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Biochemical Genetics (v.45, #7-8)

Arg753Gln Polymorphism of the Human Toll-like Receptor-2 Gene in Children with Recurrent Febrile Infections by Necil Kutukculer; Betül Sozeri Yeniay; Guzide Aksu; Afig Berdeli (pp. 507-514).

Polymorphisms in toll-like receptors (TLRs) have been reported to increase susceptibility for some diseases. TLR-2 gene polymorphisms in Turkish children with recurrent respiratory tract infections and without well-known humoral immunodeficiencies were examined. The study consisted of 52 children with recurrent infections (study group) and 91 healthy children with a maximum of two infections in a year (control group). Recurrent infection was defined as the presence of at least six febrile bacterial infection episodes in a year. Not only TLR-2 gene polymorphisms but also immunoglobulins (IgG, IgM, IgA), IgG subsets (G1, G2, G3), and specific antibody levels (anti-tetanus and anti-hemophilus influenza) were determined to exclude humoral immunodeficiencies. The Arg753Gln and Arg677Trp polymorphisms were genotyped by polymerase chain reaction restriction fragment length polymorphism. The Arg753Arg genotype was significantly decreased in the study group compared to the control (P < 0.05). Children with recurrent infections were also found to be more frequently Arg753Gln heterozygous (P < 0.05), and their Gln allele distribution was higher than that of the control subjects (23% vs. 4.9%; P < 0.001). In contrast to these results, we did not detect any case with Arg677Trp polymorphism in both groups. These results have indicated that there is a strong significant relationship between susceptibility to recurrent bacterial infections and Arg753Gln polymorphism of the TLR-2 gene.

Keywords: TLR-2 gene polymorphism; Single nucleotide polymorphism; Recurrent infections; Children

Genetic diversity of local geese of varying productivity and feather color in Kars by Alparslan Kadir Devrim; Necati Kaya; Aysel Guven; Buket Kocer (pp. 515-522).

The local geese in the transition region between the Caucasus Mountains and Anatolia have economically significant differences in productivity and are identified by four feather colors, white, black, piebald, and yellow. This study was undertaken to determine the genetic structure, evolutionary relationships, and genetic diversity among these birds. DNA samples were obtained from 100 animals, and 50 random primers were screened. Genetic relationships were determined by random amplified polymorphic DNA polymorphisms obtained from a total of 48 loci, showing 40 bands (83.33%) that were polymorphic among all the populations investigated. A dendrogram constructed for this study revealed a close relationship between the white and the black birds. Additionally, the piebald birds showed close similarity to white and black geese, and the yellow birds displayed a clear distance from the other three populations.

Keywords: DNA fingerprinting; Genetic diversity; Goose; RAPD-PCR

Genetic Analysis of RET, EDNRB, and EDN3 Genes and Three SNPs in MCS + 9.7 in Chinese Patients with Isolated Hirschsprung Disease by Xian-Ning Zhang; Miao-Ni Zhou; Yun-Qing Qiu; Shi-Ping Ding; Ming Qi; Ji-Cheng Li (pp. 523-527).

Isolation and Characterization of a β-tubulin Gene from Trichoderma Harzianum by Min Li; Qian Yang (pp. 529-534).

Distribution of Two Asian-Related Coding SNPs in the MC1R and OCA2 Genes by I. Yuasa; K. Umetsu; S. Harihara; A. Kido; A. Miyoshi; N. Saitou; B. Dashnyam; F. Jin; G. Lucotte; P. K. Chattopadhyay; L. Henke; J. Henke (pp. 535-542).

Very little is known about the genes and mechanisms affecting skin lightening in Asian populations. In this study, two coding SNPs, c.G1129A (R163Q) at the MC1R (melanocortin 1 receptor) gene and c.A1962G (H615R) at the OCA2 (oculocutaneous albinism type II) gene, were investigated in a total of 1,809 individuals in 16 populations from various areas. The Q163 and R615 alleles prevailed almost exclusively in East and Southeast Asian populations. Wright’s F _ST was 0.445 for R163Q and 0.385 for H615R among the 16 populations. The frequency of the Q163 allele was higher in Northeast Asians than in Southeast Asians. The frequency of the R615 allele was highest in South China and unlikely to be associated with levels of ultraviolet radiation. This allele may be a good marker to study the genetic affinity among East Asians because of its restricted distribution and marked difference in allele frequency.

