Prediction ability of genome-wide markers in Pinus taeda L. within and between population is affected by relatedness to the training population and trait genetic architecture

Genomic prediction has the potential to significantly increase the rate of genetic gain in tree breeding programs. In this study, a clonally replicated population (n = 2063) was used to train a genomic prediction model. The model was validated both within the training population and in a separate population (n = 451). The prediction abilities from random (20% vs 80%) cross validation within the training population were 0.56 and 0.78 for height and stem form, respectively. Removal of all full-sib relatives within the training population resulted in ∼50% reduction in their genomic prediction ability for both traits. The average prediction ability for all 451 individual trees was 0.29 for height and 0.57 for stem form. The degree of genetic linkage (full-sib family, half sib family, unrelated) between the training and validation sets had a strong impact on prediction ability for stem form but not for height. A dominant dwarfing allele, the first to be reported in a conifer species, was discovered via genome-wide association studies on linkage Group 5 that conferred a 0.33-m mean height reduction. However, the QTL was family specific. The rapid decay of linkage disequilibrium, large genome size, and inconsistencies in marker-QTL linkage phase suggest that large, diverse training populations are needed for genomic selection in Pinus taeda L.

Major QTL confer race-nonspecific resistance in the co-evolved Cronartium quercuum f. sp. fusiforme-Pinus taeda pathosystem

Fusiform rust disease, caused by the endemic fungus Cronartium quercuum f. sp. fusiforme, is the most damaging disease affecting economically important pine species in the southeast United States. Unlike the major epidemics of agricultural crops, the co-evolved pine-rust pathosystem is characterized by steady-state dynamics and high levels of genetic diversity within environments. This poses a unique challenge and opportunity for the deployment of large-effect resistance genes. We used trait dissection to study the genetic architecture of disease resistance in two P. taeda parents that showed high resistance across multiple environments. Two mapping populations (full-sib families), each with ~1000 progeny, were challenged with a complex inoculum consisting of 150 pathogen isolates. High-density linkage mapping revealed three major-effect QTL distributed on two linkage groups. All three QTL were validated using a population of 2057 cloned pine genotypes in a 6-year-old multi-environmental field trial. As a complement to the QTL mapping approach, bulked segregant RNAseq analysis revealed a small number of candidate nucleotide binding leucine-rich repeat genes harboring SNP associated with disease resistance. The results of this study show that in P. taeda, a small number of major QTL can provide effective resistance against genetically diverse mixtures of an endemic pathogen. These QTL vary in their impact on disease liability and exhibit additivity in combination.

Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome

PREMISE

An informatics approach was used for the construction of an Axiom genotyping array from heterogeneous, high-throughput sequence data to assess the complex genome of loblolly pine (Pinus taeda).

METHODS

High-throughput sequence data, sourced from exome capture and whole genome reduced-representation approaches from 2698 trees across five sequence populations, were analyzed with the improved genome assembly and annotation for the loblolly pine. A variant detection, filtering, and probe design pipeline was developed to detect true variants across and within populations. From 8.27 million variants, a total of 642,275 were evaluated and 423,695 of those were screened across a range-wide population.

RESULTS

The final informatics and screening approach delivered an Axiom array representing 46,439 high-confidence variants to the forest tree breeding and genetics community. Based on the annotated reference genome, 34% were located in or directly upstream or downstream of genic regions.

DISCUSSION

The Pita50K array represents a genome-wide resource developed from sequence data for an economically important conifer, loblolly pine. It uniquely integrates independent projects that assessed trees sampled across the native range. The challenges associated with the large and repetitive genome are addressed in the development of this resource.

Characterizing the oligogenic architecture of plant growth phenotypes informs genomic selection approaches in a common wheat population

BACKGROUND

Genetic variation in growth over the course of the season is a major source of grain yield variation in wheat, and for this reason variants controlling heading date and plant height are among the best-characterized in wheat genetics. While the major variants for these traits have been cloned, the importance of these variants in contributing to genetic variation for plant growth over time is not fully understood. Here we develop a biparental population segregating for major variants for both plant height and flowering time to characterize the genetic architecture of the traits and identify additional novel QTL.

