Genetic diversity trend in Indian rice varieties: an analysis using SSR markers

BMC Genetics

Research Article

Rakesh Singh¹  Sundeep Kumar¹  Nivedita Singh¹  Debjani Roy Choudhury¹  Amit Kumar Singh¹  Gunjan Tiwari¹  R. K. Tyagi²  A. D. Sharma²  Kalyani Srinivasan²  N. K. Singh³ 

[1] Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, 110 012, New Delhi, India;Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, 110 012, New Delhi, India;ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, IARI, 110012, New Delhi, India;

关键词: Rice;    HvSSR markers;    Hierarchical analysis;    Model based analysis;    Decadal analysis;    India;   

DOI  :  10.1186/s12863-016-0437-7

 received in 2016-04-29, accepted in 2016-08-30,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultA 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.ConclusionOur 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.

【 授权许可】

CC BY   
© The Author(s). 2016