Evaluation of Cultivated and Wild Brinjal Germplasm against Bacterial Wilt Disease with Tollinterleukin-1 Receptors (TIR)-NBS-LRR Type R-gene Specific Degenerate Primer

The experiment was conducted at C-Block Farm of Bidhan Chandra Krishi Viswavidyalaya, Kalyani, West Bengal, India during 2017–18 to screen eight brinjal germplasm lines against BW disease using tollinterleukin-1 receptors (TIR)-NBS-LRR type R-gene specific degenerate primer. The study showed that wild genotype S. torvum was highly resistant to bacterial wilt incidence with no wilting symptom whereas two cultivated genotypes (Utkal Anushree and Utkal Madhuri) and one wild genotype S. sisymbriifolium were found to be resistant to BW disease. Out of the 7 germplasm sequences, 2 had no match with R-genes whereas the remaining 5 sequences have 70-93% homology with R-genes of other plant species submitted in Gene Bank sequence database. Nearly 90% sequence identity of brinjal NBS-LRR RGA was found by analyzing through BLASTn with NBS-LRR RGAs of other solanaceous crops. Two cultivated resistant genotypes (Utkal Madhuri and Utkal Tarini) were similar to the wild resistant type S. sisymbriifloium, while cultivable resistant genotype Utkal Anushree was highly different at sequence level. Two cultivable susceptible genotypes (BCB-30 and Garia) showed high level of similarity among them and they were strongly associated with the wild susceptible genotype S. macrocarpum. Two cultivable genotypes Utkal Anushree and Utkal Madhuri could be utilized in future breeding programme and two wild genotypes S. torvum and S. sisymbriifolium could be used as resistant rootstocks in brinjal grafting.

Genetic Diversity and Dispersal of Aspergillus fumigatus in Arctic Soils

Aspergillus fumigatus is a saprophytic mold and an opportunistic pathogen with a broad geographic and ecological distribution. A. fumigatus is the most common etiological agent of aspergillosis, affecting over 8,000,000 individuals worldwide. Due to the rising number of infections and increasing reports of resistance to antifungal therapy, there is an urgent need to understand A. fumigatus populations from local to global levels. However, many geographic locations and ecological niches remain understudied, including soil environments from arctic regions. In this study, we isolated 32 and 52 A. fumigatus strains from soils in Iceland and the Northwest Territories of Canada (NWT), respectively. These isolates were genotyped at nine microsatellite loci and the genotypes were compared with each other and with those in other parts of the world. Though significantly differentiated from each other, our analyses revealed that A. fumigatus populations from Iceland and NWT contained evidence for both clonal and sexual reproductions, and shared many alleles with each other and with those collected from across Europe, Asia, and the Americas. Interestingly, we found one triazole-resistant strain containing the TR34 /L98H mutation in the cyp51A gene from NWT. This strain is closely related to a triazole-resistant genotype broadly distributed in India. Together, our results suggest that the northern soil populations of A. fumigatus are significantly influenced by those from other geographic regions.

Genomic and Transcriptomic Analysis Provide Insights Into Root Rot Resistance in Panax notoginseng

Panax notoginseng (Panax notoginseng (Burk.) F.H. Chen), a plant of high medicinal value, is severely affected by root rot during cultivation. Here, we generated a reference genome of P. notoginseng, with a contig N50 size of 241.268 kb, and identified 66 disease-resistance genes (R-genes) as candidate genes for breeding disease-resistant varieties. We then investigated the molecular mechanism underlying the responses of resistant and susceptible P. notoginseng genotypes to Fusarium oxysporum infection at six time points by RNA-seq. Functional analysis of the genes differentially expressed between the two genotypes indicated that genes involved in the defense response biological process like hormone transduction and plant-pathogen interaction are continuously and highly expressed in resistant genotype during infection. Moreover, salicylic acid and jasmonic acid levels gradually increased during infection in the resistant genotype. Coexpression analysis showed that PnWRKY22 acts as a hub gene in the defense response of the resistant genotype. Finally, transiently overexpressing PnWRKY22 increased salicylic acid levels in P. notoginseng leaves. Our findings provide a theoretical basis for studying root rot resistance in P. notoginseng.

Genetic and Proteomic Basis of Sclerotinia Stem Rot Resistance in Indian Mustard [Brassica juncea (L.) Czern & Coss.]

