E-GWAS: an ensemble-like GWAS strategy that provides effective control over false positive rates without decreasing true positives

Genome-Wide Association Study of Body Weight Traits in Texel and Kazakh Crossbred Sheep

Background: Originating from the cold and arid regions of northwestern China, Kazakh sheep are dual-purpose breeds optimized for both meat and fat production. In contrast, Texel sheep are internationally recognized for their high-quality meat and exceptional flavor. Previous studies have indicated that the hybrids of Texel and Kazakh sheep exhibit significant quality advantages. Additionally, body weight is a crucial indicator of sheep production performance, directly correlating with meat yield and economic returns. Objective: This study aims to identify genetic variations and related genes associated with the body weight traits of hybrid lambs, thereby revealing their genetic mechanisms. Methods: This study genotyped hybrid lambs using a 50K chip and performed rigorous quality control on both genotypic and phenotypic data. The traits examined include body weight traits of lambs at various stages such as birth, pre-weaning, and post-weaning. Various genome-wide association study (GWAS) models were utilized to analyze the association between lamb body weight traits and genetic markers. The study then employed an Ensemble-like GWAS (E-GWAS) strategy to integrate these models, achieving a stable list of SNPs, rather than a mere aggregation. Multiple annotation databases were consulted to further investigate the mechanisms by which genetic markers affect body weight traits. All study results were validated through an extensive literature review. Results: Analyses with multiple statistical models revealed that 48 SNPs were significantly associated with body weight traits. The annotation process identified 24 related genes (including 4 unknown genes) and 9 quantitative trait loci (QTLs). Additionally, 6 Gene Ontology (GO) terms and 22 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were determined. Conclusions: This study identified key genes and pathways in the body weight traits of hybrids between Texel and Kazakh sheep, enhancing our understanding of their genetic mechanisms.

Identification of SNPs and Candidate Genes Associated with Monocyte/Lymphocyte Ratio and Neutrophil/Lymphocyte Ratio in Duroc × Erhualian F2 Population

Understanding the pig immune function is crucial for disease-resistant breeding and potentially for human health research due to shared immune system features. Immune cell ratios, like monocyte/lymphocyte ratio (MLR) and neutrophil/lymphocyte ratio (NLR), offer a more comprehensive view of immune status compared to individual cell counts. However, research on pig immune cell ratios remains limited. This study investigated MLR and NLR in a Duroc × Erhualian F2 resource population. Heritability analysis revealed high values (0.649 and 0.688 for MLR and NLR, respectively), suggesting a strong genetic component. Furthermore, we employed an ensemble-like GWAS (E-GWAS) strategy and functional annotation analysis to identify 11 MLR-associated and 6 NLR-associated candidate genes. These genes were significantly enriched in immune-related biological processes. These findings provide novel genetic markers and candidate genes associated with porcine immunity, thereby providing valuable insights for addressing biosecurity and animal welfare concerns in the pig industry.

Additive and Dominance Genome-Wide Association Studies Reveal the Genetic Basis of Heterosis Related to Growth Traits of Duhua Hybrid Pigs

Heterosis has been extensively used for pig genetic breeding and production, but the genetic basis of heterosis remains largely elusive. Crossbreeding between commercial and native breeds provides a good model to parse the genetic basis of heterosis. This study uses Duhua hybrid pigs, a crossbreed of Duroc and Liangguang small spotted pigs, as materials to explore the genetic basis underlying heterosis related to growth traits at the genomic level. The mid-parent heterosis (MPH) analysis showed heterosis of this Duhua offspring on growth traits. In this study, we examined the impact of additive and dominance effects on 100 AGE (age adjusted to 100 kg) and 100 BF (backfat thickness adjusted to 100 kg) of Duhua hybrid pigs. Meanwhile, we successfully identified SNPs associated with growth traits through both additive and dominance GWASs (genome-wide association studies). These findings will facilitate the subsequent in-depth studies of heterosis in the growth traits of Duhua pigs.

Unraveling the genetics of heat tolerance in chickpea landraces (Cicer arietinum L.) using genome-wide association studies

Chickpea, being an important grain legume crop, is often confronted with the adverse effects of high temperatures at the reproductive stage of crop growth, drastically affecting yield and overall productivity. The current study deals with an extensive evaluation of chickpea genotypes, focusing on the traits associated with yield and their response to heat stress. Notably, we observed significant variations for these traits under both normal and high-temperature conditions, forming a robust basis for genetic research and breeding initiatives. Furthermore, the study revealed that yield-related traits exhibited high heritability, suggesting their potential suitability for marker-assisted selection. We carried out single-nucleotide polymorphism (SNP) genotyping using the genotyping-by-sequencing (GBS) method for a genome-wide association study (GWAS). Overall, 27 marker-trait associations (MTAs) linked to yield-related traits, among which we identified five common MTAs displaying pleiotropic effects after applying a stringent Bonferroni-corrected p-value threshold of <0.05 [-log10(p) > 4.95] using the BLINK (Bayesian-information and linkage-disequilibrium iteratively nested keyway) model. Through an in-depth in silico analysis of these markers against the CDC Frontier v1 reference genome, we discovered that the majority of the SNPs were located at or in proximity to gene-coding regions. We further explored candidate genes situated near these MTAs, shedding light on the molecular mechanisms governing heat stress tolerance and yield enhancement in chickpeas such as indole-3-acetic acid-amido synthetase GH3.1 with GH3 auxin-responsive promoter and pentatricopeptide repeat-containing protein, etc. The harvest index (HI) trait was associated with marker Ca3:37444451 encoding aspartic proteinase ortholog sequence of Oryza sativa subsp. japonica and Medicago truncatula, which is known for contributing to heat stress tolerance. These identified MTAs and associated candidate genes may serve as valuable assets for breeding programs dedicated to tailoring chickpea varieties resilient to heat stress and climate change.