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.

Allelic variation for alpha-Glucan Water Dikinase is associated with starch phosphate content in tetraploid potato.

KEY MESSAGE: Association analysis resulted in the identification of specific StGWD alleles causing either an increase or decrease in starch phosphate content which was verified in diploid and tetraploid potato mapping populations. Potatoes are grown for various purposes like French fries, table potatoes, crisps and for their starch. One of the most important aspects of potato starch is that it contains a high amount of phosphate ester groups which are considered to be important for providing improved functionalization after derivatization processes. Little is known about the variation in phosphate content as such in different potato varieties and thus we studied the genetic diversity for this trait. From other studies it was clear that the phosphate content is controlled by a quantitative trait locus (QTL) underlying the candidate gene α-Glucan Water Dikinase (StGWD) on chromosome 5. We performed direct amplicon sequencing of this gene by Sanger sequencing. Sequences of two StGWD amplicons from a global collection of 398 commercial cultivars and progenitor lines were used to identify 16 different haplotypes. By assigning tag SNPs to these haplotypes, each of the four alleles present in a cultivar could be deduced and linked to a phosphate content. A high value for intra-individual heterozygosity was observed (Ho = 0.765). The average number of different haplotypes per individual (Ai) was 3.1. Pedigree analysis confirmed that the haplotypes are identical-by-descent (IBD) and offered insight in the breeding history of elite potato germplasm. Haplotypes originating from introgression of wild potato accessions carrying resistance genes could be traced. Furthermore, association analysis resulted in the identification of specific StGWD alleles causing either an increase or decrease in starch phosphate content varying from 12 nmol PO4/mg starch to 38 nmol PO4/mg starch. These allele effects were verified in diploid and tetraploid mapping populations and offer possibilities to breed and select for this trait.

The Visual Analog Scale detects exercise-induced bronchoconstriction in children with asthma.

Objective: Exercise-induced bronchoconstriction (EIB) is a specific morbidity of childhood asthma and an important sign of uncontrolled asthma. The occurrence of EIB is insufficiently identified by the Childhood Asthma Control Test (C-ACT) and Asthma Control Test (ACT). This study aimed to (1) evaluate the Visual Analog Scale (VAS) for dyspnea as a tool to detect EIB in asthmatic children and (2) assess the value of combining (C-)ACT outcomes with VAS scores. Methods: We measured EIB in 75 asthmatic children (mean age 10.8 years) with a standardized exercise challenge test (ECT) performed in cold and dry air. Children and parents reported VAS dyspnea scores before and after the ECT. Asthma control was assessed by the (C-)ACT. Results: Changes in VAS scores (ΔVAS) of children and parents correlated moderately with fall in forced expiratory volume in 1 second (FEV1), respectively rs=0.57 (p < .001) and rs=0.58 (p < .001). At a ΔVAS cutoff value of ≥3 in children, sensitivity and specificity for EIB were 80% and 79% (AUC 0.82). Out of 38 children diagnosed with EIB, 37 had a (C-)ACT score of ≤19 and/or a ΔVAS of ≥3, corresponding with a sensitivity of 97% and a negative predictive value of 96%. Conclusion: This study shows that the VAS could be an effective additional tool for diagnosing EIB in children. A reported difference in VAS scores of ≥3 after a standardized ECT combined with low (C-)ACT scores was highly effective in detecting and excluding EIB.

Routine postoperative intensive care unit admission after colorectal cancer surgery for the elderly patient reduces postoperative morbidity and mortality.

AIM: Older colorectal cancer (CRC) patients are at increased risk of postoperative morbidity and mortality. Routine postoperative overnight intensive care unit (ICU) admission might reduce this risk. This study aimed to examine the effect of routine overnight ICU admission after CRC surgery on postoperative adverse outcomes and costs in patients aged 80 years or older. METHODS: Patients aged 80 years or older who underwent CRC surgery in our centre were included in this observational cohort study. All patients in the period 2014-2017 with routine overnight ICU admission were assigned to the ICU cohort; all patients in the period 2009-2013 were assigned to the non-ICU cohort. Multivariable logistic regression was performed to compare the primary composite end-point (30-day mortality, serious complications and readmission) between the groups. Cost data from the literature were used to perform a cost analysis. RESULTS: A total of 242 patients were included, 125 in the ICU cohort and 117 in the non-ICU cohort. Routine overnight ICU admission was associated with a reduced risk of the composite end-point (OR 0.44, 95% CI 0.22-0.87, P = 0.02) after adjusting for important confounders. In the ICU cohort 28% of patients experienced ICU events requiring intervention; this was not associated with postoperative morbidity or mortality. The 9% reduction in the incidence of serious complications in the ICU cohort is sufficient to offset the additional costs of routine overnight ICU admission. CONCLUSION: Routine overnight ICU admission after CRC surgery in patients aged 80 years and older is associated with reduced risk of postoperative mortality and morbidity and seems to be cost-effective.

