Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources.

Due to evolutionary divergence, sorghum race populations exhibit significant genetic and morphological variation. A k-mer-based sorghum race sequence comparison identified the conserved k-mers of all 272 accessions from sorghum and the race-specific genetic signatures identified the gene variability in 10,321 genes (PAVs). To understand sorghum race structure, diversity and domestication, a deep learning-based variant calling approach was employed in a set of genotypic data derived from a diverse panel of 272 sorghum accessions. The data resulted in 1.7 million high-quality genome-wide SNPs and identified selective signature (both positive and negative) regions through a genome-wide scan with different (iHS and XP-EHH) statistical methods. We discovered 2,370 genes associated with selection signatures including 179 selective sweep regions distributed over 10 chromosomes. Co-localization of these regions undergoing selective pressure with previously reported QTLs and genes revealed that the signatures of selection could be related to the domestication of important agronomic traits such as biomass and plant height. The developed k-mer signatures will be useful in the future to identify the sorghum race and for trait and SNP markers for assisting in plant breeding programs.

Depth distributions of bacteria for the Pseudomonas aeruginosa-infected burn wounds treated by methylene blue-mediated photodynamic therapy in rats: effects of additives to photosensitizer.

SIGNIFICANCE: Pseudomonas(P.) aeruginosa, a common cause of infection in burns, acquires antibiotic resistance easily and forms biofilms efficiently. Thus, it is difficult to control P. aeruginosa infection in burn wounds, which causes lethal septicemia. Antimicrobial photodynamic therapy (aPDT) is attractive as a new strategy to treat burn wound infections with drug-resistant bacteria. AIM: We examined the efficacy of methylene blue (MB)-mediated aPDT with various additives in a tissue depth-resolved manner to find conditions that minimize the bacterial invasion. APPROACH: We applied MB-mediated aPDT with LED array illumination to an extensive, full-thickness burn infected with P. aeruginosa in rats for three consecutive days (days 0, 1, and 2). On day 2, the depth distributions of bacteria were assessed based on the histological analysis using Gram staining. We examined how the addition of ethylenediaminetetraacetic acid (EDTA), ethanol, and dimethyl sulfoxide (DMSO) affected the efficacy of aPDT. RESULTS: Pure MB-mediated aPDT significantly reduced the numbers of bacteria with biofilms on the wound surface and in the epidermis compared with those for the control tissue (saline only). However, there were many bacteria in the deeper region of the tissue. In contrast, MB/EDTA/ethanol/DMSO-mediated aPDT minimized the numbers of bacteria in the broad depth region of the tissue. Still, a limited number of bacteria was observed in the subcutaneous tissue. CONCLUSIONS: The depthwise analysis of bacteria demonstrated the efficacy of the MB-mediated aPDT with the addition of EDTA, ethanol, and DMSO in controlling burn wound infections. However, further improvement of the therapy is needed to suppress bacterial migration into the deep tissue completely.

Heterotic pools in African and Asian origin populations of pearl millet [Pennisetum glaucum (L.) R. Br.].

Forty-five African or Asian origin pearl millet populations bred either in Africa or Asia were investigated to generate information on heterotic pools. They were clustered into seven groups (G1 to G7) when genotyped, using 29 highly polymorphic SSRs. Fourteen parental populations representing these seven marker-based groups were crossed in diallel mating design to generate 91 population hybrids. The hybrids evaluated at three locations in India showed mean panmictic mid-parent heterosis (PMPH) and better-parent heterosis (PBPH) for grain yield ranging from - 21.7 to 62.08% and - 32.51 to 42.99%, respectively. Higher grain yield and heterosis were observed in G2 × G6 (2462 kg ha-1, 43.2%) and G2 × G5 (2455 kg ha-1, 42.8%) marker group crosses compared to the most popular Indian open-pollinated variety (OPV) ICTP 8203. Two heterotic groups, Pearl millet Population Heterotic Pool-1 (PMPHP-1) comprising G2 populations and Pearl millet Population Heterotic Pool-2 (PMPHP-2) comprising G5 and G6 populations, were identified based on hybrid performance, heterosis and combining ability among marker group crosses. Population hybrids from two heterotic groups, PMPHP-1 × PMPHP-2 demonstrated PMPH of 14.75% and PBPH of 6.8%. Populations of PMPHP-1 had linkages with either African or Asian origin populations, whereas PMPHP-2 composed of populations originating in Africa and later bred for Asian environments. Results indicated that parental populations from the two opposite heterotic groups can be used as base populations to derive superior inbred lines to develop high yielding hybrids/cultivars.