RESULTS

We find that additive genetic variation for both traits is almost entirely associated with major and moderate-effect QTL, including four novel heading date QTL and four novel plant height QTL. FT2 and Vrn-A3 are proposed as candidate genes underlying QTL on chromosomes 3A and 7A, while Rht8 is mapped to chromosome 2D. These mapped QTL also underlie genetic variation in a longitudinal analysis of plant growth over time. The oligogenic architecture of these traits is further demonstrated by the superior trait prediction accuracy of QTL-based prediction models compared to polygenic genomic selection models.

CONCLUSIONS

In a population constructed from two modern wheat cultivars adapted to the southeast U.S., almost all additive genetic variation in plant growth traits is associated with known major variants or novel moderate-effect QTL. Major transgressive segregation was observed in this population despite the similar plant height and heading date characters of the parental lines. This segregation is being driven primarily by a small number of mapped QTL, instead of by many small-effect, undetected QTL. As most breeding populations in the southeast U.S. segregate for known QTL for these traits, genetic variation in plant height and heading date in these populations likely emerges from similar combinations of major and moderate effect QTL. We can make more accurate and cost-effective prediction models by targeted genotyping of key SNPs.

Sequence-based mapping identifies a candidate transcription repressor underlying awn suppression at the B1 locus in wheat

Awns are stiff, hair-like structures which grow from the lemmas of wheat (Triticum aestivum) and other grasses that contribute to photosynthesis and play a role in seed dispersal. Variation in awn length in domesticated wheat is controlled primarily by three major genes, most commonly the dominant awn suppressor Tipped1 (B1). This study identifies a transcription repressor responsible for awn inhibition at the B1 locus. Association mapping was combined with analysis in biparental populations to delimit B1 to a distal region of 5AL colocalized with QTL for number of spikelets per spike, kernel weight, kernel length, and test weight. Fine-mapping located B1 to a region containing only two predicted genes, including C2H2 zinc finger transcriptional repressor TraesCS5A02G542800 upregulated in developing spikes of awnless individuals. Deletions encompassing this candidate gene were present in awned mutants of an awnless wheat. Sequence polymorphisms in the B1 coding region were not observed in diverse wheat germplasm whereas a nearby polymorphism was highly predictive of awn suppression. Transcriptional repression by B1 is the major determinant of awn suppression in global wheat germplasm. It is associated with increased number of spikelets per spike and decreased kernel size.

Monitoring black grouse Tetrao tetrix in Isère, northern French Alps: cofactors, population trends and potential biases

Wildlife management benefits from studies that verify or improve the reliability of monitoring protocols. In this study in Isère, France, we tested for potential links between the abundance of black grouse (Tetrao tetrix) in lek–count surveys and cofactors (procedural, geographical and meteorological cofactors) between 1989 and 2016. We also examined the effect of omitting or considering the important cofactors on the long–term population trend that can be inferred from lek–count data. Model selections for data at hand highlighted that the abundance of black grouse was mainly linked to procedural cofactors, such as the number of observers, the time of first observation of a displaying male, the day, and the year of the count. Some additional factors relating to the surface of the census sector, temperature, northing, altitude and wind conditions also appeared depending on the spatial or temporal scale of the analysis. The inclusion of the important cofactors in models modulated the estimates of population trends. The results of the larger dataset highlighted a mean increase of +17 % (+5.3 %; +29 %) of the abundance of black grouse from 1997 to 2001, and a mean increase in population of +47 % (+16 %; +87 %) throughout the study period (1989–2016). We discuss the hypothesis of plausible links between this past increase in the number of black grouse and the ecological impact of the winter storm ‘Vivian’. Findings from our study and the ecological phenomena that were concomitant with the observed population trend provide opportunities to strengthen the monitoring and management of black grouse in the Alps.

