Molecular markers for characterization and conservation of plant genetic resources

AEJAZ AHMAD DAR; REETIKA MAHAJAN; SUSHEEL SHARMA

doi:10.56093/ijas.v89i11.95286

Authors

AEJAZ AHMAD DAR National Post Doctorate Fellow, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu 180 009, India
REETIKA MAHAJAN Senior Research Fellow, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu 180 009, India
SUSHEEL SHARMA Assistant Professor, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu 180 009, India

https://doi.org/10.56093/ijas.v89i11.95286

Keywords:

AFLP, Conservation, DNA barcoding, Genetic Resources, Molecular markers, NGS, Phylogentic study, SSR

Abstract

For properly understanding the molecular basis of phenotypic variation, accelerating breeding programmes and exploiting genetic resources of a particular crop, there is a need to explore the genome of the crop. Earlier conventional methods (phenotyping) were used by the breeders for identification and conservation of genetic resource. The conventional method is laborious for assignment of known and unknown plant taxa. Thus, to overcome the limitation of the conventional method, scientists developed molecular marker systems for conservation of genetic resources. The main aim of using molecular markers is to detect genetic variation in DNA sequence within and among the species. Molecular markers also find their role in producing new sources of genetic variation by introduction of advanced and useful traits from related species. From last two decades, different molecular markers were used for genetic analysis of crops. These markers include hybridization based markers (RFLP), PCR based markers (RAPD, AFLP, SSR, ISSR, SCAR, SRAP, SCoT) and sequence based markers (SNP, DArT, NGS). Besides many genes in chloroplast, mitochondria and ribosomes act as molecular markers that are useful for the phylogenetic studies and DNA barcoding of plants. This review provides an overview of the different molecular systems and their utilization in improving crop yield and productivity and conserving genetic resources.

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References

Ahlawat S P S, Mandal A B and Pramanik S C. 2002. Integrated crop-livestock fish farming system for sustained production – Bay island perspective. (In) Proceedings of the National Symposium on Agriculture in Changing Global Scenario. (Eds) Gautam R C, Mishra B N, Shivkumar B G, Rai R K, Mishra S K and Garg R N. Indian Society of Agricultural Sciences, New Delhi.

Amjath-Babu T S and Kaechele H. 2015. Agricultural system transitions in selected Indian states: What do the related indicators say about the underlying biodiversity changes and economic trade-offs? Ecological Indicators 57: 171–81. DOI: https://doi.org/10.1016/j.ecolind.2015.04.029

ASG. 2015. Agricultural Statistics at a Glance 2014. Oxford University Press, New Delhi, India.

Ayyappan S and Arunachalam A. 2014. [Crop Diversification for Social Security of Farmer in India], pp. 1-6. (Eds) Rana D S and Singh A K). Indian Society of Agronomy, New Delhi.

Behera U K, Rautray S K and Sahoo P K. 2010. Farming system-based composite pisciculture in harvested pond water under eastern Indian situations. Journal of Soil and Water Conservation 9: 143–7.

Behera U K, Yates C M, Kebreab E and France J. 2008. Farming systems methodology for efficient resource management at the farm level: an Indian perspective. Journal of Agricultural Science, Cambridge 146: 493–505. DOI: https://doi.org/10.1017/S0021859608007995

Behera U K. 2018a. Development with Farm Development Card. ICAR News 24(2): 4–7.

Behera U K and France J. 2016. Integrated farming systems for the livelihood security of small and marginal farmers in India and other developing countries. Advances in Agronomy 138: 235–82. DOI: https://doi.org/10.1016/bs.agron.2016.04.001

Behera U K and Mahapatra I C. 1999. Income and employment generation of small and marginal farmers through integrated farming systems. Indian Journal of Agronomy 44(3): 431–9.

Behera U K and France J. 2014. Developmental Farm Model for revolutionizing agricultural growth. ICAR News 20(3): 5–6.

