In view of the predicted significant increase in global meat production, alternative sources such as horsemeat are becoming increasingly important due to their lower environmental impact and high nutritional value. This study aimed to identify SNP markers on the GeneSeek® Genomic Profiler™ Equine (Neogen, Lansing, MI, USA) that are important for horsemeat production traits. First, orthologous genes related to meat yield in cattle and common genes between horses and cattle within QTLs for body size and weight were identified. Markers for these genes were then evaluated based on predicted variant consequences, GERP scores, and positions within constrained elements and orthologous regulatory regions in pigs. A total of 268 markers in 57 genes related to meat production were analyzed. This resulted in 27 prioritized SNP markers in 22 genes, including notable markers in LCORL, LASP1, IGF1R, and MSTN. These results will benefit smallholder farmers by providing genetic insights for selective breeding that could improve meat yield. This study also supports future large-scale genetic analyses such as GWAS and Genomic Best Linear Unbiased Prediction (GBLUP). The results of this study may be helpful in improving the accuracy of genomic breeding values. However, limitations include reliance on bioinformatics without experimental validation. Future research can validate these markers and consider a wider range of traits to ensure accuracy in equine breeding.

The US beef and dairy industries have made remarkable advances in sustainability and productivity through technological advancements, including selective breeding. Yet, challenges persist due to the complex nature of quantitative traits. While the beef industry has progressed in adopting genomic technologies, the availability of phenotypic data remains an obstacle. To meet the need for sustainable production systems, novel traits are being targeted for selection. Additionally, emerging approaches such as genome editing and high-throughput phenotyping hold promise for further genetic progress. Future research should address the challenges of translating functional genomic findings into practical applications, while simultaneously harnessing analytical methods.

Increasing seawater temperatures coupled with more intense and frequent heatwaves pose an increasing threat to marine species. In this study, the New Zealand green-lipped mussel, Perna canaliculus, was used to investigate the effect of genetics and ontogeny on thermal resilience. The culturally and economically significant mussel P. canaliculus (Gmelin, 1971) has been selectively-bred in New Zealand for two decades, making it a unique biological resource to investigate genetic interactions in a temperate bivalve species. Six selectively-bred full sibling families and four different ages, from early juveniles (6, 8, 10 weeks post-fertilisation) to sub-adults (52 weeks post-fertilisation), were used for experimentation. At each age, each family was exposed to a three-hour heat challenge, followed by recovery, and survival assessments. The shell lengths of live and dead juvenile mussels were also measured. Gill tissue samples from sub-adults were collected after the thermal challenge to quantify the 70 kDa heat shock protein gene (hsp70). Results showed that genetics, ontogeny and size influence thermal resilience in P. canaliculus, with LT50 values ranging between 31.3 and 34.4 °C for all studied families and ages. Juveniles showed greater thermotolerance compared to sub-adults, while the largest individuals within each family/age class tended to be more heat sensitive than their siblings. Sub-adults differentially upregulated hsp70 in a pattern that correlated with net family survival following heat challenge, reinforcing the perceived role of inducible HSP70 protein in molluscs. This study provides insights into the complex interactions of age and genotype in determining heat tolerance of a key mussel species. As marine temperatures increase, equally complex selection pressure responses may therefore occur. Future research should focus on transcriptomic and genomic approaches for key species such as P. canaliculus to further understand and predict the effect of genetic variation and ontogeny on their survival in the context of climate change.

Atlantic salmon (Salmo salar) is an important source of food globally; however, fillet color can significantly affect consumer purchasing, leading to potential food waste. Fish diets can be supplemented with astaxanthin to increase the organic pigment, carotenoid, responsible for flesh coloration; however, there is variation in the amount of overall fillet coloration in response to feeding astaxanthin. The uptake of this pigment is influenced by the environment and genetics and has been shown to be heritable. Therefore, we set out to determine the genomic associations of two separate year classes of farmed North American Atlantic salmon with measured Minolta Chroma Meter (lightness, redness, and yellowness) and SalmoFan phenotypic traits. Using ASReml-R genome-wide association, two genetic markers on chromosome 26 were significantly associated with almost all color traits, and these two markers explained between 6.0% and 12.5% of the variances. The genomic region on chromosome 26 was importantly found to be associated with the beta-carotene oxygenase 1 (bco1) gene, which is essential in the conversion of beta-carotenoids to vitamin A, implying that this gene may also play an important role in flesh coloration in North American Atlantic salmon. Additionally, there were several genomic regions significantly associated with color traits, in which the accompanying genes had functions in line with thermogenesis, immune function, and pathogenic responses. Understanding how environmental and genetic factors work together to affect fillet quality traits will help inform genetic improvement.

