(293) Single Nucleotide Polymorphism in matK and Ribosomal ITS of Astilbe

The genus Astilbe (Saxifragaceae) comprises about 13 species and is ranked consistently among the top 10 landscape perennials. Through extensive hybridization, selection and marketing, the lineage of many Astilbehas been lost. Subdioecious Astilbebiternatais the only species in the genus native to North America while other members of the genus are endemic to Asia and monoecious. Due to the unusual geographic distribution of the species and the variation in floral development among them, development of genetic markers using single nucleotide polymorphisms (SNPs) would confirm phylogenetic relationships and establish lineage within the genus. Astilbespecies, hybrids, and cultivars were obtained from plant nurseries and botanical gardens across the country. To elucidate relationships among the genus, we conducted phylogenetic analysis of DNA sequences of the chloroplast gene matKand the internal transcriber spacer (ITS) of ribosomal rDNA genes. DNA was extracted, and gene primers trnK3914 and trnK2R were used to amplify matK, and primers 1406F and ITS2 were used to amplify the ITS1 region between 18S and 5.8S ribosomal DNA units. Both matKand ITS were sequenced for each plant specimen and sequences were aligned to identify nucleotide diversity and detect SNPs. Variation in nucleotide sequence for either gene yielded similar dendrograms. Nucleotide variation among the Astilbeutilized in this study has allowed the development of SNP markers that may be useful for fingerprinting unknown hybrids or cultivars in the industry, and may be used for species alignment within the genus.

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Heteroalleles in Common Wheat: Multiple Differences between Allelic Variants of the Gli-B1 Locus

International Journal of Molecular Sciences ◽

10.3390/ijms22041832 ◽

2021 ◽

Vol 22 (4) ◽

pp. 1832

Author(s):

Eugene Metakovsky ◽

Laura Pascual ◽

Patrizia Vaccino ◽

Viktor Melnik ◽

Marta Rodriguez-Quijano ◽

...

Keyword(s):

Common Wheat ◽

Dna Sequences ◽

Fragment Length Polymorphism ◽

Snp Markers ◽

Group Iv ◽

Nucleotide Polymorphisms ◽

High Genetic Diversity ◽

Single Nucleotide ◽

Allelic Variants ◽

B Genome

The Gli-B1-encoded γ-gliadins and non-coding γ-gliadin DNA sequences for 15 different alleles of common wheat have been compared using seven tests: electrophoretic mobility (EM) and molecular weight (MW) of the encoded major γ-gliadin, restriction fragment length polymorphism patterns (RFLPs) (three different markers), Gli-B1-γ-gliadin-pseudogene known SNP markers (Single nucleotide polymorphisms) and sequencing the pseudogene GAG56B. It was discovered that encoded γ-gliadins, with contrasting EM, had similar MWs. However, seven allelic variants (designated from I to VII) differed among them in the other six tests: I (alleles Gli-B1i, k, m, o), II (Gli-B1n, q, s), III (Gli-B1b), IV (Gli-B1e, f, g), V (Gli-B1h), VI (Gli-B1d) and VII (Gli-B1a). Allele Gli-B1c (variant VIII) was identical to the alleles from group IV in four of the tests. Some tests might show a fine difference between alleles belonging to the same variant. Our results attest in favor of the independent origin of at least seven variants at the Gli-B1 locus that might originate from deeply diverged genotypes of the donor(s) of the B genome in hexaploid wheat and therefore might be called “heteroallelic”. The donor’s particularities at the Gli-B1 locus might be conserved since that time and decisively contribute to the current high genetic diversity of common wheat.

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

Plant Genetic Resources ◽

10.1017/s1479262113000099 ◽

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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Evaluation of the Genetic Diversity of Xylella fastidiosa Strains from Citrus and Coffee Hosts by Single-Nucleotide Polymorphism Markers

Phytopathology ◽

10.1094/phyto-97-12-1543 ◽

2007 ◽

Vol 97 (12) ◽

pp. 1543-1549 ◽

Cited By ~ 9

Author(s):

Ester Wickert ◽

Marcos Antonio Machado ◽

Eliana G. M. Lemos

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphism ◽

Dna Sequences ◽

Xylella Fastidiosa ◽

Snp Markers ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Relationship Of ◽

First Time ◽

The Relationship

The aim of this study was to obtain information about genetic diversity and make some inferences about the relationship of 27 strains of Xylella fastidiosa from different hosts and distinct geographical areas. Single-nucleotide polymorphism (SNP) molecular markers were identified in DNA sequences from 16 distinct regions of the genome of 24 strains of X. fastidiosa from coffee and citrus plants. Among the Brazilian strains, coffee-dependent strains have a greater number of SNPs (10 to 24 SNPs) than the citrus-based strains (2 to 12 SNPs); all the strains were compared with the sequenced strain 9a5c. The identified SNP markers were able to distinguish, for the first time, strains from citrus plants and coffee and showed that strains from coffee present higher genetic diversity than the others. These markers also have proven to be efficient for discriminating strains from the same host obtained from different geographic regions. X. fastidiosa, the causal agent of citrus variegated chlorosis, possesses genetic diversity, and the SNP markers were highly efficient for discriminating genetically close organisms.