Stressful nurses: the effect on patient outcomes

The article describes a study that measured, over a 3-month period, staffing problems, including turnover rates; nurse incidents, including absenteeism, back injuries, and needle sticks; and patient incidents, including falls and medication errors. The self-reported stress of the nurses caring for these patients was recorded over the same 3-month period. Data showed that a relatively strong relationship exists between a hospital unit's Stress Continuum Scale (SCS) and the occurrence of patient incidents. The relationship between the SCS and personal incidents and nurse injuries appears weak, as does the relationship between staff turnover and stress. Lagging staff turnover by 1 month resulted in a moderate association with the SCS, however.

Reclassification of Lactobacillus casei subsp. casei ATCC 393 and Lactobacillus rhamnosus ATCC 15820 as Lactobacillus zeae nom. rev., designation of ATCC 334 as the neotype of L. casei subsp. casei, and rejection of the name Lactobacillus paracasei

The type strain of Lactobacillus casei subsp. casei (ATCC 393) exhibits low levels of DNA homology with other strains of L. casei subsp. casei (8 to 46%) and strains of Lactobacillus paracasei (30 to 50%), but exhibits a level of DNA similarity of 80% with Lactobacillus rhamnosus ATCC 15820, the original type strain of "Lactobacterium zeae" Kuznetsov 1959. Strains ATCC 393T (T = type strain) and ATCC 15820T are members of one protein profile cluster that is separate from the other Lactobacillus spp. The randomly amplified polymorphic DNA PCR profile of strain ATCC 393T is also different from the profiles obtained for the other species. L. casei ATCC 334T is genetically closely related to L. casei subsp. casei strains (71 to 97%) and L. paracasei strains (71 to 91%), is a member of the same protein profile cluster as these organisms, and shares several DNA amplicons with L. paracasei strains. On the basis of these results, we propose that L. casei subsp. casei ATCC 393T and L. rhamnosus ATCC 15820 should be reclassified as members of Lactobacillus zeae nom. rev. (type strain, ATCC 15820), that strain ATCC 334 should be designated the neotype strain of L. casei subsp. casei, and that the name L. paracasei should be rejected.

Active autoimmune gastritis without total atrophy of the glands

To date, autoimmune gastritis has been diagnosed for the most part only when total atrophy of the oxyntic glands is detected. On the basis of 40 patients without total atrophy of the glands, and with parietal cell antibodies in the serum, we show that the diagnosis of type A gastritis is also possible in the pre-atrophic stage. The histological criteria for the diagnosis of active autoimmune gastritis without total atrophy of the glands are 1. usually dense, diffuse locally emphasized lymphocytic infiltration of the lamina propria between the glands in the oxyntic mucosa, 2. focal destruction of individual glands in the corpus of the stomach by lymphocytes, and 3. reactive pseudohypertrophy of the parietal cells. A comparison with a group of patients with autoimmune gastritis and total atrophy of the glands shows that in active autoimmune gastritis, too, women are more frequently affected than men (in both groups, the sex ratio is approximately 3:1). Patients without atrophy of the glands are, on average, about 12 years younger than those with "burnt out" type A gastritis (average age 69.98:57.80 years). While in the case of burnt out type A gastritis, no colonisation with Helicobacter pylori was to be found, such colonisation was demonstrated for the corpus mucosa in 22.5%, and for the antral mucosa in 15.0%. In 27.5% a minimal or low-grade inactive superficial gastritis, as may be seen after eradication of Helicobacter pylori, was additionally diagnosed in the antrum. A knowledge of the histological appearance of the pre-atrophic stage of type A gastritis might be of importance for the possible prevention of pernicious anaemia.(ABSTRACT TRUNCATED AT 250 WORDS)

[General practice of colorectal cancer surgery: often still inadequate resection]

