Candidate Gene Identification with SNP Marker-Based Fine Mapping of Anthracnose Resistance Gene Co-4 in Common Bean

Anthracnose, caused by Colletotrichum lindemuthianum, is an important fungal disease of common bean (Phaseolus vulgaris). Alleles at the Co–4 locus confer resistance to a number of races of C. lindemuthianum. A population of 94 F_4:5 recombinant inbred lines of a cross between resistant black bean genotype B09197 and susceptible navy bean cultivar Nautica was used to identify markers associated with resistance in bean chromosome 8 (Pv08) where Co–4 is localized. Three SCAR markers with known linkage to Co–4 and a panel of single nucleotide markers were used for genotyping. A refined physical region on Pv08 with significant association with anthracnose resistance identified by markers was used in BLAST searches with the genomic sequence of common bean accession G19833. Thirty two unique annotated candidate genes were identified that spanned a physical region of 936.46 kb. A majority of the annotated genes identified had functional similarity to leucine rich repeats/receptor like kinase domains. Three annotated genes had similarity to 1, 3-β-glucanase domains. There were sequence similarities between some of the annotated genes found in the study and the genes associated with phosphoinositide-specific phosphilipases C associated with Co-x and the COK–4 loci found in previous studies. It is possible that the Co–4 locus is structured as a group of genes with functional domains dominated by protein tyrosine kinase along with leucine rich repeats/nucleotide binding site, phosphilipases C as well as β-glucanases.     

Response of Barley Genotypes to Fusarium Head Blight under Natural Infection and Artificial Inoculation Conditions

Forty-eight spring barley genotypes were evaluated for deoxynivalenol (DON) concentration under natural infection across 5 years at Harrington, Prince Edward Island. These genotypes were also evaluated for Fusarium head blight (FHB) severity and DON concentration under field nurseries with artificial inoculation of Fusarium graminearum by the grain spawn method across 2 years at Ottawa, Ontario, and one year at Hangzhou, China. Additionally, these genotypes were also evaluated for FHB severity under greenhouse conditions with artificial inoculation of F. graminearum by conidial suspension spray method across 3 years at Ottawa, Ontario. The objective of the study was to investigate if reactions of barley genotypes to artificial FHB inoculation correlate with reactions to natural FHB infection. DON concentration under natural infection was positively correlated with DON concentration (r = 0.47, P < 0.01) and FHB incidence (r = 0.56, P < 0.01) in the artificially inoculated nursery with grain spawn method. Therefore, the grain spawn method can be used to effectively screen for low DON. FHB severity, generated from greenhouse spray, however, was not correlated with DON concentration (r = 0.12, P > 0.05) under natural infection and it was not correlated with DON concentration (r = −0.23, P > 0.05) and FHB incidence (r = 0.19, P > 0.05) in the artificially inoculated nursery with grain spawn method. FHB severity, DON concentration, and yield were affected by year, genotype, and the genotype × year interaction. The effectiveness of greenhouse spray inoculation for indirect selection for low DON concentration requires further studies. Nine of the 48 genotypes were found to contain low DON under natural infection. Island barley had low DON and also had high yield.     

SSR-enriched genetic linkage maps of bermudagrass (<Emphasis Type="Italic">Cynodon dactylon</Emphasis> × <Emphasis Type="Italic">transvaalensis</Emphasis>), and their comparison with allied plant genomes

Key message

We report SSR-enriched genetic maps of bermudagrass that: (1) reveal partial residual polysomic inheritance in the tetraploid species, and (2) provide insights into the evolution of chloridoid genomes.

Abstract

This study describes genetic linkage maps of two bermudagrass species, Cynodon dactylon (T89) and Cynodon transvaalensis (T574), that integrate heterologous microsatellite markers from sugarcane into frameworks built with single-dose restriction fragments (SDRFs). A maximum likelihood approach was used to construct two separate parental maps from a population of 110 F₁ progeny of a cross between the two parents. The T89 map is based on 291 loci on 34 cosegregating groups (CGs), with an average marker spacing of 12.5 cM. The T574 map is based on 125 loci on 14 CGs, with an average marker spacing of 10.7 cM. Six T89 and one T574 CG(s) deviated from disomic inheritance. Furthermore, marker segregation data and linkage phase analysis revealed partial residual polysomic inheritance in T89, suggesting that common bermudagrass is undergoing diploidization following whole genome duplication (WGD). Twenty-six T89 CGs were coalesced into 9 homo(eo)logous linkage groups (LGs), while 12 T574 CGs were assembled into 9 LGs, both putatively representing the basic chromosome complement (x?=?9) of the species. Eight T89 and two T574 CGs remain unassigned. The marker composition of bermudagrass ancestral chromosomes was inferred by aligning T89 and T574 homologs, and used in comparisons to sorghum and rice genome sequences based on 108 and 91 significant blast hits, respectively. Two nested chromosome fusions (NCFs) shared by two other chloridoids (i.e., zoysiagrass and finger millet) and at least three independent translocation events were evident during chromosome number reduction from 14 in the polyploid common ancestor of Poaceae to 9 in Cynodon.

