Identification of signatures of selection for intramuscular fat and backfat thickness in two Duroc populations

Intramuscular fat (IMF) content is an important trait affecting the quality of pork. Two Duroc populations, one under positive selection for IMF and the other selected for decreased backfat but under stabilizing selection for IMF, were used to identify signatures of selection associated with IMF using 60,000 single-nucleotide polymorphism data. The effects of selection were analyzed between 2 lines or groups representing selected and control animals within each population using a discriminant analysis of principal components and Wright’s fixation index (FST). Moreover, extended haplotype homozygosity-based approaches were used to examine the changes in haplotype frequency due to recent selection. Each statistical method identified 10–20 selection signatures. A few haplotype-based signatures of selection agreed with results from a genome-wide association study (GWAS), while FST measures showed a better agreement with GWAS results. Agreement of marker-trait associations and signatures of selection was limited, and further examination will be necessary to understand the effect of selection on IMF and why some regions identified by GWAS did not appear to respond to the selection practiced. The genes in 21 consensus selection signatures were examined. Several genes with an effect on overall fatness were identified, but further research is needed to assess whether or not some of them could have a specific effect on IMF.

Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array

Background

Indigenous populations of animals have developed unique adaptations to their local environments, which may include factors such as response to thermal stress, drought, pathogens and suboptimal nutrition. The survival and subsequent evolution within these local environments can be the result of both natural and artificial selection driving the acquisition of favorable traits, which over time leave genomic signatures in a population. This study’s goals are to characterize genomic diversity and identify selection signatures in chickens from equatorial Africa to identify genomic regions that may confer adaptive advantages of these ecotypes to their environments.

Results

Indigenous chickens from Uganda (n = 72) and Rwanda (n = 100), plus Kuroilers (n = 24, an Indian breed imported to Africa), were genotyped using the Axiom® 600 k Chicken Genotyping Array. Indigenous ecotypes were defined based upon location of sampling within Africa. The results revealed the presence of admixture among the Ugandan, Rwandan, and Kuroiler populations. Genes within runs of homozygosity consensus regions are linked to gene ontology (GO) terms related to lipid metabolism, immune functions and stress-mediated responses (FDR < 0.15). The genes within regions of signatures of selection are enriched for GO terms related to health and oxidative stress processes. Key genes in these regions had anti-oxidant, apoptosis, and inflammation functions.

Conclusions

The study suggests that these populations have alleles under selective pressure from their environment, which may aid in adaptation to harsh environments. The correspondence in gene ontology terms connected to stress-mediated processes across the populations could be related to the similarity of environments or an artifact of the detected admixture.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2711-5) contains supplementary material, which is available to authorized users.

Quantitative trait loci identified for blood chemistry components of an advanced intercross line of chickens under heat stress

BACKGROUND

Heat stress in poultry results in considerable economic losses and is a concern for both animal health and welfare. Physiological changes occur during periods of heat stress, including changes in blood chemistry components. A highly advanced intercross line, created from a broiler (heat susceptible) by Fayoumi (heat resistant) cross, was exposed to daily heat cycles for seven days starting at 22 days of age. Blood components measured pre-heat treatment and on the seventh day of heat treatment included pH, pCO2, pO2, base excess, HCO3, TCO2, K, Na, ionized Ca, hematocrit, hemoglobin, sO2, and glucose. A genome-wide association study (GWAS) for these traits and their calculated changes was conducted to identify quantitative trait loci (QTL) using a 600 K SNP panel.

RESULTS

There were significant increases in pH, base excess, HCO3, TCO2, ionized Ca, hematocrit, hemoglobin, and sO2, and significant decreases in pCO2 and glucose after 7 days of heat treatment. Heritabilities ranged from 0.01-0.21 for pre-heat measurements, 0.01-0.23 for measurements taken during heat, and 0.00-0.10 for the calculated change due to heat treatment. All blood components were highly correlated within measurement days, but not correlated between measurement days. The GWAS revealed 61 QTL for all traits, located on GGA (Gallus gallus chromosome) 1, 3, 6, 9, 10, 12-14, 17, 18, 21-28, and Z. A functional analysis of the genes in these QTL regions identified the Angiopoietin pathway as significant. The QTL that co-localized for three or more traits were on GGA10, 22, 26, 28, and Z and revealed candidate genes for birds' response to heat stress.

CONCLUSIONS

The results of this study contribute to our knowledge of levels and heritabilities of several blood components of chickens under thermoneutral and heat stress conditions. Most components responded to heat treatment. Mapped QTL may serve as markers for genomic selection to enhance heat tolerance in poultry. The Angiopoietin pathway is likely involved in the response to heat stress in chickens. Several candidate genes were identified, giving additional insight into potential mechanisms of physiologic response to high ambient temperatures.

Evaluation of growth, deposition of back fat, and loin muscle for purebred Berkshire pigs housed in bedded hoop buildings

This study was conducted to evaluate the accretion of BW, back fat, and loin muscle from purebred Berkshire pigs raised in bedded hoop barns in Iowa. The growth of a total of 144 purebred Berkshire pigs (18 barrows and 18 gilts per trial) was evaluated from 4 trials (2 winter and 2 summer trials). Pigs were fed ad libitum utilizing a 5-phase standard corn-soybean meal feeding program that met or exceeded NRC nutrient requirements. Pigs were housed in bedded hoop barns (unheated) to approximate common niche market requirements. At 21-d intervals, pigs were serially weighed, and ultrasonic back fat depth and loin muscle area (LMA) measurements were taken. Live BW measurements began at the trial initiation at approximately 18 to 32 kg, but ultrasonic scans for 10th-rib back fat depth and LMA began at between 36 and 45 kg until market weight of about 122 ± 2.5 kg. The rate (µ) of live body growth (weight) and ultrasonic back fat depth were influenced ( < 0.01) by trial and sex, with no significant interactions between trial and sex. Both live BW and back fat deposition were significantly greater in trial 1 than all other trials (2, 3, and 4). The rate of accretion and maximum growth of LMA depth were not affected ( > 0.05) by trial and sex. Overall, barrows averaged 31 mm of back fat at 125 kg, whereas gilts had an average of about 23 mm at 121 kg of market weight. Results suggest that because of the sex differences in growth and back fat deposition between Berkshire barrows and gilts, it may be important to formulate their diets differently in commercial pork production systems.

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

Goats and sheep are versatile domesticates that have been integrated into diverse environments and production systems. Natural and artificial selection have shaped the variation in the two species, but natural selection has played the major role among indigenous flocks. To investigate signals of natural selection, we analyzed genotype data generated using the caprine and ovine 50K SNP BeadChips from Barki goats and sheep that are indigenous to a hot arid environment in Egypt's Coastal Zone of the Western Desert. We identify several candidate regions under selection that spanned 119 genes. A majority of the genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. In particular, selection signatures spanning several genes that directly or indirectly influenced traits for adaptation to hot arid environments, such as thermo-tolerance (melanogenesis) (FGF2, GNAI3, PLCB1), body size and development (BMP2, BMP4, GJA3, GJB2), energy and digestive metabolism (MYH, TRHDE, ALDH1A3), and nervous and autoimmune response (GRIA1, IL2, IL7, IL21, IL1R1) were identified. We also identified eight common candidate genes under selection in the two species and a shared selection signature that spanned a conserved syntenic segment to bovine chromosome 12 on caprine and ovine chromosomes 12 and 10, respectively, providing, most likely, the evidence for selection in a common environment in two different but closely related species. Our study highlights the importance of indigenous livestock as model organisms for investigating selection sweeps and genome-wide association mapping.