Implantable cardioverter defibrillators at the end of life: future perspectives on clinical practice.

The implantable cardioverter defibrillator (ICD) is effective in terminating life-threatening arrhythmias. However, in the last phase of life, ICD shocks may no longer be appropriate. Guidelines recommend timely discussion with the patient regarding deactivation of the shock function of the ICD. However, research shows that such conversations are scarce, and some patients experience avoidable and distressful shocks in the final days of life. Barriers such as physicians' lack of time, difficulties in finding the right time to discuss ICD deactivation, patients' reluctance to discuss the topic, and the fragmentation of care, which obscures responsibilities, prevent healthcare professionals from discussing this topic with the patient. In this point-of-view article, we argue that healthcare professionals who are involved in the care for ICD patients should be better educated on how to communicate with patients about ICD deactivation and the end of life. Optimal communication is needed to reduce the number of patients experiencing inappropriate and painful shocks in the terminal stage of their lives.

The assessment of field trials in GMO research around the world and their possible integration in field trials for variety registration.

Most regulations worldwide stipulate that a new genetically modified (GM) crop event has to be compared to its closest non-GM counterpart as a corner stone of the pre-market risk assessment. To this end the GM crop and its comparator should be grown in field trials for a phenotypic comparison as well as for subsequent detailed analysis of the composition of the two crop varieties. A more in-depth globally harmonised approach for the conduct of these field trials is lacking. Only a few countries have formulated detailed protocols for the set-up of GM field trials. In some countries, commercial non-GM reference varieties need to be included in a field study to compile reliable data that indicate the range of natural variation for the compounds tested at the specific location. Detailed analysis of pre-market assessment reports have so far not shown the added value of including these reference varieties in the field trials. In all cases where specific values were found to be outside of the range of the reference varieties, it proved possible to draw conclusions on the part of the pre-market risk assessment that relates to the compositional analysis, on the basis of already available compositional data. With the increasing quality of several databases on compositional data of a growing number of crop species, it seems unlikely that reference varieties will become more important on future occasions. It was furthermore investigated whether this part of the risk assessment can be related to field trial requirements for variety registration with the explicit intention of reducing the data burden on producers of new GM plant varieties. Field trials for variety registration so far include an assessment of phenotypic characteristics that do not cover safety aspects, with the exception of establishment of the glycoalkaloid content in potatoes in the Netherlands and Sweden. It may, however, under certain conditions be relatively easy to exchange data from compositional measurements between variety registration and GM testing procedures, thus laying a foundation for testing the feasibility of combining both pre-market assessment procedures in a single pre-market evaluation path.

Two different R gene loci co-evolved with Avr2 of Phytophthora infestans and confer distinct resistance specificities in potato.

Late blight, caused by the oomycete pathogen Phytophthora infestans, is the most devastating disease in potato. For sustainable management of this economically important disease, resistance breeding relies on the availability of resistance (R) genes. Such R genes against P. infestans have evolved in wild tuber-bearing Solanum species from North, Central and South America, upon co-evolution with cognate avirulence (Avr) genes. Here, we report how effectoromics screens with Avr2 of P. infestans revealed defense responses in diverse Solanum species that are native to Mexico and Peru. We found that the response to AVR2 in the Mexican Solanum species is mediated by R genes of the R2 family that resides on a major late blight locus on chromosome IV. In contrast, the response to AVR2 in Peruvian Solanum species is mediated by Rpi-mcq1, which resides on chromosome IX and does not belong to the R2 family. The data indicate that AVR2 recognition has evolved independently on two genetic loci in Mexican and Peruvian Solanum species, respectively. Detached leaf tests on potato cultivar 'Désirée' transformed with R genes from either the R2 or the Rpi-mcq1 locus revealed an overlapping, but distinct resistance profile to a panel of 18 diverse P. infestans isolates. The achieved insights in the molecular R - Avr gene interaction can lead to more educated exploitation of R genes and maximize the potential of generating more broad-spectrum, and potentially more durable control of the late blight disease in potato.

