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A comprehensive evaluation of factors affecting the accuracy of pig genotype imputation using a single or multi-breed reference population
ZHANG Kai-li, PENG Xia, ZHANG Sai-xian, ZHAN Hui-wen, LU Jia-hui, XIE Sheng-song, ZHAO Shu-hong, LI Xin-yun, MA Yun-long
2022, 21 (2): 486-495.   DOI: 10.1016/S2095-3119(21)63695-X
Abstract281)      PDF in ScienceDirect      
Genotype imputation has become an indispensable part of genomic data analysis.  In recent years, imputation based on a multi-breed reference population has received more attention, but the relevant studies are scarce in pigs.  In this study, we used the Illumina PorcineSNP50 Bead Chip to investigate the variations of imputation accuracy with various influencing factors and compared the imputation performance of four commonly used imputation software programs.  The results indicated that imputation accuracy increased as either the validation population marker density, reference population sample size, or minor allele frequency (MAF) increased.  However, the imputation accuracy would have a certain extent of decrease when the pig reference population was a mixed group of multiple breeds or lines.  Considering both imputation accuracy and running time, Beagle 4.1 and FImpute are excellent choices among the four software packages tested.  This work visually presents the impacts of these influencing factors on imputation and provides a reference for formulating reasonable imputation strategies in actual pig breeding.
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Genome-wide detection of selective signatures in a Duroc pig population
DIAO Shu-qi, LUO Yuan-yu, MA Yun-long, DENG Xi, HE Ying-ting, GAO Ning, ZHANG Hao, LI Jia-qi, CHEN Zan-mou, ZHANG Zhe
2018, 17 (11): 2528-2535.   DOI: 10.1016/S2095-3119(18)61984-7
Abstract429)      PDF in ScienceDirect      
The Duroc pig has high adaptability and feeding efficiency, making it one of the most popular pig breeds worldwide.  Over long periods of natural and artificial selection, genetic footprints, i.e., selective signatures, were left in the genome.  In this study, a Duroc pig population (n=715) was genotyped with the Porcine SNP60K Bead Chip and the GeneSeek Genomic Profiler (GGP) Porcine Chip.  The relative extended haplotype homozygosity (REHH) method was used for selective signature detection in a subset of the population (n=368), selected to represent a balanced family structure.  In total, 154 significant core regions were detected as selective signatures (P<0.01), some of which overlap with previously reported quantitative trait loci associated with several economically important traits, including average daily gain and backfat thickness.  Genome annotation for these significant core regions revealed a variety of interesting candidate genes including GATA3, TAF3, ATP5C1, and FGF1.  These genes were functionally related to anterior/posterior pattern specification, phosphatidylinositol 3-kinase signaling, embryonic skeletal system morphogenesis, and oxidation-reduction processes.  This research provides knowledge for the study of selection mechanisms and breeding practices in Duroc and other pigs.
 
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