Marker‐based estimates of between and within population kinships for the conservation of genetic diversity

Abstract

In this article coefficients of kinship between and within populations are proposed as a tool to assess genetic diversity for conservation of genetic variation. However, pedigree‐based kinships are often not available, especially between populations. A method of estimation of kinship from genetic marker data was applied to simulated data from random breeding populations in order to study the suitability of this method for livestock conservation plans. Average coefficients of kinship between populations can be estimated with low Mean Square Error of Prediction, although a bias will occur from alleles that are alike in state in the founder population. The bias is similar for all populations, so the ranking of populations will not be affected. Possible ways of diminishing this bias are discussed. The estimation of kinships between individuals is imprecise unless the number of marker loci is large (> 200). However, it allows distinction between highly related animals (full sibs, half sibs and equivalent relations) and animals that are not directly related if about 30–50 polymorphic marker genes are used. The marker‐based estimates of kinship coefficients yielded higher correlations than genetic distance measures with pedigree‐based kinships and thus to this measure of genetic diversity, although correlations were high overall. The relation between coefficients of kinship and genetic distances are discussed. Kinship‐based diversity measures conserve the founder population allele frequencies, whereas genetic distances will conserve populations in which allele frequencies are the most different. Marker‐based kinship estimates can be used for the selection of breeds and individuals as contributors to a genetic conservation programme.

Assessing priorities for conservation in Tuscan cattle breeds using microsatellites

“…The differentiated background of the breeds is also supported by the molecular coancestry and the STRUCTURE analyses. The two terms of the formula used to compute the kinship distance, D k 5 ([s i 1 s j ]/2)2f ij (Caballero and Toro, 2002), summarize the between-population differentiation after their separation (term [s i 1 s j ]/2) corrected by the genetic identity of the populations at the time of the original (ancestral) metapopulation fission (f ij ; Eding and Meuwissen, 2001). A simple comparison of bidimensional scaling plots constructed using D k and 12f ij illustrates that the present differentiation of the analyzed populations is (except for the Garfagnina breed) dependent on the ancestral differentiation component (Á lvarez et al, 2005).…”

“…The between-breed molecular coancestry (f ij ; Caballero and Toro, 2002), Nei's minimum distance (D m ; Nei, 1987) and kinship distance (D k ; Eding and Meuwissen, 2001;Caballero and Toro, 2002) matrices were also computed using the program MolKin. Additionally, F-statistics, F ST and F IT (defined, respectively, as heterozygote deficiency due to population subdivision and heterozygote deficiency in the total population) were obtained for the entire analyzed dataset and for the Tuscan breeds.…”

“…Molecular techniques can be used to assess within-population genetic diversity and between-population differentiation and, therefore, make inferences on the degree of uniqueness of the analyzed populations. A number of approaches for quantifying genetic diversity have been proposed as tools for decision making in genetic conservation programs, including phylogenetic-like approaches such as that by Weitzman (1992) and Thaon d'Arnoldi et al (1998), those focusing on the maximization of the Nei's (1987) gene diversity (Eding and Meuwissen, 2001;Caballero and Toro, 2002) or the average number of alleles per locus (Petit et al, 1998; a These authors contributed equally to this work and shall share the first authorship.…”

Combining microsatellite and pedigree data to estimate relationships among Skyros ponies

“…The fM is the molecular co-ancestry between 2 individuals (Caballero and Toro 2000;Eding and Meuwissen 2001). By definition, it is the probability that 2 alleles taken randomly (one from each individual) are identical-by-descent (IBD).…”

A review on SNP and other types of molecular markers and their use in animal genetics

“…For instance, almost twice as many loci of expected heterozygosity He = 0.62 (three alleles of frequencies 0.5, 0.3 and 0.2) are required to achieve the same accuracy as with loci of He = 0.75 (four alleles of frequency 0.25 each) [7]. To be able to accurately distinguish between non-inbred full sibs and half sibs, at least 30 to 50 unlinked markers with 5 to 10 alleles each are needed [21]. Therefore, the use of biallelic loci may not be a good solution for kinship estimation, since the numbers used will have to be very high.…”