With the aim of investigated the question as to whether surgery for colorectal carcinoma is being carried out in a standardised tumor-oriented manner, 777 surgical specimens containing colorectal carcinomas obtained from 33 hospitals were analysed. Only 4.76% of these carcinomas were pT 1 early carcinomas, the largest portion of the tumors (63.96%) was classified as pT 3. The pN stages were distributed as follows: pN 0 53.4%, pN 1 22.0%, pN 2 13.77%, pN 3 9.39%, and pN X 1.41%. The surgeons indicated an R-classification in only 24% of the specimens. Measurements of the length of the resected material, the width of the mesocoli or perirectal tissue, the distal margin of clearance, the number of lymph nodes on the vessel trunk, and the number of pericolic or perirectal lymph nodes revealed a considerable degree of fluctuation in the measurements, and thus in the operative methodology applied to colorectal carcinoma surgery. Analysis of the four hospitals with the highest operating rates taking sigmoidorectal specimens as an example, showed that some abdominal surgeons are still not performing this operation in accordance with the oncological rules for tumor-oriented surgery.

Cryptosporidiosis of the appendix vermiformis: a case report

The present case report describes a 30-year-old man with AIDS who developed cryptosporidiosis of the appendix vermiformis. The patient had been admitted to hospital with all the symptoms of appendicitis, and an appendectomy was performed. The histological work-up of the surgical specimen revealed an acute phlegmonous appendicitis, and also a welldeveloped cryptosporidiosis, which was confirmed by electron-microscopic examination. Two years later, the patient died of pneumonia contracted during a generalised CMV infection. The postmortem examination revealed cryptosporidial organisms in the biliary tract. As far as we know, this is the first ever report of cryptosporidiosis of the appendix vermiformis.

[Malignant somatostatinoma--diagnosis after 6 years]

Early symptoms of malignant somatostatinoma with dyspeptic complaints, moderate diabetes mellitus and cholecystolithiasis are the reason of primary treatment of these patients by surgeons.

CASE REPORT

In a 34-year old patient with typical anamnesis of cholecystitis and moderate diabetes mellitus liver metastases were seen during laparotomy. In the beginning the metastases were mistaken for hepatocellular carcinoma histologically. There was no deterioration until June 1988 when a high-grade stenosis of the duodenum has developed. Now a malignant somatostatinoma was diagnosed histologically and confirmed by immunohistology. Somatostatinomas are generally diagnosed by repeated measures of increased plasma SLI associated with decreased insulin, glucagon, pancreatic-polypeptide (PP) and vasoactive-intestinal-peptide (VIP). In normally or moderately increased plasma SLI concentrations provocation with tolbutamid may be helpful. Treatment should remove most of the tumor by surgical intervention, while chemotherapy must be less pronounced.

Bifidobacterium gallicum sp. nov. isolated from human feces

A bifidobacterial isolate from human feces was found to have very low genetic relatedness to any previously described species of the genus. This strain, which also contained a unique type of peptidoglycan, L-lysine-L-alanine-L-serine (A3 alpha), is considered to represent a new species, which is designated Bifidobacterium gallicum. Its description is presented. The type strain is strain DSM 20093. gallicum. Its description is presented. The type strain is strain DSM 20093.

["Brown bowel" syndrome--lipofuscinosis of the intestine as a cause of atonia]

We report on a 42 year old male patient having been ill with pseudo-pobstruction and gastroinstestinal atonid for 24 years. He was thought to suffer from Crohn's disease and was treated conservatively. Since the therapy proved to be insufficient, explorative laparatomie was performed and parts of the small and large intestine which were thought to be inflamed, were removed. The histologic examination revealed the deposition of a significant amount of lipofuscin in the muscularis propria. This so-called brown bowel syndrome is known to be responsible for the development of gastrointestinal atonia. It is generally believed that this syndrome is caused by a vitamin E deficiency which may occur due to malabsorption. The brown bowel syndrome is treated sympomatically, and until now only one case achieving a remission of the disease has been reported.

