Genome wide association mapping for agronomic, fruit quality, and root architectural traits in tomato under organic farming conditions.

BACKGROUND: Opportunity and challenges of the agriculture scenario of the next decades will face increasing demand for secure food through approaches able to minimize the input to cultivations. Large panels of tomato varieties represent a valuable resource of traits of interest under sustainable cultivation systems and for genome-wide association studies (GWAS). For mapping loci controlling the variation of agronomic, fruit quality, and root architecture traits, we used a heterogeneous set of 244 traditional and improved tomato accessions grown under organic field trials. Here we report comprehensive phenotyping and GWAS using over 37,300 SNPs obtained through double digest restriction-site associated DNA (dd-RADseq). RESULTS: A wide range of phenotypic diversity was observed in the studied collection, with highly significant differences encountered for most traits. A variable level of heritability was observed with values up to 69% for morphological traits while, among agronomic ones, fruit weight showed values above 80%. Genotype by environment analysis highlighted the strongest genotypic effect for aboveground traits compared to root architecture, suggesting that the hypogeal part of tomato plants has been a minor objective for breeding activities. GWAS was performed by a compressed mixed linear model leading to 59 significantly associated loci, allowing the identification of novel genes related to flower and fruit characteristics. Most genomic associations fell into the region surrounding SUN, OVATE, and MYB gene families. Six flower and fruit traits were associated with a single member of the SUN family (SLSUN31) on chromosome 11, in a region involved in the increase of fruit weight, locules number, and fruit fasciation. Furthermore, additional candidate genes for soluble solids content, fruit colour and shape were found near previously reported chromosomal regions, indicating the presence of synergic and multiple linked genes underlying the variation of these traits. CONCLUSIONS: Results of this study give new hints on the genetic basis of traits in underexplored germplasm grown under organic conditions, providing a framework for the development of markers linked to candidate genes of interest to be used in genomics-assisted breeding in tomato, in particular under low-input and organic cultivation conditions.

Fruit composition profile of pepper, tomato and eggplant varieties grown under uniform conditions.

The study of the diversity within and between major Solanaceae crops (pepper, tomato, eggplant) is of interest for the selection and development of balanced diets. We have measured thirty-six major fruit composition traits, encompassing sugars, organic acids, antioxidants and minerals, in a set of 10 accessions per crop for pepper, tomato and eggplant, grown under the same cultivation conditions. The aim was to evaluate the diversity within species and to provide an accurate comparison of fruit composition among species by reducing to a minimum the environmental effect. Pepper, tomato and eggplant had a clearly distinct composition profile. Pepper showed the highest average content in total sugars and organic acids. Fructose and glucose were the major sugar compounds in the three species, although in pepper and tomato sucrose was present only in trace amounts. Citric acid was the major organic acid in pepper and tomato, while in eggplant it was malic acid. Pepper and eggplant had the highest total antioxidant activity. Vitamin C content was much higher in pepper than in tomato and eggplant, while eggplant accumulated high concentrations of chlorogenic acid. Furthermore, eggplant was the species with higher content in most minerals, particularly for K, Mg and Cu, while pepper was the richest in Fe. Due to their complementary nutritional profiles, a combined regular consumption of the three vegetables would supply more than 20% of the Dietary Reference Intake of several of the analysed phytochemicals. The large diversity within each species is of interest for selecting varieties with better nutritional and organoleptic profiles, as well as for breeding new cultivars.

Variation for Composition and Quality in a Collection of the Resilient Mediterranean 'de penjar' Long Shelf-Life Tomato Under High and Low N Fertilization Levels.

