Rapid Genotyping of Soybean Cultivars Using High Throughput Sequencing

Soybean (Glycine max) breeding involves improving commercially grown varieties by introgressing important agronomic traits from poor yielding accessions and/or wild relatives of soybean while minimizing the associated yield drag. Molecular markers associated with these traits are instrumental in increasing the efficiency of producing such crosses and Single Nucleotide Polymorphisms (SNPs) are particularly well suited for this task, owing to high density in the non-genic regions and thus increased likelihood of finding a tightly linked marker to a given trait. A rapid method to develop SNP markers that can differentiate specific loci between any two parents in soybean is thus highly desirable. In this study we investigate such a protocol for developing SNP markers between multiple soybean accessions and the reference Williams 82 genome. To restrict sampling frequency reduced representation libraries (RRLs) of genomic DNA were generated by restriction digestion followed by library construction. We chose to sequence four accessions Dowling (PI 548663), Dwight (PI 597386), Komata (PI200492) and PI 594538A for their agronomic importance as well as Williams 82 as a control

Using Microsatellites to Understand the Physical Distribution of Recombination on Soybean Chromosomes

Soybean is a major crop that is an important source of oil and proteins. A number of genetic linkage maps have been developed in soybean. Specifically, hundreds of simple sequence repeat (SSR) markers have been developed and mapped. Recent sequencing of the soybean genome resulted in the generation of vast amounts of genetic information. The objectives of this investigation were to use SSR markers in developing a connection between genetic and physical maps and to determine the physical distribution of recombination on soybean chromosomes. A total of 2,188 SSRs were used for sequence-based physical localization on soybean chromosomes. Linkage information was used from different maps to create an integrated genetic map. Comparison of the integrated genetic linkage maps and sequence based physical maps revealed that the distal 25% of each chromosome was the most marker-dense, containing an average of 47.4% of the SSR markers and 50.2% of the genes. The proximal 25% of each chromosome contained only 7.4% of the markers and 6.7% of the genes. At the whole genome level, the marker density and gene density showed a high correlation (R2) of 0.64 and 0.83, respectively with the physical distance from the centromere. Recombination followed a similar pattern with comparisons indicating that recombination is high in telomeric regions, though the correlation between crossover frequency and distance from the centromeres is low (R2 = 0.21). Most of the centromeric regions were low in recombination. The crossover frequency for the entire soybean genome was 7.2%, with extremes much higher and lower than average. The number of recombination hotspots varied from 1 to 12 per chromosome. A high correlation of 0.83 between the distribution of SSR markers and genes suggested close association of SSRs with genes. The knowledge of distribution of recombination on chromosomes may be applied in characterizing and targeting genes

Intraperitoneal drain placement and outcomes after elective colorectal surgery: international matched, prospective, cohort study

Despite current guidelines, intraperitoneal drain placement after elective colorectal surgery remains widespread. Drains were not associated with earlier detection of intraperitoneal collections, but were associated with prolonged hospital stay and increased risk of surgical-site infections.Background Many surgeons routinely place intraperitoneal drains after elective colorectal surgery. However, enhanced recovery after surgery guidelines recommend against their routine use owing to a lack of clear clinical benefit. This study aimed to describe international variation in intraperitoneal drain placement and the safety of this practice. Methods COMPASS (COMPlicAted intra-abdominal collectionS after colorectal Surgery) was a prospective, international, cohort study which enrolled consecutive adults undergoing elective colorectal surgery (February to March 2020). The primary outcome was the rate of intraperitoneal drain placement. Secondary outcomes included: rate and time to diagnosis of postoperative intraperitoneal collections; rate of surgical site infections (SSIs); time to discharge; and 30-day major postoperative complications (Clavien-Dindo grade at least III). After propensity score matching, multivariable logistic regression and Cox proportional hazards regression were used to estimate the independent association of the secondary outcomes with drain placement. Results Overall, 1805 patients from 22 countries were included (798 women, 44.2 per cent; median age 67.0 years). The drain insertion rate was 51.9 per cent (937 patients). After matching, drains were not associated with reduced rates (odds ratio (OR) 1.33, 95 per cent c.i. 0.79 to 2.23; P = 0.287) or earlier detection (hazard ratio (HR) 0.87, 0.33 to 2.31; P = 0.780) of collections. Although not associated with worse major postoperative complications (OR 1.09, 0.68 to 1.75; P = 0.709), drains were associated with delayed hospital discharge (HR 0.58, 0.52 to 0.66; P < 0.001) and an increased risk of SSIs (OR 2.47, 1.50 to 4.05; P < 0.001). Conclusion Intraperitoneal drain placement after elective colorectal surgery is not associated with earlier detection of postoperative collections, but prolongs hospital stay and increases SSI risk

