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Biochemical Genetics (v.45, #3-4)


DNMT3b 39179G‎T Polymorphism and the Risk of Adenocarcinoma of the Colon in Koreans by Young-Seoub Hong; Hye-Jung Lee; Chang-Hun You; Mee-Sook Roh; Jong-Young Kwak; Myeong-Jin Lee; Joon-Youn Kim (pp. 155-163).
DNA-methyltransferase-3B (DNMT3b) plays an important role in the generation of aberrant methylation in carcinogenesis. DNMT3b SNP has been associated with susceptibility to lung, head, neck, and breast cancer, but its association with the development of colon cancer has not been reported. We investigated the relationship between the 39179G‎T polymorphism in the DNMT3b gene, which is involved in de novo methylation and is associated with the risk of adenocarcinoma of the colon in Koreans. The DNMT3b 39179G‎T genotypes were determined by a PCR-RFLP method in 248 adenocarcinomas of colon cancer patients and in 248 healthy controls matched as to age and sex. When stratified by sex and age, a significantly reduced risk of the combined GT and GG genotypes was observed in younger patients (<59, adjusted OR = 0.255, 95% CI = 0.133–0.489) and in male patients (adjusted OR = 0.383, 95% CI = 0.225–0.652). The DNMT3b 39179G‎T polymorphism may be a genetic determinant of adenocarcinoma of the colon, especially in younger Korean men.

Keywords: DNMT3b ; methylation; carcinogenesis; colon cancer


Population Structure of Wild Musk Shrews (Suncus murinus) in Asia Based on Mitochondrial DNA Variation, with Research in Cambodia and Bhutan by Megumi Kurachi; Ba-Loc Chau; Vu-Binh Dang; Tashi Dorji; Yoshio Yamamoto; Maung Maung Nyunt; Yoshizane Maeda; Loan Chhum-Phith; Takao Namikawa; Takahiro Yamagata (pp. 165-183).
The musk shrew (Suncus murinus) is a small mammalian species belonging to Insectivora. It is widely distributed in Asia. To identify the genetic relationship among wild musk shrew populations and examine its migration route, we investigated the populations of Cambodia and Bhutan by using mitochondrial DNA restriction fragment length polymorphism analysis and compared them with other Asian populations previously described. Four haplotypes were detected in Cambodia and eight in Bhutan. A total of 53 haplotypes were detected in Asia and were classified largely into two groups, the Continental and Island types, based on a minimum spanning network. From the distribution of mtDNA types in wild musk shrews, three major population groups are identified in Asia: South Asia, Southeast Asia, and Malay. It is suggested that the Malay population group was a mix of South and Southeast Asian population groups and that this was a contact area of the two groups. In addition, other contact areas between the South and Southeast Asian groups exist in Myanmar, but unlike the Malay, the Myanmar area was the border of these groups.

Keywords: Suncus murinus ; mtDNA RFLPs; population; migration route; Asia


Molecular Cloning and Comparison of Avian Preproghrelin Genes by Jing Yuan; Jianjun Zhou; Xiaoxiang Hu; Ning Li (pp. 185-194).
We report cDNA sequences for the preproghrelin gene from goose, duck, and emu. This gene is involved in stimulating the release of growth hormone in mammals and may play a similar role in avian species. The complete coding sequence of avian preproghrelin encodes a 116 amino acid (aa) protein, which is organized into three parts: the N-terminal hydrophobic signal peptide, a 26 aa peptide for mature ghrelin, and a long C-terminal polypeptide. Domain/motif structures of preproghrelin protein are highly conserved among avian species. Although the avian and mammalian homologs are not highly similar for the whole 116 aa sequence, the identity of the highly conserved “active core” sequence and the n-octanoyl modification of the serine 3 residue avian ghrelin protein with its mammalian homologs implies conserved function of ghrelin protein during evolution. Information provided in this study will be useful in further studies to determine the role the preproghrelin gene plays in the regulation of growth hormone release and body weight gain in avian species.