Keywords: MC1R ; OCA2 ; Pigmentation; Polymorphism; Population study; Skin color

Phylogeography of Wild Musk Shrew (Suncus Murinus) Populations in Asia Based on Blood Protein/Enzyme Variation by Megumi Kurachi; Yoshi Kawamoto; Yuji Tsubota; Ba-Loc Chau; Vu-Binh Dang; Tashi Dorji; Yoshio Yamamoto; Maung Maung Nyunt; Yoshizane Maeda; Loan Chhum-Phith; Takao Namikawa; Takahiro Yamagata (pp. 543-563).

The musk shrew (Suncus murinus) is an insectivore species that inhabits tropical and subtropical Asia widely. To clarify the genetic relationship among wild musk shrew populations, we examined the electrophoretic variants of biparentally inherited genetic markers at 10 loci coding for eight blood proteins/enzymes in a total of 639 animals and compared the results obtained from the mitochondrial DNA data. The principal-component analysis performed using the allele frequency data revealed that the 17 populations could be divided into two major groups, a South Asian group and a Southeast Asian group that includes several island populations bound by Myanmar. The degrees of genetic divergence among populations were higher within the Southeast Asian group than within the South Asian group. This finding was incongruent with the mtDNA diversity. Analysis conducted at the individual level showed that a shrew from the central region in Myanmar that carries a South Asian type of mtDNA showed the electrophoretic variants specific to the Southeast Asian group, suggesting that this region is a contact zone between the two major groups.

Keywords: Suncus murinus ; Blood proteins/enzymes; Mitochondrial DNA; Phylogeography; Asia

Genetic Divergence Detected by ISSR Markers and Characterization of Microsatellite Regions in Mytilus Mussels by Miguel A. Varela; Ana González-Tizón; Luis Mariñas; Andrés Martínez-Lage (pp. 565-578).

The wide distribution of microsatellites in mussels of the Mytilus edulis complex (Mytilidae) enables the analysis of inter-simple-sequence repeat (ISSR) markers. The aim of this investigation was to assess genetic differentiation in six sampling localities distributed along the European Atlantic coast to expose the potential of these markers in genetic studies requiring the detection of low polymorphism and as a source of sequences for developing microsatellite markers. We detected low genetic structuring within each member of the Mytilus edulis complex. Nei and Li distances and AMOVA clustered the individuals studied into two groups. On the basis of these results two sampling localities coming from the M. edulis × M. galloprovincialis mosaic hybrid zone in Western Europe were assigned to one species. On the other hand, mussels of a sampling locality in the Baltic Sea were not significantly different from a pure M. edulis locality supporting an extensive introgression of M. edulis in these individuals. Finally, 148 microsatellites were found in the sequences of 51 ISSR markers, and two polymorphic microsatellite markers were developed.

Keywords: Genetic variation; ISSR; Microsatellite; Mussel; Mytilus

Lack of Genetic Differentiation in the Shrimp Penaeus Chinensis in the Northwestern Pacific by Zhaoxia Cui; Chi Pang Li; In Kwon Jang; Ka Hou Chu (pp. 579-588).

Genetic differentiation of the shrimp Penaeus chinensis in the Yellow Sea and Bohai Sea was investigated using the mitochondrial control region (CR). RFLP of a partial CR segment (613 bp) shows that 106 out of 122 (86.9%) individuals from six sampling localities along the coast of northern China and the west coast of the Korean Peninsula share the same haplotype, and the haplotype frequencies among localities are not significantly different. The findings are further confirmed by sequencing the complete CR. Divergence of the complete CR (992 bp) is less than 1.6% in 14 individuals from the six localities. F-statistics based on RFLP data and the TCS network of sequencing data suggest little genetic differentiation of P. chinensis in the Yellow Sea and Bohai Sea. Mismatch analysis suggests a rapid expansion of P. chinensis population to the Yellow Sea and the Bohai Sea, which probably occurred with the rapid rise in sea level after the last glacial maximum. Despite the lack of genetic heterogeneity, we propose that P. chinensis populations in this region should be treated as separate management units, as fishery management programs have to be applied on a local basis by different governments.

Keywords: Control region; Genetic diversity; Population genetics; Fenneropenaeus

Polymorphism and Genomic Structure of the A+T-Rich Region of Mitochondrial DNA in the Oriental Mole Cricket, Gryllotalpa Orientalis (Orthoptera: Gryllotalpidae) by Iksoo Kim; So Young Cha; Mi Ae Kim; Young Shin Lee; Kwang Sik Lee; Yong Soo Choi; Jae Sam Hwang; Byung Rae Jin; Yeon Soo Han (pp. 589-610).