The 'de penjar' tomato (Solanum lycopersicum L.) is a group of local varieties from the Spanish Mediterranean region carrying the alc mutation, which provides long shelf-life. Their evolution under low-input management practices has led to the selection of resilient genotypes to adverse conditions. Here we present the first evaluation on nutritional fruit composition of a collection of 44 varieties of 'de penjar' tomato under two N fertilization levels, provided by doses of manure equivalent to 162 kg N ha-1 in the high N treatment and 49 kg N ha-1 in the low N treatment. Twenty-seven fruit composition and quality traits, as well as plant yield and SPAD value, were evaluated. A large variation was observed, with lycopene being the composition trait with the highest relative range of variation (over 4-fold) under both N treatments, and significant differences among varieties were detected for all traits. While yield and most quality traits were not affected by the reduction in N fertilization, fruits from the low N treatment had, on average, higher values for hue (5.9%) and lower for fructose (-11.5%), glucose (-15.8%), and total sweetness index (-12.9%). In addition, lycopene and ß-carotene presented a strongly significant genotype × N input interaction. Local varieties had higher values than commercial varieties for traits related to the ratio of sweetness to acidity and for vitamin C, which reinforces the appreciation for their organoleptic and nutritional quality. Highest-yielding varieties under both conditions displayed wide variation in the composition and quality profiles, which may allow the selection of specific ideotypes with high quality under low N conditions. These results revealed the potential of 'de penjar' varieties as a genetic resource in breeding for low N inputs and improving the organoleptic and nutritional tomato fruit quality.

Peritumoral immune infiltrates in primary tumours are not associated with the presence of axillary lymph node metastasis in breast cancer: a retrospective cohort study.

BACKGROUND: The axillary lymph nodes (ALNs) in breast cancer patients are the body regions to where tumoral cells most often first disseminate. The tumour immune response is important for breast cancer patient outcome, and some studies have evaluated its involvement in ALN metastasis development. Most studies have focused on the intratumoral immune response, but very few have evaluated the peritumoral immune response. The aim of the present article is to evaluate the immune infiltrates of the peritumoral area and their association with the presence of ALN metastases. METHODS: The concentration of 11 immune markers in the peritumoral areas was studied in 149 patients diagnosed with invasive breast carcinoma of no special type (half of whom had ALN metastasis at diagnosis) using tissue microarrays, immunohistochemistry and digital image analysis procedures. The differences in the concentration of the immune response of peritumoral areas between patients diagnosed with and without metastasis in their ALNs were evaluated. A multivariate logistic regression model was developed to identify the clinical-pathological variables and the peritumoral immune markers independently associated with having or not having ALN metastases at diagnosis. RESULTS: No statistically significant differences were found in the concentrations of the 11 immune markers between patients diagnosed with or without ALN metastases. Patients with metastases in their ALNs had a higher histological grade, more lymphovascular and perineural invasion and larger-diameter tumours. The multivariate analysis, after validation by bootstrap simulation, revealed that only tumour diameter (OR = 1.04; 95% CI [1.00-1.07]; p = 0.026), lymphovascular invasion (OR = 25.42; 95% CI [9.57-67.55]; p < 0.001) and histological grades 2 (OR = 3.84; 95% CI [1.11-13.28]; p = 0.033) and 3 (OR = 5.18; 95% CI [1.40-19.17]; p = 0.014) were associated with the presence of ALN metastases at diagnosis. This study is one of the first to study the association of the peritumoral immune response with ALN metastasis. We did not find any association of peritumoral immune infiltrates with the presence of ALN metastasis. Nevertheless, this does not rule out the possibility that other peritumoral immune populations are associated with ALN metastasis. This matter needs to be examined in greater depth, broadening the types of peritumoral immune cells studied, and including new peritumoral areas, such as the germinal centres of the peritumoral tertiary lymphoid structures found in extensively infiltrated neoplastic lesions.

Insights Into the Adaptation to Greenhouse Cultivation of the Traditional Mediterranean Long Shelf-Life Tomato Carrying the alc Mutation: A Multi-Trait Comparison of Landraces, Selections, and Hybrids in Open Field and Greenhouse.

