DNA Finger Printing of Salt Tolerant and Susceptible Genotypes Using MicroSatellite Markers in Rice (Oryza sativa L.)

Shanthi, P.; Jebaraj, S.; Geetha, S.; Aananthi, N.

doi:10.3923/ijpbg.2012.206.216

Cited by 12 publications

(7 citation statements)

References 14 publications

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“…Of the three clusters generated in the dendrogram, two contained all tolerant genotypes and another one was comprised of all salt susceptible genotypes exclusively. Our result is also in accordance with the result about the similar clustering pattern of Nona Bokra and Pokkali [ 50 ], CSR23, CSR10 and SR 26B [ 31 ], Hasawi and SR26B [ 51 ] and susceptible IR36 and IR64 [ 52 ]. Cluster II was consisted of two tolerant genotypes FL478 and Kala Rata.…”

Section: Discussionsupporting

confidence: 92%

Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.)

et al. 2015

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BackgroundMajority of the Asian people depend on rice for nutritional energy. Rice cultivation and yield are severely affected by soil salinity stress worldwide. Marker assisted breeding is a rapid and efficient way to develop improved variety for salinity stress tolerance. Genomic microsatellite markers are an elite group of markers, but there is possible uncertainty of linkage with the important genes. In contrast, there are better possibilities of linkage detection with important genes if SSRs are developed from candidate genes. To the best of our knowledge, there is no such report on SSR markers development from candidate gene sequences in rice. So the present study was aimed to identify and analyse SSRs from salt responsive candidate genes of rice.ResultsIn the present study, based on the comprehensive literature survey, we selected 220 different salt responsive genes of rice. Out of them, 106 genes were found to contain 180 microsatellite loci with, tri-nucleotide motifs (56%) being most abundant, followed by di-(41%) and tetra nucleotide (2.8%) motifs. Maximum loci were found in the coding sequences (37.2%), followed by in 5′UTR (26%), intron (21.6%) and 3′UTR (15%). For validation, 19 primer sets were evaluated to detect polymorphism in diversity analysis among the two panels consisting of 17 salt tolerant and 17 susceptible rice genotypes. Except one, all primer sets exhibited polymorphic nature with an average of 21.8 alleles/primer and with a mean PIC value of 0.28. Calculated genetic similarity among genotypes was ranged from 19%-89%. The generated dendrogram showed 3 clusters of which one contained entire 17 susceptible genotypes and another two clusters contained all tolerant genotypes.ConclusionThe present study represents the potential of salt responsive candidate gene based SSR (cgSSR) markers to be utilized as novel and remarkable candidate for diversity analysis among rice genotypes differing in salinity response.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0498-1) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 92%

Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.)

et al. 2015

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“…These quality groupings were based on the cost price, and confirmed by sensory analysis using a skilled panelist to exam the physical appearance, cleanliness, colour, and aroma on a six (1)(2)(3)(4)(5)(6) corresponding level as done by other authors [28]. All samples were (three replication each) were sent to the laboratory for further analysis.…”

Section: Sample Preparationmentioning

confidence: 97%

“…What is clear is that, some unscrupulous actors in the rice supply chain are selling sub-standard rice to consumers and very often these unscrupulous activities go undetected, because the existing analytical methods are cumbersome, time consuming, expensive and can involve substantial use of chemicals. For instance the DNA finger-printing method based on the genetic characteristic of rice has shown to be inappropriate for on-site application, it also involves labour intensive and skilled expertise [3,4]. The procedure is also quite cumbersome and laboratory based and limits the number of sample that can be tested due to the cost involved.…”

Section: Introductionmentioning

confidence: 99%

Innovative and rapid analysis for rice authenticity using hand-held NIR spectrometry and chemometrics

Teye

Amuah

McGrath

et al. 2019

Spectrochimica Acta Part A: Molecular and Biomolecular Spectros

112

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Rice is the second most important food staple worldwide and the demand will continue to increase with the growth of the world population. As reports grow that frauds is prevalent in many supply chains there is the need for an effective and rapid technique for monitoring the authenticity and quality of rice. This study investigated the novel application of hand-held NIR spectrometry coupled to chemometric for the estimation of rice authenticity and quality in real time. A total of 520 Rice samples from different quality grades (high quality, mid quality and low quality) and different countries (Ghana, Thailand, and Vietnam) of origin were used. Among the pre-processing methods used multiplicative scatter correction (MSC) was found to be superior. Principal component analysis (PCA) was used to extract relevant information from the spectral data set and the results showed that rice samples of different categories could be clearly clustered under the first three PCs using the MSC preprocessing method. The performance of Knearest neighbor (KNN) revealed that for authentication of rice quality grades, the classification rate gave 91.62% and 91.81% in training set and prediction set respectively while identification rate based on different country of origin was 90.84% and 90.64% in both training set and prediction set respectively. For the differentiation of local rice from the imported, KNN and SVM all had 100% in both the training set and prediction set. These gives very strong evidence that hand-held spectrometry coupled with MSC-PCA-KNN could successfully be used to

