The papers published in this Special Issue “SNP arrays” (Single Nucleotide Polymorphism Arrays) focus on several perspectives associated with arrays of this type. The range of papers vary from a case report to reviews, thereby targeting wider audienc...
The hallmarks of pediatric acute respiratory failure (ARF) are dysregulated inflammation and surfactant dysfunction. The objective is to study association of surfactant protein (SP) genes’ single nucleotide polymorphisms (SNPs) with ARF and its...
Detecting single nucleotide polymorphisms’ (SNPs) interaction is one of the most popular approaches for explaining the missing heritability of common complex diseases in genome-wide association studies. Many methods have been proposed for SNP interac...
Single nucleotide polymorphisms (SNPs) have been widely used for gene identification. Allelic discrimination for an individual SNP with high reliability and flexibility is critical for the accurate detection of beneficial genes linked to specific SNP...
DNA fingerprinting is a molecular technique applied to identify genetic differences between plant cultivars or lines and is used for genetic purity testing. The suitability of single nucleotide polymorphism (SNP) panels for the fingerprinting of tetr...
Cytogenetic analysis is essential for the diagnosis and prognosis of hematopoietic neoplasms in current clinical practice. Many hematopoietic malignancies are characterized by structural chromosomal abnormalities such as specific translocations, inve...
Single nucleotide polymorphism (SNP) is one of the most widely used molecular markers to help researchers understand the relationship between phenotypes and genotypes. SNP calling mainly consists of two steps, including read alignment and locus ident...
Single-nucleotide polymorphism (SNP) markers have great potential to identify individuals, family relations, biogeographical ancestry, and phenotypic traits. In many forensic situations, DNA mixtures of a victim and an unknown suspect exist. Extracti...
Single Nucelotide Polymorphisms (SNPs) have become the most widely used markers in many current genetic applications. Here we report the discovery of nine new SNPs in olives by direct partial sequencing of two genes (OEX and OEW) in sixteen Tunisian...
Osteoporosis is a multifactorial disease, the pathogenesis of which is caused by a complex interaction of genetic, hormonal, and metabolic factors. The challenges of early diagnosis highlight the need to identify genetic predictors to prevent bone mi...
Food authentication in local breeds has important implications from both an economic and a qualitative point of view. Meat products from autochthonous breeds are of premium value, but can easily incur fraudulent or accidental substitution or mislabel...
To strengthen the management of maize varieties and the protection of intellectual property rights to new varieties, we constructed a comprehensive single nucleotide polymorphism (SNP)-DNA standard fingerprint database of 20,075 materials covering na...
Procuring biomedical literature is a time-consuming process. The genomic sciences software solution described here indexes literature from Pubmed Central’s open access initiative, and makes it available as a web application and through an application...
Background: Alfalfa, the most economically important forage legume worldwide, features modest genetic progress due to long selection cycles and the extent of the non-additive genetic variance associated with its autotetraploid genome. Methods: To imp...
The development of efficient, robust, and high-throughput SNP genotyping platforms is pivotal for crop genetics and breeding. Recently, SNP genotyping platforms based on target capture sequencing, which is very flexible in terms of the number of SNP...
High-throughput genomic technologies are enabling the identification of thousands or even millions of single-nucleotide polymorphisms (SNPs). SNP markers are frequently used to analyze crop varieties, with the marker data summarized in a common VCF f...
Excessive abdominal fat deposition accompanying rapid growth in broiler chickens seriously affects production efficiency. Using divergently selected broiler lines from Northeast Agricultural University, we integrated transcriptome sequencing, whole-g...
Grape (Vitis vinifera spp.) accessions exhibit rich diversity, and understanding their genetic variation and evolutionary relationships is crucial for cultivar selection and utilization. A highly representative SNP marker set was developed in this st...
Masson pine (Pinus massoniana Lamb.) is an important tree species in China, but its genomic research has been hindered due to a large genome size. Genotyping-by-sequencing (GBS) has been a powerful approach to revolutionize the field of genomic resea...
Single nucleotide polymorphisms (SNPs) are usually the most frequent genomic variants. Directly pedigree-phased multi-SNP haplotypes provide a more accurate view of polymorphic population genomic structure than individual SNPs. The former are, theref...
Excessive alcohol intake is a well-known modifiable risk factor for many cancers. It is still unclear whether genetic variants or single nucleotide polymorphisms (SNPs) can modify alcohol intake’s impact on prostate cancer (PCa) aggressiveness. The o...
Before the genomics era, heritability estimates were performed using pedigree data. Data collection for pedigree analysis is time consuming and holds the risk of incorrect or incomplete data. With the availability of SNP-based arrays, heritability ca...
A high-density single nucleotide polymorphism (SNP) array is essential to enable faster progress in plant breeding for new cultivar development. In this regard, we have developed an Axiom 60K almond SNP array by resequencing 81 almond accessions. For...
Next-generation sequencing and pool sequencing have been widely used in SNP (single-nucleotide polymorphism) detection and population genetics research; however, there are few reports on SNPs related to the growth of Penaeus vannamei. The purpose of...
Genome-wide association studies (GWAS) play a critical role in identifying many loci for common diseases and traits. There has been a rapid increase in the number of GWAS over the past decade. As additional GWAS are being conducted, it is unclear whe...
