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.

   Homeobox A10 (HOXA10) is a well-known transcription factor that plays an important role in directing endometrial differentiation and establishing the conditions required for implantation. Interestingly, the expression level of HOXA10 may be associated with litter size. To study the effects of the porcine HOXA10 promoter fragment on the expression of HOXA10 gene in vivo, we generated a transgenic mouse model using pronuclear microinjection, and measured the expression of HOXA10 in the endometrium. There was no difference in the expression level of HOXA10 between transgenic and wild-type mice in the absence of hormone stimulation. However, following treatment with progesterone and estradiol benzoate, the expression level of HOXA10 was significantly increased in transgenic mice compared with that of wild-type mice. Furthermore, the litter size of transgenic females was larger than that of wild-type females (7.02±1.73 vs. 6.48±1.85; P=0.14). Moreover, the difference of litter size was greater in the later parities (7.33±1.62 vs. 6.37±2.02; P=0.08) compared with the first parity (6.76±1.81 vs. 6.61±1.67; P=0.77) between transgenic and wild-type mice. Therefore, our transgenic mouse model provides exciting insights regarding the actions of HOXA10 and its hormone-inducible promoter in vivo. The present study offers valuable proof of principle to develop transgenic pigs with a hormone-inducible promoter regulating HOXA10 to alter litter size.