Impact of merging commercial breeding lines on the genetic diversity of Landrace pigs

Abstract

Background: The pig breeding industry has undergone a large number of mergers in the past decades. Various commercial lines were merged or discontinued, which is expected to reduce the genetic diversity of the pig species. The objective of the current study was to investigate the genetic diversity of different former Dutch Landrace breeding lines and quantify their relationship with the current Dutch Landrace breed that originated from these lines.

Results: Principal component analysis clearly divided the former Landrace lines into two main clusters, which are represented by Norwegian/Finnish Landrace lines and Dutch Landrace lines. Structure analysis revealed that each of the lines that are present in the Dutch Gene bank has a unique genetic identity. The current Dutch Landrace breed shows a high level of admixture and is closely related to the six former lines. The Dumeco N-line, which is conserved in the Dutch Gene bank, is poorly represented in the current Dutch Landrace. All seven lines (the six former and the current line) contribute almost equally to the genetic diversity of the Dutch Landrace breed. As expected, the current Dutch Landrace breed comprises only a small proportion of unique genetic diversity that was not present in the other lines. The genetic diversity level, as measured by Eding's core set method, was equal to 0.89 for the current Dutch Landrace breed, whereas total genetic diversity across the seven lines, measured by the same method, was equal to 0.99.

Conclusions: The current Dutch Landrace breed shows a high level of admixture and is closely related to the six former Dutch Landrace lines. Merging of commercial Landrace lines has reduced the genetic diversity of the Landrace population in the Netherlands, although a large proportion of the original variation is maintained. Thus, our recommendation is to conserve breeding lines in a gene bank before they are merged.

Fig. 1

Timeline showing the consolidation of the Landrace breeds in the Netherlands since the 1960s (after [8]). CNF Cofok Norwegian and Finnish Landrace, DL Dumeco L-line, DN Dumeco N-line, FL Stamboek Finnish Landrace, FZ Fomeva Z1-line, SB Stamboek Dutch Landrace, TN Topigs Norsvin N-line

Fig. 2

Population structure and relationships of Landrace breeding lines in the Netherlands. a Principal component (PC) analysis, PC 1 against PC 2. b Neighbor-joining tree of the relationships between the seven lines. c Proportion of ancestry for each individual assuming different numbers of ancestral populations (K = 2 to 7). Colors of each vertical line represent the estimated proportion of an animal’s genome that is assigned to a source population

Fig. 3

Genome-wide distribution of log10 Bayes factor values in the pairwise comparison between the current TN and the six former lines. a CNF versus TN, b DL versus TN, c DN versus TN, d FL versus TN, e FZ versus TN and f SB versus TN. The threshold for significance of signatures of selection is denoted with a line (q-value ≤ 0.05)

Fig. 3

Genome-wide distribution of log10 Bayes factor values in the pairwise comparison between the current TN and the six former lines. a CNF versus TN, b DL versus TN, c DN versus TN, d FL versus TN, e FZ versus TN and f SB versus TN. The threshold for significance of signatures of selection is denoted with a line (q-value ≤ 0.05)