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Biochemical Genetics (v.48, #1-2)
Phylogeny of Local Sheep Breeds in East Asia, Focusing on the Bayanbulak Sheep in China and the Sipsu Sheep in Bhutan by Kenji Tsunoda; Hong Chang; Guobin Chang; Wei Sun; Tashi Dorji; Gyem Tshering; Yoshio Yamamoto; Takao Namikawa (pp. 1-12).
The phylogenetic positions of the Bayanbulak sheep in China and the Sipsu sheep in Bhutan in the northern Asian sheep group were determined on the basis of allele frequency data for five informative and polymorphic loci of blood protein and nonproteins, such as transferrin (TF), arylesterase (ES), hemoglobin-β (HB-β), X-protein (XP), and potassium transport (KE), using different electrophoretic and ion-densitometric techniques. Based on Nei’s genetic distance, clustering analysis by the UPGMA method showed that the Bayanbulak sheep is clustered in the northern Asian sheep group. Furthermore, the Bayanbulak sheep belongs to a subgroup containing the Khalkhas and Hu sheep of the Mongolian sheep group, which is distinguished from another subgroup of the small-tailed Han, Tan, Tong, and Wadi sheep. The Bayanbulak sheep was closest to the Hu sheep, despite a morphological difference in the fat deposits. In addition to these findings, the Sipsu sheep was verified to belong to the Baruwal sheep.
Keywords: Phylogenetic relationship; Genetic distance; Bayanbulak sheep; Sipsu sheep; Blood protein polymorphism
Prion Protein Polymorphisms and Estimation of Risk of Scrapie in East Asian Sheep by Kenji Tsunoda; Takao Namikawa; Keizo Sato; M. A. Hasnath; Maung Maung Nyunt; Heramba B. Rajbandary; Chau Ba Loc; Ts Zanchiv; Hong Chang; Wei Sun; Tasi Dorji (pp. 13-25).
Allele and genotype frequency distributions of prion protein (PrP) polymorphisms at three codons, 136, 154, and 171, in East Asian sheep were determined by PCR–RFLP analysis using 553 animals from nine local breeds of the northern group and four local breeds of the southern group. Based on the genotype distribution, the risk score for scrapie was estimated. Among the local breeds, ARQ appeared predominantly (0.7701–1), followed by ARH and ARR. From such a biased allele distribution, it was difficult to ascertain the prevalent genetic relationships. A marked difference in allele frequencies between the northern and southern groups was seen (P < 0.0001). The East Asian sheep had ARQ at the highest frequency (0.8834); in European sheep it was 0.5317. According to an assessment of scrapie risk in the PrP genotype classes, the predominant ARQ/ARQ in East Asian sheep corresponded to the risk score of R4. This finding suggests that East Asian sheep have a high level of genetic susceptibility to scrapie.
Keywords: Prion protein; RFLP; Local sheep breed; Scrapie; Asia
A Decreasing Gradient of 374F Allele Frequencies in the Skin Pigmentation Gene SLC45A2, from the North of West Europe to North Africa by Gérard Lucotte; Géraldine Mercier; Florent Diéterlen; Isao Yuasa (pp. 26-33).
The 374F mutation in the SLC45A2 gene, encoding the membrane-associated transporter protein (MATP) that plays an important role in melanin synthesis, has been suggested to be associated with skin color in Caucasians. In this study, the detailed distribution of the 374F allele has been investigated in 2063 unrelated subjects from 18 European and three North African populations. The highest allele frequency is observed in Denmark (0.980), and the lowest frequencies are observed in Tunisia (0.610) and in Morocco (0.691). A significant latitudinal cline in 374F allele frequencies was observed, ranging from the north of West Europe to North Africa (r = 0.869). The results confirm that the distribution of the 374F allele may reflect the ultraviolet radiation level and can be associated with skin color variation in these regions.
Keywords: Membrane-associated transporter protein (MATP); Skin pigmentation; SLC45A2 gene; 374F allele frequencies; Population study
Genetic Diversity Assessment of Trollius Accessions in China by RAPD Markers
by Yong Li; Wan Long Ding (pp. 34-43).
Analysis of Diversity in Chinese Cultivated Barley with Simple Sequence Repeats: Differences Between Eco-Geographic Populations by Feixue Chen; Defu Chen; María-Pilar Vallés; Zhen Gao; Xiwen Chen (pp. 44-56).
