Robust microsatellite markers for hybrid analysis between domesticated pigs and wild boar

Abstract

Hybridization between wild boar (Sus scrofa) and their domestic relative, pigs, is a global issue and gene flow between these populations has been known to negatively impact biodiversity with increased aggression, litter sizes, and growth. However, establishing a cost-effective analysis for long-term monitoring of possible gene flow of wild pigs into wild boar populations is challenging due to common alleles at multiple loci and often it is difficult to distinguish boar specific lineages. Therefore, there is a need to select loci with lineage specific alleles for hybrid detection. To determine these loci, we calculated allele frequencies and measurements from successfully amplified loci with DNA extracted from domestic pigs and wild boar populations from the period prior to, and after, the evacuations and disasters in Fukushima, Japan, in 2011, which resulted in an uncontrolled release of domestic pigs. Thirty-two loci showed pig putative alleles suggesting these selected loci can be useful genetic markers. Seventeen loci successfully distinguished pig and wild boar hybridization in Fukushima populations. Identified loci from this study provide a cost-efficient tool for genetic analysis and will provide a wealth of information on how an uncontrolled release of domestic livestock from natural or disasters may impact their wild relatives.

Introgression dynamics from invasive pigs into wild boar following the March 2011 natural and anthropogenic disasters at Fukushima

“…For 31 samples already analysed in Anderson et al [ 29 ], we used the genotypes reported therein for the 24 STR loci. The remaining 212 samples were analysed as described in Anderson et al [ 29 ]. In brief, PCR amplification was performed in 5 µl reactions using the QIAGEN Multiplex PCR Kit (QIAGEN, CA, USA) and a protocol for fluorescent labelling [ 34 ].…”

“…Nuclear microsatellite (STR) data were analysed to determine the genetic structure of wild boar and the extent of domestic pig introgression into the local wild boar population. A total of 24 STR loci were selected and genotyped for our study populations based on the allele frequencies and the amplification for each of these markers in pure species individuals (see Anderson et al [29]). All 24 markers were developed by previous studies [30][31][32] and recommended by the Food and Agriculture Organisation of the United Nations database [33].…”

Research priorities to fill knowledge gaps in the control of African swine fever: possible transmission of African swine fever virus by vectors

“…The whole weekly sample or a representative weekly subsample (i.e. 30–40%) of the blood meals is selected to assess if the blood is originating from wild boar by a validated method such as microsatellite markers (Anderson et al., 2020). Any insect caught in the traps that might be identified with a wild boar blood meal must therefore have originated from outside the fenced area where they must have had prior contact with wild boar.…”

Genetic Diversity, Admixture and Analysis of Homozygous-by-Descent (HBD) Segments of Russian Wild Boar

“…The use of molecular genetic methods makes it possible to characterize animal populations and determine the degree of their genetic differentiation. Various types of DNA markers are used to characterize the wild boar populations from Russia: mitochondrial DNA [ 10 , 11 , 12 ], Y-chromosome [ 12 , 13 ], STR [ 14 , 15 , 16 , 17 ], SNP [ 18 , 19 , 20 ].…”