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Biochemical Genetics (v.49, #7-8)

Association of Bladder Cancer Risk with an NAD(P)H:Quinone Oxidoreductase Polymorphism in an Ethnic Kashmiri Population by Arshad A. Pandith; Nighat P. Khan; Zafar A. Shah; Amin M. Shah; Saleem M. Wani; Mushtaq A. Siddiqi (pp. 417-426).

NQO1 gene polymorphism at nucleotide 609 (Pro187Ser) results in a lowering of NQO1 detoxifying activity and is associated with susceptibility to various cancers. The NQO1 genotypes were identified by RFLP in 104 bladder cancer cases and 120 control subjects in an ethnic Kashmiri population. The frequency of the variant NQO1 alleles (CT/TT) was 23.3% for controls and 32.2% for cases (P < 0.05). Overall, the variant alleles were associated with a higher risk of bladder cancer in cases than in the control group (OR = 1.90; 95% CI 1.17–3.04; P < 0.01). In addition, the variant allele genotypes (CT/TT) were associated with a risk of bladder cancer that was more than threefold higher in smokers (OR = 3.47; 95% CI 1.84–6.3; P < 0.001). Results of this study strongly suggest that the variant allele of NQO1 (Pro187Ser) may affect individual susceptibility to bladder cancer, particularly among smokers, in this ethnic Kashmiri population.

Keywords: Bladder cancer; Kashmiri; Polymorphism; NQO1 ; Quinone oxidoreductase

Genomic Structure of the Immigrant Siddis of East Africa to Southern India: A Study of 20 Autosomal DNA Markers by Mansi Gauniyal; Aastha Aggarwal; Gautam K. Kshatriya (pp. 427-442).

The Siddis are a tribal group of African origin living in Karnataka, India. They have undergone considerable cultural change due to their proximity to neighboring population groups. To understand the biological consequences of these changes, we describe the genomic structure of the Siddis and the contribution from putative ancestral populations using 20 autosomal DNA markers. The distribution of Alu indel markers and a genetic distance analysis reveals their closer affinities with Africans. The levels of genomic diversity and heterozygosity are high in all the populations of southern India. Genetic admixture analysis reveals a predominant contribution from Africans, a lesser contribution from south Indians, and a slight one from Europeans. There is no evidence of gametic disequilibrium in the Siddis. The genetic homogeneity of the Siddis, in spite of its admixed origin, suggests the utility of this population for genetic epidemiological studies.

Keywords: Siddis; Africans; Genetic distance; Average heterozygosity; Genetic; Admixture; Nonrandom association

Development of 19 Dinucleotide Microsatellite Markers from the Enriched Library of Platysternon megacephalum by Dongmei Yu; Jianjun Peng; Shijia Hu; Lili Wang; Cuina Xin; Yushu Zhang; Huijian Hu (pp. 443-448).

Genetic Variation and Relationship of Six Indian Sheep Breeds Adapted to the Northwestern Arid Zone of Rajasthan by R. Arora; S. Bhatia; B. P. Mishra (pp. 449-457).

This study illustrates the genetic diversity and relationships within and among six Indian sheep breeds of the northwestern arid region of Rajasthan, based on microsatellite markers. The range of allele diversity was 7.72–9.56, and gene diversity was 0.686–0.766, revealing that these breeds possessed substantial amounts of genetic diversity. Positive F _IS values suggested a deficit of heterozygotes in all six breeds. Despite the declining status of the Marwari, Chokla, Jaisalmeri, Magra and Pugal breeds, an absence of a recent genetic bottleneck was evident from the data. The genetic differentiation estimate (F _ST = 6.1%) suggested low levels of differentiation between the breeds. Genetic distance estimates revealed a close relationship between the Magra–Pugal and Nali–Jaisalmeri breed pairs. This information forms a framework for designing genetic management and conservation programs for these valuable ovine breeds.

Keywords: Arid; Genetic diversity; Indian sheep; Microsatellite markers

Evolutionary Features and Intracellular Behavior of the PRTB Protein by Miki Matsunami; Takashi Yoshioka; Tokiko Minoura; Yukio Okano; Yoshinori Muto (pp. 458-473).

Human PRTB encodes a proline-rich protein of 168 amino acids (PRTB). We analyzed the evolutionary patterns of PRTB from various vertebrate species. Maximum likelihood analyses indicated that while mammalian PRTB has been very well conserved and underwent a significantly slower rate of evolution, only the branch leading to fish PRTB has undergone adaptive evolution. We generated several mutant PRTBs fused to the GFP variant, Venus, and found that the degradation of PRTB was enhanced by the transfection of an E2, UbcH5. Since mutation of the K153 site in PRTB was refractory to its degradation, proteolysis was suggested to be mediated by ubiquitination of K153. The subcellular localization of PRTB was also investigated, which showed that mutation of the K4 site completely prevented the nuclear localization of this protein. Together, these results suggest that Lys residues might play important roles in regulating the intracellular dynamics of the PRTB protein.

