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

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.

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

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1081E-1082
Author(s):  
Brian W. Trader ◽  
Richard E. Veilleux ◽  
Holly L. Scoggins
Keyword(s):  
Dna Sequences ◽  
Nucleotide Diversity ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Its1 Region ◽  
Rdna Genes ◽  
Species Hybrids ◽  
Plant Specimen

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.

Molecular characterisation of novel LMW-m and LMW-s genes from four Aegilops species (Sitopsis section) and comparison with those from the Glu-B3 locus of common wheat

2016 ◽  
Vol 67 (9) ◽  
pp. 938 ◽  
Author(s):  
Susana Cuesta ◽  
Carlos Guzmán ◽  
Juan B. Alvarez
Keyword(s):  
Common Wheat ◽  
Viscoelastic Properties ◽  
Wheat Breeding ◽  
Low Molecular Weight ◽  
Nucleotide Polymorphisms ◽  
Aegilops Species ◽  
Glutenin Subunits ◽  
Single Nucleotide ◽  
B Genome ◽  
S Genes

Low-molecular-weight glutenin subunits (LMW-GS) are a component of the gluten network and play a key role in determining the viscoelastic properties of wheat dough. Aegilops species have been shown to be an important source of variation for valuable traits for wheat breeding. However, very little is known about LMW-GS genes in section Sitopsis species, which are closely related to the B genome of common wheat. Ten accessions of Sitopsis species were evaluated for variability of LMW-GS genes, and 20 novel genes were obtained, of which nine were LMW-m and 11 were LMW-s genes. Only two were pseudogenes, corresponding to one LMW-m and one LMW-s gene. Six groups of genes were detected: three for each of the LMW-m and LMW-s genes. All groups of LMW-s genes and one of LMW-m genes (pGluU) detected were not related to B-genome genes from common wheat, whereas the remaining genes were. The single-nucleotide polymorphisms, and insertions and deletions, detected in active variants compared with those from common wheat could affect structure protein. The analysis of reactive epitopes for coeliac disease revealed that LMW-s subunits lacked toxicity, as did the pGluU LMW-m subunits; the other LMW-m subunits were less toxic than that from common wheat.

scholarly journals Thiopurine S-methyltransferase genetic polymorphisms in adult patients with inflammatory bowel diseases in the Latvian population

2020 ◽  
Vol 13 ◽  
pp. 175628482093742
Author(s):  
Polina Zalizko ◽  
Juris Stefanovics ◽  
Jelizaveta Sokolovska ◽  
Natalia Paramonova ◽  
Evija Klavina ◽  
...  
Keyword(s):  
Gene Polymorphisms ◽  
Fragment Length Polymorphism ◽  
Nucleotide Polymorphisms ◽  
Wild Type ◽  
Single Nucleotide ◽  
Allelic Variants ◽  
Bowel Diseases ◽  
Inflammatory Bowel ◽  
Tpmt Gene ◽  
European Populations

Background: Thiopurine methyltransferase (TPMT) plays a significant role in the metabolism of thiopurines, and, for patients with inflammatory bowel disease (IBD), it is useful to perform TPMT genotyping prior to azathioprine (AZA) treatment. In this study, we determined TPMT gene polymorphisms in a cohort of IBD patients in Latvia. Methods: DNA samples were obtained from 244 IBD patients, and qPCR was performed for detection of rs1800462, rs1800460, and rs1142345 single-nucleotide polymorphisms (SNPs). Three common, non-functional TPMT alleles ( TPMT*2, *3B, and *3C) were identified (women, 51%; men, 49%). TPMT*2, *3A, *3B, and *3C allelic variants detected using qPCR were consistent with restriction fragment length polymorphism (RFLP) data. Results: Among patients, 78% had ulcerative colitis and 22% had Crohn’s disease, with 93.9% of the former carrying a wild-type homozygous TPMT*1/*1 genotype and 6.1% carrying heterozygous genotypes. The most frequent polymorphisms were TPMT*1/*3A (5.3%: two variants: TPMT*3B and TPMT*3C), TPMT*1/*3C (0.4%), and TPMT*1/*2 (0.4%). None of the patients carried a TPMT*3B polymorphism and no patients were homozygous for any mutation. Conclusion: This is the first study to identify TPMT gene polymorphisms in adult IBD patients in Latvia. The results indicate that the frequency of common TPMT alleles is similar to that of other European populations.

