U.S. flag

An official website of the United States government

PubAg

Main content area

You searched for: Subject "genotyping" Remove constraint Subject: "genotyping"
Start Over

Search

11,305  Search Results

« Previous | 1 - 20 of 11,305 |
Number of results to display per page

Search Results

1. Developing KASP Markers for Identification of Basmati Rice Varieties

Author:
Steele, Katherine; Tulloch, Mark Quinton; Burns, Malcolm; Nader, Werner
Source:
Food analytical methods 2021 v.14 no.4 pp. 663-673
ISSN:
1936-9751
Subject:
genotyping,   etc   ; industry; microsatellite repeats; rice;     Show all 4 Subjects
Abstract:
... Authentication of Basmati rice has relied on microsatellite markers since 2004, but microsatellites cannot distinguish between all of the forty-one Basmati varieties approved in 2017. This study investigated whether single nucleotide polymorphisms (SNP) and insertion/deletion (InDel) variations developed into KASP™ (Kompetitive Allele Specific PCR; LGC Biosearch Technologies) could be used to dist ...
DOI:
10.1007/s12161-020-01892-3

2. Transmission dynamics and molecular characterization of HIV-1 epidemic among therapeutic failure patients in Santa Catarina state, southern Brazil

Author:
Fritsch, Hegger M.; Tanuri, Amilcar; Pinto, Aguinaldo R.; Gräf, Tiago
Source:
Infection, genetics, and evolution 2021 v.92 pp. 104854
ISSN:
1567-1348
Subject:
genotyping,   etc   ; databases; infection; mortality; phylogeny; therapeutics; Brazil;     Show all 7 Subjects
Abstract:
... The HIV-1 epidemic in southern Brazil is mostly caused by subtype C, which contrasts the dominance of subtype B in the other regions of the country. Santa Catarina (SC), although the smallest state in the southern region, presents one of the highest incidences and mortality rates in Brazil due to AIDS. This work investigated the HIV-1 molecular diversity and phylogenetic transmission networks in S ...
DOI:
10.1016/j.meegid.2021.104854

3. A reference‐free approach to analyse RADseq data using standard next generation sequencing toolkits

Author:
Heller, Rasmus; Nursyifa, Casia; Garcia‐Erill, Genís; Salmona, Jordi; Chikhi, Lounes; Meisner, Jonas; Korneliussen, Thorfinn Sand; Albrechtsen, Anders
Source:
Molecular ecology resources 2021 v.21 no.4 pp. 1085-1097
ISSN:
1755-098X
Subject:
genotyping by sequencing,   etc   ; computer software; ecology; genomics; heterozygosity; humans; zebras;     Show all 7 Subjects
Abstract:
... Genotyping‐by‐sequencing methods such as RADseq are popular for generating genomic and population‐scale data sets from a diverse range of organisms. These often lack a usable reference genome, restricting users to RADseq specific software for processing. However, these come with limitations compared to generic next generation sequencing (NGS) toolkits. Here, we describe and test a simple pipeline ...
DOI:
10.1111/1755-0998.13324

4. Pairwise linkage disequilibrium estimation for polyploids

Author:
Gerard, David
Source:
Molecular ecology resources 2021 v.21 no.4 pp. 1230-1242
ISSN:
1755-098X
Subject:
genotyping,   etc   ; diploidy; ecology; genotype; linkage disequilibrium; polyploidy; uncertainty;     Show all 7 Subjects
Abstract:
... Many tasks in statistical genetics involve pairwise estimation of linkage disequilibrium (LD). The study of LD in diploids is mature. However, in polyploids, the field lacks a comprehensive characterization of LD. Polyploids also exhibit greater levels of genotype uncertainty than diploids, yet no methods currently exist to estimate LD in polyploids in the presence of such genotype uncertainty. Fu ...
DOI:
10.1111/1755-0998.13349