In various organisms, sequencing of selectively bred lines at apparent selection limits has demonstrated that genetic variation can remain at many loci, implying that evolution at the genetic level may continue even if the population mean phenotype remains constant. We compared selection signatures at generations 22 and 61 of the \"High Runner\" mouse experiment, which includes 4 replicate lines bred for voluntary wheel-running behavior (HR) and 4 non-selected control (C) lines. Previously, we reported multiple regions of differentiation between the HR and C lines, based on whole-genome sequence data for 10 mice from each line at generation 61, which was >31 generations after selection limits had been reached in all HR lines. Here, we analyzed pooled sequencing data from ~20 mice for each of the 8 lines at generation 22, around when HR lines were reaching limits. Differentiation analyses of allele frequencies at ~4.4 million SNP loci used the regularized T-test and detected 258 differentiated regions with FDR = 0.01. Comparable analyses involving pooling generation 61 individual mouse genotypes into allele frequencies by line produced only 11 such regions, with almost no overlap among the largest and most statistically significant peaks between the two generations. These results implicate a sort of \"genetic churn\" that continues at loci relevant for running. Simulations indicate that loss of statistical power due to random genetic drift and sampling error are insufficient to explain the differences in selection signatures. The 13 differentiated regions at generation 22 with strict culling measures include 79 genes related to a wide variety of functions. Gene ontology identified pathways related to olfaction and vomeronasal pathways as being overrepresented, consistent with generation 61 analyses, despite those specific regions differing between generations. Genes Dspp and Rbm24 are also identified as potentially explaining known bone and skeletal muscle differences, respectively, between the linetypes.

Bottlenecks in moving genomics to real-life applications also include phenomics. This is true not only for genomics medicine and public health genomics but also in ecology and livestock phenomics. This expert narrative review explores the intricate relationship between genetic makeup and observable phenotypic traits across various biological levels in the context of livestock research. We unpack and emphasize the significance of precise phenotypic data in selective breeding outcomes and examine the multifaceted applications of phenomics, ranging from improvement to assessing welfare, reproductive traits, and environmental adaptation in livestock. As phenotypic traits exhibit strong correlations, their measurement alongside specific biological outcomes provides insights into performance, overall health, and clinical endpoints like morbidity and disease. In addition, automated assessment of livestock holds potential for monitoring the dynamic phenotypic traits across various species, facilitating a deeper comprehension of how they adapt to their environment and attendant stressors. A key challenge in genetic improvement in livestock is predicting individuals with optimal fitness without direct measurement. Temporal predictions from unmanned aerial systems can surpass genomic predictions, offering in-depth data on livestock. In the near future, digital phenotyping and digital biomarkers may further unravel the genetic intricacies of stress tolerance, adaptation and welfare aspects of animals enabling the selection of climate-resilient and productive livestock. This expert review thus delves into challenges associated with phenotyping and discusses technological advancements shaping the future of biological research concerning livestock.

Haliotis midae is one of the most important molluscs in South African commercial aquaculture. In this study, a high-resolution integrated linkage map was constructed, and QTL identified using 2b-RADseq for genotyping SNPs in three families. The final integrated linkage map was composed by merging the individual family maps, resulting in 3290 informative SNPs mapping to 18 linkage groups, conforming to the known haploid chromosome number for H. midae. The total map spanned 1798.25 cM with an average marker interval of 0.55 cM, representing a genome coverage of 98.76%. QTL analysis, across all three families, resulted in a total of five QTL identified for growth-related traits, shell width, shell length, and total body weight. For shell width and total body weight, one QTL was identified for each trait respectively, whilst three QTL were identified for shell length. The identified QTL respectively explained between 7.20% and 11.40% of the observed phenotypic variance. All three traits were significantly correlated (r = 0.862-0.970; p < 0.01) and shared overlapping QTL. The QTL for growth traits were mapped back to the H. midae draft genome and BLAST searches revealed the identity of candidate genes, such as egf-1, megf10, megf6, tnx, sevp1, kcp, notch1, and scube2 with possible functional roles in H. midae growth. The constructed high-density linkage map and mapped QTL have given valuable insights regarding the genetic architecture of growth-related traits and will be important genetic resources for marker-assisted selection. It remains, however, important to validate causal variants through linkage disequilibrium fine mapping in future.

