Comparative population genomics analysis uncovers genomic footprints and genes influencing body weight trait in Chinese indigenous chicken.

Body weight of chicken is a typical quantitative trait, which shows phenotypic variations due to selective breeding. Despite some QTL loci have been obtained, the body weight of native chicken breeds in different geographic regions varies greatly, its genetic basis remains unresolved questions. To address this issue, we analyzed 117 Chinese indigenous chickens from 10 breeds (Huiyang Bearded, Xinhua, Hotan Black, Baicheng You, Liyang, Yunyang Da, Jining Bairi, Lindian, Beijing You, Tibetan). We applied fixation index (FST) analysis to find selected genomic regions and genes associated with body weight traits. Our study suggests that NELL1, XYLT1, and NCAPG/LCORL genes are strongly selected in the body weight trait of Chinese indigenous chicken breeds. In addition, the IL1RAPL1 gene was strongly selected in large body weight chickens, while the PCDH17 and CADM2 genes were strongly selected in small body weight chickens. This result suggests that the patterns of genetic variation of native chicken and commercial chicken, and/or distinct local chicken breeds may follow different evolutionary mechanisms.

Morphometric measurements and carcass characteristics of Black Australorp, Naked Neck, and Rhode Island Red crossbreds under alternative production systems / Medições morfométricas e características de carcaça de Black Australorp, Naked Neck e Rhode Island Red crossbreds sob sistemas de produção alternativos

The present trial explained the effect of alternative production systems on growth, morphometric and carcass traits of four different chicken genotypes. The second generation of two genotypes RNN (Rhode Island Red × Naked Neck) and BNN (Black Australorp × Naked Neck) obtained by two self-crosses (RNN × RNN = RR and BNN × BNN = BB) and two reciprocal crosses (RNN × BNN = RB and BNN × RNN = BR) were evaluated in three alternative production systems (conventional cages, enriched cages, and aviary). At the 6th week of age after sexing, a total of 600 birds, comprising 150 from each crossbred with a total of 300 pullets and 300 cockerels were divided into conventional cages, enriched cages, and aviary systems having 200 birds in each.Birds were organized into 3×4 factorial arrangements under Completely Randomized Design (3 production systems × 4 genotypes × 2 sexes × 25 birds = 600 birds). Regarding genotypes, RB and BR males showed higher (p < 0.01) carcass yield, drumstick weight, breast weight, and thigh weight than BB and RR genotypes. Females of BR genotype showed higher (p < 0.01) breast weight, thigh weight and drumstick weight. As far as production systems are concerned, higher (p < 0.01) liver weight, heart weight, breast weight, intestinal weight, drumstick weight, and thigh weight were observed in the males reared in enriched cages compared with conventional cages and aviary system. Females reared in enriched cages showed higher (p < 0.01) heart weight, breast weight, intestinal weight, drumstick weight, and thigh weight when compared with those reared in conventional cages and aviary. It is concluded that chickens (both sexes) of BR and RB genotypes had better morphological measurements and carcass traits than those of RR and BB genotype chickens. Among alternative production systems, chickens reared in enriched cages had better traits than those of reared in conventional cages and aviary during the growing phase.

O presente estudo explicou o efeito de sistemas alternativos de produção sobre o crescimento, características morfométricas e carcaças de quatro genótipos de frango diferentes. A segunda geração de dois genótipos RNN (Rhode Island Red × Naked Neck) e BNN (Black Australorp × Naked Neck) obtida por duas autocruzes (RNN × RNN = RR e B ANN × BNN = BB) e duas cruzes recíprocas (RNN × BNN = RB e BNN × RNN = BR) foi avaliada em três sistemas de produção alternativos (gaiolas convencionais, gaiolas enriquecidas e aviário). Na 6ª semana de idade após o sexo, um total de 600 aves, compostas por 150 de cada raça cruzada com um total de 300 pullets e 300 galos, foi dividido em gaiolas convencionais, gaiolas enriquecidas e sistemas aviários com 200 aves em cada. As aves foram organizadas em 3×4 arranjos fatoriais sob projeto completamente randomizado (3 sistemas de produção × 4 genótipos × 2 sexos × 25 aves = 600 aves). Em relação aos genótipos, os machos RB e BR apresentaram maior rendimento de carcaça (p < 0,01), peso da baqueta, peso mamário e peso da coxa do que os genótipos BB e RR. As fêmeas do genótipo BR apresentaram maior (p < 0,01) peso mamário, peso da coxa e peso da baqueta. No que diz respeito aos sistemas de produção, maior (p < 0,01) peso hepático, peso cardíaco, peso mamário, peso intestinal, peso da baqueta e peso da coxa foram observados nos machos criados em gaiolas enriquecidas em comparação com gaiolas convencionais e sistema aviário. As fêmeas criadas em gaiolas enriquecidas apresentaram maior (p < 0,01) peso cardíaco, peso mamário, peso intestinal, peso da baqueta e peso da coxa quando comparadas com as criadas em gaiolas convencionais e aviárias. Conclui-se que as galinhas (ambos os sexos) dos genótipos BR e RB apresentaram melhores medidas morfológicas e traços de carcaça do que os de frangos genótipos RR e BB. Entre os sistemas de produção alternativos, [...].