Identification of heterotic groups in South-Asian-bred hybrid parents of pearl millet.

KEY MESSAGE: Pearl millet breeding programs can use this heterotic group information on seed and restorer parents to generate new series of pearl millet hybrids having higher yields than the existing hybrids. Five hundred and eighty hybrid parents, 320 R- and 260 B-lines, derived from 6 pearl millet breeding programs in India, genotyped following RAD-GBS (about 0.9 million SNPs) clustered into 12 R- and 7 B-line groups. With few exceptions, hybrid parents of all the breeding programs were found distributed across all the marker-based groups suggesting good diversity in these programs. Three hundred and twenty hybrids generated using 37 (22 R and 15 B) representative parents, evaluated for grain yield at four locations in India, showed significant differences in yield, heterosis, and combining ability. Across all the hybrids, mean mid- and better-parent heterosis for grain yield was 84.0% and 60.5%, respectively. Groups G12 B × G12 R and G10 B × G12 R had highest heterosis of about 10% over best check hybrid Pioneer 86M86. The parents involved in heterotic hybrids were mainly from the groups G4R, G10B, G12B, G12R, and G13B. Based on the heterotic performance and combining ability of groups, 2 B-line (HGB-1 and HGB-2) and 2 R-line (HGR-1 and HGR-2) heterotic groups were identified. Hybrids from HGB-1 × HGR-1 and HGB-2 × HGR-1 showed grain yield heterosis of 10.6 and 9.3%, respectively, over best hybrid check. Results indicated that parental groups can be formed first by molecular markers, which may not predict the best hybrid combination, but it can reveal a practical value of assigning existing and new hybrid pearl millet parental lines into heterotic groups to develop high-yielding hybrids from the different heterotic groups.

Molecular Evidence for Two Domestication Events in the Pea Crop.

Pea, one of the founder crops from the Near East, has two wild species: Pisum sativum subsp. elatius, with a wide distribution centered in the Mediterranean, and P. fulvum, which is restricted to Syria, Lebanon, Israel, Palestine and Jordan. Using genome wide analysis of 11,343 polymorphic single nucleotide polymorphisms (SNPs) on a set of wild P. elatius (134) and P. fulvum (20) and 74 domesticated accessions (64 P. sativum landraces and 10 P. abyssinicum), we demonstrated that domesticated P. sativum and the Ethiopian pea (P. abyssinicum) were derived from different P. elatius genepools. Therefore, pea has at least two domestication events. The analysis does not support a hybrid origin of P. abyssinicum, which was likely introduced into Ethiopia and Yemen followed by eco-geographic adaptation. Both P. sativum and P. abyssinicum share traits that are typical of domestication, such as non-dormant seeds. Non-dormant seeds were also found in several wild P. elatius accessions which could be the result of crop to wild introgression or natural variation that may have been present during pea domestication. A sub-group of P. elatius overlaps with P. sativum landraces. This may be a consequence of bidirectional gene-flow or may suggest that this group of P. elatius is the closest extant wild relative of P. sativum.

Molecular Mapping of QTLs for Heat Tolerance in Chickpea.

