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Biochemical Genetics (v.48, #11-12)

DNA Oligonucleotides and Plasmids Perform Equally as Donors for Targeted Gene Conversion by Stefan Wagner; Judi McCracken; Sally Cole; Götz Laible (pp. 897-908).

Site-specific gene modifications in cells are initiated by the introduction of exogenous DNA. We used a recently established cell assay to compare the ability of DNA donors to induce a single point mutation that converts a target gene encoding blue fluorescent protein (BFP) into expressing green fluorescent protein (GFP). In a chromosomal assay with cells stably expressing BFP, we showed that fluorescently labeled single-stranded oligonucleotides and a donor plasmid cotranscribing a red fluorescent protein provide similar efficiencies in triggering BFP–GFP conversions. In transient cotransfections, an isogenic donor plasmid comprising a nonfunctional GFP gene yielded a greater efficiency for the conversion of the BFP target gene than a nonisogenic donor, and all plasmid donors were superior to oligonucleotides.

Keywords: Gene conversion; Green fluorescent protein; Plasmid; Oligonucleotide; Transfection

Subtelomeric Microduplications in Three Sisters with Moderate Mental Retardation by Lamia Hila; Hedia Tébourbi; Leila Abeid; Imen Rejeb; Habiba Chaabouni (pp. 909-914).

Copy number changes of subtelomeric regions are a common cause of mental retardation, occurring in approximately 5% of mentally retarded patients. New molecular techniques allow the identification of subtelomeric microduplications. We report a Tunisian family of three sisters with moderate mental retardation, facial dysmorphism, cardiopathy, and bilateral clinodactyly of the third and fourth toes, explored by MLPA, showing the same associated microduplications, 15q and Xq, without a concurrent deletion.

Keywords: Duplications; Mental retardation; Multiplex ligation-dependent probe amplification (MLPA)

Association of COX-2 Promoter Polymorphism with Gastrointestinal Tract Cancer in Iran by Firouzeh Biramijamal; Shaghayegh Basatvat; Arash Hossein-Nezhad; Maryam Sadat Soltani; Kambiz Akbari Noghabi; Guity Irvanloo; Kourosh Shamimi (pp. 915-923).

Mitochondrial DNA-Based Genetic Structure Analysis of Pudong White Pigs by Minghui Wang; Zhonghua Sheng; Xiao Wu; Qishan Wang; Yuchun Pan (pp. 924-937).

There are extensive debates concerning the origin and the necessity of conservation of Pudong White pigs in the Taihu region of China. To elucidate their genetic ancestry, we sequenced the complete mtDNA D-loop sequences of 25 Pudong White pigs and 9 Shawutou pigs from the Taihu region and reanalyzed 158 published sequences of other breeds in GenBank. Haplotypes of all pigs were classified into two clades, A and E, but Pudong White pigs were found only in clade A. The results of population differentiation demonstrated that there were few genetic exchanges among the eight populations. Furthermore, divergence time estimates suggested that the Pudong White pigs split from four types of Taihu pigs at about 0.26–0.75 million years ago. Overall, the results suggest that the Pudong White pig is a unique population, and conservation practice should concentrate on preserving this isolated population.

Keywords: Pudong White pig; mtDNA; Haplotype; Population differentiation; Phylogenetic position

The Origin of the White Roman Goose by C. M. Wang; T. D. Way; Y. C. Chang; N. T. Yen; C. L. Hu; P. C. Nien; Y. S. Jea; L. R. Chen; J. Y. Kao (pp. 938-943).

In order to avoid interference from nuclear copies of mitochondrial DNA (numts), mtDNA of the white Roman goose (domestic goose) was extracted from liver mitochondria. The mtDNA control region was amplified using a long PCR strategy and then sequenced. Neighbor-joining, maximum parsimony, and maximum-likelihood approaches were implemented using the 1,177 bp mtDNA control region sequences to compute the phylogenetic relationships of the domestic goose with other geese. The resulting identity values for the white Roman geese were 99.1% (1,166/1,177) with western graylag geese and 98.8% (1,163/1,177) with eastern graylag geese. In molecular phylogenetic trees, the white Roman goose was grouped in the graylag lineage, indicating that the white Roman goose came from the graylag goose (Anser anser). Thus, the scientific name of the white Roman goose should be Anser anser ‘White Roman.’