Long shelf-life tomato (Solanum lycopersicum) landraces, characterized by carrying the alc allele in the NOR.NAC locus, have been traditionally cultivated in the Mediterranean region. These materials are adapted to open field conditions under low input conditions. However, cultivation under greenhouse is expanding fueled by increasing demand of these traditional tomatoes. We hypothesize that the large diversity in the long shelf-life landraces and derived materials can be exploited for adaptation to these new cultivation conditions. We have evaluated 12 varieties (seven landraces, three selections and two hybrids) carrying the alc mutation under open field (OF) and greenhouse (GH) cultivation, and evaluated them for 52 morphological, agronomic, chemical properties, and chemical composition descriptors. All descriptors, except six morphological ones, were variable. The variety effect was the greatest contributor to variation for most morphological traits, as well as for fruit weight, fruit shape, dry matter, and soluble solids content. However, significant environmental and genotype × environment interaction were found for 36 and 42 descriptors, respectively. Fruits from GH plants had lower weight and firmness and were less red than those from OF. On average, in GH yield was 35% lower and daily fruit weight loss in post-harvest 41% higher than in OF. However, fruits from GH had on average higher dry matter and soluble solids contents, antioxidant activity, glucose, fructose, and ascorbic acid concentrations, but lower contents in lycopene and ß-carotene than those from OF. A principal components analysis clearly separated varieties according to the cultivation environment. However, the distribution pattern of varieties within each of the two clusters (GH and OF) was similar, despite the strong G × E interaction for many descriptors. Landraces from the same origin plotted in the same area of each cluster, and selections and hybrids plotted together with the landraces. The results reveal a high impact of the cultivation environment on morphological, agronomic, chemical properties, and chemical composition of Mediterranean long shelf-life traditional tomato varieties. This suggests that breeding programs specifically focused to adaptation to greenhouse conditions should be developed.

A Comparison of Landraces vs. Modern Varieties of Lettuce in Organic Farming During the Winter in the Mediterranean Area: An Approach Considering the Viewpoints of Breeders, Consumers, and Farmers.

The interest of farmers in growing lettuce landraces is increasing, as landrace varieties prove particularly appealing to consumers striving to purchase natural, local, and high-quality produce. Although high genetic diversity exists in the landrace gene pool, this has scarcely been studied, thus hindering landrace utilization in agriculture. In this study, we analyzed the genetic diversity and the agronomic and quality traits of lettuce landraces in organic agrosystems, by characterizing 16 landraces and 16 modern varieties. We compared 29 morphological descriptors, and several traits relating to agronomic behavior (total and commercial weight, resistance to Bremia lactucae) and quality (color, chlorophyll, dry matter, and total sugars). Trials were conducted in two localities and managed following organic farming practices. Moreover, farmers and consumers participated in the phenotyping of accessions by scoring yield, resistance to B. lactucae, appearance, and taste acceptance. Results show that cultivar group, rather than the genetic origin (modern vs. landrace), is the major source of variation for all agronomic and quality traits. Batavia and Butterhead were highly homogeneous cultivar groups, while Cos accessions showed a much higher intra-varietal diversity. There was also a clear separation between modern and landrace varieties of Oak leaf. Fifteen out of the 16 evaluated landraces presented a high susceptibility to the particular B. lactucae race isolated from the experimental field - a new race not reported before. Breeding programs intended to introgress genetic resistance to this pathogen are a major priority to recover the cultivation of lettuce landraces. Principal component analysis (PCA), conducted on all quantitative data, showed a clear differentiation between modern varieties and landraces, mostly related to their commercial weight and susceptibility to B. lactucae. These seem the most important traits influencing farmer and consumer evaluations. Farmers showed a high capacity for characterizing the samples and agreed with consumers when scoring for the external appearance. It is proposed that farmers and consumers should be included in the phenotyping platforms in future research projects aiming for recovery of landraces.

Competing risks model in screening for preeclampsia by maternal factors and biomarkers at 19-24 weeks' gestation.

