Fisheries management units—i.e. ’stocks’—frequently match poorly with biological variation. This mismatch poses a management challenge particularly when within-species units differ in their resilience to harvesting. It is therefore essential to both identify the distinct biological units and adjust fishing pressure accordingly. In the northern Baltic Sea, the European whitefish (Coregonus lavaretus) has two ecotypes, anadromous and sea-spawning, harvested primarily with gillnets. The former is endangered due to river connectivity issues and fishing pressure, while the latter is faring better. However, the key elements of effective management, accurate stock component identification and stock-component-specific fishing pressure adjustment, have not been assessed in this mixed-stock fishery. To address this knowledge gap, we compared ecotype identification methods and examined how fishing depth, season, and gillnet mesh size influence the whitefish catch composition. First, we assessed how well the ecotypes could be identified using phenotypic traits (gill rakers and growth) and genetic data (SNP genotyping). While both approaches were useful, many individuals exhibited intermediate characteristics and were not reliably identified, with phenotypic and genetic identification approaches agreeing only moderately. The prevalence of individuals with intermediate traits may reflect past stocking practices, habitat degradation, or inherently inconsistent homing behaviour. Nevertheless, we caught a higher share of sea-spawner-like individuals from deeper waters, earlier in the season, and with gillnets of smaller mesh size. The fact that it was possible to markedly affect the catch composition suggests that spatial and temporal fishing regulations have potential in the management of whitefish mixed-stock fisheries.

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.

Objectives European whitefish ( Coregonus lavaretus L .) is a freshwater salmonid that inhabits cold regions of central and north Europe and Siberia. It is an important aquaculture species in Finland, selectively bred since 1999. The breeding programme has applied genomic selection that uses SNP markers and phenotypic data to improve traits such as growth, product quality, and fish health. Salmonids are known for chromosomal rearrangements, and the current C. lavaretus reference genome that is based on an individual from Switzerland may deviate from the Finnish one. Therefore, we have assembled a genome for the Finnish European whitefish. This allows us to better assess the genetic basis of fish traits and to enhance the accuracy of genomic selection. Data description The genome of European whitefish was sequenced using a combination of Illumina and PacBio technologies and assembled using wtbg2 and HiRise software. The assembly has a size of 2.94 Gb and comprises 6,706 scaffolds with the scaffold N50 of 1.36 Mb.

