Rice is one of the important crops grown worldwide and is considered as an important crop for global food security. Rice is being affected by various fungal, bacterial and viral diseases resulting in huge yield losses every year. Deployment of resistance genes in various crops is one of the important methods of disease management. However, identification, cloning and characterization of disease resistance genes is a very tedious effort. To increase the life span of resistant cultivars, it is important to understand the molecular basis of plant host–pathogen interaction. With the advancement in rice genetics and genomics, several rice varieties resistant to fungal, bacterial and viral pathogens have been developed. However, resistance response of these varieties break down very frequently because of the emergence of more virulent races of the pathogen in nature. To increase the durability of resistance genes under field conditions, understanding the mechanismof resistance response and its molecular basis should be well understood. Some emerging concepts like interspecies transfer of pattern recognition receptors (PRRs) and transgenerational plant immunitycan be employed to develop sustainable broad spectrum resistant varieties of rice.

Here, we present the draft genome (377.3 Mbp) of Corchorus olitorious cv. JRO-524 (Navin), which is a leading dark jute variety developed from a cross between African (cv. Sudan Green) and indigenous (cv. JRO-632) types. We predicted from the draft genome a total of 57,087 protein-coding genes with annotated functions. We identified a large number of 1765 disease resistance-like and defense response genes in the jute genome. The annotated genes showed the highest sequence similarities with that of Theobroma cacao followed by Gossypium raimondii. Seven chromosome-scale genetically anchored pseudomolecules were constructed with a total size of 8.53 Mbp and used for synteny analyses with the cocoa and cotton genomes. Like other plant species, gypsy and copia retrotransposons were the most abundant classes of repeat elements in jute. The raw data of our study are available in SRA database of NCBI with accession number SRX1506532. The genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession LLWS00000000, and the version described in this paper will be the first version (LLWS01000000).

Mango (Mangifera indica L.) is called “king of fruits” due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties ‘Neelam’, ‘Dashehari’ and their hybrid ‘Amrapali’ using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango.

Pigeonpea (Cajanus cajan L.), a protein-rich legume, is a major food component of the daily diet for residents in semi-arid tropical regions of the word. Pigeonpea is also known for its high level of tolerance against biotic and abiotic stresses. In this regard, understanding the genes involved in stress tolerance has great importance. In the present study, identification, and characterization of WRKY, a large transcription factor gene family involved in numerous biological processes like seed germination, metabolism, plant growth, biotic and abiotic stress responses was performed in pigeonpea. A total of 94 WRKY genes identified in the pigeonpea genome were extensively characterized for gene-structures, localizations, phylogenetic distribution, conserved motif organizations, and functional annotation. Phylogenetic analysis revealed three major groups (I, II, and III) of pigeonpea WRKY genes. Subsequently, expression profiling of 94 CcWRKY genes across different tissues like root, nodule, stem, petiole, petal, sepal, shoot apical meristem (SAM), mature pod, and mature seed retrieved from the available RNAseq data identified tissue-specific WRKY genes with preferential expression in the vegetative and reproductive stages. Gene co-expression networks identified four WRKY genes at the center of maximum interaction which may play a key role in the entire WRKY regulations. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) expression analysis of WRKY genes in root and leaf tissue samples from plants under drought and salinity stress identified differentially expressed WRKY genes. The study will be helpful to understand the evolution, regulation, and distribution of the WRKY gene family, and additional exploration for the development of stress tolerance cultivars in pigeonpea and other legumes crops.

Grain Amaranth is the most promising C₄ dicotyledonous pseudocereal and is distributed globally. It has an excellent nutritional profile and adaptability against a broad range of environmental factors. These traits have renewed the interest of researchers and breeders in exploring this underutilized orphan crop. The present study aimed to validate the genome-wide SSR to assess the genetic diversity among 94 Amaranthus hypochondriacus accessions using 57 genomic SSR (g-SSR) markers developed in-house. A total of 36 g-SSRs were recorded as polymorphic and amplified 138 alleles, with an average of 3.83 alleles per locus. Major allele frequency ranged from 0.29 to 0.98, with an average of 0.63 per marker. The expected heterozygosity ranged from 0.03 to 0.81, with an average of 0.46 per locus. Polymorphism information content (PIC) ranged from 0.03 to 0.79, with an average of 0.40, indicating a high level of polymorphism across amaranth accessions. Population structure analysis resulted into two major genetic clusters irrespective of their geographical origin, which suggests there may be sharing of common genomic regions across the accessions. High allelic frequency and heterozygosity levels indicate significant genetic variability in the germplasm, which can be further used in future breeding programs.