5. Cultivar specific gene pool may play an important role in Musa acuminata Colla evolution

Author:
Jeensae, Rossamon; Kongsiri, Nongluck; Fluch, Silvia; Burg, Kornel; Boonruangrod, Ratri
Source:
Genetic resources and crop evolution 2021 v.68 no.4 pp. 1589-1601
ISSN:
0925-9864
Subject:
genotyping,   etc   ; alleles; bananas; cultivars; diploidy; evolution; gene pool; triploidy; Taiwan;     Show all 9 Subjects
Abstract:
... Edible bananas are hybrids of various inter- and intraspecific combinations of Musa acuminata Colla and M. balbisiana Colla at different ploidy levels brought up by coexisting selection by farmers and nature. Our current study, based on a 461-bp-long sequence of the 5′ETS rDNA of 35 diploids and 19 cultivated varieties harboring 87 informative SNPs, revealed five groups of M. acuminata subspecies; ...
DOI:
10.1007/s10722-020-01088-y

6. Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results?

Author:
Cumer, Tristan; Pouchon, Charles; Boyer, Frédéric; Yannic, Glenn; Rioux, Delphine; Bonin, Aurélie; Capblancq, Thibaut
Source:
Molecular genetics and genomics 2021 v.296 no.2 pp. 457-471
ISSN:
1617-4615
Subject:
genotyping,   etc   ; DNA; Fagus sylvatica; bioinformatics; butterflies; genetic variation; genomics; heterozygosity;     Show all 8 Subjects
Abstract:
... Next-generation sequencing technologies have opened a new era of research in population genetics. Following these new sequencing opportunities, the use of restriction enzyme-based genotyping techniques, such as restriction site-associated DNA sequencing (RAD-seq) or double-digest RAD-sequencing (ddRAD-seq), has dramatically increased in the last decade. From DNA sampling to SNP calling, the labora ...
DOI:
10.1007/s00438-020-01756-9

7. Sexing chickens (Gallus gallus domesticus) with high-resolution melting analysis using feather crude DNA

Author:
England, A.D.; Kheravii, S.K.; Musigwa, S.; Kumar, A.; Daneshmand, A.; Sharma, N.K.; Gharib-Naseri, K.; Wu, S.B.
Source:
Poultry science 2021 v.100 no.3 pp. 100924
ISSN:
0032-5791
Subject:
genotyping,   etc   ; DNA; cost effectiveness; dissection; females; genes; heterozygosity; homozygosity; males;     Show all 9 Subjects
Abstract:
... Identification of sex in broiler chickens allows researchers to reduce the level of variation in an experiment caused by the sex effect. Broiler breeds commonly used in research are no longer feather sexable because of the change in their genetics. Other alternate sexing methods are costly and difficult to apply on a large scale. Therefore, a sexing method is required that is both cost effective a ...
DOI:
10.1016/j.psj.2020.12.022

8. Discovery of a Major QTL Controlling Trichome IV Density in Tomato Using K-Seq Genotyping

Author:
Mata-Nicolás, Estefanía; Montero-Pau, Javier; Gimeno-Paez, Esther; García-Pérez, Ana; Ziarsolo, Peio; Blanca, José; van der Knaap, Esther; Díez, María José; Cañizares, Joaquín
Source:
Genes 2021 v.12 no.2
ISSN:
2073-4425
Subject:
genotyping,   etc   ; chromosome mapping; chromosomes; genetic relationships; introgression; tomatoes; trichomes;     Show all 7 Subjects
Abstract:
... Trichomes are a common morphological defense against pests, in particular, type IV glandular trichomes have been associated with resistance against different invertebrates. Cultivated tomatoes usually lack or have a very low density of type IV trichomes. Therefore, for sustainable management of this crop, breeding programs could incorporate some natural defense mechanisms, such as those afforded b ...
DOI:
10.3390/genes12020243

