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Despite substantial efforts in the past decades towards the development of microsatellites or SSR (simple sequence repeat) markers in jute, there is still an urgent necessity for additional SSR markers for performing genetic and breeding investigations. The availability of reference genomic sequences for both diploid cultivated jute species enabled us to identify a total of 154,715 and 160,173 SSRs from the C. capsularis and C. olitorius genomes, respectively. 6,337 and 7,012 total SSRs with a density of 187.6 and 185.01 SSR/Mb were also mined in coding sequences (CDS). 12bp was the most common repeat length in both genomic and CDS. Di- and tetra-nucleotide motifs were prevailed in the genomic sequences, while trinucleotides in the CDS. SSR frequency declined with increasing repeat units in both species. ATT and AT motifs were the most common in the genome. AG and CTT were prevalent in the CDS of both species while GC and CGC motifs were infrequent. Further, we used the flanking sequences of identified SSRs (from both species) to design a total of 1,117 SSR primer pairs. Genetic diversity analysis based on 110 sampled SSRs in 24 genotypes displayed high polymorphism. The first physical map with 535 PCR-based polymorphic SSRs were constructed by taking C. capsularis as the reference genome. These resources will advance genetics and breeding research in jute.

Jute is an essential fibrous crop worldwide. However, salt- and drought-induced stresses affect its production. The complex inheritance for such traits makes Quantitative Trait Loci (QTL) detection cumbersome when using the approach to understand and improve the plant’s tolerance to these stresses. There is a need to identify the underlying mechanistic events under these stress conditions at the seedling stage. Therefore, this study uses genetic and transcriptomic approaches to identify the markers, QTL and candidate genes related to salt and drought tolerance in jute. We also analyzed some phenotypes, including dry root weight (DRW), dry shoot weight (DSW), root fresh weight (RFW), root length (RL), relative water content (RWC), shoot fresh weight (SFW) and Shoot length (SL). One hundred (100) recombinant inbred lines (RILs) of the white Jute and the parents were evaluated under control, salt and drought conditions. Analysis of variance indicates significant differences (p

Kenaf (Hibiscus cannabinus L.) is an important bast fiber crop, and a source of fiber to many industries. This crop is diploid (2n = 2x = 36) in nature, and belongs to Malvaceae family. Kenaf breed...

Soil salinization is a serious agricultural issue that is severely affecting crop production across the world. Salt induced stresses are mainly included osmotic and ionic stresses, which could lead to other stresses e.g., oxidative stress in plants. The evolved plant mechanisms in salt tolerance are categorized into osmotic tolerance and ionic homeostasis mediated by ion exclusion and ions sequestration into vacuole. Osmotic tolerance involves long-distance signaling which still has many unknowns in crops, while ionic homeostasis is achieved by Na+/K+/H+ transporters and H+-pumps. Besides, the mechanisms of salt tolerance are regulated by various signaling pathways and transcription factors. A better understanding on the mechanisms of salt tolerance and its involved candidate genes is a prerequisite for increasing/maintaining yield potential of crops in saline soils. This review focuses on various mechanisms, signaling pathways and transcriptional regulations of salt tolerance in crops. We also review the various examples of underlying candidate genes that have been engineered to develop the salt tolerant crops, and may also have worth in next crop breeding.

Association mapping (AM) is an approach that accounts for thousands of polymorphisms to evaluate the effects of quantitative trait loci (QTL). It is an important instrument for identification of alleles and new genes as well as dissection of complex characters. AM is more advantageous than linkage analysis due to the comparatively high-resolution provided, which is based on the structure of linkage disequilibrium (LD). Marker density, population, sample sizes and population structure are among the critical factors that should be considered when AM is used. It is necessary to note that, the choice of germplasm, genotypic and phenotypic data quality, the use of appropriate statistical analysis for marker-phenotype association detections and verifications are key to association analysis. Great potentials to enhance crop genetic improvement are offered by AM. However, to understand its application, extensive research is needed, such as improvements in computational and statistical methods and its integration with gene annotation data or functional analysis. Statistical apparatuses that are user-friendly and genetic resources are also needed and must be enhanced. Rare allele/variant analysis is an important area to be considered to enhance AM studies. Joint linkage association mapping has now been proposed to improve linkage-based QTL mapping and AM limitations. In the future, new candidate genes and QTL can be easily identified if genome-wide association studies (GWAS) are combined with functional genomics. As such, this review describes association mapping, its utilization in plant breeding, limitations as well as advantages over linkage mapping.

