Genome-wide transcriptional changes of ramie (Boehmeria nivea L. Gaud) in response to root-lesion nematode infection

Gene ◽  
2014 ◽  
Vol 552 (1) ◽  
pp. 67-74 ◽  
Author(s):  
Siyuan Zhu ◽  
Shouwei Tang ◽  
Qingming Tang ◽  
Touming Liu
2021 ◽  
Vol 12 ◽  
Author(s):  
Selamawit A. Kidane ◽  
Solveig Haukeland ◽  
Beira H. Meressa ◽  
Anne Kathrine Hvoslef-Eide ◽  
Danny L. Coyne

Enset (Ensete ventricosum), is a perennial herbaceous plant belonging to the family Musaceae, along with banana and plantain. Despite wild populations occurring in eastern, central and southern Africa, it is only in Ethiopia that the crop has been domesticated, where it is culturally and agriculturally symbolic as a food security crop. Although an under-researched orphan crop, enset serves as a staple food for about 20% of the Ethiopian population, comprising more than 20 million people, demonstrating its value in the country. Similar to banana and plantain, enset is heavily affected by plant-parasitic nematodes, with recent studies indicating record levels of infection by the root lesion nematode Pratylenchus goodeyi. Enset is propagated vegetatively using suckers that are purposely initiated from the mother corm. However, while banana and plantain suckers have proven to be a key source of nematode infection and spread, knowledge on the infection levels and role of enset suckers in nematode dissemination is lacking. Given the high levels of plant-parasitic nematodes reported in previous surveys, it is therefore speculated that planting material may act as a key source of nematode dissemination. To address this lack of information, we assessed enset planting material in four key enset growing zones in Ethiopia. A total of 340 enset sucker samples were collected from farmers and markets and analyzed for the presence of nematodes. Nematodes were extracted using a modified Baermann method over a period of 48 h. The root lesion nematode P. goodeyi was present in 100% of the samples, at various levels of infection. These conclusive results show that planting material is indeed a key source of nematode infection in enset, hence measures taken to ensure clean suckers for planting will certainly mitigate nematode infection and spread. The effect of nematode infection on yield and quality on enset remains to be investigated and would be a way forward to complement the nematode/disease studies conducted so far and add valuable knowledge to the current poorly known impact of pests and diseases.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Deepak Kumar ◽  
Shiveta Sharma ◽  
Rajiv Sharma ◽  
Saksham Pundir ◽  
Vikas Kumar Singh ◽  
...  

AbstractRoot lesion nematode (RLN; Pratylenchus thornei) causes extensive yield losses in wheat worldwide and thus pose serious threat to global food security. Reliance on fumigants (such as methyl bromide) and nematicides for crop protection has been discouraged due to environmental concerns. Hence, alternative environment friendly control measures like finding and deployment of resistance genes against Pratylenchus thornei are of significant importance. In the present study, genome-wide association study (GWAS) was performed using single-locus and multi-locus methods. In total, 143 wheat genotypes collected from pan-Indian wheat cultivation states were used for nematode screening. Genotypic data consisted of  > 7K SNPs with known genetic positions on the high-density consensus map was used for association analysis. Principal component analysis indicated the existence of sub-populations with no major structuring of populations due to the origin. Altogether, 25 significant marker trait associations were detected with − log10 (p value) > 4.0. Three large linkage disequilibrium blocks and the corresponding haplotypes were found to be associated with significant SNPs. In total, 37 candidate genes with nine genes having a putative role in disease resistance (F-box-like domain superfamily, Leucine-rich repeat, cysteine-containing subtype, Cytochrome P450 superfamily, Zinc finger C2H2-type, RING/FYVE/PHD-type, etc.) were identified. Genomic selection was conducted to investigate how well one could predict the phenotype of the nematode count without performing the screening experiments. Prediction value of r = 0.40 to 0.44 was observed when 56 to 70% of the population was used as a training set. This is the first report where GWAS has been conducted to find resistance against root lesion nematode (P. thornei) in Indian wheat germplasm.


Rhizosphere ◽  
2021 ◽  
pp. 100359
Author(s):  
Monique Thiara Rodrigues e Silva ◽  
Angélica Calandrelli ◽  
Luanna Karoline Rinaldi ◽  
Angélica Miamoto ◽  
Beatriz Pereira Moreno ◽  
...  

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Karen R. Mifsud ◽  
Clare L. M. Kennedy ◽  
Silvia Salatino ◽  
Eshita Sharma ◽  
Emily M. Price ◽  
...  

AbstractGlucocorticoid hormones (GCs) — acting through hippocampal mineralocorticoid receptors (MRs) and glucocorticoid receptors (GRs) — are critical to physiological regulation and behavioural adaptation. We conducted genome-wide MR and GR ChIP-seq and Ribo-Zero RNA-seq studies on rat hippocampus to elucidate MR- and GR-regulated genes under circadian variation or acute stress. In a subset of genes, these physiological conditions resulted in enhanced MR and/or GR binding to DNA sequences and associated transcriptional changes. Binding of MR at a substantial number of sites however remained unchanged. MR and GR binding occur at overlapping as well as distinct loci. Moreover, although the GC response element (GRE) was the predominant motif, the transcription factor recognition site composition within MR and GR binding peaks show marked differences. Pathway analysis uncovered that MR and GR regulate a substantial number of genes involved in synaptic/neuro-plasticity, cell morphology and development, behavior, and neuropsychiatric disorders. We find that MR, not GR, is the predominant receptor binding to >50 ciliary genes; and that MR function is linked to neuronal differentiation and ciliogenesis in human fetal neuronal progenitor cells. These results show that hippocampal MRs and GRs constitutively and dynamically regulate genomic activities underpinning neuronal plasticity and behavioral adaptation to changing environments.


Author(s):  
Md Motiur Rahaman ◽  
Rebecca S. Zwart ◽  
Thusitha W. T. Rupasinghe ◽  
Helen L. Hayden ◽  
John P. Thompson

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