Keywords: goose; duck; emu; preproghrelin; cDNA


Genetic Structure and Differentiation of Three Chinese Indigenous Cattle Populations by Yongjiang Mao; Hong Chang; Zhangping Yang; Liu Zhang; Ming Xu; Wei Sun; Guobin Chang; Guangming Song (pp. 195-209).
Levels of genetic differentiation, gene flow, and genetic structure of three indigenous cattle populations (Luxi, Bohai, and Minnan) and two reference cattle populations (Chinese Holstein and Qinhai yak) in China were estimated using the information from 12 microsatellites, and 141 microsatellite alleles were identified. The mean number of alleles per locus ranged from 2.9005 in yak to 4.9722 in Holstein. The observed heterozygosity ranged from 0.5325 (yak) to 0.7719 (Holstein); 29 private alleles were detected. The global heterozygote deficit across all populations amounted to 58.5% (p < 0.001). The overall significant (p < 0.001) deficit of heterozygotes because of inbreeding within breeds amounted to 43.2%. The five cattle populations were highly differentiated (F st = 26.9%, p < 0.001) at all loci. The heterozygote deficit within the population was highest in Luxi cattle and lowest in yak. The average number of effective migrants exchanged per generation was highest (1.149) between Luxi and Holstein, and lowest (0.509) between Luxi and yak. With the application of prior population information, cluster analysis achieved posterior probabilities from 91% to 98% of correctly assigning individuals to populations. Combining the information of cluster analysis, gene flow, and Structure analysis, the five cattle populations belong to three genetic clusters, a taurine (Luxi and Chinese Holstein), a zebu (Bohai and Minnan), and a yak cluster. This indicates that Bohai black is closer to Bos indicus than Luxi cattle. The evolution and development of three indigenous cattle populations are discussed.

Keywords: Genetic structure; genetic differentiation; Chinese indigenous cattle; microsatellite


Cloning and Characterization of a Rice Field Eel vasa-Like Gene cDNA and Its Expression in Gonads During Natural Sex Transformation by Ding Ye; Daoyuan Lv; Ping Song; Maoyu Peng; Yungui Chen; Ming Guo; Qiwen Yang; Yinchang Hu (pp. 211-224).
The vasa (vas)-related gene encodes an RNA helicase protein member of the DEAD-box family and plays key roles in germ-cell formation in higher metazoans. Using degenerate PCR and RACE, we cloned the vasa gene of the rice field eel (Monopterus albus), which is homologous to the Drosophila vasa gene. We named it ma-vas (Monopterus albus vas). Ma-vas encodes a protein of 618 amino acids, which contains all of the known characteristics of vasa homologs. RT-PCR analysis revealed that ma-vas was exclusively expressed in the gonads of the female, intersex, and male. During gonadal natural sex reversal, ma-vas is expressed in oocytes at all stages of oogenesis, in degenerating oocytes of ovotestis, and in spermatogonia and spermatocytes at early stages. The vasa positive signal was also observed in the peripheral layer of late ovary. It was not found, however, in that layer of the testis. Alkaline phosphatase (AKP) staining on the ovary and testis also indicated that some cells had differentiational potential in the peripheral layer of the ovary, suggesting that spermatogonia might arise from cells with AKP and vasa-positive staining in the peripheral layer of the female gonad.

Keywords: vasa ; rice field eel; sex transformation


Partial Characterization and Evolution of Adh-Adhr in Drosophila dunni by Wilma V. Colón-Parrilla; Ivette Pérez-Chiesa (pp. 225-238).
We sequenced 2123 bp of the Adh-Adhr genomic region of Drosophila dunni of the cardini group from two cloned DNA PCR fragments and from two cDNA clones of an Adh transcript. This comprises the Adh coding region and introns, 3′ UTR, intergenic sequence, and most of Adhr, which is 260 bp downstream of Adh. Both genes have the typical Drosophila melanogaster Adh structure of three exons and two introns, except for changes in the putative 8 bp sequence involved in downregulation within the 3′ UTR of Adh. Two amino acid substitutions could explain the low activity previously reported for this enzyme in D. dunni: Thr → Lys at position 191 and Val → Thr at position 189. D. dunni's Adh has the lowest codon bias reported so far for Drosophila species, and based on analysis of the nucleotide substitution rate, it is less conserved than Adhr.

Keywords: Drosophila dunni ; cardini group of Drosophila ; Adh-Adhr ; downregulator; Hirtodrosophila-Tripunctata radiation

Assignment of Dicer Gene to Chicken Chromosome 5 by Radiation Hybrid Panel Mapping by Yong Tian; Lizhi Lu; Yan Fu; Jin Zhao; Cun Zhang; Qingyan Yuan; Junda Shen (pp. 239-243).

