Akshay Nag

Next Generation Sequencing Technologies: The Doorway to the Unexplored Genomics of Non-Model Plants

Non-model plants i.e., the species which have one or all of the characters such as long life cycle, difficulty to grow in the laboratory or poor fecundity, have been schemed out of sequencing projects earlier, due to high running cost of Sanger sequencing. Consequently, the information about their genomics and key biological processes are inadequate. However, the advent of fast and cost effective next generation sequencing (NGS) platforms in the recent past has enabled the unearthing of certain characteristic gene structures unique to these species. It has also aided in gaining insight about mechanisms underlying processes of gene expression and secondary metabolism as well as facilitated development of genomic resources for diversity characterization, evolutionary analysis and marker assisted breeding even without prior availability of genomic sequence information. In this review we explore how different Next Gen Sequencing platforms, as well as recent advances in NGS based high throughput genotyping technologies are rewarding efforts on de-novo whole genome/transcriptome sequencing, development of genome wide sequence based markers resources for improvement of non-model crops that are less costly than phenotyping.

Genetic diversity of high-elevation populations of an endangered medicinal plant

Despite its wide distribution across the entire Himalayan range, the current status of Podophyllum hexandrum, a highly important anti-cancerous herb, remains endangered. Genetic diversity characterization of 24 populations comprising of 209 individuals representing the whole of the Indian Himalayas revealed that regardless of geographic location, all of the populations are intermixed and are composed broadly of two types of genetic populations. Our findings also suggested that these populations have evolved well in response to the environment. This study will help in the formulation of conservation programs for P. hexandrum populations in this region.

Prospects of Understanding the Molecular Biology of Disease Resistance in Rice

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.

Genetic diversity and population structure of endangered Aquilaria malaccensis revealed potential for future conservation

The endangered Aquilaria malaccensis, is an important plant with high economic values. Characterization of genetic diversity and population structure is receiving tremendous attention for effective conservation of genetic resources. Considering important repositories of biological diversity, the genetic relationships of 127 A. malaccensis accessions from 10 home gardens of three states of northeast India were assessed using amplified fragment length polymorphism (AFLP). Of the 1153 fragments amplified with four AFLP primer combinations, 916 (79.4%) were found to be polymorphic. Polymorphic information content (PIC) and marker index (MI) of each primer combination correlate significantly with the number of genotypes resolved. Overall, a high genetic diversity (avg. 71.85%) was recorded. Further, high gene flow (Nm: 3.37), low genetic differentiation (FST: 0.069) and high within population genetic variation (93%) suggests that most of the genetic diversity is restricted within population. Neighbour joining (NJ), principal coordinate analysis (PCoA) and Bayesian-based STRUCTURE grouped all the accessions in two clusters with significant intermixing between populations, therefore, revealed that two genetically distinct gene pools are operating in the A. malaccensis populations cultivated in home gardens. Based on the various diversity inferences, five diverse populations (JOH, FN, HLF, DHM and ITN) were identified, which can be potentially exploited to develop conservation strategies for A. malaccensis.

Functionally relevant novel microsatellite markers for efficient genotyping in Stevia rebaudiana Bertoni

Stevia rebaudiana Bertoni is a perennial herb that belongs to family Asteraceae. It produces rebaudioside which is one of the key components responsible for extraordinary sweetness of stevia. It produces steviol glycosides which are proved beneficial for diabetes type II patients and controlling blood pressure in hypertension patients (Hsieh et al. 2003; Gregersen et al. 2004). Moreover, stevia is a rich source of antioxidants, antimicrobial and antifungal compounds (Lemus-Mondaca et al. 2012), imparting great economic and commercial value to this crop. Stevia is indigenous to Central and South America (Brandle et al. 2002). However, it was introduced in the late 1990s in India. Selfincompatibility, poor-seed viability, low germination rates and entomophilous pollination are among the major challenges in management and genetic improvement of stevia through conventional breeding approaches (Mitra and Pal 2007). To date, population genetic analysis in S. rebaudiana has been performedusing arbitrary markers such as RAPD, AFLP and ISSRs (Yao et al. 1999; Heikal et al. 2008; Hassanen and Khalil 2013) which lead to underestimation of the recessive allele frequency in a population causing a bias in the estimates of genetic diversity and differentiation (Nybom 2004). Further, limitations such as low reproducibility rate, inability to detect heterozygous individual or/and locus nonspecificity, makes them less preferred markers (Kalia et al. 2011). In contrast, unigene derived microsatellite markers developed from public database, supersede other markers due to their codominant nature, hypervariability, genomewide occurrence, robustness and ability to establish

Morphological and molecular characterization revealed high species level diversity among cultivated, introduced and wild roses (Rosa sp.) of western Himalayan region

High level of genetic diversity and morphological variations were observed among and within the different Rosa species studied. The key traits which differentiated the species were nature of plant, habit, shape of prickles, shape of stipules, leaflet shape, type of leaf margin, vestiture of ventral side of leaflet and flower shape, whereas, traits for distinguishing the accessions within a species (as in case of accessions from western Himalayan region) were flower colour, petal number, shape of hip and hip colour. Some of the accessions from western Himalayan region formed out-groups (IHBT-WR-18, IHBT-WR-21, IHBT-WR-31and IHBT-WR-43B) and could not be classified at the species level. High degree of variations among the accessions of R. multiflora group as compared to variations among the accessions of R. moschata, R. brunonii and R. cathayensis, suggests high level of out-breeding in R. multiflora which may contribute to further variations. Desirable variations were observed for flower colour, petal number, lack of prickles, perpetual flowering, large flower diameter and large fruit size which contribute significantly to diversity of the roses and have potential use in breeding programs.