A Genetic Method to Distinguish Crossbred Inobuta from Japanese Wild Boars

Abstract

To distinguish pig-wild boar crossbred Inobuta from Japanese wild boar populations, a genetic method by using mitochondrial DNA (mtDNA) haplotypes and the nuclear glucosephosphate isomerase-processed pseudogene (GPIP) was developed. Sixteen mtDNA haplotypes from 152 wild boars from Kyushu, Shikoku and Honshu islands of Japan were distinct from those from Asian and European domestic pigs. Five alleles of GPIP were classified into two groups: 1). alleles GPIP*1, GPIP*3 and GPIP*3a from Japanese wild boars, Asian wild boars and domestic pigs; 2). alleles GPIP*4 and GPIP*4a from European wild boars and domestic pigs. An extensive genetic survey was done to distinguish the crossbred Inobuta from 60 wild boars hunted on Tsushima Island, Goto Islands, and Nagasaki and Ooita Prefectures. The mtDNA haplotypes from the 60 samples showed Japanese wild boars, but four wild boar samples from Nagasaki Prefecture had the European GPIP allele, GPIP*4. These results showed that nuclear DNA polymorphism analysis is useful, in addition to mtDNA haplotype assay, to detect "Inobuta" having the European genotype from Japanese wild boar populations.

Genetic Profile and Serosurvey for Virus Infections of Japanese Wild Boars in Shikoku Island

“…The DNA sequence of the 507-bp GPIP sequence was determined by the direct sequence method, as described previously [6]. The GPIP alleles (GPIP*1, GPIP*3, GPIP*3a, GPIP*4 and GPIP*4a) were determined by comparison with previously reported GPIP sequences [6,9].…”

“…Recently, Ishiguro et al [6] developed a genetic method that uses haplotypes of mitochondrial DNA (mtDNA) and genotypes of the nuclear glucosephosphate isomerase-processed pseudogene (GPIP) [4] to distinguish crossbred Inobuta from Japanese wild boars. There is the potential for transmission of infectious diseases between domestic pigs and feral wild boars.…”

“…The mtDNA D-loop region (574 bp) was amplified with 2 primers (mt112 and mit106), and purified with a QIAquick PCR Purification Kit (Qiagen). The DNA sequence of the mtDNA D-loop region was determined by the direct sequence method using 2 primers (mit11 and mit12), as described previously [6,9]. Multiple sequence alignment was performed using GENETYX-MAC software (Software Development Co., Tokyo, Japan).…”

“…Haplotypes of the 574-bp mtDNA were used in neighbor-joining analysis [12], which was performed using the PHYLIP program package, version 3.572 [3]. Sixty-three previously reported haplotypes (accession nos: D42170-D42174, D42178-D42185, AB015087-AB015086, AB041465-AB041473, AB041474-AB041476, AB041479-AB041485, AB041487-AB041493, AB041495-AB041499, AB053623-AB053627, D42176, AB071706, AB071707 and AB055222) [6,10,11,14,15] were used as reference sequences in NJ analysis.…”

Morphological and molecular phylogenetic characteristics of dwarf <i>Sus</i> specimens from the Noguni shell middens in the Ryukyu Islands

“…) and mitH106 (5′-ACGTGTACGCACGTGTACGC 704 ) for set C amplify 273, 305, and 229 bp fragments, respectively (Watanobe et al, 2001;Ishiguro et al, 2002). The numbers shown at the upper right of the primers denote the nucleotide positions in the D-loop region (Okumura et al, 1996).…”