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Design and development of exome capture sequencing for the domestic pig (Sus scrofa).

ABSTRACT: BACKGROUND:The domestic pig (Sus scrofa) is both an important livestock species and a model for biomedical research. Exome sequencing has accelerated identification of protein-coding variants underlying phenotypic traits in human and mouse. We aimed to develop and validate a similar resource for the pig. RESULTS:We developed probe sets to capture pig exonic sequences based upon the current Ensembl pig gene annotation supplemented with mapped expressed sequence tags (ESTs) and demonstrated proof-of-principle capture and sequencing of the pig exome in 96 pigs, encompassing 24 capture experiments. For most of the samples at least 10x sequence coverage was achieved for more than 90% of the target bases. Bioinformatic analysis of the data revealed over 236,000 high confidence predicted SNPs and over 28,000 predicted indels. CONCLUSIONS:We have achieved coverage statistics similar to those seen with commercially available human and mouse exome kits. Exome capture in pigs provides a tool to identify coding region variation associated with production traits, including loss of function mutations which may explain embryonic and neonatal losses, and to improve genomic assemblies in the vicinity of protein coding genes in the pig.

SUBMITTER: Robert C

PROVIDER: S-EPMC4099480 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature

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Design and development of exome capture sequencing for the domestic pig (Sus scrofa).

Robert Christelle C Fuentes-Utrilla Pablo P Troup Karen K Loecherbach Julia J Turner Frances F Talbot Richard R Archibald Alan L AL Mileham Alan A Deeb Nader N Hume David A DA Watson Mick M

BMC genomics 20140703

<h4>Background</h4>The domestic pig (Sus scrofa) is both an important livestock species and a model for biomedical research. Exome sequencing has accelerated identification of protein-coding variants underlying phenotypic traits in human and mouse. We aimed to develop and validate a similar resource for the pig.<h4>Results</h4>We developed probe sets to capture pig exonic sequences based upon the current Ensembl pig gene annotation supplemented with mapped expressed sequence tags (ESTs) and demo ...[more]

PMID: 24988888

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Project description:IntroductionOver the last 40 years, the domestic pig has emerged as a prominent preclinical model as this species shares similarities with humans with regard to immunity, gastrointestinal physiology, and neurodevelopment. Artificial rearing of pigs provides a number of advantages over conventional rearing (i.e., true maternal care), including careful control of nutrient intake and environment conditions. Yet there remains a gap in knowledge when comparing brain development between sow-reared and artificially reared domestic pigs. Thus, our research sought to model brain development and assess recognition memory in a longitudinal manner by directly comparing rearing environments.MethodsForty-four intact (i.e., not castrated) male pigs were artificially reared or sow-reared from postnatal day 2 until postnatal week 4. After postnatal week 4, all pigs were housed in a group setting within the same environment until postnatal week 24. Magnetic resonance imaging was conducted on pigs at 8 longitudinal time-points to model developmental trajectories of brain macrostructural and microstructural outcomes. Additionally, pigs behavior were tested using the novel object recognition task at postnatal weeks 4 and 8.ResultsThroughout the 24-week study, no differences between rearing groups were noted in weekly body weights, average growth and feed intake patterns, or feed efficiency. Whole brain, gray matter, white matter, and cerebrospinal fluid growth patterns also did not differ between pigs assigned to different early-life rearing environments. Moreover, minimal differences in regional absolute volumes and fractional anisotropy developmental trajectories were identified, though artificially reared pigs exhibited higher initial rates of myelination in multiple brain regions compared with sow-reared pigs. Furthermore, behavioral assessment at both PNW 4 and 8 suggested little influence of rearing environment on recognition memory, however, an age-dependent increase in object recognition memory was observed in the sow-reared group.ConclusionOur findings suggest that early-life rearing environment influences the rate of development in some brain regions but has little influence on overall brain growth and object recognition memory and exploratory behaviors in the domestic pig. Artificial rearing may promote maturation in certain brain areas but does not appear to elicit long-term effects in outcomes including brain structure or object recognition memory.