Ultrastructure of the islets of Langerhans after long-term occlusion of the pancreatic duct system

The long-term effect of surgically induced atrophy and fribrosis of the exocrine parenchyma of the pancreas on the islets of Langerhans was examined electron-microscopically in animal experiments in mini-pigs. Ligature of the pancreatic duct, occlusion of the pancreatic duct system with an alcoholic solution of amino acids and the combination of this occlusion with ligature of the pancreatic duct were compared. A largely similar result was found in all three experimental groups 9 months post-operatively: The islets of Langerhans are mostly subdivided into predominantly small and apparently intact islet cell complexes by peri- and intra-insular fibrosis, and, where larger islet cell complexes are found, these are, in places, also destroyed in the peripheral region. The diffusion distance between the capillaries and the endocrine cells is, in part, considerably dilated by the interposition of collagen fibres. In the capillaries, thickenings and duplications of the basement membrane, as well as swelling of the endothelial cells can be found. There are rarely signs of atrophy in the islet cells lying in clusters. Only the granular structure of the B-cells diverges from the norm. From our morphological findings a delayed and diminished hormone output after pancreatic duct occlusion can be deduced, whereby, compared to earlier short-term experiments of our own, no significant progression of the peri- and intra-insular fibrosis can be determined.

Partial purification and properties of neuraminidase from Bifidobacterium lactentis

Bifidobacterium lactentis 659 a gram-positive, nonsporeforming anaerobic bacterium originally isolated from the feces of breast-fed infants produces neuraminidase after enzyme induction with 2mM N-acetylmannosamine added to the culture medium. Bacteria were transferred and grown in a medium containing casein hydrolysate, lactose, sodium acetate, amino acids, vitamins, salts and 2% human milk for 48 h at 37 degrees C under N2/CO2 atmosphere. Two subcultures derived from the original strain B. lactentis 659 were investigated separately because of different growth characteristics. However, their taxonomic identity was not doubtful. Neuraminidase was liberated from the bacterial sediments by ultrasonic treatment in 0.15M NaCl and was isolated by 60% ammonium sulfate precipitation, dialysis, concentration, and column chromatography on Sepharose CL-6B and Sephadex G-100. The enzyme exhibits a molecular weight of 38000 and a pH optimum in the range of pH 5--6 in barbital/acetate buffers. Starch gel electrophoresis and neuraminidase-specific staining with NeuAc alpha 2 leads to (3-methoxyphenyl) glycoside revealed two major and three minor enzyme bands. Michaelis constants (Km) were determined to be 7.1 mM for the (alpha 2 leads to 3) linkage of II3NeuAc-Lac, 7.5mM for the (alpha 2 leads to 6) linkage of II6Neu-Ac-Lac and 15mM for the (alpha 2 leads to 8) linkage in II3(leads from 2NeuAc8)2-Lac. Among the different groups of naturally occurring NeuAc-containing substrates, i.e. glycoproteins, gangliosides and oligosaccharides, B. lactentis neuraminidase cleaves oligosaccharides preferentially without remarkable differences between (alpha 2 leads to 3) and (alpha 2 leads to 6) linkages. Globular glycoproteins and mucins are poor substrates and gangliosides are practically not affected. In contrast, enzyme activity towards synthetic NeuAc glycosides is very high. The enzyme is activated by 50% with 50mM Ca2 and inhibited by 20mM EDTA accordingly. In general, B. lactentis neuraminidase shows a substrate specificity pattern similar to those found in other non-pathogenic and non-invasive representatives of the human bacterial flora. The potential biological role of intestinal Bifidobacteria will be discussed.

[Mechanism of the variation of the acetate/lactate/ratio during glucose fermentation by bifidobacteria (author's transl)]

It is demonstrated that most strains of bifidobacteria form much more acetate and less lactic acid from glucose than is to be expected according to the breakdown of glucose via the "bifidoshunt". The analysis of isotope distribution among the fermentation products of glucose labeled in different positions showed that the excess of acetate is the result of the phosphoroclastic splitting of a part of the pyruvate arising from carbons 4, 5, and 6 of glucose. In addition to acetate (carbons 5 and 6), formate is formed from carbon 4 and some acetate is reduced to ethanol. The formation of "extra" acetate occurs mainly during the log phase and is less pronounced in resting cells. The extent of the phosphoroclastic splitting of pyruvate varies considerably among different strains even among those from the same species.