What factors are important in smoking cessation and relapse in women from deprived communities? A qualitative study in Southeast England.

OBJECTIVES: Women are relatively more susceptible to smoking-related diseases and find it more difficult to quit; however, little research exists on factors associated with smoking cessation and relapse in women. We examined attitudes towards and perceptions of factors associated with smoking cessation and relapse in women from deprived communities. STUDY DESIGN: Qualitative interview study. METHODS: Participants included eleven women, smokers and ex-smokers, from disadvantaged communities in East Sussex, England, who had used the National Health Service (NHS) stop smoking service. Data were collected through a focus group and semi-structured interviews, and subjected to thematic analysis. RESULTS: Participants opined that it is more difficult for women to quit smoking than men. Women felt that postcessation weight gain was inevitable and acted as a barrier to quitting. Hormonal fluctuations during the menstrual cycle and greater levels of stress were perceived as obstacles to quitting and reasons for relapse. Conversely, the women cited effects of smoking on physical appearance, oral hygiene and guilt about exposing children to passive smoke as powerful motivators to quit; and highlighted the impact of public health campaigns that focused on these factors. Views diverged on whether quitting with someone close to you is a help or hindrance. Other themes including alcohol intake, daily routine and being in the presence of smokers emerged as situational triggers of relapse. CONCLUSIONS: Interventions that address women's concerns related to postcessation weight gain, hormonal fluctuations during the menstrual cycle and stress may aid with smoking cessation and reduce relapse. Public health campaigns should consider the impact of smoking on physical appearance and the effect of passive smoke on children.

First successful reduction of clinical allergenicity of food by genetic modification: Mal d 1-silenced apples cause fewer allergy symptoms than the wild-type cultivar.

BACKGROUND: Genetic modification of allergenic foods such as apple has the potential to reduce their clinical allergenicity, but this has never been studied by oral challenges in allergic individuals. METHODS: We performed oral food challenges in 21 apple-allergic individuals with Elstar apples which had undergone gene silencing of the major allergen of apple, Mal d 1, by RNA interference. Downregulation of Mal d 1 gene expression in the apples was verified by qRT-PCR. Clinical responses to the genetically modified apples were compared to those seen with the wild-type Elstar using a visual analogue scale (VAS). RESULTS: Gene silencing produced two genetically modified apple lines expressing Mal d 1.02 and other Mal d 1 gene mRNA levels which were extensively downregulated, that is only 0.1-16.4% (e-DR1) and 0.2-9.9% (e-DR2) of those of the wild-type Elstar, respectively. Challenges with these downregulated apple lines produced significantly less intense maximal symptoms to the first dose (Vmax1) than with Elstar (Vmax1 Elstar 3.0 mm vs 0.0 mm for e-DR1, P = 0.017 and 0.0 mm for e-DR2, P = 0.043), as well as significantly less intense mean symptoms per dose (meanV/d) than with Elstar (meanV/d Elstar 2.2 mm vs 0.2 mm for e-DR1, P = 0.017 and 0.0 mm for e-DR2, P = 0.043). Only one subject (5%) remained symptom-free when challenged with the Elstar apple, whereas 43% did so with e-DR1 and 63% with e-DR2. CONCLUSION: These data show that mRNA silencing of Mal d 1 results in a marked reduction of Mal d 1 gene expression in the fruit and reduction of symptoms when these apples are ingested by allergic subjects. Approximately half of the subjects developed no symptoms whatsoever, and virtually all subjects wished to consume the apple again in the future.

The impact of discussing exercise test results of young asthmatic children on adherence to maintenance medication.