The blunt snout bream (Megalobrama amblycephala, BSB) is a freshwater economic fish with Chinese characteristics, and its genetic characteristics have unique value for studying fish evolution. The gynogenetic blunt snout bream (GBSB) obtained through...
(1) Background: Prostate cancer treatment efficacy is significantly influenced by androgen receptor (AR) signaling pathways. SLC22A3, a membrane transporter, has been linked to SNP rs9364554 risk loci for drug efficacy in prostate cancer. (2) Methods...
The G105G SNP (rs11554137) in the IDH1 gene is observed in about 10–15% of patients with a diffuse glioma. Data regarding its impact on gliomas are poor and partially conflicting, possibly due to the evolving classification of CNS tumors. The a...
Germplasm identification is essential for plant breeding and conservation. In this study, we developed a new method, DT-PICS, for efficient and cost-effective SNP selection in germplasm identification. The method, based on the decision tree concept,...
Taro (Colocasia esculenta) is the fifth most cultivated root crop in the world. During the asexual reproduction of taro, the frequent mutation of somatic cells leads to high genetic diversity. With the continuous increase in the amount of taro germpl...
Traditional expression quantitative trait locus (eQTL) mapping associates single nucleotide polymorphisms (SNPs) with gene expression, where the SNPs are derived from large-scale whole-genome sequencing (WGS) data or transcriptome data. While WGS pro...
Identifying single nucleotide polymorphism (SNP) interactions is considered as a popular and crucial way for explaining the missing heritability of complex diseases in genome-wide association studies (GWAS). Many approaches have been proposed to dete...
The autotetraploid potato (Solanum tuberosum L.) is an important crop in China, and it is widely cultivated from Northeast China to South China. Thousands of varieties are bred by breeding institutions or companies, and distinguishing the different v...
Herein, the genetic diversity of the local Přeštice Black-Pied pig breed was assessed by the simultaneous analysis of the pedigree and single nucleotide polymorphism (SNP) data. The information about sire line, dam, date of birth, sex, br...
Increasing evidence suggests that a single individual is insufficient to capture the genetic diversity within a species due to gene presence absence variation. In order to understand the extent to which genomic variation occurs in a species, the cons...
Transitioning from traditional to new genotyping technologies requires the development of bridging methodologies to avoid extra genotyping costs. This study aims to identify the optimum number of single nucleotide polymorphisms (SNPs) necessary to ac...
In this study we identified single nucleotide polymorphism (SNP) and sequence characteristic amplification region (SCAR) markers for specific identification of antler-shaped Ganoderma lucidum strains. When the partial mitochondrial SSU rDNA gene sequ...
Auricularia heimuer is the second most widely cultivated edible fungus in China, with significant food and medicinal value, and is highly popular throughout Asia and globally. However, the differentiation of A. heimuer is simple, as its morphology is...
Traits related to flowering time are the most promising agronomic traits that directly impact the seed yield and oil quality of rapeseed (Brassica napus L.). Developing early flowering and maturity rapeseed varieties is an important breeding objectiv...
The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) is the only extant freshwater cetacean species inhabiting the Yangtze River in China. Facing significant threats from habitat degradation and human activities, this critically...
Needles play key roles in photosynthesis and branch growth in Larix olgensis. However, genetic variation and SNP marker mining associated with needle and branch-related traits have not been reported yet. In this study, we examined 131 samples of unre...
Recently, research on detecting SNP interactions has attracted considerable attention, which is of great significance for exploring complex diseases. The formulation of effective swarm intelligence optimization algorithms is a primary resolution to t...
Single-nucleotide polymorphisms (SNPs), as disease-related biogenetic markers, are crucial in elucidating complex disease susceptibility and pathogenesis. Due to computational inefficiency, it is difficult to identify high-dimensional SNP interaction...
Growth performance is a complex economic trait for avian production. The swan goose (Anser cygnoides) has never been exploited genetically like chickens or other waterfowl species such as ducks. Traditional phenotypic selection is still the main meth...
(1) Background: The clinical course of multiple sclerosis (MS) is critically influenced by the expression of different pro-inflammatory and anti-inflammatory cytokines. Interleukin 6 (IL-6) represents a major inflammatory molecule previously associat...
Late blight, caused by oomycetes Phytophthora infestans is one of the most challenging fungal diseases to manage in tomato plants (Solanum lycopersicum L.). Toward managing the disease, conventional breeding has successfully introgressed genetic loci...
Aquaculture has become a crucial component of global food production, yet catfish (10.8% of global finfish production) breeding programs often lack sufficient genetic data to fully utilize their production potential. In the last 15 years, there have...
The species of Pimpinella, one of the largest genera of the family Apiaceae, are traditionally cultivated for medicinal purposes. In this study, high-throughput double digest restriction-site associated DNA sequencing technology (ddRAD-seq) was used...
Radiata pine (Pinus radiata D.Don) is one of the world’s most domesticated pines and a key economic species in New Zealand. Thus, the development of genomic resources for radiata pine has been a high priority for both research and commercial br...
The application of whole-genome resequencing in genetic research is rapidly expanding, yet the impact of sequencing depth on data quality and variant detection remains unclear, particularly in aquaculture species. This study re-sequenced 31 Litopenae...
of 155