Abstract
Simple sequence repeat (SSR) and Single Nucleotide Polymorphic (SNP), the two most robust markers for identifying rice varieties were compared for assessment of genetic diversity and population structure. Total 375 varieties of rice from various regions of India archived at the Indian National GeneBank, NBPGR, New Delhi, were analyzed using thirty six genetic markers, each of hypervariable SSR (HvSSR) and SNP which were distributed across 12 rice chromosomes. A total of 80 alleles were amplified with the SSR markers with an average of 2.22 alleles per locus whereas, 72 alleles were amplified with SNP markers. Polymorphic information content (PIC) values for HvSSR ranged from 0.04 to 0.5 with an average of 0.25. In the case of SNP markers, PIC values ranged from 0.03 to 0.37 with an average of 0.23. Genetic relatedness among the varieties was studied; utilizing an unrooted tree all the genotypes were grouped into three major clusters with both SSR and SNP markers. Analysis of molecular variance (AMOVA) indicated that maximum diversity was partitioned between and within individual level but not between populations. Principal coordinate analysis (PCoA) with SSR markers showed that genotypes were uniformly distributed across the two axes with 13.33% of cumulative variation whereas, in case of SNP markers varieties were grouped into three broad groups across two axes with 45.20% of cumulative variation. Population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD) derived Δk was plotted against the K to determine the number of populations. In case of SSR maximum Δk was at K=5 whereas, in case of SNP maximum Δk was found at K=15, suggesting that resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis.
Highlights
Rice (Oryza sativa L.) is a staple food crop in the world and accounts for 21, 14 and 2% of global energy, protein and fat supply, respectively [1]
The utility of Simple Sequence Repeat (SSR)/ single nucleotide polymorphism (SNP) marker in crop improvement will depend on the quality of information they provide with respect to parameters for genetic diversity and population structure
This is the first such study where SSR and SNP marker system were assessed for their efficiency in assessing genetic diversity and population structure in the large collection of Indian rice varieties
Summary
Rice (Oryza sativa L.) is a staple food crop in the world and accounts for 21, 14 and 2% of global energy, protein and fat supply, respectively [1]. It serves as a model plant for genetic breeding and genomics research. Earlier RAPD, ISSR and AFLP have been used very frequently for fingerprinting and characterization of varieties and germplasm accessions of different crop species. Since these markers can be utilized without prior genomic information on the target crop for analysis, they were generally used as markers of choice. Application of SNP markers on plant cultivar identification have been reported, in grape [14], grapevine [15], melon [16] and rice [17]
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