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You searched for: Subject "single nucleotide polymorphism" Remove constraint Subject: "single nucleotide polymorphism"
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1. Candidate sex-associated gene identification in Trachinotus ovatus (Carangidae) using an integrated SLAF-seq and bulked segregant analysis approach

Author:
Pingping He; Pinyuan Wei; Yuan Ma; Shenhua Hu; Jiuxiang Yao; Xiaozhen Jiang; Youhou Xu; Peng Zhu; Mingli Wei; Weiming Jiang; Jinxia Peng
Source:
Gene 2022 v.809 pp. 146026
ISSN:
0378-1119
Subject:
single nucleotide polymorphism,   etc   ; DNA; Trachinotus ovatus; chromosomes; genes;     Show all 5 Subjects
Abstract:
... It is difficult to distinguish the sexes of Trachinotus ovatus based on appearance, and little data about sex-determining genes are available for this species. Here, we generated 200 F2 individuals using the parents R404 and R403. DNA samples were collected from 50 individuals of each sex and aggregated into sex-specific DNA pools. Specific-locus amplified fragment sequencing was integrated with b ...
DOI:
10.1016/j.gene.2021.146026

2. Encoded hydrogel microparticles with universal mismatch-incorporated DNA probes for highly specific multiplex detection of SNPs

Author:
Hyun June Moon; Seok Joon Mun; Jun Ho Lee; Yoon Ho Roh; Yong Jun Lim; Ki Wan Bong
Source:
Talanta 2022 v.245 pp. 123480
ISSN:
0039-9140
Subject:
single nucleotide polymorphism,   etc   ; DNA; hybridization; hydrogels; ionic strength;     Show all 5 Subjects
Abstract:
... Hydrogel microparticle-based nucleic acid assays are an attractive detection platform based on their multiplexing capabilities with high sensitivity and specificity. A particular area of interest is single-nucleotide polymorphism (SNP) sensing, where multiple SNPs should be identified in a highly reliable yet economical manner. However, hydrogel microparticles leveraging probe-target hybridization ...
DOI:
10.1016/j.talanta.2022.123480

3. Development of SNP Marker Sets for Marker-Assisted Background Selection in Cultivated Cucumber Varieties

Author:
Eun Su Lee; Hee-Bum Yang; Jinhee Kim; Hye-Eun Lee; Ye-Rin Lee; Do-Sun Kim
Source:
Agronomy 2022 v.12 no.2 pp. -
ISSN:
2073-4395
Subject:
single nucleotide polymorphism,   etc   ; agronomy; cucumbers; genomics; genotyping; phylogeny; transcriptome;     Show all 7 Subjects
Abstract:
... Marker-assisted background selection is a powerful molecular tool that can enhance breeding efficiency through the analysis of a large number of markers representing the entire genomic background for precise selection. In the present study, the transcriptomes of 38 cucumber inbred lines with diverse traits were sequenced for single nucleotide polymorphism (SNP) mining for practical application to ...
DOI:
10.3390/agronomy12020487

4. Development of Single Nucleotide Polymorphism (SNP)-Based Triplex PCR Marker for Serotype-specific Escherichia coli Detection

Author:
Md-Mafizur Rahman; Sang-Jin Lim; Yung-Chul Park
Source:
Pathogens 2022 v.11 no.2 pp. -
ISSN:
2076-0817
Subject:
single nucleotide polymorphism,   etc   ; Escherichia coli O157; genetic variation; monitoring; phylogeny; temperature;     Show all 6 Subjects
Abstract:
... Single-nucleotide polymorphisms (SNPs) are one of the most common forms of genetic variation and as such are powerful tools for the identification of bacterial strains, their genetic diversity, phylogenetic analysis, and outbreak surveillance. In this study, we used 15 sets of SNP-containing primers to amplify and sequence the target Escherichia coli. Based on the combination of the 15-sequence pr ...
DOI:
10.3390/pathogens11020115

5. Relationship between genetic distance based on single nucleotide polymorphism markers and hybrid performance in Robusta coffee (Coffea canephora)

