Genetic diversity and population structure in lines of chickens divergently selected for high and low 8-week body weight

Sexual dimorphism for juvenile body weight in chickens divergently selected for 8-week body weight

There is a dearth of literature on the genetics of sexual dimorphism for juvenile body weight in meat-type chickens given its biological and economic relevance. Herein, we report the sexual dimorphism for 4- and 8-week body weights in White Plymouth Rock chicken lines that have undergone 67 generations of selection. Fluctuations in the degree of dimorphism occurred across generations, with greater dimorphism and less variation at 8 weeks than 4 weeks. Over the 67 generations, there was a significant decrease in the degree of dimorphism in the high line, with no changes in the low line. It is very difficult to genetically modify sexual dimorphism in a particular population using the currently available conventional tools, and nature possesses homeostatic mechanisms that maintain stasis in a population.

Pedigree analysis of Korean native chickens: unraveling inbreeding and genetic diversity

This study assessed the trends in inbreeding, effective population size, and genetic diversity across six Korean native chicken lines using pedigree records from 54,383 chickens. Understanding these genetic parameters is significantly important for maintaining healthy and viable chicken populations. The primary objective was to analyze the pedigree data to assess the levels of inbreeding and genetic diversity and to evaluate the effective population size across the different lines. Pedigree analysis revealed that pedigree completeness peaked in the first generation and declined in subsequent generations for all lines. Line A exhibited a mean inbreeding coefficient of 0.0201, whereas the other lines displayed lower mean values ranging from 0.0009 to 0.0098, indicating that inbreeding levels were within an acceptable range and considered safe from extinction. Average relatedness consistently increased with time. Individual increases in inbreeding were the highest in Line A (0.62%), with smaller increases in the other lines ranging from 0.02 to 0.23%. Effective population sizes varied from 81 to 2500, with average coancestry within parental populations ranging from 0.0032 to 0.0290. The fe/fa ratio between 1.00 and 1.69 in the 6 lines suggested a moderate impact during bottleneck events, with subsequent populations recovering well. The genetic diversity loss due to genetic drift and unequal founder contributions ranged from 0.66-3.15%, indicating that considerable genetic variability remains within the populations. The results of this study have practical applications in the management and conservation of genetic resources in poultry breeding programs. By highlighting the importance of monitoring inbreeding and maintaining genetic diversity, the findings can help develop strategies to ensure the long-term sustainability of these chicken lines. This study provides valuable insights into the genetic management of Korean native chicken lines, emphasizing the need for strategic breeding practices to preserve genetic health and diversity.

Comparison of differences in performance between pigs whose sires were identified using different selection strategies after experimental infection with PRRSV

The objective of this study was to evaluate differences in the performance of offspring of boars selected with an index emphasizing resilience and boars selected based on a traditional index, emphasizing feed efficiency and carcass quality (traditional) index vs. a customized (resilience) index. The resilience index was identical to the traditional index, except that extra emphasis was placed on piglet vitality (increased by 66%), growth rate (decreased by 14%), and feed intake (increased substantially by 5,157%). Sows were mated to either boars selected based on the resilience index or boars selected on the traditional index. Weaned offspring were vaccinated for Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and experimentally infected with PRRSV RFLP 1-7-4 four weeks later. Offspring were allocated to pens (n ~ 27 pigs/pen; n = 27 pens/group) by sire-selection group for a total of 1,458 pigs in 54 pens. The weight of each pen was recorded on 0, 42, and 110 d postinfection (DPI) and used to calculate average daily gain (ADG), average daily feed intake (ADFI), and feed conversion ratio (FCR). Mortalities were recorded from 0 to 110 DPI and necropsies were routinely performed to characterize pathogens present within the barn. Pigs classified as full value (i.e., >104 kg and void of defects) were slaughtered and hot carcass weight (HCW), backfat, loin depth, and lean weight were obtained from the slaughter plant. Effects of progeny group on performance, carcass characteristics, and mortality rate were estimated with a mixed linear model. Differences between progeny groups in ADG (P > 0.27), HCW (P = 0.68), backfat (P = 0.13), or loin depth (P = 0.39), and mortality rate (P = 0.29) were not detected. From 0 to 42 DPI, offspring of boars selected based on the resilience index had higher ADFI (0.06 kg/d, P = 0.01) and higher FCR (0.12, P = 0.01). In summary, results from this study do not support selection of boars for increased feed intake, piglet viability, and robustness in order to prevent losses caused by PRRSV, but selection response was only measured after one generation of male selection. The impact of multiple generations of selection, or the development of an index including traits derived from data collected under disease-challenged conditions should be explored. The data collected for this study are a valuable resource to explore additional genetic selection strategies for enhanced resilience to a multifactorial PRRS challenge.

Complex genetic architecture of the chicken Growth1 QTL region

The genetic complexity of polygenic traits represents a captivating and intricate facet of biological inheritance. Unlike Mendelian traits controlled by a single gene, polygenic traits are influenced by multiple genetic loci, each exerting a modest effect on the trait. This cumulative impact of numerous genes, interactions among them, environmental factors, and epigenetic modifications results in a multifaceted architecture of genetic contributions to complex traits. Given the well-characterized genome, diverse traits, and range of genetic resources, chicken (Gallus gallus) was employed as a model organism to dissect the intricate genetic makeup of a previously identified major Quantitative Trait Loci (QTL) for body weight on chromosome 1. A multigenerational advanced intercross line (AIL) of 3215 chickens whose genomes had been sequenced to an average of 0.4x was analyzed using genome-wide association study (GWAS) and variance-heterogeneity GWAS (vGWAS) to identify markers associated with 8-week body weight. Additionally, epistatic interactions were studied using the natural and orthogonal interaction (NOIA) model. Six genetic modules, two from GWAS and four from vGWAS, were strongly associated with the studied trait. We found evidence of both additive- and non-additive interactions between these modules and constructed a putative local epistasis network for the region. Our screens for functional alleles revealed a missense variant in the gene ribonuclease H2 subunit B (RNASEH2B), which has previously been associated with growth-related traits in chickens and Darwin's finches. In addition, one of the most strongly associated SNPs identified is located in a non-coding region upstream of the long non-coding RNA, ENSGALG00000053256, previously suggested as a candidate gene for regulating chicken body weight. By studying large numbers of individuals from a family material using approaches to capture both additive and non-additive effects, this study advances our understanding of genetic complexities in a highly polygenic trait and has practical implications for poultry breeding and agriculture.

Early intestinal development of chickens divergently selected for high or low 8-wk body weight and a commercial broiler

The early posthatch period is crucial to intestinal development, shaping long-term growth, metabolism, and health of the chick. The objective of this study was to determine the effect of genetic selection on morphological characteristics and gene expression during early intestinal development. Populations of White Plymouth Rocks have been selected for high weight (HWS) and low weight (LWS) for over 63 generations, and some LWS display symptoms of anorexia. Intestinal structure and function of these populations were compared to a commercial broiler Cobb 500 (Cobb) during the perihatch period. Egg weights, yolk-free embryo BW, yolk weights, and jejunal samples from HWS, LWS, and Cobb were collected on embryonic day (e) 17, e19, day of hatch, day (d) 3, d5, and d7 posthatch for histology and gene expression analysis. The RNAscope in-situ hybridization method was used to localize expression of the stem cell marker, olfactomedin 4 (Olfm4). Villus height (VH), crypt depth (CD), and VH/CD were measured from Olfm4 stained images using ImageJ. mRNA abundance for Olfm4, stem cell marker Lgr5, peptide transporter PepT1, goblet cell marker Muc2, marker of proliferation Ki67, and antimicrobial peptide LEAP2 were examined. Two-factor ANOVA was performed for measurements and Turkey's HSD was used for mean separation when appropriate. Cobb were heaviest and LWS the lightest (P < 0.01). at each timepoint. VH increased in Cobb and CD increased in HWS compared to LWS (P < 0.01). PepT1 mRNA was upregulated in LWS (P < 0.01), and Muc2 mRNA was decreased in both HWS and LWS compared to Cobb (P < 0.01). Selection for high or low 8-wk body weight has caused differences in intestinal gene expression and morphology when compared to a commercial broiler.