The genetic diversity of 116 barley accessions, representing five Chinese eco-geographic populations, was studied using simple sequence repeat (SSR) markers. The 21 SSR loci revealed 128 alleles with an average of 6.1 alleles per locus. The highest values of proportion of polymorphic loci (P) and gene diversity index (He) were obtained in the Northern (P = 1.00; He = 0.60) and the Yangtze River reaches and Southern populations (P = 1.00; He = 0.59). The lowest values were in the populations of the Yellow River reaches (P = 0.86; He = 0.44). The highest average number of alleles per locus (4.52) and number of unique alleles (7) were found in the Qinghai–Tibet plateau population. Cluster analysis revealed that together with the row type, strong eco-geographic variables influenced the classification. Associations of SSR and eco-geographic values were established for 11 SSR loci. Four to six markers were found to discriminate among geographic groups, which may serve as tools for diagnosis of the eco-geographic populations and provide evidence for the adaptive nature of SSR markers.
Keywords: Barley; Eco-geographic variable; Genetic diversity; Natural selection; Simple sequence repeats
Genetic Diversity and Population Structure of Teucrium polium (Lamiaceae) in Tunisia by Abdennacer Boulila; Afef Béjaoui; Chokri Messaoud; Mohamed Boussaid (pp. 57-70).
Random amplified polymorphic DNA markers were used to assess the genetic diversity within and among seven Tunisian diploid and polyploid populations of Teucrium polium L. from five bioclimatic areas. Out of the 141 bands generated from eight selected primers, 124 were polymorphic. The genetic diversity within a population (Shannon’s index) was high and varied according both the ploidal levels and bioclimatic zones. The genetic differentiation among populations assessed by G ST and ΦST statistics was high, suggesting a low level of gene flow among them. The major proportion of the variation was attributable to individual differences within populations. The UPGMA analysis based on Nei and Li’s coefficient showed that individuals from each population clustered together. In a dendrogram using the ΦST distance matrix, population grouping is concordant with bioclimates and cytotypes. Conservation strategies should take into account the level of the genetic diversity of the populations according to their bioclimate and ploidal levels.
Keywords: Teucrium polium ; Genetic diversity; Bioclimate; Ploidy; Tunisia
Microsatellite Variability and Its Relationship with Growth, Egg Production, and Immunocompetence Traits in Chickens by Rudranath Chatterjee; Ramashraya P. Sharma; Tarun K. Bhattacharya; Matam Niranjan; B. Loknath Reddy (pp. 71-82).
Variability of microsatellites and a possible relationship with growth, egg production, and immunocompetence traits were estimated for six crossbred chicken populations of White Leghorn. Nine microsatellite markers were explored; an association study used the least square maximum-likelihood method on 170 birds of six genetic groups. Seven microsatellites were polymorphic, with two to four alleles. The polymorphism information content (PIC) of five markers was more than 52%. Microsatellites MCW0041, ADL0210, and MCW0110 were significantly (P < 0.05) associated with egg production traits. Genotype 33 of MCW0041 had the highest egg production, up to 64 and 72 weeks of age. Genotypes 11 and 13 of this marker produced the lowest number of eggs. The heterozygous genotype 34 of ADL0210 had the highest egg production, up to 52, 64, and 72 weeks of age. Homozygote 11 of MCW0110 produced the highest number of eggs, up to 28 weeks of age. MCW0041 was significantly (P < 0.05) associated with body weight at 28 and 40 weeks of age. No microsatellite was significantly associated with egg weight at any age, with age at sexual maturity, or with immune response to sheep RBC.
Keywords: Microsatellites; Growth; Egg production; Immunocompetence; Chicken
Genetic Relationships Within and Between Capsicum Species by Ayşe Gul Ince; Mehmet Karaca; A. Naci Onus (pp. 83-95).
Genetic relationships were estimated among 24 accessions belonging to 11 species of Capsicum, using 2,760 RAPD markers based on touch-down polymerase chain reactions (Td-RAPD-PCR). These markers were implemented in analyses of principal coordinates, unweighted pair group mean average, and 2,000 bootstrap replications. The accessions were divided into four groups, corresponding to previously described Capsicum complexes: C. annuum complex (CA), C. baccatum complex (CB), C. pubescens complex (CP), and C. chacoense accessions (CA/B). Their overall mean genetic similarity index was 0.487 ± 0.082, ranging from 0.88 to 0.32, based on Jaccard’s coefficient. The highest genetic variation was observed among the accessions in CP; the accessions in CB had a low level of variation as judged from the standard deviations of the genetic similarity indices. Based on the Td-RAPD-PCR markers, the 24 accessions were divided into four major groups, three of which corresponded to the three distinct Capsicum complexes. Accessions of C. chacoense were found to be equally related to complexes CA, CB, and CP.
