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 i...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 Porcine SNP50 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.展开更多
Homeobox A10(Hoxa10) gene is one of the most important candidate genes associated with the reproductive performance of humans and mice. Overexpression of Hoxa10 in mouse endometrium can increase litter size. Moreover,...Homeobox A10(Hoxa10) gene is one of the most important candidate genes associated with the reproductive performance of humans and mice. Overexpression of Hoxa10 in mouse endometrium can increase litter size. Moreover, Hoxa10 plays a key role in regulating the embryo implantation of sows. This study aimed to generate transgenic pigs using Hoxa10 via somatic cell nuclear transfer(SCNT). We established seven Hoxa10-transgenic cell lines, and two of the cell lines were selected as nuclear donors for the transfer. A total of 1 270 cloned embryos were generated and transferred to five surrogate mothers(Landrace×Yorkshire). Eight cloned male piglets were produced including one with cryptorchidism. Six transgenic piglets grew up healthy and produced 56 offspring. Finally, we obtained six transgenic male pigs and 26 transgenic positive offspring that can be used to further study the regulatory mechanism of Hoxa10 on the reproductive performance of pigs.展开更多
基金supported by the China Agriculture Research System of MOF and MARA(CARS-35)the National Natural Science Foundation of China(32072696,31790414 and 31601916)the Fundamental Research Funds for the Central Universities(2662019PY011)。
文摘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 Porcine SNP50 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.
基金supported by the National Major Special Project on New Varieties Cultivation for Transgenic Organisms,China(2014ZX08006-005 and 2014ZX0800950B)
文摘Homeobox A10(Hoxa10) gene is one of the most important candidate genes associated with the reproductive performance of humans and mice. Overexpression of Hoxa10 in mouse endometrium can increase litter size. Moreover, Hoxa10 plays a key role in regulating the embryo implantation of sows. This study aimed to generate transgenic pigs using Hoxa10 via somatic cell nuclear transfer(SCNT). We established seven Hoxa10-transgenic cell lines, and two of the cell lines were selected as nuclear donors for the transfer. A total of 1 270 cloned embryos were generated and transferred to five surrogate mothers(Landrace×Yorkshire). Eight cloned male piglets were produced including one with cryptorchidism. Six transgenic piglets grew up healthy and produced 56 offspring. Finally, we obtained six transgenic male pigs and 26 transgenic positive offspring that can be used to further study the regulatory mechanism of Hoxa10 on the reproductive performance of pigs.