Identification of quantitative trait loci for body temperature, body weight, breast yield, and digestibility in an advanced intercross line of chickens under heat stress

Background

Losses in poultry production due to heat stress have considerable negative economic consequences. Previous studies in poultry have elucidated a genetic influence on response to heat. Using a unique chicken genetic resource, we identified genomic regions associated with body temperature (BT), body weight (BW), breast yield, and digestibility measured during heat stress. Identifying genes associated with a favorable response during high ambient temperature can facilitate genetic selection of heat-resilient chickens.

Methods

Generations F18 and F19 of a broiler (heat-susceptible) × Fayoumi (heat-resistant) advanced intercross line (AIL) were used to fine-map quantitative trait loci (QTL). Six hundred and thirty-one birds were exposed to daily heat cycles from 22 to 28 days of age, and phenotypes were measured before heat treatment, on the 1st day and after 1 week of heat treatment. BT was measured at these three phases and BW at pre-heat treatment and after 1 week of heat treatment. Breast muscle yield was calculated as the percentage of BW at day 28. Ileal feed digestibility was assayed from digesta collected from the ileum at day 28. Four hundred and sixty-eight AIL were genotyped using the 600 K Affymetrix chicken SNP (single nucleotide polymorphism) array. Trait heritabilities were estimated using an animal model. A genome-wide association study (GWAS) for these traits and changes in BT and BW was conducted using Bayesian analyses. Candidate genes were identified within 200-kb regions around SNPs with significant association signals.

Results

Heritabilities were low to moderate (0.03 to 0.35). We identified QTL for BT on Gallus gallus chromosome (GGA)14, 15, 26, and 27; BW on GGA1 to 8, 10, 14, and 21; dry matter digestibility on GGA19, 20 and 21; and QTL of very large effect for breast muscle yield on GGA1, 15, and 22 with a single 1-Mb window on GGA1 explaining more than 15 % of the genetic variation.

Conclusions

This is the first study to estimate heritabilities and perform GWAS using this AIL for traits measured during heat stress. Significant QTL as well as low to moderate heritabilities were found for each trait, and these QTL may facilitate selection for improved animal performance in hot climatic conditions.

Microbiome analyses of pacific white shrimp (Litopenaeus vannamei) collected from disparate geographical locations

In this study, the tail muscle microbiota of pacific white shrimp (Litopenaeus vannamei) sourced from five countries across Central and South America and Southeast Asia were determined and compared. The genomic DNA was sequenced at around 10 × coverage for each geographical location and was assembled de novo for comparative analysis. The assembled sequences for all the lines were classified based on their similarity to the sequences in the public database. We found that there is high correlation among the microbiota of shrimp from disparate regions, as well as the presence of some DNA from bacteria known to cause food poisoning in humans. Sequencing data has been deposited at NCBI-SRA database and can be found under the BioProject ID PRJNA282154.

The Relationship between Runs of Homozygosity and Inbreeding in Jersey Cattle under Selection

Inbreeding is often an inevitable outcome of strong directional artificial selection but on average it reduces population fitness with increased frequency of recessive deleterious alleles. Runs of homozygosity (ROH) representing genomic autozygosity that occur from mating between selected and genomically related individuals may be able to reveal the regions affecting fitness. To examine the influence of genomic autozygosity on fitness, we used a genome-wide association test to evaluate potential negative correlations between ROH and daughter pregnancy rate (DPR) or somatic cell score (SCS) in US Jersey cattle. In addition, relationships between changes of local ROH and inbreeding coefficients (F) were assessed to locate genomic regions with increased inbreeding. Despite finding some decreases in fertility associated with incremental increases in F, most emerging local ROH were not significantly associated with DPR or SCS. Furthermore, the analyses of ROH could be approximated with the most frequent haplotype(s), including the associations of ROH and F or traits. The analysis of the most frequent haplotype revealed that associations of ROH and fertility could be accounted for by the additive genetic effect on the trait. Thus, we suggest that a change of autozygosity is more likely to demonstrate footprints of selected haplotypes for production rather than highlight the possible increased local autozygosity of a recessive detrimental allele resulting from the mating between closely related animals in Jersey cattle.

Recent artificial selection in U.S. Jersey cattle impacts autozygosity levels of specific genomic regions

BACKGROUND

Genome signatures of artificial selection in U.S. Jersey cattle were identified by examining changes in haplotype homozygosity for a resource population of animals born between 1953 and 2007. Genetic merit of this population changed dramatically during this period for a number of traits, especially milk yield. The intense selection underlying these changes was achieved through extensive use of artificial insemination (AI), which also increased consanguinity of the population to a few superior Jersey bulls. As a result, allele frequencies are shifted for many contemporary animals, and in numerous cases to a homozygous state for specific genomic regions. The goal of this study was to identify those selection signatures that occurred after extensive use of AI since the 1960, using analyses of shared haplotype segments or Runs of Homozygosity. When combined with animal birth year information, signatures of selection associated with economically important traits were identified and compared to results from an extended haplotype homozygosity analysis.

RESULTS

Overall, our results reveal that more recent selection increased autozygosity across the entire genome, but some specific regions increased more than others. A genome-wide scan identified more than 15 regions with a substantial change in autozygosity. Haplotypes found to be associated with increased milk, fat and protein yield in U.S. Jersey cattle also consistently increased in frequency.

CONCLUSIONS

The analyses used in this study was able to detect directional selection over the last few decades when individual production records for Jersey animals were available.

Transcriptome analysis of post-hatch breast muscle in legacy and modern broiler chickens reveals enrichment of several regulators of myogenic growth

Agriculture provides excellent model systems for understanding how selective pressure, as applied by humans, can affect the genomes of plants and animals. One such system is modern poultry breeding in which intensive genetic selection has been applied for meat production in the domesticated chicken. As a result, modern meat-type chickens (broilers) exhibit enhanced growth, especially of the skeletal muscle, relative to their legacy counterparts. Comparative studies of modern and legacy broiler chickens provide an opportunity to identify genes and pathways affected by this human-directed evolution. This study used RNA-seq to compare the transcriptomes of a modern and a legacy broiler line to identify differentially enriched genes in the breast muscle at days 6 and 21 post-hatch. Among the 15,945 genes analyzed, 10,841 were expressed at greater than 0.1 RPKM. At day 6 post-hatch 189 genes, including several regulators of myogenic growth and development, were differentially enriched between the two lines. The transcriptional profiles between lines at day 21 post-hatch identify 193 genes differentially enriched and still include genes associated with myogenic growth. This study identified differentially enriched genes that regulate myogenic growth and differentiation between the modern and legacy broiler lines. Specifically, differences in the ratios of several positive (IGF1, IGF1R, WFIKKN2) and negative (MSTN, ACE) myogenic growth regulators may help explain the differences underlying the enhanced growth characteristics of the modern broilers.