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

Parasitology ◽

10.1017/s0031182007000054 ◽

2007 ◽

Vol 134 (8) ◽

pp. 1077-1086 ◽

Cited By ~ 76

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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Developmentof 84 single nucleotide polymorphism (SNP) markers for the three-spot swimming crab (Portunus sanguinolentus) by using RAD appoach Guidong Miao1,2,3 Feng Wang1,2,3 Jihua Guo1,2,3, Pei Zhang1,2,3 Hongyu Ma4

10.21203/rs.3.rs-790065/v1 ◽

2021 ◽

Author(s):

Guidong Miao ◽

Feng Wang ◽

Jihua Guo ◽

Pei Zhang ◽

Hongyu Ma

Keyword(s):

Dna Sequences ◽

Average Frequency ◽

Snp Markers ◽

Swimming Crab ◽

Nucleotide Polymorphism ◽

Base Pairs ◽

Single Nucleotide ◽

Large Size ◽

Pcr Products ◽

Hardy Weinberg Equilibrium

Abstract The three-spot swimming crab (Portunus sanguinolentus) is one of most important large size economic crab in China. In this study, we first isolated and characterized a set of 84 SNP loci in P. sanguinolentus. 10 pairs of primers PCR products were sequenced and a total of 3181bp high-quality DNA sequences were obtained from which 84 polymorphic SNP loci were identifed and 84 SNP loci were identified and accurated genotyped. The average frequency of SNP loci was one locus every 38 base pairs in P. sanguinolentus genome. Of these 84 SNP loci, each had bi-alleles with the minor allele frequency ranging from 0.0167 to 0.5000. The observed heterozygosity varied from 0.0333 to 0.7143, while the expected heterozygosity ranged from 0.0333 to 0.5085 per locus. 51 loci showed low variation (HO ≤ 0.3) and fourteen SNP loci showed high variation (HO ≥ 0.5). Among 84 SNP loci, 11 loci showed significant deviation from Hardy–Weinberg Equilibrium. The SNP markers developed herein will provide valuable information for elucidating population genetic diversity, population dynamics, and conservation genetics of this germplasm resource and other related crab species.

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Development of Highly Validated SNP Markers for Genetics Analyses of Chestnut Species.

10.21203/rs.3.rs-314998/v1 ◽

2021 ◽

Author(s):

Clement LARUE ◽

Erwan Guichoux ◽

Benoît Laurent ◽

Teresa Barreneche ◽

Cécile Robin ◽

...

Keyword(s):

Quality Criteria ◽

Snp Markers ◽

Nucleotide Polymorphism ◽

Mendelian Segregation ◽

Single Nucleotide ◽

Sufficient Power ◽

Ssr Loci ◽

Species Hybrids ◽

Stringent Quality ◽

Clonal Identification

Abstract To better study and manage chestnut trees and species, we identified nuclear single nucleotide polymorphism (SNP) markers using restriction-associated DNA sequencing. Out of 343 loci tested, 68 SNP markers were selected that withhold stringent quality criteria such as quasi-systematic amplification across species and Mendelian segregation in both purebred and hybrid individuals. They provide sufficient power for species, hybrids and backcross characterization as well as for clonal identification, as shown by a comparison with single sequenced repeat (SSR) loci.

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Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice

Plants ◽

10.3390/plants10040705 ◽

2021 ◽

Vol 10 (4) ◽

pp. 705

Author(s):

John Carlos I. Ignacio ◽

Maricris Zaidem ◽

Carlos Casal ◽

Shalabh Dixit ◽

Tobias Kretzschmar ◽

...

