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.

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.

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.

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 TCRβ, C3, cathelicidins 1 and 2 and SAA, suggesting these genes to be associated with protection.

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.

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.

Transcriptomic Response to Selective Breeding for Fast Growth in Rainbow Trout (Oncorhynchus mykiss)

Genetic improvement for faster growth is a conventional approach to increase growth rates in aquaculture species; however, the genetic and physiological factors regulating growth performance in fish are not fully characterized. The objective of this study was to identify physiological mechanisms associated with faster growth rates by comparing the liver and muscle transcriptome of a rainbow trout line selectively bred for fast growth (growth line, GL) and a contemporary randomly mated control line (synthetic control, SC) from the same selective breeding program. A third genetic line from a commercial egg supplier (commercial A, CA) was also included to characterize differences in gene expression profiles between populations. Body weight of the GL at harvest was approximately 20% and 8% heavier (p < 0.05) than SC and CA, respectively. There were 145 and 36 differentially expressed genes (DEG) in liver and white muscle, respectively, between the GL and SC that were enriched for the growth hormone/insulin-like growth factor axis (GH/IGF) and PI3K-Akt, JAK-STAT, MAPK, and cAMP signal transduction pathways. A greater concentration of plasma IGF-I was detected in the GL compared with SC (p < 0.05). A unique gene profile was detected in CA, with 11 and 210 DEG in liver and white muscle; these genes associated with innate immunity, complement systems, and metabolic pathways. Collectively, these findings provide a more extensive characterization of the fast-growth phenotype in fish that furthers knowledge of the physiological basis for genetic variation in growth performance in selectively bred rainbow trout.

Selective Inbreeding: Genetic Crosses Drive Apparent Adaptive Mutation in the Cairns-Foster System of Escherichia coli

The Escherichia coli system of Cairns and Foster employs a lac frameshift mutation that reverts rarely (10-9/cell/division) during unrestricted growth. However, when 108 cells are plated on lactose medium, the nongrowing lawn produces ∼50 Lac+ revertant colonies that accumulate linearly with time over 5 days. Revertants carry very few associated mutations. This behavior has been attributed to an evolved mechanism ("adaptive mutation" or "stress-induced mutagenesis") that responds to starvation by preferentially creating mutations that improve growth. We describe an alternative model, "selective inbreeding," in which natural selection acts during intercellular transfer of the plasmid that carries the mutant lac allele and the dinB gene for an error-prone polymerase. Revertant genome sequences show that the plasmid is more intensely mutagenized than the chromosome. Revertants vary widely in their number of plasmid and chromosomal mutations. Plasmid mutations are distributed evenly, but chromosomal mutations are focused near the replication origin. Rare, heavily mutagenized, revertants have acquired a plasmid tra mutation that eliminates conjugation ability. These findings support the new model, in which revertants are initiated by rare pre-existing cells (105) with many copies of the F'lac plasmid. These cells divide under selection, producing daughters that mate. Recombination between donor and recipient plasmids initiates rolling-circle plasmid over-replication, causing a mutagenic elevation of DinB level. A lac+ reversion event starts chromosome replication and mutagenesis by accumulated DinB. After reversion, plasmid transfer moves the revertant lac+ allele into an unmutagenized cell, and away from associated mutations. Thus, natural selection explains why mutagenesis appears stress-induced and directed.

Breeding Top Genotypes and Accelerating Response to Recurrent Selection by Selecting Parents with Greater Gametic Variance

Because of variation in linkage phase and heterozygosity among individuals, some individuals produce genetically more variable gametes than others. With the availability of genomic EBVs (GEBVs) or estimates of SNP-effects together with phased genotypes, differences in gametic variability can be quantified by simulating a set of virtual gametes of each selection candidate. Previous results in dairy cattle show that gametic variance can be large. Here, we show that breeders can increase the probability of breeding a top-ranking genotype and response to recurrent selection by selecting parents that produce more variable gametes, using the index [Formula: see text] where [Formula: see text] is the standardized normal truncation point belonging to selected proportion p, and SDgGEBV is the SD of the GEBV of an individual's gametes. Benefits of the index were considerably larger in an ongoing selection program with equilibrium genetic parameters than in an initially unselected population. Superiority of the index over selection on GEBV increased strongly with the magnitude of the [Formula: see text] indicating that benefits of the index may vary considerably among populations. Compared to selection on ordinary GEBV, the probability of breeding a top-ranking individual can be increased by ∼36%, and response to selection by ∼3.6% when selection is strong (P = 0.001) based on values for the Holstein-Friesian dairy cattle population. Two-stage selection, with a preselection on GEBV and a final selection on the index, considerably reduced computational requirements with little loss of benefits. Response to multiple generations of selection and inheritance of the SDgEBV require further study.