Chickpea (Cicer arietinum L.), a cool-season legume, is increasingly affected by heat-stress at reproductive stage due to changes in global climatic conditions and cropping systems. Identifying quantitative trait loci (QTLs) for heat tolerance may facilitate breeding for heat tolerant varieties. The present study was aimed at identifying QTLs associated with heat tolerance in chickpea using 292 F8-9 recombinant inbred lines (RILs) developed from the cross ICC 4567 (heat sensitive) × ICC 15614 (heat tolerant). Phenotyping of RILs was undertaken for two heat-stress (late sown) and one non-stress (normal sown) environments. A genetic map spanning 529.11 cM and comprising 271 genotyping by sequencing (GBS) based single nucleotide polymorphism (SNP) markers was constructed. Composite interval mapping (CIM) analysis revealed two consistent genomic regions harbouring four QTLs each on CaLG05 and CaLG06. Four major QTLs for number of filled pods per plot (FPod), total number of seeds per plot (TS), grain yield per plot (GY) and % pod setting (%PodSet), located in the CaLG05 genomic region, were found to have cumulative phenotypic variation of above 50%. Nineteen pairs of epistatic QTLs showed significant epistatic effect, and non-significant QTL × environment interaction effect, except for harvest index (HI) and biomass (BM). A total of 25 putative candidate genes for heat-stress were identified in the two major genomic regions. This is the first report on QTLs for heat-stress response in chickpea. The markers linked to the above mentioned four major QTLs can facilitate marker-assisted breeding for heat tolerance in chickpea.

Construction of genotyping-by-sequencing based high-density genetic maps and QTL mapping for fusarium wilt resistance in pigeonpea.

Fusarium wilt (FW) is one of the most important biotic stresses causing yield losses in pigeonpea. Genetic improvement of pigeonpea through genomics-assisted breeding (GAB) is an economically feasible option for the development of high yielding FW resistant genotypes. In this context, two recombinant inbred lines (RILs) (ICPB 2049 × ICPL 99050 designated as PRIL_A and ICPL 20096 × ICPL 332 designated as PRIL_B) and one F2 (ICPL 85063 × ICPL 87119) populations were used for the development of high density genetic maps. Genotyping-by-sequencing (GBS) approach was used to identify and genotype SNPs in three mapping populations. As a result, three high density genetic maps with 964, 1101 and 557 SNPs with an average marker distance of 1.16, 0.84 and 2.60 cM were developed in PRIL_A, PRIL_B and F2, respectively. Based on the multi-location and multi-year phenotypic data of FW resistance a total of 14 quantitative trait loci (QTLs) including six major QTLs explaining >10% phenotypic variance explained (PVE) were identified. Comparative analysis across the populations has revealed three important QTLs (qFW11.1, qFW11.2 and qFW11.3) with upto 56.45% PVE for FW resistance. This is the first report of QTL mapping for FW resistance in pigeonpea and identified genomic region could be utilized in GAB.

Genotyping-by-sequencing of three mapping populations for identification of candidate genomic regions for resistance to sterility mosaic disease in pigeonpea.

Sterility mosaic disease (SMD) is one of the serious production constraints that may lead to complete yield loss in pigeonpea. Three mapping populations including two recombinant inbred lines and one F2, were used for phenotyping for SMD resistance at two locations in three different years. Genotyping-by-sequencing approach was used for simultaneous identification and genotyping of SNPs on above mentioned populations. In total, 212,464, 89,699 and 64,798 SNPs were identified in ICPL 20096 × ICPL 332 (PRIL_B), ICPL 20097 × ICP 8863 (PRIL_C) and ICP 8863 × ICPL 87119 (F2) respectively. By using high-quality SNPs, genetic maps were developed for PRIL_B (1,101 SNPs; 921.21 cM), PRIL_C (484 SNPs; 798.25 cM) and F2 (996 SNPs; 1,597.30 cM) populations. The average inter marker distance on these maps varied from 0.84 cM to 1.65 cM, which was lowest in all genetic mapping studies in pigeonpea. Composite interval mapping based QTL analysis identified a total of 10 QTLs including three major QTLs across the three populations. The phenotypic variance of the identified QTLs ranged from 3.6 to 34.3%. One candidate genomic region identified on CcLG11 seems to be promising QTL for molecular breeding in developing superior lines with enhanced resistance to SMD.

