Identification of informative EST-SSR markers capable of distinguishing popular Indian rice varieties and their utilization in seed genetic purity assessments

Abstract Genetic purity is conventionally performed through Grow-Out-Test (GOT) with morphological characters. Simple sequence repeat (SSR) markers are independent of G X E interaction. Herewith, 16 high yielding varieties of rice were analyzed using 55 SSR markers for DNA fingerprinting and identification of genetic impurities: 14 were found to be polypmorphic and amplified 48 alleles with an average of 3.43 alleles per each primer pair. The number of alleles amplified ranged from 2 to 6 and the size of the PCR products amplified from these 14 primer pairs ranged from 80–450 bp with polymorphic information content (PIC) from 0.14 (RM 346) to 0.99 (RM 5900). PICs at 0.5 or higher are highly informative SSR markers for genetic studies, DNA fingerprinting and scoring polymorphism rate of SSR markers pertinent to specific locus. The 14 polymorphic SSR markers can be used for DUS testing, genetic purity and DNA finger printing of rice varieties.

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Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽

10.3390/plants8110471 ◽

2019 ◽

Vol 8 (11) ◽

pp. 471

Author(s):

Jae-Ryoung Park ◽

Won-Tae Yang ◽

Yong-Sham Kwon ◽

Hyeon-Nam Kim ◽

Kyung-Min Kim ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Germplasm Collection ◽

Group Method ◽

Sequence Repeat ◽

Rice Varieties ◽

Red Pericarp ◽

Simple Sequence ◽

Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

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Genetic purity analysis of cotton (Gossypium spp.) hybrids using SSR markers

Seed Science and Technology ◽

10.15258/sst.2010.38.2.09 ◽

2010 ◽

Vol 38 (2) ◽

pp. 358-366 ◽

Cited By ~ 5

Author(s):

P. Selvakumar ◽

R. Ravikesavan ◽

A. Gopikrishnan ◽

K. Thiyagu ◽

S. Preetha ◽

...

Keyword(s):

Ssr Markers ◽

Genetic Purity ◽

Gossypium Spp ◽

Purity Analysis

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Identification and characterization of popular rice (Oryza sativa L.) varieties through chemical tests

Journal of Phytology ◽

10.25081/jp.2020.v12.6513 ◽

2020 ◽

pp. 82-85

Author(s):

M.S. Nagendra ◽

P. Selvaraju ◽

R. Jerlin ◽

K. Ganesamurthy ◽

N. Senthil

Keyword(s):

Tamil Nadu ◽

Oryza Sativa L ◽

Colour Change ◽

Gelatinization Temperature ◽

Genetic Purity ◽

Rice Varieties ◽

Seed Supply ◽

Crop Varieties ◽

Identification And Characterization

Identification and characterization of crop varieties are crucial for ensuring the genetic purity of seeds. The present investigation was carried out to identify suitable chemical methods that are fast, reliable and easy for seed analysts, breeders and seed producers for identification of a variety. Twenty-five popular rice varieties in the seed supply chain of Tamil Nadu were subjected to phenol, modified phenol, NaOH, aroma, gelatinization temperature (alkali spreading value), GA3 and 2,4-D tests. The results of the experiment revealed that phenol and modified phenol tests changed the colour of TKM 9 and TRY 1 variety to brown but no colour change was observed in the variety I.W. Ponni variety. The NaOH test is useful for the identification of TKM 9 variety as it changed the colourless solution to red. GA3 and 2,4-D tests characterized the varieties based on the shoot growth into two and three groups respectively. However, all the variety lacked aroma and exhibited a high gelatinization temperature.

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DNA Fingerprinting for Identification of Rice Varieties and Seed Genetic Purity Assessment

Agricultural Research ◽

10.1007/s40003-018-0324-8 ◽

2018 ◽

Vol 7 (4) ◽

pp. 379-390 ◽

Cited By ~ 4

Author(s):

Vanisri Satturu ◽

Durga Rani ◽

Swathi Gattu ◽

Jamal Md ◽

Sreedhar Mulinti ◽

...