scholarly journals Investigation of Genetic Relationships within Miscanthus using SNP Markers Identified using SLAF-Seq

2021 ◽  
Author(s):  
ZHIYONG Chen ◽  
Yancen He ◽  
Yasir Iqbal ◽  
Yanlan Shi ◽  
Hongmei Huang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genetic Relationships ◽  
Female Parent ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Sequencing Method ◽  
Specific Locus

Abstract Background: Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships and the evolution of gene function in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.Results: We identified 800,081 SLAF tags, of which 160,368 were polymorphic. Each tag was 264–364 bp long. The obtained SNPs were used to investigate genetic relationships within Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs, and found that the germplasms fell into two clades: one clade of M. sinensis only and one clade that included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis indicated that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.Conclusions: As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs utilizing Miscanthus cultivars with elite biomass- or fiber-production potential.

scholarly journals An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes

2021 ◽  
Author(s):  
Thomas K. F. Wong ◽  
Teng Li ◽  
Louis Ranjard ◽  
Steven Wu ◽  
Jeet Sukumaran ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Real Data ◽  
Reference Sequence ◽  
Nucleotide Polymorphisms ◽  
Data Set ◽  
Single Nucleotide ◽  
Short Read ◽  
Pooled Samples ◽  
Haplotype Information

AbstractA current strategy for obtaining haplotype information from several individuals involves short-read sequencing of pooled amplicons, where fragments from each individual is identified by a unique DNA barcode. In this paper, we report a new method to recover the phylogeny of haplotypes from short-read sequences obtained using pooled amplicons from a mixture of individuals, without barcoding. The method, AFPhyloMix, accepts an alignment of the mixture of reads against a reference sequence, obtains the single-nucleotide-polymorphisms (SNP) patterns along the alignment, and constructs the phylogenetic tree according to the SNP patterns. AFPhyloMix adopts a Bayesian model of inference to estimates the phylogeny of the haplotypes and their relative frequencies, given that the number of haplotypes is known. In our simulations, AFPhyloMix achieved at least 80% accuracy at recovering the phylogenies and frequencies of the constituent haplotypes, for mixtures with up to 15 haplotypes. AFPhyloMix also worked well on a real data set of kangaroo mitochondrial DNA sequences.

scholarly journals Association of non-synonymous SNPs of <i>OPN</i> gene with litter size traits in pigs

2015 ◽  
Vol 58 (2) ◽  
pp. 317-323 ◽  
Author(s):  
T. Kumchoo ◽  
S. Mekchay
Keyword(s):  
Litter Size ◽  
Reproductive Traits ◽  
Snp Markers ◽  
Strong Linkage Disequilibrium ◽  
Nucleotide Polymorphisms ◽  
Large White ◽  
Single Nucleotide ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Acid Exchange

Abstract. Osteopontin (OPN) gene is a secreted phosphoprotein which appears to play a key function in the conceptus implantation, placentation and maintenance of pregnancy in pigs. The objectives of this study were to verify the non-synonymous single nucleotide polymorphisms (SNPs) and their association with litter size traits in commercial Thai Large White pigs. A total of 320 Thai Large White sows were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Three SNPs at c.425G> A, c.573T> C and c.881C> T revealed amino acid exchange rates of p.110Ala> Thr, p.159Val> Ala and p.262Pro> Ser, respectively, and were then segregated. These three SNPs were significantly associated with total number born (TNB) and number born alive (NBA) traits. No polymorphisms of the two SNP markers (c.278A> G and c.452T> G) were observed in this study. Moreover, the SNPs at c.425G> A and c.573T> C were found to be in strong linkage disequilibrium. The association of OPN with litter size emphasizes the importance of porcine OPN as a candidate gene for reproductive traits in pig breeding.

scholarly journals Genotyping Single-Nucleotide Polymorphisms by the Invader Assay with Dual-Color Fluorescence Polarization Detection

2001 ◽  
Vol 47 (8) ◽  
pp. 1373-1377 ◽  
Author(s):  
Tony M Hsu ◽  
Scott M Law ◽  
Shenghui Duan ◽  
Bruce P Neri ◽  
Pui-Yan Kwok
Keyword(s):  
Fluorescence Polarization ◽  
Cost Effective ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Clear Cut ◽  
Pcr Product ◽  
Invader Assay ◽  
Pcr Products ◽  
Incorporation Assay

