Natural alleles of the abscisic acid catabolism gene ZmAbh4 modulate water use efficiency and carbon isotope discrimination in maize.

Altering plant water use efficiency (WUE) is a promising approach for achieving sustainable crop production in changing climate scenarios. Here, we show that WUE can be tuned by alleles of a single gene discovered in elite maize (Zea mays) breeding material. Genetic dissection of a genomic region affecting WUE led to the identification of the gene ZmAbh4 as causative for the effect. CRISPR/Cas9-mediated ZmAbh4 inactivation increased WUE without growth reductions in well-watered conditions. ZmAbh4 encodes an enzyme that hydroxylates the phytohormone abscisic acid (ABA) and initiates its catabolism. Stomatal conductance is regulated by ABA and emerged as a major link between variation in WUE and discrimination against the heavy carbon isotope (Δ13C) during photosynthesis in the C4 crop maize. Changes in Δ13C persisted in kernel material, which offers an easy-to-screen proxy for WUE. Our results establish a direct physiological and genetic link between WUE and Δ13C through a single gene with potential applications in maize breeding.

Theoretical and experimental assessment of genome-based prediction in landraces of allogamous crops.

Discovery and enrichment of favorable alleles in landraces are key to making them accessible for crop improvement. Here, we present two fundamentally different concepts for genome-based selection in landrace-derived maize populations, one based on doubled-haploid (DH) lines derived directly from individual landrace plants and the other based on crossing landrace plants to a capture line. For both types of populations, we show theoretically how allele frequencies of the ancestral landrace and the capture line translate into expectations for molecular and genetic variances. We show that the DH approach has clear advantages over gamete capture with generally higher prediction accuracies and no risk of masking valuable variation of the landrace. Prediction accuracies as high as 0.58 for dry matter yield in the DH population indicate high potential of genome-based selection. Based on a comparison among traits, we show that the genetic makeup of the capture line has great influence on the success of genome-based selection and that confounding effects between the alleles of the landrace and the capture line are best controlled for traits for which the capture line does not outperform the ancestral population per se or in testcrosses. Our results will guide the optimization of genome-enabled prebreeding schemes.

Unrestricted vs 3-day low-residue diet for colonoscopy preparation. Results of a feasibility randomized trial.

AIM: To compare the impact of an unrestricted diet with a 3-day low-residue diet before colonoscopy on bowel preparation quality. METHODS: A randomized, multicenter, researcher-blinded, parallel-group feasibility trial was conducted to assess the efficacy of an unrestricted diet versus a 3-day low-residue diet for colonoscopy preparation. Participants, aged 50 to 69, were enrolled in a colorectal cancer screening program with no factors linked to poor bowel cleansing. The Boston Bowel Preparation Scale was used to evaluate colon preparation during intubation and withdrawal. Secondary outcomes included bowel exploration time, adenoma and polyp detection rates, and preparation and diet tolerability. The trial is registered under Clinical Trials (NCT04664543). RESULTS: One hundred and two individuals (mean age 59.3 ± 5.5 years, 40.1% female) were randomly assigned to each diet. All participants in both groups achieved adequate preparation (Boston scores ≥ 2 in each segment). Complete adherence to preparation was observed in the majority of participants in both groups. No significant differences were noted between groups in withdrawal or cecal intubation times, or in adenoma detection rates. The unrestricted diet was better tolerated than the 3-day low-residue diet (82.5% vs. 32.3%). Preparation assessed during intubation was adequate in 82.5% of the unrestricted diet group and in 90.3% of the 3-day low-residue diet group. CONCLUSIONS: It is feasible to test the impact of an unrestricted diet for adequate bowel preparation. Comparable cleansing results were achieved, but the unrestricted diet showed better tolerability.

Diagnostic accuracy of the Oakland score versus haemoglobin for predicting outcomes in lower gastrointestinal bleeding.

