Relationship between genealogical and microsatellite information characterizing losses of genetic variability: Empirical evidence from the rare Xalda sheep breed

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Abstract

Preservation of rare genetic stocks requires continual monitoring of populations to avoid losses of genetic variability. Genetic variability can be described using genealogical and molecular parameters characterizing variation in allelic frequencies over time and providing interesting information on differentiation that occurred after the foundation of a conservation program. Here we analyze the pedigree of the rare Xalda sheep breed (1851 individuals) and the polymorphism of 14 microsatellites in 239 Xalda individuals. Individuals were assigned to a base population (BP) or 4 different cohorts (from C1 to C4) according to their pedigree information. Genetic parameters were computed at a genealogical and molecular level, namely inbreeding (F), observed (Ho) and expected (He) heterozygosity, individual coancestry coefficients (f and fm), average relatedness (AR), mean molecular kinship (Mk), average number of allele per locus (A), effective number of ancestors (fa), effective population size (Ne and Ne(m)) and founder genome equivalents (Ng and Ng(m)). In general, the computed parameters increased with pedigree depth from BP to C4, especially for the genealogical information and molecular coancestry-based parameters (fm, Mk and Ng(m)). However, Ho and He showed the highest values for C1 and the molecular heterozygote deficiency within population (FIS(m)) showed the lowest value for C1, thus indicating that loss of genetic variability occurs very soon after the implementation of conservation strategies. Although no genealogical or molecular parameters are sufficient by themselves for monitoring populations at the beginning of a conservation program, our data suggests that coancestry-based parameters may be better criteria than those of inbreeding or homozygosity because of the rapid and strong correlation established between f and f(m). However, the obtaining of molecular information in well-established conservation programs could not be justified, at least in economic terms.

Introduction

The breeding goal in small populations is the conservation of genetic diversity. Genetic variability can be described at the genealogical level using parameters like inbreeding or kinship coefficients (Caballero and Toro, 2000). At the molecular level, highly variable loci provide a large amount of information on individual genotypes that is useful for clarifying population structure (Balloux and Lugon-Moulin, 2002, Álvarez et al., 2004). Even though genealogical analyses assume that each individual in the base population has unique alleles on each locus and molecular data are referred to finite sampling (thus being more pronouncedly affected by time forces), both sources of information are based on similar assumptions (Rochambeau et al., 2001): criteria based on pedigree information refer to any neutral autosomal locus, while criteria based on observed genetic polymorphisms mirror phenomena related to neutral genes or non-coding regions.

Allelic frequencies vary over time as populations are of finite size. The degree of temporal genetic differentiation can be assessed over time, thus providing interesting information on the differentiation that occurred after founder events or bottlenecks (Hansson et al., 2000). Preservation of rare genetic stocks requires continual monitoring of populations (Caballero and Toro, 2000), especially when pedigree information is shallow and the management structure leads to losses of genetic variability by drift or unobserved selection (Goyache et al., 2003). When the available sample size is small and genealogies are scarce, the combined use of pedigree information and molecular markers might be recommendable. Recent studies have formalized the computation of coancestry coefficients from molecular information (Caballero and Toro, 2000, Caballero and Toro, 2002, Eding and Meuwissen, 2001).With these findings researchers can use theoretically equivalent parameters at the genealogical and molecular level to monitor small populations (Toro et al., 2002, Toro et al., 2003, Royo et al., 2007).

This study aims to test the interest of combining genealogical and molecular information to monitor genetic variability in small populations. We shall test this approach on real data from the rare Xalda sheep breed of Asturias (Álvarez Sevilla et al., 2004, Goyache et al., 2003), which has recently undergone a conservation program, providing empirical evidence of interrelationship between molecular and genealogical estimators of genetic diversity.

Section snippets

Data and sampling

We obtained the information registered in the Xalda herd book, which includes a total of 1851 animals (217 males), of the breeders’ association (ACOXA). Up to 1505 individuals (130 males) were alive at the moment of carry out sampling and 1152 animals (107 males) were considered reproductive individuals (older than 1 year). The Xalda flockbook includes a large number of very small sized flocks. Although some of these flocks have a short duration and do not remain within ACOXA for long the

Results

Average values of the parameters characterizing the genetic variability of the Xalda population assessed from both genealogical and molecular information using each defined cohort as reference population are given in Table 1. The S.E. of the average ge corresponding to the sampled individuals varied from 0.04 to 0.07 thus being confident in assignment of individuals to their cohorts. The computed parameters increased, in general, with pedigree depth from the BP to C4, especially for the

Discussion

At the beginning of in situ conservation programs of livestock breeds, the homogenization of type characteristics and the small number of available breeding individuals leads to losses of genetic variability. In this study, we analyzed real data from a small, rare population (the Xalda sheep breed) undergoing a program for preservation of its genetic variability in order to ascertain the importance of genealogical and molecular information on the population’s monitoring during the early stages

Conclusions

Here we provide empirical evidence on genetic variation over time in real populations using data from the rare Xalda sheep breed as an example. Neither genealogical nor molecular information by themselves are sufficient for monitoring small populations when the pedigree is shallow. A depletion of genetic variability occurs very soon after the commencement of conservation program and each available parameter offers partial information for monitoring populations. In practical terms, no clear

Acknowledgments

This work was partially funded by grants from MEC-INIA, No. RZ2004-00007-C02 and from the Regional Government of the Principado de Asturias No. PC-REC04-27. The authors are indebted to the Xalda Breeders Association (ACOXA; http://www.xalda.com/) for its kind collaboration.

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