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Genetic diversity trend in Indian rice varieties: an analysis using SSR markers
Nivedita Singh1, Debjani Roy Choudhury1, Gunjan Tiwari1
1Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
BMC Genetics
|September 7, 2016
Summary
Indian rice varieties possess significant genetic diversity. However, recent breeding programs have led to a decline in this diversity, necessitating a broader genetic base for future crop improvement.
Area of Science:
- Agricultural Science
- Genetics
- Plant Breeding
Background:
- Understanding crop genetic diversity is crucial for effective crop improvement strategies.
- Indian rice varieties, a staple food, have seen numerous releases, but concerns exist about potential diversity loss post-Green Revolution.
- A comprehensive study on the trend of genetic diversity in Indian rice varieties was lacking.
Purpose of the Study:
- To characterize and assess trends in genetic diversity within a large collection of Indian rice varieties.
- To utilize SSR markers for evaluating genetic diversity and relationships in rice germplasm.
- To analyze genetic diversity patterns in Indian rice varieties released between 1940 and 2013.
Main Methods:
- Genotyping of 729 Indian rice varieties using 36 HvSSR markers.
- Analysis of allele number, Polymorphic Information Content (PIC), and genetic relationships.
- Application of cluster analysis and model-based population structure analysis.
- Analysis of Molecular Variance (AMOVA) to determine genetic variation between populations.
- Decadal analysis of gene diversity and allele number trends.
Main Results:
- A total of 112 alleles were amplified with an average of 3.11 alleles per locus and a mean PIC of 0.29.
- Cluster and population structure analyses revealed two and three distinct groups, respectively.
- AMOVA indicated 3% and 11% variation between populations.
- Gene diversity and PIC showed an increasing trend until 2005, followed by a decrease from 2006-2013.
- Allele number increased until 1985, remained stable until 2005, and increased again.
Conclusions:
- Indian rice varieties exhibit substantial genetic diversity.
- Intensive trait-based breeding programs have led to a reduction in gene diversity between 2006 and 2013 due to reliance on a few parents.
- Broadening the genetic base of Indian rice varieties by incorporating diverse parents is recommended for future breeding efforts.
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