Hybrid rice (Oryza sativa L.): identification and parentage determination by RAPD fingerprinting

Wang, Gejiao; Castiglione, Stefano; Zhang, Jian; Fu, Rong; Ma, Ju; Li, Wenbin; Sun, Yujun; Sala, F.

doi:10.1007/bf00233772

Cited by 24 publications

(12 citation statements)

References 14 publications

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“…In the beginning, PCR based RAPD marker was used for DNA fingerprinting of hybrids/ genotypes of rice (Wang 1994), but after the developments of microsatellite markers (Mc Couch , 1997, STMS and STS, which are co-dominant in nature, has chromosomal specificity and can generate variety specific profiles with high fidelity and capable to differentiate between the homozygous and heterozygous genotypes (Yun 2005;Antonova , 2006;Sundaram , 2008;Vikas 2014). There are more than nineteen thousands of well distributed and mapped STMS and STS markers reported in the rice (Tamilkumar , 2009;Lea , 2010; that have constituted a large group of markers for detecting polymorphism between parental lines of hybrids.…”

Section: Methodsmentioning

confidence: 99%

Genetic purity assessment of indica rice hybrids through DNA fingerprinting and grow out test

Verma¹,

Singh²,

Kumar³

et al. 2017

JEB

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Aim : Methodology :Results : Interpretation :Varietal identity and their purity assessment is essential to assert intellectual rights to breeder, helps seed testing and certification agencies to ensure pure seeds to the farmers, buyers, processors and consumers.In the present study, molecular characterization and genetic purity analysis of nine indica rice hybrids and respective 13 parental lines (22 genotypes) were done utilizing grow out test grow out test and micro-satellite markers based DNA fingerprinting approach. A total of 48 microsatellite (SSR and STMS) markers spanning over whole rice genome were screened.he statistical analysis of grow out test revealed that 88.25 per cent genetic purity was assessed in 3 hybrids tested. Twelve out of 48 microsatellite used were found polymorphic and amplified a total of 29 alleles among the genotypes with an average polymorphic information content value of 0.45. Out of 12 informative markers, nine were found polymorphic across the genotypes and produced unique fingerprints. Five STMS markers (RM154, RM164, RM234, RM258 and RM519) showed polymorphism over all the genotypes and were identified as referral marker for use in unambiguous identification and protection of nine hybrids. Nevertheless, marker RM 19 amplified allele was specific to the parental lines of CNRH 3 and APHR 2 (having common CMS line, IR62829). The results on genetic purity test through GOT had highly significant positive correlation (r=0.96) with molecular marker analysis.Genotype specific STMS markers identified in the study and their close association with the ability of grow out test, emphasizes immense scope for molecular approaches t o b e a n a l t e r n a t i v e s i n unambiguous assessment of genetic purity of hybrids and their parents. The molecular markers based genetic purity assessment may serve as a probable substitute to grow out test, which is a c u m b e r s o m e a n d t i m e consuming task and would benefit the farmers and agencies involved in this venture, hybrid rice seed production and cultivation.

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Section: Methodsmentioning

confidence: 99%

Genetic purity assessment of indica rice hybrids through DNA fingerprinting and grow out test

Verma¹,

Singh²,

Kumar³

et al. 2017

JEB

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“…8,9) RAPD analysis was revealed to be reproducible and amenable for identification of each single plant line of F1 hybrid rice in China 10) and Australian rice cultivars.…”

Section: )mentioning

confidence: 99%

“…8,9) RAPD analysis was revealed to be reproducible and amenable for identification of each single plant line of F1 hybrid rice in China 10) and Australian rice cultivars. 11) Diversified rice cultivars were classified into separate groups by PCR using RAPD markers, but many primers were needed to resolve closely related japonica cultivars.…”

mentioning

confidence: 99%

Cultivar Identification of Rice (Oryza sativa L.) by PCR Method and its Application to Processed Rice Products