Tarve eläinperäisen lisävalkuaisen saannille omalta tilalta tai lähialueelta on suuri siipikarjan ja sian rehuissa yleisesti käytettävien kalajauhon ja luomusoijan kohonneiden hintojen, käyttörajoitusten sekä saantivaikeuksien takia. Haasteet ovat erityisen suuret luomutuotannossa. Hyönteisiä ei tällä hetkellä voi sertifioida luomuksi, mutta sertifioinnin mahdollistava lainsäädäntö on valmisteilla. Valkuaisomavaraisuuden lisäksi hyönteistuotannon avulla voidaan parantaa myös lannoiteomavaraisuutta, sillä tuotannon sivuvirtana syntyvä toukanpuru eli frassi on ensiluokkaista lannoitetta. Tutkimusten mukaan mustasotilaskärpäsen (Hermetia illucens) toukka sopii erinomaisen hyvin siipikarjan rehuksi. Esimerkiksi kananpoikien varhaisen vaiheen kasvua voidaan parantaa lisäämällä niiden rehuun 3–10% Hermetiaa. Munituskanoilla soija on voitu korvata kokonaan mustasotilaskärpäsen proteiinilla ja rasvalla ja broilerin rehusta on korvattu kalajauhoa mustasotilaskärpäsellä aina 15%:iin asti ilman syönnin ja kasvun heikkenemistä. Hyönteistä sisältävä rehu tuottaa eläimelle terveyshyötyjä. Mustasotilaskärpäsen rasvan runsas lauriinihappo vähentää suoliston enterobakteereja, kuten kolibakteereja. Kitiini ja sen pilkkoutumistuotteet parantavat suoliston mikrobistoa. Mustasotilaskärpänen sisältää myös bakteereja tappavia peptidejä ja sen proteiinit ja kitiini voimistavat eläinten luontaista immuunijärjestelmää. Kokeellisissa infektioissa 3–10%:n hyönteislisä on vähentänyt sairastavuutta ja kuolleisuutta. Hyönteisrehun immuniteettia voimistava ja sairastavuutta vähentävä vaikutus voi vähentää antibioottien tarvetta ja pienentää riskiä uusien antibioottiresistenssien bakteerikantojen kehittymiseen kotieläintuotannon yhteydessä. Luomutuotannossa, jossa eläimet ovat osan ajastaan ulkona eikä antibiootteja käytetä, taudinvastustuskyvyn vahvistaminen on erityisen tarpeen. Kanalle lähitoukkaa -hankkeen tavoitteena on parantaa siipikarja- ja sikatilojen valkuaisomavaraisuutta, huoltovarmuutta ja kriisinkestävyyttä korvaamalla tuontivalkuaista hyönteisproteiinilla. Hankkeessa tuotetaan ja pilotoidaan maatilamittakaavaan sopiva, skaalattava ja yleistettävä toimintamalli hyönteistoukan ja sen proteiinirikasteen tuotantoon. Toimintamalli kattaa tiedon laitteista ja menetelmistä mustasotilaskärpäsen proteiinin tuottamiseen sekä yleistettävissä olevat laskentatyökalut hyönteistuotannon tilakohtaisten kannattavuuslaskelmien laatimiseen. Hankkeessa hyödynnetään maatilan omia kasvisivuvirtoja toukkien rehuina. Alustavien tulosten mukaan viljojen lajittelun sivuvirta sopii Hermetian toukkien rehuiksi. Hankkeessa testataan parasta tapaa koostaa kasvatusmassa, sillä kasvatusalustan rakenne on olennaisen tärkeä toukkien kasvun optimoinnin kannalta. Kanalle lähitoukkaa -hanke on Manner-Suomen maaseudun kehittämisohjelman 2014–2020 rahoittama maaseudun innovaatioryhmä (EIP) hanke. Sen toteuttavat Luonnonvarakeskus (Luke), Jyväskylän ammattikorkeakoulu Oy (Jamk) ja Kaistin tila Oy.

Abstract Saprolegnia oomycete infection causes serious economic losses and reduces fish health in aquaculture. Genomic selection based on thousands of DNA markers is a powerful tool to improve fish traits in selective breeding programs. Our goal was to develop a single nucleotide polymorphism (SNP) marker panel and to test its use in genomic selection for improved survival against Saprolegnia infection in European whitefish Coregonus lavaretus, the second most important farmed fish species in Finland. We used a double digest restriction site associated DNA (ddRAD) genotyping by sequencing method to produce a SNP panel, and we tested it analyzing data from a cohort of 1,335 fish, which were measured at different times for mortality to Saprolegnia oomycete infection and weight traits. We calculated the genetic relationship matrix (GRM) from the genome-wide genetic data, integrating it in multivariate mixed models used for the estimation of variance components and genomic breeding values (GEBVs), and to carry out Genome-Wide Association Studies for the presence of quantitative trait loci (QTL) affecting the phenotypes in analysis. We identified one major QTL on chromosome 6 affecting mortality to Saprolegnia infection, explaining 7.7% to 51.3% of genetic variance, and a QTL for weight on chromosome 4, explaining 1.8% to 5.4% of genetic variance. Heritability for mortality was 0.20 to 0.43 on the liability scale, and heritability for weight was 0.44 to 0.53. The QTL for mortality showed an additive allelic effect. We tested whether integrating the QTL for mortality as a fixed factor, together with a new GRM calculated excluding the QTL from the genetic data, would improve the accuracy estimation of GEBVs. This test was done through a cross-validation approach, which indicated that the inclusion of the QTL increased the mean accuracy of the GEBVs by 0.28 points, from 0.33 to 0.61, relative to the use of full GRM only. The area under the curve of the receiver–operator curve for mortality increased from 0.58 to 0.67 when the QTL was included in the model. The inclusion of the QTL as a fixed effect in the model increased the correlation between the GEBVs of early mortality with the late mortality, compared to a model that did not include the QTL. These results validate the usability of the produced SNP panel for genomic selection in European whitefish and highlight the opportunity for modeling QTLs in genomic evaluation of mortality due to Saprolegnia infection.

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.