Keywords: RAPD-PCR; DNA markers; Species relationships; Capsicum complex; Touch-down PCR
Spatial Pattern and Fine-Scale Genetic Structure Indicating Recent Colonization of the Palm Euterpe edulis in a Brazilian Atlantic Forest Fragment
by Fábio de Almeida Vieira; Dulcinéia de Carvalho; Pedro Higuchi; Evandro Luiz Mendonça Machado; Rubens Manoel dos Santos (pp. 96-103).
Identification of NF-κB1 and NF-κBIΑ Polymorphisms Using PCR–RFLP Assay in a Turkish Population by Serap Senol Tuncay; Pinar Okyay; Fevzi Bardakci (pp. 104-112).
A polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) assay was used in a Turkish population to determine the frequency of polymorphisms of the nuclear factor-kappa (NF-κB1) and NF-κBIA genes, which have been shown to be related to several inflammatory diseases and cancer pathogenesis. Total genomic DNA was isolated from peripheral blood samples taken from 565 healthy volunteers living in Aydın Province. The genomic regions in question were amplified by PCR, and the polymorphisms in these regions were detected by a PCR–RFLP assay. The frequencies were 10.3% for the NF-κB1 −94ins/delATTG del/del genotype, 49.1% for del/ins, and 40.6% for ins/ins. The genotype frequencies of the NF-κBIA 3′UTR A → G genotypes were A/A 19.2%, A/G 42.3%, and G/G 38.5%. Distribution of genotype frequencies was tested by Hardy–Weinberg; the NF-κB1 gene was in Hardy–Weinberg equilibrium (χ2 = 3.402, P > 0.05), the NF-κBIA gene was not (χ2 = 8.293, P < 0.05).
Keywords: NF-κB1 ; NF-κBIA ; PCR–RFLP; Genetic polymorphism; Turkish
Expression of Human A4V Mutant Cu,Zn Superoxide Dismutase in Schizosaccharomyces pombe: Investigations of its Toxic Properties by Semian Karaer; Cagatay Tarhan; Murat Pekmez; Ismail Hamad; Nazli Arda; Aysegul Topal Sarikaya (pp. 113-124).
Cu,Zn superoxide dismutase (SOD1) is an antioxidant enzyme that catalyzes the removal of superoxide radicals generated in various biological oxidations. Amyotrophic lateral sclerosis (ALS) is one of the most common neurodegenerative disorders, occurring in families (FALS) and sporadically (SALS). FALS and SALS are distinguishable genetically but not clinically. More than 100 point mutations in the human SOD 1 gene have been identified that cause FALS. In order to determine the effects of mutant SOD protein, we first cloned wild-type and A4V mutant human SOD1 into Schizosaccharomyces pombe. This study shows viabilities and some antioxidant properties including SOD, catalase, proteasomal activity, and protein carbonyl levels of transformants in SOD1 deleted strain (MN415); and its parental strain (JY741) at different stress conditions. There was no more oxidative damage in the human mutant SOD carrying the transformant strain compared with other strains. These results may help to explain whether ALS progresses as a consequence of cellular oxidative damage.
Keywords: Copper–zinc superoxide dismutase; A4V mutant human SOD1; Amyotrophic lateral sclerosis; Fission yeast; Schizosaccharomyces pombe
Genetic Differentiation Among Peripheral Populations of Bombina bombina from Thrace and Anatolia: An Allozyme Analysis by Nursen Alpagut-Keskin; Ethem I. Cevik; Huseyin Arikan (pp. 125-140).