Keyword(s):

Dna Fingerprinting ◽

Genetic Purity ◽

Rice Varieties ◽

Purity Assessment

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DNA fingerprinting and genetic purity testing of a new broccoli hybrid using SSR markers

Seed Science and Technology ◽

10.15258/sst.2013.41.3.13 ◽

2013 ◽

Vol 41 (3) ◽

pp. 464-468

Author(s):

H.F. Yu ◽

J.S. Wang ◽

Z.Q. Zhao ◽

X.G. Sheng ◽

H.H. Gu

Keyword(s):

Dna Fingerprinting ◽

Ssr Markers ◽

Genetic Purity ◽

Purity Testing

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Association Mapping of Drought Avoidance and Agronomic Traits in Rice (Oryza Sativa L.) Landraces with SSR Markers and Genotyping-By-Sequencing Approach

10.21203/rs.3.rs-127517/v1 ◽

2020 ◽

Author(s):

Beena R ◽

Silvas Kirubakaran ◽

Nithya N ◽

Sah R.P ◽

Abida P.S ◽

...

Keyword(s):

Ssr Markers ◽

Genome Wide Association Study ◽

Agronomic Traits ◽

Oryza Sativa L ◽

Genotyping By Sequencing ◽

Plant Production ◽

Plant Performance ◽

Chromosome 1 ◽

Production Traits ◽

Rice Varieties

Abstract Development of rice varieties suited to varying drought stress level, and crop stages, relies mainly on identifying new genetic resources and genomic targets to improve whole plant physiological processes and productivity. This study with 99 rice germplasm adapted to Southwestern Indian peninsular region genotyped with 100 SSR markers evaluated over five different seasons/field trials to characterize plant physiological, root traits and yield related traits under different intensity and crop stage experienced water limitation. Traits like chlorophyll stability index, leaf rolling, days to 50% flowering, chlorophyll content, root volume and root biomass were identified as best predictors of grain yield under stress. Genome-Wide Association Study revealed genetic variation and genomic targets underlying major QTLs for different physiological, root and plant production traits. Combined analysis with trials 1-4 revealed 14 genomic regions governing multiple traits that contribute to plant performance and productivity under water stress. Genetic characterization of nine selected landraces and two elite cultivars using genotyping-by-sequencing (GBS) revealed haplotype variation within genomic targets on chromosome 1, 4, 6 and 11 for potential use as molecular markers. The genetic and genomic resources identified will enable combining traits with agronomic value to optimize yield under stress and hasten trait introgression into elite cultivars.

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Development of SSR Marker Set to Identify Fourty Two Indonesian Soybean Varieties

Jurnal AgroBiogen ◽

10.21082/jbio.v11n2.2015.p49-58 ◽

2016 ◽

Vol 11 (2) ◽

pp. 49

Author(s):

Andari Risliawati ◽

Eny I. Riyanti ◽

Puji Lestari ◽

Dwinita W. Utami ◽

Tiur S. Silitonga

Keyword(s):

Ssr Markers ◽

Ssr Marker ◽

Variety Identification ◽

Polymorphism Analysis ◽

Dna Fingerprints ◽

Soybean Variety ◽

Genetic Purity ◽

Electrophoresis System ◽

Simple Sequence ◽

Genetic Analyzer

Profile of molecular marker can be used for variety identification, genetic purity monitoring of germplasm and additional requirement in proposing intellectual property protection. DNA fingerprinting of soybean had been applied at the ICABIOGRADIAARD since 2004 using simple sequence repeat (SSR) markers which were run automatically by CEQ 8000 Genetic Analyzer platform based on capillary electrophoresis system. This method had produced unique DNA fingerprints of the varieties tested, but the marker set to efficiently identify the varieties had not yet been developed. This study aimed to develop a set of SSR markers as a tool to identify the Indonesian soybean varieties. Fourty two soybean varieties were analyzed using 14 random SSR markersA total of 168 alleles that were obtained from the polymorphism analysis. The average of polymorphic information content (PIC) value observed was 0.7337 per SSR locus. Based on marker reproducibility rate, PIC value, number of rare alleles, frequency of dominant alleles, and percentage of SSR fragment detected by genetic analyzer, we identified five SSR markers i.e. Satt414, Satt147, Satt308, Satt009, and Satt516 as a SSR marker set to be used for soybean variety identification purposes. This marker set was used to develop the identity (ID) of the 42 Indonesian soybean varieties.

