Using pedigree information to monitor genetic variability of endangered populations: the Xalda sheep breed of Asturias as an example

Abstract

SummaryThe aim of this work is to highlight the need of monitoring small populations to conserve their genetic variability by using a set of parameters to characterize both the structure of populations and management practices. As a representative example we analyse the pedigree information of the endangered Xalda sheep breed of Asturias. The herdbook of Xalda sheep included a total of 805 animals and 62 herds. The number of founders was 329. Nowadays, there are 562 live animals and 26 active herds. The breed is in risk of losing genetic diversity because of the abusive use of certain individuals as parents. The effective number of founder animals is 81.1. The effective number of founder herds is 9.9. The average value of inbreeding in the whole Xalda population was 1.5%. The average relatedness (AR) coefficient reached 1.8% in the whole pedigree. The genetic representation of the lines of founders is unbalanced. Inbreeding trends and effective size do not provide realistic information concerning the risk of loss of diversity as a result of the shallowness of the genealogical information. We suggest the monitoring of the breed using AR to unbalance the genetic contributions of specific individuals, equalizing the genetic representation of the founders and lines in the population. In addition, AR can suggest the introduction of new, under-represented animals in herds showing high average AR values relative to the population. Our results can be useful to improve the development of conservation initiatives involving open herdbooks to avoid the risk of loss of genetic diversity caused by incorrect management practices. Zusammenfassung

Individual increase in inbreeding allows estimating effective sizes from pedigrees

“…Effective size from pedigrees Table I gives the main parameters describing the real pedigree file. The pedigree size was 6318 and the size for the fitted RS was 1464 individuals for RS 77-89 and 1721 for RS 10 . The mean equivalent generation ± standard deviation was the following: 6.6 ± 2.75 for the whole pedigree (WP), 9.1 ± 0.68 for RS 10 and 8.2 ± 0.64 for RS [77][78][79][80][81][82][83][84][85][86][87][88][89] .…”

“…In most cases the definition of a 'previous' generation is quite difficult to establish. In fact, taking the average inbreeding of a pre-defined reference subpopulation and referring it to the founder population in which inbreeding is null by definition, fits poorly in any given real population and is only acceptable in small populations with shallow pedigree files [1,10,12] leading to the risk of overestimating the actual effective population size.…”

An effective rotational mating scheme for inbreeding reduction in captive populations illustrated by the rare sheep breed Kempisch Heideschaap

“…The advantage of rotational mating schemes is that inbreeding restriction can be achieved in a relatively simple way. There is no pedigree needed as in, for example, the method of Goyache et al (2003), nor estimation of relatedness using molecular markers. Utilisation of animals from outside the subpopulation will generally reduce inbreeding rates but the advantage of rotational mating schemes is that this is done in a systematic way so that in the long run low inbreeding rates are assured.…”

Investigation of genetic variability and inbreeding characteristics in a population of Zandi sheep

“…Ne is defined as the number of animals that would produce the observed rate of inbreeding if bred under ideal conditions in the current generation. Whatever the way to compute Ne, this parameter fits poorly in small populations with shallow pedigrees, giving an overestimate of the actual effective population size (Goyache et al 2003). To better characterize this, we estimated three additional values of Ne by computing the regression coefficient (b) of the individual inbreeding coefficient over: (i) the number of full traced generations; (ii) the maximum number of generations traced and (iii) the equivalent complete generations for each animals in pedigree data.…”

“…In addition, registration of the high number of founders in the herdbook kept inbreeding at a relatively low level. The computation of the individual coefficient of inbreeding is highly sensitive to the quality of the available pedigree information, thus making this parameter difficult to interpret (Goyache et al 2003). In such a situation, an unobserved genetic drift may lead to losses in genetic diversity.…”