Keywords: PRTB; Molecular evolution; Mammal; Ubiquitination; Proteolysis

Association Between the M268T Polymorphism in the Angiotensinogen Gene and Essential Hypertension in a South Indian Population by M. Gopi Chand; J. Srinath; R. S. Rao; Bhaskar V. K. S. Lakkakula; Satish Kumar; V. R. Rao (pp. 474-482).

Essential hypertension is a complex multifactorial disease caused by interactions between genetic and environmental factors. It is an independent determinant of cardiovascular risk. The main aim of this study was to investigate the possible influence of angiotensinogen M268T polymorphisms on hypertension in two endogamous caste populations of South India. Systolic and diastolic blood pressure, anthropometric variables, and lipid profiles were assessed. Direct sequencing of PCR products was adopted for genotyping. This polymorphism was found to be in Hardy–Weinberg equilibrium in the patients and controls of both populations. Binary odds ratios showed significant association between the M268T polymorphism and hypertension in both populations. Multivariate analysis revealed significant differences in body mass index, chest girth, calf circumference, skinfold measurements, total cholesterol, and triglyceride levels between these genotypes in the Gavara and Vaishya populations. These data further support the hypothesis that hypertension is influenced by the AGT M268T polymorphism.

Keywords: Angiotensinogen; SNP; M268T; Essential hypertension; Indian populations

Dominant Contribution of Northern Chinese to the Paternal Genetic Structure of Chaoshanese in South China by Sheng-Ping Hu; Hui Li; Feng-Huan Zhang; Li-Qun Huang; Yan Lu (pp. 483-498).

We investigated the Y chromosome of various Chinese populations to determine the patrilineal origin of the Chaoshanese population. Admixture analysis of six specific Y short tandem repeat (STR) loci in 6,292 individual samples taken from 51 populations, including Chaoshanese and Minnanese of our earlier studies, showed that over 85% of the Chaoshanese Y chromosomes were derived from the Central China Han (M _RH: 0.8614; M _BE: 1.1868 ± 0.2054), and a very small portion were from the southern aborigines. These results support a Central China Han origin of the Chaoshanese and additionally reveal that males from the Central China Han were the predominant contributor to the patrilineal genetics of the Chaoshanese. A phylogenetic tree and analysis of molecular variance signified a strong association between Y chromosomes of Chinese populations and their linguistic affiliations, revealing a coevolution of Y chromosome diversity and languages in East Asia.

Keywords: Central China Han; Chaoshanese; Paternal genetic affinity; Southern indigenous population; Y-chromosomal short tandem repeat

Genetic Differentiation of the Stingless Bee Tetragonula pagdeni in Thailand Using SSCP Analysis of a Large Subunit of Mitochondrial Ribosomal DNA by Sirikul Thummajitsakul; Sirawut Klinbunga; Siriporn Sittipraneed (pp. 499-510).

Genetic diversity and population differentiation of the stingless bee Tetragonula pagdeni (Schwarz) was assessed using single-strand conformational polymorphism (SSCP) analysis of a large subunit of the ribosomal RNA gene (16S rRNA). High levels of genetic variation among individuals within each population (North, Northeast, Central, Prachuap Khiri Khan, Chumphon, and Peninsular Thailand) of T. pagdeni were observed. Analysis of molecular variance indicated significant genetic differentiation among the six geographic populations (Φ _PT = 0.28, P < 0.001) and between samples collected from north and south of the Isthmus of Kra (Φ _PT = 0.18, P < 0.001). In addition, Φ _PT values between all pairwise comparisons were statistically significant (P < 0.01), indicating strong degrees of intraspecific population differentiation. Therefore, PCR-SSCP is a simple and cost-effective technique applicable for routine population genetic analyses in T. pagdeni and other stingless bees. The results also provide an important baseline for the conservation and management of this ecologically important species.

Keywords: Meliponini; Tetragonula ; SSCP; Genetic diversity; Population differentiation

Genetic Structure and Variation of Van Cats by Vahdettin Altunok; Nazmi Yüksek; Ceren C. Berkman; Zahid Tevfik Ağaoğlu; İnci Togan (pp. 511-522).