BACKGROUND: Preeclampsia (PE) affects 2-3% of all pregnancies and is a major cause of maternal and perinatal morbidity and mortality. The traditional approach to screening for PE is to use a risk-scoring system based on maternal demographic characteristics and medical history (maternal factors), but the performance of such an approach is very poor. OBJECTIVE: To develop a model for PE based on a combination of maternal factors with second-trimester biomarkers. STUDY DESIGN: The data for this study were derived from prospective screening for adverse obstetric outcomes in women attending their routine hospital visit at 19-24 weeks' gestation in 3 maternity hospitals in England between January 2006 and July 2014. We had data from maternal factors, uterine artery pulsatility index (UTPI), mean arterial pressure (MAP), serum placental growth factor (PLGF), and serum soluble fms-like tyrosine kinase-1 (SFLT) from 123,406, 67,605, 31,120, 10,828, and 8079 pregnancies, respectively. Bayes' theorem was used to combine the a priori risk from maternal factors with various combinations of biomarker multiple of the median (MoM) values. The modeled performance of screening for PE requiring delivery at <32, <37, and ≥37 weeks' gestation was estimated. The modeled performance was compared to the empirical one, which was derived from 5-fold cross validation. We also examined the performance of screening based on risk factors from the medical history, as recommended by the American Congress of Obstetricians and Gynecologists (ACOG). RESULTS: In pregnancies that developed PE, the values of MAP, UTPI, and SFLT were increased and PLGF was decreased. For all biomarkers the deviation from normal was greater for early than for late PE, and therefore the performance of screening was inversely related to the gestational age at which delivery became necessary for maternal and/or fetal indications. Screening by maternal factors predicted 52%, 47%, and 37% of PE at <32, <37, and ≥37 weeks' gestation, respectively, at a false-positive rate of 10%. The respective values for combined screening with maternal factors and MAP, UTPI, and PLGF were 99%, 85%, and 46%; the performance was not improved by the addition of SFLT. In our population of 123,406 pregnancies, the DR of PE at <32, <37, and ≥37 weeks with the ACOG recommendations was 91%, 90%, and 91%, respectively, but at a screen positive rate of 67%. CONCLUSION: The performance of screening for PE by maternal factors and biomarkers in the middle trimester is superior to taking a medical history.

Characterization of composition traits related to organoleptic and functional quality for the differentiation, selection and enhancement of local varieties of tomato from different cultivar groups.

Tomato (Solanum lycopersicum) local varieties are having an increasing demand. We characterized 69 local tomato accessions from eight cultivar groups for proximate composition traits, major sugars, acids and antioxidants. A large diversity was found, with differences among accessions of almost tenfold for lycopene. Significant differences were found among cultivar group means for most traits. The Cherry and Penjar groups generally presented higher dry matter, soluble solids content, titratable acidity, taste index, ß-carotene, ascorbic acid, total phenolics, and antioxidant activity that the other groups. Wide ranges of variation were found within each cultivar group. Positive correlations were found between proximate traits related to taste and antioxidants. The multivariate principal components analysis confirms the distinct profile of the Cherry and Penjar groups and the large variation within groups. The results will be useful for the differentiation, enhancement and selection of local tomato varieties with improved organoleptic properties and functional quality.

Infección tuberculosa latente en trabajadores sanitarios de un hospital general básico en Cataluña / Latent tuberculosis infection in healthcare personnel at a primary level general hospital in Catalonia, Spain

El objetivo del trabajo ha sido evaluar la presencia de infección tuberculosa latente en el personal sanitario del Hospital de Tortosa Verge de la Cinta (HTVC). Para ello se analizaron las historias clínicas laborales de 398 trabajadores de dicho hospital a los que se había realizado la prueba de tuberculina durante el periodo 2001-2012. La presencia de infección tuberculosa latente (ITL) se analizó en relación a las variables edad, sexo, categoría profesional, personal de áreas de trabajo de alto y bajo riesgo de exposición a la tuberculosis y personal de riesgo no definido. La prevalencia total de ITL en el grupo estudiado fue del 11,1% (IC 95%: 8,3%-14,5%), estando dicha prevalencia asociada a la edad y al área de trabajo. El análisis multivariable mostró que el riesgo de sufrir ITL se incrementa un 6,4% por cada año de edad. La prevalencia de ITL en el centro de estudio era similar a la de la población profesionalmente no expuesta de España

The aim was to analyze the prevalence of latent tuberculosis infection and associated risk factors in healthcare personnel at the Hospital de Tortosa Verge de la Cinta (Tarragona, Spain). This was a cross-sectional study of 398 workers at this hospital who underwent tuberculin skin testing for latent tuberculosis infection (LTBI) between 2001 and 2012.We also analyzed the relationship between LTBI and age, sex, job and work area according to their risk of exposure to tuberculosis(high, low, uncertain). The total prevalence of LTBI in our sample was 11.1% (95%CI 8.3%-14.5%). LBTI was associated with age and work area. Multivariate analysis showed that the risk of LTBI increased by 6.4% per 1 year increase in age. The prevalence of LTBI in this population approximates that of the general population in Spain

[Latent tuberculosis infection in healthcare personnel at a primary level general hospital in Catalonia, Spain]. / Infección tuberculosa latente en trabajadores sanitarios de un hospital general básico en Cataluña.

