Potentiality of evenly distributed hypervariable microsatellite markers in marker‐assisted breeding of rice

Narshimulu, Gonela; Jamaloddin, Mohammed; Vemireddy, Lakshminarayana R.; Anuradha, G.; Siddiq, E. A.

doi:10.1111/j.1439-0523.2010.01834.x

Cited by 23 publications

(22 citation statements)

References 31 publications

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“…In addition, microsatellite markers have the potential to be used for unequivocal detection and quantification of adulteration in Basmati rice (Bligh 2000;Archak et al 2007;Vemireddy et al 2007). Recently, evenly-distributed hypervariable microsatellite markers were reported to be showed more polymorphism than non-hypervariable SSRs (Narshimulu et al 2011) and also used for estimating the temporal trends of the genetics diversity over decadal periods (Choudhury et al 2013). …”

Section: Molecular Markers Systemsmentioning

confidence: 99%

Review of methods for the detection and quantification of adulteration of rice: Basmati as a case study

et al. 2014

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Rice is a staple and widely grown crop endowed with rich genetic diversity. As it is difficult to differentiate seeds of various rice varieties based on visual observation accurately, the harvested seeds and subsequent processed products are highly prone to adulteration with look-alike and low quality seeds by the dishonest traders. To protect the interests of importing countries and consumers, several methods have been employed over the last few decades for unambiguous discrimination of cultivars, accurate quantification of the adulterants, and for determination of cultivated geographical area. With recent advances in biotechnology, DNA based techniques evolved rapidly and proved successful over conventional non-DNA based methods to purge the problem of adulteration at commercial level. In the current review, we made an attempt to summarize the existing methods of adulteration detection and quantification in a comprehensive manner by providing Basmati as a case study to enable the traders to arrive at a quick resolution in choosing the apt method to eliminate the adulteration practice in the global rice industry.

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Section: Molecular Markers Systemsmentioning

confidence: 99%

Review of methods for the detection and quantification of adulteration of rice: Basmati as a case study

et al. 2014

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“…Despite such large number of varieties developed using diverse germplasm, molecular marker based diversity analysis has shown the genetic base of Indian rice gene pool to be surprisingly narrow [13], [14]. Moreover, with regard to trends of genetic diversity in major Indian rice cultivars, however, little work has been done Recently, hypervariable microsatellite markers evenly distributed in rice genome have been demonstrated to be quite effective in estimating genetic diversity [15] Keeping the foregoing, the present study was undertaken to understand the level and trend of genetic diversity in the high yielding varieties developed in India over decadal periods between 1970s and 2000s employing hypervariable microsatellite markers.…”

Section: Introductionmentioning

confidence: 99%

Molecular Genetic Diversity of Major Indian Rice Cultivars over Decadal Periods

et al. 2013

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Genetic diversity in representative sets of high yielding varieties of rice released in India between 1970 and 2010 was studied at molecular level employing hypervariable microsatellite markers. Of 64 rice SSR primer pairs studied, 52 showed polymorphism, when screened in 100 rice genotypes. A total of 184 alleles was identified averaging 3.63 alleles per locus. Cluster analysis clearly grouped the 100 genotypes into their respective decadal periods i.e., 1970s, 1980s, 1990s and 2000s. The trend of diversity over the decadal periods estimated based on the number of alleles (Na), allelic richness (Rs), Nei’s genetic diversity index (He), observed heterozygosity (Ho) and polymorphism information content (PIC) revealed increase of diversity over the periods in year of releasewise and longevitywise classification of rice varieties. Analysis of molecular variance (AMOVA) suggested more variation in within the decadal periods than among the decades. Pairwise comparison of population differentiation (Fst) among decadal periods showed significant difference between all the pairs except a few. Analysis of trends of appearing and disappearing alleles over decadal periods showed an increase in the appearance of alleles and decrease in disappearance in both the categories of varieties. It was obvious from the present findings, that genetic diversity was progressively on the rise in the varieties released during the decadal periods, between 1970s and 2000s.

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“…The marker profiles could be a powerful tool for the characterization of rice accessions, avoiding redundancy and duplicates in the germplasm being collected and conserved in the gene banks. The evenly distributed eight hypervariable SSR markers exhibiting higher PIC values and higher allele numbers (0.87 and 3.63) compared to the randomly selected markers (0.77 and 2.48) could be used as potential background markers in marker assisted selection as reported earlier (Narshimulu et al 2011).…”

Section: Discussionmentioning

confidence: 99%

“…In our previous study, we have shortlisted 840 hypervariable rice microsatellite markers (hvRM) from the publicly available 18,882 Class I SSR markers (Narshimulu et al 2011). Of the 840 hvRM markers, 52 were chosen for the present study based on their distribution and evenness over all the 12 chromosomes to screen the 90 genotypes.…”

Section: Dna Fingerprintingmentioning

confidence: 99%

“…SSRs containing perfect repeats ( = 20 nucleotides in length) and also known as hypervariable SSRs. Recently, evenly distributed hypervariable SSRs have been shortlisted and demonstrated to be quite handy in studies of genetic diversity, population structure analysis, DNA fingerprinting and marker-assisted selection/breeding in rice (Narshimulu et al 2011). Also, very recently, hypervariable SSR markers have been used to estimate the genetic diversity of major Indian rice cultivars released from 1970 to 2010 (Choudhary et al 2013).…”

Section: Introductionmentioning

confidence: 99%

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Molecular Profiling of Major Indian Rice Cultivars Using a Set of Eight Hypervariable Microsatellite Markers

Vemireddy¹,

Ranjithkumar²,

Vipparla³

et al. 2015

Cereal Research Communications

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India bred high yielding rice varieties have enriched to a great extent the global rice germplasm since the mid-sixties. Systematic research efforts for development of cultivar-specific DNA fingerprints of major Indian rice cultivars, however, have not received due attention. The present investigation was aimed at development of DNA fingerprints for 90 high yielding rice varieties using hypervariable microsatellite (hvRM) markers. A panel of eight markers, viz. RM11313, RM13584, RM15004, RM5844, RM22250, RM22565, RM24260 and RM8207 was chosen from 52 polymorphic markers based on their highly polymorphic nature, SSR repeat type and number and ability to distinguish genotypes, in order to develop DNA fingerprints of 90 varieties. The remaining high polymorphic hvRM markers could be of immense value in future to distinguish new cultivars, in case they could not be distinguished by the 8 marker panel. Four of the 8 markers, viz. RM22250, RM13584, RM24260 and RM5844 were located in expressed genes and could be of value in DUS (Distinctness, Uniformity and Stability) testing. Thus we suggested, that this set of 8 loci could be used as standard for DNA fingerprinting of Indian rice cultivars.

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Potentiality of evenly distributed hypervariable microsatellite markers in marker‐assisted breeding of rice

Cited by 23 publications

References 31 publications

Review of methods for the detection and quantification of adulteration of rice: Basmati as a case study

Review of methods for the detection and quantification of adulteration of rice: Basmati as a case study

Molecular Genetic Diversity of Major Indian Rice Cultivars over Decadal Periods

Molecular Profiling of Major Indian Rice Cultivars Using a Set of Eight Hypervariable Microsatellite Markers

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