Genomic adaptation of admixed dairy cattle in East Africa

Dairy cattle in East Africa imported from the U.S. and Europe have been adapted to new environments. In small local farms, cattle have generally been maintained by crossbreeding that could increase survivability under a severe environment. Eventually, genomic ancestry of a specific breed will be nearly fixed in genomic regions of local breeds or crossbreds when it is advantageous for survival or production in harsh environments. To examine this situation, 25 Friesians and 162 local cattle produced by crossbreeding of dairy breeds in Kenya were sampled and genotyped using 50K SNPs. Using principal component analysis (PCA), the admixed local cattle were found to consist of several imported breeds, including Guernsey, Norwegian Red, and Holstein. To infer the influence of parental breeds on genomic regions, local ancestry mapping was performed based on the similarity of haplotypes. As a consequence, it appears that no genomic region has been under the complete influence of a specific parental breed. Nonetheless, the ancestry of Holstein-Friesians was substantial in most genomic regions (>80%). Furthermore, we examined the frequency of the most common haplotypes from parental breeds that have changed substantially in Kenyan crossbreds during admixture. The frequency of these haplotypes from parental breeds, which were likely to be selected in temperate regions, has deviated considerably from expected frequency in 11 genomic regions. Additionally, extended haplotype homozygosity (EHH) based methods were applied to identify the regions responding to recent selection in crossbreds, called candidate regions, resulting in seven regions that appeared to be affected by Holstein-Friesians. However, some signatures of selection were less dependent on Holsteins-Friesians, suggesting evidence of adaptation in East Africa. The analysis of local ancestry is a useful approach to understand the detailed genomic structure and may reveal regions of the genome required for specialized adaptation when combined with methods for searching for the recent changes of haplotype frequency in an admixed population.

RNA-seq analysis of broiler liver transcriptome reveals novel responses to high ambient temperature

BACKGROUND

In broilers, high ambient temperature can result in reduced feed consumption, digestive inefficiency, impaired metabolism, and even death. The broiler sector of the U.S. poultry industry incurs approximately $52 million in heat-related losses annually. The objective of this study is to characterize the effects of cyclic high ambient temperature on the transcriptome of a metabolically active organ, the liver. This study provides novel insight into the effects of high ambient temperature on metabolism in broilers, because it is the first reported RNA-seq study to characterize the effect of heat on the transcriptome of a metabolic-related tissue. This information provides a platform for future investigations to further elucidate physiologic responses to high ambient temperature and seek methods to ameliorate the negative impacts of heat.

RESULTS

Transcriptome sequencing of the livers of 8 broiler males using Illumina HiSeq 2000 technology resulted in 138 million, 100-base pair single end reads, yielding a total of 13.8 gigabases of sequence. Forty genes were differentially expressed at a significance level of P-value < 0.05 and a fold-change ≥ 2 in response to a week of cyclic high ambient temperature with 27 down-regulated and 13 up-regulated genes. Two gene networks were created from the function-based Ingenuity Pathway Analysis (IPA) of the differentially expressed genes: "Cell Signaling" and "Endocrine System Development and Function". The gene expression differences in the liver transcriptome of the heat-exposed broilers reflected physiological responses to decrease internal temperature, reduce hyperthermia-induced apoptosis, and promote tissue repair. Additionally, the differential gene expression revealed a physiological response to regulate the perturbed cellular calcium levels that can result from high ambient temperature exposure.

CONCLUSIONS

Exposure to cyclic high ambient temperature results in changes at the metabolic, physiologic, and cellular level that can be characterized through RNA-seq analysis of the liver transcriptome of broilers. The findings highlight specific physiologic mechanisms by which broilers reduce the effects of exposure to high ambient temperature. This information provides a foundation for future investigations into the gene networks involved in the broiler stress response and for development of strategies to ameliorate the negative impacts of heat on animal production and welfare.

Total cost estimation for implementing genome-enabled selection in a multi-level swine production system

BACKGROUND

Determining an animal's genetic merit using genomic information can improve estimated breeding value (EBV) accuracy; however, the magnitude of the accuracy improvement must be large enough to recover the costs associated with implementing genome-enabled selection. One way to reduce costs is to genotype nucleus herd selection candidates using a low-density chip and to use high-density chip genotyping for animals that are used as parents in the nucleus breeding herd. The objective of this study was to develop a tool to estimate the cost structure associated with incorporating genome-enabled selection into multi-level commercial breeding programs.

RESULTS

For the purpose of this deterministic study, it was assumed that a commercial pig is created from a terminal line sire and a dam that is a cross between two maternal lines. It was also assumed that all male and female selection candidates from the 1000 sow maternal line nucleus herds were genotyped at low density and all animals used for breeding at high density. With the assumptions used in this analysis, it was estimated that genome-enabled selection costs for a maternal line would be approximately US$0.082 per weaned pig in the commercial production system. A total of US$0.164 per weaned pig is needed to incorporate genome-enabled selection into the two maternal lines. Similarly, for a 600 sow terminal line nucleus herd and genotyping only male selection candidates with the low-density panel, the cost per weaned pig in the commercial herd was estimated to be US$0.044. This means that US$0.21 per weaned pig produced at the commercial level and sired by boars obtained from the nucleus herd breeding program needs to be added to the genetic merit value in order to break even on the additional cost required when genome-enabled selection is used in both maternal lines and the terminal line.

CONCLUSIONS

By modifying the input values, such as herd size and genotyping strategy, a flexible spreadsheet tool developed from this work can be used to estimate the additional costs associated with genome-enabled selection. This tool will aid breeders in estimating the economic viability of incorporating genome-enabled selection into their specific breeding program.

Genome-wide scans to detect positive selection in Large White and Tongcheng pigs

Due to the direction, intensity, duration and consistency of genetic selection, especially recent artificial selection, the production performance of domestic pigs has been greatly changed. Therefore, we reasoned that there must be footprints or selection signatures that had been left during domestication. In this study, with porcine 60K BeadChip genotyping data from both commercial Large White and local Chinese Tongcheng pigs, we calculated the extended haplotype homozygosity values of the two breeds using the long-range haplotype method to detect selection signatures. We found 34 candidate regions, including 61 known genes, from Large White pigs and 25 regions comprising 57 known genes from Tongcheng pigs. Many selection signatures were found on SSC1, SSC4, SSC7 and SSC14 regions in both populations. According to quantitative trait loci and network pathway analyses, most of the regions and genes were linked to growth, reproduction and immune responses. In addition, the average genetic differentiation coefficient FST was 0.254, which means that there had already been a significant differentiation between the breeds. The findings from this study can contribute to further research on molecular mechanisms of pig evolution and domestication and also provide valuable references for improvement of their breeding and cultivation.

Identification of species-specific novel transcripts in pig reproductive tissues using RNA-seq

Although structural properties of the porcine reproductive system are shared by many placental mammals, some combination of these properties is unique to pigs. To explore whether genomic elements specific to pigs could potentially underlie this uniqueness, we made the first step to identify novel transcripts in two representative pig reproductive tissues by the technique of massively parallel sequencing. To automate the whole process, we built a computational pipeline, which can also be easily extended for similar studies in other species. In total, 5516 and 9061 novel transcripts were found, and 159 and 252 novel transcripts appear to be specific to pigs for the placenta and testis respectively. Furthermore, these novel transcripts were found to be enriched in quantitative trait loci (QTL) regions for reproduction traits in pigs. We validated eight of these novel transcripts by quantitative real-time PCR. With respect to their genomic organization and their functional relationship to reproduction, these transcripts need to be further validated and explored in various pig breeds to better comprehend the relevant aspects of pig physiology that contribute to reproductive performance.

Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig

BACKGROUND

Residual feed intake (RFI), a measure of feed efficiency, is the difference between observed feed intake and the expected feed requirement predicted from growth and maintenance. Pigs with low RFI have reduced feed costs without compromising their growth. Identification of genes or genetic markers associated with RFI will be useful for marker-assisted selection at an early age of animals with improved feed efficiency.

