Construction of a strawberry breeding core collection to capture and exploit genetic variation.

BACKGROUND: Genetic diversity is crucial for the success of plant breeding programs and core collections are important resources to capture this diversity. Many core collections have already been constructed by gene banks, whose main goal is to obtain a panel of a limited number of genotypes to simplify management practices and to improve shareability while retaining as much diversity as possible. However, as gene banks have a different composition and goal than plant breeding programs, constructing a core collection for a plant breeding program should consider different aspects. RESULTS: In this study, we present a novel approach for constructing a core collection by integrating both genomic and pedigree information to maximize the representation of the breeding germplasm in a minimum subset of genotypes while accounting for future genetic variation within a strawberry breeding program. Our stepwise approach starts with selecting the most important crossing parents of advanced selections and genotypes included for specific traits, to represent also future genetic variation. We then use pedigree-genomic-based relationship coefficients combined with the 'accession to nearest entry' criterion to complement the core collection and maximize its representativeness of the current breeding program. Combined pedigree-genomic-based relationship coefficients allow for accurate relationship estimation without the need to genotype every individual in the breeding program. CONCLUSIONS: This stepwise construction of a core collection in a strawberry breeding program can be applied in other plant breeding programs to construct core collections for various purposes.

Capturing flavors from Capsicum baccatum by introgression in sweet pepper.

KEY MESSAGE: Biochemical characterization in combination with genetic analyses in BC 2 S 1 plants and near-isogenic lines led to the detection and validation of C. baccatum loci affecting flavor, terpenoid content and Brix level. The species Capsicum baccatum includes the most common hot peppers of the Andean cuisine, known for their rich variation in flavors and aromas. So far the C. baccatum genetic variation remained merely concealed for Capsicum annuum breeding, due to post-fertilization genetic barriers encountered in interspecific hybridization. However, to exploit the potential flavor wealth of C. baccatum we combined interspecific crossing with embryo rescue, resulting in a multi-parent BC2S1 population. Volatile and non-volatile compounds plus some physical characters were measured in mature fruits, in combination with taste evaluation by a sensory panel. An enormous variation in biochemical composition and sensory attributes was found, with almost all traits showing transgression. A population-specific genetic linkage map was developed for QTL mapping. BC2S1 QTLs were validated in an experiment with near-isogenic lines, resulting in confirmed genetic effects for physical, biochemical and sensory traits. Three findings are described in more detail: (1) A small C. baccatum LG3 introgression caused an extraordinary effect on flavor, resulting in significantly higher scores for the attributes aroma, flowers, spices, celery and chives. In an attempt to identify the responsible biochemical compounds few consistently up- and down-regulated metabolites were detected. (2) Two introgressions (LG10.1 and LG1) had major effects on terpenoid content of mature fruits, affecting at least 15 different monoterpenes. (3) A second LG3 fragment resulted in a strong increase in Brix without negative effects on fruit size. The mapping strategy, the potential application of studied traits and perspectives for breeding are discussed.

The mode of inheritance in tetraploid cut roses.

Tetraploid hybrid tea roses (Rosa hybrida) represent most of the commercial cultivars of cut roses and form the basis for breeding programmes. Due to intensive interspecific hybridizations, modern cut roses are complex tetraploids for which the mode of inheritance is not exactly known. The segregation patterns of molecular markers in a tetraploid mapping population of 184 genotypes, an F(1) progeny from a cross of two heterozygous parents, were investigated for disomic and tetrasomic inheritance. The possible occurrence of double reduction was studied as well. We can exclude disomic inheritance, but while our observations are more in line with a tetrasomic inheritance, we cannot exclude that there is a mixture of both inheritance modes. Two novel parental tetraploid linkage maps were constructed using markers known from literature, combined with newly generated markers. Comparison with the integrated consensus diploid map (ICM) of Spiller et al. (Theor Appl Genet 122:489-500, 2010) allowed assigning numbers to each of the linkage groups of both maps and including small linkage groups. So far, the possibility of using marker-assisted selection in breeding of tetraploid cut roses and of other species with a tetrasomic or partly tetrasomic inheritance, is still limited due to the difficulties in establishing marker-trait associations. We used these tetraploid linkage maps to determine associations between markers, two morphological traits and powdery mildew resistance. The knowledge on inheritance and marker-trait associations in tetraploid cut roses will be of direct use to cut rose breeding.

A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits.

Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

Integrated statistical analysis of cDNA microarray and NIR spectroscopic data applied to a hemp dataset.

Both cDNA microarray and spectroscopic data provide indirect information about the chemical compounds present in the biological tissue under consideration. In this paper simple univariate and bivariate measures are used to investigate correlations between both types of high dimensional analyses. A large dataset of 42 hemp samples on which 3456 cDNA clones and 351 NIR wavelengths have been measured, was analyzed using graphical representations. For this purpose we propose clustered correlation and clustered discrimination images. Large, tissue-related differences are seen to dominate the cDNA-NIR correlation structure but smaller, more difficult to detect, variety-related differences can be found at specific cDNA clone/NIR wavelength combinations.

