Discovering the regulators of heat stress tolerance in Ziziphus nummularia (Burm.f) wight and walk.-arn.

Ziziphus nummularia an elite heat-stress tolerant shrub, grows in arid regions of desert. However, its molecular mechanism responsible for heat stress tolerance is unexplored. Therefore, we analysed whole transcriptome of Jaisalmer (heat tolerant) and Godhra (heat sensitive) genotypes of Z. nummularia to understand its molecular mechanism responsible for heat stress tolerance. De novo assembly of 16,22,25,052 clean reads yielded 276,029 transcripts. A total of 208,506 unigenes were identified which contains 4290 and 1043 differentially expressed genes (DEG) in TGO (treated Godhra at 42 °C) vs. CGO (control Godhra) and TJR (treated Jaisalmer at 42 °C) vs. CJR (control Jaisalmer), respectively. A total of 987 (67 highly enriched) and 754 (34 highly enriched) pathways were obsorved in CGO vs. TGO and CJR vs. TJR, respectively. Antioxidant pathways and TFs like Homeobox, HBP, ARR, PHD, GRAS, CPP, and E2FA were uniquely observed in Godhra genotype and SET domains were uniquely observed in Jaisalmer genotype. Further transposable elements were highly up-regulated in Godhra genotype but no activation in Jaisalmer genotype. A total of 43,093 and 39,278 simple sequence repeats were identified in the Godhra and Jaisalmer genotypes, respectively. A total of 10 DEGs linked to heat stress were validated in both genotypes for their expression under different heat stresses using quantitative real-time PCR. Comparing expression patterns of the selected DEGs identified ClpB1 as a potential candidate gene for heat tolerance in Z. nummularia. Here we present first characterized transcriptome of Z. nummularia in response to heat stress for the identification and characterization of heat stress-responsive genes. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-024-01431-y.

Degradation dynamics, correlations, and residues of carfentrazone-ethyl, fenoxaprop-p-ethyl, and pinoxaden under the continuous application in the wheat field.

Weed infestation is a major biotic limitations in wheat cultivation; thus, various herbicides are being applied to control these weeds. Therefore, this study was undertaken for two successive years to assess degradation behaviours, persistence and residue risk imposed by carfentrazone, fenoxaprop-p-ethyl and pinoxaden sprayed as post-emergence herbicides in the wheat crop for management of weeds. Soil and crop samples were collected at periodically at after two hour of herbicide application till harvest of wheat crop and analysed by a high-performance liquid chromatograph. Degradation of carfentrazone, pinoxaden and fenoxaprop-p-ethyl, in the soil of wheat field occurred rapid to moderately with the mean half-life 9.92, 11.7 and 11.8 days, respectively. Persistence was found to be dependent on the weather parameters as well as physicochemical properties of the soil and herbicides. Half-life of studied herbicides was found to be negatively correlated with persistence (R2 0.38, p = 0.05, n = 3) and vapour pressure (R2 0.99, p = 0.05, n = 3). Principal component analysis revealed that the first two Principal Components (PCs) had eigenvalues more than 1, and the first and second PCs contributed 77.4 and 22.6% in herbicide residues and different parameters variation, respectively. Terminal residues of carfentrazone, pinoxaden and fenoxaprop-p-ethyl in the wheat straw, grains and soil were found below the maximum residue limits. Owing to the moderate persistence under wheat field conditions, carfentrazone, pinoxaden and fenoxaprop-p-ethyl are supposed to be safe for control of weeds in wheat crop and hence, suspected risk on the human and environment or crop produce under evaluated doses is negligible.

Status and Prospects of Next Generation Sequencing Technologies in Crop Plants.

The history of DNA sequencing dates back to 1970s. During this period the two first generation nucleotide sequencing techniques were developed. Subsequently the Sanger's dideoxy method of sequencing gained popularity over Maxam and Gilbert's chemical method of sequencing. However, in the last decade, we have observed revolutionary changes in DNA sequencing technologies leading to the emergence of next-generation sequencing (NGS) techniques. NGS technologies have enhanced the throughput and speed of sequencing combined with bringing down the overall cost of the process over a time. The major applications of NGS technologies being genome sequencing and resequencing, transcriptomics, metagenomics in relation to plant-microbe interactions, exon and genome capturing, development of molecular markers and evolutionary studies. In this review, we present a broader picture of evolution of NGS tools, its various applications in crop plants, and future prospects of the technology for crop improvement.

Identification of long non-coding RNA in rice lines resistant to Rice blast pathogen Maganaporthe oryzae.

Rice blast disease caused by a fungus Magnaporthae oryzae is one of the most important biotic factors that severely damage the rice crop. Several molecular approaches are now being applied to tackle this issue in rice. It is of interest to study long non-coding RNA (lncRNA) in rice to control the disease. lncRNA, a non-coding transcript that does not encode protein, is known to play an important role in gene regulation of various biological processes. Here we describe a computational pipeline to identify lncRNA from a resistant rice line. The number of lncRNA found in resistant line was 1429, 1927 and 1981 in mock and M. oryzae (ZB13 and Zhong) inoculated samples, respectively. Functional classification of these lncRNA reveals a higher number of long intergenic non-coding RNA compared to antisense lncRNA in both mock and M. oryzae inoculated resistant rice lines. Many intergenic lncRNA candidates were identified from resistant rice line and their role to regulate the resistance mechanism in rice during M. oryzae invasion is implied.

A web-based microsatellite database for the Magnaporthe oryzae genome.

Microsatellites have been widely utilized for molecular marker development. Codominant and multiallelic nature of these simple repeats have several advantages over other types of molecular markers. Their broad applicability in the area of molecular biology like gene mapping, genome characterization, genome evolution, and gene regulation has been reported in various crop plants, animals and fungi. Considering these benefits of the SSR markers, a MMDB (Magnaporthe oryzae Microsatellite Database) was developed to help in understanding about the pathogen and its diversity at strains level of a particular geographic region, which can help us to make a proper utilization of blast resistance genes in the region. This microsatellite database is based on whole genome sequence of two M. oryzae isolates, RML-29 (2665 SSRs from 43037792 bp) and RP-2421 (3169 SSRs from 45510614 bp). Although, first M. oryzae genome (70-15) was sequenced in 2005, but this sequenced isolate is not a true field isolate of M. oryzae. Therefore, MMDB has great potential in the study of diversification and characterization of M. oryzae and other related fungi. AVAILABILITY: http://14.139.229.199/home.aspx.