Population dynamics of a long-term selection experiment in White Plymouth Rock chickens selected for low or high body weight

The population dynamics of 2 lines of chickens from a long-term (59 generations) selection experiment were assessed based on pedigree data. These lines were propagated from phenotypic selection for low and high 8-wk BW in White Plymouth Rock chickens. Our objective was to determine whether the 2 lines maintained similar population structures over the selection horizon to allow meaningful comparisons of their performance data. A complete pedigree of 31,909 individuals, consisting of 102 founders, 1,064 from the parental generation, and 16,245 low weight (LWS) and 14,498 high weight (HWS) select chickens, was available. Inbreeding (F) and average relatedness (AR) coefficients were computed. Average F per generation and AR coefficients were 1.3 (SD 0.8) % and 0.53 (SD 0.001) for LWS, and 1.5 (SD 1.1) % and 0.66 (SD 0.001) for HWS. Mean F for the entire pedigree was 0.26 (0.16) and 0.33 (0.19), and maximum F was 0.64 and 0.63, in LWS and HWS, respectively. Based on Wright's fixation index, at generation 59, substantial genetic differences were established between lines. The effective population size was 39 in LWS and 33 in HWS. The effective number of founders was 17 and 15, effective number of ancestors were 12 and 8, and genome equivalents were 2.5 and 1.9 in LWS and HWS, respectively. About 30 founders explained the marginal contribution to both lines. By generation 59, only 7 male and 6 female founders contributed to both lines. Moderately high levels of inbreeding and low effective population sizes were inevitable, as this was a closed population. However, effects on the fitness of the population were expected to be less substantial because founders were a combination of 7 lines. The effective numbers of founders and ancestors were relatively low compared to the actual number of founders, as few ancestors contributed to descendants. Based on these evaluations, it can be inferred that LWS and HWS had similar population structures. Comparisons of selection responses in the 2 lines therefore should be reliable.

Dynamics of Small Non-coding RNA Profiles and the Intestinal Microbiome of High and Low Weight Chickens

The host and its symbiotic bacteria form a biological entity, holobiont, in which they share a dynamic connection characterized by symbiosis, co-metabolism, and coevolution. However, how these collaborative relationships were maintained over evolutionary time remains unclear. In this research, the small non-coding RNA (sncRNA) profiles of cecum and their bacteria contents were measured from lines of chickens that have undergone long-term selection for high (HWS) or low (LWS) 56-day body weight. The results from these lines that originated from a common founder population and maintained under the same husbandry showed an association between host intestinal sncRNA expression profile (miRNA, lncRNA fragment, mRNA fragment, snoRNA, and snRNA) and intestinal microbiota. Correlation analyses suggested that some central miRNAs and mRNA fragments had interactions with the abundance of intestinal microbial species and microbiota functions. miR-6622-3p, a significantly differentially expressed (DE) miRNA was correlated with a body weight gain related bacterium, Alistipes putredinis. Our results showed that host sncRNAs may be mediators of interaction between the host and its intestinal microbiome. This provides additional clue for holobiont concepts.

Epigenetic modifiers identified as regulators of food intake in a unique hypophagic chicken model

DNA methylation is an epigenetic modification that influences gene transcription; however, the effects of methylation-influencing chemicals on appetite are unknown. We evaluated the effects of single administration of a methyl donor, S-Adenosylmethionine (SAM), or methylation inhibitor, 5-Azacytidine (AZA), on immediate and later-age food intake in an anorexic chick model. The doses of intracerebroventricularly-injected SAM were 0 (vehicle), 0.1, 1, and 10 μg, and of AZA were 0 (vehicle), 1, 5, and 25 μg. When injected on day 5 posthatch, there was no effect of SAM on food intake in either fed or fasted chicks, whereas AZA increased food consumption in the fasted state but decreased it in fed chicks. We then performed a single injection (same doses) at hatch and measured food intake on day 5 in response to neuropeptide Y (NPY; 0.2 μg) injection. Irrespective of NPY, chicks injected with 1 μg of SAM ate more than others on day 5. In contrast, chicks injected with AZA (5 and 25 μg doses) consumed less on day 5. In conclusion, we identified DNA methylation-regulating chemicals as regulators of food intake. AZA but not SAM affected food intake in the short-term, feeding state dependently. Later, both chemicals injected on the day of hatch were associated with food intake changes at a later age, suggesting that feeding pathways might be altered through changes in methylation.

Evolutionary pressures rendered by animal husbandry practices for avian influenza viruses to adapt to humans

Commercial poultry operations produce and crowd billions of birds every year, which is a source of inexpensive animal protein. Commercial poultry is intensely bred for desirable production traits, and currently presents very low variability at the major histocompatibility complex. This situation dampens the advantages conferred by the MHC’s high genetic variability, and crowding generates immunosuppressive stress. We address the proteins of influenza A viruses directly and indirectly involved in host specificities. We discuss how mutants with increased virulence and/or altered host specificity may arise if few class I alleles are the sole selective pressure on avian viruses circulating in immunocompromised poultry. This hypothesis is testable with peptidomics of MHC ligands. Breeding strategies for commercial poultry can easily and inexpensively include high variability of MHC as a trait of interest, to help save billions of dollars as a disease burden caused by influenza and decrease the risk of selecting highly virulent strains.

Researching on the fine structure and admixture of the worldwide chicken population reveal connections between populations and important events in breeding history

Here, we have evaluated the general genomic structure and diversity and studied the divergence resulting from selection and historical admixture events for a collection of worldwide chicken breeds. In total, 636 genomes (43 populations) were sequenced from chickens of American, Chinese, Indonesian, and European origin. Evaluated populations included wild junglefowl, rural indigenous chickens, breeds that have been widely used to improve modern western poultry populations and current commercial stocks bred for efficient meat and egg production. In-depth characterizations of the genome structure and genomic relationships among these populations were performed, and population admixture events were investigated. In addition, the genomic architectures of several domestication traits and central documented events in the recent breeding history were explored. Our results provide detailed insights into the contributions from population admixture events described in the historical literature to the genomic variation in the domestic chicken. In particular, we find that the genomes of modern chicken stocks used for meat production both in eastern (Asia) and western (Europe/US) agriculture are dominated by contributions from heavy Asian breeds. Further, by exploring the link between genomic selective divergence and pigmentation, connections to functional genes feather coloring were confirmed.