Background: The jute plant is of great significance and economic relevance to humanity, but its production has been hindered due to abiotic influences, especially salt stress. Hitherto, the molecular bases for this vital feature await future exploration. The abscisic acid (ABA) signaling pathway comprises many regulated genes and plays a role in plant response to stress, however, a balance between the multiple pathways is always needed for any plant developmental process. In this study, we used a transcriptomic approach to unveil the molecular bases behind this trait. Salt tolerant (J194) and sensitive (J7) germplasms were subjected to sodium chloride (NaCl) stress at a different time point, from which leaf and roots samples were taken for transcriptome analyses. Result: The plant hormone signal transduction pathway was the most abundant observed in the study; the Pyrrolysine (PYL) gene (Cc.03G0016680) was up-regulated, which supports the basic model of abscisic acid (ABA). The quantitative reverse transcription-PCR (qRT –PCR) and the correlation analysis validated the Ribonucleic acid sequence (RNA-seq) results. The candidate genes’ relative expression level was higher in J194, especially in protein phosphate 2C (PP2C). Corchorus capsularis PP2C gene family revealed 38 members, phylogenetic analysis categorized PP2C into 15 based upon conserved domains. Eleven conserved motifs were identified, and most of the genes had the same number of conserved motifs. The exon-intron ranges of (3-21) and (2-20), respectively. Moreover, among the plant hormone signal transduction pathway PP2C genes, Cc.03G0016550 and Cc.07G0028160 were up-regulated in J194 root tissues at 6-hour exposure NaCl, as such recommended to be salt-tolerant candidature genes. It was noted that most of the Corchorus capsularis PP2C genes were involved from segmental duplication, and analysis of the key stress marker salt-tolerant PP2C genes validated the salt tolerance individuals. Conclusion: These results provided valuable insight into salt tolerance transcriptome and indicated that PP2C had provided a stepping-stone to the molecular mechanism in Corchorus capsularis. Furthermore, differentially expressed genes, motifs, gene structure, and the chromosomal location of salt tolerance candidate genes might have experienced functional divergence. As such, their further study will enhance salt tolerance in Corchorus capsularis.

For survival in the surrounding environment, plants have to acclimatize to environmental stresses through proper identification and response to stress signals. Understanding these plant responses is indispensable for all efforts aimed at sustainable crop production. An important feature of plant response to stress signals is the modulation of transcript level. Due to the progress in high-throughput sequencing techniques during recent past, long noncoding RNAs (lncRNAs) have earned far-reaching attention. As significant regulators of biological processes, lncRNAs have been employed in a comprehensive range of disease control and developmental pathways. However, knowledge about lncRNAs’ importance for stress tolerance in plants is limited. We have reviewed recent developments on various aspects of lncRNAs during the response to biotic stresses, and in this chapter, we also discussed some workable future research areas.

Microbial pathogens attack every plant tissue, including leaves, roots, shoots, and flowers during all growth stages. Thus, they cause several diseases resulting in a plant's failure or loss of the whole crop in severe cases. To combat the pathogens attack, plants produce some biologically active toxic compounds known as saponins. The saponins are secondary metabolic compounds produced in healthy plants with potential anti-pathogenic activity and serve as potential chemical barriers against pathogens. Saponins are classified into two major groups the steroidal and terpenoid saponins. Here, we reported the significance of saponin toxins in the war against insect pests, fungal, and bacterial pathogens. Saponins are present in both cultivated (chilies, spinach, soybean, quinoa, onion, oat, tea, etc.) and wild plant species. As they are natural toxic constituents of plant defense, breeders and plant researchers aiming to boost plant imm unity should focus on transferring these compounds in cash crops.

Different types of molecular approaches have been used for improving resistance against pathogens to secure food. Efficient and advanced genome editing tool as paralleled to earlier techniques like Zinc Finger Nuclease (ZFN), transcription activator-like effector nucleases (TALENs), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR). The approach of CRISPR/Cas9 has updated our abilities of genetic manipulation in many crops. The assembly of purposes that can be achieved through CRISPR/Cas9 and its related products make it a powerful system that will expose novel prospects in the complex domain of plant-pathogen interactions and will help to develop crop resistance against pathogens. CRISPR/Cas9 engineering permits DNA endonuclease guided by an RNA for a range of genome engineering applications across various eukaryotic species and provides an effective platform to create resistance against bacteria, viruses, insects, and fungi. In this review, we discuss CRISPR-Cas9 engineered crop plants resistant to specific pathogens.