Keyword(s):

Genetic Basis ◽

Snp Markers ◽

Nucleotide Polymorphism ◽

Rice Varieties ◽

Single Nucleotide ◽

Genotyping Platform ◽

Anaerobic Germination ◽

Direct Seeded ◽

Mapping By Sequencing ◽

Simple Sequence

Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded fields, including tolerance to anaerobic germination (AG). To map the genetic basis of its tolerance, we examined a population of 200 F2:3 families derived from a cross between IR64 and ASD1 using the restriction site-associated DNA sequencing (RAD-seq) technology. This genotyping platform enabled the identification of 1921 single nucleotide polymorphism (SNP) markers to construct a high-resolution genetic linkage map with an average interval of 0.9 cM. Two significant quantitative trait loci (QTLs) were detected on chromosomes 7 and 9, qAG7 and qAG9, with LOD scores of 7.1 and 15.0 and R2 values of 15.1 and 29.4, respectively. Here, we obtained more precise locations of the QTLs than traditional simple sequence repeat and low-density SNP genotyping methods and may help further dissect the genetic factors of these QTLs.

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

Plant Genetic Resources ◽

10.1017/s1479262121000034 ◽

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.

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A Cotton-Fiber-Associated Cyclin-Dependent Kinase A Gene: Characterization and Chromosomal Location

International Journal of Plant Genomics ◽

10.1155/2012/613812 ◽

2012 ◽

Vol 2012 ◽

pp. 1-10 ◽

Cited By ~ 3

Author(s):

Weifan Gao ◽

Sukumar Saha ◽

Din-Pow Ma ◽

Yufang Guo ◽

Johnie N. Jenkins ◽

...

Keyword(s):

Cotton Fiber ◽

Sequence Data ◽

Snp Markers ◽

Pcr Analysis ◽

Cyclin Dependent Kinase ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Gene Characterization ◽

Protein Levels ◽

Catalytic Domains

A cotton fiber cDNA and its genomic sequences encoding an A-type cyclin-dependent kinase (GhCDKA) were cloned and characterized. The encoded GhCDKA protein contains the conserved cyclin-binding, ATP binding, and catalytic domains. Northern blot and RT-PCR analysis revealed that the GhCDKA transcript was high in 5–10 DPA fibers, moderate in 15 and 20 DPA fibers and roots, and low in flowers and leaves. GhCDKA protein levels in fibers increased from 5–15 DPA, peaked at 15 DPA, and decreased from 15 t0 20 DPA. The differential expression of GhCDKA suggested that the gene might play an important role in fiber development. The GhCDKA sequence data was used to develop single nucleotide polymorphism (SNP) markers specific for the CDKA gene in cotton. A primer specific to one of the SNPs was used to locate the CDKA gene to chromosome 16 by deletion analysis using a series of hypoaneuploid interspecific hybrids.

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Single nucleotide polymorphisms of CBF4 locus region of Arabidopsis thaliana correspond to drought tolerance

Chinese Journal of Agricultural Biotechnology ◽

10.1079/cjb200440 ◽

2004 ◽

Vol 1 (3) ◽

pp. 181-190 ◽

Cited By ~ 1

Author(s):

Hao Gang-Ping ◽

Wu Zhong-Yi ◽

Chen Mao-Sheng ◽

Cao Ming-Qing ◽

Dominique Brunel ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Drought Tolerance ◽

World Wide ◽

Nucleotide Variation ◽

Nucleotide Polymorphisms ◽

Water Deficiency ◽

Coding Region ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Adaptation To Drought

AbstractThe levels of drought tolerance and nucleotide polymorphism at the CBF4 locus were examined in a world-wide sample of 17 core accessions of Arabidopsis thaliana. The results showed that different accessions exhibited considerable differences in adaptation to drought stress. Compared with Columbia accession, the frequency of nucleotide polymorphism at the CBF4 locus of 25av, 203av and 244av accessions, including single nucleotide polymorphism (SNP) and insertion/deletion (Indel), was high, on average 1 SNP per 35.8 bp and 1 Indel per 143 bp. No significance in all regions of Tajima's D test indicated that the neutral mutation hypothesis could explain the nucleotide polymorphism in this CBF4 gene region. The higher polymorphism was the result of purification selection. Nucleotide polymorphism in the non-coding region was three times higher than in the coding region. This might indicate a recent relaxation of selection pressures on the non-coding region of CBF4 gene. In the coding region of CBF4, SNP frequency was 1 SNP per 96.4 bp and one non-synonymous mutation was detected from 25av, 203av and 244av accessions: the amino acid variation gly↔val at position 205, caused by the nucleotide variation G↔T at position 1034 (corresponding to the nucleotide at position 19 696 of GenBank accession no. AB015478 as 1). Furthermore, four differential SNPs were discovered in haplotype 6 constituted by 203av, one of them located in the 3′ non-coding region (A↔C at position 1106) and the others in the 5′ non-coding region (A↔G, A↔C and G↔A at positions 27, 129 and 171, respectively). The drought tolerance assay indicated that accession 203av was the best at tolerating water deficiency. We propose that haplotype 6 is consistent with its drought tolerance.

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