Analysis of genetic diversity in four Canadian swine breeds using pedigree data

Abstract

Melka, M. G. and Schenkel, F. 2010. Analysis of genetic diversity in four Canadian swine breeds using pedigree data. Can. J. Anim. Sci. 90: 331Á340. Conservation of animal genetic resources entails judicious assessment of genetic diversity as a first step. The objective of this study was to analyze the trend of within-breed genetic diversity and identify major causes of loss of genetic diversity in four swine breeds based on pedigree data. Pedigree files from Duroc (DC), Hampshire (HP), Lacombe (LC) and Landrace (LR) containing 480 191, 114 871, 51 397 and 1 080 144 records, respectively, were analyzed. Pedigree completeness, quality and depth were determined. Several parameters derived from the in-depth pedigree analyses were used to measure trends and current levels of genetic diversity. Pedigree completeness indexes of the four breeds were 90.4, 52.7, 89.6 and 96.1%, respectively. The estimated percentage of genetic diversity lost within each breed over the last three decades was approximately 3, 22, 12 and 2%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in DC, HP, LC and LR was 74.5, 63.6, 72.9 and 60.0%, respectively. The estimated current effective population size for DC, HP, LC and LR was 72, 14, 36 and 125, respectively. Therefore, HP and LC have been found to have lost considerable genetic diversity, demanding priority for conservation. Key words: Genetic drift, effective population size Melka, M. G. and Schenkel, F. 2010. Analyse de la diversite´ge´ne´tiquediversite´ge´diversite´ge´ne´diversite´ge´ne´tique de quatre races de porc canadiennes a` partir des donneés ge´neálogiquesge´neálogiques. Can. J. Anim. Sci. 90: 331Á340. La pre´servationpre´servation des ressources ge´ne´tiquesge´ne´ge´ne´tiques animales suppose avant tout une e´valuatione´valuation judicieuse de la diversite´ge´ne´tiquediversite´ge´diversite´ge´ne´diversite´ge´ne´tique. L'e´tudee´tude devait analyser les tendances de la diversite´ge´ne´tiquediversite´ge´diversite´ge´ne´diversite´ge´ne´tique au sein de la race et identifier les principales raisons pour lesquelles cette diversite´sdiversite´s'amoindrit chez quatre races de porc, daprè s les donneés ge´neálogiquesge´neálogiques. A ` cette fin, les auteurs ont analyseí'ascendance des races Duroc (DC), Hampshire (HP), Lacombe (LC) et Landrace (LR) graˆcegraˆce aux dossiers contenant respectivement 480 191, 114 871, 51 397 et 1 080 144 entreés. Ils ont de´termineíade´termineía comple´tudecomple´tude, la qualiteét l'e´tenduee´tendue de la ge´neálogiege´neálogie. Plusieursparamè tres de´rive´sde´rive´de´rive´s de ces analyses approfondies ont permis de mesurer les tendances et le degreáctuel de diversite´ge´ne´tiquediversite´ge´diversite´ge´ne´diversite´ge´ne´tique. L'indice de comple´tudecomple´tude pour chacune des quatre race s'e´tablissaite´tablissait respectivement a` 90,4, 52,7, 89,6 et 96,1%. Le pourcentage de diversite´ge´ne´tiquediversite´ge´diversite´ge´ne´diversite´ge´ne´tique qu'on estime avoir perdu au sein de chaque race au cour...

Genealogical analysis of the Gochu Asturcelta pig breed: insights for conservation

“…In any case, the general scenario of the Gochu Asturcelta pig breed can hardly be compared with others in the literature. Indeed, pedigree depth is substantially lower than the depths reported for the well-established commercial pig breeds of Canada and the United States (Melka and Schenkel 2010;Welsh et al 2010) which included, in general, more than 11 complete generation equivalents. Nevertheless, the mean inbreeding in the breed is up to seven-fold higher than that reported for these American pig populations, ranging from 0.032 to 0.078.…”

“…Average generation interval computed for Gochu Asturcelta (1.8 years) is consistently the same as the others previously reported in the literature for non-endangered pig breeds. Melka and Schenkel (2010) reported generation intervals of 1.6 and 1.7 years for Canadian Duroc and Landrace, respectively; Welsh et al (2010), analyzing the pedigree of five United States pig breeds, reported generations intervals ranging from 1.7 (Berkshire) to 2.2 (Yorkshire) years; Tang et al (2013), in three cosmopolitan pig breeds imported into China, reported generation intervals ranging between 1.8 and 1.9 years.…”

“…Reports analyzing pedigree data in pig are scant Melka and Schenkel 2010;Welsh et al 2010;Tang et al 2013). Despite the local origin and development of the breed, the analysis of the very particular genetic scenario of the Gochu Asturcelta pig breed will give insights of general interest for breeders and conservationists.…”

Using pedigree analysis to monitor the local Piau pig breed conservation program

“…Despite the upper limit being above 50, the lower limit is well below the recommended threshold value, supporting the recommendation to increase the effective population size. In an analysis of four Canadian pig breeds Melka and Schenkel (2010) found small effective population sizes for the Hampshire (14) and Lacombe (22) breeds and emphasized that these breeds should be the subjects of conservation practices, as a small effective population size will lead to lower genetic diversity in the future. These findings highlight the importance of larger effective population sizes for the maintenance of genetic variability within a breed.…”

“…Barros et al (2011), evaluating the Brazilian goat breed Marota, found the effective number of founders and ancestors was 48 animals and the number of ancestors that explained 50 % of population variability was 22. In an analysis of four Canadian pig breeds, Melka and Schenkel (2010) determined the effective number of founders to be 275, 11, 56 and 54 for the Duroc, Hampshire, Lacombe and Landrace breeds, respectively. In addition, the number of ancestors that explained 50 % of the gene pool were especially low for the Hampshire (4 animals) and Lacombe (7 animals) breeds.…”