Rumen microbiota modulation during the pre-weaning period has been suggested as means to affect animal performance later in life. In this follow-up study, we examined the post-weaning rumen microbiota development differences in monozygotic twin-heifers that were inoculated (T-group) or not inoculated (C-group) (n = 4 each) with fresh adult rumen liquid during their pre-weaning period. We also assessed the treatment effect on production parameters and methane emissions of cows during their 1st lactation period. The rumen microbiota was determined by the 16S rRNA gene, 18S rRNA gene, and ITS1 amplicon sequencing. Animal weight gain and rumen fermentation parameters were monitored from 2 to 12 months of age. The weight gain was not affected by treatment, but butyrate proportion was higher in T-group in month 3 (p = 0.04). Apart from archaea (p = 0.084), the richness of bacteria (p < 0.0001) and ciliate protozoa increased until month 7 (p = 0.004) and anaerobic fungi until month 11 (p = 0.005). The microbiota structure, measured as Bray–Curtis distances, continued to develop until months 3, 6, 7, and 10, in archaea, ciliate protozoa, bacteria, and anaerobic fungi, respectively (for all: p = 0.001). Treatment or age × treatment interaction had a significant (p < 0.05) effect on 18 bacterial, 2 archaeal, and 6 ciliate protozoan taxonomic groups, with differences occurring mostly before month 4 in bacteria, and month 3 in archaea and ciliate protozoa. Treatment stimulated earlier maturation of prokaryote community in T-group before month 4 and earlier maturation of ciliate protozoa at month 2 (Random Forest: 0.75 month for bacteria and 1.5 month for protozoa). No treatment effect on the maturity of anaerobic fungi was observed. The milk production and quality, feed efficiency, and methane emissions were monitored during cow’s 1st lactation. The T-group had lower variation in energy-corrected milk yield (p < 0.001), tended to differ in pattern of residual energy intake over time (p = 0.069), and had numerically lower somatic cell count throughout their 1st lactation period (p = 0.081), but no differences between the groups in methane emissions (g/d, g/kg DMI, or g/kg milk) were observed. Our results demonstrated that the orally administered microbial inoculant induced transient changes in early rumen microbiome maturation. In addition, the treatment may influence the later production performance, although the mechanisms that mediate these effects need to be further explored.

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 Reduction of genetic diversity can lead to reduced fitness of species, such as the loss of adaptability to changing environments. The native Eurasian beaver (Castor fiber) was hunted to extinction from Finland and many other countries in Europe in the nineteenth century. In Finland, the species was re-introduced in the 1930s with only a few individuals from Norway. Re-introductions were performed also in other countries of northern Europe and as a result, Eurasian beaver populations have undergone population bottlenecks leading to low levels of genetic diversity. Materials and Methods Here, 200 Eurasian beaver samples from Finland, Estonia, Lithuania, and Russian Karelia were investigated using 12 microsatellite markers to examine the level of genetic diversity and relationship between the populations. Results While Russian and Estonian populations were genetically the closest, the Finnish population was clearly distinct from all others and had the lowest genetic variability among the study populations. This may be deleterious to the population especially in a changing environment. Conclusions Genetic rescue could be the best solution to increase the genetic diversity and improve the future prospects of the population, although more studies are required to resolve the optimal source population.

Economic activities of the population living in the rural areas of the world is 70% dependent on traditional livestock production systems based on indigenous breeds. Consequently, it is very important to protect and preserve the heritage breeds of animals resistant to any diseases and better adapted to the changing environmental conditions. The effects of the natural environmental factors on the formation of the genetic structure in 24 coarse-wool breeds of sheep reared in nine countries of Europe and Asia have been studied. Genetic surveys of 20 microsatellite loci were carried out. The most significant environmental factors causing the genetic variation in the analyzed sheep breeds turned out to be the geographical latitude and the annual mean temperature. The genetic variation in the coarse-wool sheep breeds was generally higher at low geographical latitudes, which corresponds to the data obtained for the other animal species. Therefore, the protection of animal populations inhabiting the areas at the low geographical latitudes can contribute to a higher intraspecific diversity than the protection of the same number of populations distributed in the high latitude ranges. This fact should be especially considered when planning the programs to preserve the biodiversity of animals since the breeds of sheep reared near the centers of animal domestication have a higher genetic variation. Hence, they can serve as the source of genes contributing to adaptation under the conditions of global climate change.