METHODOLOGY/PRINCIPAL FINDINGS

Whole genome association studies (WGAS) for RFI, average daily feed intake (ADFI), average daily gain (ADG), back fat (BF) and loin muscle area (LMA) were performed on 1,400 pigs from the divergently selected ISU-RFI lines, using the Illumina PorcineSNP60 BeadChip. Various statistical methods were applied to find SNPs and genomic regions associated with the traits, including a Bayesian approach using GenSel software, and frequentist approaches such as allele frequency differences between lines, single SNP and haplotype analyses using PLINK software. Single SNP and haplotype analyses showed no significant associations (except for LMA) after genomic control and FDR. Bayesian analyses found at least 2 associations for each trait at a false positive probability of 0.5. At generation 8, the RFI selection lines mainly differed in allele frequencies for SNPs near (<0.05 Mb) genes that regulate insulin release and leptin functions. The Bayesian approach identified associations of genomic regions containing insulin release genes (e.g., GLP1R, CDKAL, SGMS1) with RFI and ADFI, of regions with energy homeostasis (e.g., MC4R, PGM1, GPR81) and muscle growth related genes (e.g., TGFB1) with ADG, and of fat metabolism genes (e.g., ACOXL, AEBP1) with BF. Specifically, a very highly significantly associated QTL for LMA on SSC7 with skeletal myogenesis genes (e.g., KLHL31) was identified for subsequent fine mapping.

CONCLUSIONS/SIGNIFICANCE

Important genomic regions associated with RFI related traits were identified for future validation studies prior to their incorporation in marker-assisted selection programs.

Genome-wide prediction of age at puberty and reproductive longevity in sows

Traditional selection for sow reproductive longevity is ineffective due to low heritability and late expression of the trait. Incorporation of DNA markers into selection programs is potentially a more practical approach for improving sow lifetime productivity. Using a resource population of crossbred gilts, we explored pleiotropic sources of variation that influence age at puberty and reproductive longevity. Of the traits recorded before breeding, only age at puberty significantly affected the probability that females would produce a first parity litter. The genetic variance explained by 1-Mb windows of the sow genome, compared across traits, uncovered regions that influence both age at puberty and lifetime number of parities. Allelic variants of SNPs located on SSC5 (27-28 Mb), SSC8 (36-37 Mb) and SSC12 (1.2-2 Mb) exhibited additive effects and were associated with both early expression of puberty and a greater than average number of lifetime parities. Combined analysis of these SNPs showed that an increase in the number of favorable alleles had positive impact on reproductive longevity, increasing number of parities by up to 1.36. The region located on SSC5 harbors non-synonymous alleles in the arginine vasopressin receptor 1A (AVPR1A) gene, a G-protein-coupled receptor associated with social and reproductive behaviors in voles and humans and a candidate for the observed effects. This region is characterized by high levels of linkage disequilibrium in different lines and could be exploited in marker-assisted selection programs across populations to increase sow reproductive longevity.

Novel microRNA families expanded in the human genome

Background

Most studies on the origin and evolution of microRNA in the human genome have been focused on its relationship with repetitive elements and segmental duplications. However, duplication events at a smaller scale (<1 kb) could also contribute to microRNA expansion, as demonstrated in this study.

Results

Using comparative genome analysis and bioinformatics methods, we found nine novel expanded microRNA families enriched in short duplicated sequences in the human genome. Furthermore, novel genomic regions were found to contain microRNA paralogs for microRNA families previously analyzed to be related to segmental duplications. We found that for microRNA families expanded in the human genome, 14 families are specific to the primate lineage, and nine are non-specific, respectively. Two microRNA families (hsa-mir-1233 and hsa-mir-622) appear to be further expanded in the human genome, and were confirmed by fluorescence in situ hybridization. These novel microRNA families expanded in the human genome were mostly embedded in or close to proteins with conserved functions. Furthermore, besides the Alu element, L1 elements could also contribute to the origination of microRNA paralog families.

Conclusions

Together, we found that small duplication events could also contribute to microRNA expansion, which could provide us novel insights on the evolution of human genome structure and function.

Small RNA profile of the cumulus-oocyte complex and early embryos in the pig

Small RNA represent several unique noncoding RNA classes that have important function in the development of germ cells and early embryonic development. Deep sequencing was performed on small RNA from cumulus cells (recovered from germinal vesicle [GV] and metaphase II-arrested [MII] oocytes), GV and MII oocytes, in vitro fertilization-derived embryos at 60 h postfertilization (4- to 8-cell stage), and Day 6 blastocysts. Additionally, a heterologous miRNA microarray method was also used to identify miRNA expressed in the oocyte during in vitro maturation. Similar to the results of expression analysis of other species, these data demonstrate dynamic expression regulation of multiple classes of noncoding RNA during oocyte maturation and development to the blastocyst stage. Mapping small RNA to the pig genome indicates dynamic distribution of small RNA organization across the genome. Additionally, a cluster of miRNA and Piwi-interacting RNA (piRNA) was discovered on chromosome 6. Many of the small RNA mapped to annotated repetitive elements in the pig genome, of which the SINE/tRNA-Glu and LINE/L1 elements represented a large proportion. Two piRNA (piR84651 and piR16993) and seven miRNA (MIR574, MIR24, LET7E, MIR23B, MIR30D, MIR320, and MIR30C) were further characterized using quantitative RT-PCR. Secretory carrier membrane protein 4 (SCAMP4) was predicted to be subject to posttranscriptional gene regulation mediated by small RNA, by annotating small RNA reads mapped to exonic regions in the pig genome. Consistent with the prediction results, SCAMP4 was further confirmed to be differentially expressed at both transcriptional and translational levels. These data establish a small RNA expression profile of the pig cumulus-oocyte complex and early embryos and demonstrate their potential capacity to be utilized for predictions of functional posttranscriptional regulatory events.

Analyses of pig genomes provide insight into porcine demography and evolution

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

A missense mutation in AGTPBP1 was identified in sheep with a lower motor neuron disease

A type of lower motor neuron (LMN) disease inherited as autosomal recessive in Romney sheep was characterized with normal appearance at birth, but with progressive weakness and tetraparesis after the first week of life. Here, we carried out genome-wide homozygosity mapping using Illumina Ovine SNP50 BeadChips on lambs descended from one carrier ram, including 19 sheep diagnosed as affected and 11 of their parents that were therefore known carriers. A homozygous region of 136 consecutive single-nucleotide polymorphism (SNP) loci on chromosome 2 was common to all affected sheep and it was the basis for searching for the positional candidate genes. Other homozygous regions shared by all affected sheep spanned eight or fewer SNP loci. The 136-SNP region contained the sheep ATP/GTP-binding protein 1 (AGTPBP1) gene. Mutations in this gene have been shown to be related to Purkinje cell degeneration (pcd) phenotypes including ataxia in mice. One missense mutation c.2909G>C on exon 21 of AGTPBP1 was discovered, which induces an Arg to Pro substitution (p.Arg970Pro) at amino-acid 970, a conserved residue for the catalytic activity of AGTPBP1. Genotyping of this mutation showed 100% concordant rate with the recessive pattern of inheritance in affected, carrier, phenotypically normal and unrelated normal individuals. This is the first report showing a mutant AGTPBP1 is associated with a LMN disease in a large mammal animal model. Our finding raises the possibility of human patients with the same etiology caused by this gene or other genes in the same pathway of neuronal development.