Temporal Trends in Performance and Hatchability Traits of Eight Strains of Hens Covered by the Gene Pool Protection Programme in Poland

The aim of the study was to determine trends in performance and hatchability traits of eight strains of hens that have been covered by the gene pool protection programme in Poland over ten years/generations. The study involved conservation populations of laying hens: Greenleg Partridge (Z-11), Yellowleg Partridge (Ż-33), Sussex (S-66), Leghorn (H-22, G99), Rhode Island Red (R-11, K-22) and Rhode Island White (A-33), which were maintained at the Experimental Station of the National Research Institute of Animal Production in Chorzelów. The following productive traits were analysed for each population: body weight at 20 wk (g), egg weight at 33 and 53 wk, sexual maturity and number of eggs laid per hen up to 56 wk of age. Mortality and culling were also recorded during rearing and production periods. Furthermore, effective population size (Ne) and inbreeding coefficient in the population (Fx) were calculated for each strain. The analysis of the performance results of the eight strains of hens and their trends indicate that the methods of conservation breeding adopted for these populations enable effective implementation of the conservation programme. The strains were found to differ in all the performance traits subjected to evaluation. Over the 10 generations, the strains examined showed high survival and hatchability parameters during both rearing and production periods. The currently used random mating system proved effective to prevent the populations from an increase of inbreeding. However, a worrying downward trend in body weight was observed in some strains.

Haplotype Purging After Relaxation of Selection in Lines of Chickens that Had Undergone Long-Term Selection for High and Low Body Weight

Bi-directional selection for increased and decreased 56-day body weights (BW56) has been applied to two lines of White Plymouth Rock chickens—the Virginia high (HWS) and low (LWS) body weight lines. Correlated responses have been observed, including negative effects on traits related to fitness. Here, we use high and low body weight as proxies for fitness. On a genome-wide level, relaxed lines (HWR, LWR) bred from HWS and LWS purged some genetic variants in the selected lines. Whole-genome re-sequencing was here used to identify individual loci where alleles that accumulated during directional selection were purged when selection was relaxed. In total, 11 loci with significant purging signals were identified, five in the low (LW) and six in the high (HW) body weight lineages. Associations between purged haplotypes in these loci and BW56 were tested in an advanced intercross line (AIL). Two loci with purging signals and haplotype associations to BW56 are particularly interesting for further functional characterization, one locus on chromosome 6 in the LW covering the sour-taste receptor gene PKD2L1, a functional candidate gene for the decreased appetite observed in the LWS and a locus on chromosome 20 in the HW containing a skeletal muscle hypertrophy gene, DNTTIP1.

A genomic inference of the White Plymouth Rock genealogy

Crossing of populations has been, and still is, a central component in domestication and breed and variety formation. It is a way for breeders to utilize heterosis and to introduce new genetic variation into existing plant and livestock populations. During the mid-19th century, several chicken breeds that had been introduced to America from Europe and Asia became the founders for those formed in the USA. Historical records about the genealogy of these populations are often unclear and inconsistent. Here, we used genomics in an attempt to describe the ancestry of the White Plymouth Rock (WPR) chicken. In total, 150 chickens from the WPR and 8 other stocks that historical records suggested contributed to its formation were whole-genome re-sequenced. The admixture analyses of the autosomal and sex chromosomes showed that the WPR was likely founded as a cross between a paternal lineage that was primarily Dominique, and a maternal lineage where Black Java and Cochin contributed in essentially equal proportions. These results were consistent and provided quantification with the historical records that they were the main contributors to the WPR. The genomic analyses also revealed genome-wide contributions (<10% each) by Brahma, Langshan, and Black Minorca. When viewed on an individual chromosomal basis, contributions varied considerably among stocks.

Glucose Tolerance and Plasma Non-Esterified Fatty Acid Levels in Chickens Selected for Low Body Weight, Red Junglefowl, and their Reciprocal Cross

Responses of an individual to food deprivation, such as a 16-h fast, are complex, and are influenced by environmental and genetic factors. Domestication is an ongoing process during which adaptations to changing environments occur over generations. Food deprivation by their caretakers is less for domestic chickens than for their junglefowl ancestors. Unlike domestic chicken, the junglefowl adapted over generations to periods of food deprivation, which may be reflected in differences in metabolic responses to brief periods without food. Here, we compared the blood glucose and plasma levels of non-esterified fatty acids (NEFA) among four populations when deprived of feed for 16 h. The four populations included a domestic White Rock experimental line (LWS) maintained for generations under ad libitum feeding, adult red junglefowl (RJF), and a reciprocal cross of the lines. Although there were significant differences in adult (31-week) body weight between the RJF (683 g) and LWS (1282 g), with the weight of F₁ crosses being intermediate, the amount of abdominal fat relative to body weight was similar for all populations. Patterns for blood glucose responses to a glucose bolus after a 16-h fast were similar for the initial and final points in the parental and cross populations. However, RJF reached their peak faster than LWS, with the reciprocal cross intermediate to the parental populations. Plasma NEFA concentrations were higher after the 16-h fast than in fed states, with no population differences for the fasting state. However, in the fed state, NEFA levels were lesser for LWS than for others, which was reflected further in percentage change from fed to fasted. This larger change in LWS suggests differences in mobilization of energy substrates and implies that during domestication or development of the LWS line, thresholds for responses to acute stressors may have increased.

Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach

BACKGROUND

Experimental intercrosses between outbred founder populations are powerful resources for mapping loci that contribute to complex traits i.e. quantitative trait loci (QTL). Here, we present an approach and its accompanying software for high-resolution reconstruction of founder mosaic genotypes in the intercross offspring from such populations using whole-genome high-coverage sequence data on founder individuals (~ 30×) and very low-coverage sequence data on intercross individuals (< 0.5×). Sets of founder-line informative markers were selected for each full-sib family and used to infer the founder mosaic genotypes of the intercross individuals. The application of this approach and the quality of the estimated genome-wide genotypes are illustrated in a large F₂ pedigree between two divergently selected lines of chickens.

RESULTS

We describe how we obtained whole-genome genotype data for hundreds of individuals in a cost- and time-efficient manner by using a Tn5-based library preparation protocol and an imputation algorithm that was optimized for this application. In total, 7.6 million markers segregated in this pedigree and, within each full-sib family, between 10.0 and 13.7% of these were fully informative, i.e. fixed for alternative alleles in the founders from the divergent lines, and were used for reconstruction of the offspring mosaic genotypes. The genotypes that were estimated based on the low-coverage sequence data were highly consistent (> 95% agreement) with those obtained using individual single nucleotide polymorphism (SNP) genotyping. The estimated resolution of the inferred recombination breakpoints was relatively high, with 50% of them being defined on regions shorter than 10 kb.

CONCLUSIONS

A method and software for inferring founder mosaic genotypes in intercross offspring from low-coverage whole-genome sequencing in pedigrees from heterozygous founders are described. They provide high-quality, high-resolution genotypes in a time- and cost-efficient manner. The software is freely available at https://github.com/CarlborgGenomics/Stripes .