Project description:Introduction and aimAlthough the sense of smell in pigs is widely recognized as being highly developed, surprisingly little is known about their sensory ability. This study aimed to (a) identify which non-social odors pigs were able to detect and distinguish between, (b) investigate the types of behavior expressed when exploring odors and, (c) compare pigs' responses to the different odors to evaluate their interest in the odors.MethodsGrowing pigs (N = 192) of crossbred commercial breeds were enrolled in the experiment (32-110 days of age, weighing 64.9 ± 10.1kg). Littermate pairs of opposite sex were tested in test pens with two odor insertion points in the pen wall, 55 cm apart. All pigs were habituated to the test pens and experimenters. Twelve odors were tested (eight essential oils and four synthetic perfumes) in groups of three odors, with each pig pair tested once with one set of three odors (all possible orders of the three odors were tested on 24 pairs in total), always against a non-odor control (demineralized water). In a test, each of the three odors were presented during three trials in a row (a total of 9 trials per test; trial duration: 1 min; inter-trial breaks: 2 min; total test duration: 25 min). Response variables included: duration of sniffing, feeding-related behavior (licking, biting and rooting), agonistic behavior (biting, displacement and pushing) and no approach of the odor or control, recorded throughout each 1-min odor presentation.ResultsAll pigs sniffed an odor less when repeatedly presented (LMM: all odors P < 0.05), and significantly longer at the subsequent presentation of a new odor [LMM (3rd vs. 1st presentations): P < 0.001]. Specific odor and odor type (essential oil vs. synthetic perfume) had no significant effect on sniffing duration. Overall, feeding-related behavior and agonistic behavior were expressed significantly more when pigs explored the odor compared with the control insertion point (Paired t-tests: P < 0.001), and specific odor only affected the expression of feeding-related behavior.ConclusionCollectively, pigs express sniffing, agonistic, and feeding-related behavior when exploring odors, which suggests that pigs perceive odors of non-social origin as a resource. Odors may thus constitute relevant enrichment material for pigs.

Project description:BackgroundIn recent years, the wildlife/livestock interface has attracted increased attention due to disease transmission between wild and domestic animal populations. The ongoing spread of African swine fever (ASF) in European wild boar (Sus scrofa) emphasize the need for further understanding of the wildlife/livestock interface to prevent disease spill-over between the wild and domestic populations. Although wild boar may also act as a potential source for other infectious disease agents, ASF is currently the most severe threat from wild boar to domestic pigs. To gather information on the wild boar situation at commercial pig producing farms in Sweden, a digital questionnaire survey was distributed through the animal health services.ResultsMost pigs produced for commercial purposes in Sweden are raised without outdoor access. Of the 211 responding pig producers, 80% saw wild boar or signs of wild boar activity in the vicinity of their farm at least once during the year. Observations were significantly correlated with geographical region, but there was no correlation between farm characteristics (farm size, main type of production, outdoor access) and observed wild boar presence or proximity. However, a reported higher frequency of wild boar observations was positively correlated with the observations being made in closer proximity to the farm. Hunting and strategic baiting were the most common mitigation strategies used to keep wild boar at bay. Of the 14 farms raising pigs with outdoor access, 12 responded that these pigs could be raised solely indoors if needed. Pigs with outdoor access are required to be fenced in, but double fencing in these outdoor pig enclosures was not practiced by all. A perimeter fence surrounding any type of pig farm was very rare. More than half of the producers that grew crops with intended use for pigs reported crop damage by wild boar.ConclusionThis study shows that although pigs raised for commercial purposes in Sweden are, to a large extent, kept indoors the potential for indirect contact with wild boar exists and must be considered. Variable local situations regarding wild boar abundance may require an adaptive approach regarding biosecurity efforts.

Dataset Information

Design and development of exome capture sequencing for the domestic pig (Sus scrofa).

Publications

Design and development of exome capture sequencing for the domestic pig (Sus scrofa).

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