Integration von Expressions- und genomweiten Assoziations-Analysen in Kreuzungspopulationen kommerzieller Rassen zur Kartierung von QTL Regionen mit verbesserter Auflösung und funktionelle Analyse von Kandidatengenen für Wasserbindungsvermögen
Final Report Abstract
Interactions among genes, transcripts, proteins, metabolites and with environmental factors finally determine the organismal phenotype in its environment. Variability in meat quality traits like water holding capacity (WHC) is a major concern for producers and consumers. The conversion of muscle to meat is important not only as an economic factor in pork production, but also because these events mimic pathological processes associated with muscle injury or damage in humans. Holistic microarray studies (Affymetrix GeneChip porcine Genome Array) revealed biological pathways that were correlated with WHC including extracellular matrix receptor interaction, calcium signalling, oxidative phosphorylation, mitochondrial pathways, actin cytoskeleton signalling, PDGF signalling, EGF signalling, ERK/MAPK signalling, as well as TR/RXR activation. In order to validate and refine these results in terms of knowledge of the genetic foundation of meat quality and also in terms of priorisation of candidate genes, we integrated here phenotypic records related to WHC, genomewide SNP genotypes, and holistic data of mRNA and miRNA abundance obtained of 207 performance-tested pigs from commercial herds of the crossbred Plx(DLxDE). A porcine muscle eQTL map based on microarray expression profiles was established. The integration of eQTL mapping data and information of trait correlated expression led to a list of genes exhibiting cis eQTL and trait dependent expression. Another level of integration of was accomplished by the construction of porcine muscle co-expression transcript networks that correlated to meat quality traits. The coexpression networks were highly enriched for genes involved in glucose metabolism, response to wounding, mitochondrial energy metabolism, and extracellular matrix. For the first time, expression and co-expression of miRNAs - functioning as a fine-tuning of mRNA transcription and translation - was integrated with mRNA transcript abundance measures and phenotypic data to reveal an additional hierarchical level in the molecular regulation of muscle-to-meat conversion. Next, we assessed genome wide association of more than 45,000 SNP (Illumina PorcineSNP60 BeadChip) with meat quality traits. The GWAS revealed numerous trait-associated SNPs, most of which display peaks of closely linked loci at particular genomic regions. In order to promote the identification of candidate genes within these regions, we propose addressing the association of these markers with abundances of transcripts of trait-correlated expressed genes. Following this strategy, ZNF704, PIHIDI, SIGLECIO, TBCB, LOC100518735. KIFIB, and LOC100514845 were identified as candidate genes for meat quality showing trait-correlated expression and transcript abundances associated with markers, which at the same time show significant trait-association. Thus, eQTL analysis and trait-correlated expression data enhanced the nomination of candidate genes flanking traitassociated GWAS-markers. Exemplarily candidate genes encoding proteins of the extracellular matrix and the ubiquitination system were analysed by addressing the triangular relationship of genetic variation, phenotype, and expression which consistently promote the candidacy of these genes. Finally, we establish the relationship between specific miRNAs and mitochondrial genes as well as the cellular ATP levels in C2C12 cell cultures experiments. Thus, the project provides new knowledge of the molecular pathways critical for meat quality and it led to the identification of genes with multiple evidences of their role for meat quality traits.
