Conservation and Utilization of Livestock Genetic Diversity in the United States of America through Gene Banking

Abstract

A germplasm collection curated by the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Animal Germplasm Program contains of over one million samples from over 55,000 animals, representing 165 livestock and poultry breeds. The collection was developed to provide genetic conservation and security for the U.S. livestock sector. Samples in the collection span 60 years, suggesting a wide range of genetic diversity and genetic change is represented for rare and major breeds. Classifying breeds into four groups based upon registration or census estimates of population size of < 1000, < 5000, < 20,000, and > 20,000 indicated that 50% of the collection is comprised of rare breeds in the < 1000 category. As anticipated, collections for breeds in the < 20,000 and > 20,000 are more complete (86% and 98%, respectively) based upon an index combining the number of germplasm samples and the number of animals. For the rarest breeds (< 1000), collection completeness was 45%. Samples from over 6000 animals in the collection have been used for adding diversity to breeds, genomic evaluation, reconstituting populations, or various research projects. Several aspects of collecting germplasm samples from rare breeds are discussed. In addition, approaches that could be used to enhance the status of rare breeds via the repository use are presented. However, given the array of obstacles confronting rare breeds, the gene bank may be the most secure prospect for the long-term conservation of rare breed genetics.

A computational framework for improving genetic variants identification from 5,061 sheep sequencing data

“…The collected data were from the Flock54℠ program ( https://www.flock54.com ), which was created by Superior Farms in coordination with the University of Idaho and aimed to promote the usage of marker assisted selection in breeding [ 28 ]. The key component for genotyping germplasm is finding DNA sequence polymorphisms and assaying the markers across a full set of samples, and the excellent germplasm resources can be used as breeding materials [ 47 ]. Some investigations on decoding sheep traits were beginning to emerge from whole genome-wide sequencing and association studies, such as productivity [ 48 ], wool and skin [ 49 – 51 ], weight [ 52 ], preweaning growth [ 53 ], and disease resistance [ 54 ].…”

A gene bank's collection of genetic diversity among minor chicken breeds

“…The samples used in this study were all sourced from the national gene bank ( Blackburn, 2018 ; Blackburn et al, 2019 ) which currently holds 17,352 tissue samples from 2,192 chickens, representing 145 chicken subpopulations and 23 chicken breeds. The data suggest that the gene bank has acquired substantial genetic variation from the breeds tested.…”

Assessing the potential of germplasm collections for the management of genetic diversity: the case of the French National Cryobank

“…In order to evaluate the potential of cryopreserved genetic resources, it is first necessary to identify the main features of the stocks in the cryobank. For example, 50% of the collections in the US National Gene Bank represent rare breeds with small population sizes and do not necessarily meet the requirements to reconstitute a breed, whereas collections for breeds with larger populations tend to be more complete (Blackburn et al, 2019). For Dutch cattle, collections have been partially optimized to maximize diversity within seven native breeds, and their gene bank could therefore play a major role in the conservation and maintenance of these breeds over time (van Breukelen et al, 2019).…”