scholarly journals Multiple nucleotide polymorphism DNA markers for the accurate evaluation of genetic variations

2021 ◽  
Author(s):  
Zhiwei Fang ◽  
Lun Li ◽  
Junfei Zhou ◽  
Aiqing You ◽  
Lifen Gao ◽  
...  
Keyword(s):  
Dna Markers ◽  
Dna Marker ◽  
Hybrid Rice ◽  
Model Organism ◽  
Polymorphic Marker ◽  
Difficult Problem ◽  
Genetic Variations ◽  
Nucleotide Polymorphism ◽  
Micro Organisms ◽  
Diploid Rice

AbstractDNA markers are an essential tool for the detection and evaluation of genetic variations, a central theme in genetics and biology. Effective markers must be highly reproducible, polymorphic, accurate and efficient to profile. We developed multiple dispersed nucleotide polymorphism (MNP) DNA marker and an efficient MNP genotyping method called MNP-Seq. The MNP marker was 17.48% more polymorphic than the highly polymorphic marker of microsatellites on a collection of hybrid rice plants. When applied to genotype more than 80,000 individual MNP markers of diploid rice and polyploidy hybrid cotton varieties which were notoriously difficult to genotype accurately, MNP-Seq finished in two days and achieved accuracies of 99.999% and 99.988%, respectively. We adopted MNP-Seq to reveal the ubiquitous, albeit subtle and neglected, genetic heterogeneities in homonyms of Nipponbare rice, a popular model organism for plant biology. This result raised a question on the consistency of the published results using the model plant. We also used MNP-Seq to accurately and efficiently determine the identities of plant varieties, a key but difficult problem for the protection of plant intellectual property rights. While being applied to plants in the current study, the MNP marker and MNP-Seq are general and readily applicable to similar problems in animals and micro-organisms.

scholarly journals Detection of a single nucleotide polymorphism (SNP) DNA marker linked to cocoon traits in the mulberry silkworm, Bombyx mori (Lepidoptera: Bombycidae)

2011 ◽  
Vol 108 (3) ◽  
pp. 347-354 ◽  
Author(s):  
Sivaramakurup SREEKUMAR ◽  
Southekal K. ASHWATH ◽  
Monika SLATHIA ◽  
Sundaramurthy N. KUMAR ◽  
Syed M.H. QADRI
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Bombyx Mori ◽  
Dna Marker ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Mulberry Silkworm ◽  
Silkworm Bombyx Mori

scholarly journals Ultrasonic Cleaning of Conveyor Belt Materials Using Listeria monocytogenes as a Model Organism

2007 ◽  
Vol 70 (3) ◽  
pp. 758-761 ◽  
Author(s):  
RIINA TOLVANEN ◽  
JANNE LUNDÉN ◽  
HANNU KORKEALA ◽  
GUN WIRTANEN
Keyword(s):  
Stainless Steel ◽  
Listeria Monocytogenes ◽  
Model Organism ◽  
Conveyor Belt ◽  
Difficult Problem ◽  
Cleaning Efficiency ◽  
Ultrasonic Cleaning ◽  
Plastic Materials ◽  
Significant Difference ◽  
Logarithmic Reduction

Persistent Listeria monocytogenes contamination of food industry equipment is a difficult problem to solve. Ultrasonic cleaning offers new possibilities for cleaning conveyors and other equipment that are not easy to clean. Ultrasonic cleaning was tested on three conveyor belt materials: polypropylene, acetal, and stainless steel (cold-rolled, AISI 304). Cleaning efficiency was tested at two temperatures (30 and 45°C) and two cleaning times (30 and 60 s) with two cleaning detergents (KOH, and NaOH combined with KOH). Conveyor belt materials were soiled with milk-based soil and L. monocytogenes strains V1, V3, and B9, and then incubated for 72 h to attach bacteria to surfaces. Ultrasonic cleaning treatments reduced L. monocytogenes counts on stainless steel 4.61 to 5.90 log units; on acetal, 3.37 to 5.55 log units; and on polypropylene, 2.31 to 4.40 log units. The logarithmic reduction differences were statistically analyzed by analysis of variance using Statistical Package for the Social Sciences software. The logarithmic reduction was significantly greater in stainless steel than in plastic materials (P < 0.001 for polypropylene, P = 0.023 for acetal). Higher temperatures enhanced the cleaning efficiency in tested materials. No significant difference occurred between cleaning times. The logarithmic reduction was significantly higher (P = 0.013) in cleaning treatments with potassium hydroxide detergent. In this study, ultrasonic cleaning was efficient for cleaning conveyor belt materials.

scholarly journals Resequencing of 1,143 indica rice accessions reveals important genetic variations and different heterosis patterns

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Qiming Lv ◽  
Weiguo Li ◽  
Zhizhong Sun ◽  
Ning Ouyang ◽  
Xin Jing ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Hybrid Rice ◽  
Indica Rice ◽  
Genetic Variations ◽  
Hybrid Breeding ◽  
Rice Grain ◽  
Kinship Analysis ◽  
Cadmium Absorption ◽  
Hybrid Lines ◽  
Rice Genetic