     

Rural-urban differences on the rates and factors associated with early initiation of breastfeeding in Nigeria: further analysis of the Nigeria demographic and health survey, 2013

Background

This study investigates and compares the rates and factors associated with early initiation of breastfeeding (EIBF) within one hour of birth in rural and urban Nigeria.

Methods

Data from the 2013 Nigeria Demographic and Health Survey (NDHS) were analyzed. The rates of EIBF were reported using frequency tabulation. Associated factors were examined using Chi-Square test and further assessed on multivariable logistic regression analysis.

Results

The rates of EIBF were 30.8% (95% confidence interval [CI] 29.0, 32.6) and 41.9% (95% CI 39.6, 44.3) in rural and urban residences, respectively (p?<?0.001). The North-Central region had the highest EIBF rates both in rural (43.5%) and urban (63.5%) residences. Greater odds of EIBF in rural residence were significantly associated with higher birth order (Adjusted Odds Ratio [AOR] 1.29, 95% CI 1.10, 1.60), large birth size (AOR 1.33, 95% CI 1.10, 1.60), and health facility delivery (AOR 1.46, 95% CI 1.23, 1.72). Rural mothers in the rich wealth index, not working and whose husbands obtained at least a secondary school education had significantly higher odds of early initiation of breastfeeding. Regardless of residence, greater odds of EIBF were significantly associated with non-cesarean delivery (Rural AOR 3.50, 95% CI 1.84, 6.62; Urban AOR 2.48, 95% CI 1.60, 3.80) and living in North-Central (Rural AOR 1.84, 95% CI 1.34, 2.52; Urban AOR 4.40, 95% CI 3.15, 6.15) region. Also, higher odds of EIBF were significantly associated with living in North-East (Rural AOR 1.48, 95% CI 1.05, 2.08; Urban AOR 3.50, 95% CI 2.55, 4.83), South-South (Rural AOR 1.51, 95% CI 1.11, 2.10; Urban AOR 2.84, 95% CI 2.03, 3.97) and North-West (Urban residence only AOR 2.08, 95% CI 1.54, 2.80) regions.

Conclusions

Rural-urban differences in the rates and factors associated with EIBF exist in Nigeria with rural residence having significantly lower rates. Intervention efforts which address the risk factors identified in this study may contribute to improved EIBF rates. Efforts need to prioritize rural mothers generally, (particularly, those in rural North-West region) as well as mothers in urban South-West region of Nigeria.

     

Membrane receptor-initiated signaling in 1,25(OH)2D3-stimulated calcium uptake in intestinal epithelial cells

Demonstrating 1,25(OH)2D3-stimulated calcium uptake in isolated chick intestinal epithelial cells has been complicated by simultaneous enhancement of both uptake and efflux. We now report that in intestinal cells of adult birds, or those of young birds cultured for 72 h, 1,25(OH)2D3-stimulates 45Ca uptake to greater than 140% of corresponding controls within 3 min of addition. Such cells have lost hormone-stimulated protein kinase C (PKC) activity, believed to mediate calcium efflux. To further test this hypothesis, freshly isolated cells were preincubated with calphostin C, and calcium uptake monitored in the presence or absence of steroid. Only cells treated with the PKC inhibitor demonstrated a significant increase in 45Ca uptake in response to 1,25(OH)2D3, relative to corresponding controls. In addition, phorbol ester was shown to stimulate efflux, while forskolin stimulated uptake. To further investigate the mechanisms involved in calcium uptake, we assessed the role of TRPV6 and its activation by beta-glucuronidase. beta-Glucuronidase secretion from isolated intestinal epithelial cells was significantly increased by treatment with 1,25(OH)2D3, PTH, or forskolin, but not by phorbol ester. Treatment of cells with beta-glucuronidase, in turn, stimulated 45Ca uptake. Finally, transfection of cells with siRNA to either beta-glucuronidase or TRPV6 abolished 1,25(OH)2D3-enhanced calcium uptake relative to controls transfected with scrambled siRNA. Confocal microscopy further indicated rapid redistribution of enzyme and calcium channel after steroid. 1,25(OH)2D3 and PTH increase calcium uptake by stimulating the PKA pathway to release beta-glucuronidase, which in turn activates TRPV6. 1,25(OH)2D3-enhanced calcium efflux is mediated by the PKC pathway.     

