Mapping of genes associated with leptine content of tetraploid potato

High content of leptine glycoalkaloids present in Solanum chacoense has been associated with genetic resistance to Colorado potato beetle (Leptinotarsa decemlineata [Say]). From an unrecorded accession of S. chacoense, the North Dakota State University breeding program has developed a tetraploid genotype, ND4382-19, that contains foliar leptines. In this study, using a segregating population, ND5873 (ND4382-19 × Chipeta), and GC-MS to analyze foliar content of alkaloids, two loci, involved in the synthesis of leptines were identified. They segregated as two complementary epistatic genes that allowed the synthesis of leptinidine (Lep) and acetyl-leptinidine (AL), respectively. Partial AFLP maps for both parents were developed using 97 individuals from population ND5873. The total lengths mapped for ND4382-19 and Chipeta were 1,883 and 1,021 cM, respectively. The marker for Lep was located at the distal end of simplex-coupling linkage group R37. Expansion of the initial mapping population and analysis of Lep-containing individuals allowed us to identify the linkage group (R35) that enabled synthesis of AL. By the use of simple sequence repeat markers, linkage group R37 (Lep) and linkage group R35 (AL) have been identified as homologs of chromosomes II and VIII, respectively.H. Casper (deceased)     

Gel formation in mixtures of high amylopectin potato starch and potato starch

The effects of starch granules on the rheological behaviour of gels of native potato and high amylopectin potato (HAPP) starches have been studied with small deformation oscillatory rheometry. The influence of granule remnants on the rheological properties of samples treated at 90 °C was evident when compared with samples treated at 140 °C, where no granule remnants were found. The presence of amylose in native potato starch gave to stronger network formation since potato starch gave higher moduli values than HAPP, after both 90 and 140 °C treatments. In addition, amylose may have strengthened the network of HAPP because higher moduli values were obtained when native potato starch was added to the system. The moduli values of the mixtures also increased with increasing polysaccharide concentration in the system, which is due to an increment in the polysaccharide chain contacts and entanglements. Finally, it was found that a mixture of commercial amylose from potato starch and HAPP resulted in lower values of G′ compared to native potato starch. This indicates that the source of amylose is important for the properties in a blend with native amylopectin.     

Deep-freezing of potato starch

Samples of oven-dried, air-dried, and moisturised potato starch (5, 13, and 24% w/w moisture content, respectively) were frozen in liquid nitrogen. Samples after thawing were studied by means of cross-polarised light beam microscope (CLBM), Fourier Transformation Infrared Spectroscope (FT-IR), powder X-ray diffractometer, and non-contact Atomic Force Microscope (nc-AFM). Rapid deep-freezing followed by thawing produced changes on the granule surface. They were accompanied by internal alteration manifested by FT-IR spectra and powder X-ray diffractograms. The results depended on the water content in the sample. Deep-freezing of moistened starch resulted in increased crystallinity of granules. It had minor effect on the granule aqueous solubility and characteristics of gelation.     

Population structure and linkage disequilibrium unravelled in tetraploid potato

Association mapping is considered to be an important alternative strategy for the identification of quantitative trait loci (QTL) as compared to traditional QTL mapping. A necessary prerequisite for association analysis to succeed is detailed information regarding hidden population structure and the extent of linkage disequilibrium. A collection of 430 tetraploid potato cultivars, comprising two association panels, has been analysed with 41 AFLP^® and 53 SSR primer combinations yielding 3364 AFLP fragments and 653 microsatellite alleles, respectively. Polymorphism information content values and detected number of alleles for the SSRs studied illustrate that commercial potato germplasm seems to be equally diverse as Latin American landrace material. Genome-wide linkage disequilibrium (LD)—reported for the first time for tetraploid potato—was observed up to approximately 5 cM using r ² higher than 0.1 as a criterion for significant LD. Within-group LD, however, stretched on average twice as far when compared to overall LD. A Bayesian approach, a distance-based hierarchical clustering approach as well as principal coordinate analysis were adopted to enquire into population structure. Groups differing in year of market release and market segment (starch, processing industry and fresh consumption) were repeatedly detected. The observation of LD up to 5 cM is promising because the required marker density is not likely to disable the possibilities for association mapping research in tetraploid potato. Population structure appeared to be weak, but strong enough to demand careful modelling of genetic relationships in subsequent marker-trait association analyses. There seems to be a good chance that linkage-based marker-trait associations can be identified at moderate marker densities.     