BACKGROUND: Acute lower gastrointestinal bleeding (ALGIB) is a common cause of hospitalization. Recent guidelines recommend the use of prognostic scales for risk stratification. However, it remains unclear whether risk scores are more accurate than some simpler prognostic variables. OBJECTIVE: To compare the predictive values of haemoglobin alone and the Oakland score for predicting outcomes in ALGIB patients. DESIGN: Single-centre, retrospective study at a University Hospital. Data were extracted from the hospital's clinical records. The Oakland score was calculated at admission. Study outcomes were defined according to the original article describing the Oakland score: safe discharge (the primary Oakland score outcome), transfusion, rebleeding, readmission, therapeutic intervention and death. Area under the receiver operating characteristics (AUROC) curve and accuracy using haemoglobin and the Oakland score were calculated for each outcome. RESULTS: Two hundred and fifty-eight patients were included. Eighty-four (32.6%) needed transfusion, 50 (19.4%) presented rebleeding, 31 (12.1%) required therapeutic intervention, 20 (7.8%) were readmitted and six (2.3%) died. There were no differences in the AUROC curve values for haemoglobin versus the Oakland score with regard to safe discharge (0.82 (0.77-0.88) vs 0.80 (0.74-0.86), respectively) or to therapeutic intervention and death. Haemoglobin was significantly better for predicting transfusion and rebleeding, and the Oakland score was significantly better for predicting readmission. CONCLUSION: In our study, the Oakland score did not perform better than haemoglobin alone for predicting the outcome of patients with ALGIB. The usefulness of risk scores for predicting outcomes in clinical practice remains uncertain.

Joint analysis of days to flowering reveals independent temperate adaptations in maize.

Domesticates are an excellent model for understanding biological consequences of rapid climate change. Maize (Zea mays ssp. mays) was domesticated from a tropical grass yet is widespread across temperate regions today. We investigate the biological basis of temperate adaptation in diverse structured nested association mapping (NAM) populations from China, Europe (Dent and Flint) and the United States as well as in the Ames inbred diversity panel, using days to flowering as a proxy. Using cross-population prediction, where high prediction accuracy derives from overall genomic relatedness, shared genetic architecture, and sufficient diversity in the training population, we identify patterns in predictive ability across the five populations. To identify the source of temperate adapted alleles in these populations, we predict top associated genome-wide association study (GWAS) identified loci in a Random Forest Classifier using independent temperate-tropical North American populations based on lines selected from Hapmap3 as predictors. We find that North American populations are well predicted (AUC equals 0.89 and 0.85 for Ames and USNAM, respectively), European populations somewhat well predicted (AUC equals 0.59 and 0.67 for the Dent and Flint panels, respectively) and that the Chinese population is not predicted well at all (AUC is 0.47), suggesting an independent adaptation process for early flowering in China. Multiple adaptations for the complex trait days to flowering in maize provide hope for similar natural systems under climate change.

Comparable quality of bowel preparation with single-day versus three-day low-residue diet: Randomized controlled trial.

BACKGROUND AND AIMS: There is controversy about the length of low-residue diet (LRD) for colonoscopy preparation. The aim of the study was to compare one-day vs. three-day LRD associated to standard laxative treatment for achieving an adequate colonoscopy preparation in average risk subjects with positive fecal immunochemical test undergoing screening colonoscopy. METHODS: A non-inferiority, randomized, controlled, parallel-group clinical trial was performed in the setting of average risk colorectal cancer screening program. Participants were randomized to receive 1-day vs. 3-day LRD in addition to standard polyethilenglicol treatment. Adequacy of preparation was evaluated using the Boston Bowel Preparation Scale (BBPS). Primary outcome was achieving a BBPS ≥ 2 in all colon segments. Analysis was performed for a non-inferiority margin of 5%, a 95% statistical power and one-sided 0.05 significance level. RESULTS: A total of 855 patients were randomized. Adequate bowel preparation was similar between groups: 97.9% of patients in the 1-day LRD group vs 96.9% in the 3-day LRD group achieved the primary outcome (P-value for non-inferiority < 0.001). The percentage of patients with BBPS scores ≥ 8 was superior in the 1-day LRD group (254 vs 221 in the 3-day LRD group, P = 0.032). The 1-day regimen was better tolerated than the 3-day diet. 47.7% (vs 28.7%, P < 0.05) of patients rated the 1-day LRD as very easy to follow. CONCLUSION: The 1-day LRD is non-inferior to 3-day LRD for achieving an adequate colon cleansing before average risk screening colonoscopy and it is better tolerated.