Polymorphism of the Porcine Leptin Gene Promoter and Analysis of Its Association with Gene Expression and Fatness Traits by M. Stachowiak; M. Mackowski; Z. Madeja; M. Szydlowski; A. Buszka; P. Kaczmarek; B. Rubis; P. Mackowiak; K. W. Nowak; M. Switonski (pp. 245-253).
We describe for the first time a 245 bp fragment of the porcine leptin gene promoter in the proximity of the transcription start site. Altogether, 720 pigs were screened with the PCR-SSCP technique for polymorphism in this region. Four SNPs, segregating as two haplotypes, have been identified, one of them (C113G) in the putative consensus site for the AP-2 transcription factor. This polymorphism was evenly distributed in the Duroc breed (n=21) and was absent in the Polish Landrace (n=248) and Pietrain breed (n=12). In the Polish Large White (n=191) and synthetic line 990 (n=243), allele G occurred with a very low frequency. The investigation was performed to test if the C113G SNP affects leptin mRNA level in subcutaneous fat and leptin protein concentration in serum. Additionally, the effect of this polymorphism on fatness traits was statistically analyzed. Although there was a trend toward decreased expression in GG animals, the differences were not significant between genotypes. We also found no evidence for an association of the LEP promoter genotype with the analyzed fatness traits.

Keywords: leptin promoter; pig; fat; single nucleotide polymorphism (SNP); quantitative trait locus (QTL)


Genetic Differentiation of Native Sheep Populations in East and South Asia by Rongqing Geng; Hong Chang; Lanping Wang; K. Tsunoda; Zhangping Yang; Wei Sun; Dejun Ji; Yonghong Li (pp. 263-279).
Variations of four sheep populations in China were examined by multiloci electrophoresis, and similar data are quoted to analyze the degree of genetic differentiation of native sheep populations in East and South Asia. Among 15 populations, the average heterozygosity is 0.2746, and the effective number of alleles is 1.559. Mongolian sheep possess the highest genetic diversity, and diversity decreases sequentially in the Chinese, Vietnamese, Bangladeshi, and Nepalese populations. Coefficients of genetic differentiation are 0.0126–0.3083, with an average of 0.148, demonstrating that the major genetic variation (85%) exists within populations. Genetic identity and genetic distance all show relatively low genetic differentiation. No relationship was found between geographic distance and genetic distance. Gene flow is common among the mass of populations, which leads to the inconsistency between geographic distance and genetic distance. The 15 native sheep populations in East and South Asia can be divided into two groups, one group including part of the Chinese and Mongolian populations and another including theYunnan population of China and part of the Nepalese and Bangladeshi populations. Other populations did not separate into groups, merging instead into the two main groups.

Keywords: sheep populations; genetic differentiation; phylogenetic relationship; East and South Asia


Genotypic Analysis of Multidrug-Resistant Mycobacterium tuberculosis Isolates Recovered From Central China by Shu-Lin Zhang; Hua Qi; Dun-Lian Qiu; Da-Xu Li; Jie Zhang; Chang-Mei Du; Guo-Bin Wang; Zhi-Rong Yang; Qun Sun (pp. 281-290).
DNA sequencing analysis was used to investigate genetic alterations in the rpoB, katG, and inhA regulatory region and embB in 66 Mycobacterium tuberculosis isolates recovered from Central China. Of the 36 multidrug-resistant isolates, 33 (92%) had mutations in the amplified region of rpoB. The most frequent mutation (58%, 19/36) was S531L (TCG→TTG). At least one mutation was found in the katG and inhA regulatory region in 83% (30/36) of the multidrug-resistant isolates, and mutations at katG codon 315 were identified in 78% (28/36). Alterations at embB306 may not confer resistance to EMB, and embB306 mutants were more frequently accompanied by rpoB mutations (100%, 16/16) than by katG 315 mutations (75%, 12/16). Our results show that geographic variation in the molecular genetic mechanism is responsible for drug resistance in multidrug-resistant M. tuberculosis. This observation will facilitate the development of a rapid molecular drug resistance screening approach for drug-resistant M. tuberculosis.