Selectively Bred Diabetes Models: GK Rats, NSY Mice, and ON Mice

The polygenic background of selectively bred diabetes models mimics the etiology of type 2 diabetes. So far, three different rodent models (Goto-Kakizaki rats, Nagoya-Shibata-Yasuda mice, and Oikawa-Nagao mice) have been established in the diabetes research field by continuous selective breeding for glucose tolerance from outbred rodent stocks. The origin of hyperglycemia in these rodents is mainly insulin secretion deficiency from the pancreatic β-cells and mild insulin resistance in insulin target organs. In this chapter, we summarize backgrounds and phenotypes of these rodent models to highlight their importance in diabetes research. Then, we introduce experimental methodologies to evaluate β-cell exocytosis as a putative common defect observed in these rodent models.

Simulations reveal challenges to artificial community selection and possible strategies for success

Multispecies microbial communities often display "community functions" arising from interactions of member species. Interactions are often difficult to decipher, making it challenging to design communities with desired functions. Alternatively, similar to artificial selection for individuals in agriculture and industry, one could repeatedly choose communities with the highest community functions to reproduce by randomly partitioning each into multiple "Newborn" communities for the next cycle. However, previous efforts in selecting complex communities have generated mixed outcomes that are difficult to interpret. To understand how to effectively enact community selection, we simulated community selection to improve a community function that requires 2 species and imposes a fitness cost on one or both species. Our simulations predict that improvement could be easily stalled unless various aspects of selection are carefully considered. These aspects include promoting species coexistence, suppressing noncontributors, choosing additional communities besides the highest functioning ones to reproduce, and reducing stochastic fluctuations in the biomass of each member species in Newborn communities. These considerations can be addressed experimentally. When executed effectively, community selection is predicted to improve costly community function, and may even force species to evolve slow growth to achieve species coexistence. Our conclusions hold under various alternative model assumptions and are therefore applicable to a variety of communities.

Genome-Wide Association Studies Based on Equine Joint Angle Measurements Reveal New QTL Affecting the Conformation of Horses

The evaluation of conformation traits is an important part of selection for breeding stallions and mares. Some of these judged conformation traits involve joint angles that are associated with performance, health, and longevity. To improve our understanding of the genetic background of joint angles in horses, we have objectively measured the angles of the poll, elbow, carpal, fetlock (front and hind), hip, stifle, and hock joints based on one photograph of each of the 300 Franches-Montagnes (FM) and 224 Lipizzan (LIP) horses. After quality control, genome-wide association studies (GWASs) for these traits were performed on 495 horses, using 374,070 genome-wide single nucleotide polymorphisms (SNPs) in a mixed-effect model. We identified two significant quantitative trait loci (QTL) for the poll angle on ECA28 (p = 1.36 × 10⁻⁷), 50 kb downstream of the ALX1 gene, involved in cranial morphology, and for the elbow joint on ECA29 (p = 1.69 × 10⁻⁷), 49 kb downstream of the RSU1 gene, and 75 kb upstream of the PTER gene. Both genes are associated with bone mineral density in humans. Furthermore, we identified other suggestive QTL associated with the stifle joint on ECA8 (p = 3.10 × 10⁻⁷); the poll on ECA1 (p = 6.83 × 10⁻⁷); the fetlock joint of the hind limb on ECA27 (p = 5.42 × 10⁻⁷); and the carpal joint angle on ECA3 (p = 6.24 × 10⁻⁷), ECA4 (p = 6.07 × 10⁻⁷), and ECA7 (p = 8.83 × 10⁻⁷). The application of angular measurements in genetic studies may increase our understanding of the underlying genetic effects of important traits in equine breeding.