Keywords: Mitochondrial DNA; Phylogenetic relationship; Geese

Genetic Diversity of the Melanocortin 4 Receptor (MC4R) Gene and its Association with Slaughter Traits in the Landes Goose by Yi Huang; Yan Wang; Daqian He; Yiping Liu (pp. 944-953).

Melanocortin 4 receptor (MC4R) plays a crucial part in regulating feeding behavior in humans and rodents. We detected two single nucleotide polymorphisms (SNPs; c.108G → A and c.627C → T) in the goose MC4R gene and genotyped 94 Landes geese for association analysis with several carcass traits. Significant associations (P < 0.05) were obtained for c.108G → A with carcass weight, breast muscle percentage, and leg muscle percentage, and for c.627C → T with body weight, carcass weight, semi-eviscerated weight, and eviscerated weight. We re-constructed haplotypes based on the two SNPs and analyzed diplotypes in association with carcass traits, obtaining significant associations with several of the traits. These results suggest that polymorphisms in the MC4R gene could have effects on carcass traits in Landes geese. More study is required to confirm these results.

Keywords: MC4R ; Landes goose; SNP; Carcass trait; Haplotype

Analysis of Genetic Diversity of Chukar Partridge (Alectoris chukar) Populations in Khorasan-e-Razavi Province of Iran by RAPD-PCR by Hassan Abbasi; Mojtaba Tahmoorespour; Mohammad R. Nassiri; Shahrokh Ghovvati (pp. 954-961).

RAPD markers were used to investigate population genetic parameters of an endangered partridge, Alectoris chukar, in four areas of Iran, as a part of a genetic conservation program. The aim of this study was to analyze the genetic similarity among these populations. Blood samples from 75 birds were used for DNA extraction and RAPD-PCR analysis of 67 loci, with 28 polymorphic bands (41.79%). The populations of Kalat-e-Nader and Mashhad were found to be closely related, as were the Torbat-e-Jaam and the Quchan populations. Mean heterozygosity for all populations was 0.4405 ± 0.0755. The results indicate that chukar partridge genetic diversity in Khorasan-e-Razavi province is sufficient and the amount of gene flow among populations is acceptable.

Keywords: Chukar partridge; Genetic diversity; RAPD-PCR (random amplified polymorphic DNA-polymerase chain reaction); Khorasan-e-Razavi province; Gene flow

Molecular Characterization of the Full-Length Coding Sequence of the Caprine Laminin Receptor Gene (RPSA) by Rongyan Zhou; Xianglong Li; Huiqin Zheng; Lanhui Li; Weiyao Quan; Zunan Shen; Jun Tong; Qingfang Yang; Qiang Fu (pp. 962-969).

Scrapie is a prion disease in sheep and goats. Ribosomal protein SA (RPSA), also called 37 kDa laminin receptor precursor/67 kDa laminin receptor has been demonstrated to be a putative cell surface receptor for prion. To investigate the caprine RPSA, we cloned the full-length coding sequence of the gene of goat and submitted it to GenBank. The length of the open reading frame is 888 bp, encoding 295 amino acids. The putative amino acid sequence is highly similar to that of other mammals. The caprine amino acid sequence of RPSA is shown to be identical to the sequence of species susceptible to scrapie at positions 241, 272, and 291. The phylogenetic tree analysis revealed that the genetic distance between sheep and goat is the smallest. Moreover, RT-PCR results of 11 tissues indicated that RPSA mRNA is expressed in all selected caprine tissues.

Keywords: RPSA; 37/67-kDa laminin receptor gene; Goat; Expression

Polymorphisms in Promoter Sequences of the p15 INK4B and PTEN Genes of Normal Japanese Individuals by Yasuhito Ohsaka; Shingo Yogosawa; Ryoko Nakanishi; Toshiyuki Sakai; Hoyoku Nishino (pp. 970-986).

Gene promoter regions of p15^INK4B, a cyclin-dependent kinase inhibitor, and phosphatase and tensin homolog (PTEN), a dual-function protein and lipid phosphatase, interact with regulatory factors for gene transcription and methylation. Normal individuals exhibit sequence polymorphisms in these regulatory genes. We isolated genomic DNA from whole blood of healthy Japanese individuals and sequenced promoter regions of the p15 INK4B and PTEN genes. We also examined the influence of polymorphisms on promoter activity in several cell lines. We identified polymorphisms at positions −699, −394, and −242 and an insertion at position −320 in the p15 INK4B gene and a polymorphism at position −1142 in the PTEN gene. Reporter gene analysis revealed that these polymorphisms influenced transcriptional regulation in their cell lines. Our results indicate for the first time that promoter sequences of the p15 INK4B and PTEN genes differ among normal Japanese individuals and that promoter polymorphisms can influence gene transcription.

