Genetic diversity trend in Indian rice varieties: an analysis using SSR markers.
The knowledge of the extent and pattern of diversity in the crop species is a prerequisite for any crop improvement as it helps breeders in deciding suitable breeding strategies for their future improvement. Rice is the main staple crop in India with the large number of varieties released every year. Studies based on the small set of rice genotypes have reported a loss in genetic diversity especially after green revolution. However, a detailed study of the trend of diversity in Indian rice varieties is lacking. SSR markers have proven to be a marker of choice for studying the genetic diversity. Therefore, the present study was undertaken with the aim to characterize and assess trends of genetic diversity in a large set of Indian rice varieties (released between 1940-2013), conserved in the National Gene Bank of India using SSR markers.



A set of 729 Indian rice varieties were genotyped using 36 HvSSR markers to assess the genetic diversity and genetic relationship. A total of 112 alleles was amplified with an average of 3.11 alleles per locus with mean Polymorphic Information Content (PIC) value of 0.29. Cluster analysis grouped these varieties into two clusters whereas the model based population structure divided them into three populations. AMOVA study based on hierarchical cluster and model based approach showed 3 % and 11 % variation between the populations, respectively. Decadal analysis for gene diversity and PIC showed increasing trend from 1940 to 2005, thereafter values for both the parameters showed decreasing trend between years 2006-2013. In contrast to this, allele number demonstrated increasing trend in these varieties released and notified between1940 to 1985, it remained nearly constant during 1986 to 2005 and again showed an increasing trend.



Our results demonstrated that the Indian rice varieties harbors huge amount of genetic diversity. However, the trait based improvement program in the last decades forced breeders to rely on few parents, which resulted in loss of gene diversity during 2006 to 2013. The present study indicates the need for broadening the genetic base of Indian rice varieties through the use of diverse parents in the current breeding program.
Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
Nivedita
N
Singh
Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
Debjani Roy
DR
Choudhury
Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
Gunjan
G
Tiwari
Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
Amit Kumar
AK
Singh
Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
Sundeep
S
Kumar
Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
Kalyani
K
Srinivasan
Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
R K
RK
Tyagi
Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
A D
AD
Sharma
ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, IARI, New Delhi, 110012, India.
N K
NK
Singh
Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India. singhnbpgr@yahoo.com.
Rakesh
0000-0001-7269-6420
R
Singh
D000483:Alleles; D016000:Cluster Analysis; D005787:Gene Frequency; D005819:Genetic Markers; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D018895:Microsatellite Repeats; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny
D005819:Genetic Markers
Decadal analysis; Hierarchical analysis; HvSSR markers; India; Model based analysis; Rice