To determine the genetic structure and variation of Van cats and some other cats, seven enzyme loci were examined using horizontal starch gel electrophoresis. ME bands were observed for the first time in cats. For the enzyme loci CA 1, SOD, GPI, and GOT, neither the individual Van cats nor the specimens of other cat species exhibited any variation. These enzymes presented identical bands, all of which were homozygous. With respect to the PGD, ME, and ESD loci, however, genetic variation was observed in all of the cats. Hence, three of the seven gene–enzyme systems (43%) were polymorphic with two alleles, contributing to an estimate of average heterozygosity of 0.33–0.49 for the Van cats. PGD was the most discriminatory among the three polymorphic loci. The phylogenetic tree indicated that the Van, Persian, Turkish Angora, and Turkish Tekir cats are distinct from Siamese and Bombay cats.

Keywords: Van cat; Genetic diversity; Enzyme electrophoresis

Polymorphism of the Goat Agouti Signaling Protein Gene and Its Relationship with Coat Color in Italian and Spanish Breeds by B. Badaoui; M. D’Andrea; F. Pilla; J. Capote; A. Zidi; J. Jordana; A. Ferrando; J. V. Delgado; A. Martínez; O. Vidal; M. Amills (pp. 523-532).

Agouti signaling protein (ASIP) is one of the key players in the modulation of hair pigmentation in mammals. Binding to the melanocortin 1 receptor, ASIP induces the synthesis of phaeomelanin, associated with reddish brown, red, tan, and yellow coats. We have sequenced 2.8 kb of the goat ASIP gene in 48 individuals and identified two missense (Cys126Gly and Val128Gly) and two intronic polymorphisms. In silico analysis revealed that the Cys126Gly substitution may cause a structural change by disrupting a highly conserved disulfide bond. We studied its segregation in 12 Spanish and Italian goat breeds (N = 360) with different pigmentation patterns and found striking differences in the frequency of the putative loss-of-function Gly₁₂₆ allele (Italian 0.43, Spanish Peninsular 0.08), but we did not observe a clear association with coat color. This suggests that the frequency of this putative loss-of-function allele has evolved under the influence of demographic rather than selection factors in goats from these two geographical areas.

Keywords: Goat; Agouti signaling protein; Coat color

Polymorphism in a Microsatellite of the Acrp30 Gene and Its Association with Growth Traits in Goats by Xingtang Fang; Yu Du; Chunlei Zhang; Xiuying Shi; Danxia Chen; Jiajie Sun; Qijiang Jin; Xianyong Lan; Hong Chen (pp. 533-539).

Acrp30 plays a critical role in the regulation of glucose and lipid homeostasis. In this study, polymorphism of the Acrp30 gene was detected by PCR-SSCP and DNA sequencing methods in 321 individuals from three goat breeds, and the association of Acrp30 gene polymorphism with growth traits in the three goat breeds was analyzed. A novel insert/deletion (GT)₅ microsatellite sequence was detected in the 5′ flanking region of the gene. Three genotypes (AA, AB, and BB) were found in three breeds. There was moderate genetic diversity in the locus in the analyzed populations. Significant associations were observed between the genotypes of the locus and growth traits in the Boer goat population. The chest circumference of individuals with genotype BB was significantly greater than that of individuals with genotype AA.

Keywords: Goat; Acrp30 gene; Polymorphism; Single-strand conformation polymorphism (SSCP); Microsatellite; Association analysis

ISSR Markers as a Tool for the Assessment of Genetic Diversity in Passiflora by Lucas Ferraz dos Santos; Eder Jorge de Oliveira; Aline dos Santos Silva; Fabiana Moraes de Carvalho; Juliana Leles Costa; Juliano Gomes Pádua (pp. 540-554).

Genetic variation among sweet, purple, and yellow passion fruit accessions was assessed using inter-simple sequence repeat (ISSR) markers. Eighteen ISSR primers were used to evaluate 45 accessions. The number of polymorphic bands per primer varied from 4 to 22, with 12.4 bands per primer on average. Nei’s genetic distance between accessions ranged from 0.04 to 0.35. Clustering using the neighbor-joining method resulted in the formation of 11 major clusters. It was not possible to classify the accessions according to their geographic origin, showing that there is no structure in the gene bank. The overall mean Shannon–Weaver diversity index was 0.32, indicating good resolution of genetic diversity in passion fruit germplasm using ISSR markers. Our results indicate that ISSR can be useful for genetic diversity studies, to provide practical information for parental selection and to assist breeding and conservation strategies.

Keywords: Passion fruit; Genetic variability; Molecular markers; Genetic resources

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