Using fecal microbiota as biomarkers for predictions of performance in the selective breeding process of pedigree broiler breeders

Much work has been dedicated to identifying members of the microbial gut community that have potential to augment the growth rate of agricultural animals including chickens. Here, we assessed any correlations between the fecal microbiome, a proxy for the gut microbiome, and feed efficiency or weight gain at the pedigree chicken level, the highest tier of the production process. Because selective breeding is conducted at the pedigree level, our aim was to determine if microbiome profiles could be used to predict feed conversion or weight gain in order to improve selective breeding. Using 16s rRNA amplicon sequencing, we profiled the microbiomes of high and low weight gain (WG) birds and good and poor feed efficient (FE) birds in two pedigree lineages of broiler chickens. We also aimed to understand the dynamics of the microbiome with respect to maturation. A time series experiment was conducted, where fecal samples of chickens were collected at 6 points of the rearing process and the microbiome of these samples profiled. We identified OTUs differences at different taxonomic levels in the fecal community between high and low performing birds within each genetic line, indicating a specificity of the microbial community profiles correlated to performance factors. Using machine-learning methods, we built a classification model that could predict feed conversion performance from the fecal microbial community. With respect to maturation, we found that the fecal microbiome is dynamic in early life but stabilizes after 3 weeks of age independent of lineage. Our results indicate that the fecal microbiome profile can be used to predict feed conversion, but not weight gain in these pedigree lines. From the time series experiments, it appears that these predictions can be evaluated as early as 20 days of age. Our data also indicates that there is a genetic factor for the microbiome profile.

Removal of alleles by genome editing (RAGE) against deleterious load

BACKGROUND

In this paper, we simulate deleterious load in an animal breeding program, and compare the efficiency of genome editing and selection for decreasing it. Deleterious variants can be identified by bioinformatics screening methods that use sequence conservation and biological prior information about protein function. However, once deleterious variants have been identified, how can they be used in breeding?

RESULTS

We simulated a closed animal breeding population that is subject to both natural selection against deleterious load and artificial selection for a quantitative trait representing the breeding goal. Deleterious load was polygenic and was due to either codominant or recessive variants. We compared strategies for removal of deleterious alleles by genome editing (RAGE) to selection against carriers. When deleterious variants were codominant, the best strategy for prioritizing variants was to prioritize low-frequency variants. When deleterious variants were recessive, the best strategy was to prioritize variants with an intermediate frequency. Selection against carriers was inefficient when variants were codominant, but comparable to editing one variant per sire when variants were recessive.

CONCLUSIONS

Genome editing of deleterious alleles reduces deleterious load, but requires the simultaneous editing of multiple deleterious variants in the same sire to be effective when deleterious variants are recessive. In the short term, selection against carriers is a possible alternative to genome editing when variants are recessive. Our results suggest that, in the future, there is the potential to use RAGE against deleterious load in animal breeding.

A novel polymorphism in the fatty acid desaturase 2 gene (Fads2): A possible role in the basal metabolic rate

Fatty acyl composition of cell membrane lipids, particularly the abundance of highly unsaturated docosahexaenoic fatty acid (22:6n-3, DHA), is likely to be an important predictor of basal metabolic rate (BMR). Our study was performed using two lines of laboratory mice divergently selected for either high or low BMR. We describe a novel single nucleotide polymorphism in the Fads2 gene encoding Δ6-desaturase, a key enzyme in the metabolic pathways of polyunsaturated fatty acids (PUFAs). The allele frequencies of Fads2 were significantly different in both lines of mice. The analysis of genetic distances revealed that the genetic differentiation between the two studied lines developed significantly faster at the Fads2 locus than it did at neutral loci. Such a pattern suggests that the Fads2 polymorphism is related to the variation in BMR, i.e. the direct target of selection. The Fads2 polymorphism significantly affected abundance of several PUFAs; however, the differences in PUFA composition between lines were compatible with the difference in frequency of Fads2 alleles only for DHA. We hypothesize that the polymorphism in the Fads2 gene affects the BMR through modification of DHA abundance in cell membranes. This may be the first example of a significant link between a polymorphism in a gene responsible for fatty acyl composition and variation in BMR.