A Polygenic Genetic Architecture of Flowering Time in the Worldwide Arabidopsis thaliana Population

Here, we report an empirical study of the polygenic basis underlying the evolution of complex traits. Flowering time variation measured at 10 and 16°C in the 1,001-genomes Arabidopsis thaliana collection of natural accessions were used as a model. The polygenic architecture of flowering time was defined as the 48 loci that were significantly associated with flowering time-at 10 and/or 16°C and/or their difference-in this population. Contributions from alleles at flowering time associated loci to global and local adaptation were explored by evaluating their distribution across genetically and geographically defined subpopulations across the native range of the species. The dynamics in the genetic architecture of flowering time in response to temperature was evaluated by estimating how the effects of these loci on flowering changed with growth temperature. Overall, the genetic basis of flowering time was stable-about 2/3 of the flowering time loci had similar effects at 10°C and 16°C-but many loci were involved in gene by temperature interactions. Globally present alleles, mostly of moderate effect, contributed to the differences in flowering times between the subpopulations via subtle changes in allele frequencies. More extreme local adaptations were, on several occasions, due to regional alleles with relatively large effects, and their linkage disequilibrium-patterns suggest coevolution of functionally connected alleles within local populations. Overall, these findings provide a significant contribution to our understanding about the possible modes of global and local evolution of a complex adaptive trait in A. thaliana.

Changes in adipose tissue physiology during the first two weeks posthatch in chicks from lines selected for low or high body weight

Chickens from lines selected for low (LWS) or high (HWS) body weight (BW) differ in appetite and adiposity. Mechanisms associated with the predisposition to becoming obese are unclear. The objective of the experiment was to evaluate developmental changes in depot-specific adipose tissue during the first 2 wk posthatch. Subcutaneous (SQ), clavicular (CL), and abdominal (AB) depots were collected at hatch (DOH) and days 4 (D4) and 14 (D14) posthatch for histological and mRNA measurements. LWS chicks had decreased SQ fat mass on a BW basis with reduced adipocyte size from DOH to D4 and increased BW and fat mass with unchanged adipocyte size from D4 to D14. HWS chicks increased in BW from DOH to D14 and increased in fat mass in all three depots with enlarged adipocytes in the AB depot from D4 to D14. Meanwhile, CCAAT/enhancer-binding protein-α, neuropeptide Y, peroxisome proliferator-activated receptor-γ, and acyl-CoA dehydrogenase mRNAs differed among depots between lines at different ages. Plasma nonesterified fatty acids were greater in LWS than HWS at D4 and D14. From DOH to D4, LWS chicks mobilized SQ fat and replenished the reservoir through hyperplasia, whereas HWS chicks were dependent on hyperplasia and hypertrophy to maintain adipocyte size and depot mass. From D4 to D14, adipose tissue catabolism and adipogenesis slowed. Whereas LWS fat depots and adipocyte sizes remained stable, HWS chicks rapidly accumulated fat in CL and AB depots. Chicks predisposed to be anorexic or obese have different fat development patterns during the first 2 wk posthatch.

Bidirectional Selection for Body Weight on Standing Genetic Variation in a Chicken Model

Experimental populations of model organisms provide valuable opportunities to unravel the genomic impact of selection in a controlled system. The Virginia body weight chicken lines represent a unique resource to investigate signatures of selection in a system where long-term, single-trait, bidirectional selection has been carried out for more than 60 generations. At 55 generations of divergent selection, earlier analyses of pooled genome resequencing data from these lines revealed that 14.2% of the genome showed extreme differentiation between the selected lines, contained within 395 genomic regions. Here, we report more detailed analyses of these data exploring the regions displaying within- and between-line genomic signatures of the bidirectional selection applied in these lines. Despite the strict selection regime for opposite extremes in body weight, this did not result in opposite genomic signatures between the lines. The lines often displayed a duality of the sweep signatures, where an extended region of homozygosity in one line, in contrast to mosaic pattern of heterozygosity in the other line. These haplotype mosaics consisted of short, distinct haploblocks of variable between-line divergence, likely the results of a complex demographic history involving bottlenecks, introgressions and moderate inbreeding. We demonstrate this using the example of complex haplotype mosaicism in the growth1 QTL. These mosaics represent the standing genetic variation available at the onset of selection in the founder population. Selection on standing genetic variation can thus result in different signatures depending on the intensity and direction of selection.

Central injection of oxytocin reduces food intake and affects hypothalamic and adipose tissue gene expression in chickens

Oxytocin (OT) is a well-characterized neurotransmitter that participates in a wide range of physiological processes including the inhibition of food intake. The avian ortholog, mesotocin (MT), differs from OT by a single amino acid. Little is known regarding the function of OT in regulating energy balance in birds; thus, this study was designed to determine the effects of central OT injection on food intake and adipose tissue physiology in chicks. At 4-d post-hatch, broiler chicks were fasted for 3 h and injected intracerebroventricularly with 0 (vehicle), 0.63, 2.5, 5.0, or 10 nmol OT. Oxytocin decreased food and water intake during the entire 180-min observation period. The reduction in water intake was likely not prandial because chicks that were food restricted after OT injection also drank less. There was increased c-Fos immunoreactivity in several appetite-associated hypothalamic nuclei in OT-injected chicks at 1 h, including the arcuate (ARC), dorsomedial nucleus (DMN), lateral hypothalamus (LH), paraventricular nucleus (PVN), and ventromedial hypothalamus (VMH). OT treatment was associated with reduced hypothalamic corticotropin-releasing factor (CRF) mRNA and increased cloacal temperature at 1 h post-injection. We then investigated appetite- and adipose tissue-associated effects of OT in chicks from lines that have undergone long-term selection for either low (LWS) or high (HWS) juvenile body weight. Central injection of OT decreased food intake in both lines with the magnitude of response greater in the HWS than LWS chicks. Adipose tissue abundance of fatty acid-binding protein 4, monoglyceride lipase (MGLL), MT, and perilipin-1 mRNA was greater in LWS than HWS chicks. Lipoprotein lipase, MGLL, and MT mRNAs increased in response to OT injection in LWS but not HWS chicks. In conclusion, central injection of OT induced anorexia, reduced water intake, increased body temperature, and was associated with activation of the ARC, DMN, LH, PVN, and VMH in the hypothalamus. The effects on appetite and body temperature may involve CRF signaling in the hypothalamus and lipolysis in the adipose tissue, respectively. There were differences in the appetite, and adipose tissue response to OT in body weight-selected lines of chicks supports that MT plays a role in energy balance regulation in chickens.

Fasting differentially alters the hypothalamic proteome of chickens from lines with the propensity to be anorexic or obese

BACKGROUND

The hypothalamus is the ultimate modulator of appetite and energy balance and therefore sensitive to changes in nutritional state. Chicks from lines selected for low (LWS) and high (HWS) body weight are hypophagic and compulsive eaters, respectively, and differ in their propensity to become obese and in their hypothalamic mRNA response to fasting.

METHODS

As fasting-induced changes in hypothalamic proteins are unknown, we investigated the hypothalamic proteomes of 5-day old LWS and HWS chicks in the fed and fasted states using a label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach.

RESULTS

A total of 744 proteins were identified in the chicken hypothalamus, and 268 differentially abundant proteins were identified among four pairwise comparisons. Ninety-five proteins were associated with the response to fasting in HWS chicks, and 23 proteins were associated with the response to fasting in LWS chicks. Fasting-responsive proteins in HWS chicks were significantly enriched in ATP metabolic processes, glyoxylate/dicarboxylate metabolism, and ribosome function. There was no enrichment for any pathways in LWS chicks in response to fasting. In the fasted and fed states, 159 and 119 proteins differed between HWS and LWS, respectively. Oxidative phosphorylation, citric acid cycle, and carbon metabolism were the main pathways associated with differences between the two lines of chicks. Enzymes associated with metabolic pathways differed between HWS and LWS in both nutritional states, including fumarase, aspartate aminotransferase, mitochondrial GOT2, 3-hydroxyisobutyrate dehydrogenase, chondrogenesis associated lipocalin, sialic acid synthase, arylamine N-acetyltransferase, pineal gland isozyme NAT-3, and succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial.