Behera U K, Babu A, Kaechele H and France J. 2015. Energy self-sufficient sustainable integrated farming systems for livelihood security under a changing climate scenario in an Indian context: a case-study approach. CAB Reviews 10(19): 11. DOI: https://doi.org/10.1079/PAVSNNR201510019

Behera U K, Bhargavi B, Meena S L, Bhattacharyya R, Singh R, Singh R K, Singh V K, Gupta N and Rana K S. 2018. Research Bulletin on Integrated farming system model for livelihood security of small and marginal farmers. Division of Agronomy, Indian Agricultural Research Institute.

Behera U K, Choudhary A K, Dass A and Vyas A K. 2013. Integrated Farming Systems for Livelihood Security of Small and Marginal Farmers. Division of Agronomy, Indian Agricultural Research Institute 327 p.

Behera U K, Sharma A R and Mahapatra I C. 2007. Crop diversification for efficient resource management in India: Problems, prospects and policy. Journal of Sustainable Agriculture 30(3): 97–127. DOI: https://doi.org/10.1300/J064v30n03_08

Upadhyay P K, Rajanna G A, Sepat S, Bana R S, Choudhary A K, Singh T, Singh R K, Rathore S S, Kumar D, Nath C P, Shiva Dhar, Ghosh P K and Yadav R L. 2018. Doubling farmers’ income through agronomic interventions under changing scenario. (In) Extended summaries of XXI Biennial National Symposium. Indian Society of Agronomy, IARI, New Delhi 110 012, p 652.

Behera U K, Jha K P and Mahapatra I C. 2004. Integrated management of available resources of the small and marginal farmers for generation of income and employment in eastern India. Crop Research 27(1): 83–9.

Bianchi F J J A, Mikkos V, Brussaard L, Delbalre B and Pulleman M M. 2013. Opportunities and limitations for functional agro-biodiversity in the European context. Environmental Science Policy 27: 223–31. DOI: https://doi.org/10.1016/j.envsci.2012.12.014

Borthakur A and Singh P. 2013. History of agricultural research in India. Current Science 105: 587–93.

Chopra K. 1993. Sustainability of agriculture. Indian Journal of Agricultural Economics 48(3): 527–35.

Dalsgaard J P T and Prein M. 1999. Integrated smallholder agriculture-aquaculture in Asia: Optimising tropic flows. Nutrient disequilibria in agro-ecosystems: Concepts and case studies pp. 141-155. (Eds) Smaling E M A, Oenema O, Fresco L O), CABI, Wallingford, UK.

de Haan C, Steinfeld H and Blackburn H. 1997. Livestock and environment: Finding a balance. FAO/USAID/The World Bank. WRENmedia, Eye, Suffolk, UK.

Dent J B. 1990. [Systems Theory Applied to Agriculture and the Food Chain]. Elsevier, Amsterdam.

Devendra C and Thomas D. 2002b. Crop-animal interactions in mixed farming systems in Asia. Agricultural Systems 71: 27–40. DOI: https://doi.org/10.1016/S0308-521X(01)00034-8

Devendra C, Thomas D, Jabbar M A and Zerbini E. 2000. Improvement of livestock production in crop-animal systems in agro-ecological zones of South Asia. ILRI, Nairobi, Kenya.

Devendra C. 1997. Crop residues for feeding animals in Asia: Technology assessment and adoption in crop/livestock systems. Crop residues in Sustainable Mixed Crop/Livestock farming System pp. 241-267. (Ed) Renard C., . CABI, Wallingford, UK.

Devendra C. 2007. Small farm systems to feed hungry Asia. Outlook on Agriculture 36(1): 7–20. DOI: https://doi.org/10.5367/000000007780223641

Devendra C and Thomas D. 2002a. Smallholder farming systems in Asia. Agricultural Systems 71: 17-25. DOI: https://doi.org/10.1016/S0308-521X(01)00033-6

Dhyani S K, Newaj R and Sharma A R. 2009. Agroforestry: Its relation with agronomy, challenges and opportunities. Indian Journal of Agronomy 54(3): 249–66.