Accuracy of the Narrow-Band Imaging International Colorectal Endoscopic Classification System in Identification of Deep Invasion in Colorectal Polyps.

BACKGROUND & AIMS: T1 colorectal polyps with at least 1 risk factor for metastasis to lymph node should be treated surgically and are considered endoscopically unresectable. Optical analysis, based on the Narrow-Band Imaging International Colorectal Endoscopic (NICE) classification system, is used to identify neoplasias with invasion of the submucosa that require endoscopic treatment. We assessed the accuracy of the NICE classification, along with other morphologic characteristics, in identifying invasive polyps that are endoscopically unresectable (have at least 1 risk factor for metastasis to lymph node). METHODS: We performed a multicenter, prospective study of data collected by 58 endoscopists, from 1634 consecutive patients (examining 2123 lesions) at 17 university and community hospitals in Spain from July 2014 through June 2016. All consecutive lesions >10 mm assessed with narrow-band imaging were included. The primary end point was the accuracy of the NICE classification for identifying lesions with deep invasion, using findings from histology analysis as the reference standard. Conditional inference trees were fitted for the analysis of diagnostic accuracy. RESULTS: Of the 2123 lesions analyzed, 89 (4.2%) had features of deep invasion and 91 (4.3%) were endoscopically unresectable. The NICE classification system identified lesions with deep invasion with 58.4% sensitivity (95% CI, 47.5-68.8), 96.4% specificity (95% CI, 95.5-97.2), a positive-predictive value of 41.6% (95% CI, 32.9-50.8), and a negative-predictive value of 98.1% (95% CI, 97.5-98.7). A conditional inference tree that included all variables found the NICE classification to most accurately identify lesions with deep invasion (P < .001). However, pedunculated morphology (P < .007), ulceration (P = .026), depressed areas (P < .001), or nodular mixed type (P < .001) affected accuracy of identification. Results were comparable for identifying lesions that were endoscopically unresectable. CONCLUSIONS: In an analysis of 2123 colon lesions >10 mm, we found the NICE classification and morphologic features identify those with deep lesions with >96% specificity-even in non-expert hands and without magnification. ClinicalTrials.gov number NCT02328066.

Prediction of advanced colonic neoplasm in symptomatic patients: a scoring system to prioritize colonoscopy (COLONOFIT study).

BACKGROUND: Fast-track colonoscopy to detect patients with colorectal cancer based on high-risk symptoms is associated with low sensitivity and specificity. The aim was to derive a predictive score of advanced colonic neoplasia in symptomatic patients in fast-track programs. METHODS: All patients referred for fast-track colonoscopy were evaluated. Faecal immunological haemoglobin test (3 samples; positive> 4 µg Hb/g), and a survey to register clinical variables of interest were performed. Colorectal cancer and advanced adenoma were considered as advanced colonic neoplasia. A sample size of 600 and 500 individuals were calculated for each phase 1 and phase 2 of the study, respectively (Phase 1, derivation and Phase 2, validation cohort). A Bayesian logistic regression analysis was used to derive a predictive score. RESULTS: 1495 patients were included. Age (OR, 21), maximum faecal-Hb value (OR, 2.3), and number of positive samples (OR, 28) presented the highest ORs predictive of advanced colonic neoplasia. The additional significant predictive variables adjusted for age and faecal-Hb variables in Phase 1 were previous colonoscopy (last 5 years) and smoking (no, ex/active). With these variables a predictive score of advanced colonic neoplasia was derived. Applied to Phase 2, patients with a Score > 20 had an advanced colonic neoplasia probability of 66% (colorectal cancer, 32%), while those with a Score ≤ 10, a probability of 10% (colorectal cancer, 1%). Prioritizing patients with Score > 10, 49.4% of patients would be referred for fast-track colonoscopy, diagnosing 98.3% of colorectal cancers and 77% of advanced adenomas. CONCLUSIONS: A scoring system was derived and validated to prioritize fast-track colonoscopies according to risk, which was efficient, simple, and robust.

Testcross performance of doubled haploid lines from European flint maize landraces is promising for broadening the genetic base of elite germplasm.

