Reintroducing genetic diversity in populations from cryopreserved material: the case of Abondance, a French local dairy cattle breed

Abstract

Background: Genetic diversity is a necessary condition for populations to evolve under natural adaptation, artificial selection, or both. However, genetic diversity is often threatened, in particular in domestic animal populations where artificial selection, genetic drift and inbreeding are strong. In this context, cryopreserved genetic resources are a promising option to reintroduce lost variants and to limit inbreeding. However, while the use of ancient genetic resources is more common in plant breeding, it is less documented in animals due to a longer generation interval, making it difficult to fill the gap in performance due to continuous selection. This study investigates one of the only concrete cases available in animals, for which cryopreserved semen from a bull born in 1977 in a lost lineage was introduced into the breeding scheme of a French local dairy cattle breed, the Abondance breed, more than 20 years later.

Results: We found that this re-introduced bull was genetically distinct with respect to the current population and thus allowed part of the genetic diversity lost over time to be restored. The expected negative gap in milk production due to continuous selection was absorbed in a few years by preferential mating with elite cows. Moreover, the re-use of this bull more than two decades later did not increase the level of inbreeding, and even tended to reduce it by avoiding mating with relatives. Finally, the reintroduction of a bull from a lost lineage in the breeding scheme allowed for improved performance for reproductive abilities, a trait that was less subject to selection in the past.

Conclusions: The use of cryopreserved material is an efficient way to manage the genetic diversity of an animal population, by mitigating the effects of both inbreeding and strong selection. However, attention should be paid to mating of animals to limit the disadvantages associated with incorporating original genetic material, notably a discrepancy in the breeding values for selected traits or an increase in inbreeding. Therefore, careful characterization of the genetic resources available in cryobanks could help to ensure the sustainable management of populations, in particular local or small populations. These results could also be transferred to the conservation of wild threatened populations.

Fig. 1

Production of Naif’s direct progeny and total annual pedigree-based genetic contribution from 1980 to 2017. Blue: first period of the use of Naif; and green: second period of the use of Naif

Fig. 2

Old and recent contribution of Naif evaluated from pedigree data from 2004 to 2017. In blue: old contribution from the first period of the use of Naif; and in green: recent contribution from the second period of the use of Naif

Fig. 3

Average heterozygosity of contemporary cohorts for both uses of the Naif bull. The 62 bulls in Cohort 1 are shown in pink, the 165 bulls in Cohort 2 are shown in blue, Naif is represented by the purple triangle, the mean of each cohort corresponds to the yellow square

Fig. 4

Inbreeding of individuals of cohort 2017 depending on their link with the recent use of Naif. Blue: individuals that do not originate from the recent use of Naif; and green: individuals that originate from the recent use of Naif

Fig. 5

Principal component analysis of genotyping data for Cohort 1 (a) and Cohort 2 (b). Naif is represented by the blue dot

Fig. 6

Between-class analysis of genotyping data of cohort 2017. Red: individuals not related to Naif; green: individuals with one old link with Naif; orange: individuals with two old links with Naif; blue: individuals with one old and one recent link with Naif; purple: individuals with one recent link with Naif; and magenta: individual with two recent links with Naif

Fig. 7

Distribution of INEL (a), reproduction index (b) and ISU (c) for Cohort 1 and Cohort 2. The 62 bulls in Cohort 1 are shown in pink, the 165 bulls in Cohort 2 are shown in blue, Naif is represented by the black dashed line, the mean of each cohort is represented by the solid line and the different gaps between Naif and the mean of each cohort by the arrows

Fig. 8

Average values of INEL (a), reproduction index (b) and ISU (c) in the two generations following the second use of Naif. The average values of the offspring from the reuse of Naif’s frozen semen are represented in blue and those of the offspring from the other sire families are represented in yellow. Error bars correspond to confidence intervals

Fig. 9

Distribution of INEL (a) and a milk index (b) for females mated with Cohort 1 and Cohort 2. The 2443 cows in Cohort 1a are shown in pink, the 4092 cows in Cohort 2a are shown in blue, the mean of each cohort is represented by the solid line, the performance mean of the Cohort 1b and Cohort 2b are represented by the black dashed lines and the gaps between the different cohort means by the arrows