CONCLUSIONS

These results provide insights into the hypothalamic metabolic pathways that are affected by nutritional status and the regulation of appetite and eating behavior.

Genomic signatures of 60 years of bidirectional selection for 8-week body weight in chickens

Sixty years, constituting 60 generations, have passed since the founding of the Virginia body weight lines, an experimental population of White Plymouth Rock chickens. Using a stringent breeding scheme for divergent 8-week body weight, the lines, which originated from a common founder population, have responded to bidirectional selection with an approximate 15-fold difference in the selected trait. They provide a model system to study the genetics of complex traits in general and the influences of artificial selection on quantitative genetic architectures in particular. As we reflect on the 60th anniversary of the initiation of the Virginia body weight lines, there is opportunity to discuss the findings obtained using different analytical and experimental genetic and genomic strategies and integrate them with a recent pooled genome resequencing dataset. Hundreds of regions across the genome show differentiation between the 2 lines, reinforcing previous findings that response to selection relied on standing variation across many genes and giving insights into the haplotype complexity underlying regions associated with body weight.

Growth patterns for three generations of an intercross between red junglefowl and chickens selected for low body weight

Growth is a complex and dynamic process that may be measured at a specific point or over a period of time. Compared was the growth of male and female chickens over a three-generation period. Involved were red junglefowl (RJF; Gallus gallus), a line of White Plymouth Rock chickens (LWS; Gallus gallus domesticus) selected for low body weight, and their reciprocal F1 and F2 crosses. In both sexes, Gompertz's description of growth showed that RJF had significantly lower asymptotes, earlier inflection points, and faster growth rates than LWS. Heterosis for these measures was positive for asymptote and negative for growth rate and inflection point. The RJF commenced egg production at a significantly younger age and lower body weight than LWS. Although F1 and F2 reciprocal crosses were similar for body weight and for age at first egg, the F1 reciprocal crosses began lay at significantly younger ages than the F2 crosses and parental lines. When viewed on a physiological basis where age and body weight were simultaneously standardized, both parental lines and reciprocal F1 and F2 crosses had differing rapid and lag growth phases. Overall, sexual dimorphism increased in all populations from hatch to sexual maturity. The LWS males had a longer growth period consistent with their female counterparts who became sexually mature at older ages. Comprehensively, these results indicate additive and nonadditive genetic variation for distinct growth patterns and changes in resource allocation strategies over time.

Correlated responses to long-term divergent selection for 8-week body weight in female White Plymouth Rock chickens: Sexual maturity

Reported here are correlated responses for reproductive traits to long-term divergent selection (54 generations) for 8-week body weight (BW8). Comparisons involved both selected and relaxed lines. Traits measured were age at first egg (AFE), body weight at first egg (WFE), and ratio of body weight and age at first egg (WAFE). Although sexual maturity was delayed in the selected lines, the effect was more pronounced in the low than high selected and relaxed lines. Selection for low BW resulted in decreases in WFE and WAFE. Correlated responses to selection for high BW were increased WFE and WAFE. Minimum AFE, WFE, and WAFE in relation to sexual maturity were line specific and influenced by selection for BW8. WAFE provided a "yardstick" for target body weights that were optimum for successful attainment of sexual maturity and higher reproductive rates. Such may be line specific. There was opposition between relaxed and artificial selection, resulting in a higher reproductive performance and fitness for the former.

Asymmetries, heterosis, and phenotypic profiles of red junglefowl, White Plymouth Rocks, and F1 and F2 reciprocal crosses

During the domestication of farm animals, humans have manipulated genetic variation for growth and reproduction through artificial selection. Here, data are presented for growth, reproductive, and behavior traits for the red junglefowl, a line of White Plymouth Rock chickens, and their F₁ and F₂ reciprocal crosses. Intra- and intergenerational comparisons for growth related traits reflected considerable additive genetic variation. In contrast, those traits associated with reproduction exhibited heterosis. The role of sexual selection was seen in the evolution of prominent secondary sexual ornaments that lend to female choice and male-male competition. The large differences between parental lines in fearfulness to humans were only mitigated slightly in the intercross generations. Whereas, overall F₁ generation heterosis was not transferred to the F₂, there was developmental stability in the F₂, as measured by relative asymmetry of bilateral traits. Through multigenerational analyses between the red junglefowl and the domestic White Plymouth Rocks, we observed plasticity and considerable residual genetic variation. These factors likely facilitated the adaptability of the chicken to a broad range of husbandry practices throughout the world.

On the relationship between epistasis and genetic variance heterogeneity

Epistasis and genetic variance heterogeneity are two non-additive genetic inheritance patterns that are often, but not always, related. Here we use theoretical examples and empirical results from earlier analyses of experimental data to illustrate the connection between the two. This includes an introduction to the relationship between epistatic gene action, statistical epistasis, and genetic variance heterogeneity, and a brief discussion about how genetic processes other than epistasis can also give rise to genetic variance heterogeneity.

Differential expression of appetite-regulating genes in avian models of anorexia and obesity

Chickens from lines that have been selected for low (LWS) or high (HWS) juvenile body weight for more than 57 generations provide a unique model by which to research appetite regulation. The LWS display different severities of anorexia, whereas all HWS become obese. In the present study, we measured mRNA abundance of various factors in appetite-associated nuclei in the hypothalamus. The lateral hypothalamus (LHA), paraventricular nucleus (PVN), ventromedial hypothalamus (VMH), dorsomedial nucleus (DMN) and arcuate nucleus (ARC) were collected from 5 day-old chicks that were fasted for 180 minutes or provided with continuous access to food. Fasting increased neuropeptide Y receptor subtype 1 (NPYR1) mRNA in the LHA and c-Fos in the VMH, at the same time as decreasing c-Fos in the LHA, neuropeptide Y receptor subtype 5 and ghrelin in the PVN, and neuropeptide Y receptor subtype 2 in the ARC. Fasting increased melanocortin receptor subtype 3 (MC3R) expression in the DMN and NPY in the ARC of LWS but not HWS chicks. Expression of NPY was greater in LWS than HWS in the DMN. neuropeptide Y receptor subtype 5 mRNA was greater in LWS than HWS in the LHA, PVN and ARC. Expression of orexin was greater in LWS than HWS in the LHA. There was greater expression of NPYR1, melanocortin receptor subtype 4 and cocaine- and amphetamine-regulated transcript in HWS than LWS and mesotocin in LWS than HWS in the PVN. In the ARC, agouti-related peptide and MC3R were greater in LWS than HWS and, in the VMH, orexin receptor 2 and leptin receptor were greater in LWS than HWS. Greater mesotocin in the PVN, orexin in the LHA and ORXR2 in the VMH of LWS may contribute to their increased sympathetic tone and anorexic phenotype. The results of the present study also suggest that an increased hypothalamic anorexigenic tone in the LWS over-rides orexigenic factors such as NPY and AgRP that were more highly expressed in LWS than HWS in several nuclei.