Genetic structures of Bombina bombina populations, located as peripheral isolates in Turkish Thrace and northwestern Anatolia, were analyzed by polyacrylamide gel electrophoresis using 20 allozyme loci, to investigate the populations’ current genetic variation and possible colonization history. Significant genetic variability was detected in most of the loci and all populations. Allozyme pairwise F ST matrices and distribution of allele frequencies indicate their very close genetic relationships and relatively recent formation. Mean genetic distance values between Thracian and Anatolian populations indicate a Middle or Upper Pleistocene lineage separation before the formation of the Bosporus as an isolating geographic barrier. All the samples show substantial heterozygosity excess, and there was statistically significant evidence of recent bottlenecks. The extent and patterns of genetic divergence indicate that the Anatolian and Thracian populations have probably experienced bottlenecks, and incipient speciation may have occurred in Anatolian populations of B. bombina.
Keywords: Fire-bellied toad; Bombina bombina ; Peripheral isolates; Allozyme variations; Founder effects; Bottleneck; Anatolia; Thrace
Characterization of Mutations in the FOXE1 Gene in a Cohort of Unrelated Malaysian Patients with Congenital Hypothyroidism and Thyroid Dysgenesis by In-Nee Kang; Maslinda Musa; Fatimah Harun; Sarni Mat Junit (pp. 141-151).
The FOXE1 gene was screened for mutations in a cohort of 34 unrelated patients with congenital hypothyroidism, 14 of whom had thyroid dysgenesis and 18 were normal (the thyroid status for 2 patients was unknown). The entire coding region of the FOXE1 gene was PCR-amplified, then analyzed using single-stranded conformational polymorphism, followed by confirmation by direct DNA sequencing. DNA sequencing analysis revealed a heterozygous A>G transition at nucleotide position 394 in one of the patients. The nucleotide transition changed asparagine to aspartate at codon 132 in the highly conserved region of the forkhead DNA binding domain of the FOXE1 gene. This mutation was not detected in a total of 104 normal healthy individuals screened. The binding ability of the mutant FOXE1 protein to the human thyroperoxidase (TPO) promoter was slightly reduced compared with the wild-type FOXE1. The mutation also caused a 5% loss of TPO transcriptional activity.
Keywords: Congenital hypothyroidism; FOXE1 gene; N132D mutation
Sequencing of Part of the Goat agouti Gene and SNP Identification
by Xiang-long Li; Jing-wen Zhao; Chun-juan Tang; Rong-yan Zhou; Guiru Zheng; Lan-hui Li; Xiu-li Guo (pp. 152-156).
A 9-bp Deletion Homoplasmy in Women with Polycystic Ovary Syndrome Revealed by Mitochondrial Genome-Mutation Screen by Guangchao Zhuo; Guofang Feng; Jianhang Leng; Lin Yu; Yan Jiang (pp. 157-163).
Polycystic ovary syndrome (PCOS) is a complex and heterogeneous disorder presenting a challenge for clinical investigators. To investigate the association of a mitochondrial genetic basis with PCOS, we screened mutations of the whole mitochondrial genome in 57 women patients with PCOS and 38 healthy control individuals. Two-step PCR reactions were adopted to amplify and sequence the whole mitochondrial genome. A 9-bp deletion variant appeared in homoplasmy between PCOS patients and control individuals. In the 62 individuals with complete sequences, eight of 34 (23.5%) patients showed the 9-bp deletion, compared with only two of 28 (7.1%) in healthy controls. The 9-bp deletion variant in region V of mitochondrial DNA may be associated with the heterogeneous disorder PCOS.
Keywords: Polycystic ovary syndrome; Mitochondrial genome; 9-bp deletion
Expression of New Red Cell–Related Genes in Erythroid Differentiation by Tiago De Andrade; Luciana Moreira; Adriana Duarte; Carolina Lanaro; Dulcinéia De Albuquerque; Sara Saad; Fernando Costa (pp. 164-171).
Using a suppression subtractive hybridization method, we have previously identified genes differentially expressed in erythroid cells heterozygous for large deletions in β-like globin cluster. Herein, we investigated the expression of four newly detected red cell–related genes in erythroid differentiation. ARID1B and TSPYL1, genes with chromatin remodeling properties, presented similar patterns of expression with an upregulation after erythropoietin (EPO) addition, similar to previous data found in reticulocytes. ZHX2, a transcriptional repressor, was downregulated, and a redoxin-related gene, SH3BGRL2, had higher levels of expression on differentiation. These are the first investigations of these newly described genes in erythroid differentiation and demonstrate that the expression of these genes is affected by EPO stimulation. These genes may participate in globin regulation and may be important in the normal physiology of erythrocytes.
Keywords: Globin; Transcription; Erythroid differentiation; Chromatin remodeling; Oxidative stress