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The application of high-throughput SNP genotyping is a great challenge for many research projects in the plant genetics domain. The GOOD assay for mass spectrometry, Amplifluor and TaqMan are three methods that rely on different principles for allele discrimination and detection, specifically, primer extension, allele-specific PCR and hybridization, respectively. First, with the goal of assessing allele frequencies by means of SNP genotyping, we compared these methods on a set of three SNPs present in the herbicide resistance genes CSR, AXR1 and IXR1 of Arabidopsis thaliana. In this comparison, we obtained the best results with TaqMan based on PCR specificity, flexibility in primer design and success rate. We also used mass spectrometry for genotyping polyploid species. Finally, a combination of the three methods was used for medium- to high-throughput genotyping in a number of different plant species. Here, we show that all three genotyping technologies are successful in discriminating alleles in various plant species and discuss the factors that must be considered in assessing which method to use for a given application.
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http://dx.doi.org/10.1007/s00122-006-0213-6 | DOI Listing |
Front Endocrinol (Lausanne)
December 2024
Department of Obstetrics and Gynecology, The First Affiliated Hospital of Ningbo University, Ningbo, China.
Background: Observational studies suggest the risk of primary ovarian insufficiency (POI) is increased in autoimmune disorders (AIDs), but it is unclear whether there is a causal relationship. Therefore, we aimed to investigate the bidirectional causality between 20 AIDs and POI using Mendelian randomization (MR) analysis.
Methods: A bidirectional two-sample MR investigation was designed by using publicly accessible summary-level data from genome-wide association studies (GWAS).
Anim Genet
February 2025
College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China.
Body mass index (BMI) can serve as a reasonable indicator of overall body fat content in pigs. This study aimed to identify underlying variants and candidate genes associated with BMI in Yunong-black pigs. A single-step genome-wide association analysis (GWAS) was performed on 1405 BMI records and 924 Yunong-black pigs genotyped using a 50 K SNP Chip.
View Article and Find Full Text PDFJ Orthop Surg Res
December 2024
Department of Endocrinology, Hebei Medical University Third Hospital, Shijiazhuang, Hebei, China.
Background: The influence of the glucagon-like peptide-1 receptor (GLP-1R) on bone metabolism is well-established. However, it has been observed that single nucleotide polymorphisms (SNPs) in the GLP-1R gene can partially affect its function. Therefore, this study aims to investigate the association between SNPs in the GLP-1R gene and postmenopausal osteoporosis (PMOP) within the Chinese Han population.
View Article and Find Full Text PDFTrop Anim Health Prod
December 2024
Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India.
Genome-wide association studies (GWAS) offer potential for discovering genomic regions that can be exploited to increase milk production. However, available GWAS and single nucleotide polymorphism (SNP) datasets are heavily skewed towards taurine breeds, which restricts their utility for genomic research in indicine cattle breeds. This study conducts a GWAS on the Badri breed of Indicine cattle to estimate variance components and identify significant variants associated with milk composition traits, utilizing double digest restriction-site associated DNA (ddRAD) sequencing data.
View Article and Find Full Text PDFPLoS One
December 2024
Infection Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh.
CXCR4, a chemokine receptor known as Fusin or CD184, spans the outer membrane of various human cells, including leukocytes. This receptor is essential for HIV infection as well as for many vital cellular processes and is implicated to be associated with multiple pathologies, including cancers. This study employs various computational tools to investigate the molecular effects of disease-vulnerable germ-line missense and non-coding SNPs of the CXCR4 gene.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!