KEY MESSAGE: Selected doubled haploid lines averaged similar testcross performance as their original landraces, and the best of them approached the yields of elite inbreds, demonstrating their potential to broaden the narrow genetic diversity of the flint germplasm pool. Maize landraces represent a rich source of genetic diversity that remains largely idle because the high genetic load and performance gap to elite germplasm hamper their use in modern breeding programs. Production of doubled haploid (DH) lines can mitigate problems associated with the use of landraces in pre-breeding. Our objective was to assess in comparison with modern materials the testcross performance (TP) of the best 89 out of 389 DH lines developed from six landraces and evaluated in previous studies for line per se performance (LP). TP with a dent tester was evaluated for the six original landraces, ~ 15 DH lines from each landrace selected for LP, and six elite flint inbreds together with nine commercial hybrids for grain and silage traits. Mean TP of the DH lines rarely differed significantly from TP of their corresponding landrace, which averaged in comparison with the mean TP of the elite flint inbreds ~ 20% lower grain yield and ~ 10% lower dry matter and methane yield. Trait correlations of DH lines closely agreed with the literature; correlation of TP with LP was zero for grain yield, underpinning the need to evaluate TP in addition to LP. For all traits, we observed substantial variation for TP among the DH lines and the best showed similar TP yields as the elite inbreds. Our results demonstrate the high potential of landraces for broadening the narrow genetic base of the flint heterotic pool and the usefulness of the DH technology for exploiting idle genetic resources from gene banks.

European maize landraces made accessible for plant breeding and genome-based studies.

KEY MESSAGE: Doubled-haploid libraries from landraces capture native genetic diversity for a multitude of quantitative traits and make it accessible for breeding and genome-based studies. Maize landraces comprise large allelic diversity. We created doubled-haploid (DH) libraries from three European flint maize landraces and characterized them with respect to their molecular diversity, population structure, trait means, variances, and trait correlations. In total, 899 DH lines were evaluated using high-quality genotypic and multi-environment phenotypic data from up to 11 environments. The DH lines covered 95% of the molecular variation present in 35 landraces of an earlier study and represent the original three landrace populations in an unbiased manner. A comprehensive analysis of the target trait plant development at early growth stages as well as other important agronomic traits revealed large genetic variation for line per se and testcross performance. The majority of the 378 DH lines evaluated as testcrosses outperformed the commercial hybrids for early development. For total biomass yield, we observed a yield gap of 15% between mean testcross yield of the commercial hybrids and mean testcross yield of the DH lines. The DH lines also exhibited genetic variation for undesirable traits like root lodging and tillering, but correlations with target traits early development and yield were low or nonsignificant. The presented diversity atlas is a valuable, publicly available resource for genome-based studies to identify novel trait variation and evaluate the prospects of genomic prediction in landrace-derived material.

Carbon isotope composition, water use efficiency, and drought sensitivity are controlled by a common genomic segment in maize.

KEY MESSAGE: A genomic segment on maize chromosome 7 influences carbon isotope composition, water use efficiency, and leaf growth sensitivity to drought, possibly by affecting stomatal properties. Climate change is expected to decrease water availability in many agricultural production areas around the globe. Therefore, plants with improved ability to grow under water deficit are urgently needed. We combined genetic, phenomic, and physiological approaches to understand the relationship between growth, stomatal conductance, water use efficiency, and carbon isotope composition in maize (Zea mays L.). Using near-isogenic lines derived from a maize introgression library, we analysed the effects of a genomic region previously identified as affecting carbon isotope composition. We show stability of trait expression over several years of field trials and demonstrate in the phenotyping platform Phenodyn that the same genomic region also influences the sensitivity of leaf growth to evaporative demand and soil water potential. Our results suggest that the studied genomic region affecting carbon isotope discrimination also harbours quantitative trait loci playing a role in maize drought sensitivity possibly via stomatal behaviour and development. We propose that the observed phenotypes collectively originate from altered stomatal conductance, presumably via abscisic acid.

Hemostatic spray powder TC-325 for GI bleeding in a nationwide study: survival and predictors of failure via competing risks analysis.

