Dr. Arvind Kumar is the director of International Rice Research Institute (IRRI) South Asia Regional Centre (ISARC). His group recently analyzed the 3000 Rice Genomes panel (3K-RGP) to improve rice grain quality and yield. This study, published in Plant Biotechnology Journal, paves the way for rice enhancement through a novel strategy called haplotype-based breeding. The NGSF Blog team got in touch with Dr. Arvind to learn more about this exciting work.
What does a haplotype mean? How does haplotype-based breeding differ from conventional breeding?
Inside the cell of every living organism, resides the genome, made up of four nucleotides – A, T, G, and C. Even within the same species, there is considerable variation in the genome, which gives rises to variability in the population. A single base variation in the DNA sequence is called Single Nucleotide Polymorphism (SNP). A haplotype is a particular pattern of SNPs found in a gene or genomic region that is tightly linked and inherited together. Whole-genome resequencing of a large number of diverse accessions provides an opportunity to identify haplotypes of target genes that are superior and can subsequently be utilized in breeding programs.
Contrary to conventional breeding programs, which mostly depend on phenotypic selection for parents and identification of superior lines among the offspring, haplotype-based breeding refers to a comprehensive strategy where superior haplotypes of interest are identified, and later combined to develop tailored rice varieties suiting future demands.
Has any crop been previously developed using haplotype-based breeding?
Although in the past, several crop varieties that were released might have coincidentally possessed superior haplotypes, haplotype-based breeding is a new strategy. Hence there arises a need to establish proof-of-concept before making it a regular practice. Once realized, we strongly believe that in the coming years, this strategy would pave the way for developing climate resilient and nutritious rice varieties. We also expect that this strategy can be extended to any crop of interest.
How was this work initiated and funded?
The establishment of the final pipeline for haplotype-based breeding was the result of many discussions held over 6 months, as this is the first time, to the best of our knowledge, that efforts are being made in this direction. This work was jointly funded by Department of Biotechnology (DBT), Government of India, Indian Council of Agricultural Research (ICAR) and Bill and Melinda Gates Foundation (BMGF).
What was the source of the rice varieties used in your study? How diverse were they?
The entire 3K RGP consisting of 12 diverse sub-populations, and originating from over 100 countries, was used for the haplotype analysis of 120 key genes. We also phenotyped 150 diverse rice accessions from 30 different countries for certain traits across two crop seasons at IRRI, South Asia Hub, Hyderabad.
In recent times, rice has been thought to have poorer nutrient quality than other grains. Its consumption is being linked to diabetes as well. How do you see such accusations and does your work focus on improving the nutrient quality of rice?
We are making considerable efforts to enhance iron and zinc concentration in rice with our collaborators in India. Few promising lines with high zinc content have already been released through our national partners under All India Coordinated Rice Improvement Project (AICRIP) and several other potential biofortified lines are waiting to be released. In addition, we also identified superior haplotypes for high iron and zinc content, which are currently used in haplotype-based breeding to develop nutritious rice varieties.
To address diabetes, our team in Philippines and in India are involved in the identification of superior haplotypes with low glycaemic index (Low GI) using a variety of genomic approaches. As soon as reliable haplotypes are verified, they will be rapidly utilized in the haplotype-based breeding pipeline for developing Low GI rice varieties.
There has been a rising trend toward organic farming. Have you looked into traits that can make rice more amenable to such approaches?
We believe that the lines developed through haplotype-based breeding using superior haplotypes that are associated with grain yield, nutrient use efficiency, and biotic stress resistance, are expected to perform well under organic farming.
Are efforts being made by national and international organizations to improve pulses and millets on a large scale similar to rice?
Pulses and millets are important dietary sources. Considerable efforts are being made by various international and national organizations to improve these crops. For instance, a lot of whole-genome resequencing efforts were recently made by International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, for different crops including chickpea, pigeon pea, groundnut, pearl millet, sorghum etc. which pave the way for haplotype-based breeding in these crops.
IRRI has set up regional centres in Hyderabad and Varanasi. What do these centers have to offer young Indian students in terms of opportunities and research infrastructure? Are Internship/Doctoral studies possible in such centers?
ISARC in Varanasi will undertake basic and applied research to improve grain quality, cooking quality, and nutritional quality of rice as well as to develop climate-smart agriculture for the rice based agri-food system. ISARC will also direct training programs for scholars, scientists, Agriculture Department officials as well as farmers to increase their effectiveness and knowledge. They will also be given an opportunity to undertake joint scholars research programs with institutes in South Asia and Africa. Yes, internships as well as joint Ph.D. studies are possible at ISARC.
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