Use of Genome Sequence Information for Meat Quality Trait QTL Mining for Causal Genes and Mutations on Pig Chromosome 17

The newly available pig genome sequence has provided new information to fine map quantitative trait loci (QTL) in order to eventually identify causal variants. With targeted genomic sequencing efforts, we were able to obtain high quality BAC sequences that cover a region on pig chromosome 17 where a number of meat quality QTL have been previously discovered. Sequences from 70 BAC clones were assembled to form an 8-Mbp contig. Subsequently, we successfully mapped five previously identified QTL, three for meat color and two for lactate related traits, to the contig. With an additional 25 genetic markers that were identified by sequence comparison, we were able to carry out further linkage disequilibrium analysis to narrow down the genomic locations of these QTL, which allowed identification of the chromosomal regions that likely contain the causative variants. This research has provided one practical approach to combine genetic and molecular information for QTL mining.

Advances in pig genomics and functional gene discovery

Advances in pig gene identification, mapping and functional analysis have continued to make rapid progress. The porcine genetic linkage map now has nearly 3000 loci, including several hundred genes, and is likely to expand considerably in the next few years, with many more genes and amplified fragment length polymorphism (AFLP) markers being added to the map. The physical genetic map is also growing rapidly and has over 3000 genes and markers. Several recent quantitative trait loci (QTL) scans and candidate gene analyses have identified important chromosomal regions and individual genes associated with traits of economic interest. The commercial pig industry is actively using this information and traditional performance information to improve pig production by marker-assisted selection (MAS). Research to study the co-expression of thousands of genes is now advancing and methods to combine these approaches to aid in gene discovery are under way. The pig's role in xenotransplantation and biomedical research makes the study of its genome important for the study of human disease. This review will briefly describe advances made, directions for future research and the implications for both the pig industry and human health.

A novel nonsense mutation in the DMP1 gene identified by a genome-wide association study is responsible for inherited rickets in Corriedale sheep

Inherited rickets of Corriedale sheep is characterized by decreased growth rate, thoracic lordosis and angular limb deformities. Previous outcross and backcross studies implicate inheritance as a simple autosomal recessive disorder. A genome wide association study was conducted using the Illumina OvineSNP50 BeadChip on 20 related sheep comprising 17 affected and 3 carriers. A homozygous region of 125 consecutive single-nucleotide polymorphism (SNP) loci was identified in all affected sheep, covering a region of 6 Mb on ovine chromosome 6. Among 35 candidate genes in this region, the dentin matrix protein 1 gene (DMP1) was sequenced to reveal a nonsense mutation 250C/T on exon 6. This mutation introduced a stop codon (R145X) and could truncate C-terminal amino acids. Genotyping by PCR-RFLP for this mutation showed all 17 affected sheep were "T T" genotypes; the 3 carriers were "C T"; 24 phenotypically normal related sheep were either "C T" or "C C"; and 46 unrelated normal control sheep from other breeds were all "C C". The other SNPs in DMP1 were not concordant with the disease and can all be ruled out as candidates. Previous research has shown that mutations in the DMP1 gene are responsible for autosomal recessive hypophosphatemic rickets in humans. Dmp1_knockout mice exhibit rickets phenotypes. We believe the R145X mutation to be responsible for the inherited rickets found in Corriedale sheep. A simple diagnostic test can be designed to identify carriers with the defective "T" allele. Affected sheep could be used as animal models for this form of human rickets, and for further investigation of the role of DMP1 in phosphate homeostasis.

Probing genetic control of swine responses to PRRSV infection: current progress of the PRRS host genetics consortium

Background

Understanding the role of host genetics in resistance to porcine reproductive and respiratory syndrome virus (PRRSV) infection, and the effects of PRRS on pig health and related growth, are goals of the PRRS Host Genetics Consortium (PHGC).

Methods

The project uses a nursery pig model to assess pig resistance/susceptibility to primary PRRSV infection. To date, 6 groups of 200 crossbred pigs from high health farms were donated by commercial sources. After acclimation, the pigs were infected with PRRSV in a biosecure facility and followed for 42 days post infection (dpi). Blood samples were collected at 0, 4, 7, 10, 14, 21, 28, 35 and 42 dpi for serum and whole blood RNA gene expression analyses; weekly weights were recorded for growth traits. All data have been entered into the PHGC relational database. Genomic DNAs from all PHGC1-6 pigs were prepared and genotyped with the Porcine SNP60 SNPchip.

Results

Results have affirmed that all challenged pigs become PRRSV infected with peak viremia being observed between 4-21 dpi. Multivariate statistical analyses of viral load and weight data have identified PHGC pigs in different virus/weight categories. Sera are now being compared for factors involved in recovery from infection, including speed of response and levels of immune cytokines. Genome-wide association studies (GWAS) are underway to identify genes and chromosomal locations that identify PRRS resistant/susceptible pigs and pigs able to maintain growth while infected with PRRSV.

Conclusions

Overall, the PHGC project will enable researchers to discover and verify important genotypes and phenotypes that predict resistance/susceptibility to PRRSV infection. The availability of PHGC samples provides a unique opportunity to continue to develop deeper phenotypes on every PRRSV infected pig.

A whole-genome association study for pig reproductive traits

A whole-genome association study was performed for reproductive traits in commercial sows using the PorcineSNP60 BeadChip and Bayesian statistical methods. The traits included total number born (TNB), number born alive (NBA), number of stillborn (SB), number of mummified foetuses at birth (MUM) and gestation length (GL) in each of the first three parities. We report the associations of informative QTL and the genes within the QTL for each reproductive trait in different parities. These results provide evidence of gene effects having temporal impacts on reproductive traits in different parities. Many QTL identified in this study are new for pig reproductive traits. Around 48% of total genes located in the identified QTL regions were predicted to be involved in placental functions. The genomic regions containing genes important for foetal developmental (e.g. MEF2C) and uterine functions (e.g. PLSCR4) were associated with TNB and NBA in the first two parities. Similarly, QTL in other foetal developmental (e.g. HNRNPD and AHR) and placental (e.g. RELL1 and CD96) genes were associated with SB and MUM in different parities. The QTL with genes related to utero-placental blood flow (e.g. VEGFA) and hematopoiesis (e.g. MAFB) were associated with GL differences among sows in this population. Pathway analyses using genes within QTL identified some modest underlying biological pathways, which are interesting candidates (e.g. the nucleotide metabolism pathway for SB) for pig reproductive traits in different parities. Further validation studies on large populations are warranted to improve our understanding of the complex genetic architecture for pig reproductive traits.

Genome-wide association study identifies Loci for body composition and structural soundness traits in pigs

BACKGROUND

The recent completion of the swine genome sequencing project and development of a high density porcine SNP array has made genome-wide association (GWA) studies feasible in pigs.

METHODOLOGY/PRINCIPAL FINDINGS

Using Illumina's PorcineSNP60 BeadChip, we performed a pilot GWA study in 820 commercial female pigs phenotyped for backfat, loin muscle area, body conformation in addition to feet and leg (FL) structural soundness traits. A total of 51,385 SNPs were jointly fitted using Bayesian techniques as random effects in a mixture model that assumed a known large proportion (99.5%) of SNPs had zero effect. SNP annotations were implemented through the Sus scrofa Build 9 available from pig Ensembl. We discovered a number of candidate chromosomal regions, and some of them corresponded to QTL regions previously reported. We not only have identified some well-known candidate genes for the traits of interest, such as MC4R (for backfat) and IGF2 (for loin muscle area), but also obtained novel promising genes, including CHCHD3 (for backfat), BMP2 (for loin muscle area, body size and several FL structure traits), and some HOXA family genes (for overall leg action). The candidate regions responsible for body conformation and FL structure soundness did not overlap greatly which implied that these traits were controlled by different genes. Functional clustering analyses classified the genes into categories related to bone and cartilage development, muscle growth and development or the insulin pathway suggesting the traits are regulated by common pathways or gene networks that exert roles at different spatial and temporal stages.