BACKGROUND AND AIMS: TC-325 (Hemospray, Cook Medical, Winston-Salem, NC) is an inorganic hemostatic powder recently approved by the U.S. Food and Drug Administration. This study aimed to examine the effectiveness, safety, and predictors of TC-325 failure in a large real-life cohort. METHODS: This was a retrospective study conducted at 21 Spanish centers. All patients treated with TC-325 until September 2018 were included. The primary outcome was treatment failure, defined as failed intraprocedural hemostasis or recurrent bleeding within the first 30 postprocedural days. Secondary outcomes included safety and survival. Risk and predictors of failure were assessed via competing-risk models. RESULTS: The cohort comprised 261 patients, of whom 219 (83.9%) presented with upper gastrointestinal bleeding (GIB). The most common causes were peptic ulcer (28%), malignancy (18.4%), and therapeutic endoscopy-related GIB (17.6%). TC-325 was used as rescue therapy in 191 (73.2%) patients. The rate of intraprocedural hemostasis was 93.5% (95% confidence interval [CI], 90%-96%). Risks of TC-325 failure at postprocedural days 3, 7, and 30 were 21.1%, 24.6%, and 27.4%, respectively. On multivariate analysis, spurting bleeding (P = .004), use of vasoactive drugs (P = .02), and hypotension (P = .008) were independent predictors of failure. Overall 30-day survival was 81.9% (95% CI, 76%-86%) and intraprocedural hemostasis was associated with a better prognosis (adjusted hazard ratio, 0.29; P = .006). Two severe adverse events were noted. CONCLUSION: TC-325 was safe and effective for intraprocedural hemostasis in more than 90% of patients, regardless of the cause or site of bleeding and its use as rescue therapy. In this high-risk cohort treated with TC-325, the 30-day failure rate exceeded 25% and was highest with spurting bleeding or hemodynamic instability.

Nonacceptance of negative emotions in women with borderline personality disorder: association with neuroactivity of the dorsal striatum

Background: Emotion dysfunction is a key symptom in patients with borderline personality disorder (BPD) and is considered a consequence of dysfunctional emotion regulation (e.g., reduced emotion acceptance). In the present functional MRI (fMRI) study, we investigated the neural correlates of habitual emotion acceptance in individuals with BPD. Methods: Female patients with BPD and female healthy controls passively viewed negative and neutral movie clips of faces during fMRI. We assessed emotion acceptance using the Emotion Acceptance Questionnaire (EAQ). To examine brain activation associated with habitual emotional acceptance of negative stimuli, the EAQ score was included as a regressor of interest in brain data analyses of activation intensity during negative compared with neutral movies. Results: We included 20 women with BPD and 20 heatlhy controls in our analysis. Compared with healthy controls, patients with BPD showed significantly more activation in frontostriatal brain regions (i.e., left superior frontal gyrus, right caudate) as well as in the left precuneus, left precentral gyrus, left posterior cingulate cortex and left hippocampus when confronted with negative (v. neutral) stimuli. Patients with BPD reported decreased emotion acceptance compared with healthy controls, and habitual emotion acceptance was inversely associated with activation of striatal areas (i.e., left putamen, left caudate) in patients with BPD. Limitations: Causal conclusions are not possible. Comorbid diagnoses were not excluded, and only female participants were investigated. Stimuli were not rated immediately and may not be generalizable to all negative emotions. We cannot make any statements about other emotion-regulation strategies that may have been applied here. Conclusion: Data indicate that striatal hyperactivation during the processing of negative stimuli in women with BPD is related to their decreased disposition to accept unpleasant emotional states. Thus, individuals with BPD may benefit from therapy approaches that focus on emotion acceptance in order to normalize emotional reactions.

Utility of histology for the diagnosis of portal hypertensive gastroenteropathy. Concordance between the endoscopic image and gastrointestinal biopsies. Role of the CD34 marker. / Utilidad de la histología para el diagnóstico de la gastroenteropatía por hipertensión portal. Concordancia entre la imagen endoscópica y las biopsias gastrointestinales. Papel del marcador CD34.