Keywords: Mycobacterium tuberculosis ; multidrug resistant; gene; mutation; sequence


Allozyme Variation and Phylogenetic Relationships in Picea jezoensis (Pinaceae) Populations of the Russian Far East by V. V. Potenko (pp. 291-304).
Genetic variation and differentiation of 12 populations of Picea jezoensis from the Russian Far East were studied using 20 allozyme loci. The mean number of alleles per locus was 2.63, the percent of polymorphic loci was 88.1%, the observed heterozygosity was 0.181, and the mean value of expected heterozygosity amounted to 0.189. The values of expected heterozygosity of the northern and central mainland populations were higher than in the southern part of the natural range. A significant bias of Hardy–Weinberg heterozygosity to equilibrium heterozygosity (Heq) suggests that most of the mainland populations have recently experienced a severe expansion in population size while populations from Kamchatka Peninsula have undergone a reduction in population size. Unbiased Nei’s genetic distance values were low within and between the mainland and Sakhalin Island populations (DN=0.008). The largest values (DN=0.063) were found between the mainland/Sakhalin and Kamchatka Peninsula populations. Based on genetic distance, P. jezoensis and P. kamtschatkensis could be considered as distinct taxa, but P. ajanensis, P. microsperma, and P. komarovii do not warrant taxonomic recognition.

Keywords: Picea jezoensis ; isozymes; genetic variation; phylogeny


Mitochondrial CR-1 Variation in Sardinian Hares and Its Relationships with Other Old World Hares (Genus Lepus) by Massimo Scandura; Laura Iacolina; Hichem Ben Slimen; Franz Suchentrunk; Marco Apollonio (pp. 305-323).
Among the European fauna, the Sardinian hare (Lepus sp.) is peculiar in that it differs from all other hares inhabiting the continent. Here, we report on the variation of a 461 bp sequence of hypervariable domain 1 of the mitochondrial control region, examined in 42 hares collected throughout Sardinia and compared to the corresponding sequences of different Lepus taxa. Seventeen novel haplotypes were found in the Sardinian population, resulting in a haplotype diversity of 0.840 and a nucleotide diversity of 0.012. As a result of Bayesian and principal coordinates analyses, Sardinian hares were grouped with North African hares, constituting a monophyletic clade that diverges from all other Old World hares, including Cape hares from South Africa and East Asia. Hence, our data agree that populations inhabiting North Africa and Sardinia form a distinct taxon, which could possibly be included in the L. capensis superspecies. Moreover, two corresponding lineages can be found in Sardinia and Tunisia, providing evidence of a common origin of the two populations and thus supporting the hypothesis that North African hares were introduced into the island in historical times. Our data show that the two lineages differ in their geographic distribution throughout the island and that the wild Sardinian population also shows the signature of a postintroduction demographic expansion.

Keywords: Sardinian hare; mtDNA; Lepus capensis ; phylogeography; population structure

Three New SNPs in Coding and Noncoding Regions of the Bovine CATB Gene by Edyta Juszczuk-Kubiak; Joanna Wyszyńska-Koko; Krystyna Wicińska; Stanisław Rosochacki (pp. 325-333).

Hox Genes from the Tapeworm Taenia asiatica (Platyhelminthes: Cestoda) by Kyu-Heon Kim; Yong Seok Lee; Hyeong-Kyu Jeon; Joong-Ki Park; Chang-Bae Kim; Keeseon S. Eom (pp. 335-343).
Hox genes are important in forming the anterior-posterior body axis pattern in the early developmental stage of animals. The conserved nature of the genomic organization of Hox genes is well known in diverse metazoans. To understand the Hox gene architecture in human-infecting Taenia tapeworms, we conducted a genomic survey of the Hox gene using degenerative polymerase chain reaction primers in Taenia asiatica. Six Hox gene orthologs from 276 clones were identified. Comparative analysis revealed that T. asiatica has six Hox orthologs, including two lab/Hox1, two Hox3, one Dfd/Hox4, and one Lox2/Lox4. The results suggest that Taenia Hox genes may have undergone independent gene duplication in two Hox paralogs. The failure to detect Post1/2 orthologs in T. asiatica may suggest that sequence divergence or the secondary loss of the posterior genes has occurred in the lineage leading to the cestode and trematode.

