Identification of RAPD marker for the White Backed Plant Hopper (WBPH) resistant gene in rice (original) (raw)
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Brown planthopper (Nilaparvata lugens Stål) is one of the most damaging pests causing hopper burn in rice, and thereby reducing the productivity and also the quality of the product. The effective management strategy to control this pest is the identification and transfer of desirable genes to local rice cultivars. The most important approach for developing resistant cultivars is the identification of markers, which can help in marker-assisted selection of more durable resistant genotype. The susceptible parent IR50 and the resistant parent Ptb33, and their F 2 populations were used in bulked segregant analysis for identification of resistant genes with random amplified polymorphic DNA marker (RAPD) primers. The primers OPC7 and OPAG14 showed both dominant and susceptible specific banding pattern so called co-dominant markers. Moreover, OPC7 697 and OPAG14 680 showed resistant specific bands and thus being in coupling phase, whereas OPC7 846 and OPAG14 650 showed susceptible specific genotypic bands in bulked segregant analysis. Therefore, the coupling phase markers, OPC7 697 and OPAG14 680 , are considered to be more useful in marker-assisted selection of rice genotypes in crop improvement.
Gene Validation for Brown Plant Hopper Resistance in Rice Varieties Using SSR Markers
International Journal of Plant & Soil Science
The Brown Plant Hopper (BPH), Nilaparvata lugens (Homoptera: Delphacidae) is one of the most destructive insect pests causing significant yield loss in most of the rice cultivars of Asia. Marker-assisted backcrossing is used to introgress the genes for BPH resistance in which the selection of donor parents to confer durable resistance and validation of the presence of genes is a prerequisite. Jyothi the most popular, widely cultivated rice variety in Kerala is screened along with four parental lines viz., PTB33 (Variety released from RARS, Pattambi), IRRI introgressed lines- IR65482-7-216-1-2, IR7103-121-15-B, and a breeding line RP2068-13-5-8 for validating the presence of genes Bph3, BPH18, Bph20, and Bph21 using SSR markers. Parental polymorphism was shown for markers specific to Bph3, BPH18, and Bph20. Besides this, cluster analysis using the UPGMA method produced 4 clusters. The variety ‘PTB33’ was obtained in a separate cluster which can be attributed to its resistant characte...
Journal of Pharmacognosy and Phytochemistry, 2016
The brown planthopper (BPH), Nilaparvata lugens Stal (Homoptera: Delphacidae), is the most-significant insect pest of rice (Oryza sativa L.) throughout rice-growing countries. In this study DNA-based SSR molecular marker technique was deployed to estimate genetic diversity among 30 rice accessions using seven SSR primers which produced a total of 32 polymorphic markers with the average number of 4.57 markers per primer. The PIC value for all 7 microsatellite loci in the present study ranged from 0.500-0.833. The PIC value was maximum in case of RM186 (0.833) and all the SSR markers were more informative since they recorded more than 0.500 as PIC value. The seven primer pairs showed 3-6 alleles across 30 genotypes grouping the genotypes into 7 groups of different composition indicating that even seven SSR primer pairs can differentiate the cultivars. The analysis indicated that co efficient of similarity among 30 varieties ranged from 0.67 to 1. In the present study, SSR markers were...
Development and large-scale genotyping of single-nucleotide polymorphism (SNP) is required to use identified sequence variation in the alleles of different genes to determine their functional relevance to the candidate gene(s). In the present study, Illumina GoldenGate assay was used to validate and genotype SNPs in a set of six major rice blast resistance genes, viz. Pi-ta, Piz(t), Pi54, Pi9, Pi5(1) and Pib, distributed over five chromosomes, to understand their functional relevance and study the population structure in rice. All the selected SNPs loci (96) of six blast (Magnaporthe oryzae) resistance genes were genotyped successfully in 92 rice lines with an overall genotype call rate of 92.0 % and minimum GenTrain cutoff score of C0.448. The highest genotyped SNPs were found in japonica type (97.1 %) rice lines, followed by indica (92.12 %), indica basmati (91.84 %) and minimum in case of wild species (82.0 %). Among the genotyped loci, the highest score (98.68 %) was observed in case of Piz(t), followed by Pi-ta, Pi5(1), Pib, Pi54 and Pi9. Polymorphism was obtained in 87.5 % SNPs loci producing 7,728 genotype calls. Minor allele frequency ranged from 0.01 to 0.49 and has good differentiating power for distinguishing different rice accessions. Population structure analysis revealed that a set of genotypes from four rice subpopulations had ‘‘admix’’ ancestry ([26 %) with more than one genetic background of indica, japonica and wild types. SNPs markers were validated in a set of 92 rice lines and converted into CAPS markers which can be used in blast resistance breeding programme.
