Skip to main content
ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #343745
Title: Genomic analysis reveals specific patterns of homozygosity in inbred pigs

Author
item WANG, LIGANG - Chinese Academy Of Agricultural Sciences
item XU, LINYANG - Chinese Academy Of Agricultural Sciences
item MU, YULIAN - Chinese Academy Of Agricultural Sciences
item LI, KUI - Chinese Academy Of Agricultural Sciences
item HAN, JIANLIN - Chinese Academy Of Agricultural Sciences
item WU, TIANWEN - Chinese Academy Of Agricultural Sciences
item LIU, LAN - Chinese Academy Of Agricultural Sciences
item GAO, QIAN - Chinese Academy Of Agricultural Sciences
item XIA, YING - Chinese Academy Of Agricultural Sciences
item DONG, KUNZHE - Chinese Academy Of Agricultural Sciences
item HOU, GUANYU - Chinese Academy Of Agricultural Sciences
item HUANG, LEI - Chinese Academy Of Agricultural Sciences
item TANG, FANG - Chinese Academy Of Agricultural Sciences
item CHENG, YING - Chinese Academy Of Agricultural Sciences
item LIU, YANG - Chinese Academy Of Agricultural Sciences
item WANG, CHEN - Chinese Academy Of Agricultural Sciences
item WANG, ZISHUAI - Chinese Academy Of Agricultural Sciences
item YANG, SHULIN - Chinese Academy Of Agricultural Sciences
item HE, XIAOHONG - Chinese Academy Of Agricultural Sciences
item QIAN, LILI - Chinese Academy Of Agricultural Sciences
item Liu, Ge - George
item FENG, SHUTANG - Chinese Academy Of Agricultural Sciences

Submitted to: Animals
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/28/2019
Publication Date: 6/1/2019
Citation: Wang, L., Xu, L., Mu, Y., Li, K., Han, J., Wu, T., Liu, L., Gao, Q., Xia, Y., Dong, K., Hou, G., Huang, L., Tang, F., Cheng, Y., Liu, Y., Wang, C., Wang, Z., Yang, S., He, X., Qian, L., Liu, G., Feng, S. 2019. Genomic analysis reveals specific patterns of homozygosity in inbred pigs. Animals. 9(6):314. https://doi.org/10.3390/ani9060314.
DOI: https://doi.org/10.3390/ani9060314

Interpretive Summary: The inbred strain of miniature pig is an ideal model for animal genetics, breeding and conservation. Using SNP array data collected from both inbred and non-inbred Wuzhishan pigs, we systematically investigated their distinct genetic structures. These results fill our knowledge gaps and provide insights into the mechanisms of inbreeding in farm animals. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enable animal selection will benefit from this study.

Technical Abstract: The inbred strain of miniature pig is an ideal model for conservation genetics due to its high level of homozygosity. In this study, we investigated the genetic diversity, relatedness and homozygosity using Porcine SNP60 BeadChip array in both inbred and non-inbred Wuzhishan pigs (WZSPs). Our results from multidimensional scaling, admixture and phylogenetic analyses suggested the inbred WZSP has its unique genetic properties, and can be considered as a novel genetic resource for pig genome study. Run of homozygosity (ROH) analysis revealed an average of 61 and 12 ROH regions in the inbred and non-inbred genomes of WZSP, respectively. Further, we detected 56 SNPs showing constant heterozygosity with He=1 across six generations in inbred pigs, while only one of them in non-inbred population. Among these SNPs, we observed 9 SNPs located in swine RefSeq genes. In addition, we found the estimated heterozogosity for 76 SNPs in 22 genes showed a decreasing trend through six generations. Among them, three genes (i.e., FANCM, GCNT1 and TXN) were found to be involved with immune rejection pathway. Together, our findings indicate that the inbred-specific pattern of homozygosity in inbred pigs can offer value insights for elucidate the mechanisms of inbreeding in farm animals.