contribution of imPrIntome to PiglET birTh wEight - a targeted integrative -omics strategy – PIPETTE
Do imprinted genes contribute to the variability of birth weight in piglets?
While most genes are expressed from both parental copies (paternal and maternal), a small group of genes (imprinted genes) are expressed from only one of the two copies, either the paternal or the maternal. These imprinted genes are essential for fetal and postnatal development and growth in humans and mice, but what about in pigs, a species in which birth weight is linked to stillbirth problems?
The birth weight of piglets: a challenge for the sustainability of pig farming
In pigs, birth weight is a trait that is (i) of major economic interest, as it significantly determines the animal's growth and therefore has an impact on the farmer's economic results, and (ii) of significant health and societal interest, given its links to the risk of stillbirth and pre-weaning mortality, which are essential criteria for animal welfare. Therefore, deciphering the genetic determinism of birth weight in piglets is a major challenge for the pig industry and contributes to more sustainable production systems. Imprinted genes contribute to the variability of complex traits in mammals given their key roles in fetal and postnatal growth and development functions. However, most of the knowledge on the phenotypic effects of imprinted genes comes from mouse models and human pathologies known as imprinting disorders. Few studies have been conducted to date in livestock species, two mutations in the IGF2 and DLK1 imprinted genes have been associated with hypermuscularity in pigs and sheep, respectively. Genomic imprinting is a particularly interesting example of epigenetic regulation, because in a single cell, one of the two parental alleles is stably repressed by epigenetic modifications, while the other allele is maintained in an active state. This allele-specific regulation depends entirely on whether the allele is inherited from the mother or the father. Since the discovery of genomic imprinting, approximately 200 imprinted genes have been identified in murine and human species. In farm animals, only about 20 have been experimentally validated to date. Thus, farm animals represent models for both enriching fundamental knowledge about the number of imprinted genes in these species and understanding parental effects through the contribution of imprinted genes in genome-phenome links.
To map the imprinted genes and their regulatory regions, two experimental reciprocal crosses between Large White and Meishan animals were produced. In the first experimental design, genomic sequencing data were generated for all individuals (n=15) and transcriptomic sequencing data (muscle and hypothalamus) were generated for 1-day-old piglets (n=9). The sequencing data were generated at the GeT-PlaGe platform (https://get.genotoul.fr/la-plateforme/get-plage/). For the second experimental design, we retrieved data from the ANR COLOCATION project available in public databases. The data were analyzed on the Genotoul-bioinof platform's computing cluster (https://bioinfo.genotoul.fr/) using standard bioinformatics tools, and statistical tests were applied.
To develop high-throughput molecular tools targeting imprinted genes and their regulatory regions, we worked with the biotechnology companies Agilent (https://www.agilent.com) and Twist Biosciences (https://www.twistbioscience.com). These developments are based on the capture of genomic regions of interest, with or without a DNA methylation step to evaluate regulatory regions.
To set up the dedicated experimental system, approximately 500 litters of piglets were produced by maximizing paternal (n=347) and maternal (n=348) genetic diversity. For each litter, we selected three piglets: the lightest, the heaviest, and the one with average weight. Each of these 1,487 piglets was weighed at one day old, and their body length and abdominal circumference were also measured.
To quantify the direct and indirect heritabilities of birth weight, all individuals produced as part of the experimental setup (n=10,000) were analyzed based on their birth weight. Classical quantitative genetic models using the REML procedure of the ASREML software were used to discriminate between the three components.
Finally, to characterize the genetic architecture of birth weight in Large White piglets, high-throughput molecular tools targeting imprinted genes and their regulatory regions were used on blood samples taken from individuals that had been phenotyped as part of the previously established program. Based on these large heterogeneous datasets, linear statistical models of association genetics will be used, as well as more subtle models aimed at evaluating imprinting phenomena and therefore parental effects.
Several notable results have already been obtained and exploited or are in the process of being exploited, with others to come:
- The direct and indirect genetic components of various traits in Large White piglets have been determined. In piglets, the estimated values of direct and maternal heritability were as follows: h²d=0.02 and h²m=0.13 for birth weight, showing that the sow's genome influences the birth weight of the piglet.
- A total of 141 imprinted genes, including 70, 48, and 51 in the hypothalamus, muscle, and placenta, respectively, were identified. Low conservation of the identified genes between tissues and with murine and human species was observed.
- Approximately 50 regions differentially methylated according to parental origin were identified. Among these regions, some colocalize with identified imprinted genes, and importantly, all known imprinting control centers in humans and mice were found.
- A molecular capture tool dedicated to imprinted genes in piglets was developed and then optimized for high-throughput production.
Research onto genomic imprinting mechanisms in farm animals offers multiple prospects. First, the fundamental knowledge acquired through imprinted gene mapping allows for a more detailed analysis of the evolutionary aspects of imprinting in artiodactyls. Second, analyses of the contribution of imprinted genes to birth weight variability can enable these results to be taken into account in selection schemes in order to improve the sustainability of livestock farming. Finally, other traits that are important for animal production (such as maternal behavior or feeding behavior) could also be studied through the prism of imprinted genes, given their major roles in neurodevelopmental functions and behavioral traits. In addition, the data generated as part of this project also provide answers to other scientific questions targeting the phenomenon of allele-specific expression and the RNA editing process.
Birth weight (BW) is a complex trait associated with important economic and welfare issues in pig production. We propose to dissect the molecular architecture of BW by focusing on imprinted genes given their crucial role in pre- and post-natal growth and development.
Genomic imprinting is an attractive mechanism of epigenetic regulation leading to the parental origin-specific expression of genes. The role of genomic imprinting in the variability of complex traits has never been extensively assessed in farm animals although two mutations in imprinted genes associated with agronomic traits have already been identified. To tackle this challenging question, we will (i) design a dedicated experimental protocol harnessing extreme BW phenotypes, (ii) develop -omics molecular tools targeting the whole imprintome and (iii) perform multiple association analyses to integrate genetic, epigenetic and transcriptomic data for a better understanding of the molecular architecture of piglet BW.
This project will have scientific, applied and transversal impacts by highlighting the significant contribution of imprinted genes to the determinism of BW in piglets.
Project coordination
Julie Demars (Génétique Physiologie et Systèmes d'Elevage)
The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.
Partnership
GenPhySE Génétique Physiologie et Systèmes d'Elevage
Help of the ANR 598,236 euros
Beginning and duration of the scientific project:
August 2019
- 48 Months