Genomic polymorphisms at the crhr2 locus improve feed conversion efficiency through alleviation of hypothalamus-pituitary-interrenal axis activity in gibel carp (Carassius gibelio).

Improvement in fish feed conversion efficiency (FCE) is beneficial for sustaining global food fish supplies. Here, we show that a set of polymorphisms at locus of the corticotropin releasing hormone receptor 2 (crhr2), which is involved in hypothalamus-pituitary-interrenal (HPI) axis signaling, is associated with improved FCE in farmed allogynogenetic gibel carp strain CAS III compared with that in the wild gibel carp strain Dongting (DT). This set of polymorphisms downregulates the expression levels of crhr2 mRNA in the brain and pituitary tissues in gibel carp strain CAS III compared with those in strain DT. Furthermore, compromised HPI axis signaling is observed in gibel carp strain CAS III, such as decreased α-melanocyte stimulating hormone protein levels, plasma cortisol content, and stress responses. Moreover, enhanced activation of protein kinase B/mammalian target of rapamycin complex 1 signaling observed in the muscle tissue of strain CAS III in comparison to that in strain DT indicated elevated anabolic metabolism in strain CAS III. Thus, these studies demonstrate that the genetic markers associated with compromised HPI axis signaling, such as crhr2, are potentially useful for genetic selection toward improvement in farmed fish growth and FCE, which would reduce fishmeal consumption and thereby indirectly facilitate sustainable fisheries.

Genomic Signatures of Domestication Selection in the Australasian Snapper (Chrysophrys auratus).

Domestication of teleost fish is a recent development, and in most cases started less than 50 years ago. Shedding light on the genomic changes in key economic traits during the domestication process can provide crucial insights into the evolutionary processes involved and help inform selective breeding programmes. Here we report on the recent domestication of a native marine teleost species in New Zealand, the Australasian snapper (Chrysophrys auratus). Specifically, we use genome-wide data from a three-generation pedigree of this species to uncover genetic signatures of domestication selection for growth. Genotyping-By-Sequencing (GBS) was used to generate genome-wide SNP data from a three-generation pedigree to calculate generation-wide averages of FST between every generation pair. The level of differentiation between generations was further investigated using ADMIXTURE analysis and Principal Component Analysis (PCA). After that, genome scans using Bayescan, LFMM and XP-EHH were applied to identify SNP variants under putative selection following selection for growth. Finally, genes near candidate SNP variants were annotated to gain functional insights. Analysis showed that between generations FST values slightly increased as generational time increased. The extent of these changes was small, and both ADMIXTURE analysis and PCA were unable to form clear clusters. Genome scans revealed a number of SNP outliers, indicative of selection, of which a small number overlapped across analyses methods and populations. Genes of interest within proximity of putative selective SNPs were related to biological functions, and revealed an association with growth, immunity, neural development and behaviour, and tumour repression. Even though few genes overlapped between outlier SNP methods, gene functionalities showed greater overlap between methods. While the genetic changes observed were small in most cases, a number of outlier SNPs could be identified, of which some were found by more than one method. Multiple outlier SNPs appeared to be predominately linked to gene functionalities that modulate growth and survival. Ultimately, the results help to shed light on the genomic changes occurring during the early stages of domestication selection in teleost fish species such as snapper, and will provide useful candidates for the ongoing selective breeding in the future of this and related species.

