Romesh Kumar Salgotra

Genomic Selection in the Era of Next Generation Sequencing for Complex Traits in Plant Breeding

Genomic selection (GS) is a promising approach exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. In plant breeding, it provides opportunities to increase genetic gain of complex traits per unit time and cost. The cost-benefit balance was an important consideration for GS to work in crop plants. Availability of genome-wide high-throughput, cost-effective and flexible markers, having low ascertainment bias, suitable for large population size as well for both model and non-model crop species with or without the reference genome sequence was the most important factor for its successful and effective implementation in crop species. These factors were the major limitations to earlier marker systems viz., SSR and array-based, and was unimaginable before the availability of next-generation sequencing (NGS) technologies which have provided novel SNP genotyping platforms especially the genotyping by sequencing. These marker technologies have changed the entire scenario of marker applications and made the use of GS a routine work for crop improvement in both model and non-model crop species. The NGS-based genotyping have increased genomic-estimated breeding value prediction accuracies over other established marker platform in cereals and other crop species, and made the dream of GS true in crop breeding. But to harness the true benefits from GS, these marker technologies will be combined with high-throughput phenotyping for achieving the valuable genetic gain from complex traits. Moreover, the continuous decline in sequencing cost will make the WGS feasible and cost effective for GS in near future. Till that time matures the targeted sequencing seems to be more cost-effective option for large scale marker discovery and GS, particularly in case of large and un-decoded genomes.

Genetic Diversity and Population Structure of Basmati Rice (Oryza sativa L.) Germplasm Collected from North Western Himalayas Using Trait Linked SSR Markers

One hundred forty one basmati rice genotypes collected from different geographic regions of North Western Himalayas were characterized using 40 traits linked microsatellite markers. Number of alleles detected by the abovementioned primers were 112 with a maximum and minimum frequency of 5 and 2 alleles, respectively. The maximum and minimum polymorphic information content values were found to be 0.63 and 0.17 for the primers RM206 and RM213, respectively. The genetic similarity coefficient for the most number of pairs ranged between of 0.2-0.9 with the average value of 0.60 for all possible combinations, indicating moderate genetic diversity among the chosen genotypes. Phylogenetic cluster analysis of the SSR data based on distance divided all genotypes into four groups (I, II, III and IV), whereas model based clustering method divided these genotypes into five groups (A, B, C, D and E). However, the result from both the analysis are in well agreement with each other for clustering on the basis of place of collection and geographic region, except the local basmati genotypes which clustered into three subpopulations in structure analysis comparison to two clusters in distance based clustering. The diverse genotypes and polymorphic trait linked microsatellites markers in the present study will be used for the identification of quantitative trait loci/genes for different economically important traits to be utilized in molecular breeding programme of rice in the future.

Plant Genetic Resources and Traditional Knowledge for Food Security

Genetic resources and indigenous/traditional knowledge are the major resources on which human being has relied for their very livelihood and their demand will increase in the future due to increase in global population. The relation between plant genetic resources and traditional knowledge is of recent origin. Plant genetic resources are the heritable materials contained within and among plant species of present and potential value. On the other hand, traditional/indigenous knowledge is the outcome of intellectual practice in a traditional perspective. The genetic resources and indigenous knowledge protect biological resilience that exists in a natural way. The problems of food security are of global signifi cance and are further compounded by precedential increase in world population resulting in over-exploitation of genetic resources and diversity. Nevertheless, these resources are lost at alarming rates due to anthropogenic effects such as climate change, pollution, genetic erosion, gross mismanagement of these resources and population growth. A vast amount of genetic resources are threatened and endangered, and some have even gone extinct due to genetic erosion and environmental changes. In order to meet current global challenges, it is obligatory for all nations and institutions to discover, collect and conserve potentially valuable plant genetic resource and traditional knowledge and utilise them sustainably. R. K. Salgotra , Ph.D. (*) School of Biotechnology , Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu , Jammu 180009 , Jammu and Kashmir , India e-mail: rks_2959@rediffmail.com 1 B. B. Gupta , Ph.D. Division of Plant Breeding and Genetics , Sher-eKashmir University of Agricultural Sciences and Technology of Jammu , Chatha, Jammu 180009 , Jammu and Kashmir , India e-mail: dr_bbgupta@ymail.com

Plant-Bacterial Partnership: A Major Pollutants Remediation Approach

Environmental pollution due to global industrialization and urbanization has become a serious matter of concern for human inhabitants throughout the world. As safety point of human health and environmental issues, it required an efficient removal for the sake of minimized inlet of these hazard materials into the food chain generated by organic and inorganic pollutants. The physical and chemical means need specialized equipment, labor intensive and highly costs inputs which make less familiar to remove the pollutants, but it seems biological methods especially phytoremediation, gaining comprehensive remedial measure approach. The green technology based Phytoremediation carried out the process with the help of altogether action of plants and their specific attached microbial communities to remove, transform, degrade or immobilize various toxic organic and inorganic contaminants deposits in soil and polluted water and air pollutants could be treated well with this approach which is nowadays publicly high acclaimed, less disturbance to the environment remediate various form of pollutants and lower cost investment input. The symbiotic nature of plants combination with related beneficial bacteria (rhizobacteria or endophytic) offers tremendous potential as bacteria possess set of catabolic genes which produce catabolic enzymes to decontaminate complex organic compounds and inorganic pollutants with an effective way and in return of these bacteria increase plant growth promoting activities and gain more biomass in the plants. This chapter highlighted the remediation approach of major pollutants by phytoremediation with the main focal point on rhizoremediation and plant-bacterial partnerships and discuss how to improve the efficiency of phytoremediation by various approaches.

