A genetic diversity analysis and identification of plant germplasms and varieties are important and necessary for plant breeding. Deoxyribonucleotide (DNA) fingerprints based on genomic molecular markers play an important role in accurate germplasm identification. In this study, Specific-Locus Amplified Fragment Sequencing (SLAF-seq) was conducted for a sugarcane population with 103 cultivated and wild accessions. In total, 105,325 genomic single nucleotide polymorphisms (SNPs) were called successfully to analyze population components and genetic diversity. The genetic diversity of the population was complex and clustered into two major subpopulations. A principal component analysis (PCA) showed that these accessions could not be completely classified based on geographical origin. After filtration, screening, and comparison, 192 uniformly-distributed SNP loci were selected for the 32 chromosomes of sugarcane. An SNP complex genotyping detection system was established using the SNaPshot typing method and used for the precise genotyping and identification of 180 sugarcane germplasm samples. According to the stability and polymorphism of the SNPs, 32 high-quality SNP markers were obtained and successfully used to construct the first SNP fingerprinting and quick response codes (QR codes) for sugarcane. The results provide new insights for genotyping, classifying, and identifying germplasm and resources for sugarcane breeding.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9408448 | PMC |
| http://dx.doi.org/10.3390/genes13081477 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
An integrative taxonomic approach reveals two putatively novel species of phlebotomine sand fly (Diptera: Psychodidae) in Thailand.
Parasit Vectors
January 2025
Center of Excellence in Veterinary Parasitology, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
Background: The subfamily Phlebotominae comprises 1028 species of sand fly, of which only 90 are recognized as vectors of pathogenic agents such as Trypanosoma, Leishmania, and Bartonella. In Thailand, leishmaniasis-a sand fly-borne disease-is currently endemic, with 36 documented sand fly species. However, many cryptic species likely remain unidentified.
View Article and Find Full Text PDFDeep analysis of the major histocompatibility complex genetic associations using covariate analysis and haploblocks unravels new mechanisms for the molecular etiology of Elite Control in AIDS.
BMC Immunol
January 2025
Laboratoire Génomique, Bioinformatique, et Chimie Moléculaire, Conservatoire National des Arts et Métiers, 2 rue Conté 75003, Paris, EA7528, France.
Introduction: We have reanalyzed the genomic data from the International Collaboration for the Genomics of HIV (ICGH), focusing on HIV-1 Elite Controllers (EC).
Methods: A genome-wide association study (GWAS) was performed, comparing 543 HIV-1 EC individuals with 3,272 uninfected controls (CTR) of European ancestry. 8 million single nucleotide polymorphisms (SNPs) and HLA class I and class II gene alleles were imputed to compare EC and CTR.
Novel compound heterozygous mutations in the LARS2 gene in a Chinese family with hearing loss.
Neurogenetics
January 2025
Department of Otolaryngology & Head and Neck, Liuzhou Worker's Hospital of Guangxi Zhuang Autonomous Region, 156 Heping Road, Liuzhou, 545007, China.
Background: Mutations in the LARS2 gene are correlated with Perrault syndrome, a rare autosomal recessive genetic disorder, that is typically characterized by sensorineural hearing loss and ovarian insufficiency.
Methods: Whole-exome sequencing and mutational analysis were employed to identify hearing loss-causing genes in a Chinese family from the Guangxi Zhuang Autonomous Region. Clinical phenotypes, audiological data, and color Doppler ultrasound of the family were collected, and a series of computer software were used to analyze the impact of genetic variations on protein structure and function.
High-resolution melting analysis for detection of nucleotide mutation markers in the polymerase-acidic (PA) gene of influenza virus that are associated with baloxavir marboxil resistance.
Arch Virol
January 2025
Department Experimental and Clinical Medicine, University of Florence, Florence, Italy.
The I38T substitution in the influenza virus polymerase-acidic (PA) subunit is a resistance marker of concern for treatment with the antiviral baloxavir marboxil (BXM). Thus, monitoring PA/I38T mutations is of clinical importance. Here, we developed three rapid and sensitive assays for the detection and monitoring of the PA/I38T mutation.
View Article and Find Full Text PDFMediating role of blood metabolites in the relationship between immune cell traits and sepsis: a Mendelian randomization and mediation analysis.
Inflamm Res
January 2025
Department of Emergency Medicine, Institute of Disaster Medicine and Institute of Emergency Medicine, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, 610041, People's Republic of China.
Background: A significant association between immune cells and sepsis has been suggested by observational studies. However, the precise biological mechanisms underlying this association remain unclear. Therefore, we employed a Mendelian randomization (MR) approach to investigate the causal relationship between immune cells and genetic susceptibility to sepsis, and to explore the potential mediating role of blood metabolites.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!