Implications of biofuel policy‐driven land cover change for rainfall erosivity and soil erosion in the United States

Large‐scale conversion of traditional agricultural cropping systems to biofuel cropping systems is predicted to have significant impact on the hydrologic cycle. Changes in the hydrologic cycle lead to changes in rainfall and its erosive power, and consequently soil erosion that will have onsite impacts on soil quality and crop productivity, and offsite impacts on water quality and quantity. We examine regional change in rainfall erosivity and soil erosion resulting from biofuel policy‐induced land use/land cover (LULC) change. Regional climate is simulated under current and biofuel LULC scenarios for the period 1979–2004 using the Weather Research Forecast (WRF) model coupled to the NOAH land surface model. The magnitude of change in rainfall erosivity under the biofuel scenario is 1.5–3 times higher than the change in total annual rainfall. Over most of the conterminous United States (~56%), the magnitude of the change in erosivity is between ?2.5% and +2.5%. A decrease in erosivity of magnitude 2.5–10% is predicted over 23% of the area, whereas an increase of the same magnitude is predicted over 14% of the area. Corresponding to the changes in rainfall erosivity and crop cover, a decrease in soil loss is predicted over 60% of the area under the biofuel scenario. In Kansas and Oklahoma, the states in which a large fraction of land area is planted with switchgrass under the biofuel scenario, soil loss is estimated to decrease 12% relative to the baseline. This reduction in soil loss is due more to changes in the crop cover factor than changes in rainfall or rainfall erosivity. This indicates that the changes in LULC, due to future cellulosic biofuel feedstock production, can have significant implications for regional soil and water resources in the United States and we recommend detailed investigation of the trade‐offs between land use and management options.     

In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterization

In this study, we followed the genomic, lipidomic and metabolomic changes associated with the selection of miltefosine (MIL) resistance in two clinically derived Leishmania donovani strains with different inherent resistance to antimonial drugs (antimony sensitive strain Sb‐S; and antimony resistant Sb‐R). MIL‐R was easily induced in both strains using the promastigote‐stage, but a significant increase in MIL‐R in the intracellular amastigote compared to the corresponding wild‐type did not occur until promastigotes had adapted to 12.2 μM MIL. A variety of common and strain‐specific genetic changes were discovered in MIL‐adapted parasites, including deletions at the LdMT transporter gene, single‐base mutations and changes in somy. The most obvious lipid changes in MIL‐R promastigotes occurred to phosphatidylcholines and lysophosphatidylcholines and results indicate that the Kennedy pathway is involved in MIL resistance. The inherent Sb resistance of the parasite had an impact on the changes that occurred in MIL‐R parasites, with more genetic changes occurring in Sb‐R compared with Sb‐S parasites. Initial interpretation of the changes identified in this study does not support synergies with Sb‐R in the mechanisms of MIL resistance, though this requires an enhanced understanding of the parasite's biochemical pathways and how they are genetically regulated to be verified fully.     

Using the knowns to discover the unknowns: MS‐based dereplication uncovers structural diversity in 17‐hydroxygeranyllinalool diterpene glycoside production in the Solanaceae

Exploring the diversity of plant secondary metabolism requires efficient methods to obtain sufficient structural insights to discriminate previously known from unknown metabolites. De novo structure elucidation and confirmation of known metabolites (dereplication) remain a major bottleneck for mass spectrometry‐based metabolomic workflows, and few systematic dereplication strategies have been developed for the analysis of entire compound classes across plant families, partly due to the complexity of plant metabolic profiles that complicates cross‐species comparisons. 17‐hydroxygeranyllinalool diterpene glycosides (HGL‐DTGs) are abundant defensive secondary metabolites whose malonyl and glycosyl decorations are induced by jasmonate signaling in the ecological model plant Nicotiana attenuata. The multiple labile glycosidic bonds of HGL‐DTGs result in extensive in‐source fragmentation (IS‐CID) during ionization. To reconstruct these IS‐CID clusters from profiling data and identify precursor ions, we applied a deconvolution algorithm and created an MS/MS library from positive‐ion spectra of purified HGL‐DTGs. From this library, 251 non‐redundant fragments were annotated, and a workflow to characterize leaf, flower and fruit extracts of 35 solanaceous species was established. These analyses predicted 105 novel HGL‐DTGs that were restricted to Nicotiana, Capsicum and Lycium species. Interestingly, malonylation is a highly conserved step in HGL‐DTG metabolism, but is differentially affected by jasmonate signaling among Nicotiana species. This MS‐based workflow is readily applicable for cross‐species re‐identification/annotation of other compound classes with sufficient fragmentation knowledge, and therefore has the potential to support hypotheses regarding secondary metabolism diversification.