A Puccinia striiformis f. sp tritici secreted protein activates plant immunity at the cell surface

Pathogens secrete effector proteins to suppress host immunity, mediate nutrient uptake and subsequently enable parasitism. However, on non-adapted hosts, effectors can be detected as non-self by host immune receptors and activate non-host immunity. Nevertheless, the molecular mechanisms of effector triggered non-host resistance remain unknown. Here, we report that a small cysteine-rich protein PstSCR1 from the wheat rust pathogen Puccinia striiformis f. sp. tritici (Pst) activates immunity in the non-host solanaceous model plant Nicotiana benthamiana. PstSCR1 homologs were found to be conserved in Pst, and in its closest relatives, Puccinia graminis f. sp. tritici and Puccinia triticina. When PstSCR1 was expressed in N. benthamiana with its signal peptide, it provoked the plant immune system, whereas no stimulation was observed when it was expressed without its signal peptide. PstSCR1 expression in N. benthamiana significantly reduced infection capacity of the oomycete pathogens. Moreover, apoplast-targeted PstSCR1 triggered plant cell death in a dose dependent manner. However, in Brassinosteroid insensitive 1-Associated Kinase 1 (SERK3/BAK1) silenced N. benthamiana, cell death was remarkably decreased. Finally, purified PstSCR1 protein activated defence related gene expression in N. benthamiana. Our results show that a Pst-secreted protein, PstSCR1 can activate surface mediated immunity in non-adapted hosts and contribute to non-host resistance

No relation of tuberculin reactivity with quantitative analysis of peripheral blood lymphocyte subsets in haemodialysis patients

Anergic response to tuberculin (PPD) is well known in haemodialysis patients (HDp). This cross-sectional controlled study was conducted to analyse the correlation of PPD response with demographical features, nutritional parameters and the distribution of peripheral blood lymphocyte (PBL) subtypes. In this study 29 HDp (17 men, 12 women; mean age 30.9 +/- 9.5 years) and 13 controls (eight men, five women; mean age 29.2 +/- 6.4 years) were included. The mean time spent on dialysis was 20.5 +/- 17.4 months. The mean PPD response was lower in HDp than controls (7.5 +/- 8 mm vs. 15 +/- 4 mm, P=0.001). Fourteen patients (48%) were PPD (-) (eight men, six women; mean age 34.1 +/- 11.1 years) and 15 were PPD (+) (normergic) (nine men, six women, mean age 26.8 +/- 3.4 years). No difference was observed between PPD (-)and(+) groups for age, sex and time spent on dialysis. As nutritional parameters, body mass index, serum albumin: creatinine and cholesterol levels were measured and no differences were found between controls and the PPD (-) and (+) groups. Absolute lymphocyte counts were lower in HDP compared to controls (1290 +/- 296 vs. 1570 +/- 307 cells ml(-1); P=0.01). PBL subtype percentages and absolute counts (CD3, CD4, CD8, CD4/CD8, HLADR(+)CD3(+), CD16(+)56(+), CD19) were also similar between PPD(-) and (+) HDp

Systolic time intervals in haemodialysis patients with normal ejection fraction: An echocardiographic study

In this controlled study, systolic time intervals (STI) and diastolic functions were investigated in haemodialysis patients (HDp) with ejection fraction (EF) within normal limits. Echocardiographic findings in 86 HDp (M: F, 47:39, mean age 36+/-13 years) and 51 healthy controls (M: F, 22:29, mean age 37+/-10 years) were compared for STI parameters (prejection period (PEP), left ventricular ejection time (LVET) and STI index (PEP/LVET)) and diastolic dysfunction (isovolumetric relaxation time (IVRT) and E/A ratio and deceleration time). The pre-ejection period (114+/-21 vs 94+/-4 msec, P100 msec and latent systolic dysfunction (STI index>0.4) were randomly distributed, with nearly half (48%) of the patients with prolonged IVRT having an STI index within the normal limits and the other half of the patients with deteriorated STI index having a normal IVRT. The combined systolic and diastolic dysfunction was observed in 30% of the patients. It was concluded that STI indexes deteriorate before an overt systolic dysfunction (normal EF), and that systolic and/or diastolic dysfunction of the myocardium may appear singly or simultaneously because of a common pathogenetic mechanism of myocardial fibrosis