Ehrlich P R and Pingle R M. 2008. Where does biodiversity go from here? A grim business as usual forecast and a hopeful portfolio of partial solutions. (In) Proceedings of the US National Academy of Sciences 105: 11579–86. DOI: https://doi.org/10.1073/pnas.0801911105

Evenson R E and Gollin D. 2003. Assessing the impact of the Green Revolution - 1960 to 2000. Science 300: 758–62. DOI: https://doi.org/10.1126/science.1078710

Falcon W and Naylor R L. 2005. Rethinking food security for the 21st century. American Journal of Agricultural Economics 87(5): 1113–27. DOI: https://doi.org/10.1111/j.1467-8276.2005.00797.x

Gangwar B. 1993. Farming systems research for accelerating agricultural development in less developed countries: A review. Agricultural Reviews 14(3): 149–59.

Gill M S, Singh J P and Gargwar K S. 2010. Integrated farming systems and agriculture sustainability. Indian Journal of Agronomy 54(20): 128–39.

IOBC 1983. International organization for biological and integrated control. Technical bulletin 16(1):45.

Jain T C. 2008. New paradigms in agronomic research and development. Indian Journal of Agronomy 53(4): 241-4.

Jha D. 2003. An overview of farming systems research in India. Annals of Agricultural Research 24(4): 695-706.

Korikanthimath V S and Manjunath B L. 2009. Integrated farming systems for sustainability in agriculture production. Indian Journal of Agronomy 54(2): 140-8.

Kumar S and Jain D K. 2005. Are linkages between crops and livestock important for the sustainability of the farming system? Asian Economic Review 47(1): 90-101.

Kumar S, Shivani and Singh S S. 2013. Sustainable food and nutritional security through IFS. Indian Farming 63(7): 30-36.

Kumar S, Singh S S, Shivani and Dey A. 2011. Integrated faming system for eastern India. Indian Journal of Agronomy 56(4): 297-304.

Kumar S, Singh S S, Meena M K, Shivani and Dey A. 2012. Resources recycling and their management under an integrated faming system for lowlands of Bihar. Indian Journal of Agricultural Science 82(6): 504-510.

Lal R and Miller F P. 1990. Sustainable farming system for the tropics. Sustainable Agriculture: Issues and Prospectives, pp 69-89. R.P. Singh (Ed.) . Indian Society of Agronomy, IARI, New Delhi.

Lightfoot C, Bimbao M P, Dalsgaard J P T and Pullin R S V. 1993. Aquaculture and sustainability through integrated resources management. Outlook on Agriculture 22(3): 143-150.

Lightfoot C, Bimbao M P, Dalsgaard J P T and Pullin R S V. 1993. Aquaculture and sustainability through integrated resources management. Outlook on Agriculture 22(3): 143-150. DOI: https://doi.org/10.1177/003072709302200303

Mahapatra I C and Behera U K. 2011. Rice-based farming systems for livelihood improvement of Indian farmers. Indian Journal of Agronomy 56(1): 1-19.

Maheswarappa H P, Hegde M R, Dhanpal R and Biddappa C C. 1998. Mixed farming in coconut garden: its impact on soil, physical, chemical properties, coconut nutrition and yield. Journal of Plantation Crops 26(2): 139-43.

Maheswarappa H P, Hegde M R, Dhanpal R, Sairam C V and Singh TV. 2001. Impact of integrated mixed farming systems in coconut garden on coconut yield and economic analysis. Indian Journal of Agronomy 46(1): 56-63.

Manjunath B L and Itnal C J. 2003b. Farming system options for small and marginal holdings in different topographics of Goa. Indian Journal of Agronomy 48(1): 4-7.

Manjunath B L and Itnal C J. 2003a. Integrated farming system in enhancing the productivity of marginal rice (Oryza sativa) holdings in Goa. Indian Journal of Agronomy 48(1): 1-3.