The aim was to analyze the prevalence of latent tuberculosis infection and associated risk factors in healthcare personnel at the Hospital de Tortosa Verge de la Cinta (Tarragona, Spain). This was a cross-sectional study of 398 workers at this hospital who underwent tuberculin skin testing for latent tuberculosis infection (LTBI) between 2001 and 2012.We also analyzed the relationship between LTBI and age, sex, job and work area according to their risk of exposure to tuberculosis(high, low, uncertain). The total prevalence of LTBI in our sample was 11.1% (95%CI 8.3%-14.5%). LBTI was associated with age and work area. Multivariate analysis showed that the risk of LTBI increased by 6.4% per 1 year increase in age. The prevalence of LTBI in this population approximates that of the general population in Spain.

El objetivo del trabajo ha sido evaluar la presencia de infección tuberculosa latente en el personal sanitario del Hospital de Tortosa Verge de la Cinta (HTVC). Para ello se analizaron las historias clínicas laborales de 398 trabajadores de dicho hospital a los que se había realizado la prueba de tuberculina durante el periodo 2001-2012. La presencia de infección tuberculosa latente (ITL) se analizó en relación a las variables edad, sexo, categoría profesional, personal de áreas de trabajo de alto y bajo riesgo de exposición a la tuberculosis y personal de riesgo no definido. La prevalencia total de ITL en el grupo estudiado fue del 11,1% (IC 95%: 8,3%-14,5%), estando dicha prevalencia asociada a la edad y al área de trabajo. El análisis multivariable mostró que el riesgo de sufrir ITL se incrementa un 6,4% por cada año de edad. La prevalencia de ITL en el centro de estudio era similar a la de la población profesionalmente no expuesta de España.

Additive effect of factors related to assisted conception on the reduction of maternal serum pregnancy-associated plasma protein A concentrations and the increased false-positive rates in first-trimester Down syndrome screening.

OBJECTIVE: To analyze whether assisted conceptions need adjustments in first-trimester Down syndrome screening and why modifications in screening markers occur. DESIGN: Eleven-year cohort retrospective analysis. SETTING: Maternal-fetal medicine unit. PATIENT(S): Two thousand eleven naturally conceived normal singleton pregnancies and 2,042 normal singleton pregnancies achieved with assisted conception: 350 by IUI and 1,692 with IVF (n = 328) or intracytoplasmic sperm injection (ICSI; n = 1,364), using nondonor (n = 1,086) or donated ova (n = 606), with fresh (n = 1,432) or frozen (n = 260) embryos. INTERVENTION(S): Comparison of ultrasound and biochemical markers of first-trimester Down syndrome screening according to the mode of conception and considering the clinical and laboratory parameters related. MAIN OUTCOME MEASURE(S): Nuchal translucency (NT), PAPP-A and free ßhCG maternal serum concentrations, and false-positive rates (FPRs). RESULT(S): NT is unaffected by the mode of conception. Singleton pregnancies achieved by IVF and ICSI with nondonor oocytes have reduced maternal serum PAPP-A and increased FPR, which are significant only in ICSI cycles. Pregnancies from frozen embryos with hormone therapy also show decreased PAPP-A but without affecting the FPR. Elevated maternal serum fßhCG levels in oocyte donation do not influence the FPR. CONCLUSION(S): Among assisted conceptions, only nondonor IVF/ICSI singleton pregnancies need adjustments of the maternal serum PAPP-A in first-trimester Down syndrome screening.

Self-similar focusing with generalized devil's lenses.

We introduce the generalized devil's lenses (GDLs) as a new family of diffractive kinoform lenses whose structure is based on the generalized Cantor set. The focusing properties of different members of this family are analyzed. It is shown that under plane wave illumination the GDLs give a single main focus surrounded by many subsidiary foci. It is shown that the total number of subsidiary foci is higher than the number of foci corresponding to conventional devil's lenses; however, the self-similar behavior of the axial irradiance is preserved to some extent.