Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers

Abstract

Genetic relationships among Indian aromatic and quality rice (Oryza sativa) germplasm were assessed using 30 fluorescently labeled rice microsatellite markers. The 69 rice genotypes used in this study included 52 Basmati and other scented/quality rice varieties from different parts of India and 17 indica and japonica varieties that served as controls. A total of 235 alleles were detected at the 30 simple sequence repeat (SSR) loci, 62 (26.4%) of which were present only in Basmati and other scented/quality rice germplasm accessions. The number of alleles per locus ranged from 3 to 22, with an average of 7.8, polymorphism information content (PIC) values ranged from 0.2 to 0.9, with an average of 0.6, and the size range between the smallest and the largest allele for a given microsatellite locus varied between 3 bp and 68 bp. Of the 30 SSR markers, 20 could distinguish traditional Basmati rice varieties, and a single panel of eight markers could be used to differentiate the premium traditional Basmati, cross-bred Basmati, and non-Basmati rice varieties having different commercial value in the market-place. When estimates of inferred ancestry or similarity coefficients were used to cluster varieties, the high-quality Indian aromatic and quality rice genotypes could be distinguished from both indica and japonica cultivars, and crossbred varieties could be distinguished from traditional Basmati rices. The results indicate that Indian aromatic and quality germplasm is genetically distinct from other groups within O. sativa and is the product of a long independent pattern of evolution. The data also suggest that there is scope for exploiting the genetic diversity of aromatic/quality rice germplasm available in India for national Basmati rice breeding programs.

Genetic Diversity Studies on Selected Rice (Oryza sativa L.) Genotypes based on Gel Consistency and Alkali Digestion

“…Similar null allele occurrence was reported by [36] in Indian rice genotypes. In general, the markers indicating a high number of alleles per locus also detected rare alleles.…”

“…The many rare alleles observed in a germplasm indicates that there is a unique source of genetic diversity amongst the genotypes. Presence of rare alleles are important in fingerprinting rice genotypes [36].…”

Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium

“…The PIC values can guide us to select the most informative SSRs for calculating genetic divergence (Candida et al 2006), Table 5 Genetic similarity coefficient between tetraploid species and A-/D-genome species Table 6 Genetic similarity coefficients of 36 cotton species using two types of markers (EST-SSRs and gSSRs) Pros and cons of using genomic SSRs and EST-SSRs 567 thus the number of SSRs can be reduced substantially (Candida et al 2006) before initiating the genetic diversity and variety identification experiments (Macaulay et al 2001;Masi et al 2003;Jain et al 2004). In this study, we proposed 22 (11 BNLs and 11 MGHES) out of the 75 SSRs-based on their high PIC values (PIC C 5.0) and potential to amplify distinct DNA fragments for calculating the extent of genetic diversity among the 36 Gossypium species.…”

Aerobic rice genotypes displayed greater adaptation to water-limited cultivation and tolerance to polyethyleneglycol-6000 induced stress

“…A small set of three previously developed rice microsatellite markers (RM212, RM302 and RM3825) associated with drought resistant traits were used for the identification and discrimination of polymorphism (Kanagaraj et al 2010). PCR amplification, denaturing polyacrylamide gel electrophoresis and silver staining were carried out as described earlier (Jain et al 2004). …”