Жизнедеятельность сельского населения мира на 70% зависит от традиционных систем животноводства, основанных на местных породах. По этой причине очень важно сохранение локальных пород, обладающих устойчивостью к болезням и лучше адаптированных к меняющимся условиям окружающей среды. Изучено влияние факторов внешней среды на формирование генетической структуры 24 грубошерстных пород овец, разводимых в 9 странах Европы и Азии. Генетические исследования проводили по 20 микросателлитным локусам. Наиболее важными средовыми факторами, объясняющими генетическую изменчивость исследованных пород овец, оказались географическая широта и средняя годовая температура воздуха. Генетическая изменчивость грубошерстных пород овец была выше в низких широтах, что соотносится с данными, полученными на других видах животных. Таким образом, защита популяций, обитающих в низких широтах, может сохранить разнообразие внутри вида в значительно большей степени, чем охрана такого же количества популяций в высоких широтах. Этот факт важно учитывать в программах по сохранению биоразнообразия животных, поскольку породы, разводимые ближе к центрам одомашнивания, обладают более высокой генетической изменчивостью и могут служить источником генов, способствующим адаптации при глобальном изменении климата.

Edible insect rearing could provide one alternative for protein production by having a smaller environmental impact than traditional livestock farming due to insects’ ability to convert organic side streams. Currently, the insect rearing industry utilizes soybeans as a major source of protein in the feeds. Protein-rich by-products of food industry could be used to replace them in insect feeds, but it is not known if they also meet the insects’ nutritional requirements. Our study evaluated the growth performance of two widely used edible cricket species, Acheta domesticus and Gryllus bimaculatus (Orthoptera: Gryllidae), on 18 experimental diets. The experimental diets included commercial chicken feeds and cricket diets, where soybean was partly and completely replaced with by-products from food industry: potato protein, barley mash, barley feed, compressed leftover of turnip rape and mix of broad bean and pea on three levels of protein. We found that the high- and medium-protein turnip rape and barley mash diets produced the highest yield and an increase in all performance variables. Overall, the high- and medium-protein diets produced the highest yield, growth and fastest development. Our results showed that by-products of food industry could be utilized as a part of the cricket feeds and thus advance the goals of circular economy.

Milk production and milk composition of various cattle breeds and their crosses in the North Central Peanut Basin of Senegal have been analysed.In total, 6082 records were collected from 1447 cows.But finally, only 1923 test-day records of milk volume were evaluated from 319 cows with 370 lactations during a longitudinal survey.A subset of 227 cows was used to determine the milk composition of the main breed-groups that were present and which were clustered into four groups: Indigenous zebus (Zebu Gobra; Zebu Maure), Indigenous zebu by Guzerat (Indigenous zebu cross with 25% to 50% Guzerat), Indigenous zebu by Bos taurus taurus (Indigenous zebu cross with 25% to 50% Bos taurus taurus where the Bos taurus taurus includes breeds such as Montbeliarde and Holstein-Friesian) and High Bos taurus taurus (cows with a high component of Bos taurus taurus, typically 75% to 100% of previous Bos taurus taurus).The daily milk yield, cumulative milk yield of 305 days, milk fat and protein percentages were determined for each cluster.The daily milk yield varied from 1.43 L/day in indigenous zebus to 7.04 L/day in High Bos taurus taurus.In general, the daily milk yield increased with the number of parturitions.Indigenous zebus showed the lowest 305-day milk yield (466 L and 496 L for first and later lactations, respectively) whilst High Bos taurus taurus cows showed the highest milk production (1408 L and 2108 L for first and later lactations, respectively).Fat percentage increased from the primiparous to the multiparous cows.Primiparous Indigenous zebus by Bos taurus taurus cows showed the highest fat content (5.10%), followed by Indigenous zebus (4.44%).The average calving interval ranged from 519 days for Indigenous zebus by Bos taurus taurus to 580 days for Indigenous zebus.The average lactation length for all cows was 370 days.