Field evaluation of tetraploid somatic potato hybrids

Tetraploid somatic hybrids, derived from ten different fusion combinations, were grown in the field to study the inheritance of quantitatively-controlled agronomic traits. The data from two seasons showed that the heterosis in yield varied between 70% and 230% compared to the mid-parent value of the dihaploid fusion clones. The relative yield of the hybrids compared to two standard varieties (= 100%) ranged from 47% to 106%. Despite large differences in yield between the single hybrids of the same fusion combination, no significant differences could be detected between the hybrids. The analysis of the yield components revealed that the heterosis was mainly due to a highly increased tuber weight, whereas the tuber number was in general intermediate to that of the parent clones. In three combinations, the starch content of the hybrids was 15–20% higher than the midparent value and in the others it was intermediate. Fusion of clones with long oval tubers and with round or round-oval ones showed the round/round-oval form was dominant. Fusion combinations of tuber flesh colour indicated that in most cases yellow was dominant to white, while red skin colour was dominant over yellow.     

QTL mapping of internal heat necrosis in tetraploid potato

Internal heat necrosis (IHN) is a physiological disorder of potato tubers. We developed a linkage map of tetraploid potato using AFLP and SSR markers, and mapped QTL for mean severity and percent incidence of IHN. Phenotypic data indicated that the distribution of IHN is skewed toward resistance. Late foliage maturity was slightly but significantly correlated with increased IHN symptoms. The linkage map for ‘Atlantic’, the IHN-susceptible parent, covered 1034.4 cM and included 13 linkage groups, and the map for B1829-5, the IHN-resistant parent, covered 940.2 cM and contained 14 linkage groups. QTL for increased resistance to IHN were located on chromosomes IV, V, and groups VII and X of ‘Atlantic’, and on group VII of B1829-5 in at least 2 of 3 years. The QTL explained between 4.5 and 29.4% of the variation for mean severity, and from 3.7 to 14.5% of the variation for percent incidence. Most QTL detected were dominant, and associated with decreased IHN symptoms. One SSR and 13 AFLP markers that were linked to IHN were tested in a second population. One AFLP marker was associated with decreased symptoms in both populations. The SSR marker was not associated with IHN in the second population, but was closely linked in repulsion to another marker that was associated with IHN, and had the same (negative) effect on the trait as the SSR marker did in the first population. The correlation between maturity and IHN may be partially explained by the presence of markers on chromosome V that are linked to both traits. This research represents the first molecular genetic research of IHN in potato.     

Composition of endogenous alleles can influence the level of antisense inhibition of granule-bound starch synthase gene expression in tetraploid potato plants

The T-DNA composition was analysed of twelve potato genotypes obtained after transforming a tetraploid cultivar with an antisense granule-bound starch synthase (GBSSI) gene. In five transformants (labelled TB50 nos.) the antisense GBSSI gene was driven by the CaMV 35S promoter, while in the remaining seven (labelled TBK50 nos.) the GBSSI promoter was used. In these twelve transformants the antisense effect on amylose production in potato tuber starch ranged from complete suppression to no discernible inhibition, and the number of T-DNA insertions ranged from one to at least fifteen. The antisense effect of individual T-DNA loci in progeny of these transformants was studied. Progeny containing a single T-DNA showed no inhibition of GBSSI activity. Only multiple, linked T-DNA insertions resulted in substantial antisense inhibition. T-DNA fragments present in duplex in selfed progeny resulted in a larger antisense effect than that in the parent (which contained the T-DNA insertions in simplex). Furthermore, the antisense effects of some T-DNA-containing linkage groups were influenced by the composition of endogenous GBSSI alleles. For practical breeding this implies that (1) the efficiency of obtaining primary potato transformants showing complete inhibition of GBSSI gene expression by antisense RNA is genotype-dependent, and (2) many transformants have to be produced per genotype to be able to select plants with maximum suppression of GBSSI and a minimum number of T-DNA loci.     

