As an important genotyping platform, SNP chips are essential for implementing genomic selection. In this article, we introduced the development of a liquid SNP chip panel for dairy goats. This panel contains 54,188 SNPs based on genotyping by targete...
This study investigated novel quantitative traits loci (QTLs) associated with the control of grain shape and size as well as grain weight in rice. We employed a joint-strategy multiple GAPIT (Genome Association and Prediction Integrated Tool) models...
This research is designed to examine the genetic diversity and kinship among Hu sheep, as well as to discover genes associated with crucial economic traits. A selection of 50 unrelated adult male Hu sheep underwent genotyping with the SNP50K BeadChip...
Background: Beagle dogs are widely used in biomedical research, but their genetic diversity and population structure require further investigation. This study aimed to assess genetic diversity, population structure, and selection signals in a foundat...
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...
The genetic markers associated with economic traits have been widely explored for animal breeding. Among these markers, single-nucleotide polymorphism (SNPs) are gradually becoming a prevalent and effective evaluation tool. Since SNPs only focus on t...
The Jiangshan black pig is an indigenous pig breed in China, renowned for its superior meat quality and adaptability to roughage. However, the population of Jiangshan black pigs has dwindled due to the introduction of cosmopolitan pig breeds and the...
Caucasian tur (Capra caucasica) is native to Greater Caucasus Mountain Chain from Azerbaijan and Georgia in the East to Krasnodar region of Russia in the West. This species is divided into two subspecies (by some authors into species)—East-Caucasian...
Genomic models that incorporate dense marker information have been widely used for predicting genomic breeding values since they were first introduced, and it is known that the relationship between individuals in the reference population and selectio...
The aim of this study was to determine the breed boundary of the Hungarian Short-haired Vizsla (HSV) dog breed. Seventy registered purebred HSV dogs were genotyped on approximately 145,000 SNPs. Principal Component Analysis (PCA) and Admixture analys...
The Korean native pig (KNP; Sus scrofa coreanus) is an indigenous porcine breed in South Korea considered as a valuable but dwindling genetic resource. Studies using diverse methodologies and genetic markers suggest that this population originated fr...
Design of low-density SNP chips provides an opportunity for wide application of genomic selection at lower cost. A novel strategy referred to as the “block-free” method is proposed in this study to select a subset of SNPs from a high-dens...
Genomic improvement and sustainable breeding of Mediterranean buffalo are hampered by the lack of breed-specific genomic resources compared with bovine. To address this gap, we aimed to identify a comprehensive set of high-confidence single-nucleotid...
Sheep play a critical role in the agricultural and livestock sector in Egypt. For sheep meat production, growth traits such as birth and weaning weights are very important and determine the supply and income of local farmers. The Barki sheep originat...
(1) Background: The Hu sheep is a renowned breed characterized by high reproduction, year-round estrus, and resistance to high humidity and temperature conditions. However, the breed exhibits lower growth rates and meat yields, which necessitate impr...
Hair follicle development and wool shedding in sheep are poorly understood. This study investigated the population structures and genetic differences between sheep with different wool types to identify candidate genes related to these traits. We used...
This study developed a 60K single-nucleotide polymorphism (SNP) liquid-phase chip (‘Shenxin I’) based on genotyping by target sequencing (GBTS) technology. The chip was used to genotype 1451 individuals spanning five conserved local pig b...
Aggressive behavior has negative effects on animal welfare and growth performance in pigs. The dopamine receptor D2 (DRD2) has a critical neuromodulator role in the dopamine signal pathway within the brain to control behavior. A functional single-nuc...
Improving the prediction accuracies of economically important traits in genomic selection (GS) is a main objective for researchers and breeders in the livestock industry. This study aims at utilizing potentially functional SNPs and QTLs identified wi...
Differentiation of cells by flow cytometry provides informative somatic cell counts (SCCs) that allow analyzing leukocyte population patterns in udder infections of different etiologies. Postulating that this approach also enhances the statistical po...
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...
pH was one of the important meat quality traits, which was an important factor affecting the storage/shelf life and quality of meat in meat production. In order to find a way to extend the storage/shelf life, the pH values (pH45min, pH24h, pH48h and...
Understanding the genetic diversity and population structure of farm animals is key to developing effective breeding strategies and conserving genetic resources. The aim of this study was to assess the genetic diversity and population structure of th...
Background: Genetic diversity and genetic differentiation between Gossypium hirsutum-Gossypium barbadense introgression lines (ILs) and early-maturing upland cotton lines are critical for resolving the core breeding contradiction in Xinjiang cotton r...
Autochthonous taurine and later introduced zebu cattle from Cameroon differ considerably in their resistance to endemic pathogens with little to no reports of the underlying genetic make-up. Breed history and habitat variations are reported to contri...