Comparison of echocardiographic methods with magnetic resonance imaging for assessment of right ventricular function in children.

Assessment of right ventricular (RV) function is clinically relevant in the follow-up of various forms of congenital heart disease. Agreement on the value of different echocardiographic approaches for this purpose is lacking. Magnetic resonance imaging (MRI) provides dimensionally accurate RV volumes and ejection fraction. Transthoracic 2-dimensional echocardiography from 3 different views and gradient-echo tomographic MRI were performed in 16 children with congenital heart disease and 17 age-matched healthy children. RV volumes and ejection fraction were calculated with 5 mono- and biplane area-length and multiple-slice echocardiographic methods. Adequate MRI and echocardiographic apical 4-chamber images could be obtained in all 33 children. The best correlation between MRI and echocardiographic volumes was with the biplane pyramidal approximation method. End-diastolic volume by MRI was 92 +/- 27 ml: systematic difference with echocardiography was +14 +/- 16 ml (r = 0.86). End-systolic volume by MRI was 33 +/- 13 ml: systematic difference with echocardiography was -4 +/- 7 ml (r = 0.82). Ejection fraction by MRI was 65 +/- 8%: systematic difference with echocardiography was +5 +/- 7% (r = 0.72), using monoplane ellipsoid approximation. For all echocardiographic methods, significant effects of RV geometry were noted. Echocardiographic mono- and biplane area-length and multiple-slice calculations demonstrated moderate correlation and significant systematic errors compared with MRI-derived RV volumes. Echocardiographic results were influenced by RV geometry. The relatively simple monoplane area-length method provides ejection fraction results acceptable for clinical practice; results are not improved by more complex biplane and/or multislice methods.

Quantitative assessment of the presence of a single leg separation in Björk-Shiley convexoconcave prosthetic heart valves.

RATIONALE AND OBJECTIVES: The authors developed an analytic software package for the objective and reproducible assessment of a single leg separation (SLS) in the outlet strut of Björk-Shiley convexoconcave (BSCC) prosthetic heart valves. METHODS: The radiographic cinefilm recordings of 18 phantom valves (12 intact and 6 SLS) and of 43 patient valves were acquired. After digitization of regions of interest in a cineframe, several processing steps were carried out to obtain a one-dimensional corrected and averaged density profile along the central axis of each strut leg. To characterize the degree of possible separation, two quantitative measures were introduced: the normalized pit depth (NPD) and the depth-sigma ratio (DSR). The group of 43 patient studies was divided into a learning set (25 patients) and a test set (18 patients). RESULTS: All phantom valves with an SLS were detected (sensitivity, 100%) at a specificity of 100%. The threshold values for the NPD and the DSR to decide whether a fracture was present or not were 3.6 and 2.5, respectively. On the basis of the visual interpretations of the 25 patient studies (learning set) by an expert panel, it was concluded that none of the patients had an SLS. To achieve a 100% specificity by quantitative analysis, the threshold values for the NPD and the DSR were set at 5.8 and 2.5, respectively, for the patient data. Based on these threshold values, the analysis of patient data from the test set resulted in one false-negative detection and three false-positive detections. CONCLUSIONS: An analytic software package for the detection of an SLS was developed. Phantom data showed excellent sensitivity (100%) and specificity (100%). Further research and software development is needed to increase the sensitivity and specificity for patient data.

A metabolomics approach to identify factors influencing glucosinolate thermal degradation rates in Brassica vegetables.

Thermal processing of Brassica vegetables can lead to substantial loss of potential health-promoting glucosinolates (GLs). The extent of thermal degradation of a specific GL varies in different vegetables, possibly due to differences in the composition of other metabolites within the plant matrices. An untargeted metabolomics approach followed by random forest regression was applied to identify metabolites associated to thermal GL degradation in a segregating Brassica oleracea population. Out of 413 metabolites, 15 were associated with the degradation of glucobrassicin, six with that of glucoraphanin and two with both GLs. Among these 23 metabolites three were identified as flavonols (one kaempferol- and two quercetin-derivatives) and two as other GLs (4-methoxyglucobrassicin, gluconasturtiin). Twenty quantitative trait loci (QTLs) for these metabolites, which were associated with glucoraphanin and glucobrassicin degradation, were identified on linkage groups C01, C07 and C09. Two flavonols mapped on linkage groups C07 and C09 and co-localise with the QTL for GL degradation determined previously.

A taste of sweet pepper: Volatile and non-volatile chemical composition of fresh sweet pepper (Capsicum annuum) in relation to sensory evaluation of taste.

