Efficient feed utilization in dairy cows is crucial for economic and environmental reasons. The rumen microbiota plays a significant role in feed efficiency, but studies utilizing microbial data to predict host phenotype are limited. In this study, 87 primiparous Nordic Red dairy cows were ranked for feed efficiency during their early lactation based on residual energy intake, and the rumen liquid microbial ecosystem was subsequently evaluated using 16S rRNA amplicon and metagenome sequencing. The study used amplicon data to build an extreme gradient boosting model, demonstrating that taxonomic microbial variation can predict efficiency (r_test = 0.55). Prediction interpreters and microbial network revealed that predictions were based on microbial consortia and the efficient animals had more of the highly interacting microbes and consortia. Rumen metagenome data was used to evaluate carbohydrate-active enzymes and metabolic pathway differences between efficiency phenotypes. The study showed that an efficient rumen had a higher abundance of glycoside hydrolases, while an inefficient rumen had more glycosyl transferases. Enrichment of metabolic pathways was observed in the inefficient group, while efficient animals emphasized bacterial environmental sensing and motility over microbial growth. The results suggest that inter-kingdom interactions should be further analyzed to understand their association with the feed efficiency of animals.

Just like traditional livestock, farmed insects harbour genetic variation and can be selectively bred to optimise traits of interest. This BugBook article presents a comprehensive overview of how genetics can contribute to improving insect production for food and feed. Molecular genetics and genomics approaches for generating the data essential for understanding species biology are presented, as well as their implementation in dedicated selective breeding programmes, and options for health and quality control of mass rearing operations. To harness the breeding potential of farmed insects, methods to investigate population genetic diversity and structure through population and evolutionary genetic principles are provided as well as tools for monitoring genetic variation and assessing genetic consequences of captive breeding to adequately manage populations. An overview is given on quantitative genetics of farmed insects, how to record phenotypes and pedigrees, estimate genetic parameters, and design optimal breeding programmes. Lastly, the role of functional genetics in insect production is discussed, the biological link between DNA and phenotypic variation, and key to effectively apply genetic improvement strategies through selective breeding. This article identifies knowledge gaps in insect breeding and provides recommendations for application and future research. Major challenges in the field of genetics of farmed insects include how to phenotype large numbers of individual insects over generations; how environmental factors affect trait expression, including interaction with genetics; and how to translate results from laboratory settings to mass rearing environments. This article will contribute to further develop the area of genetics of insects for food and feed.

In Lithuania, there are two recognised native sheep breeds: old native Lithuanian Coarsewooled and Lithuanian Blackface. In addition, in 2005, primitive Heidschnucke-type Skudde sheep were imported to Lithuania and were argued to possibly represent a lost Lithuanian sheep type. The aim of the study was to investigate the genetic variation in the two Lithuanian native sheep breeds, compare them with the imported Skudde sheep and establish the historical patterns of admixture and the genetic relatedness of Lithuanian sheep to British, Central European and Nordic sheep breeds included in the SheepHapMap study. In total, 72 individuals, representing two Lithuanian native and imported Skudde sheep breeds, were genotyped using a Neogen 12K Illumina Infinium chip. The population analysis was carried out by model-based clustering, principal component analysis and neighbour net analysis, and showed similar patterns for the Lithuanian sheep populations. Lithuanian Coarsewooled and Skudde in Lithuania have unique divergence and possibly some shared ancestry, while the Lithuanian Blackface conforms to a modern synthetic breed. The study clearly showed that the Coarsewooled and the Skudde breeds are distinct from each other. Historical data strongly suggest that the Coarsewooled breed represents a local breed, while the Skudde origin is less directly linked to the geographical area of modern-day Lithuania. Within the modern-day Lithuanian context, the Lithuanian Coarsewooled sheep is very important historical sheep type for conservation.

Background Diversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack efficient genotyping solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data was used to automate the bioinformatic analysis. The application of the optimization was demonstrated on non-model European whitefish data. Results DdRAD data generation was designed for a reliable estimation of relatedness and is scalable to up to 384 samples. The GBS sequencing yielded approximately one million reads for each of the around 100 assessed samples. Optimizing various strategies to create a de-novo reference genome for variant calling (mock reference) showed that using three samples outperformed other building strategies with single or very large number of samples. Adjustments to most pipeline tuning parameters had limited impact on high-quality data, except for the identity criterion for merging mock reference genome clusters. For each species, over 15k GBS variants based on the mock reference were obtained and showed comparable results with the ones called using an existing reference genome. Repeatability analysis showed high concordance over replicates, particularly in bovine while in European whitefish data repeatability did not exceed earlier observations. Conclusions The proposed cost-effective ddRAD strategy, coupled with an efficient bioinformatics workflow, enables broad adoption of ddRAD GBS across diverse farmed species. While beneficial, a reference genome is not obligatory. The integration of Snakemake streamlines the pipeline usage on computer clusters and supports customization. This user-friendly solution facilitates genotyping for both model and non-model species.

Small, threatened populations often suffer from a limited gene pool, which increases inbreeding and reduces their adaptability. We investigated the phenotypic and genomic effects of hybridization (resulting from backcrossing) on the critically endangered Lake Saimaa landlocked salmon, Salmo salar m. sebago , focusing on a particularly sensitive alevin‐fry life stage. The Saimaa salmon has undergone severe genetic bottlenecks and relies exclusively on a hatchery‐based conservation program. Since 2017, crossings with geographically proximate anadromous Baltic Sea salmon populations (Neva and Tornio) have been conducted as a possible means to restore genetic diversity. Here, we used a maternal half‐sib design to compare early viability of purebred Saimaa salmon with their first‐generation Neva and Tornio backcrosses in semi‐natural conditions. The backcrossed fry survived better than purebreds, showing a 9–12 percentage‐point increase in viability, whereas no significant cross differences were found in body mass. Quantitative genetic analysis further showed that hybrid sires conferred higher genetic merit for survival. Genomic analyses using a high‐density SNP array (47,901 loci) confirmed clear differentiation between pure and backcross groups, validating admixture. Pure Saimaa salmon had heterozygosity ( H _S ) of 0.13 (over 50% of loci monomorphic), while backcrosses possessed H _S of 0.25 and substantially more polymorphism (96%–97% of loci). Analysis of homozygous genomic segments showed that the inbreeding of Saimaa salmon has predominantly accumulated prior to the conservation program. Widespread reductions in autozygosity were found in both cross types, though introgression varied across the genome and also showed substantial donor‐ and family‐specificity. Overall, the results suggest that hybridization improved early survival through additive and potential dominance effects (reduced genetic load, heterozygote advantage), and expanded genomic variation without immediate indication of outbreeding depression. However, sequential backcrossing across multiple generations is necessary to ensure the preservation of Saimaa salmon's unique genetic identity while enhancing its resilience through the life cycle.