Marker-assisted selection for the rice blast resistance gene Pi-ar in a backcross population
Cropp Breeding and Applied Biotechnology, 2010
A doubled-haploid (DH) population, obtained by anther culture of F 1 plants from a cross between a highly susceptible rice cultivar Lijiangxintuanheigu and the resistant somaclone (SC09), of the cultivar Araguaia, was used to identify RAPD markers linked to the blast resistance gene Pi-ar. The 86 DH plants, inoculated with the race IB-9 of Magnaporthe oryzae, segregated in 1:1 ratio of resistant and susceptible plants. Of the 67 primers used 31 produced DNA profiles that differentiated resistant and susceptible bulks as well as the parental cultivars. The resistance gene was found linked to the primer OPS16 2072 ('AGGGGGTTCC') at a distance of 3.6 cM. The selection efficiency of this primer was assessed in a BC 3 F 1 population derived from another cross between a susceptible cultivar IAC 201 and SC09. The marker OPS16 showed efficiency of 86.9%, when six resistant and two susceptible plants were considered as negatives in RAPD analysis.
2015
Brown planthopper is one of the most destructive insect pest of rice in Indonesia and other Asian countries. Pyramiding some brown planthopper resistance genes is a valuable approach to create more durable resistance against the pest. The objective of this study was to identify polymorphisms of Brown Planthopper Resistance genes (Bph) on 20 genotypes of rice, and to obtain genetic relationship among genotypes tested. The experiment was conducted from June to September 2012 at Green House and Laboratory of Plant Analysis and Biotechnology, Faculty of Agriculture, Universitas Padjadjaran, Jatinangor. Twenty genotypes were analyzed, and two of them were used as check varieties. Simple Sequence Repeat (SSR) markers were applied to detect Bph3, Bph4, Qbph3, and Qbph4 genes. Polymorphic levels were analyzed by calculating PIC (Polymorphic Information Content). The grouping of rice genotypes were done based on principal components analysis (PCA) of SSR data, and the genetic relationship ba...
Molecular tagging of a gene for resistance to brown planthopper in rice (Oryza sativa L.)
2003
An introgression line derived from an interspecific cross between Oryza sativa and Oryza officinalis, IR54741-3-21-22 was found to be resistant to an Indian biotype of brown planthopper (BPH). Genetic analysis of 95 F 3 progeny rows of a cross between the resistant line IR54741-3-21-22 and a BPH susceptible line revealed that resistance was controlled by a single dominant gene. A comprehensive RAPD analysis using 275 decamer primers revealed a low level of (7.1%) polymorphism between the parents. RAPD polymorphisms were either co-dominant (6.9%), dominant for resistant parental fragments (9.1%) or dominant for susceptible parental fragments (11.6%). Of the 19 co-dominant markers, one primer, OPA16, amplified a resistant parental band in the resistant bulk and a susceptible parental band in the susceptible bulk by bulked segregant analysis. RAPD analysis of individual F 2 plants with the primer OPA16 showed marker-phenotype co-segregation for all, with only one recombinant being identified. The linkage between the RAPD marker OPA16 938 and the BPH resistance gene was 0.52 cM in coupling phase. The 938 bp RAPD amplicon was cloned and used as a probe on 122 Cla I digested doubled haploid (DH) plants from a IR64xAzucena mapping population for RFLP inheritance analysis and was mapped onto rice chromosome 11. The OPA16 938 RAPD marker could be used in a cost effective way for marker-assisted selection of BPH resistant rice genotypes in rice breeding programs.
DNA tagging of blast resistant gene(s) in three Brazilian rice cultivars
Genetics and Molecular Biology, 2003
Rice blast is the most important fungal disease of rice and is caused by Pyricularia oryzae Sacc. (Telomorph Magnoporthe grisea Barr.). Seven randomly amplified polymorphic DNA (RAPD) markers OPA5, OPG17, OPG18, OPG19, OPF9, OPF17 and OPF19 showed very clear polymorphism in resistant cultivar lines which differed from susceptible lines. By comparing different susceptible lines, nine DNA amplifications of seven primers (OPA5 1000 , OPA5 1200, OPG17 700 , OPG18 850 , OPG19 500 , OPG19 600 , OPF9 600 , OPF17 1200 and OPF19 600) were identified as dominant markers for the blast resistant gene in resistant cultivar lines. These loci facilitate the indirect scoring of blast resistant and blast susceptible genotypes. The codomine RAPDs markers will facilitate marker-assisted selection of the blast resistant gene in two blast resistant genotypes of rice (Labelle and Line 11) and will be useful in rice breeding programs.