Author:
Abraham Akpertey; Francis Kwame Padi; Lyndel Meinhardt; Dapeng Zhang
Source:
Plant breeding 2022 v.141 no.2 pp. 286-300
ISSN:
0179-9541
Subject:
single nucleotide polymorphism,   etc   ; Bayesian theory; Coffea canephora; genetic distance; hybrids; trees; yields;     Show all 7 Subjects
Abstract:
... The choice of parents is a vital first step in any variety development process. This is particularly imperative in tree crops that require minimally 15–20 years to complete a varietal development. The present study was conducted to determine genetic distances (GDs) between parental clones of Robusta coffee hybrids and assess the relationship between GD and hybrid performance. The experimental mate ...
DOI:
10.1111/pbr.13005

6. Breeding peppers for industrial uses: Progress and prospects

Author:
Satyaprakash Barik; Naresh Ponnam; Anand C. Reddy; Lakshmana Reddy D.C; Koushik Saha; Acharya G.C.; Madhavi Reddy K.
Source:
Industrial crops and products 2022 v.178 pp. 114626
ISSN:
0926-6690
Subject:
single nucleotide polymorphism,   etc   ; capsaicinoids; carotenoids; cosmetics; genes; germplasm; hot peppers; marker-assisted selection; oleoresins; pepper;     Show all 10 Subjects
Abstract:
... Pepper is a crucial vegetable as well as spice crop, fruits of which contain numerous bioactive compounds such as capsaicinoids, capsinoids, carotenoids, and oleoresin. Because of the increased demand for eco-friendly products, increasing attention has been paid toward the bioactive compounds in pepper. Hot pepper fruits have potential applications in the pharmaceutical and cosmeceutical industrie ...
DOI:
10.1016/j.indcrop.2022.114626

7. Exploiting single-marker and haplotype-based genome-wide association studies to identify QTL for the number of teats in Italian Duroc pigs

Author:
Samuele Bovo; Mohamad Ballan; Giuseppina Schiavo; Anisa Ribani; Silvia Tinarelli; Stefania Dall'Olio; Maurizio Gallo; Luca Fontanesi
Source:
Livestock science 2022 v.257 pp. 104849
ISSN:
1871-1413
Subject:
single nucleotide polymorphism,   etc   ; Duroc; Sus scrofa; chromosomes; genes; genomics; genotyping; haplotypes; industry; quantitative traits; swine;     Show all 11 Subjects
Abstract:
... The number of teats is a morphological trait of high economic relevance for the pig industry. Here, to dissect the genomic architecture of this trait in the Italian Duroc pig population, we present the results of genome-wide association studies in this Italian heavy pig breed. A total of 1,162 pigs, for which the number of teats was recorded, was genotyped with two high-throughput single nucleotid ...
DOI:
10.1016/j.livsci.2022.104849

8. Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds

Author:
Rosalia Di Gerlando; Salvatore Mastrangelo; Marco Tolone; Ilaria Rizzuto; Anna Maria Sutera; Angelo Moscarelli; Baldassare Portolano; Maria Teresa Sardina
Source:
Animals 2022 v.12 no.2 pp. -
ISSN:
2076-2615
Subject:
single nucleotide polymorphism,   etc   ; gene ontology; genes; genetic relationships; immune response; lipid metabolism; phenotypic variation; sheep;     Show all 8 Subjects
Abstract:
... Copy number variants (CNVs) are one of the major contributors to genetic diversity and phenotypic variation in livestock. The aim of this work is to identify CNVs and perform, for the first time, a CNV-based population genetics analysis with five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs with an average length of 1.81 Mb. The bre ...
DOI:
10.3390/ani12020217