OBJECTIVE: Parents' awareness of their child's asthma may improve by discussing an exercise challenge test (ECT) result with them. We investigated the influence of discussing an ECT result with parents on adherence to inhaled maintenance medication, parental illness perceptions and medication beliefs in young asthmatic children. METHODS: A total of 79 children, 4-7 years old and enrolled in our standard comprehensive asthma care program, performed an ECT to assess exercise induced bronchoconstriction (EIB). The result of the ECT was immediately discussed with the parents. Median medication adherence level was measured with electronic medication loggers from six weeks before the ECT till six weeks afterwards. Parental beliefs about medicines and illness perceptions were measured with the Beliefs about Medicines Questionnaire (BMQ) and the Brief Illness Perceptions Questionnaire (B-IPQ). RESULTS: The median baseline adherence level was high (83%) and showed a small significant decline after the ECT. There was no significant difference in the decrease in median adherence level between the children with or without EIB. Most parents (82.1%) showed a positive necessity-concern ratio at baseline, as measured with the BMQ. There was no clinical relevant change in medication concerns and necessity scores or in illness perceptions. CONCLUSION: Discussing ECT results with parents does not modify median adherence levels to inhaled maintenance medication nor medication beliefs of highly adherent young asthmatic children who are already enrolled in a comprehensive asthma care program.

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.

Exerted force on the face mask in preterm infants at birth is associated with apnoea and bradycardia.

BACKGROUND: During stabilisation of preterm infants at birth, a face mask is used to provide respiratory support. However, application of these masks may activate cutaneous stretch receptors of the trigeminal nerve, causing apnoea and bradycardia. This study investigated the amount of force exerted on the face mask during non-invasive ventilation of preterm infants at birth and whether the amount of exerted force is associated with apnoea and bradycardia. METHODS: A prospective observational study was performed in preterm infants born <32 weeks of gestation who were stabilised at birth. During the first 10 minutes of respiratory support, we measured breathing and heart rate as well as the amount of force exerted on a face mask using a custom-made pressure sensor placed on top of the face mask. RESULTS: Thirty infants were included (median (IQR) gestational age(GA) 28+3 (27+0-30+0) weeks, birthweight 1104 (878-1275) grams). The median exerted force measured was 297 (198-377) grams, ranging from 0 to 1455 grams. Significantly more force was exerted on the face mask during positive pressure ventilation when compared to CPAP (410 (256-556) vs 286 (190-373) grams, p = 0.009). In a binary logistic regression model, higher forces were associated with an increased risk of apnoea (OR = 1.607 (1.556-1.661), p < 0.001) and bradycardia (OR = 1.140 (1.102-1.180), p < 0.001) during the first 10 minutes of respiratory support at birth. CONCLUSION: During mask ventilation, the median exerted force on a face mask was 297 grams with a maximum of 1455 grams. Higher exerted forces were associated apnoea and bradycardia during the first 10 minutes of respiratory support at birth.

The enigma to achieve normal postnatal growth in preterm infants--using parenteral or enteral nutrition?

AIM: To evaluate whether increasing the amount of amino acids and energy in parenteral nutrition combined with rapid increment of enteral feeding improves postnatal growth in preterm infants. METHODS: Observational study; two consecutive year-cohorts of preterm infants; Cohort 2 received higher supplementation of parenteral amino acids and energy with more rapid enhancement of enteral feeding than Cohort 1. Nutritional intake, weight and head circumference (HC) were compared. RESULTS: Cohort 2 [N: 79, gestational age (GA): 29.8 ± 2.2 weeks, birth weight (BW): 1248 ± 371 g] achieved full enteral feeds earlier (p < 0.001) and had a higher protein/energy intake during the first week (p < 0.001) than Cohort 1 (N: 68, GA: 29.5 ± 2.3 weeks, BW: 1261 ± 339 g). Both cohorts developed cumulative protein/energy deficits, but less in Cohort 2 (p < 0.01). Appropriate for gestational age infants (AGA) of Cohort 2 improved weight gain until week 5 (p < 0.01) compared to AGA of Cohort 1, nevertheless all infants demonstrated a decline in mean standard deviation score (>1) for weight at term. Small for GA infants failed to improve HC. CONCLUSION: Improved parenteral intake may lead to improved short-term postnatal weight gain. Faster increase of enteral nutrition was well tolerated but failed to prevent nutritional deficits. Practising early enteral feeding with higher supplementation of nutrients may be needed and requires further study.

Field testing and exploitation of genetically modified cassava with low-amylose or amylose-free starch in Indonesia.

