Assessing the genetic diversity in small farm animal populations

Toro, M. Á.; Meuwissen, Theo H. E.; Fernández, Jesús; Shaat, I.; Mäki‐Tanila, Asko

doi:10.1017/s1751731111000498

Cited by 31 publications

(27 citation statements)

References 91 publications

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“…Leroy et al (2013) found significant correlations between N e (Hill), and N e (DF) and N e (Wright) in relatively small data sets of French cattle, sheep and horses. N e (Hill) has also been found to track other measures of N e over time (Toro et al, 2011). Previous work on Hill's equation (figures 13 and 14 of Hall, 2013), showed that when N e (Hill) for a breed is compared with N e (Wright) in the same breed they can be similar where conservation is being practised, but the former is subsequently less than the latter in numerically stronger breeds where genetic conservation is not a priority.…”

Section: Discussionmentioning

confidence: 90%

Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data

Hall¹

2016

Animal

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Accurate measures of effective population sizes ( N e ) in livestock require good quality data and specialized skills for their computation and analysis. N e can be estimated by Wright's equation N e = 4MF/( M + F) (M, F being sires and dams, respectively), but this requires assumptions which are often not met. Total census sizes N c of livestock breeds are collated globally. This paper investigates whether estimates of N e can be made from N c ; this would facilitate conservation monitoring. Some N e methodologies avoid the assumptions of Wright's equation and permit measurement, rather than estimation, of N e . Those considered here employ, respectively, linkage disequilibrium (LD) of single-nucleotide polymorphisms (yielding N e ( LD)), and genealogical analysis (rate of increase of inbreeding, DF), yielding N e (DF). Considering breeds of cattle, sheep, horses, pigs and goats for which N c and either N e ( LD) or N e ( DF) are known (totals of 203 breeds and 321 breeds, respectively), proportionality has been investigated between N c and these measures of N e . N e ( LD) was found to increase with N c , significantly in sheep and horses, less so in cattle, but not at all in pigs. N e ( DF) was correlated with log 10 ( N c ) in cattle, sheep and horses (53, 56, 43 breeds, respectively). N e ( LD) was correlated in cattle (73 breeds) and pigs (31 breeds) with the log 10 transformation of N e as calculated by Wright's equation.Further verification and refinement are needed, particularly of census data, but credible predictions of N e are obtainable by applying the following multipliers to log 10 ( N c ): cattle 17.61, sheep 97.72, horse 70.78. For cattle and pigs, multiplying log 10 ( N e (Wright)) by, respectively, 40.69 and 60.09, also gives credible predictions. Such census-based estimates of N e could in principle be generated by non-specialists and are likely to be suited to audits of conservation activity when financial resources or availability of data are limiting. The ratio N e /N c varied among species with an overall median value of 0.03, less than a tenth of that typically observed in wild mammals. Characteristics were also investigated of a distinct herdbook-based methodology, namely the development of Wright's equation to take into account variances of progeny numbers to yield what has been termed here N e (Hill). Comparison of these values with N e (Wright) could help to identify breeds with breeding structures conducive or inimical to genetic conservation. However, N e (Hill) requires breed-specific values for these variances, and this restricts its applicability.

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Section: Discussionmentioning

confidence: 90%

Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data

Hall¹

2016

Animal

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“…La variabilité morphologique peut être considérée comme un bon indicateur de la variabilité génétique et ainsi du potentiel adaptatif de la race (Toro et al, 2011). La variabilité génétique intraraciale est cruciale, seule à même de permettre à la race de s'adapter à des environnements naturels et de production changeants (Meuwissen, 2009), et de répondre de manière significative à la sélection artificielle (Toro et Caballero, 2005).…”

Section: Remerciementsunclassified

Caractérisation phénotypique de la race ovine Rembi d’Algérie

Laoun¹,

Harkat²,

Benali³

et al. 2015

Rev. Elev. Med. Vet. Pays Trop.

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Le cheptel ovin algérien reste méconnu, malgré son intérêt économique et les qualités très précieuses des races locales qui montrent des adaptations exceptionnelles dans des conditions environnementales extrêmes. La variabilité phénotypique de la Rembi, race algérienne menacée, a été étudiée au moyen d’une analyse discriminante multivariée. L’échantillonnage a pris en considération la diversité des environnements de production présents dans le pays selon les recommandations de la FAO. Au total 722 femelles et 60 mâles ont été phénotypés sur une grande zone incluant le berceau de la race, en utilisant 21 variables quantitatives et 12 variables qualitatives. Les résultats montrent une forte homogénéité phénotypique qui suggère une homogénéité intraraciale au niveau génétique, à confirmer par des analyses moléculaires. En effet, aucune structuration phénotypique n’a été mise en évidence, que ce soit en considérant le statut de la ferme (privée/étatique), la zone climatique (aride/semi-aride/subhumide), la mobilité du troupeau (sédentaire/semi-sédentaire/transhumant) ou encore la variété. Seule la considération du facteur région a permis la mise en évidence de sous-groupes au sein de la race. Les échanges commerciaux, organisés autour de marchés principaux, favorisent les flux d’individus à l’intérieur des différentes régions et semblent responsables d’un modèle phénotypique unique. Ces résultats permettent pour la première fois de caractériser finement la Rembi. Les indices morphologiques la situent notamment parmi les races à viande. Cette étude est la première étape vers la mise en place de programmes de conservation de cette race très menacée par des croisements avec la Ouled-Djellal, la race algérienne dominante.

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“…In livestock breeding, knowledge of relationships is used routinely to estimate genetic variation and animal breeding values (EBV;VanRaden, 2008;Hayes et al, 2009;Su et al, 2012), monitor inbreeding Toro et al, 2011), and for conservation of animal genetic resources (Eding and Meuwissen, 2001). Traditionally, relationship coefficients are calculated from the pedigree data.…”

Section: Introductionmentioning

confidence: 99%

The estimation of genomic relationships using breedwise allele frequencies among animals in multibreed populations

Makgahlela

Strandén

Nielsen

et al. 2013

Journal of Dairy Science

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Different approaches of calculating genomic measures of relationship were explored and compared with pedigree relationships (A) within and across base breeds in a crossbreed population, using genotypes for 38,194 loci of 4,106 Nordic Red dairy cattle. Four genomic relationship matrices (G) were calculated using either observed allele frequencies (AF) across breeds or within-breed AF. The G matrices were compared separately when the AF were estimated in the observed and in the base population. Breedwise AF in the current and base population were estimated using linear regression models of individual genotypes on breed composition. Different G matrices were further used to predict direct estimated genomic values using a genomic BLUP model. Higher variability existed in the diagonal elements of G across breeds (standard deviation=0.06, on average) compared with A (0.01). The use of simple observed AF across base breeds to compute G increased coefficients for individuals in distantly related populations. Estimated breedwise AF reduced differences in coefficients similarly within and across populations. The variability of the current adjusted G matrix decreased from 0.055 to 0.035 when breedwise AF were estimated from the base breed population. The direct estimated genomic values and their validation reliabilities were, however, unaffected by AF used to compute G when estimated with a genomic BLUP model, due to inclusion of breed means in the model. In multibreed populations, G adjusted with breedwise AF from the founder population may provide more consistency among relationship coefficients between genotyped and ungenotyped individuals in an across-breed single-step evaluation.

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Assessing the genetic diversity in small farm animal populations

Cited by 31 publications

References 91 publications

Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data

Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data

Caractérisation phénotypique de la race ovine Rembi d’Algérie

The estimation of genomic relationships using breedwise allele frequencies among animals in multibreed populations

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