All tropically adapted humped cattle (Bos indicus or "zebu"), descend from a domestication process that took place >8,000 years ago in South Asia. Here we present an intercontinental survey of Y-chromosome diversity and a comprehensive reconstruction of male-lineage zebu cattle history and diversity patterns. Phylogenetic analysis revealed that all the zebu Y-chromosome haplotypes in our dataset group within three different lineages: Y3A, the most predominant and cosmopolitan lineage; Y3B, only observed in West Africa; and Y3C, predominant in South and Northeast India. The divergence times estimated for these three Zebu-specific lineages predate domestication. Coalescent demographic models support either de novo domestication of genetically divergent paternal lineages or more complex process including gene flow between wild and domestic animals. Our data suggest export of varied zebu lineages from domestication centres through time. The almost exclusive presence of Y3A haplotypes in East Africa is consistent with recent cattle restocking in this area. The cryptic presence of Y3B haplotypes in West Africa, found nowhere else, suggests that these haplotypes might represent the oldest zebu lineage introduced to Africa ca. 3,000 B.P. and subsequently replaced in most of the world. The informative ability of Interspersed Multilocus Microsatellites and Y-specific microsatellites to identify genetic structuring in cattle populations is confirmed.

The domestication of animal species was a major innovation for human societies. A framework, based on DNA research for understanding the animal domestication processes is emerging. The animal domestication is a co-evolutionary process with multiple stages along different pathways. Humans were not always the initiator of the process, but humans became important later for the survival of the domesticated species. The chapter focuses on domestication processes of common terrestrial animals and general genomic observations. Natural and artificial selection, demographic changes and gene-flow influenced genomic variation of the domesticated animal species in the domestication process. Admixture with the wild types likely loosened the domestication induced population reductions greatly, explaining the rich genetic variability in the domesticated species. Management of animal populations has intensified along the domestication history influencing the distribution of genetic diversity. The domestication process continues as a response to the continuous change of human needs.

The government of Senegal has initiated a National Program for Livestock Development (PNDE) seeking to achieve self-sufficiency in the production of animal-source foods and increase the economic vitality of the value chain by 2026. Improving the productivity and competitiveness of the livestock sector is a key component of the plan. This brief seeks to facilitate the implementation of the dairy cattle sector components of the PNDE, particularly in relation to improving productivity. In doing so it sets out the evidence-based rationale for keeping different dairy cattle breeds/ crossbreeds under different management systems, and makes recommendations regarding key investments to improve dairy cattle productivity.

The ruminal microbiome, comprising large numbers of bacteria, ciliate protozoa, archaea and fungi, responds to diet and dietary additives in a complex way. The aim of this study was to investigate the benefits of increasing the depth of the community analysis in describing and explaining responses to dietary changes. Quantitative PCR, ssu rRNA amplicon based taxa composition, diversity and co-occurrence network analyses were applied to ruminal digesta samples obtained from four multiparous Nordic Red dairy cows fitted with rumen cannulae. The cows received diets with forage:concentrate ratio either 35:65 (diet H) or 65:35 (L), supplemented or not with sunflower oil (SO) (0 or 50 g/kg diet dry matter), supplied in a 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments and four 35-day periods. Digesta samples were collected on days 22 and 24 and combined. QPCR provided a broad picture in which a large fall in the abundance of fungi was seen with SO in the H but not the L diet. Amplicon sequencing showed higher community diversity indices in L as compared to H diets and revealed diet specific taxa abundance changes, highlighting large differences in protozoal and fungal composition. Methanobrevibacter ruminantium and Mbb. gottschalkii dominated archaeal communities, and their abundance correlated negatively with each other. Co-occurrence network analysis provided evidence that no microbial domain played a more central role in network formation, that some minor-abundance taxa were at nodes of highest centrality, and that microbial interactions were diet specific. Networks added new dimensions to our understanding of the diet effect on rumen microbial community interactions.

Animal domestication involves a process of evolutionary change in the genetics of animal populations, brought about by human intervention. Mankind shaped the genome of domestic species by managing populations ancestral demography as well as selecting for desirable characteristics such as behavioral, pigmentation, growth rate, elevated reproduction, companionship, sport and fashion traits. The overwhelming diversity among animal populations is a result of diversification in a small set of major genes with large phenotypic effects and selective breeding within distinct phenotypic or functional groups. Natural and artificial selection directed the domestication and left detectable signatures within the genome of domestic species. Genome-wide screenings based on population techniques provide analytical tools to detect these signatures in relation to the act of selection. This chapter intends to provide a nonmathematical treatment of the theories and approaches available to find evidence of past selection along with relative strengths, weaknesses and also the remaining challenges.