Keywords: Normal individuals; p15^INK4B ; Promoter polymorphism; PTEN; Transcription

Genetic Polymorphisms of Sulfotransferases (SULT1A1 and SULT1A2) in a Turkish Population by Serdal Arslan (pp. 987-994).

Sulfotransferases (SULTs) play a significant role in the biotransformation of a variety of xenobiotics and endogenous compounds. SULTs are genetically polymorphic enzymes; to date, 12 human cytosolic SULT isoforms have been identified. This study investigated SULT1A1 and SULT1A2 gene polymorphism using a PCR-RFLP method (n = 303). The frequency of the SULT1A1*1 allele was 76.2% and SULT1A1*2 was 23.8%. The SULT1A1*3 allele could not be identified. The SULT1A2 frequencies were 69.2% (SULT1A2*1), 18.3% (SULT1A2*2), and 12.5% (SULT1A2*3). The SULT1A1 and SULT1A2 loci were in Hardy–Weinberg equilibrium (SULT1A1 χ² = 0.58, P = 0.44; SULT1A2 χ² = 7.28, P = 0.06). Linkage analysis indicated a close linkage between these two genes (χ² = 5.31, P < 0.01); therefore, the statistical hypothesis that SULT1A1 and SULT1A2 alleles are independently distributed was rejected. Additionally, a strongly positive linkage was detected between SULT1A1*2 and SULT1A2*2 alleles in this population (D′ = 0.79, χ² = 33.33).

Keywords: Sulfotransferases; Linkage disequilibrium; SULT1A1 ; SULT1A2

Genetic Structure of Brown Trout (Salmo trutta) Populations from Turkey Based on Microsatellite Data by Serdal Arslan; Fevzi Bardakci (pp. 995-1014).

This present study investigated micro- and macro-geographic microsatellite DNA variations using five polymorphic microsatellite loci from 27 brown trout populations in Turkey. Average number of alleles and average observed heterozygosity were 7.4 and 0.254, respectively. Even populations from the same sea basin and river system (the so called micro-geographic regions) had unique alleles. Genetic variation among the populations from macro-geographic regions (different sea basins and river systems) was 45.78%. The mtDNA lineages of brown trout that have previously been identified by mtDNA analyses were supported by the analysis of the microsatellite DNA data in general. The Çatak population, which belongs to the Tigris lineage, was clustered together with the Euphrates populations within the Adriatic mtDNA lineage, based on microsatellite data. Both mitochondrial and microsatellite DNA analyses have made it possible to determine a secondary contact between Adriatic and Tigris lineages.

Keywords: Salmo trutta ; Microsatellite DNA; Anatolia; Brown trout; Phylogeny; Phylogeography; Turkey

Genetic Relationships Among 22 Taxa of Bamboo Revealed by ISSR and EST-Based Random Primers by Arup K. Mukherjee; Shibani Ratha; Sujaya Dhar; Akhil K. Debata; Pradosh K. Acharya; Sudhamoy Mandal; Pratap C. Panda; Ajay K. Mahapatra (pp. 1015-1025).

Genetic relationships among 22 taxa of bamboo were evaluated using 12 inter simple sequence repeats (ISSR) and four expressed sequence tag (EST)-based random primers, resulting in amplification of 220 loci. The grouping of species based on Jaccard’s similarity matrix using UPGMA and principal coordinate analysis agreed with earlier published reports on molecular phylogenetic studies in bamboos with few deviations. In the dendrogram, however, species of one genus were placed in different clusters along with members of other genera. This calls for correct taxonomic delineation at the genus and species level using both vegetative and reproductive characters and correlation of molecular data with morphologically definable taxonomic groupings at the proper taxonomic level.

Keywords: Bamboo; ISSR; EST–SSR; Genetic diversity

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Biochemical Genetics (v.48, #11-12)

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Biochemical Genetics (v.48, #11-12)