Genomic Tools for Effective Conservation of Livestock Breed Diversity

Abstract

Human concern about the status of genetic diversity in livestock breeds and their conservation has increased, as intense selection and reduced population sizes in many breeds has caused losses on the global livestock genetic biodiversity. Traditionally, pedigree data provided by the breeders were used to estimate genetic diversity parameters, but over the past decades, technology has made possible the development of genomic markers. The result has been new opportunities to estimate genetic diversity in more detail, and to improve selection as well as prioritizing animals for conservation of genetic resources. The aim of the review is to summarize the evolution of livestock genomic markers and to explore the potential of the newest high-throughput technologies for estimation and conservation of livestock genetic diversity. More accurate diversity parameters are observed when genomic information is used for selection decisions instead of the traditional estimates using pedigree data. It is also possible to estimate additional parameters such as linkage disequilibrium to calculate effective population size or to minimize the genetic relatedness among the selected individuals based on runs of homozygosity. For long-term perspectives, new methods on genome editing are considered as new perspectives to reach a genetic diversity balance.

Genomic Characterization of a Set of Iberian Peninsula Bovine Local Breeds at Risk of Extinction: Morenas Gallegas

“…The knowledge of the within breed genetic diversity and between breeds genetic relationships are important tools for enhancing efficient use of the breeds and for implementing conservation programs. The availability of high-throughput genotyping platforms has favored detailed analysis of cattle genetic diversity and SNPs have been used in a large number of articles focused on the analysis of genetic diversity within and among cattle breeds [21]. However, although the assessment of the genetic diversity of local breeds is an important task for conservation and management of local biodiversity and to avoid the loss of an important genetic resource, local breeds have been less analyzed than cosmopolitan ones.…”

“…Caldelá and Cachena breeds evidenced the higher genetic differentiation level as revealed by ADMIXTURE, ASD, and Reynolds genetic distance dendrogram. Caldelá is the unique Morenas Gallegas breed belonging to the Black Iberian lineage origin, one of the three main historical bovine lineages in the Iberian Peninsula (Cantabrian, Iberian Black, and Chestnut) [21].…”

Insight into the Current Genetic Diversity and Population Structure of Domestic Reindeer (Rangifer tarandus) in Russia

“…Recent improvements in the speed, cost, and accuracy of next-generation sequencing have contributed to an obtainment of new information about the whole genome of most domestic animals, and have led to the widespread use of single-nucleotide polymorphism (SNP) markers as a powerful tool for addressing a great number of genetic tasks [21,22]. The discovery and genotyping of hundreds of thousands of SNPs in a single assay are enabled by the use of SNP high-throughput arrays, which are available for the majority of the livestock species, thus targeting wide genetic variants that are spread along the entire genome [23,24]. In distinction from the other model species, a genomic era in the study of both the reindeer and the North American caribou has been established recently, and several versions of the Rangifer tarandus genome have occurred [25][26][27].…”

Conserving the Genetic Diversity of Domesticated Livestock

“…An approach based on molecular genetics is possible in some countries, most notably those with sufficient infrastructure and finances. Strategies based on such techniques have been used in the Netherlands for cattle [10] and in several other countries for breeds of several species, all to good effect [11,12]. Strategies for long-term conservation involve cryopreservation, which is organized at both governmental and non-governmental levels [13][14][15].…”