Abstract Obtaining genetic variation information from indica rice hybrid parents and identification of loci associated with heterosis are important for hybrid rice breeding. Here, we resequence 1,143 indica accessions mostly selected from the parents of superior hybrid rice cultivars of China, identify genetic variations, and perform kinship analysis. We find different hybrid rice crossing patterns between 3- and 2-line superior hybrid lines. By calculating frequencies of parental variation differences (FPVDs), a more direct approach for studying rice heterosis, we identify loci that are linked to heterosis, which include 98 in superior 3-line hybrids and 36 in superior 2-line hybrids. As a proof of concept, we find two accessions harboring a deletion in OsNramp5, a previously reported gene functioning in cadmium absorption, which can be used to mitigate rice grain cadmium levels through hybrid breeding. Resource of indica rice genetic variation reported in this study will be valuable to geneticists and breeders.

scholarly journals A putative resistant DNA marker for wool yellowing susceptibility in sheep

2000 ◽  
Vol 23 (2) ◽  
pp. 341-346
Author(s):  
M.V. Benavides ◽  
S. Damak ◽  
A.P. Maher
Keyword(s):  
Candidate Genes ◽  
Differential Display ◽  
Dna Sequences ◽  
Dna Markers ◽  
Dna Marker ◽  
Transmembrane Signalling ◽  
Breeding Values ◽  
Wide Range ◽  
Resistant Group ◽  
Australian Merino

An Australian Merino flock was screened for low (resistant) and high (susceptible) yellow predictive colour (YPC) breeding values in order to compare extreme individuals using the differential display of mRNA technique. One differentially expressed cDNA band was visualised only in the resistant group. This band showed no identity with the DNA sequences of public databases; however, they showed short homologies with three database sequences related to transmembrane signalling functions. The use of these candidate genes as DNA markers needs to be confirmed against sheep with a wide range of susceptibility to wool yellowing to verify the results.

The TG5 thyroglobulin gene test for a marbling quantitative trait loci evaluated in feedlot cattle

2004 ◽  
Vol 44 (7) ◽  
pp. 669 ◽  
Author(s):  
W. Barendse ◽  
R. Bunch ◽  
M. Thomas ◽  
S. Armitage ◽  
S. Baud ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Quantitative Trait Loci ◽  
Dna Sequence ◽  
Dna Markers ◽  
Quantitative Trait ◽  
Allelic Association ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Trait Loci ◽  
Thyroglobulin Gene

The TG5 (thyroglobulin 5′ leader sequence) single nucleotide polymorphism has been associated with marbling in cattle fed for periods longer than 250 days. To test whether the association could be detected in diverse cattle, fed for less than 250 days, and to measure the size of the effect, we sampled 1750 cattle from the AMH Toowoomba feedlot. These cattle were sampled on 28 separate days, over 9 months. Their marbling scores covered the complete range. We found that the TG5 single nucleotide polymorphism was associated with marbling scores (P<0.05) and estimated that TG5 genotypes explained 6.5% of the residual deviance for the marbling phenotype. We also found that the '3' allele was more frequent in animals with higher marbling scores. The consistency of the allelic association between studies and, in particular, the association found in diverse cattle, indicate that the TG5 polymorphism can be used as a breeding tool and possibly a feedlot entry tool. To estimate the size of the genetic region in which the marbling quantitative trait loci are located, we tested the nearby DNA markers CSSM66 and BMS1747. These do not show allelic associations to marbling. The consistency of the allelic association between studies, the lack of association to nearby DNA markers and the complementary information on gene action of genes near Thyroglobulin suggest that DNA sequence variations, in or near the Thyroglobulin gene sequence, are the likely causes for the marbling quantitative trait loci. Further studies of single nucleotide polymorphism in and near the Thyroglobulin DNA sequence should allow causal mutations for the effect to be identified.

scholarly journals Intestinal lactobacilli and the DC-SIGN gene for their recognition by dendritic cells play a role in the aetiology of allergic manifestations

Microbiology ◽  
2010 ◽  
Vol 156 (11) ◽  
pp. 3298-3305 ◽  
Author(s):  
John Penders ◽  
Carel Thijs ◽  
Monique Mommers ◽  
Ellen E. Stobberingh ◽  
Edward Dompeling ◽  
...  
Keyword(s):  
Pattern Recognition ◽  
Dendritic Cells ◽  
Birth Cohort ◽  
Statistical Significance ◽  
Genetic Variations ◽  
Microbial Interactions ◽  
Birth Cohort Study ◽  
Faecal Samples ◽  
Micro Organisms ◽  
Allergic Disorders