Microwave-assisted silication of potato starch

Silication of potato starch was performed by microwave irradiation and convectional heating of starch with sodium metasilicate. The study has shown that microwaves offered more selective silication than convectional heating. Depending on the dose of metasilicate products of either monoesterification or crosslinking esterification were formed. Increase in the amount of the silicating agent favoured crosslinking of starch. In the case of microwave irradiation, the C–O–SiO₂Na moieties were formed, whereas the convectional heating generated the C–O–Si–O–Si–O–C crosslinks.     

Gelatinization mechanism of potato starch

The non-Newtonian behavior and dynamic viscoelasticity of potato starch (Jaga kids red ’90, 21.0% amylose content) solutions after storage at 25 and 4°C for 24 h were measured with a rheogoniometer. The flow curves, at 25°C, of potato starch showed plastic behavior >1.0% (w/v) after heating at 100°C for 30 min. A gelatinization of potato starch occurred above 1.0% at room temperature. A very large dynamic viscoelasticity was observed when potato starch solution (3.0%) was stored at 4°C for 24 h and stayed at a constant value with increasing temperature. A small dynamic modulus of potato starch was observed upon addition of urea (4.0 M) at low temperature (0°C) even after storage at 25 and 4°C for 24 h. A small dynamic modulus was also observed in 0.05 M NaOH solution. Possible models of gelatinization and retrogradation mechanism of potato starch were proposed.     

Decreased sucrose content triggers starch breakdown and respiration in stored potato tubers (Solanum tuberosum)

To change the hexose-to-sucrose ratio within phloem cells, yeast-derived cytosolic invertase was expressed in transgenic potato (Solanum tuberosum cv. Desirée) plants under control of the rolC promoter. Vascular tissue specific expression of the transgene was verified by histochemical detection of invertase activity in tuber cross-sections. Vegetative growth and tuber yield of transgenic plants was unaltered as compared to wild-type plants. However, the sprout growth of stored tubers was much delayed, indicating impaired phloem-transport of sucrose towards the developing bud. Biochemical analysis of growing tubers revealed that, in contrast to sucrose levels, which rapidly declined in growing invertase-expressing tubers, hexose and starch levels remained unchanged as compared to wild-type controls. During storage, sucrose and starch content declined in wild-type tubers, whereas glucose and fructose levels remained unchanged. A similar response was found in transgenic tubers with the exception that starch degradation was accelerated and fructose levels increased slightly. Furthermore, changes in carbohydrate metabolism were accompanied by an elevated level of phosphorylated intermediates, and a stimulated rate of respiration. Considering that sucrose breakdown was restricted to phloem cells it is concluded that, in response to phloem-associated sucrose depletion or hexose elevation, starch degradation and respiration is triggered in parenchyma cells. To study further whether elevated hexose and/or hexose-phosphates or decreased sucrose levels are responsible for the metabolic changes observed, sucrose content was decreased by tuber-specific expression of a bacterial sucrose isomerase. Sucrose isomerase catalyses the reversible conversion of sucrose into palatinose, which is not further metabolizable by plant cells. Tubers harvested from these plants were found to accumulate high levels of palatinose at the expense of sucrose. In addition, starch content decreased slightly, while hexose levels remained unaltered, compared with the wild-type controls. Similar to low sucrose-containing invertase tubers, respiration and starch breakdown were found to be accelerated during storage in palatinose-accumulating potato tubers. In contrast to invertase transgenics, however, no accumulation of phosphorylated intermediates was observed. Therefore, it is concluded that sucrose depletion rather than increased hexose metabolism triggers reserve mobilization and respiration in stored potato tubers.     