9. Detection of deletion/insertion polymorphism profiles from single human hair shafts

Author:
Jian Tie; Seisaku Uchigasaki; Eiji Isobe; Etsuko Iwakami; Takahisa Okuda
Source:
Molecular biology reports 2022 v.49 no.2 pp. 1017-1025
ISSN:
0301-4851
Subject:
single nucleotide polymorphism,   etc   ; DNA; capillary electrophoresis; genetic markers; genotyping; hairs; microsatellite repeats; molecular biology; nuclear genome;     Show all 9 Subjects
Abstract:
... BACKGROUND: Hair is a frequently encountered biological evidence in personal identification. The amount of nuclear DNA that can be extracted from a single strand of rootless hair is most limited, making the detection of short tandem repeat (STR) polymorphisms difficult. To overcome these limitations, deletion/insertion polymorphisms (DIP) as a new type of genetic marker have shown their benefits i ...
DOI:
10.1007/s11033-021-06921-w

10. Genetic Diversity and Phylogenetic Structures of Four Tibet Yak Populations Using CytB Gene Sequence of Mitochondrial DNA

Author:
Z. D. Pingcuo; W. D. Basang; Q. Zhang; D. Z. Luosang; K. J. Hua; Y. L. Dawa; Y. B. Zhu; D. Ba; D. J. Suolang
Source:
Russian journal of genetics 2022 v.58 no.3 pp. 347-352
ISSN:
1022-7954
Subject:
single nucleotide polymorphism,   etc   ; genes; genetic variation; haplotypes; mitochondria; mitochondrial DNA; nucleotide sequences; pastoralism; phylogeny; yaks; China;     Show all 11 Subjects
Abstract:
... The yak is one of the important livestock unique to the pastoral areas of the Qinghai–Tibet Plateau. In this study, the genetic diversity and phylogenetic relationships of four yak populations in Tibet Naqu and Ali were assessed using mitochondrial cytochrome genes (CytB). Results showed that the full length of the CytB gene sequences of 129 yak individuals in the four populations was 1140 bp, and ...
DOI:
10.1134/S1022795422030103

11. Molecular characterization of parental lines and validation of SNP markers for anthracnose and angular leaf spot in common bean

Author:
Lucas Matias Gomes-Messias; Rosana Pereira Vianello; Joney Pereira Monteiro-Júnior; Luana Alves Rodrigues; Ana Paula Simplício Mota; Helton Santos Pereira; Leonardo Cunha Melo; Bodo Raatz; Thiago Lívio Pessoa Oliveira de Souza
Source:
Euphytica 2022 v.218 no.5 pp. 49
ISSN:
0014-2336
Subject:
single nucleotide polymorphism,   etc   ; anthracnose; beans; disease resistance; early selection; leaf spot; marker-assisted selection; resistance genes;     Show all 8 Subjects
Abstract:
... The implementation of molecular tools that help the early selection of genotypes carrying target alleles increases efficiency and reduces the time and costs of breeding programs. The present study aimed the molecular characterization and validation of Single Nucleotide Polymorphism (SNP) targeting disease resistance alleles for assisted selection. A total of 376 common bean lines with contrasting ...
DOI:
10.1007/s10681-022-03002-2

12. Different Shades of Kale—Approaches to Analyze Kale Variety Interrelations

Author:
Christoph Hahn; Nicholas P. Howard; Dirk C. Albach
Source:
Genes 2022 v.13 no.2 pp. -
ISSN:
2073-4425
Subject:
single nucleotide polymorphism arrays,   etc   ; Brassica oleracea var. sabellica; cabbage; chromosome mapping; genetic variation; haplotypes; kale; vegetable crops;     Show all 8 Subjects
Abstract:
... Brassica oleracea is a vegetable crop with an amazing morphological diversity. Among the various crops derived from B. oleracea, kale has been in the spotlight globally due to its various health-benefitting compounds and many different varieties. Knowledge of the existing genetic diversity is essential for the improved breeding of kale. Here, we analyze the interrelationships, population structure ...
DOI:
10.3390/genes13020232

