Priyanka Gangwar

Phytophthora nicotianae is a persistent and highly destructive soilborne oomycete that causes black shank of tobacco and continues to threaten its production despite integrated management. Although soil microbiomes are increasingly recognized as important components of disease outcomes, little is known about how soil microbial communities vary with P. nicotianae DNA concentrations and black shank pressure under field conditions. We examined relationships among 17 soil physicochemical properties, microbial community features, P. nicotianae DNA levels, and black shank outcomes in three flue-cured tobacco fields sampled repeatedly throughout one growing season. Phytophthora nicotianae DNA concentrations were associated with several soil physicochemical properties. The field with the lowest disease pressure had higher microbial alpha diversity, the simplest bacterial network, and a moderately complex fungal network. In contrast, the field with the highest black shank mortality showed the lowest alpha diversity, the most complex bacterial network, and the least complex fungal network. Over the growing season, microbial alpha diversity declined, and disease outcomes were associated with field-specific shifts in microbial community composition. Trichoderma , Fusarium , and Globodera were most abundant in the high-disease field, whereas multiple bacterial groups within Firmicutes, Proteobacteria, and Actinobacteriota were negatively associated with P. nicotianae in the lower-disease fields. These results indicate that P. nicotianae DNA abundance and black shank pressure are associated with soil physicochemical properties and field-dependent patterns in microbial diversity, community composition, network topology, and several microbial taxa. Our study provides a field-based foundation for future research to experimentally test candidate microbial indicators and microbe–pathogen relationships relevant to black shank risk assessment. IMPORTANCE: Black shank is a persistent soilborne disease that threatens tobacco production and is difficult to manage because the pathogen survives in soil and disease outcomes vary from field to field. This study shows that measuring the pathogen alone may not fully explain disease risk. Across three Virginia tobacco fields, black shank pressure was linked to soil properties and differences in the soil microbial community. Fields with lower disease pressure had higher microbial diversity and different groups of bacteria associated with lower levels of Phytophthora nicotianae , the causal agent of black shank. These findings suggest that future disease-risk assessment may be improved by considering soil conditions and microbial indicators together with pathogen detection. The work provides a foundation for identifying soil and microbial features that could support more targeted and sustainable black shank management strategies.

The rich genetic diversity existing within exotic, indigenous, and diverse germplasm lays the foundation for the continuous improvement of crop cultivars. The composite collection has been suggested as a gateway to identifying superior germplasm for use in crop improvement programs. Here, a chickpea global composite collection was evaluated at five locations in India over two years for five agronomic traits to identify agronomically superior accessions. The desi, kabuli, and intermediate types of chickpea accessions differed significantly for plant height (PLHT) and 100-seed weight (100 SW). In contrast, the intermediate type differed substantially from kabuli for days to maturity (DM). Several highly significant trait correlations were detected across different locations. The most stable and promising accessions from each of the five locations were prioritised based on their superior performance over the best-performing check cultivar. Accordingly, the selected germplasm accessions of desi type showed up to 176% higher seed yield (SY), 29% lower flowering time, 21% fewer maturity days, 64% increase in PLHT, and 183% larger seeds than the check cultivar JG11 or Annigeri. The prioritised kabuli accessions displayed up to 270% more yield, 13% less flowering time, 8% fewer maturity days, 111% increase in PLHT, and 41% larger seeds over the check cultivar KAK2. While the intermediate type accessions had up to 169% better yield, 1% early flowering, 3% early maturity, 54% taller plants, and 25% bigger seeds over the check cultivar JG 11 or KAK2. These accessions can be utilised in chickpea improvement programs to develop high-yielding, early flowering, short duration, taller, and large-seeded varieties with a broad genetic base.