Selective Breeding for Disease-Resistant PRNP Variants to Manage Chronic Wasting Disease in Farmed Whitetail Deer.

Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy (TSE) of cervids caused by a misfolded variant of the normal cellular prion protein, and it is closely related to sheep scrapie. Variations in a host's prion gene, PRNP, and its primary protein structure dramatically affect susceptibility to specific prion disorders, and breeding for PRNP variants that prevent scrapie infection has led to steep declines in the disease in North American and European sheep. While resistant alleles have been identified in cervids, a PRNP variant that completely prevents CWD has not yet been identified. Thus, control of the disease in farmed herds traditionally relies on quarantine and depopulation. In CWD-endemic areas, depopulation of private herds becomes challenging to justify, leading to opportunities to manage the disease in situ. We developed a selective breeding program for farmed white-tailed deer in a high-prevalence CWD-endemic area which focused on reducing frequencies of highly susceptible PRNP variants and introducing animals with less susceptible variants. With the use of newly developed primers, we found that breeding followed predictable Mendelian inheritance, and early data support our project's utility in reducing CWD prevalence. This project represents a novel approach to CWD management, with future efforts building on these findings.

Twelve new microsatellite loci of Eurasian perch Perca fluviatilis Linnaeus, 1758.

The Eurasian perch (Perca fluviatilis Linnaeus, 1758) is native to almost entire Eurasia. For over the last two decades, this species became an important candidate for intensive freshwater aquaculture due to its high consumer's acceptance and overall market value. Hence, the intensive production of Eurasian perch has increased considerably allowing effective domestication; there is still a need for the development of effective selective breeding programmes allowing its further expansion. This process, in turn, can be significantly facilitated by molecular genetics. The genetic information of Eurasian perch and its populations is limited. Up to date information of regarding genetic diversity of many populations is still missing, including microsatellites for Eurasian perch, which could be useful during the selective breeding programmes allowing parental assignment and/or to follow heritability of desired traits. In this study, we have developed and characterized new polymorphic microsatellites. Subsequently, those 12 markers have been used further to compare two Hungarian and one Polish Eurasian perch populations. The Hungarian stocks had high genetic similarity (with low diversity), as we assumed, while the Polish population differed significantly. All populations deviated significantly from the Hardy-Weinberg equilibrium, and heterozygote deficiency was detected in all, showing the presence of an anthropogenic effect.

On-farm evaluation of growth and reproductive performances of Washera and Gumuz sheep in northwestern Ethiopia: Basics for setting up breeding objectives/goals.

Growth and reproductive performance traits are traits of economic importance for sheep selection and productivity improvement interventions. This study aimed at comparative evaluation of growth and reproductive performance traits of sheep in the highland and lowland agro-ecologies of northwestern Ethiopia. Data on growth performance traits were collected from 144 Washera (78 males and 66 females) lambs and 72 Gumuz (37 males and 35 females) lambs. Data on reproductive performance traits were collected from 260 Washera (130 rams and 130 ewes) sheep and 150 Gumuz (75 rams and 75 ewes) sheep. General linear model univariate procedure was employed to analyze the collected data. Breed, the interaction effect between breed and season of birth as well as the interaction effect between breed and type of birth all exerted very high significant effect (P<0.001) on live weight at all age groups. Breed type affected pre-weaning average daily weight gain significantly (P<0.01). Pre-weaning average daily weight gain of Washera (70 g/day) was found much better performance than 60 g/day of Gumuz. Breed type exerts significant (P<0.05) effect on age at first lambing, lambing interval, annual reproductive rate and number of lambs born per ewe life time. Average age at first lambing and lambing interval of Washera sheep were 11.69 months and 9.27 months, respectively. The corresponding values for Gumuz sheep were 12.51 months and 10.43 months, respectively. Production and reproduction performance values of traits varied across the two breeds and sexes as well. These values can be used to set up breeding objectives or goals for selective breeding of sheep giving special emphasis to growth traits believed to have medium heritability values.

Nest acceptance, clutch, and oviposition traits are promising selection criteria to improve egg production in cage-free system.

