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...
VTRNA2-1 is a metastable epiallele with accumulating evidence that methylation at this region is heritable, modifiable and associated with disease including risk and progression of cancer. This study investigated the influence of genetic variation an...
Genome-wide association studies (GWAS) are commonly employed to study the genetic basis of complex traits/diseases, and a key question is how much heritability could be explained by all single nucleotide polymorphisms (SNPs) in GWAS. One widely used...
With a perspective future ban on surgical castration in Europe, selecting pigs with reduced ability to accumulate boar taint (BT) compounds (androstenone, indole, skatole) in their tissues seems a promising strategy. BT compound concentrations were q...
Litopenaeus vannamei, the most widely farmed crustacean, relies on family-based selection where accurate pedigree information is essential. Although SNP-based tools offer high-accuracy pedigree assignment, adoption in commercial breeding remains limi...
Egg production traits are crucial in the poultry industry, including age at first egg (AFE), egg number (EN) at different stages, and laying rate (LR). Ducks exhibit higher egg production capacity than other poultry species, but the genetic mechanism...
IgA nephropathy is the most common primary glomerulonephritis worldwide and a leading cause of chronic kidney disease and kidney failure in young and middle-aged adults, characterized by considerable ethnic differences in incidence and prognosis. Thi...
Eucalyptus globulus (Labill.) is one of the most important cultivated eucalypts in temperate and subtropical regions and has been successfully subjected to intensive breeding. In this study, Bayesian genomic models that include the effects of haploty...
Alzheimer’s disease (AD) is the main cause of dementia worldwide, and the genetic mechanism of which is not yet fully understood. Much evidence has accumulated over the past decade to suggest that after the first large-scale genome-wide associa...
Dogs represent a unique spontaneous cancer model. Osteosarcoma (OSA) is the most common primary bone tumor in dogs (OMIA 001441-9615), and strongly resembles human forms of OSA. Several large- to giant-sized dog breeds, including the Leonberger, have...
Genomic selection (GS) is a technique that integrates genomic data, pedigree information, and individual phenotypes to enhance genetic improvements of economically important traits in livestock. While it has shown significant effects in dairy cattle,...
Cancer ranks as the second leading cause of death worldwide, and, being a genetic disease, it is highly heritable. Over the past few decades, genome-wide association studies (GWAS) have identified many risk-associated loci harboring hundreds of singl...
The Body Mass Index (BMI), integrating body weight and length, is a widely used metric for obesity assessment in humans. As pigs serve as crucial biomedical models, the application of BMI in swine and its genetic basis remain poorly explored. This st...
High-throughput genotyping techniques have enabled large-scale genomic analysis to precisely predict complex traits in many plant species. However, not all species can be well represented in commercial SNP (single nucleotide polymorphism) arrays. In...
The contributions of additive, dominance, haplotype, and epistasis effects up to the third order to the accuracy of predicting daughter pregnancy rate (DPR) phenotypic values and to the phenotypic variance in U.S. Holstein cows were investigated usin...
Coeliac disease (CeD) is a gastrointestinal enteropathy triggered by the consumption of gluten in predisposed individuals. A recent study showed that individuals were at more than 10% risk of having CeD if a first-degree relative also had the disease...
This study investigates the efficacy of various genomic prediction models—Genomic Best Linear Unbiased Prediction (GBLUP), Random Forest (RF), Support Vector Machine (SVM), Extreme Gradient Boosting (XGB), and Multilayer Perceptron (MLP)—...
This study systematically measured gross hair weight and hair length traits across five body regions of 759 Tianzhu White Yak individuals. The BSL trait exhibited moderate heritability, while the BL trait demonstrated high heritability (h2 = 0.450)....
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...
(1) Background: Litter size traits are critical for pig breeding efficiency but pose challenges due to low heritability and sex-limited influences. This study aimed to elucidate the genetic architecture and identify candidate genes for these traits i...
Portuguese oyster (Magallana angulata) is one of the most important shellfish species worldwide. Although significant improvements in growth have been achieved through artificial selection breeding, the genetic basis underlying these traits remains u...
Background/Objectives: Genome-wide association studies (GWAS) based on single-step genomic BLUP (ssGBLUP) commonly assume equal single nucleotide polymorphism (SNP) variances, which may not reflect the biological architecture of complex traits. Alter...
The goal of our study was to identify the SNPs, metabolic pathways (KEGG), and gene ontology (GO) terms significantly associated with calving and workability traits in dairy cattle. We analysed direct (DCE) and maternal (MCE) calving ease, direct (DS...
Background/Objectives: Soybean first pod insertion height (FPIH) is a key trait established during plant development, but its genetic architecture in Eurasian germplasm remains largely unknown. Methods: We performed a GWAS and fine-mapping for FPIH u...
The aim of this study was the identification of candidate genomic regions associated with fiber diameter in alpacas. DNA samples were collected from 1011 female Huacaya alpacas from two geographical Andean regions in Peru (Pasco and Puno), and three...