Copy number variations (CNVs) critically influence individual genetic diversity and phenotypic traits. In this study, we employed whole-genome resequencing technology to conduct an in-depth analysis of 50 pigs from five local swine populations [Rongchang pig (RC), Wuzhishan pig (WZS), Tibetan pig (T), Yorkshire (YL) and Landrace (LR)], aiming to assess their genetic potential and explore their prospects in the field of animal model applications. We identified a total of 96,466 CNVs, which were subsequently integrated into 7112 non-redundant CNVRs, encompassing 1.3% of the swine genome. Functional enrichment analysis of the genes within these CNVRs revealed significant associations with sensory perception, energy metabolism, and neural-related pathways. Further selective scan analyses of the local pig breeds RC, T, WZS, along with YL and LR, uncovered that for the RC variety, the genes PLA2G10 and ABCA8 were found to be closely related to fat metabolism and cardiovascular health. In the T breed, the genes NCF2 and CSGALNACT1 were associated with immune response and connective tissue characteristics. As for the WZS breed, the genes PLIN4 and CPB2 were primarily linked to fat storage and anti-inflammatory responses. In summary, this research underscores the pivotal role of CNVs in fostering the diversity and adaptive evolution of pig breeds while also offering valuable insights for further exploration of the advantageous genetic traits inherent to China\'s local pig breeds. This facilitates the creation of experimental animal models tailored to the specific characteristics of these breeds, contributing to the advancement of livestock and biomedical research.

Changes in body shape are linked to swimming performance and become relevant for selective breeding programmes in cultured finfish. We studied how the selection for fast growth could affect phenotypes by investigating the relationship between swimming performance and body shape. We also investigated how swimming might affect plasma metabolite concentrations. Critical swimming speed (UCrit), body traits (e.g., BW, body weight; BL, body length; K, condition factor), and plasma lactate and glucose concentrations were evaluated in two cohorts of Australasian snapper (Chrysophrys auratus): one derived from wild broodstock (F1), and the other selected for fast growth (F4). UCrit tests (n = 8) were applied in groups of 10 snapper of similar BW (71.7 g) and BL (14.6 cm). The absolute or relative UCrit values of both cohorts were similar (0.702 m⋅s-1 and 4.795 BL⋅s-1, respectively), despite the F4 cohort displaying a higher K. A positive correlation between K and absolute UCrit (Pearson\'s r = 0.414) was detected in the F4 cohort, but not in the F1 cohort, which may be linked to differences in body shape. A negative correlation between relative UCrit and body size (Pearson\'s r between -0.682 and -0.501), but no correlation between absolute UCrit and body size, was displayed in both cohorts. Plasma lactate and glucose concentrations were higher in the F4 cohort at UCrit. Whether a longer selective breeding programme could result in more changes in body shape, potentially affecting swimming performance, should be explored, along with the potential outcomes of the differences in metabolic traits detected.

This study examined the influence of genetic background on cognitive performance in a selectively bred high nicotine-preferring (NP) rat line. Using the novel object recognition (NOR), novel location recognition (NLR), and Morris water maze (MWM) tests, we evaluated object memory, spatial memory, and spatial navigation in nicotine-naive NP rats compared to controls. Our results demonstrate that in the NOR test, both male and female NP rats spent more time exploring the novel object (higher discrimination index) compared to sex-matched controls. In the NLR, the discrimination index differed significantly from zero chance (no preference) in both NP males and females but not in controls, indicating enhanced spatial memory in the NP line. During MWM acquisition, the NP groups and control males took a shorter path to reach the platform compared to control females. On the probe trial, the distance traveled in the target quadrant was longer for NP males and females compared to their respective controls, suggesting enhanced spatial navigation and learning in the NP rats. The interesting preference for novel objects and locations displayed by NP rats may indicate a potential novelty-seeking phenotype in this line. These results highlight the complex interplay between genetic factors, cognitive function, and nicotine preference.