Pedigree Analysis and Inbreeding Investigation in Lori-Bakhtiari Sheep

Introduction Control and management of genetic diversity of breeds is necessary for their sustainable use in the future because a limited number of breeding animals will unavoidably lead to increased inbreeding and thus to a reduction in additive genetic variance, and maybe to inbreeding depression. Managing inbreeding is usually one of the major goals in conservation and selection programs of breeds. Some of descriptive parameters of population structure are the inbreeding coefficient, effective population size, effective number of founders, effective number of ancestors, effective number of founder genomes, effective number of non-founder genomes and average generation interval, which are indicative of genetic diversity levels in a population. In a breeding program, the inbreeding coefficient and the rate of annual inbreeding should be monitored because of their influence on production and on the estimation of genetic parameters. The Lori-Bakhtiari sheep is one of the most important native breeds of Iran. With more than 1.7 million head population are mostly kept on village or semi-migratory system in Chaharmahal and Bakhtiari province. This breed has the largest fat-tail size among all of sheep breeds in Iran. The objective of this study was to investigate genetic structure and genetic diversity of Lori–Bakhtiari sheep using pedigree analysis and the inbreeding depression of body weight traits was estimated.
Materials and methods The pedigree information of 7693 Lori–Bakhtiari lambs (2478 male and 5215 female) from 274 rams and 2006 ewes collected from 1990 to 2011, were used. The data were collected at Shooli sheep breeding station in Shahrekord, Chaharmahal and Bakhtiari province. Estimation of inbreeding coefficients was done by CFC software and Endog (v4.8) software was used to compute other pedigree analyses including mean coancestry, effective population size, probability of gene origin parameters and average generation interval. Parameters based on the probability of gene origin were used to describe genetic variability. To investigate the effect of inbreeding on body weight traits, the data of birth weights, weaning weights, weights at six months of age, weights at nine months of age and weights at 12 months of age were used. Inbreeding depression was estimated as the regression of these performance records on the individual inbreeding coefficients by fitting an animal model. WOMBAT software was used for estimating the inbreeding depression of body weight traits.
Results and Discussion Total number of founders, effective number of founders, effective number of ancestors, effective number of founder genomes and effective number of non-founder genomes were 506, 105, 90, 65, 181 heads, respectively. Average generation interval and effective population size were 4.23 years and 249 heads, respectively. The generation interval in the dam-progeny pathway was shorter than in sire-progeny pathway. Estimated average coancestry and inbreeding coefficient were 0.76 and 0.56, respectively. Animals with progeny were 29.7 % and those of without progeny 70.3 % of the total animals. Animals with both known parents and one unknown parent constituted 92 % of the population. Between all the registered animals, 28 % were inbred. The average inbreeding coefficient during the study period for inbred and all animals were 2 and 0.56 %, respectively. The most inbred animals, equivalent to 25% of the inbreeds, had inbreeding coefficients equal to or lower than 5 %. The regression coefficients for birth weight, weaning weight, weight at 6, 9 and 12 months of age on inbreeding were -11, -106.6, -259.7, -161.2 and -239.9 g, respectively.
Conclusion Considering the parameters obtained from the probability of gene origin analysis, the contribution rate of founders and major ancestors have been unbalanced due to the selection of animals that led to decrease of genetic diversity. Estimated inbreeding depression of body weight traits for this breed was higher than other sheep breeds of Iran and showed high degree of close mating in this herd. Due to the deleterious effect of inbreeding on body weight traits it is suggested that this breeding station should use a better breeding plan to avoid mating of close relative animals. At this study, the presence of inbreeding depression for body weight traits also confirmed reduction of genetic diversity in this population. The results of this study also indicate that genetic variability within this population has to be monitored constantly in order to prevent or minimize loss of founder alleles due to genetic drift or selection. The authors suggested that pedigree analysis should be done periodically in this breeding station. Doing this analysis would also prevent or control kinship in this breeding population.