Genetic diversity and population structure of the synthetic Pannon White rabbit revealed by pedigree analyses1

Abstract

Demographic history, current status, and efficiency of the mating strategy were analyzed using the pedigree of Pannon White (PW) rabbits born between 1992 and 2007. Potential accumulation of detrimental effects and loss of genetic diversity were also considered. Calculations and estimates were done most often for rabbits born in 2007, whereas other reference populations (REFPOPXXXX) were specified explicitly. The pedigree contained 4,749 individuals and 580 founders, and its completeness was 82.1% up to 10 and 94.5% up to 5 generations, respectively. Generation intervals through different pathways averaged 1.2 yr. When adjusted to the pedigree completeness, the amount of inbreeding (F(i)) of rabbits was comparable (5.54%) with that of other livestock populations, whereas the 10 (30) founders contributing the most to inbreeding explained a large part of the population inbreeding [i.e., 42.24% (73.18%)]. The ancestral inbreeding coefficient of REFPOP2004 (10.67%) was one-half that of REFPOP2007 (20.66%), showing its strong dependence on pedigree length. Family variance, inbreeding, and realized effective population size were 84.18 (REFPOP2006; this variable could not be calculated for the last year examined), 37.19, and 91.08, respectively. The effective numbers of ancestors, founders, and founder genomes were 48, 26, and 7.33, respectively. Although the circular mating scheme applied was generally effective, the large accumulated reduction in genetic variability indicates the need to revise and improve the current breeding strategy.

Equivalent effective population size mating as a useful tool in the genetic management of the Ibicenco rabbit breed (Conill Pages d'Eivissa)

“…Anyway, it is possible that with the entry of other farmers in the herd book, these values could be significantly altered, since the current results are based on data from two farms. Nevertheless, this generation interval is similar to that obtained in a commercial breed, the Pannon White rabbit in Hungary (1.2 years) (Nagy et al 2010). …”

“…Mean inbreeding coefficient for the reference population was 10.8%. This value is higher than the 6.4% found in Pannon White rabbit (Nagy et al 2010). The evolution of mean inbreeding coefficients jointly with those of the equivalent generations across years is shown in Figure 2.…”

“…Thus, the minimum number of ancestors explaining 50% of the genetic diversity was 4. These values of effective number of founders and ancestors are very low if we compare them with values attained with other commercial breeds such as the Pannon White in Hungary (Nagy et al 2010), with 52 and 26 for f e and f a , respectively. But these comparisons should be made with caution because of the differences in the census and information about pedigree content.…”

“…This parameter decreased to almost 6, but it was higher than 5 one year before (Martin de la Rosa et al 2013). Even though this number is very low, a bigger population such as the Pannon White rabbit, had a value of 7 for this parameter (Nagy et al 2010), but with a much deeper pedigree depth of about 11 equivalent generations. The genetic diversity that remained from the foundation was 60% (f g /f e ), and the reasons, other than unbalancing of founders or ancestors, were additional random losses of genes during the segregations, and also others besides bottlenecks such as drift.…”

Application possibilities of selection indices in Pannon White rabbits’ breeding programme

“…To avoid inbreeding a circular mating scheme was applied dividing the population into four subgroups. This method was described in detail by Nagy et al (2010).…”