Genome-wide association study and a post replication analysis revealed a promising genomic region and candidate genes for chicken eggshell blueness

The eggshell blueness is an interesting object for chicken genetic studies and blue-shelled chicken industry, especially after the discovery of the causative mutation of chicken blue eggshell. In the present study, genome wide association study (GWAS) was conducted in Chinese Dongxiang blue-shelled chicken underlying four traits of blue eggshell pigments: quantity of biliverdin (QB), quantity of protoporphyrin (QP), quantity of total pigment (QT), and color density trait (CD). A total of 139 individuals were randomly collected for GWAS. We detected two SNPs in genome-wise significance and 35 in suggestive significance, 24 out of the 37 SNP were located either within intron/exon or near 15 genes in a range of ~1.17 Mb on GGA21. For further confirmation of the identified SNP loci by GWAS, the follow-up replication studies were performed in two populations. A total of 146 individuals of the second generation derived from the former GWAS population, as well as 280 individuals from an alternative independent population were employed for genotyping by MALDI-TOF MS in a genotype-phenotype association study. Eighteen SNPs evenly distributed on the GGA21 significant region were successfully genotyped in the two populations, of which 4 and 6 SNP loci were shown significantly associated with QB, QT and QP in the two repeat populations, respectively. Further, the SNPs were narrowed down to a region of ~ 653.819 Kb on GGA21 that harbors five candidate genes: AJAP1, TNFRSF9, C1ORF174, CAMTA1, and CEP104. Shell gland of chickens laying dark and light blue eggshell was chosen for detection of mRNA expression of the five candidate genes. The results showed differential expression levels of these genes in the two groups. The specific function of these genes has not yet been defined clearly in chickens and further in-depth studies are needed to explore the new functional role in chicken eggshell blueness.

Comparative transcriptomics identifies genes differentially expressed in the intestine of a new fast-growing strain of common carp with higher unsaturated fatty acid content in muscle

We have created a new, fast-growing strain of common carp with higher unsaturated fatty acid content in muscle. To better understand the impacts of gene regulation in intestinal tissue on growth and unsaturated fatty acid content, we conducted a comparative RNA-Seq transcriptome analysis between intestine samples of Selected and Control groups (and corroborated selected results by PCR). After eight weeks of cage culture, weight gain of the Selected group was 20.84% higher. In muscles of the control group, monounsaturated fatty acids (FAs) were more abundant, whereas polyunsaturated FAs were more abundant in muscles of the Selected group. In total, we found 106 differentially expressed genes (DEGs) between the two groups. Only the endocytosis pathway was significantly enriched in DEGs, with two upregulated genes: il2rb and ehd1. The latter is involved in the growth hormone/insulin-like growth factor (Gh/Igf) axis, which plays a key role in the regulation of growth in animals. tll2, which is known to be associated with intestinal regeneration, was extremely highly upregulated in both transcriptomic (infinite) and qPCR (610.70) analyses. Two of the upregulated genes are associated with the fatty acid metabolism, several genes are likely to be indicators of heightened transcription levels, several are associated with metabolic and developmental roles, several with neuronal functions (including two with vision), several with the immune system, and two downregulated genes with the development of vasculature. The higher growth rate of the Selected group is likely to be at least partially attributed to increased endocytosis efficiency and genetically-driven behavioural differences (higher aggression levels). There are some indications that this new strain might have slightly impaired immune responses, and a higher propensity for inherited diseases leading to sight impairment, as well for neurodegenerative diseases in general, but these indications still need to be confirmed.

Comparison of the gastrointestinal tract of a dual-purpose to a broiler chicken line: A qualitative and quantitative macroscopic and microscopic study