Mijatovic D, van Oudenhoven F, Eyzaguirre P and Hodgkin T. 2013. The role of agricultural biodiversity in strengthening resilience to climate change: Towards an analytical framework. International Journal of Agricultural Sustainability 11(2): 95-107. DOI: https://doi.org/10.1080/14735903.2012.691221

Paroda R. 2014. Sustainable livelihoods through agriculture diversification and climate smart agriculture. (Eds.) D S Rana and A K Singh. Indian Society of Agronomy, New Delhi.

Rangaswamy A, Venkitaswamy R, Purushothaman S and Palaniappan S P. 1996. Rice-poultry-fish-mushroom integrated farming systems for the lowlands of Tamil Nadu. Indian Journal of Agronomy 41(3): 344-8.

Rathore S S and Bhatt B P. 2008. Productivity improvement in jhum fields through an integrated farming system. Indian Journal of Agronomy 53(4): 167–171.

Rautaray S K, Das,P C and Sinhababu D P. 2005. Increasing farm income through a rice-fish based integrated farming system in rainfed lowlands of Assam. Indian Journal of Agricultural Sciences 75(2): 79–82.

Ravisankar N, Pramanik S C, Rai R B, Nawaz S, Biswas T K and Bibi N. 2007. Study of an integrated farming system in hilly upland areas of Bay Islands. Indian Journal of Agronomy 52(1): 7–10.

Ravisankar N, Subrmani T, Ambast S K and Srivasyava R C. 2010. Enhancing farm income in an island ecosystem. Indian Farming 60(6): 16–9.

Reidsma P, Tekelenburg T, van de Berg M and Alkemade R. 2006. Impact of land use change on biodiversity: an assessment of agricultural biodiversity in the European Union. Agricultural Ecosystems and Environment 114: 86–102. DOI: https://doi.org/10.1016/j.agee.2005.11.026

Rhoades R E and Booth R H. 1982. Farmer-back to back farmers: a model for generating acceptable agricultural technology. Agricultural Administration 11: 127–37. DOI: https://doi.org/10.1016/0309-586X(82)90056-5

Sharma A R and Behera U K. 2004. Fertiliser use and option for diversification in rice-wheat cropping systems in India. Fertiliser News 49(12): 115–31.

Shukla A K, Shukla N D and Singh V K. 2002. Farming system approach for food security and sustained rural economy. Indian Journal of Fertilizers 47(11): 55–62.

Singh G. 2015. Agriculture diversification for food, nutrition, livelihood and environmental security: Challenges and opportunities. Indian Journal of Agronomy. 60(2): 172–84.

Singh K, Bohra J S, Singh Y and Singh J P. 2006. Development of farming system models for the north-eastern plain zone of Uttar Pradesh. Indian Farming 56(2): 5–11.

Singh D P, Singh K P and Yadavika. 1998. Integrated farming systems – a key issue for research education – extension linkages to sustain food security and ecofriendly environment in 21st Century, pp 474-486. (In) Proceedings of the First International Agronomy Congress: Agronomy, Environment and Food Security for the 21st Century , pp. 474-486. Singh P, Prasad R, Ahlawat I P S (Eds.). Indian Society of Agronomy, New Delhi.

Singh G. 2015. Agriculture diversification for food, nutrition, livelihood and environmental security: Challenges and opportunities. Indian Journal of Agronomy 60(2): 172–84.

Singh J P, Gill M S and Tripathi D. 2007. Development of integrated farming system models for marginal and small farmers. (In) Extended summaries of 3rd national symposium on integrated farming system and its role towards livelihood improvement, pp 51-57. ARS, Durgapura, Jaipur, 26-28 November 2007.

Yadav R L and Prasad K. 1998. Farming systems research in India: needs and strategies. (In) Proceedings of first international agronomy congress: Agronomy, environment and food security for 21st century (Eds.). Singh P, Prasad R and Ahlawat I P S, pp 333-341. Indian Society of Agronomy, New Delhi.