B Singh

CRISPR/Cas9: a promising way to exploit genetic variation in plants

Creation of variation in existing gene pool of crop plants is the foremost requirement in crop improvement programmes. Genome editing is a tool to produce knock out of target genes either by introduction of insertion or by deletion that disrupts the function of a specific gene. The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) system is the most recent addition to the toolbox of sequence-specific nucleases that includes ZFNs and TALENs. The CRISPR/Cas9 system allows targeted cleavage of genomic DNA guided by a small noncoding RNA, resulting in gene modifications by both non-homologous end joining and homology-directed repair mechanisms. Here, we present an overview of mechanisms of CRISPR, its potential roles in creating variation in germplasm and applications of this novel interference pathway in crop improvement. The availability of the CRISPR/Cas9 system holds promise in facilitating both forward and reverse genetics and will enhance research in crops that lack genetic resources.

SSR and morphological trait based population structure analysis of 130 diverse flax (Linum usitatissimum L.) accessions

A total of 130 flax accessions of diverse morphotypes and worldwide origin were assessed for genetic diversity and population structure using 11 morphological traits and microsatellite markers (15 gSSRs and 7 EST-SSRs). Analysis performed after classifying these accessions on the basis of plant height, branching pattern, seed size, Indian/foreign origin into six categories called sub-populations viz. fibre type exotic, fibre type indigenous, intermediate type exotic, intermediate type indigenous, linseed type exotic and linseed type indigenous. The study assessed different diversity indices, AMOVA, population structure and included a principal coordinate analysis based on different marker systems. The highest diversity was exhibited by gSSR markers (SI=0.46; He=0.31; P=85.11). AMOVA based on all markers explained significant difference among fibre type, intermediate type and linseed type populations of flax. In terms of variation explained by different markers, EST-SSR markers (12%) better differentiated flax populations compared to morphological (9%) and gSSR (6%) markers at P=0.01. The maximum Neis unbiased genetic distance (D=0.11) was observed between fibre type and linseed type exotic sub-populations based on EST-SSR markers. The combined structure analysis by using all markers grouped Indian fibre type accessions (63.4%) in a separate cluster along with the Indian intermediate type (48.7%), whereas Indian accessions (82.16%) of linseed type constituted an independent cluster. These findings were supported by the results of the principal coordinate analysis. Morphological markers employed in the study found complementary with microsatellite based markers in deciphering genetic diversity and population structure of the flax germplasm.

Abiotic Stress Responsive miRNA-Target Network and Related Markers (SNP, SSR) in Brassica juncea

Abiotic stress is one of the major factors responsible for huge yield loss in crop plants. MicroRNAs play a key role in adaptive responses of plants under abiotic stress conditions through post-transcriptional gene regulations. In present study, 95 potential miRNAs were predicted in Brassica juncea using comparative genomics approach. It was noted that these miRNAs, target several transcription factors (TFs), transporter family proteins, signaling related genes, and protease encoding genes. Nineteen distinct miRNA-target regulatory networks were observed with significant involvement in regulation of transcription, response to stimulus, hormone and auxin mediated signaling pathway related gene ontology (GO) term. The sucrose-starch metabolism and pentose-gluconate interconversion pathways were found significantly enriched for these target genes. Molecular markers such as Simple Sequence Repeats (SSR) and Single Nucleotide Polymorphism (SNPs) were identified on miRNAs (miR-SSRs and miR-SNPs) and their target genes in B. juncea. Notably, one of the miR-SNP (C/T) was found at the 5th position on mature region of miR2926. This C/T transition led to the distorted and unstable hairpin structure of miR2926, consequently complete loss of target function. Hence, findings from this study will lay a foundation for marker assisted breeding for abiotic stress tolerant varieties of B. juncea.

Perceived Effectiveness of Indigenous Technological Knowledge (ITK) of Insect and Vertebrate Pests Management in Eastern Uttar Pradesh, India

Abstract Indigenous technological knowledge is considered as a traditional knowledge that inherited from their ancestors, unique to a culture, society and environment. In this article we documented uses of such local knowledge used by the local farmers of seven villages form Varanasi, Deoria and Mirzapur districts of eastern Uttar Pradesh, India for their crop protection. Data were collected from 140 respondents (twenty from each village) and 60 respondents who had visited the institute from these three districts during farmers’ fair and farmers’ training and whole making a total of 200 respondents. The farmers in the study developed notable innovations to control major pests of agricultural and horticultural crops such as use of ashes to control vegetable insect pests; use of onion/garlic bulbs, neem leaves, salt crystals, wheat straw, brick kiln powder etc. to prevent store grain pests of cereals; ash and kerosene mixture to repel the sucking pests of rice at milky stage; well-rotted fish scales against Nilgai (Boselaphus tragocamelus); red chilli pods against bruchids in pulses; salt and turmeric powder mixture against ants; use of neem cake to repel termite and other soil insects etc. The local farmers were following these practices because of easy availability, eco-friendly, easy to handle, do not leave any harmful residue, pose any threat to develop resistance and resurgence of secondary pests, easy to apply and compatible with other pest management techniques and socio-cultural situation of the farmers.

Recent Perspective of Next Generation Sequencing: Applications in Molecular Plant Biology and Crop Improvement

Nearly after three decades of Sanger sequencing method dominating the field of nucleotide sequencing, the new age of novel sequencing techniques commenced with 454-pyrosequencing in the year 2005 and thus started the era of next generation sequencing techniques. Since then many other novel sequencing techniques with increased accuracy, simplicity and cost-effectiveness have come up and called next to next generation sequencing techniques or third generation sequencing techniques. The scientific knowledge generated from next generation sequencing techniques has transformed the field of structural and functional genomic studies in different crop plants. In this review, various next generation sequencing techniques are described, with their applications and future prospective.

Ovule Fertility and Seed Set in Oilseed Brassicas

Present study illustrates the effect of number of ovules/gynoecium and their fertility on seed yield in oilseed Brassicas. Amongst the nine different species of the family Brassicaceae analyzed, the maximum number of ovules/gynoecium was recorded in Brassica napus (2830) followed by Eruca sativa (22–24), B. carinata (20–22) and B. juncea cv. Geeta (18–20), while the minimum was observed in Crambe abyssinica (01). The number of seeds developed in each siliqua was in accordance with the number of fertilized embryo sacs, indicating little or no embryo abortion during seed development. Moreover, it was also revealed that the number of ovules with embryo sac is more closely correlated to ovule fertility than to the number of ovules/gynoecium. The observation indicates that ovule fertility, rather than the number of ovules/gynoecium, determines seed yield in oilseed Brassicas.