Population structure of Mazandaran native fowls using pedigree analysis

The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability of the Mazandaran native fowls in Iran by quantifying the pedigree completeness index, effective population size, genetic diversity, inbreeding level, and individual increase in inbreeding. The pedigree completeness analysis showed 3.31 full, 10.19 maximum, and 6.30 equivalent generations. The effective number of founders (f _e) was 131, representing 5% of the potential number of founders. The effective number of ancestors (f _a) was 81, and the genetic contribution of the 37 most influent ancestors explained 50% of the genetic variability in the population. The ratio f _e/f _a (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.62. The inbreeding coefficient increased over generations and the average was 1.93%. The average relatedness coefficient between individuals of the population was estimated to be 2.59%. The effective population size, based on the number of full generations, was 56. Family size analysis showed that fewer males than females were used, resulting in the observed levels of inbreeding. Average inbreeding coefficient in the Mazandaran native fowls can be regarded to be below critical levels. However, considering the relationship coefficients of individuals is recommended to aid maintaining genetic diversity of Mazandaran native fowls.

Imputation-Based Fine-Mapping Suggests That Most QTL in an Outbred Chicken Advanced Intercross Body Weight Line Are Due to Multiple, Linked Loci

The Virginia chicken lines have been divergently selected for juvenile body weight for more than 50 generations. Today, the high- and low-weight lines show a >12-fold difference for the selected trait, 56-d body weight. These lines provide unique opportunities to study the genetic architecture of long-term, single-trait selection. Previously, several quantitative trait loci (QTL) contributing to weight differences between the lines were mapped in an F₂-cross between them, and these were later replicated and fine-mapped in a nine-generation advanced intercross of them. Here, we explore the possibility to further increase the fine-mapping resolution of these QTL via a pedigree-based imputation strategy that aims to better capture the genetic diversity in the divergently selected, but outbred, founder lines. The founders of the intercross were high-density genotyped, and then pedigree-based imputation was used to assign genotypes throughout the pedigree. Imputation increased the marker density 20-fold in the selected QTL, providing 6911 markers for the subsequent analysis. Both single-marker association and multi-marker backward-elimination analyses were used to explore regions associated with 56-d body weight. The approach revealed several statistically and population structure independent associations and increased the mapping resolution. Further, most QTL were also found to contain multiple independent associations to markers that were not fixed in the founder populations, implying a complex underlying architecture due to the combined effects of multiple, linked loci perhaps located on independent haplotypes that still segregate in the selected lines.

Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance

Mitochondrial genomes represent a valuable source of data for evolutionary research, but studies of their short-term evolution have typically been limited to invertebrates, humans and laboratory organisms. Here we present a detailed study of 12 mitochondrial genomes that span a total of 385 transmissions in a well-documented 50-generation pedigree in which two lineages of chickens were selected for low and high juvenile body weight. These data allowed us to test the hypothesis of time-dependent evolutionary rates and the assumption of strict maternal mitochondrial transmission, and to investigate the role of mitochondrial mutations in determining phenotype. The identification of a non-synonymous mutation in ND4L and a synonymous mutation in CYTB, both novel mutations in Gallus, allowed us to estimate a molecular rate of 3.13 × 10(-7) mutations/site/year (95% confidence interval 3.75 × 10(-8)-1.12 × 10(-6)). This is substantially higher than avian rate estimates based upon fossil calibrations. Ascertaining which of the two novel mutations was present in an additional 49 individuals also revealed an instance of paternal inheritance of mtDNA. Lastly, an association analysis demonstrated that neither of the point mutations was strongly associated with the phenotypic differences between the two selection lines. Together, these observations reveal the highly dynamic nature of mitochondrial evolution over short time periods.

Stimulation of food intake after central administration of gonadotropin-inhibitory hormone is similar in genetically selected low and high body weight lines of chickens

Gonadotropin-inhibitory hormone (GnIH), first isolated from the brain of the Japanese quail (Coturnix japonica), when centrally administered exerts orexigenic effects in birds. However, the precise mechanisms mediating this effect are poorly understood and limited information is available on this effect in models of body weight dysfunction. Thus, the purpose of the present study was to investigate appetite-associated effects of GnIH in chicks from lines that have been selected for either low or high body weight, and are anorexic or become obese, respectively. Central GnIH injection increased food intake in both lines with a similar magnitude of response. There was no effect on water intake. Hypothalamic GnIH mRNA was greater in the low than high weight lines and was greater in the fasted than fed chicks. GnIH receptor mRNA was similarly expressed in both lines, and was greater in fed than fasted chicks. Thus, although selection for body weight did not alter the effect of GnIH on feeding, fasting increased GnIH mRNA in both lines implying that it is an innate hunger factor.

Anorexia is Associated with Stress-Dependent Orexigenic Responses to Exogenous Neuropeptide Y

Chicken lines that have been divergently selected for either low (LWS) or high (HWS) body weight at 56 days of age for more than 57 generations have different feeding behaviours in response to a range of i.c.v. injected neurotransmitters. The LWS have different severities of anorexia, whereas the HWS become obese. Previously, we demonstrated that LWS chicks did not respond, whereas HWS chicks increased food intake, after central injection of neuropeptide Y (NPY). The present study aimed to determine the molecular mechanisms underlying the loss of orexigenic function of NPY in LWS. Chicks were divided into four groups: stressed LWS and HWS on day of hatch, and control LWS and HWS. The stressor was a combination of food deprivation and cold exposure. On day 5 post-hatch, each chick received an i.c.v. injection of vehicle or 0.2 nmol of NPY. Only the LWS stressed group did not increase food intake in response to i.c.v. NPY. Hypothalamic mRNA abundance of appetite-associated factors was measured at 1 h post-injection. Interactions of genetic line, stress and NPY treatment were observed for the mRNA abundance of agouti-related peptide (AgRP) and synaptotagmin 1 (SYT1). Intracerebroventricular injection of NPY decreased and increased AgRP and SYT1 mRNA, respectively, in the stressed LWS and increased AgRP mRNA in stressed HWS chicks. Stress was associated with increased NPY, orexin receptor 2, corticotrophin-releasing factor receptor 1, melanocortin receptor 3 (MC3R) and growth hormone secretagogue receptor expression. In conclusion, the loss of responsiveness to exogenous NPY in stressed LWS chicks may be a result of the decreased and increased hypothalamic expression of AgRP and MC3R, respectively. This may induce an intensification of anorexigenic melanocortin signalling pathways in LWS chicks that block the orexigenic effect of exogenous NPY. These results provide insights onto the anorexic condition across species, and especially for forms of inducible anorexia such as human anorexia nervosa.

Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment

Background

Artificial selection provides a powerful approach to study the genetics of adaptation. Using selective-sweep mapping, it is possible to identify genomic regions where allele-frequencies have diverged during selection. To avoid false positive signatures of selection, it is necessary to show that a sweep affects a selected trait before it can be considered adaptive. Here, we confirm candidate, genome-wide distributed selective sweeps originating from the standing genetic variation in a long-term selection experiment on high and low body weight of chickens.

Results

Using an intercross between the two divergent chicken lines, 16 adaptive selective sweeps were confirmed based on their association with the body weight at 56 days of age. Although individual additive effects were small, the fixation for alternative alleles across the loci contributed at least 40 % of the phenotypic difference for the selected trait between these lines. The sweeps contributed about half of the additive genetic variance present within and between the lines after 40 generations of selection, corresponding to a considerable portion of the additive genetic variance of the base population.