INTRODUCTION: Upper gastroscopy in patients with cirrhosis often reveals non-specific lesions, which are usually oriented as portal hypertensive gastropathy (PHG). However, the diagnosis of PHG can be difficult, both from an endoscopic and histological point of view. The study of CD34 expression, which enhances the endothelial cells of the microvasculature, could help the differential diagnosis. The objectives of this study were to evaluate the correlation between endoscopy and histology in the diagnosis of PHG and to assess the utility of CD34 in the diagnosis of PHG. MATERIAL AND METHODS: The results of immunostaining with CD34 gastric fundus biopsies from 100 cirrhotic patients and 20 controls were compared with the endoscopic images. RESULTS: The correlation between the histology and the endoscopic diagnosis of PHG was very low (kappa=0.15). In addition, the measurement of the diameter of the gastric vessels enhanced by the use of immunohistochemical staining (CD34) did not show good correlation with the endoscopic diagnosis (p=.26) and did not provide relevant information for the histological diagnosis of PHG either. DISCUSSION: The correlation between histology and endoscopy is low for the diagnosis of PHG. The use of immunostaining for CD34 does not seem to improve the diagnostic yield of the histological study.

Towards a whole-genome sequence for rye (Secale cereale L.).

We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.

Inter and intra-observer concordance for the diagnosis of portal hypertension gastropathy.

INTRODUCTION: At present there is no fully accepted endoscopic classification for the assessment of the severity of portal hypertensive gastropathy (PHG). Few studies have evaluated inter and intra-observer concordance or the degree of concordance between different endoscopic classifications. OBJECTIVES: To evaluate inter and intra-observer agreement for the presence of portal hypertensive gastropathy and enteropathy using different endoscopic classifications. METHODS: Patients with liver cirrhosis were included into the study. Enteroscopy was performed under sedation. The location of lesions and their severity was recorded. Images were videotaped and subsequently evaluated independently by three different endoscopists, one of whom was the initial endoscopist. The agreement between observations was assessed using the kappa index. RESULTS: Seventy-four patients (mean age 63.2 years, 53 males and 21 females) were included. The agreement between the three endoscopists regarding the presence or absence of PHG using the Tanoue and McCormack classifications was very low (kappa scores = 0.16 and 0.27, respectively). CONCLUSIONS: The current classifications of portal hypertensive gastropathy have a very low degree of intra and inter-observer agreement for the diagnosis and assessment of gastropathy severity.

Fine mapping of the restorer gene Rfp3 from an Iranian primitive rye (Secale cereale L.).

KEY MESSAGE: A comparative genetics approach allowed to precisely determine the map position of the restorer gene Rfp3 in rye and revealed that Rfp3 and the restorer gene Rfm1 in barley reside at different positions in a syntenic 4RL/6HS segment. Cytoplasmic male sterility (CMS) is a reliable and striking genetic mechanism for hybrid seed production. Breeding of CMS-based hybrids in cereals requires the use of effective restorer genes as an indispensable pre-requisite. We report on the fine mapping of a restorer gene for the Pampa cytoplasm in winter rye that has been tapped from the Iranian primitive rye population Altevogt 14160. For this purpose, we have mapped 41 gene-derived markers to a 38.8 cM segment in the distal part of the long arm of chromosome 4R, which carries the restorer gene. Male fertility restoration was comprehensively analyzed in progenies of crosses between a male-sterile tester genotype and 21 recombinant as well as six non-recombinant BC4S2 lines. This approach allowed us to validate the position of this restorer gene, which we have designated Rfp3, on chromosome 4RL. Rfp3 was mapped within a 2.5 cM interval and cosegregated with the EST-derived marker c28385. The gene-derived conserved ortholog set (COS) markers enabled us to investigate the orthology of restorer genes originating from different genetic resources of rye as well as barley. The observed localization of Rfp3 and Rfm1 in a syntenic 4RL/6HS segment asks for further efforts towards cloning of both restorer genes as an option to study the mechanisms of male sterility and fertility restoration in cereals.

Is there an optimum level of diversity in utilization of genetic resources?

