Analyzing pedigree and estimating inbreeding depression and genetic parameters of reproductive traits in a synthetic pig strain

Pigs are commercially produced in Japan by three-way crossing. However, the performance of crossbred pigs usually varies widely if the pure breeds used for crossing are not genetically improved by raising them as closed herds. Tokyo X was developed by crossing Berkshire, Duroc, and Beijing black pigs at the Tokyo Prefecture Animal Industry Experiment Station in 1997 as the first synthetic pig strain in Japan and has been maintained for 17 years. Consequently, genetic diversity of this strain may be decreased. In this study, a pedigree analysis was conducted to calculate the observed inbreeding coefficient (F), expected inbreeding coefficient under random mating (f), the observed relationship coefficient (R), and genetic contribution rate (GCR). Further, estimation of the inbreeding depression of reproductive traits was conducted using a general regression model. The data analyzed were the pedigree records from 1990 to 2014 and the reproductive records from 1997 to 2014. The reproductive traits analyzed were the total number of piglets born including mummified piglets (TNB), number of piglets born, number of piglets born alive (NBA), number of piglets born dead (NBD), number of piglets mummified, number of piglets suckled, number of piglets that died during the suckling period, and number of piglets weaned (NW). TNB, NBA, NBD, and NW were also used to estimate genetic parameters. In 1997, the mean F, f, and R values were 6.9%, 9.3%, and 20.0%, respectively. In 2014, the mean F, f, and R values reached 11.8%, 14.7%, and 26.6%, respectively. GCR in male founders began to change in 2000 but has plateaued since 2004. In 2014, GCR differed widely depending on the individuals. A similar result was shown in female founders. The effects of F in dams, sires, and litters were not significant for all traits (p>0.05). The effects of F in dams tended to decrease reproductive activity. In particular, TNB tended to decrease 0.88 piglets as F increased by 10%. The estimates of heritability for TNB, NBA, NW, and NBD were 0.11, 0.07, 0.05, and 0.03, respectively. This result indicates that the reproductive traits of Tokyo X could be improved.