13. Establishment and application of an SNP molecular identification system for grape cultivars

Author:
Fu-qiang WANG; Xiu-cai FAN; Ying ZHANG; Lei SUN; Chong-huai LIU; Jian-fu JIANG
Source:
Journal of integrative agriculture 2022 v.21 no.4 pp. 1044-1057
ISSN:
2095-3119
Subject:
single nucleotide polymorphism,   etc   ; DNA; agriculture; alleles; cluster analysis; cultivars; genetic distance; grapes; loci; markets; population structure; China;     Show all 12 Subjects
Abstract:
... We aimed to develop a set of single nucleotide polymorphism (SNP) markers that can be used to distinguish the main cultivated grape (Vitis L.) cultivars in China and provide technical support for domestic grape cultivar protection, cultivar registration, and market rights protection. A total of 517 high-quality loci were screened from 4 241 729 SNPs obtained by sequencing 304 grape accessions usin ...
DOI:
10.1016/S2095-3119(21)63654-7

14. Genomic markers linked to Meloidogyne chitwoodi resistance introgressed from Solanum bulbocastanum to cultivated potato and their utility in marker-assisted selection

Author:
Sapinder Bali; Charles Brown; Hassan Majtahedi; Solomon Yilma; Russell E. Ingham; Launa Cimrhakl; Rich Quick; Vidyasagar Sathuvalli
Source:
Molecular breeding 2022 v.42 no.3 pp. 12
ISSN:
1380-3743
Subject:
single nucleotide polymorphism,   etc   ; Meloidogyne chitwoodi; Solanum bulbocastanum; chromosomes; genomics; marker-assisted selection; microsatellite repeats; phenotype; potatoes; profitability;     Show all 10 Subjects
Abstract:
... Meloidogyne chitwoodi is a major threat to potato production in the Pacific Northwest region of the United States. Infected tubers are rendered unmarketable; hence, growers’ profitability is adversely affected. Breeding for nematode resistance is a long-term process and phenotyping the segregating populations for nematode resistance is the most time-consuming and laborious part of the process. Usi ...
DOI:
10.1007/s11032-022-01285-w

15. Development of polymerase chain reaction-based marker for identification of a nonsense mutation in a Pseudomonas-responsive receptor like protein gene of tomato

Author:
Tirthartha Chattopadhyay; Deepak Maurya; Bhagya Shree; Shirin Akhtar; Chandan Roy
Source:
Journal of horticultural science & biotechnology 2022 v.97 no.1 pp. 113-121
ISSN:
2380-4084
Subject:
single nucleotide polymorphism,   etc   ; biotechnology; computer simulation; exons; genetic markers; heterozygosity; horticulture; loci; nonsense mutation; polymerase chain reaction; tomatoes;     Show all 11 Subjects
Abstract:
... The present study was undertaken to develop a simple, robust, and reliable polymerase chain reaction-based molecular marker that can identify a critical nonsense mutation in a receptor like protein (RLP) gene of tomato. The Solyc04g014400 locus was found to code for a RLP with leucine-rich repeats, a trans-membrane domain, and characteristic three-dimensional structure. In silico analysis revealed ...
DOI:
10.1080/14620316.2021.1947905

16. Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice

Author:
Haidong Yan; David C. Haak; Song Li; Linkai Huang; Aureliano Bombarely
Source:
Plant communications 2022 v.3 no.3 pp. 100270
ISSN:
2590-3462
Subject:
single nucleotide polymorphism,   etc   ; alleles; domestication; genome-wide association study; genotype; genotyping; linkage disequilibrium; panicles; phenotype; plant height; rice;     Show all 11 Subjects
Abstract:
... Transposable elements (TEs) are a major force in the production of new alleles during domestication; nevertheless, their use in association studies has been limited because of their complexity. We have developed a TE genotyping pipeline (TEmarker) and applied it to whole-genome genome-wide association study (GWAS) data from 176 Oryza sativa subsp. japonica accessions to identify genetic elements a ...
DOI:
10.1016/j.xplc.2021.100270
CHORUS:
10.1016/j.xplc.2021.100270

17. Genomic Analysis of Escherichia coli Longitudinally Isolated from Broiler Breeder Flocks after the Application of an Autogenous Vaccine

