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Integrative multi-omics analysis of growth plate regulation underlying body size in miniature pigs

ABSTRACT: Body size represents a complex phenotype driven by genetic variation and epigenetic regulation, with the molecular processes underlying this trait remaining a central challenge to disentangle. To elucidate these fundamental mechanisms, we applied a multi-omics approach to investigate the regulatory architecture of growth in the growth plates of the long bones from pigs, a valuable model species for skeletal development. Taking advantage of divergent selection that separates pig breeds into miniature and larger-sized types, we targeted homozygous genomic regions under this intense selection for height, which harbor functional variants with pronounced effects. We sampled two miniature breeds, namely Aachen Minipig (AM) and Mini-LEWE (ML), as well as two larger pig breeds, Angeln Saddleback (AS) and Mangalitza (MA) and assembled an integrated multi-omics dataset comprising the results of WGS, Hi-C, ATAC-seq and RNA-seq, available at ENA Browser with accession number provided in our manuscript, and LC-MS analyses (data available with this submission). Data analyses led to the identification of 23 homozygous mutant variants in Aachen Minipigs and 13 distinct variants in Mini-LEWE predicted to affect cis-regulatory elements and potentially interact with differentially expressed genes that drive body size in breed-dependent ways. Our results pointed to HPX, an lncRNA (ENSSSCG00000048200) located near SDR16C5 and PLAG1, as well as NET-related pathways, as central players in impaired growth in the growth plates. Furthermore, protein-protein interaction networks highlighted 16 proteins that interacted significantly, of which GC vitamin D binding was identified as a regulatory element acting downstream of the key variants for body size across miniature pig breeds. In summary, our study offers a multi-layered characterization of regulatory mechanisms in the growth plates, using miniature pigs as a model to understand the genetic and epigenetic control of long-bone growth.

INSTRUMENT(S):

ORGANISM(S): Sus Scrofa (pig)

TISSUE(S): Long Bone

SUBMITTER: Karsten Cirksena

LAB HEAD: Gisa Gerold

PROVIDER: PXD069390 | Pride | 2026-06-11

REPOSITORIES: Pride

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			Action	DRS
	240821_AP_2426JM_01_S01.raw	Raw
	240821_AP_2426JM_02_S05.raw	Raw
	240821_AP_2426JM_03_S09.raw	Raw
	240821_AP_2426JM_05_S02.raw	Raw
	240821_AP_2426JM_06_S06.raw	Raw

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Project description:BACKGROUND: Litter size in pigs is a major factor affecting the profitability in the pig industry. The peri-implantation window in pigs is characterized by the coordinated interactions between the maternal uterine endometrium and the rapidly elongating conceptuses and represents a period of time during which a large percentage of the developing conceptuses are lost. However, the gene expression and regulatory networks in the endometrium contributing to the establishment of the maternal: placental interface remain poorly understood. RESULTS: We characterized the endometrial gene expression profile during the peri-implantation stage of development by comparing two breeds that demonstrate very different reproductive efficiencies. We employed the porcine Affymetrix GeneChip® to assay the transcriptomic profiles of genes expressed in the uterine endometrium obtained from Meishan and Yorkshire gilts (n = 4 for each breed) on day 12 of gestation (M12 and Y12, respectively). Total of 17,076 probesets were identified as "present" in at least two arrays. A mixed model-based statistical analysis predicted a total of 2,656 (q < 0.1) transcripts as differentially expressed between Meishan and Yorkshire pigs. Eighteen differentially expressed transcripts of interest were validated by quantitative real-time PCR. Gene ontology (GO) annotation revealed that the known functions of the differentially expressed genes were involved in a series of important biological processes relevant to early pregnancy establishment in the pig. CONCLUSIONS: The results identified endometrial gene expression profiles of two breeds differing in litter size and identified candidate genes that are related to known physiological pathways related to reproductive prolificacy. These findings provide a deeper understanding of molecular pathways differing between two breeds at the critical peri-implantation stage of pregnancy, which can be utilized to better understand the events contributing to pregnancy establishment in the pig. Meishan and Yorkshire breeds endometirum were selected and RNA been extracted and hybridized to the Affymetrix microarray. A number of genes have been shown differently expressed on two breeds.

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Integrative multi-omics analysis of growth plate regulation underlying body size in miniature pigs

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