9. Identification of the Source for Salmonella Contamination of Carcasses in a Large Pig Slaughterhouse

Author:
Zeng, Hang; Rasschaert, Geertrui; De Zutter, Lieven; Mattheus, Wesley; De Reu, Koen
Source:
Pathogens 2021 v.10 no.1
ISSN:
2076-0817
Subject:
genotyping,   etc   ; Salmonella; dehairing; evisceration; mouth; rectum; recycled water; slaughterhouses; swine;     Show all 9 Subjects
Abstract:
... To identify the major source of Salmonella contamination in a pig slaughterhouse, samples were collected from the clean and unclean area and Salmonella isolates were further typed. Carcasses entering the clean area showed a Salmonella contamination rate of 96.7% in the oral cavity and 55.0% in the rectum content samples. Evisceration seemed not to be critical as the contamination rate of the carca ...
DOI:
10.3390/pathogens10010077

10. Ultra-small four-emission-point spectral-detection system using seven-dichroic-mirror array

Author:
Anazawa, Takashi; Yamazaki, Motohiro; Yamamoto, Shuhei; Inaba, Ryoji
Source:
Talanta 2021 v.222 pp. 121667
ISSN:
0039-9140
Subject:
genotyping,   etc   ; detection; electrophoresis; fluorescence; fluorescent dyes; sequence analysis; thickness;     Show all 7 Subjects
Abstract:
... An ultra-small and highly efficient spectral-detection system for four emission points was developed by integrating an injection-molded-plastic four-lens array, a seven-dichroic-mirror array, and an image sensor as one device. The seven-dichroic-mirror array was further miniaturized compared to our previous four-dichroic-mirror array by measures including reduction of the thickness of each dichroi ...
DOI:
10.1016/j.talanta.2020.121667

11. Vitamin D Receptor (VDR) Gene Polymorphism in Patients Diagnosed with Colorectal Cancer

Author:
Latacz, Maria; Rozmus, Dominika; Fiedorowicz, Ewa; Snarska, Jadwiga; Jarmołowska, Beata; Kordulewska, Natalia; Savelkoul, Huub; Cieślińska, Anna
Source:
Nutrients 2021 v.13 no.1
ISSN:
2072-6643
Subject:
genotyping,   etc   ; colorectal neoplasms; genetic polymorphism; haplotypes; people; prevalence; risk;     Show all 7 Subjects
Abstract:
... Colorectal cancer (CRC) is one of the most commonly occurring neoplasias in humans. The prevalence of CRC rates is still rising. Although the exact background of the disease still remains unknown, it is believed that CRC may not only be a result of environmental factors, but also genetic ones. One of the mechanisms underlying CRC might be the vitamin D pathway, as CRC is the most closely linked ne ...
DOI:
10.3390/nu13010200

12. Can Previous Associations of Single Nucleotide Polymorphisms in the TLR2, NOD1, CXCR5, and IL10 Genes in the Susceptibility to and Severity of Chlamydia trachomatis Infections Be Confirmed?

Author:
Jukema, Jelmer B.; Hoenderboom, Bernice M.; van Benthem, Birgit H. B.; van der Sande, Marianne A. B.; de Vries, Henry J. C.; Hoebe, Christian J. P. A.; Dukers-Muijrers, Nicole H. T. M.; Bax, Caroline J.; Morré, Servaas A.; Ouburg, Sander
Source:
Pathogens 2021 v.10 no.1
ISSN:
2076-0817
Subject:
genotyping,   etc   ; Chlamydia trachomatis; algorithms; genetic variation; interleukin-10; pregnancy; risk;     Show all 7 Subjects
Abstract:
... Clear inter-individual differences exist in the response to C. trachomatis (CT) infections and reproductive tract complications in women. Host genetic variation like single nucleotide polymorphisms (SNPs) have been associated with differences in response to CT infection, and SNPs might be used as a genetic component in a tubal-pathology predicting algorithm. Our aim was to confirm the role of four ...
DOI:
10.3390/pathogens10010048