Sclerotinia stem rot is one of the utmost important disease of mustard, causing considerable losses in seed yield and oil quality. The study of the genetic and proteomic basis of resistance to this disease is imperative for its effective utilization in developing resistant cultivars. Therefore, the genetic pattern of Sclerotinia stem rot resistance in Indian mustard was studied using six generations (P1, P2, F1, F2, BC1P1, and BC1P2) developed from the crossing of one resistant (RH 1222-28) and two susceptible (EC 766300 and EC 766123) genotypes. Genetic analysis revealed that resistance was governed by duplicate epistasis. Comparative proteome analysis of resistant and susceptible genotypes indicated that peptidyl-prolyl cis-trans isomerase (A0A078IDN6 PPIase) showed high expression in resistant genotype at the early infection stage while its expression was delayed in susceptible genotypes. This study provides important insight to mustard breeders for designing effective breeding programs to develop resistant cultivars against this devastating disease.

Inducible Enrichment of Osa-miR1432 Confers Rice Bacterial Blight Resistance through Suppressing OsCaML2

MicroRNAs (miRNAs) handle immune response to pathogens by adjusting the function of target genes in plants. However, the experimentally documented miRNA/target modules implicated in the interplay between rice and Xanthomonas oryzae pv. oryzae (Xoo) are still in the early stages. Herein, the expression of osa-miR1432 was induced in resistant genotype IRBB5, but not susceptible genotype IR24, under Xoo strain PXO86 attack. Overexpressed osa-miR1432 heightened rice disease resistance to Xoo, indicated by enhancive enrichment of defense marker genes, raised reactive oxygen species (ROS) levels, repressed bacterial growth and shortened leaf lesion length, whilst the disruptive accumulation of osa-miR1432 accelerated rice susceptibility to Xoo infection. Noticeably, OsCaML2 (LOC_Os03g59770) was experimentally confirmed as a target gene of osa-miR1432, and the overexpressing OsCaML2 transgenic plants exhibited compromised resistance to Xoo infestation. Our results indicate that osa-miR1432 and OsCaML2 were differently responsive to Xoo invasion at the transcriptional level and fine-tune rice resistance to Xoo infection, which may be referable in resistance gene discovery and valuable in the pursuit of improving Xoo resistance in rice breeding.

Evaluation of Growth and Yield Characters of Garden Pea Genotypes at Dailekh, Mid-Western Nepal

Knowledge of phenotypic variation among the germplasm is important for the breeding program of garden pea. This study was conducted to evaluate the growth and yield traits of garden pea genotypes and to identify high yielding, and powdery mildew resistant genotype at Horticulture Research Station (HRS), Dailekh, Mid-western Nepal. Eleven garden pea genotypes were evaluated in the main production season (2018-2019) and compared with 'Sikkim Local' as standard variety, and the experiment was laid out in randomized complete block design with three replications. The analysis of variance revealed that genotypes had significant variation for all the traits studied except few insignificant traits. Significantly higher number of green pod/plant, green pod yield/plant, seed number/pod and seed yield/plant were recorded in genotypes DGP-12-18-2 and DGP-12-18-1 as compared with other studied genotypes. Genotype DGP-12-18-2, and DGP-12-18-1 exhibited resistant (2) to powdery mildew disease and these genotypes showed 45.8% and 16.6% yield advantage over the standard check 'Sikkim Local' variety. Therefore, genotypes DGP-12-18-2 and DGP-12-18-1 can be recommended to produce for fresh green pod and seed yield at on-farm condition of Mid-Western Nepal.

Integrated Transcriptomic and Metabolomic Analyses of the Molecular Mechanisms of Two Highland Barley Genotypes with Differential Pyroxsulam Responses

Background: Highland barley is one of the few crops that can be grown at high elevations, making it a key resource within the Tibet Plateau. Weeds are a significant threat to highland barley production and new herbicides and tolerant barley varieties are needed to control this ever-growing problem. Results: A better understanding of existing herbicide resistance mechanisms is therefore needed. In this study, transcriptomic and metabolomic analyses were used to identify molecular and physiological changes in two highland barley genotypes with differing sensitivities to pyroxsulam. We identified several stress-responsive metabolites, including flavonoids and antioxidants, which accumulated to significantly higher levels in the pyroxsulam-resistant genotype. Additionally, we found key genes in both the flavonoid biosynthesis pathway and the antioxidant system were up-regulated in pyroxsulam-resistant barley. Conclusions: This work significantly expands on the current understanding of the molecular mechanisms underlying differing pyroxsulam tolerance among barley genotypes and provides several new avenues to explore for breeding or engineering tolerant barley.

