of markers it can handle (currently 800 is the maximum) and the need to manually assign marker phase, which may become infeasible with large data sets.One autopolyploid species in which large advances in genetic analysis have been made is tetraploid potato (Solanum tuberosum L.), in terms of the availability of a high-quality reference sequence (Potato Genome Sequencing Consortium 2011), many published linkage maps (Meyer et al 1998;van Os et al 2006;Felcher et al 2012;Hackett et al 2013) as well as methods for performing linkage mapping at the polyploid level (Luo et al 2001;Bradshaw et al 2004;Hackett et al 2013). In comparison with other economically important autotetraploid species such as alfalfa, rose, and leek, the pairing behavior of potato is thought to be relatively well understood, with random bivalent pairing during prophase I of meiosis being generally assumed (Swaminathan and Howard 1953;Milbourne et al 2009).…”

The novel, major locus Rpi-phu1 for late blight resistance maps to potato chromosome IX and is not correlated with long vegetation period

“…The few QTLs for vegetation period length tagged in population 97-30 are in accordance with published data. The most important QTL for vegetation period length has been repeatedly identiWed on potato chromosome V in the vicinity of the R1 locus and overlapped with QTL for late blight resistance (Collins et al 1999;Oberhagemann et al 1999;Bormann et al 2004;Bradshaw et al 2004;Visker et al 2003Visker et al , 2005. QTLs for vegetation period length on chromosomes IV, VIII and IX have also been detected in the QTLs tagging experiment of Bormann et al (2004).…”

Constructing Genetic Linkage Maps Under a Tetrasomic Model

“…It causes not only distorted segregation of marker alleles but also a more complicated distribution of offspring genotypes. To avoid the analytical complexity of double reduction in linkage analysis of tetraploids, the current literature on linkage analysis of tetraploids has relied on a random bivalent pairing model (Ripol et al 1999;Hackett et al 2001;Luo et al 2001;Bradshaw et al 2004;Cao et al 2005) or on an oversimplified assumption (refer to Luo and Zhang 2005 for details). The methods based on the bivalent pairing model may not be used to analyze the data properly when double reduction does exist.…”

“…The marker data set comprised 197 AFLP markers and 4 microsatellite markers scored on 228 offspring from a cross between two parental lines: the advanced potato breeding line 1260lab1 and the cultivar Stirling (Bradshaw et al 2004). Some of the AFLP markers were present in one parent and absent in the other and some were present in both parents.…”

“…In addition to the aforementioned complexities (i-iii), challenges in modeling these PCRbased genetic markers involve (iv) occurrence of null alleles due to experimental failure to identify the presence of some alleles and (v) one phenotype representing several genotypes. Linkage analyses of autopolyploids in the current literature have been based either on the use of single-dose (simplex) dominant markers (e.g., AFLPs and RAPDs) that segregate in a simple 1:1 ratio in mapping populations (Wu et al 1992;Meyer et al 1998;Brouwer and Osborn 1999;Barcaccia et al 2003) or on assuming solely random bivalent pairing among homologous chromosomes (Ripol et al 1999;Hackett et al 2001;Luo et al 2001;Bradshaw et al 2004;Cao et al 2005). These have effectively avoided the analytical complexities but at the same time ignored some essential features of the problems.…”