13. Nested Association Mapping (NAM) Populations: Present Status and Future Prospects in the Genomics Era

Author:
Gireesh, Channappa; Sundaram, Raman. M.; Anantha, Siddaiah M.; Pandey, Manish K.; Madhav, Maganti S.; Rathod, Santosha; Yathish, Kondajji R.; Senguttuvel, Ponnuvel; Kalyani, Barbadikar M.; Ranjith, Ellur; Venkata Subbarao, Lella; Kumar Mondal, Tapan; Swamy, Mallikarjuna; Rakshit, Sujay
Source:
Critical reviews in plant sciences 2021 v.40 no.1 pp. 49-67
ISSN:
1549-7836
Subject:
genotyping,   etc   ; barley; corn; dissection; genomics; prediction; rice; soybeans; wheat;     Show all 9 Subjects
Abstract:
... Development of mapping population is a prerequisite for genetic dissection of genomic regions underlying complex traits. Nested Association Mapping (NAM) is an integrated multi-parent population approach that combines the advantages of linkage mapping and association mapping for high resolution and high-power mapping of complex traits. The NAM population is constituent of independent RIL populatio ...
DOI:
10.1080/07352689.2021.1880019

14. Frequency of Mutations Associated with the Development of Hereditary Hemochromatosis Type I, Wilson–Konovalov Disease, and Familial Mediterranean Fever and Peculiarities of Their Distribution in the Russian Population

Author:
Abramov, D. D.; Kadochnikova, V. V.; Yakimova, E. G.; Belousova, M. V.; Maerle, A. V.; Sergeev, I. V.; Kozlov, I. B.; Donnikov, A. E.; Kofiadi, I. A.; Trofimov, D. Yu.
Source:
Russian journal of genetics 2021 v.57 no.1 pp. 83-89
ISSN:
1022-7954
Subject:
genotyping,   etc   ; Russia; blood; familial Mediterranean fever; genes; hemochromatosis; penetrance; phenotype;     Show all 8 Subjects
Abstract:
... This article is a continuation of the series of works devoted to determining the frequency of mutations associated with the development of common monogenic diseases among the representatives of the Russian population. The frequencies of mutations in the genes HFE, ATP7B, and MEFV in primary blood donors who identify themselves as Russians and permanently reside in the Russian Federation were estab ...
DOI:
10.1134/S1022795421010026

15. Marker genotyping error effects on genomic predictions under different genetic architectures

Author:
Akbarpour, Tahere; Ghavi Hossein-Zadeh, Navid; Shadparvar, Abdol Ahad
Source:
Molecular genetics and genomics 2021 v.296 no.1 pp. 79-89
ISSN:
1617-4615
Subject:
genotyping errors,   etc   ; genomics; heritability; phenotype; prediction; quantitative traits;     Show all 6 Subjects
Abstract:
... This study aimed to determine the effect of different rates of marker genotyping error on the accuracy of genomic prediction that was examined under distinct marker and quantitative trait loci (QTL) densities and different heritability estimates using a stochastic simulation approach. For each scenario of simulation, a reference population with phenotypic and genotypic records and a validation pop ...
DOI:
10.1007/s00438-020-01728-z

16. Genotyping structural variants in pangenome graphs using the vg toolkit

Author:
Hickey, Glenn; Heller, David; Monlong, Jean; Sibbesen, Jonas A.; Sirén, Jouni; Eizenga, Jordan; Dawson, Eric T.; Garrison, Erik; Novak, Adam M.; Paten, Benedict
Source:
Genome biology 2020 v.21 no.1 pp. 35
ISSN:
1474-760X
Subject:
genotyping,   etc   ; graphs; point mutation; yeasts;     Show all 4 Subjects
Abstract:
... Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging SV catalogs for short-read SV genotyping experiments. We benchmark vg against state-of-the-art SV genotypers using three sequence-resolved SV catalogs generat ...
DOI:
10.1186/s13059-020-1941-7
PubMed:
32051000
PubMed Central:
PMC7017486