In cage-free systems, laying hens must lay their eggs in the nests. Selecting layers based on nesting behavior would be a good strategy for improving egg production in these breeding systems. However, little is known about the genetic determinism of nest-related traits. Laying rate in the nests (LRN), clutch number (CN), oviposition traits (OT), and nest acceptance for laying (NAL) of 1,430 Rhode Island Red (RIR) hens and 1,008 White Leghorn (WL) hens were recorded in floor pens provided with individual electronic nests. Heritability and genetic and phenotypic correlations of all traits were estimated over two recording periods-the peak (24-43 weeks of age) and the middle (44-64 weeks of age) of production-by applying the restricted maximum likelihood method to an animal model. The mean oviposition time (MOT) ranged from 2 h 5 min to 3 h and from 3 h 35 min to 3 h 44 min after turning on the lights for RIR and WL hens, respectively. The mean oviposition interval ranged from 24 h 3 min to 24 h 16 min. All heritability and correlation estimates were similar for RIR and WL. Low to moderate heritability coefficients were estimated for LRN (0.04-0.25) and moderate to high heritability coefficients for CN and OT (0.27-0.68). CN and OT were negatively genetically correlated with LRN (-0.92 to -0.39) except during peak production for RIR (-0.30 to +0.43). NAL was weakly to moderately heritable (0.13-0.26). Genetic correlations between NAL and other traits were low to moderate (-0.41 to +0.44). In conclusion, CN and OT are promising selection criteria to improve egg production in cage-free systems. NAL can be also used to reduce the number of eggs laid off-nest in these breeding systems. However, variability in MOT must be maintained to limit competition for the nests.

The impact of identity by descent on fitness and disease in dogs.

Domestic dogs have experienced population bottlenecks, recent inbreeding, and strong artificial selection. These processes have simplified the genetic architecture of complex traits, allowed deleterious variation to persist, and increased both identity-by-descent (IBD) segments and runs of homozygosity (ROH). As such, dogs provide an excellent model for examining how these evolutionary processes influence disease. We assembled a dataset containing 4,414 breed dogs, 327 village dogs, and 380 wolves genotyped at 117,288 markers and data for clinical and morphological phenotypes. Breed dogs have an enrichment of IBD and ROH, relative to both village dogs and wolves, and we use these patterns to show that breed dogs have experienced differing severities of bottlenecks in their recent past. We then found that ROH burden is associated with phenotypes in breed dogs, such as lymphoma. We next test the prediction that breeds with greater ROH have more disease alleles reported in the Online Mendelian Inheritance in Animals (OMIA). Surprisingly, the number of causal variants identified correlates with the popularity of that breed rather than the ROH or IBD burden, suggesting an ascertainment bias in OMIA. Lastly, we use the distribution of ROH across the genome to identify genes with depletions of ROH as potential hotspots for inbreeding depression and find multiple exons where ROH are never observed. Our results suggest that inbreeding has played a large role in shaping genetic and phenotypic variation in dogs and that future work on understudied breeds may reveal new disease-causing variation.

RNA-sequencing and behavioral testing reveals inherited physical inactivity co-selects for anxiogenic behavior without altering depressive-like behavior in Wistar rats.

Physical inactivity is positively associated with anxiety and depression. Considering physical inactivity, anxiety, and depression each have a genetic basis for inheritance, our lab used artificial selectively bred low-voluntary running (LVR) and wild type (WT) female Wistar rats to test if physical inactivity genes selected over multiple generations would lead to an anxiety or depressive-like phenotype. We performed next generation RNA sequencing and immunoblotting on the dentate gyrus to reveal key biological functions from heritable physical inactivity. LVR rats did not display depressive-like behavior. However, LVR rats did display anxiogenic behavior with gene networks associated with reduced neuronal development, proliferation, and function compared to WT counterparts. Additionally, immunoblotting revealed LVR deficits in neuronal development and function. To our knowledge, this is the first study to show that by selectively breeding for physical inactivity genes, anxiety-like genes were co-selected. The study also reveals molecular insights to the genetic influences that physical inactivity has on anxiety-like behavior.

Microsatellite characterization and development of unified STR panel for big cats in captivity: a case study from a Seoul Grand Park Zoo, Republic of Korea.