CONCLUSIONS/SIGNIFICANCE

This study is one of the earliest GWA reports on important quantitative traits in pigs, and the findings will contribute to the further biological function analysis of the identified candidate genes and potential utilization of them in marker assisted selection.

The pig genome project has plenty to squeal about

Significant progress on pig genetics and genomics research has been witnessed in recent years due to the integration of advanced molecular biology techniques, bioinformatics and computational biology, and the collaborative efforts of researchers in the swine genomics community. Progress on expanding the linkage map has slowed down, but the efforts have created a higher-resolution physical map integrating the clone map and BAC end sequence. The number of QTL mapped is still growing and most of the updated QTL mapping results are available through PigQTLdb. Additionally, expression studies using high-throughput microarrays and other gene expression techniques have made significant advancements. The number of identified non-coding RNAs is rapidly increasing and their exact regulatory functions are being explored. A publishable draft (build 10) of the swine genome sequence was available for the pig genomics community by the end of December 2010. Build 9 of the porcine genome is currently available with Ensembl annotation; manual annotation is ongoing. These drafts provide useful tools for such endeavors as comparative genomics and SNP scans for fine QTL mapping. A recent community-wide effort to create a 60K porcine SNP chip has greatly facilitated whole-genome association analyses, haplotype block construction and linkage disequilibrium mapping, which can contribute to whole-genome selection. The future 'systems biology' that integrates and optimizes the information from all research levels can enhance the pig community's understanding of the full complexity of the porcine genome. These recent technological advances and where they may lead are reviewed.

Use of SNP genotyping to determine pedigree and breed composition of dairy cattle in Kenya

High levels of inbreeding in East African dairy cattle are a potential concern because of use of a limited range of imported germplasm coupled with strong selection, especially by disease, and sparse performance recording. To address this, genetic relationships and breed composition in an admixed population of Kenyan dairy cattle were estimated by means of a 50K SNP scan. Genomic DNA from 3 worldwide Holstein and 20 Kenyan bulls, 71 putative cow-calf pairs, 25 cows from a large ranch and 5 other Kenyan animals were genotyped for 37 238 informative SNPs. Sires were predicted and 89% of putative dam-calf relationships were supported by genotype data. Animals were clustered with the HapMap population using Structure software to assess breed composition. Cows from a large ranch primarily clustered with Holsteins, while animals from smaller farms were generally crosses between Holstein and Guernsey. Coefficients of relatedness were estimated and showed evidence of heavy use of one AI bull. We conclude that little native germplasm exists within the genotyped populations and mostly European ancestry remains.

Whole-genome association analyses for lifetime reproductive traits in the pig

Profits for commercial pork producers vary in part because of sow productivity or sow productive life (SPL) and replacement costs. During the last decade, culling rates of sows have increased to more than 50% in the United States. Both SPL and culling rates are influenced by genetic and nongenetic factors. A whole-genome association study was conducted for pig lifetime reproductive traits, including lifetime total number born (LTNB), lifetime number born alive (LNBA), removal parity, and the ratio between lifetime nonproductive days and herd life. The proportion of phenotypic variance explained by markers was 0.15 for LTNB and LNBA, 0.12 for removal parity, and 0.06 for the ratio between lifetime nonproductive days and herd life. Several informative QTL regions (e.g., 14 QTL regions for LTNB) and genes within the regions (e.g., SLC22A18 on SSC2 for LTNB) were associated with lifetime reproductive traits in this study. Genes associated with LTNB and LNBA were similar, reflecting the high genetic correlation (0.99 ± 0.003) between these traits. Functional annotation revealed that many genes at the associated regions are expressed in reproductive tissues. For instance, the SLC22A18 gene on SSC2 associated with LTNB has been shown to be expressed in the placenta of mice. Many of the QTL regions showing associations coincided with previously identified QTL for fat deposition. This reinforces the role of fat regulation for lifetime reproductive traits. Overall, this whole-genome association study provides a list of genomic locations and markers associated with pig lifetime reproductive traits that could be considered for SPL in future studies.

Pig genome sequence--analysis and publication strategy

Background

The pig genome is being sequenced and characterised under the auspices of the Swine Genome Sequencing Consortium. The sequencing strategy followed a hybrid approach combining hierarchical shotgun sequencing of BAC clones and whole genome shotgun sequencing.

Results

Assemblies of the BAC clone derived genome sequence have been annotated using the Pre-Ensembl and Ensembl automated pipelines and made accessible through the Pre-Ensembl/Ensembl browsers. The current annotated genome assembly (Sscrofa9) was released with Ensembl 56 in September 2009. A revised assembly (Sscrofa10) is under construction and will incorporate whole genome shotgun sequence (WGS) data providing > 30× genome coverage. The WGS sequence, most of which comprise short Illumina/Solexa reads, were generated from DNA from the same single Duroc sow as the source of the BAC library from which clones were preferentially selected for sequencing. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement the data have been released into public sequence repositories (Genbank/EMBL, NCBI/Ensembl trace repositories) in a timely manner and in advance of publication.

Conclusions

In this marker paper, the Swine Genome Sequencing Consortium (SGSC) sets outs its plans for analysis of the pig genome sequence, for the application and publication of the results.

Mining ESTs to determine the usefulness of SNPs across shrimp species

Expressed sequence tag (EST) libraries from members of the Penaeidae family and brine shrimp (Artemia franciscana) are currently the primary source of sequence data for shrimp species. Penaeid shrimp are the most commonly farmed worldwide, but selection methods for improving shrimp are limited. A better understanding of shrimp genomics is needed for farmers to use genetic markers to select the best breeding animals. The ESTs from Litopenaeus vannamei have been previously mined for single nucleotide polymorphisms (SNPs). This present study took publicly available ESTs from nine shrimp species, excluding L. vannamei, clustered them with CAP3, predicted SNPs within them using SNPidentifier, and then analyzed whether the SNPs were intra- or interspecies. Major goals of the project were to predict SNPs that may distinguish shrimp species, locate SNPs that may segregate in multiple species, and determine the genetic similarities between L. vannamei and the other shrimp species based on their EST sequences. Overall, 4,597 SNPs were predicted from 4,600 contigs with 703 of them being interspecies SNPs, 735 of them possibly predicting species' differences, and 18 of them appearing to segregate in multiple species. While sequences appear relatively well conserved, SNPs do not appear to be well conserved across shrimp species.

Investigation of LDHA and COPB1 as candidate genes for muscle development in the MYOD1 region of pig chromosome 2

Porcine MYOD1 gene has been mapped to swine chromosome (SSC) 2p14-p17, which is involved in the regulation of the proliferation and differentiation of skeletal muscle cells. The LDHA (lactate dehydrogenase A) and COPB1 (coatomer protein complex, subunit beta 1) genes, which map close to MYOD1, are involved in energy metabolism and protein transport processes. Both genes might play important roles in muscle development. However, little is known about the porcine LDHA and COPB1 genes. In the present study, the full-length cDNA of these two genes were cloned. The mapping results demonstrated that porcine LDHA and COPB1 were all mapped to SSC 2p14-p17. In this region, there are several QTL for growth and carcass traits, including average backfat thickness, lean and fat percentage. The RT-PCR results revealed that both LDHA and COPB1 were highly expressed in porcine skeletal muscle tissues, implying their potential regulatory function of muscle development. LDHA and COPB1 were then mapped to the region and multipoint analyses generated a best sex-averaged map order of each gene between linked markers: MYOD1_75.2 cM _LDHA_79 cM _CSRP3_83.8 cM _TEF-1_86.5 cM _COPB1_90 cM. Association analyses revealed that the substitution of c.423A>G had a significant effect on average daily gain on test, average backfat thickness (BFT), loin muscle area, lumbar BFT, marbling score, tenth rib BFT, average drip loss and fiber type II ratio. The substitution of c.3096C>T had a significant effect on average BFT, lumbar BFT, tenth rib BFT, carcass weight and last rib BFT. Interestingly, both SNPs were all associated with average BFT, lumbar BFT and tenth rib BFT.

