Ambika B Gaikwad* and Akansha Bajpai
Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi-110012
*E-mail: [email protected]
Plants are the basic support system of life and therefore conservation of their genetic resources for sustainable use to feed tomorrow’s population is of utmost importance. The genome is an organism’s complete set of DNA. The omics era has brought forth ‘Genomics’ as an interdisciplinary field of biology relating to the structure, function, evolution, mapping, and editing of genomes. Genomics has a considerable role to play when it comes to management of the Plant Genetic Resources (PGR). The PGR describe variability within plants whether it comes from natural selection or through human intervention, over the time. Taking the way forward from the application of first generation DNA based markers such as Restriction Fragment Length Polymorphism (RFLP), to PCR based markers such as SSRs, to the recent breakthroughs in the sequencing based technologies, genomics has played a major role in the management of the plant genetic resources and their utilization (Figure 1).
Figure 1: Schematic representation of potential application of genomics in germplasm utilization (Wambugu et al., 2018)
Page | 121 Next generation sequencing technologies have revolutionized research by allowing an economic elucidation of the genome of any organism. Genome projects of any selected plant species encompass three major elements: DNA sequencing of whole genome, assembly of the reads representing genome, annotation and analysis of the assembled data. The technology has found application in many areas, and PGR management is not an exception. Crop germplasm resources are the raw material for crop improvement programs leading to development of varieties that fulfil the food requirement of the world. Increased population, reduction in arable lands and environmental degradation combined with biotic and abiotic stresses and erosion of genetic pools have made sustainable exploitation of plant genetic resources a key to the new green revolution that aims towards higher productivity, lower inputs and improvement of human nutrition.
Assessment of genetic diversity is a prerequisite for analyzing as well as utilizing the variability occurring in a cultivated species and its wild and weedy relatives. At NBPGR, generation, validation and utilization of genomic resources is the major objective of the Division of Genomic Resources. These resources are utilized for value addition to the plant germplasm resources harbored in the gene bank and for generating molecular profiles varieties of agri- horticultural crops. The availability of NGS technologies has made possible analyzing a large number of genebank accessions thereby targeting maximum allelic variability. The combination of genomics and conventional genetic approaches has led to the development of
“genomics- based germplasm research” (GPGR) that encompasses the characterization and utilization of plant germplasm using these tools. The concept of development of a core collection that defines a minimum set of accessions capturing the maximum proportion of genetic diversity is primary to any genebank curator. Subsequent to the identification of a core collection based on morphological and geographical information, the use of molecular markers in further reducing the core to a minicore has been adopted as a strategy for many crops. Further characterization of the minicore to an applied core collection using the focused identification of germplasm strategy (FIGS) has been accelerated using the next generation sequencing technologies. These include characterization of the germplasm using low coverage sequencing strategies such as genotyping by sequencing (GBS) with the advantage that a large number of samples can be multiplexed at low cost inputs. The identification of high throughput Single nucleotide polymorphisms (SNPs) the ultimate molecular markers, through NGS, has facilitated the characterization of germplasm, particularly for crops like rice and wheat.
Gene discovery, the final goal of any breeding programme has been greatly accelerated through the genomics tools using map based, genome wide association studies (GWAS), allele-mining and comparative genomics approaches. The utilization of NGS technologies on the characterization of germplasm has opened up a plethora of information for the efficient and sustainable utilization of these invaluable resources.
Genomics thus has a wide application on the conservation and utilization of genetic resources and will restructure the way of managing gene banks. In addition to understanding the diversity
Page | 122 of plant species, genomics approaches enable studying gene duplication and identifying lateral gene transfer, one of the driving forces of evolution. The current genotyping and sequencing techniques and the value addition to the genebanks through the genomics approaches have thus minimized the challenges that limit germplasm utility.
References
Jia J, H Li, X Zhang, Z Li and L Qiu (2017) Genomics-based plant germplasm research (GPGR). The Crop Journal 5(2): 166-174.
Kilian B and A Graner (2012) NGS technologies for analyzing germplasm diversity in genebanks.
Briefings in functional genomics. 2(1): 38-50.
Mccouch SR, KL Mcnally, W Wang and RS Hamilton (2012) Genomics of gene banks: a case study in rice. American Journal of Botany 99(2): 407–423.
Tuberosa R, Graner A and Frison E. (2014). Genomics of Plant Genetic Resources: Volume 1.
Managing, sequencing and mining genetic resources. Springer. DOI: 10.1007/978-94-007- 7572-5.
Wambugu P W, Ndjiondjop M and Henry R J. (2018). Role of genomics in promoting the utilization of plant genetic resources in gene banks. Briefings in Functional Genomics. 17(3), 2018, 198–
206.
Warthmann N (2017) Plant genetic resources and genomics: Mainstreaming agricultural research through genomics. The national treaty on plant genetic resources for food and agriculture, FAO. http://www.planttreaty.org/content/background-study-paper-5.
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