The transition to using dual-purpose chickens is an alternative to killing male hatchlings of high performance egg-laying chickens. This study aimed to compare the gastrointestinal tract of a recently developed genetic line of dual purpose male chicken, Lohmann Dual (LD), with that of a broiler line, Ross 308. Eighty birds from each line were grown until they reached an average body weight 2000 g (5 weeks for Ross and 9 for LD birds). Six birds of each line were sampled weekly. Body weight (BW), normalized mass of gastrointestinal segments and relative length of intestine were determined. Histologically the villus height, epithelium height, crypt depth, mucosal enlargement factor and the tunica muscularis thickness were measured in jejunum and ileum. Data were regressed against body weight and genetic line. Jejunal enterocyte microvilli and junctional complexes length were measured. Normalized mass and relative length of the gastrointestinal segments were greater in LD birds than in Ross birds at all ages. After day 7 these decreased steadily over the lifetime of the birds in both genetic lines. The growth curves of the gastrointestinal segments of the LD birds were similar to those of the Ross birds. In birds of the same BW, LD birds had a significantly heavier gizzard, shorter intestine, higher jejunal villi, thicker ileal tunica muscularis and smaller ileal mucosal enlargement factor than were found in Ross birds. The large gizzard in LD chickens presumably increases the degree of food processing and enhances availability of nutrients in the orad part of the intestine leading to a lower nutrient concentration and a smaller absorption surface area in the ileum of the LD compared to the Ross chickens. The anatomical differences between the two lines are important criteria for further selection and should be considered in their feeding management.

Selective breeding for high alcohol consumption and response to nicotine: locomotor activity, dopaminergic in the mesolimbic system, and innate genetic differences in male and female alcohol-preferring, non-preferring, and replicate lines of high-alcohol drinking and low-alcohol drinking rats

RATIONALE

There is evidence for a common genetic link between alcohol and nicotine dependence. Rodents selectively bred for high alcohol consumption/responsivity are also more likely to self-administer nicotine than controls.

OBJECTIVES

The experiments examined the response to systemic nicotine, the effects of nicotine within the drug reward pathway, and innate expression of nicotine-related genes in a brain region regulating drug reward/self-administration in multiple lines of rats selectively bred for high and low alcohol consumption.

METHODS

The experiments examined the effects of systemic administration of nicotine on locomotor activity, the effects of nicotine administered directly into the (posterior ventral tegmental area; pVTA) on dopamine (DA) release in the nucleus accumbens shell (AcbSh), and innate mRNA levels of acetylcholine receptor genes in the pVTA were determined in 6 selectively bred high/low alcohol consuming and Wistar rat lines.

RESULTS

The high alcohol-consuming rat lines had greater nicotine-induced locomotor activity compared to low alcohol-consuming rat lines. Microinjections of nicotine into the pVTA resulted in DA release in the AcbSh with the dose response curves for high alcohol-consuming rats shifted leftward and upward. Genetic analysis of the pVTA indicated P rats expressed higher levels of α2 and β4.

CONCLUSION

Selective breeding for high alcohol preference resulted in a genetically divergent behavioral and neurobiological sensitivity to nicotine. The observed behavioral and neurochemical differences between the rat lines would predict an increased likelihood of nicotine reinforcement. The data support the hypothesis of a common genetic basis for drug addiction and identifies potential receptor targets.

Genetic diversity and origin of the feral horses in Theodore Roosevelt National Park

Feral horses in Theodore Roosevelt National Park (TRNP) represent an iconic era of the North Dakota Badlands. Their uncertain history raises management questions regarding origins, genetic diversity, and long-term genetic viability. Hair samples with follicles were collected from 196 horses in the Park and used to sequence the control region of mitochondrial DNA (mtDNA) and to profile 12 autosomal short tandem repeat (STR) markers. Three mtDNA haplotypes found in the TRNP horses belonged to haplogroups L and B. The control region variation was low with haplotype diversity of 0.5271, nucleotide diversity of 0.0077 and mean pairwise difference of 2.93. We sequenced one mitochondrial genome from each haplotype determined by the control region. Two complete mtDNA sequences of haplogroup L were closely related to the mtDNA of American Paint horse. The TRNP haplotype B did not have close matches in GenBank. The phylogenetic test placed this sequence in a group consisting of two horses from China, one from Yakutia, and one from Italy raising a possibility of historical transportation of horses from Siberia and East Asia to North America. Autosomal STR loci were polymorphic and indicated that the TRNP horses were distinctly different from 48 major horse breeds. Heterozygosity, mean number of alleles, and other measures of diversity indicated that TRNP herd diversity was below that observed for most other feral herds and domestic breeds. Both mtDNA and STRs demonstrated that the existing genetic data sets of horses are insufficient to determine the exact origins of the TRNP horses. However, measures of nuclear and mitochondrial diversity have elucidated management needs. It is recommended that new genetic stock be introduced and that adaptive management principles are employed to ensure that unique mitochondrial lineages are preserved and genetic diversity is increased and maintained over time.