Comparative Time Series RNA-seq Analysis of Pigeonpea Root Tissues in Response to Fusarium udum Infection

Unravelling the genetic architecture underlying yield components and agronomic traits is important for enhancing crop productivity. Here, a recombinant inbred line (RIL) population, developed from ICC 4958 and DCP 92–3 cross, was used for constructing linkage map and QTL mapping analysis. The RIL population was genotyped using a high-throughput Axiom^®CicerSNParray, which enabled the development of a high-density genetic map consisting of 3,818 SNP markers and spanning a distance of 1064.14 cM. Analysis of phenotyping data for yield, yield components and agronomic traits measured across three years together with genetic mapping data led to the identification of 10 major-effect QTLs and six minor-effect QTLs explaining up to 59.70% phenotypic variance. The major-effect QTLs identified for 100-seed weight, and plant height possessed key genes, such as C3HC4 RING finger protein, pentatricopeptide repeat (PPR) protein, sugar transporter, leucine zipper protein and NADH dehydrogenase, amongst others. The gene ontology studies highlighted the role of these genes in regulating seed weight and plant height in crop plants. The identified genomic regions for yield, yield components, and agronomic traits, and the closely linked markers will help advance genetics research and breeding programs in chickpea.

Grass pea (Lathyrus sativus L.) is an important food crop cultivated in dryland agricultural ecosystem. It is an important source of dietary protein to millions of people living in low-income countries in South-east Asia and Africa. The present study emphasises the development of genomic resources and their application in marker–trait association for plant phenology and yield-related traits in lathyrus. In silico mining of nucleotide sequences identified 203 simple sequence repeat (SSR) motifs, of which trimer repeats (62%) were most abundant followed by tetramer (19%), hexamer (10%), pentamer (6%) and dimer (3%) nucleotide repeats. Of 150 SSR markers screened, 60 markers were amplified 75 alleles from 50 germplasm lines with 2–3 alleles per locus and the polymorphic information content of 0.45 was observed. We report 6 significant marker–trait associations using the developed SSR markers for plant phenology and yield-related traits following mixed linear model (Q+K) analysis. Gene ontology search of trait linked markers revealed marker regions encoding genes related to homeobox-leucine zipper protein ATHB-6-like, rubredoxin family protein, and cationic peroxidise. Understanding the association of novel alleles in trait expression will play a significant role in future lathyrus crop improvement programmes.

Background Chickpea (Cicer arietinum L.) contributes 75% of total pulse production. Being cheaper than animal protein, makes it important in dietary requirement of developing countries. Weed not only competes with chickpea resulting into drastic yield reduction but also creates problem of harbouring fungi, bacterial diseases and insect pests. Chemical approach having new herbicide discovery has constraint of limited lead molecule options, statutory regulations and environmental clearance. Through genetic approach, transgenic herbicide tolerant crop has given successful result but led to serious concern over ecological safety thus non-transgenic approach like marker assisted selection is desirable. Since large variability in tolerance limit of herbicide already exists in chickpea varieties, thus the genes offering herbicide tolerance can be introgressed in variety improvement programme. Transcriptome studies can discover such associated key genes with herbicide tolerance in chickpea. Results This is first transcriptomic studies of chickpea or even any legume crop using two herbicide susceptible and tolerant genotypes exposed to imidazoline (Imazethapyr). Approximately 90 million paired-end reads generated from four samples were processed and assembled into 30803 contigs using reference based assembly. We report 5759 differentially expressed genes (DEGs), of which 3037 were regulated by 980 miRNAs, 1528 transcription factors associated with 897 DEGs, 47 Hub proteins, 3540 putative Simple Sequence Repeat-Functional Domain Marker (SSR-FDM), 13778 genic Single Nucleotide Polymorphism (SNP) putative markers and 1174 Indels. Randomly selected 20 DEGs were validated using qPCR. Pathway analysis suggested that xenobiotic degradation related gene, glutathione S-transferase (GST) were only up-regulated in presence of herbicide. Down-regulation of DNA replication genes and up-regulation of abscisic acid pathway genes were observed. Study further reveals the role of cytochrome P450, xyloglucan endotransglucosylase/hydrolase, glutamate dehydrogenase, methyl crotonoyl carboxylase and of thaumatin-like genes in herbicide resistance. Conclusion Reported DEGs can be used as genomic resource for future discovery of candidate genes associated with herbicide tolerance. Reported markers can be used for future association studies in order to develop marker assisted selection (MAS) for refinement. In endeavour of chickpea variety development programme, these findings can be of immense use in improving productivity of chickpea germplasm.