Publications
- Association of gene expression profiles with growth and carcass traits in Duroc-Pietrain F2 population. In: Internationaler Dummerstorf Workshop 2009 "Prenatal and early postnatal effects on muscle properties and growth" (FBN; Hrsg.): 21
Cinar U, Wimmers K, Ponsuksili S, Tholen E, Looft C, Tesfaye D, Schellander K, Phatsara C
- Expression profiles and eQTL associated with meat quality in pigs. In: International Dummerstorf Workshop 2009 "Prenatal and early postnatal effects on muscle properties and growth" (FBN; Hrsg.): 22
Ponsuksili S, Murani E, Wimmers K
- Expression profiles of M. longissimus with relevance for meat quality traits in pigs. Seminar, Chiang Mai University, 27.7.2009-29.7.2009, Chiang Mai, Thailand
Ponsuksili S
- Functional Genomics and genetical genomics approaches towards elucidating networks of genes affecting water holding capacity of pork. In: Animbiogen Workshop, 22.-23.10.2009 (Institute of Genetics and Animal Breeding of Polish Academy of Science; Hrsg.): 47-57
Wimmers K, Murani E, Ponsuksili S
- Pre- and postnatal differential gene expression with relevance for meat and carcass traits in pigs. In: Animbiogen Workshop, 14.-15. 05.2009 (Institute of Genetics and Animal Breeding of the Polish Academy of Science; Hrsg.): 54-59
Wimmers K, Murani E, Ponsuksili
- Effect of interferon alpha-inducible protein 6 (IFI6) gene on drip loss in pig. Vortragstagung der DGfZ und GfT am 15./16. September 2010 in Kiel, 15.9.2010-16.9.2010, Kiel, Deutschland
Kayan A, Uddin M, Cinar U, Wimmers K, Ponsuksili S, Tesfaye D, Looft C, Jüngst H, Tholen E, Phatsara C, Schellander K
- Identification of porcine candidate genes for water-holding capacity using QTL-region-specific BAC-arrays. In: Proceedings of the 9th World Congress on Genetics Applied to Livestock Production (Gesellschaft für Tierzuchtwissenschaften e.V.; Hrsg.) (978-00-031608) (2010): 455
Wimmers K, Dolle K, Leeb T, Schellander K, Brunner RM, Murani E, Ponsuksili S
- Integrating expression profiling and whole genome association in crossbred populations of commercial breeds for dissection of complex traits in pig. In: Proceedings 32nd Conference of the International Society for Animal Genetics (International Society for Animal Genetics (ISAG); (2010): 1-1
Ponsuksili S, Murani E, Brand B, Schwerin M, Wimmers K
- Integration of expression profiling and genome wide association studies in pigs. Seminar Advances in molecular animal breeding, Hubei Academy of Agricultural Science, 9.8.2010-9.8.2010, Wuhan, China
Ponsuksili S
- Characterization of QTL regions by transcriptome profiling with genome tiling arrays. Vortragstagung der DGfZ/GfT, Uni Halle, 12.9.2012-13.9.2012, Halle, Deutschland
Du Y, Murani E, Ponsuksili S, Wimmers K
- Genes with expression levels correlating to drip loss prove association of their polymorphism with water holding capacity of pork. Mol Biol Rep. 2012, 39:97-107
Brunner RM, Srikanchai T, Murani E, Wimmers K, Ponsuksili S
(See online at https://doi.org/10.1007/s11033-011-0714-5) - MicroRNAs and functionally linked mRNAs affecting meat and carcass traits in pigs. In: Proceedings of 33rd ISAG Conference (ISAG; Hrsg.) ISAG, Cairns 2012 (33)
Ponsuksili S, Du Y, Murani E, Brand B, Schwerin M, Wimmers K
- Polymorphism of the porcine UBXN1 gene associated with carcass and meat quality. Vortragstagung der DGfZ/GfT, Uni Halle, 12.9.2012-13.9.2012, Halle, Deutschland
Huynh L, Murani E, Brunner RM, Ponsuksili S, Wimmers K
- Correlated mRNAs and miRNAs from co-expression and regulatory networks affect porcine muscle and finally meat properties. BMC Genomics. 2013, 14:533
Ponsuksili S, Du Y, Hadlich F, Siengdee P, Murani E, Schwerin M, Wimmers K
(See online at https://doi.org/10.1186/1471-2164-14-533) - Transcriptional profiling and miRNA-dependent regulatory network analysis of longissimus dorsi muscle during prenatal and adult stages in two distinct pig breeds. Anim Genet. 2013, 44:398-407
Siengdee P, Trakooljul N, Murani E, Schwerin M, Wimmers K, Ponsuksili S
(See online at https://doi.org/10.1111/age.12032) - UBE3B and ZRANB1 polymorphisms and transcript abundance are associated with water holding capacity of porcine M. longissimus dorsi. Meat Sci. 2013, 95:166-172
Huynh TP, Murani E, Maak S, Ponsuksili S, Wimmers K
(See online at https://doi.org/10.1016/j.meatsci.2013.04.033)