Keywords: Hox genes; PCR survey; Taenia asiatica ; platyhelminthes; lophotrochozoans


Genetic Differentiation of the Giant Honey Bee (Apis dorsata) in Thailand Analyzed by Mitochondrial Genes and Microsatellites by S. Insuan; S. Deowanish; S. Klinbunga; S. Sittipraneed; H. A. Sylvester; S. Wongsiri (pp. 345-361).
Genetic diversity and population differentiation of the giant honey bee (Apis dorsata) in Thailand were examined. Six PCR-RFLP mitotypes were generated from digestion of the COI-COII, Cytb-tRNAser, ATPase6-8, and lrRNA genes with Dra I and Hin fI. Low genetic diversity (h=0.074, π=0.032%) and a lack of genetic population differentiation between A. dorsata originating from geographically different regions were observed from mtDNA polymorphisms (P > 0.05). In contrast, microsatellite (A14, A24, and A88) polymorphisms revealed a relatively high level of genetic diversity in A. dorsata (H o=0.68–0.74, average number of alleles per locus=6.0–9.0). Both A24 and A88 indicated significant population differentiation between bees from the north-to-central region (north, northeast, and central regions), peninsular Thailand, and Samui Island.

Keywords: Apis dorsata ; honey bee; genetic diversity; mtDNA; microsatellites


Allozyme Variation in a Threatened Freshwater Fish, Spotted Murrel (Channa punctatus) in a South Indian River System by Mohamed Abdulkather Haniffa; Muniyandi Nagarajan; Achamveetil Gopalakrishnan; Kochikkaran Kunjumohammed Musammilu (pp. 363-374).
Samples of the spotted murrel (Channa punctatus) were collected from three rivers of Tamil Nadu and Kerala. The allozyme variation of C. punctatus was investigated by polyacrylamide gel electrophoresis. Eighteen enzymes were detected, but only 10 (EST, PGM, G3PDH, G6PDH, SOD, GPI, ODH, GDH, XDH, and CK) showed consistent phenotypic variations. Allele frequencies were estimated at the 18 polymorphic loci representing 10 enzymes. Two rare alleles, EST-4*C and G6PDH-2*C, were noted in the Tamirabarani and Kallada populations but were absent in the Siruvani population. The allele frequencies of the Tamirabarani and Kallada populations were similar, except for a few loci. Among the three populations, the maximum genetic distance (0.026) and FST (0.203) were found between the geographically distant Siruvani and Kallada populations. Overall the study showed that among the three populations, the Tamirabarani and Kallada have similar genetic structures.

Keywords: Channa punctatus ; allozyme; population; heterozygosity


Molecular Analysis Using Mitochondrial DNA and Microsatellites to Infer the Formation Process of Japanese Native Horse Populations by Hironaga Kakoi; Teruaki Tozaki; Hitoshi Gawahara (pp. 375-395).
To assess the genetic diversity of Japanese native horse populations, we examined seven such populations using mitochondrial DNA (mtDNA) and microsatellite analyses. Four reference populations of Mongolian horses and European breeds were employed as other equids. In the mtDNA analysis, the control region (D-loop) of 411 bp was sequenced, and 12 haplotypes with 33 variable sites were identified in the Japanese native horses. The phylogenetic tree constructed by haplogrouping and using worldwide geographic references indicated that the haplotypes of the Japanese native horses were derived from six equid clusters. Compared with the foreign populations, the Japanese native populations showed lower within-population diversity and higher between-population differentiation. Microsatellite analysis, using 27 markers, found an average number of alleles per locus of 9.6 in 318 native and foreign horses. In most native populations, the within-population diversity was lower than that observed in foreign populations. The genetic distance matrix based on allelic frequency indicated that several native populations had notably high between-population differentiation. The molecular coancestry-based genetic distance matrix revealed that the European populations were differentiated from the Japanese and Mongolian populations, and no clear groups could be identified among the Japanese native horse populations. The genetic distance matrices had few correlations with the geographic distribution of the Japanese native populations. Based on the results of both mtDNA and microsatellite analyses, it could be speculated that each native population was formed by the founder populations derived from Mongolian horses. The genetic construction of each population appears to have been derived from independent breeding in each local area since the time of population fission, and this was accompanied by drastic genetic drift in recent times. This information will help to elucidate the ancestry of Japanese native horses.

Keywords: Japanese native horses; mitochondrial DNA; D-loop; microsatellite DNA; genetic diversity; phylogeny
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