Genomic prediction of breeding values using previously estimated SNP variances

Background

Genomic prediction requires estimation of variances of effects of single nucleotide polymorphisms (SNPs), which is computationally demanding, and uses these variances for prediction. We have developed models with separate estimation of SNP variances, which can be applied infrequently, and genomic prediction, which can be applied routinely.

Methods

SNP variances were estimated with Bayes Stochastic Search Variable Selection (BSSVS) and BayesC. Genome-enhanced breeding values (GEBV) were estimated with RR-BLUP (ridge regression best linear unbiased prediction), using either variances obtained from BSSVS (BLUP-SSVS) or BayesC (BLUP-C), or assuming equal variances for each SNP. Datasets used to estimate SNP variances comprised (1) all animals, (2) 50% random animals (RAN50), (3) 50% best animals (TOP50), or (4) 50% worst animals (BOT50). Traits analysed were protein yield, udder depth, somatic cell score, interval between first and last insemination, direct longevity, and longevity including information from predictors.

Results

BLUP-SSVS and BLUP-C yielded similar GEBV as the equivalent Bayesian models that simultaneously estimated SNP variances. Reliabilities of these GEBV were consistently higher than from RR-BLUP, although only significantly for direct longevity. Across scenarios that used data subsets to estimate GEBV, observed reliabilities were generally higher for TOP50 than for RAN50, and much higher than for BOT50. Reliabilities of TOP50 were higher because the training data contained more ancestors of selection candidates. Using estimated SNP variances based on random or non-random subsets of the data, while using all data to estimate GEBV, did not affect reliabilities of the BLUP models. A convergence criterion of 10⁻⁸ instead of 10⁻¹⁰ for BLUP models yielded similar GEBV, while the required number of iterations decreased by 71 to 90%. Including a separate polygenic effect consistently improved reliabilities of the GEBV, but also substantially increased the required number of iterations to reach convergence with RR-BLUP. SNP variances converged faster for BayesC than for BSSVS.

Conclusions

Combining Bayesian variable selection models to re-estimate SNP variances and BLUP models that use those SNP variances, yields GEBV that are similar to those from full Bayesian models. Moreover, these combined models yield predictions with higher reliability and less bias than the commonly used RR-BLUP model.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-014-0052-x) contains supplementary material, which is available to authorized users.     

On the presence of starch bound phosphate in potato leaf starch

The presence of starch-bound phosphate in potato leaves collected late afternoon in the middle of July when the starch content is high (12.9% dry matter basis) was studied. Starch was extracted from the leaves with dimethylsulphoxide and fragments of starch were purified by ultrafiltration in two steps in combination with an -amylase hydrolysis. The fragments were analysed with ³¹P-NMR and no signals corresponding to phosphate monoesters linked to glucose at the C₃ and/or C₆ positions were detected. The results show that starch in potato leaves does not contain any detectable amounts of phosphate monoesters.     

Genomic prediction using imputed whole-genome sequence data in Holstein Friesian cattle

Background

In contrast to currently used single nucleotide polymorphism (SNP) panels, the use of whole-genome sequence data is expected to enable the direct estimation of the effects of causal mutations on a given trait. This could lead to higher reliabilities of genomic predictions compared to those based on SNP genotypes. Also, at each generation of selection, recombination events between a SNP and a mutation can cause decay in reliability of genomic predictions based on markers rather than on the causal variants. Our objective was to investigate the use of imputed whole-genome sequence genotypes versus high-density SNP genotypes on (the persistency of) the reliability of genomic predictions using real cattle data.

Methods

Highly accurate phenotypes based on daughter performance and Illumina BovineHD Beadchip genotypes were available for 5503 Holstein Friesian bulls. The BovineHD genotypes (631,428 SNPs) of each bull were used to impute whole-genome sequence genotypes (12,590,056 SNPs) using the Beagle software. Imputation was done using a multi-breed reference panel of 429 sequenced individuals. Genomic estimated breeding values for three traits were predicted using a Bayesian stochastic search variable selection (BSSVS) model and a genome-enabled best linear unbiased prediction model (GBLUP). Reliabilities of predictions were based on 2087 validation bulls, while the other 3416 bulls were used for training.

