scholarly journals Search for and Analysis of Single Nucleotide Polymorphisms (SNPs) in Rice (Oryza sativa, Oryza rufipogon) and Establishment of SNP Markers

DNA Research ◽  
2002 ◽  
Vol 9 (5) ◽  
pp. 163-171 ◽  
Author(s):  
S. Nasu
Keyword(s):  
Oryza Sativa ◽  
Single Nucleotide Polymorphisms ◽  
Snp Markers ◽  
Oryza Rufipogon ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Characterization of Indonesian pigmented rice (Oryza sativa) based on morphology and Single Nucleotide Polymorphisms

2019 ◽  
Vol 20 (4) ◽  
pp. 1208-1214 ◽  
Author(s):  
NUR SITI KURNIASIH ◽  
RATNA SUSANDARINI ◽  
FEBRI ADI SUSANTO ◽  
TRI RINI NURINGTYAS ◽  
GLYN JENKINS ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Single Nucleotide Polymorphisms ◽  
Morphological Characters ◽  
Snp Markers ◽  
Hybrid Vigor ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pigmented Rice ◽  
Indica And Japonica Subspecies

Abstract. Kurniasih NS, Susandarini R, Susanto FA, Nuringtyas TR, Jenkins G, Purwestri YA. 2019. Characterization of Indonesian pigmented rice (Oryza sativa) based on morphology and Single Nucleotide Polymorphisms. Biodiversitas 20: 1208-1214. Indonesia has many cultivars of pigmented rice, but many variants have not been characterized using morphological characters and molecular markers. SNPs (Single Nucleotide polymorphisms) have been used in previous studies to identify the Indica and Japonica subspecies. Characterization of whether a line belongs to the Indica or Japonica subspecies is useful information for rice breeders, especially to generate line exhibiting the strong hybrid vigor. Morphological characters are used to determine the relationship between cultivars using cluster analysis. The SNP markers were amplified by PCR, sequenced and compared with sequences in the GenBank. Based on morphological characters, ten cultivars divide into two clusters. SNPs distinguish Indica and Japonica subspecies, and show that Hitam Lampung, Aek Sibundong, Melik, Hitam Toraja, Merah Kalimantan, and Merah Sumbawa belong to the Indica subspecies while Cempo Ireng and Pare Eja belong to Japonica. Abang Segreng and Hitam Toraja could not be clearly assigned to either the Indica or Japonica subspecies.

NIASGBsnp: integration of single nucleotide polymorphism data of rice (Oryzasativa L.) genetic resources

2013 ◽  
Vol 11 (3) ◽  
pp. 221-224
Author(s):  
Masaru Takeya ◽  
Fukuhiro Yamasaki ◽  
Sachiko Hattori ◽  
Kaworu Ebana
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Plant Pathology ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Resources ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Snp Data ◽  
Polymorphism Data

The NIASGBsnp system manages data on single nucleotide polymorphisms (SNPs) of rice (Oryzasativa L.) genetic resources in the National Institute of Agrobiological Science (NIAS) Genebank. NIASGBsnp currently holds data on 768 SNP markers for 301 rice accessions and plans to add the SNP data of active rice accessions in the NIAS Genebank. It can show differences between accessions by graphical genotyping. Passport, characteristics and evaluation data of accessions can be retrieved to allow phenotype to be associated with genotype. NIASGBsnp will support various research purposes such as genomic selection and plant pathology research.

scholarly journals Comparative analysis of microsatellite and SNP markers for parentage testing in the golden snub-nosed monkey (Rhinopithecus roxellana)

2020 ◽  
Vol 12 (4) ◽  
pp. 611-620
Author(s):  
Chen Ling ◽  
Wu Lixia ◽  
Hou Rong ◽  
Shen Fujun ◽  
Zhang Wenping ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Snp Markers ◽  
Rhinopithecus Roxellana ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Parentage Testing ◽  
International Human

Abstract Microsatellite markers are popular for assigning parentage, but single-nucleotide polymorphisms (SNPs) have only been applied in this area recently. To evaluate these two markers which have been previously studied in golden snub-nosed monkeys, we genotyped 12 individuals using 37 microsatellite loci and 37 SNP markers. The data showed that 32 of 37 microsatellite loci were polymorphic, and most microsatellite loci were high informative (mean PIC = 0.599). Meanwhile, 24 of 37 SNP markers were polymorphic and most were low informative (mean PIC = 0.244). For microsatellites, the combined exclusion probability with one-parent-unknown/known (CE-1P/CE-2P) nearly reached 1, while for the SNP markers, CE-2P only reached 0.9582. Under the condition of one parent known/unknown, the CE-2P and CE-1P could meet the international human parental standard (0.9973) by using five or nine microsatellite loci respectively. For SNP markers, we doubled the loci (n = 48) and simulated parentage testing, and the data showed that the CE-2P was 0.998 while the CE-1P was still low. This result indicated that the SNP loci which we used here had low polymorphism and that more loci need to be developed in the future. In addition, we corrected one case of failed identification by excluding siblings and reducing the range of candidate paternities.

Single nucleotide polymorphism (SNP) markers for benzimidazole resistance in veterinary nematodes

Parasitology ◽  
2007 ◽  
Vol 134 (8) ◽  
pp. 1077-1086 ◽  
Author(s):  
G. VON SAMSON-HIMMELSTJERNA ◽  
W. J. BLACKHALL ◽  
J. S. McCARTHY ◽  
P. J. SKUCE
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Point Mutations ◽  
Building Blocks ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Principal Mechanism ◽  
Tubulin Isotype ◽  
Veterinary Importance

SUMMARYResistance to the benzimidazole class of anthelmintics in nematodes of veterinary importance has a long history. Research into the mechanisms responsible for this resistance is subsequently at a more advanced stage than for other classes of anthelmintics. The principal mechanism of resistance to benzimidazoles is likely to involve changes in the primary structure of β-tubulins, the building blocks of microtubules. Specifically, point mutations in the β-tubulin isotype 1 gene leading to amino acid substitutions in codons 167, 198, and 200 of the protein have been associated with resistance in nematodes. These single nucleotide polymorphisms offer a means of detecting the presence of resistance within populations. In this mini-review, we focus on the prevalence and importance of these polymorphisms in three groups of nematodes: trichostrongylids, cyathostomins, and hookworms. A brief overview of existing strategies for genotyping single nucleotide polymorphisms is also presented. The CARS initiative hopes to exploit these known polymorphisms to further our understanding of the phenomenon of BZ resistance.

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