In this study volatile and non-volatile compounds, as well as some breeding parameters, were measured in mature fruits of elite sweet pepper (Capsicum annuum) lines and hybrids from a commercial breeding program, several cultivated genotypes and one gene bank accession. In addition, all genotypes were evaluated for taste by a trained descriptive sensory expert panel. Metabolic contrasts between genotypes were caused by clusters of volatile and non-volatile compounds, which could be related to metabolic pathways and common biochemical precursors. Clusters of phenolic derivatives, higher alkanes, sesquiterpenes and lipid derived volatiles formed the major determinants of the genotypic differences. Flavour was described with the use of 14 taste attributes, of which the texture related attributes and the sweet-sour contrast were the most discriminatory factors. The attributes juiciness, toughness, crunchiness, stickiness, sweetness, aroma, sourness and fruity/apple taste could be significantly predicted with combined volatile and non-volatile data. Fructose and (E)-2-hexen-1-ol were highly correlated with aroma, fruity/apple taste and sweetness. New relations were found for fruity/apple taste and sweetness with the compounds p-menth-1-en-9-al, (E)-ß-ocimene, (Z)-2-penten-1-ol and (E)-geranylacetone. Based on the overall biochemical and sensory results, the perspectives for flavour improvement by breeding are discussed.

Quantification of right ventricular function with magnetic resonance imaging in children with normal hearts and with congenital heart disease.

In clinical treatment of children with congenital heart disease (CHD) assessment of right ventricular (RV) function is important. Available imaging techniques have been of limited value because of technical factors and the complex geometry of the right ventricle. To validate magnetic resonance (MR) imaging measurements of RV function in children, gradient echo MR imaging of both ventricles and MR flow mapping of great vessel and tricuspid flow was performed in 20 children with CHD affecting the right ventricle and in 22 healthy children ranging in age from 5 to 16 years. Close correlation between RV versus LV stroke volumes (r = 0.96) and RV stroke volume versus great artery (r = 0.97) or tricuspid flow (r = 0.97) was observed with small interobserver and intraobserver variability. Results of healthy children were end-diastolic volume: 70 +/- 9 ml/m2, end-systolic volume: 21 +/- 5 ml/m2, and ejection fraction: 70% +/- 4%. In the patient groups clinically important differences were noted. We conclude that MR imaging provides accurate noninvasive measurements of RV function in healthy children and patients with (operated) CHD.

MR velocity mapping of tricuspid flow in healthy children and in patients who have undergone Mustard or Senning repair.

PURPOSE: To determine the feasibility and accuracy of measuring tricuspid volume flow with magnetic resonance (MR) velocity mapping in healthy children and in patients after a Mustard or Senning repair. MATERIALS AND METHODS: MR studies were performed in 14 healthy children (mean age, 12 years +/- 3) and in 12 patients (mean age, 17 years +/- 5) late after a Mustard or Senning repair. MR measurements of tricuspid volume flow were validated against right ventricular stroke volumes measured tomographically. Diastolic filling parameters were derived from the flow measurements. RESULTS: Tricuspid volume flow and right ventricular stroke volume showed close agreement in the healthy children (r = .98) and in the patients (r = .94). Children after Senning repair, compared with healthy children, showed a delayed and higher peak tricuspid flow rate during early filling and a lower peak flow rate during atrial contraction (P < .05). CONCLUSION: MR measurement of tricuspid flow is feasible and accurate in healthy children and in patients after a Mustard or Senning operation, who often demonstrate abnormal tricuspid flow patterns.

On-line automated border detection for echocardiographic quantification of right ventricular size and function in children.

Rapid, accurate assessment of right ventricular (RV) size is important for the management of children with congenital heart disease. The usefulness of the Acoustic Quantification system of automated border detection (ABD) and on-line quantification (AQ) for assessment of RV size was tested in 36 children. AQ data were compared to "corrected AQ" measurements (after correction for cavity areas erroneously included in the region of interest) required for AQ. Furthermore, the influence of necessary changes to gain settings was tested in "lateral gain control" (LGC) images obtained by removal of ABD overlays. All results were compared to conventional echocardiography (echo), and agreement with magnetic resonance imaging (MRI) RV areas was assessed. Systematic differences (+/-) limits of agreement with MRI (transverse plane) for conventional echo and AQ (apical four-chamber view) were as follows: end-diastolic -0.8 +/- 3.8 (conventional echo) versus -1.7 +/- 4.6 (AQ) cm2/m2 (p < 0.001); end-systolic -1.3 +/- 3.2 versus -4.9 +/- 5.8 (AQ) cm2/m2 (p < 0.001); fractional area change 7.8 +/- 17.0% versus 26.9 +/- 31.4% (AQ) (p < 0.001). Differences between conventional echo, LGC, and corrected AQ areas were not statistically significant. The best agreement between MRI and echocardiography was with conventional echo. We conclude that automated border detection of the RV can be performed successfully with the AQ system at a fixed point in the cardiac cycle. For adequate assessment of RV function manual corrections of online AQ results are still required, which results in an important reduction of the time gain of on-line quantification.