A study on genetic diversity of Raeini Cashmere Goat using pedigree analysis

The Raeini Cashmere goat is one of the most important breeds among Iranian goat. This study was conducted to characterize genetic diversity and population structure of Raeini Cashmere goat using pedigree analysis, to identify factors affected the genetic variability of this breed. By knowing these kinds of parameters especially probability of gene origin parameters animal breeders could suggest good strategies to manage inbreeding and describing decrease in genetic variability in the population.
The information of 7264 goat from 293 fathers and 2057 mothers were used. The data were collected during 1990-2013 in Raeini Cashmere goat breeding station in Baft, Kerman. Estimation of inbreeding coefficient was done by CFC software. Endog (v4.8) software was used to compute other pedigree analyses including mean coancestry, mean relationship, effective population size, probability of gene origin parameters and average generation interval.
The mean generation interval was 3.93 years. The generation interval in the dam-progeny pathway was shorter than in sire-progeny pathway. The mean coancestry of this population was estimated 0.012 percent. Average inbreeding coefficients of the population and within inbred population were 0.08 and 3.5 percent, respectively. Inbred animals formed small part of the population and included about 2 percent of total animals. The maximum inbreeding coefficient was 25 percent and the majority of inbred animals were animals with inbreeding coefficient up to 5 percent. Increase in inbreeding was 0.004 percent per year and based on 3.9 generation interval inbreeding will increase about 0.015 percent per generation. The mean relationship was 0.24 percent. The relationship coefficients estimates between male and female animals are to predict the future level of inbreeding in population. The total number of founder animals, the effective number of founders, effective number of ancestors and effective number of founder genomes, were estimated 1227, 251, 232, 240 heads, respectively. Also, the effective population size was 191 heads.
The results of this study showed that the effective population size of this population decreased during the period of research. The effective population size in Raeini Cashmere goat was in good condition according to the FAO suggestion. An effective population size of 50 determined by FAO as a critical status for animal populations. But if this trend continues in the future, the effective size of the population will approach to critical levels. The results of this study indicated that, the contribution of the founders and major ancestors to the population has been unbalanced due to the selection of animals and the genetic variability of the population decreased compared to the founder population. In comparison to other breeds, the population under study has an acceptable level of genetic variability.