The zoos manage small populations of endangered big cat species like tiger, lion, and leopard for display, research, and conservation breeding. Genetic management of these populations is essential to ensure long term survival and conservation utility. Here we propose a simple and cost effective microsatellite based protocol for the genetic management of captive big cats. We sampled 36 big cat individuals from Seoul Grand Park Zoo (Republic of Korea) and amplified 33 published microsatellite loci. Overall, allelic richness and gene diversity was found highest for leopards, followed by lions and tigers. Twelve of the thirty-three markers showed a high degree of polymorphism across all target species. These microsatellites provide a high degree of discrimination for tiger (1.45 × 10-8), lion (1.54 × 10-10), and leopard (1.88 × 10-12) and thus can be adopted for the genetic characterization of big cats in accredited zoos globally. During captive breeding, zoo authorities rely on pedigree records maintained in studbooks to ensure mating of genetically fit unrelated individuals. Several studies have reported errors in studbook records of big cat species. Microsatellites are simple and cost effective tool for DNA fingerprinting, estimation of genetic diversity, and paternity assessment. Our unified microsatellite panel (12-plex) for big cats is efficient and can easily be adopted by zoo authorities for regular population management.

Understanding the seasonality of performance resilience to climate volatility in Mediterranean dairy sheep.

As future climate challenges become increasingly evident, enhancing performance resilience of farm animals may contribute to mitigation against adverse weather and seasonal variation, and underpin livestock farming sustainability. In the present study, we develop novel seasonal resilience phenotypes reflecting milk production changes to fluctuating weather. We evaluate the impact of calendar season (autumn, winter and spring) on animal performance resilience by analysing 420,534 milk records of 36,908 milking ewes of the Chios breed together with relevant meteorological data from eastern Mediterranean. We reveal substantial seasonal effects on resilience and significant heritable trait variation (h2 = 0.03-0.17). Resilience to cold weather (10 °C) of animals that start producing milk in spring was under different genetic control compared to autumn and winter as exemplified by negative genetic correlations (- 0.09 to - 0.27). Animal resilience to hot weather (25 °C) was partially under the same genetic control with genetic correlations between seasons ranging from 0.43 to 0.86. We report both favourable and antagonistic associations between animal resilience and lifetime milk production, depending on calendar season and the desirable direction of genetic selection. Concluding, we emphasise on seasonal adaptation of animals to climate and the need to incorporate the novel seasonal traits in future selective breeding programmes.

Changes Depression- and Anxiety- like Behaviors following Selective Breeding for Cocaine Reinforcement.

The LS and HS are rat lines selectively bred for altered cocaine self-administration. Given the importance of mental health in substance use, these lines were evaluated for putative depression- and anxiety- like behaviors through forced swimming and exploration of a plus maze. We found increases of struggling in LS males, climbing in LS females, and swimming in HS males; with biphasic effects on immobility in the HS strain. HS rats had fewer entries into and less time spent in open arms of the plus maze, consistent with greater anxiety-like behavior, which may contribute to enhanced drug taking.

The evolutionary origin and domestication history of goldfish (Carassius auratus).

Goldfish have been subjected to over 1,000 y of intensive domestication and selective breeding. In this report, we describe a high-quality goldfish genome (2n = 100), anchoring 95.75% of contigs into 50 pseudochromosomes. Comparative genomics enabled us to disentangle the two subgenomes that resulted from an ancient hybridization event. Resequencing 185 representative goldfish variants and 16 wild crucian carp revealed the origin of goldfish and identified genomic regions that have been shaped by selective sweeps linked to its domestication. Our comprehensive collection of goldfish varieties enabled us to associate genetic variations with a number of well-known anatomical features, including features that distinguish traditional goldfish clades. Additionally, we identified a tyrosine-protein kinase receptor as a candidate causal gene for the first well-known case of Mendelian inheritance in goldfish-the transparent mutant. The goldfish genome and diversity data offer unique resources to make goldfish a promising model for functional genomics, as well as domestication.

Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding.