Genetic Variability, Genotype × Environment Interaction, Correlation, and GGE Biplot Analysis for Grain Iron and Zinc Concentration and Other Agronomic Traits in RIL Population of Sorghum (Sorghum bicolor L. Moench).

The low grain iron and zinc densities are well documented problems in food crops, affecting crop nutritional quality especially in cereals. Sorghum is a major source of energy and micronutrients for majority of population in Africa and central India. Understanding genetic variation, genotype × environment interaction and association between these traits is critical for development of improved cultivars with high iron and zinc. A total of 336 sorghum RILs (Recombinant Inbred Lines) were evaluated for grain iron and zinc concentration along with other agronomic traits for 2 years at three locations. The results showed that large variability exists in RIL population for both micronutrients (Iron = 10.8 to 76.4 mg kg-1 and Zinc = 10.2 to 58.7 mg kg-1, across environments) and agronomic traits. Genotype × environment interaction for both micronutrients (iron and zinc) was highly significant. GGE biplots comparison for grain iron and zinc showed greater variation across environments. The results also showed that G × E was substantial for grain iron and zinc, hence wider testing needed for taking care of G × E interaction to breed micronutrient rich sorghum lines. Iron and zinc concentration showed high significant positive correlation (across environment = 0.79; p < 0.01) indicating possibility of simultaneous effective selection for both the traits. The RIL population showed good variability and high heritabilities (>0.60, in individual environments) for Fe and Zn and other traits studied indicating its suitability to map QTL for iron and zinc.

Genome-Enabled Prediction Models for Yield Related Traits in Chickpea.

Genomic selection (GS) unlike marker-assisted backcrossing (MABC) predicts breeding values of lines using genome-wide marker profiling and allows selection of lines prior to field-phenotyping, thereby shortening the breeding cycle. A collection of 320 elite breeding lines was selected and phenotyped extensively for yield and yield related traits at two different locations (Delhi and Patancheru, India) during the crop seasons 2011-12 and 2012-13 under rainfed and irrigated conditions. In parallel, these lines were also genotyped using DArTseq platform to generate genotyping data for 3000 polymorphic markers. Phenotyping and genotyping data were used with six statistical GS models to estimate the prediction accuracies. GS models were tested for four yield related traits viz. seed yield, 100 seed weight, days to 50% flowering and days to maturity. Prediction accuracy for the models tested varied from 0.138 (seed yield) to 0.912 (100 seed weight), whereas performance of models did not show any significant difference for estimating prediction accuracy within traits. Kinship matrix calculated using genotyping data reaffirmed existence of two different groups within selected lines. There was not much effect of population structure on prediction accuracy. In brief, present study establishes the necessary resources for deployment of GS in chickpea breeding.

Laryngotracheal reconstruction in glottic-subglottic stenosis associated with DiGeorge syndrome in a four and a half-month-old infant.

Neonatal subglottic stenosis still remains a substantial challenge for paediatric ENT surgeons. Herein, we present a case of a single stage laryngotracheal reconstruction for a glottic-subglottic stenosis in an 18-week-old, 7.2 kg infant with DiGeorge syndrome. Our surgical approach was compared with those reported in the literature. Paediatric airway surgery should be tailored to individual patients according to age, weight, comorbidities and family collaboration, with the ultimate objective to minimise the invasiveness of the procedure.

Phylogenetic diversity of Mesorhizobium in chickpea.