研一¹,

澄子²

2007

J. Appl. Glycosci.

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Rice is one of the most important edible crops in the world, along with wheat and corn. There are more than several tens of thousands of varieties or cultivars of rice in the world. Rice is markedly diversified from the viewpoint of genetics, morphology and properties. On the other hand, high quality rice is closely related by inbreeding to attain high palatability, high processing suitability, characteristic aroma, etc.Rice grains of the famous cultivars are traded or distributed at higher prices as "premium rice" than the ordinary rice because of their high palatability, processing suitability, special aroma, etc. As those premium rice grains sell at high price, some dishonest rice wholesalers or retailers blend low quality cheap rice with high quality premium rice and mislabel it as "high quality premium rice. Recently, rice consumers have tended to demand more information, such as cultivar name, location of production, year of production, etc., about rice which they purchase. For example, it is required under the JAS LAW (Law Concerning Standardization and Proper Labeling of Agricultural and Forestry Products in Japan) to display the name of rice cultivar on the package. Therefore, technology to identify rice cultivars is very important for breeders, farmers, inspectors, wholesalers, retailers, food industries and consumers.Rice cultivars have been identified on the basis of morphological characteristics of rice plants or grains, ripening ratio after crossing, isozyme patterns, etc. Cultivated rice (Oryza sativa L.) is one of the most polymorphic crop species in the world. In contrast, many cultivars of high quality rice or premium rice are closely related because inbred lines are often used for their development. Therefore, it is necessary to develop a time saving technology to differentiate rice cultivars clearly and precisely.DNA fingerprinting was developed in 1985 1) and is used for criminal investigation and trial at court. Recently, a novel cultivar identification method based on DNA polymorphism has been developed accompanied with the progress in molecular biology. DNA based markers have the obvious advantage of sampling the genome directly and RFLP analysis has been widely used for assessing variation of plants.2 4) RFLP analysis has been used to distinguish between species of Oryza 5) and particularly between indica and japonica types of Oryza sativa. 6)Recently, a PCR based marker system has been developed by Williams et al . 7) In this RAPD (Random Amplified Polymorphic DNA) method, short oligo nucleotides of arbitrary sequences are used to support the amplification of regions of the test plant genome and amplified DNAs are separated by gel electrophoresis.There are some reports on RAPD analysis of rice germplasm including indica and japonica types, to identify suitable parents for linkage map construction, and for gene tagging for drought resistance. 8,9) RAPD analysis was revealed to be reproducible and amenable for identification of each single plant line of F1 hybrid rice in China 10) and A...

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“…(1990) is a simple and reproducible PCR amplification technique that is commonly used in the evaluation of genetic diversity. It is well established that RAPD is a potent marker for determining genetic diversity in rice ( Ko et al., 1994 ; Mackill, 1995 ; Virk et al., 1995 ; Fuentes et al., 1999 ) and a variety of RAPD markers have been utilized to identify, protect, and determine parents for further crop improvement ( Wang et al., 1994 ). Numerous researchers have used RAPD marker technique to determine genetic diversity in a variety of cultivated rice varieties, local rice landraces and aromatic rice cultivars ( Rekha et al., 2011 ; Hasan and Raihan, 2014 ; Xie et al., 2000 ).…”

Section: Introductionmentioning

confidence: 99%

Genetic variability analysis of partially salt tolerant local and inbred rice (Oryza sativa L.) through molecular markers

Mazumder

Hoque

Sinha

et al. 2020

Heliyon

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Random Amplified Polymorphic DNA (RAPD) analysis was performed to assess the genetic variability in sixteen selected germplasms of rice, Oryza sativa L. using eight decamer RAPD primers. The data obtained from this investigation reveals a high level of polymorphism between cultivars. The primers produced a total of 255 bands of which all 255 bands were polymorphic indicating 100% polymorphism. The size of the amplified bands ranged from 220 bp to 2290 bp. The number of polymorphic fragments ranged from 24 to 49 with an average of 32 polymorphic fragments for each primer. The primer OPX04 produced the maximum number (49) of polymorphic bands while the OPB04 and OPB17 produced the minimum number (24) of polymorphic bands. The polymorphic information content (PIC) values ranged from 0.6616 to 0.8845 with an average of 0.832. The highest PIC value (0.8845) was obtained for primer OPL03. The RAPD data was analyzed to determine the pair-wise genetic similarity coefficients which ranged from 0.00 to 0.83. The BRRIdhan 23 and the BRRIdhan 41 varieties were the closest genotypes with the highest similarity index of 83%. This was followed by 77% similarity between a pair of cultivars Kalamona and Horkuch. On the other hand, 100% dissimilarity was seen between BRRIdhan 53, BRRIdhan 50, BRRIdhan 10, BRRIdhan 70, BRRIdhan 54, BRRIdhan 40, BRRIdhan 23, BRRIdhan 47, BRRIdhan 41 and Dadsail respectively and between BRRIdhan 53 and Horkuch; indicating a high level of variability between paired genotypes. Cluster analysis was performed using Unweighted Paired Group of Arithmetic Means (UPGMA). The UPGMA dendrogram resolved the selected rice cultivars into four clusters.

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Hybrid rice (Oryza sativa L.): identification and parentage determination by RAPD fingerprinting

Cited by 24 publications

References 14 publications

Genetic purity assessment of indica rice hybrids through DNA fingerprinting and grow out test

Genetic purity assessment of indica rice hybrids through DNA fingerprinting and grow out test

Cultivar Identification of Rice (Oryza sativa L.) by PCR Method and its Application to Processed Rice Products

Genetic variability analysis of partially salt tolerant local and inbred rice (Oryza sativa L.) through molecular markers

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