Results

Prediction reliabilities ranged from 0.37 to 0.52. BSSVS performed better than GBLUP in all cases. Reliabilities of genomic predictions were slightly lower with imputed sequence data than with BovineHD chip data. Also, the reliabilities tended to be lower for both sequence data and BovineHD chip data when relationships between training animals were low. No increase in persistency of prediction reliability using imputed sequence data was observed.

Conclusions

Compared to BovineHD genotype data, using imputed sequence data for genomic prediction produced no advantage. To investigate the putative advantage of genomic prediction using (imputed) sequence data, a training set with a larger number of individuals that are distantly related to each other and genomic prediction models that incorporate biological information on the SNPs or that apply stricter SNP pre-selection should be considered.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0149-x) contains supplementary material, which is available to authorized users.     

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

Interval mapping of quantitative trait loci (QTL) for 16 yield, agronomic and quality traits in potato was performed on a tetraploid full-sib family comprising 227 clones from a cross between processing clone 12601ab1 and table cultivar Stirling. Thirty-eight AFLP primer combinations and six SSRs provided 514 informative markers which formed a molecular marker map comprising 12 linkage groups (LGs) in 12601ab1 (nine with four homologous chromosomes) which were aligned with 12 in Stirling (11 with four homologous chromosomes), with four partial groups remaining in 12601ab1. Two LGs were identified unequivocally as chromosomes IV and V and eight others were tentatively assigned with chromosomes VII and X unidentified. All of the traits scored had moderately high heritabilities with 54–92% of the variation in clone means over 3 years and two replicates being due to genetic differences. A total of 39 QTLs were identified. A QTL for maturity was identified on chromosome V which explained 56% of the phenotypic variance, whereas the other QTLs individually explained between 5.4 and 16.5%. However, six QTLs were detected for after-cooking blackening and four for each of regularity of tuber shape, fry colour both after storage at 4 and 10°C and sprouting. Just two QTLs were found for each of yield, the two ‘overall’ scores, crop emergence, tuber size and common scab and just one QTL was detected for each of dry matter content, keeping quality, growth cracks and internal condition. The implications for practical potato breeding and for practical linkage and QTL analysis in autotetraploids are discussed.     

Preparation and characteristics of oxidized potato starch films

Starch films were developed from oxidized potato starch (OPS) with glycerol as a plasticizer at different contents. The OPS films were transparent and flexible. The mechanical properties of these films were measured, and the results indicated that the film with 19.4% glycerol exhibited the desirable mechanical properties. X-ray diffraction study showed that the increase of glycerol content led to a decrease in the crystallinity for OPS films, and storage conditions such as storage time, storage temperature and relative humidity also had certain effects on the retrogradation of starch owing to re-crystallization. Anti-leakage, anti-crosslinking, and stability in acid or alkali solutions of the OPS films were also studied, and the results indicated that the OPS films had excellent anti-leakage ability for vegetable oil, good anti-crosslinking ability in saturated formaldehyde vapor, and good stability in acid aqueous medium, but poor stability in alkali aqueous medium.     

Ultrastructure of acid- and enzyme-modified cross-linked potato starch

Purified potato starch, cross-linked with epichlorohydrin (65–5.4 anhydroglucose units per cross-link) by an iterative method that preserved the native crystalline structure of the starch granule, was exposed to enzymic (B. subtilis α-amylase at 50°C) and acidic (3 N HCl at 40°C) hydrolysis. The stability of the granules to digestion by enzymes, as measured by their weight loss after incubation with the enzyme solution, increased with the degree of cross-linking; by contrast, the stability to acid attack decreased as a function of the degree of cross-linking. The morphology of these samples was studied by scanning electron microscopy. A lamellar structure, which was most evident after enzyme treatment, was observed in samples that had a weight loss of greater than 50%. The results reflect differences in accessibility, which are interpreted in terms of a statistical model of the ultrastructure with correlated fluctuations in density in the radial direction.