Analysis of the mouse high-growth region in pigs

In the mouse, homozygous animals for the high growth mutation show a 30-50% increase in growth without becoming obese. This region is homologous to the distal part of pig chromosome 5 (SSC5). A previous genome scan detected several quantitative trait loci (QTL) in this region for body composition and meat quality using a three generation Berkshire x Yorkshire resource family. In this study, the effects on swine growth, fat and meat quality traits of three genes previously identified within the mouse high growth region were analysed. The genes studied were CASP2 and RIPKI domain containing adaptor with death domain (CRADD), suppressor of cytokine signalling 2 (SOCS2) and plexinC1 (PLXNC1). In addition, the influence of two other genes located very close to this region, namely the plasma membrane calcium-transporting ATPase 1 (ATP2B1) and dual specificity phosphatase 6 (DUSP6) genes, was also investigated. Single nucleotide polymorphisms were identified and used to map these genes to the QTL region on SSC5. Results indicate significant associations between these genes and several phenotypic traits, including fat deposition and growth in pigs. The present study suggests associations of these genes with swine fat and growth related traits, but further studies are needed in order to clearly identify the genes involved in the regulation of the QTL located on SSC5.

A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannamei

Pacific white shrimp (Litopenaeus vannamei) are of particular economic importance to the global shrimp aquaculture industry. However, limited genomics information is available for the penaeid species. We utilized the limited public information available, mainly single nucleotide polymorphisms (SNPs) and expressed sequence tags, to discover markers for the construction of the first SNP genetic map for Pacific white shrimp. In total, 1344 putative SNPs were discovered, and out of 825 SNPs genotyped, 418 SNP markers from 347 contigs were mapped onto 45 sex-averaged linkage groups, with approximate coverage of 2071 and 2130 cm for the female and male maps, respectively. The average-squared correlation coefficient (r(2)), a measure of linkage disequilibrium, for markers located more than 50 cm apart on the same linkage group, was 0.15. Levels of r(2) increased with decreasing inter-marker distance from approximately 80 cm, and increased more rapidly from approximately 30 cm. A QTL for shrimp gender was mapped on linkage group 13. Comparative mapping to model organisms, Daphnia pulex and Drosophila melanogaster, revealed extensive rearrangement of genome architecture for L. vannamei, and that L. vannamei was more related to Daphnia pulex. This SNP genetic map lays the foundation for future shrimp genomics studies, especially the identification of genetic markers or regions for economically important traits.

A calcitonin receptor (CALCR) single nucleotide polymorphism is associated with growth performance and bone integrity in response to dietary phosphorus deficiency

Although concerns over the environmental impact of excess P in the excreta from pig production and governmental regulations have driven research toward reducing dietary supplementation of P to swine diets for over a decade, recent dramatic increases in feed costs have further motivated researchers to identify means to further reduce dietary P supplementation. We have demonstrated that genetic background impacts P utilization in young pigs and have identified genetic polymorphisms in several target genes related to mineral utilization. In this study, we examined the impact of a SNP in the calcitonin receptor gene (CALCR) on P utilization in growing pigs. In Exp. 1, 36 gilts representing the 3 genotypes identified by this CALCR SNP (11, 12, and 22) were fed a P-adequate (PA) or a marginally P-deficient (approximately 20% less available P; PD) diet for 14 wk. As expected, P deficiency reduced plasma P concentration, bone strength, and mineral content (P < 0.05). However, the dietary P deficiency was mild enough to not affect the growth performance of these pigs. A genotype x dietary P interaction (P < 0.05) was observed in measures of bone integrity and mineral content, with the greatest reduction in bone strength and mineral content due to dietary P deficiency being associated with the allele 1. In Exp. 2, 168 pigs from a control line and low residual feed intake (RFI) line were genotyped for the CALCR SNP and fed a PA diet. As expected, pigs from the low RFI line consumed less feed but also gained less BW when compared with the control line (P < 0.05). Although ADFI did not differ between genotypes, pigs having the 11 genotype gained less BW (P < 0.05) than pigs having the 12 or 22 genotypes. Pigs of the 11 and 12 genotypes had bones that tolerated greater load when compared with animals having the 22 genotype (P < 0.05). A similar trend was observed in bone modulus and ash % (P < 0.10). These data are supportive of the association of this CALCR SNP with bone integrity and its response to dietary P restriction. Although the allele 1 is associated with greater bone integrity and mineral content during adequate P nutrition, it is also associated with the greatest loss in bone integrity and mineral content in response to dietary P restriction. Understanding the underlying genetic mechanisms that regulate P utilization may lead to novel strategies to produce more environmentally friendly pigs.

Identification of genetic markers associated with residual feed intake and meat quality traits in the pig

Residual feed intake (RFI) has become increasingly important and is being considered as a more reasonable approach to evaluate feed efficiency in livestock. However, the cost and technical difficulties in measuring this trait restrict the extensive adoption of RFI selection, and this makes marker assisted selection (MAS) a feasible tool. In addition, the effects on meat quality caused by low RFI selection have yet to be clarified. In this study, 11 SNPs from eight candidate genes were evaluated in a Yorkshire pig experimental population (n=169) consisting of a low RFI selection line and a randomly selected control line. Associations of these SNPs with RFI, growth rate, carcass composition, and meat quality measures including water holding capacity, pH at 2d postmortem, meat color and sensory traits were analyzed. The SNPs FTO p.Ala198Ala and TCF7L2 c.646+514A>G showed significant (P<0.05) and suggestively significant (P<0.1) associations with RFI, respectively. The MC4R SNP p.Asp298Asn was associated with backfat but it was not with ADG and meat quality attributes. Both SNPs within HNF1A were associated with intramuscular lipid content and sensory juiciness. The SNPs ACC1 c(*)384C>T and TCF7L2 c.646+514A>G were significantly (P<0.05) associated with ADG. The SNPs CTSZ p.Arg64Lys and TCF7L2 c.646+514A>G were associated with both visual scoring of meat color and the objective L-value measure of meat color. This study has identified potential genetic markers suitable for MAS in improving RFI, ADG, and meat color traits, but these associations need to be validated in other larger populations.

Identification of chromosomal regions associated with cranial cruciate ligament rupture in a population of Newfoundlands

OBJECTIVE

To identify chromosomal regions associated with cranial cruciate ligament rupture (CCLR) in a population of Newfoundlands.

ANIMALS

90 client-owned Newfoundlands.

PROCEDURES

A pedigree was constructed for dogs that did or did not have CCLR (determined on the basis of physical examination and radiographic findings). From this pedigree, affected and unaffected dogs were selected for genotyping on the basis of their predicted statistical likelihood of being homozygous CCLR-unaffected (n = 53) or homozygous CCLR-affected (37) dogs. Genotyping was performed for 532 microsatellite markers (MSATs). Comparisons of genotypes and allele frequencies were made between CCLR-affected and CCLR-unaffected dogs.