17. Shelter cats host infections with multiple Trypanosoma cruzi discrete typing units in southern Louisiana

Author:
Dumonteil, Eric; Desale, Hans; Tu, Weihong; Duhon, Brandy; Wolfson, Wendy; Balsamo, Gary; Herrera, Claudia
Source:
Veterinary research 2021 v.52 no.1 pp. 53
ISSN:
1297-9716
Subject:
genotyping,   etc   ; Trypanosoma cruzi; genetic variation; parasites; risk assessment; seroprevalence; veterinary medicine; Louisiana;     Show all 8 Subjects
Abstract:
... Trypanosoma cruzi is a zoonotic parasite endemic in the southern US and the Americas, which may frequently infect dogs, but limited information is available about infections in cats. We surveyed a convenience sample of 284 shelter cats from Southern Louisiana to evaluate T. cruzi infection using serological and PCR tests. Parasites from PCR positive cats were also genotyped by PCR and deep sequenc ...
DOI:
10.1186/s13567-021-00923-z

18. Development of a 38 K single nucleotide polymorphism array and application in genomic selection for resistance against Vibrio harveyi in Chinese tongue sole, Cynoglossus semilaevis

Author:
Lu, Sheng; Zhou, Qian; Chen, Yadong; Liu, Yang; Li, Yangzhen; Wang, Lei; Yang, Yingming; Chen, Songlin
Source:
Genomics 2021 v.113 no.4 pp. 1838-1844
ISSN:
0888-7543
Subject:
genotyping,   etc   ; Cynoglossus semilaevis; Vibrio harveyi; genomics; marker-assisted selection; prediction; progeny; single nucleotide polymorphism arrays;     Show all 8 Subjects
Abstract:
... Based on 1572 re-sequenced Chinese tongue sole (Cynoglossus semilaevis), we investigated the accuracy of four genomic methods at predicting genomic estimated breeding values (GEBVs) of Vibrio harveyi resistance in C. semilaevis when SNPs varying from 500 to 500 k. All methods outperformed the pedigree-based best linear unbiased prediction when SNPs reached 50 k or more. Then, we developed an SNP a ...
DOI:
10.1016/j.ygeno.2021.03.034

19. Predicting for disease resistance in aquaculture species using machine learning models

Author:
Palaiokostas, Christos
Source:
Aquaculture reports 2021 v.20 pp. 100660
ISSN:
2352-5134
Subject:
genotyping,   etc   ; Markov chain; aquaculture; data collection; disease resistance; genomics; livestock; marker-assisted selection; prediction;     Show all 9 Subjects
Abstract:
... Predicting disease resistance is one of the most prominent applications of aquaculture selective breeding. Reductions in genotyping costs have allowed the implementation of genomic selection in an abundance of aquaculture species and their related diseases showing promising results. Machine learning (ML) models can be of value for prediction purposes, as suggested by several studies in both plants ...
DOI:
10.1016/j.aqrep.2021.100660

20. Genomic selection using a subset of SNPs identified by genome-wide association analysis for disease resistance traits in aquaculture species

Author:
Luo, Zheng; Yu, Yang; Xiang, Jianhai; Li, Fuhua
Source:
Aquaculture 2021 v.539 pp. 736620
ISSN:
0044-8486
Subject:
genotyping,   etc   ; aquaculture; disease resistance; genome-wide association study; marker-assisted selection; models; prediction;     Show all 7 Subjects
Abstract:
... Genomic selection (GS) has been proved to be a useful method for selective breeding. However, the cost for genotyping a large amount of SNPs is too expensive, especially for aquaculture species with a low individual commodity value. In this study, we proposed a strategy for GS using a subset of markers selected by genome wide association studies (GWAS), and evaluated the prediction accuracy in dif ...
DOI:
10.1016/j.aquaculture.2021.736620