Crop domestication, in general, has reduced genetic diversity in cultivated gene pool of chickpea (Cicer arietinum) as compared with wild species (C. reticulatum, C. bijugum). To explore impact of domestication on symbiosis, 10 accessions of chickpeas, including 4 accessions of C. arietinum, and 3 accessions of each of C. reticulatum and C. bijugum species, were selected and DNAs were extracted from their nodules. To distinguish chickpea symbiont, preliminary sequences analysis was attempted with 9 genes (16S rRNA, atpD, dnaJ, glnA, gyrB, nifH, nifK, nodD and recA) of which 3 genes (gyrB, nifK and nodD) were selected based on sufficient sequence diversity for further phylogenetic analysis. Phylogenetic analysis and sequence diversity for 3 genes demonstrated that sequences from C. reticulatum were more diverse. Nodule occupancy by dominant symbiont also indicated that C. reticulatum (60 percent) could have more various symbionts than cultivated chickpea (80 percent). The study demonstrated that wild chickpeas (C. reticulatum) could be used for selecting more diverse symbionts in the field conditions and it implies that chickpea domestication affected symbiosis negatively in addition to reducing genetic diversity.

Dysphagia in amyotrophic lateral sclerosis: prevalence and clinical findings.

OBJECTIVES: To characterize swallowing deficits in amyotrophic lateral sclerosis (ALS); investigate the delay in dysphagia onset; estimate correlations between dysphagia severity and patients' functional status; identify the symptom(s) most likely to predict dysphagia. MATERIALS AND METHODS: A group of 49 consecutive patients with ALS, 14 with bulbar onset and 35 with spinal onset, underwent swallowing evaluation including bedside and fiberoptic endoscopic examination to detect dysphagia. RESULTS: Patients with dysphagia were more likely than those without to have bulbar onset ALS (P = 0.02); more severely impaired chewing (P = 0.01); and tongue muscle deficits (P = 0.001). The only variable measured at first examination significantly associated with dysphagia was a more than mild tongue muscle deficit. The only variable useful in predicting dysphagia was a chewing deficit. In 10 of the 49 patients studied, swallowing evaluation disclosed an impaired cough reflex. CONCLUSIONS: Dysphagia in patients with ALS correlates significantly with bulbar onset and with oral swallowing impairment. Fiberoptic swallowing evaluation is a useful tool for detecting swallowing deficits and laryngeal sensitivity in patients with ALS. An impaired cough reflex is an unexpected finding in many patients with ALS.

Morpho-functional patterns of physiologic oropharyngeal swallowing evaluated with dynamic fast MRI.

With the advent of dynamic fast MRI sequences the act of deglutition can be dynamically visualized in cine-mode. Twenty-three healthy volunteers were enrolled in this study to define the morpho-functional patterns of oral and pharyngeal deglutition using new dynamic MRI techniques. All subjects were previously submitted to video endoscopic assessment, to exclude swallowing abnormalities. As contrast material a combination of yogurt mixed with gadolinium-diethylene diamine pentaacetic acid was used. The protocol was divided into three parts: (a) preliminary assessment of the oral cavity, pharynx and laryngeal structures; (b) morphologic assessment of tongue, soft palate, pharynx, epiglottis and larynx-hyoid bone; (c) dynamic assessment of swallowing without administrating any contrast media and, in subsequent phase, by injecting 5 ml of yogurt-based contrast medium in the patient's mouth. The time resolution was 3-4 images/s. The MR protocol revealed to be effective in the evaluation of normal motility patterns of the structures involved in swallowing. Moreover, the evaluation of the bolus progression, slowdown or stagnation, was possible. On the contrary problems were encountered in calculating precisely the bolus progression time, because of the insufficient temporal resolution. However, more energy should be invested to optimize the spatial and temporal resolution of turbo-FLASH sequences, to obtain a better dynamic representation of a complex function such as deglutition.

Myocardial infarction in nondiabetic and prediabetic population: a retrospective analysis.