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Similarity of 26 New Released Rice Varieties and Rice Parental Hybrids Based on 36 SSR Markers

Jurnal Penelitian Pertanian Tanaman Pangan ◽

10.21082/jpptp.v33n2.2014.p71-76 ◽

2014 ◽

Vol 33 (2) ◽

pp. 71

Author(s):

Untung Susanto ◽

Satoto Satoto ◽

Nofi A. Rohmah ◽

Made Jana Mejaya

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Ssr Markers ◽

Rice Varieties ◽

Average Value ◽

Modified Method ◽

Rice Chromosomes ◽

Medium Level ◽

Rice Genotypes ◽

Parental Lines

More than 200 rice varieties had been released in Indonesia, but the genetic variability among those released varieties was suspected to be relatively low. Molecular markers, especially SSR could be used as a tool to disect the distinctness among rice genotypes, albeit phenotipically similar varieties. The technique could also be used to prove the authenticity of a variety. This research was aimed to obtain DNA fingerprinting data of new released rice varieties and hybrid parental lines using SSR markers. A total of 26 rice genotypes consisted of three upland, ten irrigated, five swampy rice varieties, along with eight hybrid parental lines were used in this experiments. The DNA was extracted from young leaf samples using CTAB modified method and was amplified with 36 SSR markers linked to important rice traits which spread accross the 12 rice chromosomes. The experiment was conducted in Plant Breeding Laboratory of Indonesian Center for Rice Research (ICRR) during 2012. The results showed that PIC value of the genotypes were mostly at medium level of the genetic diversity with the average value of 0.4451. The phylogenetic analysis showed that at the genetic distance of 10%, the genotypes were separated into 9 groups, i.e. Inpago 6, Inpara 5, and BH33d each stood alone while (Inpara 1, Inpara 2 , and Inpara 3); (Inpari 18 and Inpari 19, Inpago 4, Inpago 5, and Inpara 4); (Inpari 11, Inpari 12, Inpari 13, Inpari 14, Inpari 15, Inpari 16, Inpari 17, and Inpari 20); (GMJ6B, B6, and IR79156B); (PK21, BH95E, Bio9, and R14) each belong to one group. The grouping of the genotypes in this study seemed to follow the adaptation type to agro ecosystems. The hybrid parental lines tended to stay in different group from the inbred varieties. The application of these 36 SSR markers was able to distinguish among 26 genotypes rather distinctly.The use of more markers should give more powerful data to distinguish among genotypes.

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Rapid high throughput template preparation (rHTTP) method: a novel cost effective method of direct PCR for a wide range of plants

BMC Biotechnology ◽

10.1186/s12896-019-0560-4 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Prassan Choudhary ◽

Sudipta Das ◽

Hillol Chakdar ◽

Arjun Singh ◽

Sanjay Kumar Goswami ◽

...

Keyword(s):

Ssr Markers ◽

High Throughput ◽

Field Experiments ◽

Dna Isolation ◽

Cost Effective ◽

Direct Pcr ◽

Rice Varieties ◽

Plant Materials ◽

Wide Range ◽

Commercial Kits

Abstract Background Conventional plant DNA isolation methods are complex, time consuming and require technical expertise. These limitations were overcome using the DNA isolation kits which, however significantly add to the research costs. Hence the present study was aimed to develop a high throughput, rapid and inexpensive method of PCR ready DNA template preparation from plant materials. Methods Concentration of SDS in lysis buffer, amount of starting material, period and temperature for lysis were optimized for obtaining PCR ready templates from plant materials. The method was tested using RAPD and ITS specific primers for different plant species like rice, wheat, mustard, pea, soybean, pigeonpea, tomato, maize, march lilly, bougainvillea, Indian blanket flower, nerium, petunia, purple pirouette petunia, moses-in-the-cradle, golden cane palm, duranta, periwinkle, chrysanthemum and two xerophytes viz. Dipterygium glaucum and Crotaleria burhia. SSR markers RM18398 and RM26108 showed successful amplification in rice varieties Improved Pusa Basmati 1 and KS Dev 12. The effectiveness of the method was tested using fresh as well as 1 year old tissues. The storability of the lysate was also tested. Results In this report, we developed a novel method called rapid high throughput template preparation (rHTTP) method to prepare PCR ready DNA templates. Most striking feature of this technique is that it can be done anywhere where water can be boiled by any means. Using rHTTP method, PCR ready templates can be prepared in just 10 min. Robust and reproducible amplification for all the test plants were recorded with RAPD, plant ITS primers and SSR markers following this method. rHTTP methods works well for both fresh as well as old plant tissues. The lysates had a shelf life of 1 month when stored at 4 °C and 3 days when stored at room temperature. Conclusions rHTTP method has several advantages over the other protocols like ease of execution, no requirement of tissue grinding/liquid nitrogen/hazardous chemicals and above all, equally effective for both fresh and old samples. Using this method, costs per prep comes down ~ 10–50 times as compared to most commercial kits. This method can be used for on-field experiments like molecular diagnostics, varietal identification etc.

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