Genetic Engineering and Environmental Risk

Genetic engineering in today’s world is gaining much importance. It provides plant varieties with good agronomic characteristics, superior quality values and expressing traits of agricultural interest such as insect resistance and herbicide tolerance. The production and use of genetically modified organisms (GMO’s) is increasing steadily. There are various techniques by which genetic modified crops can be developed. But the issue still remains; whether altering genetic structure of any organism is ethical, will it create any problem to the people who consume it. Therefore, it is important to examine both pros and cons of genetic engineering and to determine whether this technology have place in a future. There are lots of controversies regarding the safety issue of GM crops and labeling of GMO products. Environmental risk assessment is a structural approach use to analyze the risk associated with GM crops. The goal of the risk assessment is to identify, characterize and evaluate risks by considering a wide range of potential pathways through which harm might occur. The assessment evaluates any risks posed by the genetic engineered (GE) plant in comparison to the risks posed by non-GE plant.

CRISPR/Cas approach: A new way of looking at plant-abiotic interactions

It is not the most grounded of the species that survive, nor the most shrewd, however one most receptive to change. Crop plants being sessile are subjected to various abiotic stresses resulting significant yield losses about an average of more than 50 percent, thus greatly threatening the global crop production. In this regard, plant breeding innovations and genetic engineering approaches have been used in the past for generating stress tolerant crop genotypes, but due to complex inheritance of abiotic stress tolerance these approaches are not enough to bring significant trait improvement and to guarantee worlds future sustenance security. Although, RNA interference (RNAi) technology has been utilized amid the most recent decades to produce plants tolerant to environmental stress. But this technique ordinarily prompts to down-regulate as opposed to complete inhibition of target genes. Therefore, scientist/researchers were looking for techniques that should be efficient, precise and reliable as well as have potential to solve the issues experienced by previous approaches, and hence the CRISPR/Cas system came into spotlight. Although, only few studies using CRISPR/Cas approach for targeting abiotic stress tolerance related genes have been reported, but suggested its effective role for future applications in molecular breeding to improve abiotic stress tolerance. Hence, genome engineering via CRISPR-Cas system for targeted mutagenesis promise its immense potential in generating elite cultivars of crop plants with enhanced and durable climate resilience. Lastly, CRISPR-Cas will be future of crop breeding as well as to target minor gene variation of complex quantitative traits, and thus will be the key approach to release global hunger and maintain food security.

Plant Genetic Resources and Traditional/Indigenous Knowledge: Potentials and Challenges

Genetic resources and indigenous/traditional knowledge are the major resources on which human being has relied for their very livelihood and their demand will increase in the future due to increase in global population. The relation between plant genetic resources and traditional knowledge is of recent origin. Plant genetic resources are the heritable materials contained within and among plant species of present and potential value. On the other hand, traditional/indigenous knowledge is the outcome of intellectual practice in a traditional perspective. The genetic resources and indigenous knowledge protect biological resilience that exists in a natural way. The problems of food security are of global significance and are further compounded by precedential increase in world population resulting in over-exploitation of genetic resources and diversity. Nevertheless, these resources are lost at alarming rates due to anthropogenic effects such as climate change, pollution, genetic erosion, gross mismanagement of these resources and population growth. A vast amount of genetic resources are threatened and endangered, and some have even gone extinct due to genetic erosion and environmental changes. In order to meet current global challenges, it is obligatory for all nations and institutions to discover, collect and conserve potentially valuable plant genetic resource and traditional knowledge and utilise them sustainably.

Rational of Participatory Approaches for the Management of Plant Genetic Resources and Traditional Knowledge

For timely and successful diffusion of any agro-technique to the farming communities, the participatory approach is one of the options. In participatory approach, the researchers can reach to number of farmers for diffusion of agricultural technology with in a period of time. Now participatory approaches are becoming the integral part of the researchers for diffusion of any technology. For conservation and sustainable utilisation of PGR and TK, participatory approaches play a significant role. The genetic diversity of crop species can be enhanced by conserving the PGR and TK through formal institutions and the farming communities. In developing countries, farmers are the main elements in the conservation of PGR and production of agricultural crops. The women also play a major role in the selection of plant species, their preservation and sustainable utilisation. Although women are not involved in policymaking and to take decisions, they play a main role identification of crop genetic resources for household uses and their conservation. Through participatory approaches, farmers are encouraged to take part in the selection of new varieties by using their own experiences. They can interact with the researchers freely while selecting the suitable crop genetic resources. Both participatory varietal selection and participatory plant-breeding approaches encourage the farming communities for active involvement in the selection of new genotypes from the developed and the segregating genetic materials. The farmers select the genetic material for conservation and use depending upon their need and to secure the food security.