RESULTS

In the selected population, 495 MSATs were informative with a mean interval between markers of 5.5 centimorgans. Eighty-six MSATs were significantly associated with the CCLR trait, whereas 4 markers (located on 4 chromosomes) were significantly associated with the trait when false discovery rate (q value) was controlled at the 0.05 level. Subsequent initial validation confirmed significant trait association for 3 of the 4 MSATs.

CONCLUSIONS AND CLINICAL RELEVANCE

In the population of Newfoundlands, 4 MSATs that were located on 4 chromosomes were significantly associated with the CCLR trait. Three of those markers were validated in part via genotyping additional closely located markers. The MSATs that were associated with the CCLR trait were identified in all regions (except for those on chromosome 24). Newfoundlands with CCLR could be used to study the disease process associated with anterior cruciate ligament injuries that occur in young female human athletes.

Association of HOXA10, ZFPM2, and MMP2 genes with scrotal hernias evaluated via biological candidate gene analyses in pigs

OBJECTIVE

To evaluate the associations between 14 biological candidate genes and scrotal hernias in pigs.

ANIMALS

1,534 Pietrain-based pigs, including 692 individuals from 298 pig families and 842 male pigs without family information.

PROCEDURES

Pigs were classified as affected or unaffected for scrotal hernias. Single nucleotide polymorphisms of candidate genes were analyzed via PCR assays and genotyped. Statistical analyses were performed on the family-trio and the case-control data.

RESULTS

2 genes involved in collagen metabolism (homeobox A10 [HOXA10] and matrix metalloproteinases 2 [MMP2]) and 1 gene encoding zinc finger protein multitype 2 (ZFPM2, important in the development of diaphragmatic hernia) were significantly associated with hernias. Pigs with these genotypes had high odds of developing scrotal hernias in the case and control groups (2 ZFPM2 variants: odds ratio, 4.3 [95% confidence interval, 2.78 to 6.64] and 4.45[95%confidenceinterval,2.88to6.88]). Anothergene, collagentypeII A 1(COL2A1),was potentially involved in hernia development.

CONCLUSIONS AND CLINICAL RELEVANCE

HOXA10, ZFPM2, MMP2, and COL2A1 could have important roles in pig hernia development and potentially be useful for marker-assisted selection in the pig industry.

IMPACT FOR HUMAN MEDICINE

Pigs are used for the study of many human diseases because of their physiologic similarities. Genes associated with scrotal hernias in this study may be directly used in understanding the molecular mechanisms underlying this defect in humans.

Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology

BACKGROUND

The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay.

METHODOLOGY/PRINCIPAL FINDINGS

A total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina's Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274.

CONCLUSIONS/SIGNIFICANCE

Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs.

Hitting the jackpot twice: identifying and patenting gene tests related to muscle lipid accumulation for meat quality in animals and type 2 diabetes/obesity in humans

Marbling and intramuscular fat (IMF) content are commonly used to describe or measure intramuscular fat deposition in meat, which contributes to taste, texture and flavor. Four types of genetic markers, i.e., microsatellite, random amplification of polymorphic DNA (RAPD), amplified fragment length polymorphisms (AFLP) and single nucleotide polymorphisms (SNPs) have been used in genome scans or association studies to detect quantitative trait loci (QTL) for these traits in cattle and swine. For the most part microsatellite markers help define QTL regions but have been used in limited ways to patent gene tests because of the uncertainties associated with the microsatellite marker scans. However, SNPs in candidate genes selected based on physiological, positional or comparative information often lead to patent applications once strong associations have been determined. To date, at least 22 patents have been awarded or under review for genes/markers affecting marbling or IMF in cattle and swine. Unfortunately, similar muscle lipid accumulation in humans has significant negative impacts on health, causing obesity/type 2 diabetes and their associated conditions. Many studies have also been performed on human subjects or on the mouse as a model organism to understand the genetic complexity of these conditions. A collection of over 2,000 reports on genes/markers affecting fat phenotypes in humans, mice, cattle and swine have led to construction of a mammalian concordant QTL map for lipogenesis. The concordant QTL map provides power for fine mapping and narrowing each of these QTL regions to a few genes.

The fat mass and obesity-associated (FTO) gene is associated with intramuscular fat content and growth rate in the pig

The association of the FTO gene with obesity has been implicated in various human populations. The FTO gene is also most likely involved in the regulation of energy balance and feed intake. Here, the FTO gene was studied as a candidate gene for fatness and growth rate traits in pigs. The amino acid sequence of the FTO gene showed high conservation among human, pig, and other important domestic animals. Twelve variants including ten SNPs and two indels were detected, and then five SNPs within different genomic regions were genotyped in the ISU Berkshire x Yorkshire pig resource family. The linkage disequilibrium analyses revealed that most of these FTO variants were not in strong LD with each other. The SNPs c.46-139A > T within intron 1 and a synonymous mutation c.594C > G (Ala198Ala) within exon 3 had significant (P < 0.01) associations with average daily gain on test and total lipid percentage in muscle, respectively. Five major haplotypes were identified and the subsequent association analyses suggested that haplotype 2 (-CTTGG-) was the most favorable for increased growth rate, while haplotype 1 (-CTACG-) was unfavorably associated with intramuscular fatness traits.

Assessment of the swine protein-annotated oligonucleotide microarray

The specificity and utility of the swine protein-annotated oligonucleotide microarray, or Pigoligoarray (http://www.pigoligoarray.org), has been evaluated by profiling the expression of transcripts from four porcine tissues. Tools for comparative analyses of expression on the Pigoligoarray were developed including HGNC identities and comparative mapping alignments with human orthologs. Hybridization results based on the Pigoligoarray's sets of control, perfect match (PM) and deliberate mismatch (MM) probes provide an important means of assessing non-specific hybridization. Simple descriptive diagnostic analyses of PM/MM probe sets are introduced in this paper as useful tools for detecting non-specific hybridization. Samples of RNA from liver, brain stem, longissimus dorsi muscle and uterine endothelium from four pigs were prepared and hybridized to the arrays. Of the total 20,400 oligonucleotides on the Pigoligoarray, 12,429 transcripts were putatively differentially expressed (DE). Analyses for tissue-specific expression [over-expressed in one tissue with respect to all the remaining three tissues (q < 0.01)] identified 958 DE transcripts in liver, 726 in muscle, 286 in uterine endothelium and 1027 in brain stem. These hybridization results were confirmed by quantitative PCR (QPCR) expression patterns for a subset of genes after affirming that cDNA and amplified antisense RNA (aRNA) exhibited similar QPCR results. Comparison to human ortholog expression confirmed the value of this array for experiments of both agricultural importance and for tests using pigs as a biomedical model for human disease.

Genes located on a SSC17 meat quality QTL region are associated with growth in outbred pig populations

The objective of this study was to evaluate the effect of markers developed in eight genes, located in a previously detected meat quality QTL region on SSC17, on growth, fat and meat quality traits collected in commercial pig populations of different genetic backgrounds. The genes had been previously mapped to SSC17 as part of a fine-mapping effort. Association analyses were conducted between each marker and the available phenotypic traits. Results showed that three genes (CTSZ, CSTF1 and C20orf43) were significantly associated with the growth traits. In addition, CTSZ also impacted on meat colour, with the less favourable genotype for growth being associated with darker meat. The differences observed between genotypes were substantial and may be of economic importance to pig producers. These markers may be useful for selecting for faster growth or improved meat quality.