Diminished exposure to harmless micro-organisms, such as lactobacilli, has been suggested to play a role in the increased prevalence of allergic disorders in Westernized communities. The development of allergies depends on both environmental factors and genetic variations, including polymorphisms in genes encoding pattern recognition receptors. The present study examines the effects of both colonization with specific Lactobacillus species and genetic variations in DC-SIGN, a pattern recognition receptor on dendritic cells that recognizes lactobacilli, on the development of atopic dermatitis (AD) and sensitization in infancy. Within the KOALA Birth Cohort Study, faecal samples of 681 one-month-old infants were collected and quantitatively screened for five Lactobacillus species: L. casei, L. paracasei, L. rhamnosus, L. acidophilus and L. reuteri. Eleven haplotype-tagging polymorphisms in the DC-SIGN gene were genotyped in these children. Allergic outcomes were a clinical diagnosis of AD and sensitization (specific IgE) at age 2 years. L. rhamnosus (31.5 %), L. paracasei (31.3 %) and L. acidophilus (14.4 %) were frequently detected in the faecal samples of one-month-old infants, whereas L. casei (2.5 %) and L. reuteri (<1 %) were rare. Colonization with L. paracasei decreased the risk of AD significantly (odds ratio 0.57, 95 % confidence interval 0.32–0.99), whereas effects of L. acidophilus were of borderline statistical significance (0.46, 0.20–1.04). Two DC-SIGN polymorphisms, rs11465413 and rs8112555, were statistically significantly associated with atopic sensitization. The present study supports the ‘old friends’ hypothesis suggesting that certain health-beneficial micro-organisms protect us from developing allergies and that these protective effects are species-dependent. Firm conclusions on the potential interaction between lactobacillus colonization and genetic variations in DC-SIGN in association with the development of allergic disorders cannot be drawn, given the limited power of our study. Therefore, incorporation of consecutive faecal sampling in newly started (birth) cohort studies would be a first requisite to further increase our understanding of host–microbial interactions in health and disease.

scholarly journals THE PROBLEM OF DETECTION OF HETEROZYGOUS GENOTYPES BY MUTATION OF THE FAD 2-1 GENE OF SUNFLOWER (HELIANTHUS ANNUUS L.) USING DNA MARKERS

2021 ◽  
Author(s):  
D.L. Savichenko ◽  
◽  
S.Z. Guchetl ◽  
Keyword(s):  
Dna Markers ◽  
Mutant Allele ◽  
Dna Marker ◽  
Oleic Acid Content ◽  
Wild Type ◽  
High Oleic Acid ◽  
Marker System ◽  
High Oleic ◽  
High Oleic Acid Content ◽  
Search For Information

The development of marker-associated breeding requires the development of DNA marker systems that meet the needs of the breeding process. We are looking for the opportunities to improve the efficiency of breeding for high oleic acid content in sunflower oil. One of the directions is the improvement of the existing marker system for detection the heterozygous status of the alleles of the FAD 2-1 gene. We carried out the search for information published in databases on this DNA locus. We studied the structure of the nucleotide sequences of the mutant allele and the wild-type allele. We proposed the way of improving the existing marker system.

scholarly journals Identification and Monitoring of Amomi Fructus and its Adulterants Based on DNA Barcoding Analysis and Designed DNA Markers

Molecules ◽  
2019 ◽  
Vol 24 (22) ◽  
pp. 4193 ◽  
Author(s):  
Eui Jeong Doh ◽  
Jung-Hoon Kim ◽  
Guemsan Lee
Keyword(s):  
Dna Barcoding ◽  
Dna Markers ◽  
Dna Marker ◽  
Intergenic Spacer ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Traditional Medicines ◽  
Amomum Villosum ◽  
Reliable Methods ◽  
A New Species

Amomi Fructus is one of the traditional medicines derived from the ripe fruits of the Zingiberaceae family of plants, which include Amomum villosum, A. villosum var. xanthioides, and A. longiligulare. Owing to their highly similar morphological traits, several kinds of adulterants of Amomi Fructus have been reported. Therefore, accurate and reliable methods of identification are necessary in order to ensure drug safety and quality. We performed DNA barcoding using five regions (ITS, matK, rbcL, rpoB, and trnL-F intergenic spacer) of 23 Amomi Fructus samples and 22 adulterants. We designed specific DNA markers for Amomi Fructus based on the single nucleotide polymorphisms (SNPs) in the ITS. Amomi Fructus was well separated from the adulterants and was classified with the species of origin based on the detected SNPs from the DNA barcoding results. The AVF1/ISR DNA marker for A. villosum produced a 270 bases amplified product, while the ALF1/ISF DNA marker produced a 350 bases product specific for A. longiligulare. Using these DNA markers, the monitoring of commercially distributed Amomi Fructus was performed, and the monitoring results were confirmed by ITS analysis. This method identified samples that were from incorrect origins, and a new species of adulterant was also identified. These results confirmed the accuracy and efficiency of the designed DNA markers; this method may be used as an efficient tool for the identification and verification of Amomi Fructus.

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