Author:
Liča Lozica; Kasper Rømer Villumsen; Ganwu Li; Xiao Hu; Maja Maurić Maljković; Željko Gottstein
Source:
Microorganisms 2022 v.10 no.2 pp. -
ISSN:
2076-2607
Subject:
single nucleotide polymorphism,   etc   ; Escherichia coli; animal welfare; antibiotic resistance; autogenous vaccines; broiler breeders; genomics; phylogeny; poultry production; virulence;     Show all 10 Subjects
Abstract:
... Escherichia coli is the main bacterial cause of major economic losses and animal welfare issues in poultry production. In this study, we investigate the effect of an autogenous vaccine on E. coli strains longitudinally isolated from broiler breeder flocks on two farms. In total, 115 E. coli isolates were sequenced using Illumina technologies, and compared based on a single-nucleotide polymorphism ...
DOI:
10.3390/microorganisms10020377

18. The relationship between polymorphism of insulin-like growth factor I gene and susceptibility to type 2 diabetes in Uygur population, Xinjiang, China

Author:
Tingting Wang; Gulixiati Maimaitituersun; Haonan Shi; Cheng Chen; Qi Ma; Yinxia Su; Hua Yao; Jia Zhu
Source:
Genes & genomics 2022 v.44 no.4 pp. 499-508
ISSN:
1976-9571
Subject:
single nucleotide polymorphism,   etc   ; alleles; gene interaction; genomics; genotype; genotyping; loci; models; noninsulin-dependent diabetes mellitus; pathogenesis; risk; China;     Show all 12 Subjects
Abstract:
... BACKGROUND: Type 2 diabetes (T2DM) susceptibility varies among different populations and is affected by gene single nucleotide polymorphism (SNP). Insulin-like growth factor (IGF)-1 gene, which has many SNP loci, is involved in T2DM pathogenesis. However, the relationship of IGF-1 gene polymorphism with T2DM in Uyghur population is less studied. OBJECTIVE: To investigate the relationship between T ...
DOI:
10.1007/s13258-021-01209-6

19. New resources for genetic studies in maize (Zea mays L.): a genome‐wide Maize6H‐60K single nucleotide polymorphism array and its application

Author:
Hongli Tian; Yang Yang; Hongmei Yi; Liwen Xu; Hang He; Yaming Fan; Lu Wang; Jianrong Ge; Yawei Liu; Fengge Wang; Jiuran Zhao
Source:
plant journal 2021 v.105 no.4 pp. 1113-1122
ISSN:
0960-7412
Subject:
single nucleotide polymorphism; single nucleotide polymorphism arrays,   etc   ; Zea mays; corn; decline; gene frequency; genotyping; germplasm; heterosis; inbreeding; linkage disequilibrium;     Show all 11 Subjects
Abstract:
... Despite the availability of numerous molecular markers in maize, effective evaluation of all types of germplasm resources, accurate identification of varieties and analysis of a large number of materials in a timely, low‐cost manner is challenging. Here, we present Maize6H‐60K, a genome‐wide single nucleotide polymorphism (SNP) array to facilitate maize genotyping. We first identified 160 million ...
DOI:
10.1111/tpj.15089

20. Genome-based prediction of agronomic traits in spring wheat under conventional and organic management systems

Author:
Kassa Semagn; Muhammad Iqbal; José Crossa; Diego Jarquin; Reka Howard; Hua Chen; Darcy H. Bemister; Brian L. Beres; Harpinder Randhawa; Amidou N’Diaye; Curtis Pozniak; Dean Spaner
Source:
Theoretical and applied genetics 2022 v.135 no.2 pp. 537-552
ISSN:
0040-5752
Subject:
single nucleotide polymorphism arrays,   etc   ; cultivars; grain protein; management systems; marker-assisted selection; models; organic production; phenotype; prediction; spring wheat;     Show all 10 Subjects
Abstract:
... KEY MESSAGE: Using phenotype data of three spring wheat populations evaluated at 6–15 environments under two management systems, we found moderate to very high prediction accuracies across seven traits. The phenotype data collected under an organic management system effectively predicted the performance of lines in the conventional management and vice versa. There is growing interest in developing ...
DOI:
10.1007/s00122-021-03982-0