The Use of Molecular Markers to Investigate Possible Resistance to Heartworm Preventives in Dirofilaria Immitis Samples from Heartworm Positive Dogs in Europe

Background: Dirofilaria immitis is a parasitic filarial nematode. It is the causative agent of dirofilariosis, a potentially fatal pulmonary infection which primarily infects canids and felines. dirofilariosis infections are primarily controlled with a prophylactic macrocyclic lactone (ML) regimen. Recent evidence has confirmed the development of ML-resistant isolates in the US which are genetically distinct from wild-type populations. Previous research clinically validated 9 single nucleotide polymorphism (SNP) molecular markers associated with these ML resistance phenotypes isolated from the USA. Methods: In this study, three D. immitis US laboratory-maintained isolates: two putative susceptible isolates, Berkeley, and Georgia II, one putative resistant isolate, WildCat; and eleven European D. immitis clinical samples, from Italy, Spain, and Hungary were analyzed. The samples tested were fresh microfilaria (mf) in blood or adult female worms shipped in ethanol and rehydrated in phosphate buffered saline (PBS). After DNA extraction, each sample underwent MiSeq sequencing of regions encompassing the 9 SNP sites previously correlated with ML resistance. The nucleotide frequencies of the 9 SNP sites were analyzed and the pairwise fixation index (FST) of the top 2 SNP molecular markers were calculated in order to estimate the probability of identity with known resistant isolates.Results: In the three laboratory-maintained US D. immitis isolates Berkeley had a 2-SNP pairwise FST of 0.00, indicating a ML-susceptible genotype, WildCat had a 2-SNP pairwise FST of 0.33 indicating a ML-resistant genotype, and Georgia II had a 2-SNP pairwise FST of 0.07, which may indicate early selection for ML resistance. The genotype analysis of the European clinical samples showed that all eleven European samples had 2-SNP pairwise FST of 0.00, which indicates their genotypes are consistent with ML susceptibility. Conclusions: Prior to genotyping the European samples, it was possible that the positive heartworm infections could have arisen because of the development of ML-resistance or due to lack of owner compliance or incomplete use of heartworm preventives. Our results indicate no genomic evidence of ML-resistance and suggests that resistance has not developed, so far, in Europe, or been introduced via movement of infected dogs. However, vigilance is needed to maintain susceptibility to heartworm preventives in regions of the world so far without resistance.

Transcriptome analysis reveals key genes associated with root-lesion nematode Pratylenchus thornei resistance in chickpea

The root-lesion nematode, Pratylenchus thornei, is one of the major plant-parasitic nematode species causing significant yield losses in chickpea (Cicer arietinum). In order to identify the underlying mechanisms of resistance to P. thornei, the transcriptomes of control and inoculated roots of three chickpea genotypes viz. D05253 > F3TMWR2AB001 (resistant advanced breeding line), PBA HatTrick (moderately resistant cultivar), and Kyabra (susceptible cultivar) were studied at 20 and 50 days post inoculation using the RNA-seq approach. On analyzing the 633.3 million reads generated, 962 differentially expressed genes (DEGs) were identified. Comparative analysis revealed that the majority of DEGs upregulated in the resistant genotype were downregulated in the moderately resistant and susceptible genotypes. Transcription factor families WRKY and bZIP were uniquely expressed in the resistant genotype. The genes Cysteine-rich receptor-like protein kinase 10, Protein lifeguard-like, Protein detoxification, Bidirectional sugar transporter Sugars Will Eventually be Exported Transporters1 (SWEET1), and Subtilisin-like protease were found to play cross-functional roles in the resistant chickpea genotype against P. thornei. The identified candidate genes for resistance to P. thornei in chickpea can be explored further to develop markers and accelerate the introgression of P. thornei resistance into elite chickpea cultivars.

Comparative Transcriptome Analysis Reveals Genetic Mechanisms of Sugarcane Aphid Resistance in Grain Sorghum

The sugarcane aphid, Melanaphis sacchari (Zehntner) (Hemiptera: Aphididae) (SCA), has become a major pest of grain sorghum since its appearance in the USA. Several grain sorghum parental lines are moderately resistant to the SCA. However, the molecular and genetic mechanisms underlying this resistance are poorly understood, which has constrained breeding for improved resistance. RNA-Seq was used to conduct transcriptomics analysis on a moderately resistant genotype (TAM428) and a susceptible genotype (Tx2737) to elucidate the molecular mechanisms underlying resistance. Differential expression analysis revealed differences in transcriptomic profile between the two genotypes at multiple time points after infestation by SCA. Six gene clusters had differential expression during SCA infestation. Gene ontology enrichment and cluster analysis of genes differentially expressed after SCA infestation revealed consistent upregulation of genes controlling protein and lipid binding, cellular catabolic processes, transcription initiation, and autophagy in the resistant genotype. Genes regulating responses to external stimuli and stress, cell communication, and transferase activities, were all upregulated in later stages of infestation. On the other hand, expression of genes controlling cell cycle and nuclear division were reduced after SCA infestation in the resistant genotype. These results indicate that different classes of genes, including stress response genes and transcription factors, are responsible for countering the physiological effects of SCA infestation in resistant sorghum plants.