[Generation of a new strain of NOD/SCID/IL2Rγ-/- mice with targeted disruption of Prkdc and IL2Rγ genes using CRISPR/Cas9 system]

OBJECTIVE

The NOD/SCID/IL2Rγ^-/- (NSG) mouse strain is the most widely used immunodeficient strain for xenograft transplantation. However, the existing SCID mutation is a spontaneous mutation of the Prkdc gene, which leads to leaky T cell developmental block and difficulty in genotyping. It is therefore important to develop a new strain of NSG mice with targeted disruption of Prkdc and IL2Rγ genes.

METHODS

Targeted disruption of Prkdc and IL2Rγ genes was achieved using the CRISPR/ Cas9 system. By intercrossing the knockout and NOD mice, we obtained a novel strain of NOD/SCID/IL2Rγ^-/- (NSG) mice, denoted as cNSG (Chinese NSG) mice.

RESULTS

In addition to the NOD mutation, cNSG mice exhibited a complete absence of T cells, B cells and NK cells. cNSG mice allowed more efficient engraftment of human cancer cells than the commonly used immunodeficient nude mice.

CONCLUSION

cNSG mice will provide an important xenotransplantation model for biomedical research.

Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs

Population bottlenecks, inbreeding, and artificial selection can all, in principle, influence levels of deleterious genetic variation. However, the relative importance of each of these effects on genome-wide patterns of deleterious variation remains controversial. Domestic and wild canids offer a powerful system to address the role of these factors in influencing deleterious variation because their history is dominated by known bottlenecks and intense artificial selection. Here, we assess genome-wide patterns of deleterious variation in 90 whole-genome sequences from breed dogs, village dogs, and gray wolves. We find that the ratio of amino acid changing heterozygosity to silent heterozygosity is higher in dogs than in wolves and, on average, dogs have 2-3% higher genetic load than gray wolves. Multiple lines of evidence indicate this pattern is driven by less efficient natural selection due to bottlenecks associated with domestication and breed formation, rather than recent inbreeding. Further, we find regions of the genome implicated in selective sweeps are enriched for amino acid changing variants and Mendelian disease genes. To our knowledge, these results provide the first quantitative estimates of the increased burden of deleterious variants directly associated with domestication and have important implications for selective breeding programs and the conservation of rare and endangered species. Specifically, they highlight the costs associated with selective breeding and question the practice favoring the breeding of individuals that best fit breed standards. Our results also suggest that maintaining a large population size, rather than just avoiding inbreeding, is a critical factor for preventing the accumulation of deleterious variants.

Detection of selection signatures in Piemontese and Marchigiana cattle, two breeds with similar production aptitudes but different selection histories

BACKGROUND

Domestication and selection are processes that alter the pattern of within- and between-population genetic variability. They can be investigated at the genomic level by tracing the so-called selection signatures. Recently, sequence polymorphisms at the genome-wide level have been investigated in a wide range of animals. A common approach to detect selection signatures is to compare breeds that have been selected for different breeding goals (i.e. dairy and beef cattle). However, genetic variations in different breeds with similar production aptitudes and similar phenotypes can be related to differences in their selection history.

METHODS

In this study, we investigated selection signatures between two Italian beef cattle breeds, Piemontese and Marchigiana, using genotyping data that was obtained with the Illumina BovineSNP50 BeadChip. The comparison was based on the fixation index (Fst), combined with a locally weighted scatterplot smoothing (LOWESS) regression and a control chart approach. In addition, analyses of Fst were carried out to confirm candidate genes. In particular, data were processed using the varLD method, which compares the regional variation of linkage disequilibrium between populations.

RESULTS

Genome scans confirmed the presence of selective sweeps in the genomic regions that harbour candidate genes that are known to affect productive traits in cattle such as DGAT1, ABCG2, CAPN3, MSTN and FTO. In addition, several new putative candidate genes (for example ALAS1, ABCB8, ACADS and SOD1) were detected.

CONCLUSIONS

This study provided evidence on the different selection histories of two cattle breeds and the usefulness of genomic scans to detect selective sweeps even in cattle breeds that are bred for similar production aptitudes.