The development and testing in the field of genetically modified -so called- orphan crops like cassava in tropical countries is still in its infancy, despite the fact that cassava is not only used for food and feed but is also an important industrial crop. As traditional breeding of cassava is difficult (allodiploid, vegetatively propagated, outbreeding species) it is an ideal crop for improvement through genetic modification. We here report on the results of production and field testing of genetically modified low-amylose transformants of commercial cassava variety Adira4 in Indonesia. Twenty four transformants were produced and selected in the Netherlands based on phenotypic and molecular analyses. Nodal cuttings of these plants were sent to Indonesia where they were grown under biosafety conditions. After two screenhouse tests 15 transformants remained for a field trial. The tuberous root yield of 10 transformants was not significantly different from the control. Starch from transformants in which amylose was very low or absent showed all physical and rheological properties as expected from amylose-free cassava starch. The improved functionality of the starch was shown for an adipate acetate starch which was made into a tomato sauce. This is the first account of a field trial with transgenic cassava which shows that by using genetic modification it is possible to obtain low-amylose cassava plants with commercial potential with good root yield and starch quality.

Anthocyanin production as a potential visual selection marker during plant transformation.

A mutant allele of the transcription factor gene MYB10 from apple induces anthocyanin production throughout the plant. This gene, including its upstream promoter, gene coding region and terminator sequence, was introduced into apple, strawberry and potato plants to determine whether it could be used as a visible selectable marker for plant transformation as an alternative to chemically selectable markers, such as kanamycin resistance. After transformation, red coloured calli, red shoots and red well-growing plants were scored. Red and green shoots were harvested from apple explants and examined for the presence of the MYB10 gene by PCR analysis. Red shoots of apple explants always contained the MYB10 gene but not all MYB10 containing shoots were red. Strawberry plants transformed with the MYB10 gene showed anthocyanin accumulation in leaves and roots. No visible accumulation of anthocyanin could be observed in potato plants grown in vitro, even the ones carrying the MYB10 gene. However, acid methanol extracts of potato shoots or roots carrying the MYB10 gene contained up to four times higher anthocyanin content than control plants. Therefore anthocyanin production as result of the apple MYB10 gene can be used as a selectable marker for apple, strawberry and potato transformation, replacing kanamycin resistance.

Childhood obesity in the Caribbean.

OBJECTIVE: To determine the prevalence of overweight among school children in Bonaire, an island in the Caribbean, and to obtain clues for prevention of overweight. METHODS: In a cross-sectional school-based study, weight and height were measured in all 4-16-year old children in Bonaire (n = 2148). Body mass index was categorized as defined by the International Obesity Task Force (IOTF). The children were administered a questionnaire pertaining to lifestyle and nutrition. RESULTS: The prevalence of overweight, including obesity, in boys is 24.3%, and 31.9% in girls; obesity is 9.9% and 13.7%, respectively. Approximately half of the children have an unhealthy food pattern. Significantly less overweight (49%) and obese children (45%) are physically active for > 1 hour/day compared to normal weight children (56%). CONCLUSION: The prevalence of overweight and obesity in children in Bonaire is high. Prevention of overweight should focus on stimulating healthy eating habits and more physical activity.

The effect of remote ischaemic preconditioning on postoperative cardiac and inflammatory biomarkers in pancreatic surgery: a randomized controlled trial.

BACKGROUND: Cardiac and inflammatory biomarkers have been associated with adverse outcome after major abdominal surgery. This study investigated the effect of remote ischaemic preconditioning (RIPC) on perioperative concentrations of high-sensitive cardiac troponin (hs-cTn) T and interleukin (IL) 6. METHODS: Adult patients scheduled for elective pancreatic surgery between March 2017 and February 2019 were randomized to either three cycles of upper-limb ischaemia and reperfusion (each 5 min) or a sham procedure before surgery. The primary endpoint was the maximum postoperative hs-cTnT concentration within 48 h after surgery. Secondary endpoints were postoperative myocardial injury (PMI), defined as an absolute increase of hs-cTnT of at least 14 ng/l above baseline concentration, maximum concentration of IL-6 within 48 h after surgery and postoperative complications within 30 days of surgery. RESULTS: Of 99 eligible patients, 46 underwent RIPC and 46 a sham procedure. RIPC did not reduce the maximum hs-cTnT concentration after surgery (12.6 ng/l RIPC, 16.6 ng/l controls, P = 0.225), nor did it lessen the incidence of PMI (15/45 RIPC, 18/45 controls, P = 0.375). The maximum postoperative IL-6 concentration was 265 pg/ml after RIPC versus 385 pg/ml in controls (P = 0.108). Postoperative complications occurred in 23 RIPC and 24 control patients respectively. CONCLUSIONS: Remote ischaemic preconditioning did not reduce the maximum postoperative hs-cTnT concentration. Postoperative myocardial injury, IL-6 concentrations and postoperative complications were similar between RIPC patients and controls. TRIAL REGISTRATION: Clinicaltrials.gov identifier NCT03460938.