Semantic fluency impairment has been attributed to a wide range of neurocognitive and psychiatric conditions, especially in the older population. Moderate heritability estimates on semantic fluency were obtained from both twin and family-based studie...
Sortilin-related vacuolar protein sorting 10 (VPS10) domain containing receptor 3 (SORCS3) is a neuron-specific transmembrane protein involved in the trafficking of proteins between intracellular vesicles and the plasma membrane. Genetic variation at...
Vulvar size and angle are meaningful traits in pig production. Sows with abnormal vulva generally show reproductive disorders. In order to excavate candidate loci and genes associated with pig’s vulvar traits, 270 Suhuai pigs with vulvar phenot...
Gene–environment interaction (G×E) studies are one of the most important solutions for understanding the “missing heritability” problem in genome-wide association studies (GWAS). Although many statistical methods have been 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...
Newcastle Disease (ND) is a continuing global threat to domestic poultry, especially in developing countries, where severe outbreaks of velogenic ND virus (NDV) often cause major economic losses to households. Local chickens are of great importance t...
The inclusion of meat quality traits in breeding programs is a promising strategy to improve beef by selecting animals based on both growth and meat quality. This study aimed to estimate genetic parameters for average daily gain (ADG) and Warner&ndas...
Replacement pigs’ genomic prediction for reproduction (total number and born alive piglets in the first parity), meat, fatness and growth traits (muscle depth, days to 100 kg and backfat thickness over 6–7 rib) was tested using single-step genomic be...
Linear mixed models (LMMs) are commonly used in genome-wide association studies (GWASs) to evaluate population structures and relatedness. However, LMMs have been shown to be ineffective in controlling false positive errors for the analysis of resist...
Agronomic traits and quality traits of alfalfa are of great importance to the feed industry. Genomic selection (GS) based on genotyping-by-sequencing (GBS) data, if it achieves moderate to high accuracy, has the potential to significantly shorten bre...
Forage feedstock is the greatest source of energy for livestock. Unfortunately, less than 50% of their fiber content is actually digested and assimilated by the ruminant animals. This recalcitrance is mainly due to the high concentration of plant cel...
Intermediate wheatgrass (IWG) is a perennial forage grass undergoing a rigorous domestication as a grain crop. As a young grain crop, several agronomic and domestication traits need improvement for IWG to be relevant in current agricultural landscape...
The paddle-shaped dactyl of the fifth pereiopod in the mud crab Scylla paramamosain is a specialized appendage, but the genetic basis and genomic prediction potential of its traits remain poorly understood. Using whole-genome resequencing data from 3...
GS in beef cattle faces challenges in cross-population prediction. Blind expansion of reference populations can reduce accuracy because of genetic noise, and traditional models such as GBLUP ignore functional heterogeneity of SNPs. In this study, we...
Attention Deficit Hyperactivity Disorder (ADHD) is a highly heritable and prevalent neurodevelopmental disorder that frequently persists into adulthood. Strong evidence from genetic studies indicates that single nucleotide polymorphisms (SNPs) harbou...
Fertility traits are core functional traits in dairy cattle, yet their low heritability makes traditional phenotypic selection inefficient. Weighted single-step GWAS (WssGWAS) improves detection power by integrating pedigree, phenotype, and genotype...
Castanopsis hystrix, a precious tree species in Southeast Asia, has the advantages of rapid growth and high-quality wood materials. However, there are problems such as its long breeding cycle and low efficiency, and being time-consuming, which greatl...
Swine inflammation and necrosis syndrome (SINS) is a widespread disease in pigs, causing pain, suffering, and damage. Inflammation is documented at different levels based on clinical signs, histopathology, clinical chemistry, metabolomics and transcr...
Common rust (CR), caused by Puccina sorghi, is a major foliar disease in maize that leads to quality deterioration and yield losses. To dissect the genetic architecture of CR resistance in maize, this study utilized the susceptible temperate inbred l...
The Inner Mongolia Cashmere goat (IMCG) industry is a major contributor to global cashmere production, with fleece traits serving as key economic indicators that directly impact both income and the long-term sustainability of the industry. When genom...
High-density SNP chips have been demonstrated to be effective instruments for simultaneously genotyping large numbers of loci, thereby facilitating genome-scale analyses and advancing genomic selection (GS) in poultry and livestock. The meat-type duc...
Left main coronary artery disease (LMCAD) is a particular severe phenotype of coronary artery disease (CAD) and heritability. Interleukin (IL) may play important roles in the pathogenesis of CAD. Although several single nucleotide polymorphisms (SNPs...
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,...
Background/Objectives: In gilthead seabream, the transition from fish meal/oil-based diets to diets with partial plant-based replacement is gaining ground due to price fluctuations and environmental concerns. Most studies focus on the dietary effects...
Dioscorea alata (L.), also referred to as water, winged, or greater yam, is one of the most economically important staple food crops in tropical and subtropical areas. In Côte d’Ivoire, it represents, along with other yam species, the lar...
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