Development of 84 single nucleotide polymorphism (SNP) markers for the three-spot swimming crab (Portunus sanguinolentus) by using RAD approach

2021 ◽  
Author(s):  
Guidong Miao ◽  
Feng Wang ◽  
Jihua Guo ◽  
Pei Zhang ◽  
Hongyu Ma
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Snp Markers ◽  
Swimming Crab ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Assessment of diversity in tropical soybean (Glycine max (L.) Merr.) varieties and elite breeding lines using single nucleotide polymorphism markers

2021 ◽  
Vol 19 (1) ◽  
pp. 20-28
Author(s):  
Abush Tesfaye Abebe ◽  
Adesike Oladoyin Kolawole ◽  
Nnanna Unachukwu ◽  
Godfree Chigeza ◽  
Hailu Tefera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Glycine Max ◽  
Snp Markers ◽  
Fixation Index ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Breeding Lines ◽  
Soybean Germplasm ◽  
Elite Breeding Lines

AbstractSoybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.

Discovery of single nucleotide polymorphism in Capsicum and SNP markers for cultivar identification

Euphytica ◽  
2010 ◽  
Vol 175 (1) ◽  
pp. 91-107 ◽  
Author(s):  
Jin-kee Jung ◽  
Soung-Woo Park ◽  
Wing Yee Liu ◽  
Byoung-Cheorl Kang
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Cultivar Identification ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Molecular Characterization of Cacao (Theobroma cacao) Germplasm from Jamaica Using Single Nucleotide Polymorphism (SNP) Markers

2018 ◽  
Vol 11 (3-4) ◽  
pp. 93-106 ◽  
Author(s):  
Aliza A. Lindo ◽  
Dwight E. Robinson ◽  
Paula F. Tennant ◽  
Lyndel W. Meinhardt ◽  
Dapeng Zhang
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Molecular Characterization ◽  
Theobroma Cacao ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Genetic diversity of released Malaysian rice varieties based on single nucleotide polymorphism markers

2020 ◽  
Vol 56 (No. 2) ◽  
pp. 62-70 ◽  
Author(s):  
Shahril Ab Razak ◽  
Nor Helwa Ezzah Nor Azman ◽  
Rahiniza Kamaruzaman ◽  
Shamsul Amri Saidon ◽  
Muhammad Fairuz Mohd Yusof ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Crop Improvement ◽  
Snp Markers ◽  
Group Method ◽  
Chromosome 11 ◽  
Nucleotide Polymorphism ◽  
Rice Varieties ◽  
Single Nucleotide ◽  
K Value

Understanding genetic diversity is a main key for crop improvement and genetic resource management. In this study, we aim to evaluate the genetic diversity of the released Malaysian rice varieties using single nucleotide polymorphism (SNP) markers. A total of 46 released Malaysian rice varieties were genotyped using 1536 SNP markers to evaluate their diversity. Out of 1536 SNPs, only 932 SNPs (60.7%) represented high quality alleles, whereas the remainder either failed to amplify or had low call rates across the samples. Analysis of the 932 SNPs revealed that a total of 16 SNPs were monomorphic. The analysis of the SNPs per chromosome revealed that the average of the polymorphic information content (PIC) value ranged from 0.173 for chromosome 12 to 0.259 for chromosome 11, with an average of 0.213 per locus. The genetic analysis of the 46 released Malaysian rice varieties using an unweighted pair group method with arithmetic mean (UPGMA) dendrogram revealed the presence of two major groups. The analysis was supported by the findings from the STRUCTURE analysis which indicated the ∆K value to be at the highest peak at K = 2, followed by K = 4. The pairwise genetic distance of the shared alleles showed that the value ranged from 0.000 (MR159–MR167) to 0.723 (MRIA–Setanjung), which suggested that MR159 and MR167 were identical, and that the highest dissimilarity was detected between MRIA 1 and Setanjung. The results of the study will be very useful for the variety identification, the proper management and conservation of the genetic resources, and the exploitation and utilisation in future breeding programmes.

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.

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