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High concordance between SNPs identified by the porcine 60K BeadChip genotyping array (Illumina) and the whole-genome sequencing

ABSTRACT: Crossbreeding has been an effective method to improve crossbred performance in pig industry. To have a global view of a classic three-way crossbreeding system of Duroc x (Landrace x Yorkshire) (DLY), we identified SNPs for each pig breed and crossbred individual originated from a DLY pig family to estimate the influence of purebreds on crossbred offspring using whole-genome sequencing. To confirm the accuracy of the SNPs identified by whole-genome sequencing, therefore, we performed the porcine 60K BeadChip genotyping array (Illumina) for each sequenced pig individual.

ORGANISM(S): Sus scrofa

PROVIDER: GSE123327 | GEO | 2018/12/05

REPOSITORIES: GEO

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Project description:Interactions among genomic loci have often been overlooked in genome-wide association studies, revealing the combinatorial effects of variants on phenotype or disease manifestation. Unexplained genetic variance, interactions amongst causal genes of small effects, and biological pathways could be identified using a network biology approach. The main objective of this study was to determine the genome-wide epistatic variants affecting feed efficiency traits [feed conversion ratio (FCR) and residual feed intake (RFI)] based on weighted interaction SNP hub (WISH-R) method. Herein, we detected highly interconnected epistatic SNP modules, pathways, and potential biomarkers for the FCR and RFI in Duroc and Landrace purebreds considering the whole population, and separately for low and high feed efficient groups. Highly interacting SNP modules in Duroc (1,247 SNPs) and Landrace (1,215 SNPs) across the population and for low feed efficient (Duroc - 80 SNPs, Landrace - 146 SNPs) and high feed efficient group (Duroc - 198 SNPs, Landrace - 232 SNPs) for FCR and RFI were identified. Gene and pathway analyses identified ABL1, MAP3K4, MAP3K5, SEMA6A, KITLG, and KAT2B from chromosomes 1, 2, 5, and 13 underlying ErbB, Ras, Rap1, thyroid hormone, axon guidance pathways in Duroc. GABBR2, GNA12, and PRKCG genes from chromosomes 1, 3, and 6 pointed towards thyroid hormone, cGMP-PKG and cAMP pathways in Landrace. From Duroc low feed efficient group, the TPK1 gene was found involved with thiamine metabolism, whereas PARD6G, DLG2, CRB1 were involved with the hippo signaling pathway in high feed efficient group. PLOD1 and SETD7 genes were involved with lysine degradation in low feed efficient group in Landrace, while high feed efficient group pointed to genes underpinning valine, leucine, isoleucine degradation, and fatty acid elongation. Some SNPs and genes identified are known for their association with feed efficiency, others are novel and potentially provide new avenues for further research. Further validation of epistatic SNPs and genes identified here in a larger cohort would help to establish a framework for modelling epistatic variance in future methods of genomic prediction, increasing the accuracy of estimated genetic merit for FE and helping the pig breeding industry.

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High concordance between SNPs identified by the porcine 60K BeadChip genotyping array (Illumina) and the whole-genome sequencing

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