QTL mapping of yield, agronomic and quality traits in tetraploid potato (Solanum tuberosum subsp. tuberosum)

Bradshaw, J. E.; Hackett, Christine A.; Pande, B. N.; Waugh, Robbie; Bryan, Glenn J.

doi:10.1007/s00122-007-0659-1

Cited by 160 publications

(178 citation statements)

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“…The strong correlation between reducing sugar content and chipping colour has previously been demonstrated (Scheffler et al 1992). QTLs for chipping colour in our study confirm that major QTL are present in regions on chromosomes 3, 5, 8, 9 and 10 (Douches and Freyre 1994;Menendez et al 2002;Bradshaw et al 2008;Li et al 2005), although strict comparisons with published data cannot be made due to the lack of shared markers and map resolution. For the chipping QTLs on chromosomes 3 we confirm the co-localisation with starch phosphorylase StPho1a, but the invertase locus PAIN-1 and SSS-1 have been implicated as well (Li et al 2008).…”

Section: Genetic Variation For Starch Propertiessupporting

confidence: 81%

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A limited set of starch related genes explain several interrelated traits in potato

et al. 2012

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To understand the molecular basis of potato starch related traits and the underlying starch biosynthesis and degradation, a Quantitative Trait Locus (QTL) analysis in combination with a candidate gene approach was performed. The diploid mapping population C 9 E, consisting of 249 individuals, was assayed over two consecutive years, for chipping colour, cold induced sweetening, starch content, starch granule size, starch gelling temperature, starch enthalpy, amylose content and degree of starch phosphorylation. QTLs were observed for all traits, except enthalpy on eight out of the twelve potato chromosomes. Several QTLs were found to be consistent over 2 years. Clustering of co-localizing QTLs was observed on some chromosomes, indicating common genetic factors for the different traits. On chromosome 2, Soluble Starch Synthase 2 mapped on the same position as QTLs for starch phosphorylation, starch gelling temperature and amylose content. a-glucan, water dikinase co-localizes on chromosome 5 together with QTLs for starch phosphorylation and cold induced sweetening. Furthermore, the genes coding for two phosphorylases (StPho1a and StPho2) coincide with QTLs for starch gelling temperature, chipping colour and starch granule size on chromosome 2 and a QTL for starch phosphorylation on chromosome 9, respectively. The results suggest allelic variation acting on the genetics of the different traits.

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Section: Genetic Variation For Starch Propertiessupporting

confidence: 81%

“…For the QTL on 9 and 10 the apoplastic invertases were proposed (Menendez et al 2002). QTLs for frying colour, after 4 and 10°C storage have also been identified (Bradshaw et al 2008). These QTLs are located on chromosomes 1, 6 and 11.…”

Section: Genetic Variation For Starch Propertiesmentioning

confidence: 89%

A limited set of starch related genes explain several interrelated traits in potato

et al. 2012

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“…One of the more influential publications on potato cytology has been the early review of Swaminathan and Howard (1953), who summarized the findings of previous researchers such as Cadman (1943), Lamm (1945), and Bains (1951) for the mean number of multivalents per cell at diakinesis and first metaphase in tetraploid S. tuberosum as ranging from 1.70 to 5.24. This cytological evidence has been used to support the use of a simplified pairing model in potato mapping and QTL analysis since then (Hackett et al , 2013Luo et al 2001;Bradshaw et al 2008). In our study, we have used marker data to estimate the rate of DR and from this to extrapolate the likely frequency of multivalents involved (we only consider quadrivalents).…”