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“…Due to their reliability and high discriminative power, SSR markers also have been recognized as one of the standard fingerprinting methods for genetic identification and protection of new plants varieties (UPOV 2007). SSR fingerprinting has been successfully applied for cultivars discrimination in many plant species, including Pupulous, such as P. tremuloides (Dayanandan et al 1998;Rahman et al 2000) and P. canadensis (Rajora and Rahman 2003), as well as a number of crops and horticultural plants, such as Prunus persica (Cheng and Huang 2009), Lactuca sativa (Rauscher et al 2013), and Oryza sativa (Shanthi et al 2012).…”

Section: Discussionmentioning

confidence: 99%

Genetic identification of 43 elite clonal accessions ofPopulus deltoidesby SSR fingerprinting

et al. 2016

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In this study, 43 elite clones of Populus deltoides were fingerprinted with ABI 3730 capillary electrophoresis by using six SSR primer pairs. Based on the fingerprinting profiles, 62 polymorphic bands were generated with a mean number of 10 alleles per locus, and allele numbers amplified by each primer in these clones ranged from 5 (NJFUP-poly10) to 16 (NJFUP-poly07). The power of discrimination values for these primer pairs ranged from 0.80 to 0.94, with an average value of 0.89. Among the six primer pairs, the most efficient primer pair for genetic discrimination of these elite clones was NJFUP-poly02, which could identify 22 of the 43 elite clones directly. In conclusion, all the 43 elite clones of P. deltoides could be discriminated unambiguously based on their genotypes at the six SSR loci. The combination of all six loci gave considerable reliability and accuracy for genetic identification of these clonal accessions. Subsequently, genetic relationship of these clones was plotted by the UPGMA clustering and principle component analysis. Results of both analyses indicated that clone "C7-1" had the largest genetic distance from the other clones, followed by clone "C51-1" and a subgroup comprising clone "C100-3" and "C62-3". These clones are proposed to be possibly more affected by the inter-specific gene introgression.Key words: Populus deltoides, clone identification, SSR fingerprinting, UPGMA cluster, PCA plot.Résumé : Dans cette étude, 43 clones élite de Populus deltoides ont été marqués avec six paires d'amorces SSR par électrophorèse capillaire au moyen d'un appareil ABI 3730. D'après la cartographie peptidique, la technique aboutit à 62 bandes polymorphes comprenant en moyenne 10 allèles par locus, le nombre d'allèles amplifiés dans chaque amorce variant de 5 (NJFUP-poly10) à 16 (NJFUP-poly07) chez les clones. La valeur discriminatoire des paires d'amorces variait de 0,80 à 0,94, pour une moyenne de 0,89. Sur les six paires d'amorces, celle permettant la meilleure discrimination génétique des clones élite était NJFUP-poly02, puisqu'elle a permis d'identifier directement 22 clones sur les 43. En conclusion, on est parvenu à distinguer sans ambiguïté les 43 clones élite de P. deltoides d'après leur génotype aux six locus SSR. Combiner les six locus rend l'identification génétique extrêmement fiable et précise pour ces obtentions, issues du clonage. Par la suite, les liens génétiques entre les clones ont été tracés après regroupement par la méthode des moyennes par paire non pondérée (UPGMA) et l'analyse en composantes principales. Dans les deux cas, les résultats indiquent que le clone C7-1 est génétiquement le plus éloigné des autres. Suivaient le clone C51-1 et un sous-groupe composé des clones C100-3 et C62-3. Il se peut que ces clones soient plus affectés par l'introgression des gènes interspécifiques. [Traduit par la Rédaction]

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DNA Finger Printing of Salt Tolerant and Susceptible Genotypes Using MicroSatellite Markers in Rice (Oryza sativa L.)

Cited by 12 publications

References 14 publications

Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.)

Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.)

Innovative and rapid analysis for rice authenticity using hand-held NIR spectrometry and chemometrics

Genetic identification of 43 elite clonal accessions ofPopulus deltoidesby SSR fingerprinting

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