Brazil is the largest consumer and third highest producer of common beans (Phaseolus vulgaris L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity and population structure of 185 Brazilian common bean cultivars using 2827 high-quality single-nucleotide polymorphisms (SNPs). The Andean allelic introgression in the Mesoamerican accessions was investigated, and a Carioca panel was tested using an association mapping approach. The results distinguish the Mesoamerican from the Andean accessions, with a prevalence of Mesoamerican accessions (94.6%). When considering the commercial classes, low levels of genetic differentiation were seen, and the Carioca group showed the lowest genetic diversity. However, gain in gene diversity and allelic richness was seen for the modern Carioca cultivars. A set of 1060 'diagnostic SNPs' that show alternative alleles between the pure Mesoamerican and Andean accessions were identified, which allowed the identification of Andean allelic introgression events and shows that there are putative introgression segments in regions enriched with resistance genes. Finally, genome-wide association studies revealed SNPs significantly associated with flowering time, pod maturation, and growth habit, showing that the Carioca Association Panel represents a powerful tool for crop improvements.

RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef.

RNA sequencing (RNA-seq) has allowed for transcriptional profiling of biological systems through the identification of differentially expressed (DE) genes and pathways. A total of 80 steers with extreme phenotypes were selected from the University of Florida multibreed Angus-Brahman herd. The average slaughter age was 12.91±8.69 months. Tenderness, juiciness and connective tissue assessed by sensory panel, along with marbling, Warner-Bratzler Shear Force (WBSF) and cooking loss, were measured in longissimus dorsi muscle. Total RNA was extracted from muscle and one RNA-seq library per sample was constructed, multiplexed, and sequenced based on protocols by Illumina HiSeq-3000 platform to generate 2×101 bp paired-end reads. The overall read mapping rate using the Btau_4.6.1 reference genome was 63%. A total of 8,799 genes were analyzed using two different methodologies, an expression association and a DE analysis. A gene and exon expression association analysis was carried out using a meat quality index on all 80 samples as a continuous response variable. The expression of 208 genes and 3,280 exons from 1,565 genes was associated with the meat quality index (p-value ≤ 0.05). A gene and isoform DE evaluation was performed analyzing two groups with extreme WBSF, tenderness and marbling. A total of 676 (adjusted p-value≤0.05), 70 (adjusted p-value≤0.1) and 198 (adjusted p-value≤0.1) genes were DE for WBSF, tenderness and marbling, respectively. A total of 106 isoforms from 98 genes for WBSF, 13 isoforms from 13 genes for tenderness and 43 isoforms from 42 genes for marbling (FDR≤0.1) were DE. Cytoskeletal and transmembrane anchoring genes and pathways were identified in the expression association, DE and the gene enrichment analyses; these proteins can have a direct effect on meat quality. Cytoskeletal proteins and transmembrane anchoring molecules can influence meat quality by allowing cytoskeletal interaction with myocyte and organelle membranes, contributing to cytoskeletal structure and architecture maintenance postmortem.

Genomic selection for white spot syndrome virus resistance in whiteleg shrimp boosts survival under an experimental challenge test.

White spot syndrome virus (WSSV) causes major worldwide losses in shrimp aquaculture. The development of resistant shrimp populations is an attractive option for management of the disease. However, heritability for WSSV resistance is generally low and genetic improvement by conventional selection has been slow. This study was designed to determine the power and accuracy of genomic selection to improve WSSV resistance in Litopenaeus vannamei. Shrimp were experimentally challenged with WSSV and resistance was evaluated as dead or alive (DOA) 23 days after infestation. All shrimp in the challenge test were genotyped for 18,643 single nucleotide polymorphisms. Breeding candidates (G0) were ranked on genomic breeding values for WSSV resistance. Two G1 populations were produced, one from G0 breeders with high and the other with low estimated breeding values. A third population was produced from "random" mating of parent stock. The average survival was 25% in the low, 38% in the random and 51% in the high-genomic breeding value groups. Genomic heritability for DOA (0.41 in G1) was high for this type of trait. The realised genetic gain and high heritability clearly demonstrates large potential for further genetic improvement of WSSV resistance in the evaluated L. vannamei population using genomic selection.

One-Step Homology Mediated CRISPR-Cas Editing in Zygotes for Generating Genome Edited Cattle.