Conclusions

Long-term, single-trait, bi-directional selection in the Virginia chicken lines has resulted in a gradual response to selection for extreme phenotypes without a drastic reduction in the genetic variation. We find that fixation of several standing genetic variants across a highly polygenic genetic architecture made a considerable contribution to long-term selection response. This provides new fundamental insights into the dynamics of standing genetic variation during long-term selection and adaptation.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0785-z) contains supplementary material, which is available to authorized users.

Hypothalamic differences in expression of genes involved in monoamine synthesis and signaling pathways after insulin injection in chickens from lines selected for high and low body weight

Long-term selection for juvenile body weight from a common founder population resulted in two divergent chicken lines (low-weight selected line (LWS), high-weight selected line (HWS)) that display distinct food intake and blood glucose responses to exogenous neuropeptides and insulin. The objective of this study was to elucidate putative targets affecting food intake and energy homeostasis by sequencing hypothalamic RNA from LWS and HWS chickens after insulin injection. Ninety-day-old female LWS and HWS chickens were injected with either vehicle or insulin and hypothalamus collected at 1 h postinjection. Through RNA sequencing, a total of 361 differentially expressed genes (DEGs) were identified. There was greater expression of genes, mainly tyrosine hydroxylase (TH), L-aromatic amino acid decarboxylase (DDC), and vesicular monoamine transporter (VMAT), involved in serotonin and dopamine biosynthesis and signaling in LWS than in HWS vehicle-injected chickens. In contrast, after insulin injection, these genes were more highly expressed in HWS than in LWS. We identified 90 single nucleotide polymorphisms (SNPs) existing only in the HWS and 121 SNPs specific to LWS and 5119 SNPs close to fixation (with absolute frequency difference ≥0.9). Four were located in genes encoding enzymes associated with serotonergic and dopaminergic pathways, such as DDC, TH, and solute carrier family 18, member 2 (VMAT). These data implicate differences in biogenic amines such as serotonin and dopamine in hypothalamic physiology between the chicken lines, and these differences might be associated with polymorphisms during long-term selection. Changes in serotonergic and dopaminergic signaling pathways in response to insulin injection suggest a role in whole-body energy homeostasis.

Estimating directional epistasis

Epistasis, i.e., the fact that gene effects depend on the genetic background, is a direct consequence of the complexity of genetic architectures. Despite this, most of the models used in evolutionary and quantitative genetics pay scant attention to genetic interactions. For instance, the traditional decomposition of genetic effects models epistasis as noise around the evolutionarily-relevant additive effects. Such an approach is only valid if it is assumed that there is no general pattern among interactions—a highly speculative scenario. Systematic interactions generate directional epistasis, which has major evolutionary consequences. In spite of its importance, directional epistasis is rarely measured or reported by quantitative geneticists, not only because its relevance is generally ignored, but also due to the lack of simple, operational, and accessible methods for its estimation. This paper describes conceptual and statistical tools that can be used to estimate directional epistasis from various kinds of data, including QTL mapping results, phenotype measurements in mutants, and artificial selection responses. As an illustration, I measured directional epistasis from a real-life example. I then discuss the interpretation of the estimates, showing how they can be used to draw meaningful biological inferences.

Thirty-four generations of divergent selection for 8-week body weight in chickens

Chickens of the Slovenian commercial Prelux-bro line were divergently selected over 34 generations for high and low BW at 8 wk of age. The aim of the study was to estimate responses to selection with a nonlinear model. Estimates of BW for each generation were provided by the mixed model. For fitting generation means against generation or cumulative selection differential, an exponential model was used. Estimates of realized heritability over generations were derived from regression of the response on cumulative selection differential. After 34 generations, the lines differed by approximately 2,220 g for males and 1,860 g for females. Estimates for a selection limit in the high line were 2,598.4 and 2,144.1 g, for males and females, respectively. A selection limit was not reached in the low line. Half of the selection response was obtained after approximately 6 to 8 generations in the high line and 20 to 28 generations in the low line. Estimated realized heritability decreased over generations. Heritability was larger for females than males and reduction of heritability was more rapid in the high line than in the low line. Genetic SD decreased over generations. Phenotypic SD increased over generations in the high line, but was constant in the low line in the initial 22 generations and decreased thereafter. According to the good fit of the nonlinear model and informative parameter estimates, the results confirmed the usefulness of the nonlinear model for analyzing responses to long-term selection.

Body weight selection affects quantitative genetic correlated responses in gut microbiota

The abundance of gut microbiota can be viewed as a quantitative trait, which is affected by the genetics and environment of the host. To quantify the effects of host genetics, we calculated the heritability of abundance of specific microorganisms and genetic correlations among them in the gut microbiota of two lines of chickens maintained under the same husbandry and dietary regimes. The lines, which originated from a common founder population, had undergone >50 generations of selection for high (HW) or low (LW) 56-day body weight and now differ by more than 10-fold in body weight at selection age. We identified families of Paenibacillaceae, Streptococcaceae, Helicobacteraceae, and Burkholderiaceae that had moderate heritabilities. Although there were no obvious phenotypic correlations among gut microbiota, significant genetic correlations were observed. Moreover, the effects were modified by genetic selection for body weight, which altered the quantitative genetic background of the host. Heritabilities for Bacillaceae, Flavobacteriaceae, Helicobacteraceae, Comamonadaceae, Enterococcaceae, and Streptococcaceae were moderate in LW line and little to zero in the HW line. These results suggest that loci associated with these microbiota families, while exhibiting genetic variation in LW, have been fixed in HW line. Also, long term selection for body weight has altered the genetic correlations among gut microbiota. No microbiota families had significant heritabilities in both the LW and HW lines suggesting that the presence and/or absence of a particular microbiota family either has a strong growth promoting or inhibiting effect, but not both. These results demonstrate that the quantitative genetics of the host have considerable influence on the gut microbiota.

Dynamics of adaptive alleles in divergently selected body weight lines of chickens

By studying genomic changes over time in populations subjected to strong artificial directional selection, we can gain insights to the dynamics of beneficial alleles originating from the founder population or emerging as novel mutations undergoing ongoing selection. The Virginia lines are a chicken resource population generated by long-term bi-directional, single-trait selection for juvenile body weight. We studied genome-wide allele frequency changes from generation 40 to 53 using genome-wide genotypes from directional and relaxed selection lines. Overall, there were small changes in allele frequencies at individual loci over the studied time period; but, on average, the changes were greater in lines with larger phenotypic changes. This is consistent with previous findings that much of the response to selection over the first 40 years of selection was attributable to utilization of standing genetic variation at many loci in the genome, indicating a mostly polygenic architecture for body weight. Over the course of the selection experiment, the largest phenotypic response to selection was observed in the high-weight selected line, and in this line we detected a single locus where the allele frequency changed rapidly during a late stage of the experiment. This locus likely contains a novel, beneficial mutation that appeared between generations 40 and 45 and was driven to fixation in 5 to 10 generations. This result illustrates the dependence of continued long-term selection response on standing genetic variation at many loci as well as strong, novel, beneficial mutations.