Section: Potato Cytologymentioning

confidence: 90%

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

et al. 2015

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The creation of genetic linkage maps in polyploid species has been a long-standing problem for which various approaches have been proposed. In the case of autopolyploids, a commonly used simplification is that random bivalents form during meiosis. This leads to relatively straightforward estimation of recombination frequencies using maximum likelihood, from which a genetic map can be derived. However, autopolyploids such as tetraploid potato (Solanum tuberosum L.) may exhibit additional features, such as double reduction, not normally encountered in diploid or allopolyploid species. In this study, we produced a high-density linkage map of tetraploid potato and used it to identify regions of double reduction in a biparental mapping population. The frequency of multivalents required to produce this degree of double reduction was determined through simulation. We also determined the effect that multivalents or preferential pairing between homologous chromosomes has on linkage mapping. Low levels of multivalents or preferential pairing do not adversely affect map construction when highly informative marker types and phases are used. We reveal the double-reduction landscape in tetraploid potato, clearly showing that this phenomenon increases with distance from the centromeres.KEYWORDS linkage mapping; tetraploid; double reduction; potato; multivalents P OLYPLOID species constitute a very important group among cultivated crops. Polyploids themselves can be further divided into auto-and allopolyploids, with autopolyploids showing random association between homologous chromosomes and allopolyploids showing nonrandom or preferential pairing during meiosis. Linkage mapping in autopolyploid species remains a challenging exercise despite recent advances in genotyping technology and mapping methodology. Breeding work in many autopolyploid crops has yet to benefit from the use of markers in breeding programs. 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 understo...

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“…The multilocus method confers the additional advantage of providing a direct calculation of likelihood for any given linkage map, thus achieving a step forward for the computational challenge of statistical inferring linkage order and linkage phase (17). Although active research efforts have been invested to develop theory and statistical methods for mapping QTL in tetraploid species (4,11,15,(18)(19)(20)(21), none of these have been built on a rigorous autotetrasomic model. In addition to the tools for genetic map construction, this study provides both theory and method to calculate the conditional probability distribution of genotypes at any test position given the phenotype of its linked genetic markers, a key step for QTL analysis in autotetraploid species.…”

Section: Discussionmentioning

confidence: 99%

Multilocus tetrasomic linkage analysis using hidden Markov chain model

Leach

Wang

Kearsey

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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The availability of reliable genetic linkage maps is crucial for functional and evolutionary genomic analyses. Established theory and methods of genetic linkage analysis have made map construction a routine exercise in diploids. However, many evolutionarily, ecologically, and/or agronomically important species are autopolyploids, with autotetraploidy being a typical example. These species undergo much more complicated chromosomal segregation and recombination at meiosis than diploids. In addition, there is evidence of polyploidy-induced and highly dynamic changes in the structure of the genome. These polysomic characteristics indicate the inappropriateness of the theory and methods of linkage analysis in diploids for use in these species and a gap in the theory and methodology of tetraploid map construction. This paper presents a theoretical model and statistical framework for multilocus linkage analysis in autotetraploids for use with dominant and/or codominant DNA molecular markers. The theory and methods incorporate the essential features of allele segregation and recombination under tetrasomic inheritance and the major challenges in statistical modeling and marker data analysis. We validated the method and explored its statistical properties by intensive simulation study and demonstrated its utility by analysis of AFLP and SSR marker data from an outbred autotetraploid potato population.autotetraploid species | tetrasomic inheritance | outbred populations | map construction P olyploidization, the simultaneous duplication of all genes in a genome, has been ubiquitous in plant evolutionary history, with ≈70% of angiosperms being polyploids (1). Allopolyploids display disomic inheritance and their genetic analysis follows the same principles as diploids, whereas autopolyploids display more complicated polysomic inheritance. Among autopolyploids exist important autotetraploids including agricultural crops, notably cultivated potato, and aquaculture animals such as Atlantic salmon and trout, for which active genome projects are underway. These projects will generate abundant genetic polymorphisms and, thus, enable construction of genetic maps, which are essential for dissecting quantitative trait loci (QTL) and, in turn, for improving efficiency of breeding programs through marker assisted selection.Genetic linkage maps exist or are becoming rapidly available in almost all important diploid animal and plant species and humans, providing an essential starting point for an insightful genomic investigation. In sharp contrast, progress in autopolyploid linkage analysis, the theoretical kernel for map construction, lags far behind. In autopolyploids, multivalent meiotic pairing of homologous chromosomes, followed by crossing over between the locus and spindle attachment, may cause double reduction, in which sister chromatids enter into the same gamete (2). Recombination frequency between a pair of loci can be as high as 0.75 under a tetrasomic model (compared to 0.5 in diploids), and double reduction can occur at a fr...

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QTL mapping of yield, agronomic and quality traits in tetraploid potato (Solanum tuberosum subsp. tuberosum)

Cited by 160 publications

References 28 publications

A limited set of starch related genes explain several interrelated traits in potato

A limited set of starch related genes explain several interrelated traits in potato

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

Multilocus tetrasomic linkage analysis using hidden Markov chain model

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