FISH applications for genomics and plant breeding strategies in tomato and other solanaceous crops.

This paper describes the use of advanced fluorescence in situ hybridization (FISH) technologies for genomics and breeding of tomato and related Solanum species. The first part deals with the major determinants of FISH technology: (1) spatial resolution, which depends on the diffraction limit of the microscope and the type of chromosome, chromatin or isolated DNA fibres as target for the hybridisation; (2) the detection sensitivity, which is limited by the sensitivity and dynamic range of the CCD camera and the quality of the microscope, and the amplification system of the weak signals from tiny probe molecules; (3) simultaneous detection of multiple probes labelled directly or indirectly with up to 5 different fluorophores, whether or not in different combinations and/or mixed at different ratios. The power and usability of such multicolour FISH is indispensable when large numbers of bacterial artificial chromosomes (BACs) or other vectors with genomic DNA are available. Mapping of multiple BACs on chromosomes are powerful instruments confirming their assumed genetic position, whereas pooled BACs for a given chromosome arm will reveal the gaps between the BACs or derived contigs of their physical maps. Tandem and dispersed repeats, which are abundant in the genomes of most species, can be analysed in repeat bar coding FISH, showing the major blocks of repeats in heterochromatin and euchromatin areas. Repeat-rich areas of the chromosomes can also be demonstrated by hybridisation of probed Cot fractions of sheared genomic DNA; a powerful method to elucidate the heterochromatin domains for genomic studies. In addition, unlabelled Cot DNA, as blocking agent in BAC-FISH painting, suppresses repetitive sequences from the BACs to hybridise on the chromosomes. Cross-species BAC-FISH painting with labelled probes from tomato and potato BACs and hybridised on the chromosomes of related species, under appropriate conditions, is a powerful instrument to demonstrate chromosomal rearrangements, including inversions and translocations. The technology not only supports phylogenetic studies between the taxa under study but can also be helpful in breeding programs with crops containing introgressed regions from related species when linkage drag or meiotic pairing disturbances between the homoeologues are assumed. In the next steps in comparative genomics, we now can detect smaller chromosomal and DNA rearrangements, diminutions and amplifications of repeats and changes of the epigenetic status of introgressed regions.

Estimating maize genetic erosion in modernized smallholder agriculture.

Replacement of crop landraces by modern varieties is thought to cause diversity loss. We studied genetic erosion in maize within a model system; modernized smallholder agriculture in southern Mexico. The local seed supply was described through interviews and in situ seed collection. In spite of the dominance of commercial seed, the informal seed system was found to persist. True landraces were rare and most informal seed was derived from modern varieties (creolized). Seed lots were characterized for agronomical traits and molecular markers. We avoided the problem of non-consistent nomenclature by taking individual seed lots as the basis for diversity inference. We defined diversity as the weighted average distance between seed lots. Diversity was calculated for subsets of the seed supply to assess the impact of replacing traditional landraces with any of these subsets. Results were different for molecular markers, ear- and vegetative/flowering traits. Nonetheless, creolized varieties showed low diversity for all traits. These varieties were distinct from traditional landraces and little differentiated from their ancestral stocks. Although adoption of creolized maize into the informal seed system has lowered diversity as compared to traditional landraces, genetic erosion was moderated by the distinct features offered by modern varieties.

GpaXI ( tar ) ( l ) originating from Solanum tarijense is a major resistance locus to Globodera pallida and is localised on chromosome 11 of potato.

Resistance to Globodera pallida Rookmaker (Pa3), originating from wild species Solanum tarijense was identified by QTL analysis and can be largely ascribed to one major QTL. GpaXI ( tar ) ( l ) explained 81.3% of the phenotypic variance in the disease test. GpaXI ( tar ) ( l ) is mapped to the long arm of chromosome 11. Another minor QTL explained 5.3% of the phenotypic variance and mapped to the long arm of chromosome 9. Clones containing both QTL showed no lower cyst counts than clones with only GpaXI ( tar ) ( l ) . After Mendelising the phenotypic data, GpaXI ( tar ) ( l ) could be more precisely mapped near markers GP163 and FEN427, thus anchoring GpaXI ( tar ) ( l ) to a region with a known R-gene cluster containing virus and nematode resistance genes.