KEY MESSAGE: Capitalizing upon the genomic characteristics of long-term random mating populations, sampling from pre-selected landraces is a promising approach for broadening the genetic base of elite germplasm for quantitative traits. Genome-enabled strategies for harnessing untapped allelic variation of landraces are currently evolving. The success of such approaches depends on the choice of source material. Thus, the analysis of different strategies for sampling allelic variation from landraces and their impact on population diversity and linkage disequilibrium (LD) is required to ensure the efficient utilization of diversity. We investigated the impact of different sampling strategies on diversity parameters and LD based on high-density genotypic data of 35 European maize landraces each represented by more than 20 individuals. On average, five landraces already captured ~95% of the molecular diversity of the entire dataset. Within landraces, absence of pronounced population structure, consistency of linkage phases and moderate to low LD levels were found. When combining data of up to 10 landraces, LD decay distances decreased to a few kilobases. Genotyping 24 individuals per landrace with 5k SNPs was sufficient for obtaining representative estimates of diversity and LD levels to allow an informed pre-selection of landraces. Integrating results from European with Central and South American landraces revealed that European landraces represent a unique and diverse spectrum of allelic variation. Sampling strategies for harnessing allelic variation from landraces depend on the study objectives. If the focus lies on the improvement of elite germplasm for quantitative traits, we recommend sampling from pre-selected landraces, as it yields a wide range of diversity, allows optimal marker imputation, control for population structure and avoids the confounding effects of strong adaptive alleles.

Exploring new alleles for frost tolerance in winter rye.

KEY MESSAGE: Rye genetic resources provide a valuable source of new alleles for the improvement of frost tolerance in rye breeding programs. Frost tolerance is a must-have trait for winter cereal production in northern and continental cropping areas. Genetic resources should harbor promising alleles for the improvement of frost tolerance of winter rye elite lines. For frost tolerance breeding, the identification of quantitative trait loci (QTL) and the choice of optimum genome-based selection methods are essential. We identified genomic regions involved in frost tolerance of winter rye by QTL mapping in a biparental population derived from a highly frost tolerant selection from the Canadian cultivar Puma and the European elite line Lo157. Lines per se and their testcrosses were phenotyped in a controlled freeze test and in multi-location field trials in Russia and Canada. Three QTL on chromosomes 4R, 5R, and 7R were consistently detected across environments. The QTL on 5R is congruent with the genomic region harboring the Frost resistance locus 2 (Fr-2) in Triticeae. The Puma allele at the Fr-R2 locus was found to significantly increase frost tolerance. A comparison of predictive ability obtained from the QTL-based model with different whole-genome prediction models revealed that besides a few large, also small QTL effects contribute to the genomic variance of frost tolerance in rye. Genomic prediction models assigning a high weight to the Fr-R2 locus allow increasing the selection intensity for frost tolerance by genome-based pre-selection of promising candidates.

Association mapping for cold tolerance in two large maize inbred panels.

BACKGROUND: Breeding for cold tolerance in maize promises to allow increasing growth area and production in temperate zones. The objective of this research was to conduct genome-wide association analyses (GWAS) in temperate maize inbred lines and to find strategies for pyramiding genes for cold tolerance. Two panels of 306 dent and 292 European flint maize inbred lines were evaluated per se and in testcrosses under cold and control conditions in a growth chamber. We recorded indirect measures for cold tolerance as the traits number of days from sowing to emergence, relative leaf chlorophyll content or quantum efficiency of photosystem II. Association mapping for identifying genes associated to cold tolerance in both panels was based on genotyping with 49,585 genome-wide single nucleotide polymorphism (SNP) markers. RESULTS: We found 275 significant associations, most of them in the inbreds evaluated per se, in the flint panel, and under control conditions. A few candidate genes coincided between the current research and previous reports. A total of 47 flint inbreds harbored the favorable alleles for six significant quantitative trait loci (QTL) detected for inbreds per se evaluated under cold conditions, four of them had also the favorable alleles for the main QTL detected from the testcrosses. Only four dent inbreds (EZ47, F924, NK807 and PHJ40) harbored the favorable alleles for three main QTL detected from the evaluation of the dent inbreds per se under cold conditions. There were more QTL in the flint panel and most of the QTL were associated with days to emergence and ΦPSII. CONCLUSIONS: These results open new possibilities to genetically improve cold tolerance either with genome-wide selection or with marker assisted selection.