The Fengjing pig is one of the local pig breed resources in China and has many excellent germplasm characteristics. However, research on its genome is lacking. To explore the degree of genetic diversity of the Fengjing pig and to deeply explore its e...
The nitrogen (N) use efficiency (NUE) in the roots of seedlings is beneficial for increasing crop yield. Creating marker-assisted selection for wheat root traits can assist wheat breeders in choosing robust roots to maximize nutrient uptake. Explorin...
Metabolic syndrome (MetS) is a complex condition of metabolic disorders and shows a steady onset globally. Ceramides are known as intracellular signaling molecules that influence key metabolism through various pathways such as MetS and insulin resist...
Henan Province is located in central China and rich in domestic pig populations; Huainan (HN) pigs are one of three Henan indigenous breeds with great performance, including early maturation, strong disease resistance and high meat quality. Yunan (YN...
The swimming crab (Portunus trituberculatus) is a commercially important marine aquaculture species. After multiple generations of selective breeding, the third improved variety in China, “Huangxuan No 2” (HX2), was successfully developed...
Single-step genomic evaluation became a standard procedure in livestock breeding, and the main reason is the ability to combine all pedigree, phenotypes, and genotypes available into one single evaluation, without the need of post-analysis processing...
Mastitis is one of the most frequently encountered diseases in dairy cattle, negatively affecting animal welfare and milk production. For this reason, contributions to understanding its genomic architecture are of great interest. Genome-wide associat...
The objective of this study was to identify genomic regions associated with milk fat percentage (FP), crude protein percentage (CPP), urea concentration (MU) and efficiency of crude protein utilization (ECPU: ratio between crude protein yield in milk...
Copy number variation (CNV) is an important class of genetic variations widely associated with the porcine genome, but little is known about the characteristics of CNVs in foreign and indigenous pig breeds. We performed a genome-wide comparison of CN...
Well-developed maize reference genomes and genotyping technology along with fast decreasing detection costs have enabled the chance of shifting essentially derived varieties (EDV) identification to high-throughput SNP genotyping technology. However,...
Distinctive molecular approaches and tools, particularly high-throughput SNP genotyping, have been applied to determine and discover SNPs, potential genes of interest, indicators of evolutionary selection, genetic abnormalities, molecular indicators,...
The Asian tiger mosquito (Aedes albopictus) is an invasive species that has become widespread throughout the Americas. It is a vector for several arboviruses, making it an increasing threat to human health as its range expands. To characterize popula...
This manuscript describes the use of a novel biochip platform for the rapid analysis/identification of nucleic acids, including DNA and microRNAs, with very high specificity. This approach combines a unique dynamic chemistry approach for nucleic acid...
Understanding the genetic basis of native cattle populations that have adapted to the local environment is of great significance for formulating appropriate strategies and programs for genetic improvement and protection. Therefore, it is necessary to...
The diversification of indigenous pig breeds in China has resulted from multiple climate, topographic, and human cultural influences. The numerous indigenous pig breeds can be geographically divided into six meta-populations; however, their genetic r...
Chinese Red Steppe Cattle (CRS), a composite cattle breed, is well known for its milk production, high slaughter rate, carcass traits, and meat quality. Nowadays, it is widely bred in Jilin and Hebei Province and the Inner Mongolia Autonomous region....
A pillar of wine authenticity is the variety/ies used. Ampelographic descriptors and SSR markers, included in several national and international databases, are extensively used for varietal identification purposes. Recently, SNP markers have been pro...
Our previous study suggested that the Mono-ADP ribosylhydrolase 2 (MACROD2) rs6110695 A>G polymorphism is significantly associated with white blood cell (WBC) count in the Korean population. The present study aimed to evaluate the clinical relevan...
The availability of genome sequences and single-nucleotide polymorphism (SNP) chips allows us to investigate the various genomic characteristics of species by exploring genetic diversity to aid genetic selection. The SNP chip is a cost-effective geno...
The Xinglong buffalo is a local swamp buffalo breed adapted to tropical regions in China. To facilitate the protection and utilization of valuable genetic resources, we first developed the breed-specific single nucleotide polymorphism (SNP) liquid-ph...
Genomic selection (GS) is an efficient method to improve genetically economic traits. Feature selection is an important method for GS based on whole-genome sequencing (WGS) data. We investigated the prediction performance of GS of milk production tra...
Selection of genetically resistant animals is one alternative to reduce the negative impact of gastrointestinal nematodes (GIN) on sheep production. The aim of this study was to identify genomic regions associated with GIN resistance in Corriedale sh...
Although the potato chip industry is booming, and distinct chip-processing clones have been released over the past 60 years, the genetic architecture of their chip-processing characteristics remains largely unknown. Case-control genome-wide associati...
The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is...
Microarray-based genomic selection is a central tool to increase the genetic gain of economically significant traits in dairy cattle. Yet, the effectivity of this tool is slightly limited, as estimates based on genotype data only partially explain th...
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