Selective breeding and genetic modification have been the cornerstone of animal agriculture. However, the current strategy of breeding animals over multiple generations to introgress novel alleles is not practical in addressing global challenges such as climate change, pandemics, and the predicted need to feed a population of 9 billion by 2050. Consequently, genome editing in zygotes to allow for seamless introgression of novel alleles is required, especially in cattle with long generation intervals. We report for the first time the use of CRISPR-Cas genome editors to introduce novel PRNP allelic variants that have been shown to provide resilience towards human prion pandemics. From one round of embryo injections, we have established six pregnancies and birth of seven edited offspring, with two founders showing >90% targeted homology-directed repair modifications. This study lays out the framework for in vitro optimization, unbiased deep-sequencing to identify editing outcomes, and generation of high frequency homology-directed repair-edited calves.

Quantitative trait loci (QTL) associated with resistance of rainbow trout Oncorhynchus mykiss against the parasitic ciliate Ichthyophthirius multifiliis.

The parasitic ciliate Ichthyophthirius multifiliis has a low host specificity eliciting white spot disease (WSD) in a wide range of freshwater fishes worldwide. The parasite multiplies rapidly whereby the infection may reach problematic levels in a host population within a few days. The parasite targets both wild and cultured fish but the huge economic impact of the protozoan is associated with mortality, morbidity and treatment in aquacultural enterprises. We have investigated the potential for genetic selection of WSD-resistant strains of rainbow trout. Applying the DNA typing system Affymetrix® and characterizing the genome of the individual fish by use of 57,501 single nucleotide polymorphisms (SNP) and their location on the rainbow trout chromosomes, we have genetically characterized rainbow trout with different levels of natural resistance towards WSD. Quantitative trait loci (QTL) used for the selection of breeders with specific markers for resistance are reported. We found a significant association between resistance towards I. multifiliis infection and SNP markers located on the two specific rainbow trout chromosomes Omy 16 and Omy 17. Comparing the expression of immune-related genes in fish-with and without clinical signs-we recorded no significant difference. However, trout surviving the infection showed high expression levels of genes encoding IgT, T-cell receptor TCRß, C3, cathelicidins 1 and 2 and SAA, suggesting these genes to be associated with protection.

Estimation of C-derived introgression into A. m. mellifera colonies in the Russian Urals using microsatellite genotyping.

BACKGROUND: Marker-assisted selection is well established in animal breeding method of selecting individuals with desirable traits in a breeding scheme based on DNA molecular marker patterns. OBJECTIVE: Genetic diversity and C-derived admixture into local purebred gene pool of A. m. mellifera colonies was assessed using polymorphism of nine microsatellite loci in order to provide further marker-assisted selection of desired honey bee colonies. METHODS: The genetic diversity and the level of C-derived introgression into A. m. mellifera colonies in the Shulgan-Tash Nature Reserve (Russia) was assessed based on nine microsatellite loci (ap243, 4a110, A24, A8, A43, A113, A88, Ap049, A28), which were analized using the fragment analysis of the PCR products in Applied Biosystems 3130 DNA Analyzer. Phylogenetic relationship of colonies was evaluated using Neighbor-Joining methods with Cavalli-Sforza and Edwards genetic distance using the PHYLIP 3.68. The model-based Bayesian clustering algorithm implemented in STRUCTURE 2.3.3 was employed to infer membership and introgression proportions (Q-value). RESULTS: In the Shulgan-Tash Nature Reserve colonies of A. m. mellifera subdivided into four groups by level of C-derived introgression. Only five colonies of A. m. mellifera had C-derived introgression which varied from 0.5 to 2%. The genetic diversity in colonies of A. m. mellifera varied from 0.12 to 0.40. The Neighbor-Joining tree demonstrates the genetic relationship of A. m. mellifera colonies, which subdivided into three groups with different levels of C-derived introgression. Group 1 combined five honey bee colonies Bort_1, Bort_2, Bort_3, Baisalyan_1, and Kush_7 with a fraction of introgression close to 0.000 and genetic diversity from 0.20 to 0.25. CONCLUSION: The results showed the excellence of nine microsatellite loci genotyping in estimation of genetic diversity, distinguishing the two European evolutionary lineages M and C and estimating C-derived introgression. These genetic parameters can be applied further to perform the marker-assisted selection of purebred dark European honey bees.