The complete A+T-rich region of mitochondrial DNA has been cloned and sequenced from 48 individuals of Gryllotalpa orientalis (Orthoptera: Gryllotalpidae), collected from five Korean localities. Thirty-six haplotypes acquired from 48 individuals were found to range in size from 917 to 925 bp, with a sequence divergence from 0.1% to 14.3% and an A+T content from 74.5 to 76.3%. Phylogeographic analysis of the G. orientalis haplotypes showed the presence of two clearly differentiated mitochondrial clades, separated by 13.4% of a minimum uncorrected sequence divergence, which suggests the presence of an unknown, similar Gryllotalpa species or a once isolated G. orientalis population. Structural analysis in search of the conserved structural elements previously described in the caeliferan Orthoptera and Diptera revealed that the G. orientalis A+T-rich region harbored a stretch of the [TA(A)]n sequence, which has been suggested to be involved in the control of transcription or replication. In contrast to the abundance of the sequence stretches containing the stem-and-loop structure in the G. orientalis A+T-rich region, the 3′ flanking sequence “G(A)nT,” which is well conserved in a variety of organisms, including the caeliferan Orthoptera and Diptera, was not conserved in the A+T-rich region of G. orientalis.

Keywords: Mitochondrial DNA; A+T-rich region; Control region; Gryllotalpa orientalis ; Oriental mole cricket; Intraspecific phylogeny

Molecular Cloning and Single Nucleotide Polymorphism Detection of Buffalo DGAT1 Gene by Jing Yuan; Jun Zhou; Xuemei Deng; Xiaoxiang Hu; Ning Li (pp. 611-621).

We report molecular cloning and single nucleotide polymorphism detection of the buffalo DGAT1 gene. Diacylglycerol acyltransferase (DGAT1) is considered the key enzyme in controlling the rate of synthesis of triglycerides. The DGAT1 gene was recently identified as a strong functional candidate gene affecting milk yield and composition in cattle. A full-length buffalo DGAT1 genomic DNA was amplified by iterative PCR based on homolog cloning. The buffalo DGAT1 gene comprises 17 exons and spans approximately 8.3 kb. The genomic structures of DGAT1 are highly conserved among mammal species. The deduced protein of buffalo DGAT1 contains 489 amino acids, showing high-sequence similarity with mammal homologs. Through PCR-SSCP analysis and sequencing, seven polymorphic positions were detected in the complete genomic region of buffalo DGAT1, and their frequencies were observed from a collection of 117 buffalo. The SNP (C/T) detected at position 11785 in exon 17 creates a substitution change for the amino acid sequence, resulting in an Ala residue (GCG) transition to a Val residue (GTG) in position 484 of buffalo DGAT1 protein. Information provided in this study will be useful in further studies to determine the role DGAT1 plays in the regulation of milk fat synthesis and quality improvement for milk in buffalo.

Keywords: Buffalo; DGAT1; Genomic structure; SNP

Molecular Phylogeny of Grey Mullets (Teleostei: Mugilidae) in Greece: Evidence from Sequence Analysis of mtDNA Segments by Vasilis Papasotiropoulos; Elena Klossa-Kilia; Stamatis N. Alahiotis; George Kilias (pp. 623-636).

Mitochondrial DNA sequence analysis has been used to explore genetic differentiation and phylogenetic relationships among five species of the Mugilidae family, Mugil cephalus, Chelon labrosus, Liza aurata, Liza ramada, and Liza saliens. DNA was isolated from samples originating from the Messolongi Lagoon in Greece. Three mtDNA segments (12s rRNA, 16s rRNA, and CO I) were PCR amplified and sequenced. Sequencing analysis revealed that the greatest genetic differentiation was observed between M. cephalus and all the other species studied, while C. labrosus and L. aurata were the closest taxa. Dendrograms obtained by the neighbor-joining method and Bayesian inference analysis exhibited the same topology. According to this topology, M. cephalus is the most distinct species and the remaining taxa are clustered together, with C. labrosus and L. aurata forming a single group. The latter result brings into question the monophyletic origin of the genus Liza.

Keywords: Grey mullets; Mugilidae family; Mitochondrial DNA; Sequencing; Phylogeny

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Biochemical Genetics (v.45, #7-8)

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Biochemical Genetics (v.45, #7-8)