Abstract Background: The PCR-Invader® assay is a robust, homogeneous assay that has been shown to be highly sensitive and specific in genotyping single-nucleotide polymorphism (SNP) markers. In this study, we introduce two changes to improve the assay: (a) we streamline the PCR-Invader method by assaying both alleles for each SNP in one reaction; and (b) we reduce the cost of the method by adopting fluorescence polarization (FP) as the detection method. Methods: PCR product was incubated with Invader oligonucleotide and two primary probes at 93 °C for 5 min. Signal probes corresponding to the cleaved flaps of the primary probes [labeled with fluorescein and 6-carboxytetramethylrhodamine (TAMRA) dye] and Cleavase® VIII enzyme (a flap endonuclease) were then added to the mixture. This reaction mixture was incubated at 63 °C for 5 min. FP measurements were made with a fluorescence plate reader. Results: Eighty-eight individuals were genotyped across a panel of 10 SNPs, using PCR product as template, for a total of 880 genotypes. An average “no call” rate of 3.2% was observed after first round of experiments. PCR products were remade in those samples that failed to produce any genotype in the first round, and all gave clear-cut genotypes. When the genotypes determined by the PCR-Invader assay and template-directed dye-terminator incorporation assay with FP were compared, they were in 100% concordance for all SNP markers and experiments. Conclusions: The improvements introduced in this study make PCR-Invader assay simpler and more cost-effective, and therefore more suitable for high-throughput genotyping.

scholarly journals Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1190 ◽  
Author(s):  
Eunju Seo ◽  
Kipoong Kim ◽  
Tae-Hwan Jun ◽  
Jinsil Choi ◽  
Seong-Hoon Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Principal Component ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Useful Knowledge ◽  
Population Structure Analysis ◽  
Group 3 ◽  
Genetic Diversity Study

Cowpea is one of the most essential legume crops providing inexpensive dietary protein and nutrients. The aim of this study was to understand the genetic diversity and population structure of global and Korean cowpea germplasms. A total of 384 cowpea accessions from 21 countries were genotyped with the Cowpea iSelect Consortium Array containing 51,128 single-nucleotide polymorphisms (SNPs). After SNP filtering, a genetic diversity study was carried out using 35,116 SNPs within 376 cowpea accessions, including 229 Korean accessions. Based on structure and principal component analysis, a total of 376 global accessions were divided into four major populations. Accessions in group 1 were from Asia and Europe, those in groups 2 and 4 were from Korea, and those in group 3 were from West Africa. In addition, 229 Korean accessions were divided into three major populations (Q1, Jeonra province; Q2, Gangwon province; Q3, a mixture of provinces). Additionally, the neighbor-joining tree indicated similar results. Further genetic diversity analysis within the global and Korean population groups indicated low heterozygosity, a low polymorphism information content, and a high inbreeding coefficient in the Korean cowpea accessions. The population structure analysis will provide useful knowledge to support the genetic potential of the cowpea breeding program, especially in Korea.

DNA Fingerprinting of Vegetable Soybean Cultivar ‘Zhexian No.9’ Using 101 New Developed HRM-Based SNP Markers

2019 ◽  
Author(s):  
X. J. Fu ◽  
J. X. Pei ◽  
Y. T. Zheng ◽  
D. D. Guo ◽  
Q. H. Yang ◽  
...  
Keyword(s):  
High Resolution Melting ◽  
Snp Markers ◽  
Soybean Cultivar ◽  
Polymorphic Markers ◽  
Nucleotide Polymorphisms ◽  
Analysis Method ◽  
Vegetable Soybean ◽  
Genomic Information ◽  
Single Nucleotide ◽  
Plant Genomes

Single nucleotide polymorphisms (SNPs) have been proved to be powerful markers in genetic analysis due to their high abundance and polymorphism in plant genomes. The recently developed high-resolution melting (HRM) analysis method provides a novel, quick, and close-tube PCR approach to analyze SNP variations. In present study, 101 HRM-based SNP markers from 20 soybean chromosomes were developed for genotyping vegetable soybean cultivar ‘Zhexian No.9’ with ‘Williams 82’ as reference. 33.7% of these markers were polymorphic between ‘Zhexian No.9’ and ‘Williams 82’. Polymorphic markers were found on 85% (17 of 20) of the soybean chromosomes when comparing ‘Zhexian No.9’ and ‘Williams 82’. Finally, an array of 101 in-sequence nucleotide letters was generated as the first precise SNP fingerprint of ‘Zhexian No.9’. The described marker-developing methodology could be used in other crops with known genomic information.

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