Prioritization based on neutral genetic diversity may fail to conserve important characteristics in cattle breeds

Abstract

Conservation of the intraspecific genetic diversity of livestock species requires protocols that assess between-breed genetic variability and also take into account differences among individuals within breeds. Here, we focus on variation between breeds. Conservation of neutral genetic variation has been seen as promoting, through linkage processes, the retention of useful and potentially useful variation. Using public information on beef cattle breeds, with a total of 165 data sets each relating to a breed comparison of a performance variable, we have tested this paradigm by calculating the correlations between pairwise breed differences in performance and pairwise genetic distances deduced from biochemical and immunological polymorphisms, microsatellites and single-nucleotide polymorphisms. As already observed in floral and faunal biodiversity, significant positive correlations (n=54) were found, but many correlations were non-significant (n=100) or significantly negative (n=11). This implies that maximizing conserved neutral genetic variation with current techniques may conserve breed-level genetic variation in some traits but not in others and supports the view that genetic distance measurements based on neutral genetic variation are not sufficient as a determinant of conservation priority among breeds.

Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry?

“…This illustrates that conservation of phenotypic and molecular diversity should be considered separately (Hall et al . ). The examples of the Icelandic goats and several other livestock breeds (Hall ) also show that phenotypic and molecular variation is affected in different degrees by a low population size.…”

Analysis of conservation priorities of Iberoamerican cattle based on autosomal microsatellite markers

“…Because a high number of genetic markers in coding and non-coding genomic regions can be used (e.g. SNPs), such a genomic approach can provide more reliable estimates of inbreeding coefficients when pedigree information is lacking, as well as more accurate measures of genetic diversity and of the conservation value of the different breeds [10]. Thus, and following recent FAO guidelines for the in vivo preservation of AnGR [76], it is important to investigate furthermore and carefully evaluate the usefulness of whole-genome SNPs to define conservation priorities of genetically distinct breeds of Creole cattle in addition to the microsatellite-based inferences reported in this study.…”

“…Preservation of 'neutral’ genetic diversity is expected to contribute to maintaining specific breed traits due to natural and artificial selection. Indeed, microsatellites can be present in genes associated with important traits, including adaptation [9,10]. …”

“…However, this method has been strongly criticized because it ignores within-breed diversity [11,17,19-23]. Moreover, breed uniqueness inferred from genetic distances may result from prevalence of rare alleles due to inbreeding, founder effects or strict genetic isolation, instead of a distinct evolutionary history [10,17]. …”

Genetic Relationships Among Five Zebu Breeds Naturalized in America Accessed with Molecular Markers

“…The autosomal microsatellites are molecular markers generally recommended to estimate within and among populations genetic diversity, to investigate the relationships between among breeds and set conservation priorities . In addition to its own value in assessing the genetic diversity and the structure of domestic breeds, microsatellites are useful in the analysis of conservation, since this is expected to be linked with genes associated with important features, including the adaptation (Hall et al, 2012;Medugorac et al, 2011). The aim of this paper is to analyze the within-breed American Zebu genetic diversity accessed with microsatellite markers and identify the genetic relationships among populations of GYR, BRH, SIN, GUZ and NEL, established in the American continent.…”