Diabetes mellitus (DM) is one of the important risk factors for cardiac diseases. Type 2 DM is the commonest form of diabetes, which is characterized by insulin resistance. Insulin resistance can be preceded by long term abnormality in glucose homeostasis which is called pre-diabetes. Recently, pre-diabetes has been suggested to have an increased risk of cardiovascular disease. Considering that India has been declared as a diabetic capital of the world it deemed pertinent to assess the exact load of pre diabetics and non diabetics landing in myocardial infarction. We analyzed retrospectively the data of all patients admitted for the first time for acute myocardial infarction (MI) and evaluated the load of non diabetics, pre diabetics and diabetics among them. We found difference in the severity of diseases and degree of biochemical alterations among the three groups suggesting that abnormal glucose homeostasis has no role on the severity of MI. No previous studies have investigated the difference in male and female MI patients with respect to their glucose metabolism and its impact on the severity of the disease. Our study reveals that males even with normal glucose level are at increased risk to develop MI. Males on the other hand have increased risk for MI when compared to females with normal glucose homeostasis.

Clinical spectrum and histopathologic features of chronic hepatitis C infection in children.

OBJECTIVE: To define the natural history and outcomes of children infected with hepatitis C virus (HCV) at birth or in early childhood. STUDY DESIGN: This retrospective, prospective study identified 60 HCV-infected children through a transfusion look-back program (group 1) and by referrals (group 2). Perinatal/transfusion history, clinical course, and laboratory studies were correlated with findings from 42 liver biopsy specimens. RESULTS: Mean age at infection was 7.1 months, and duration of infection 13.4 years. The sources of infection were blood transfusion (68%), perinatal transmission (13%), and both (7%). Most patients were asymptomatic; three referral patients had advanced liver disease at presentation. Mean alanine aminotransferase level was normal in 25%, 1 to 3 times normal in 62%, and greater than 3 times normal in 13%. Liver biopsy specimens showed minimal to mild inflammation in 71%, absent or minimal fibrosis in 88%, and bridging fibrosis in 12%. Age at infection and serum gamma-glutamyltranspeptidase correlated with fibrosis; serum alanine aminotransferase correlated with inflammation unless complicated by comorbidity. Repeat biopsies within 1 to 4 years in four patients showed no significant progression in three and cirrhosis in one. Two patients died after liver transplantation. CONCLUSIONS: Children with chronic HCV infection are generally asymptomatic. By 13 years after infection, 12% of patients had significant fibrosis. Patients enrolled by referral had more severe liver disease than those identified through the look-back program, demonstrating the importance of selection bias in assessing the long-term outcome of HCV infection.

Gaschromatography-mass spectrometry analysis of fatty acids in human milk from forty puerperae living in southern Italy.

Fatty acid (FA) composition of breast milk, an important factor in newborn nutrition, may change in relation to maternal diet and individual metabolic characteristics. This study was carried out on a group of 40 puerperae who lived in Southern Italy, delivered at term and feeded with common mediterranean diet. End-milk samples were collected between the 15th and 40th day (in mean at 27th day) after delivery. Analysis of fatty acids was performed using high resolution gaschromatography and mass spectrometry. It has been reported 37 different fatty acids including 6 branched chain fatty acids (BCFA).

Retained surgical gauzes: acute and chronic CT and US findings.

Surgical sponges retained after laparotomy represent a diagnostic problem if they cannot be identified by radiopaque markers on standard radiographs. We report on 9 patients from different hospitals with an abdominal gossypiboma 7 days to 21 years after the surgical procedure. Plain radiographs may suggest the diagnosis if a textile foreign body is calcified, that is, is equipped with radiopaque marker, or when a characteristic "whirl-like" pattern is present. CT and US are necessary procedures in chronic cases, since the lesion may mimic a mass; US shows specific echogenic areas with acoustic shadow; CT usually reveals a hypodense mass with a thick peripheral rim.

Angiographic and microradiographic demonstration of the linear vascular pattern in renal neoplasms.

The linear striated vascular pattern in the kidney is discussed in the light of nine new examples. Based on the histomicroangiographic findings in 2 cases, the pathogenic mechanism underlying this phenomenon is discussed, and the pattern is considered a sure sign of venous tumor infiltration.