Modelling of genetic interactions improves prediction of hybrid patterns--a case study in domestic fowl

A major challenge in complex trait genetics is to unravel how multiple loci and environmental factors together cause phenotypic diversity. Both first (F(1)) and second (F(2)) generation hybrids often display phenotypes that deviate from what is expected under intermediate inheritance. We have here studied two chicken F(2) populations generated by crossing divergent chicken lines to assess how epistatic loci, identified in earlier quantitative trait locus (QTL) studies, contribute to hybrid deviations from the mid-parent phenotype. Empirical evidence suggests that the average phenotypes of the intercross birds tend to be lower than the midpoint between the parental means in both crosses. Our results confirm that epistatic interactions, despite a relatively small contribution to the phenotypic variance, play an important role in the deviation of hybrid phenotypes from the mid-parent values (i.e. multi-locus hybrid genotypes lead to lower rather than higher body weights). To a lesser extent, dominance also appears to contribute to the mid-parent deviation, at least in one of the crosses. This observation coincides with the hypothesis that hybridization tends to break up co-adapted gene complexes, i.e. generate Bateson-Dobzhansky-Muller incompatibilities.

Quantity of glucose transporter and appetite-associated factor mRNA in various tissues after insulin injection in chickens selected for low or high body weight

Chickens from lines selected for low (LWS) or high (HWS) body weight differ by 10-fold in body weight at 56 days old with differences in food intake, glucose regulation, and body composition. To evaluate if there are differences in appetite-regulatory factor and glucose transporter ( GLUT) mRNA that are accentuated by hypoglycemia, blood glucose was measured, and hypothalamus, liver, pectoralis major, and abdominal fat collected at 90 days of age from female HWS and LWS chickens, and reciprocal crosses, HL and LH, at 60 min after intraperitoneal injection of insulin. Neuropeptide Y ( NPY) and receptor ( NPYR) subtypes 1 and 5 mRNA were greater in LWS compared with HWS hypothalamus ( P < 0.05), but greater in HWS than LWS in fat ( P < 0.05). Expression of NPYR2 was greater in LWS than HWS in pectoralis major ( P < 0.05). There was greater expression in HWS than LWS for GLUT1 in hypothalamus and liver ( P < 0.05), GLUT2 in fat and liver ( P < 0.05), and GLUT9 in liver ( P < 0.05). Insulin was associated with reduced blood glucose in all populations ( P < 0.05) and reduced mRNA of insulin receptor ( IR) and GLUT 2 and 3 in liver ( P < 0.05). There was heterosis for mRNA, most notably NPYR1 (−78%) and NPYR5 (−81%) in fat and GLUT2 (−70%) in liver. Results suggest that NPY and GLUTs are associated with differences in energy homeostasis in LWS and HWS. Reduced GLUT and IR mRNA after insulin injection suggest a compensatory mechanism to prevent further hypoglycemia.

Identification of candidate genes and mutations in QTL regions for chicken growth using bioinformatic analysis of NGS and SNP-chip data

Mapping of chromosomal regions harboring genetic polymorphisms that regulate complex traits is usually followed by a search for the causative mutations underlying the observed effects. This is often a challenging task even after fine mapping, as millions of base pairs including many genes will typically need to be investigated. Thus to trace the causative mutation(s) there is a great need for efficient bioinformatic strategies. Here, we searched for genes and mutations regulating growth in the Virginia chicken lines - an experimental population comprising two lines that have been divergently selected for body weight at 56 days for more than 50 generations. Several quantitative trait loci (QTL) have been mapped in an F2 intercross between the lines, and the regions have subsequently been replicated and fine mapped using an Advanced Intercross Line. We have further analyzed the QTL regions where the largest genetic divergence between the High-Weight selected (HWS) and Low-Weight selected (LWS) lines was observed. Such regions, covering about 37% of the actual QTL regions, were identified by comparing the allele frequencies of the HWS and LWS lines using both individual 60K SNP chip genotyping of birds and analysis of read proportions from genome resequencing of DNA pools. Based on a combination of criteria including significance of the QTL, allele frequency difference of identified mutations between the selected lines, gene information on relevance for growth, and the predicted functional effects of identified mutations we propose here a subset of candidate mutations of highest priority for further evaluation in functional studies. The candidate mutations were identified within the GCG, IGFBP2, GRB14, CRIM1, FGF16, VEGFR-2, ALG11, EDN1, SNX6, and BIRC7 genes. We believe that the proposed method of combining different types of genomic information increases the probability that the genes underlying the observed QTL effects are represented among the candidate mutations identified.

Stimulation of food intake after central galanin is associated with arcuate nucleus activation and does not differ between genetically selected low and high body weight lines of chickens

Galanin, a 29 residue peptide found in the hypothalamus, causes orexigenic effects in a variety of species. In the present study, we investigated appetite-associated effects of galanin in chicks from lines which have been selected from a common founder population for either low or high body weight. The low line consists of some anorexic individuals and there are obese individuals in the high line. Central galanin caused increased food intake in both lines with the magnitude of response similar in both lines. We also quantified the number of c-Fos immunoreactive cells in several hypothalamic nuclei that are associated with appetite. Only the arcuate nucleus had an increase in the number of reactive cells, a response that was similar for both lines. From these results we concluded that selection for body weight likely did not affect galanin function on induction of feeding in either lines, and that the effect of galanin is associated with arcuate nucleus activation in chicks.

Expression of carnitine palmitoyl-CoA transferase-1B is influenced by a cis-acting eQTL in two chicken lines selected for high and low body weight

Carnitine palmitoyl-CoA transferase-1B is a mitochondrial enzyme in the fatty acid oxidation pathway. In a previous study, CPT1B was identified as differentially expressed in the hypothalamus of two lines of chickens established by long-term selection for high (HWS) or low (LWS) body weight. Mammals have three paralogs (CPT1a, b and c) while nonmammalian vertebrates only have two (CPT1A, B). CPT1A is expressed in liver and CPT1B in muscle. CPT1c is expressed in hypothalamus, where it regulates feeding and energy expenditure. We identified an intronic length polymorphism, fixed for different alleles in the two populations, and mapped the hitherto missing CPT1B locus in the chicken genome assembly, to the distal tip of chromosome 1p. Based on molecular phylogeny and gene synteny we suggest that chicken CPT1B is pro-orthologous of the mammalian CPT1c. Chicken CPT1B was differentially expressed in both muscle and hypothalamus but in opposite directions: higher levels in hypothalamus but lower levels in muscle in the HWS than in the LWS line. Using an advanced intercross population of the lines, we found CPT1B expression to be influenced by a cis-acting expression quantitative trait locus in muscle. The increased expression in hypothalamus and reduced expression in muscle is consistent with an increased food intake in the HWS line and at the same time reduced fatty acid oxidation in muscle yielding a net accumulation of energy intake and storage. The altered expression of CPT1B in hypothalamus and peripheral tissue is likely to be a mechanism contributing to the remarkable difference between lines.

Quantitative genetic background of the host influences gut microbiomes in chickens

Host genotype and gender are among the factors that influence the composition of gut microbiota. We studied the population structure of gut microbiota in two lines of chickens maintained under the same husbandry and dietary regimes. The lines, which originated from a common founder population, had undergone 54 generations of selection for high (HW) or low (LW) 56-day body weight, and now differ by more than 10-fold in body weight at selection age. Of 190 microbiome species, 68 were affected by genotype (line), gender, and genotype by gender interactions. Fifteen of the 68 species belong to Lactobacillus. Species affected by genotype, gender, and the genotype by gender interaction, were 29, 48, and 12, respectively. Species affected by gender were 30 and 17 in the HW and LW lines, respectively. Thus, under a common diet and husbandry host quantitative genotype and gender influenced gut microbiota composite.