Check out our New Publishers' Select for Free Articles

Biochemical Genetics (v.47, #7-8)

Biological and Molecular Characterization of a Crucifer Tobamovirus Infecting Oilseed Rape by Li Cai; Kunrong Chen; Xuejiang Zhang; Liying Yan; Mingsheng Hou; Zeyong Xu (pp. 451-461).

In China, the tobamovirus that infects oilseed rape has been misdiagnosed as Tobacco mosaic virus (TMV) based on its morphological similarity and serological relatedness. Recently, a tobamovirus has been isolated from oilseed rape in China, which we named Youcai mosaic virus Br (YoMV-Br), according to its biological and molecular characteristics. It had strong infectivity to Cruciferae but less to Solanaceae, Leguminosae, and Cucurbitaceae, and its virion morphology was consistent with that of the tobamoviruses. At high concentrations, it serologically cross reacted with TMV antiserum. The 3′ terminal sequence (2,283 nucleotides) of YoMV-Br was determined, including the 3′ noncoding region, the CP and MP genes, and the C-terminal part of the replicase gene. Between the MP and CP genes, 77 nucleotides overlapped. Compared with homologous regions of 21 recognized species of Tobamovirus, YoMV-Br had a much higher identity to crucifer species than to other tobamoviruses. Phylogenetic analysis demonstrated that YoMV-Br was closely related to the YoMV cluster of tobamoviruses and distantly to TMV, so that they likely belong to different strains of the same species.

Keywords: Youcai mosaic virus (YoMV); Serology; Sequence; Phylogenetic analysis

Isoenzyme Polymorphism and Genetic Structure of Ochlerotatus taeniorhynchus (Diptera: Culicidae) in Populations from the Colombian Atlantic Coast by Felio Bello; Manuel Ruiz-García (pp. 462-470).

Genetic Assessment of Traits and Genetic Relationship in Blackgram (Vigna mungo) Revealed by Isoenzymes by Ajay Kumar Singh; Avinash Mishra; Arvind Shukla (pp. 471-485).

Sixty blackgram accessions were evaluated and classified into different clusters to assess genetic diversity and traits using isoenzymes. Trait-specific expression was assessed, and isoenzyme bands were observed: a peroxidase band (Rm 0.60) associated with dwarfness and an esterase band (Rm 0.25) with tallness. Early maturing varieties were characterized by a specific esterase isoenzyme band of Rm 0.51. All yellow mosaic virus susceptible genotypes had two bands of esterase isoenzyme, Rm 0.42 and 0.70. Resistant genotypes showed three bands (0.32, 0.33, and 0.35) of alkaline phosphatase. Peroxidase isoenzyme was helpful to differentiate green-seeded from black-seeded varieties. Two bands (0.58 and 0.83) were observed in black-seeded accessions, and two different bands (0.74 and 0.76) were observed in green-seeded accessions. Clustering of germplasm and assessment of traits will facilitate the use of germplasm for the improvement of blackgram.

Keywords: Isoenzyme; Blackgram; Cluster analysis; Dendrogram; Peroxidase; Esterase; Alkaline Phosphatase

Analysis of Genetic Diversity of Persea bombycina “Som” Using RAPD-Based Molecular Markers by Brijmohan Singh Bhau; Kalyani Medhi; Ambrish P. Das; Siddhartha P. Saikia; Kartik Neog; S. N. Choudhury (pp. 486-497).

The utility of RAPD markers in assessing genetic diversity and phenetic relationships in Persea bombycina, a major tree species for golden silk (muga) production, was investigated using 48 genotypes from northeast India. Thirteen RAPD primer combinations generated 93 bands. On average, seven RAPD fragments were amplified per reaction. In a UPGMA phenetic dendrogram based on Jaccard’s coefficient, the P. bombycina accessions showed a high level of genetic variation, as indicated by genetic similarity. The grouping in the phenogram was highly consistent, as indicated by high values of cophenetic correlation and high bootstrap values at the key nodes. The accessions were scattered on a plot derived from principal correspondence analysis. The study concluded that the high level of genetic diversity in the P. bombycina accessions may be attributed to the species’ outcrossing nature. This study may be useful in identifying diverse genetic stocks of P. bombycina, which may then be conserved on a priority basis.

Keywords: Persea bombycina ; Muga silk; Genetic diversity; Molecular markers; RAPD

Extensive Diversity of the ADRB3 Gene in Chinese Sheep Identified by PCR-SSCP by Guo Yang; Huitong Zhou; Jiang Hu; Yuzhu Luo; Jon G. H. Hickford (pp. 498-502).

The β₃-adrenergic receptor (ADRB3) is the main mediator of the lipolytic and thermogenic effects of high catecholamine concentrations. Polymorphism in the ovine ADRB3 gene has been reported to be associated with birth weight, growth rate, carcass composition, and cold survival. Eight alleles have been identified in New Zealand sheep, but to date, breeds from other countries have not been studied in detail. In this study, we employed PCR-SSCP to detect ADRB3 polymorphism in the Hu, Tan, small-tailed Han, and Tibet breeds of Chinese sheep. Thirteen SSCP patterns were observed, including the eight previously reported and five new patterns. The newly identified SSCP patterns represent five novel sequences, increasing the reported number of alleles of ADRB3 from 8 to 13. In these Chinese sheep, the most common allele was the previously reported allele C (49.0%); the A allele was the next most common (22.0%). These results suggest that Chinese sheep have more diversity in ADRB3 than New Zealand sheep and therefore have possibly been selected either naturally or via breeding for different traits.

Keywords: β₃-Adrenergic receptor (ADRB3) gene; Variation; PCR-SSCP; Chinese sheep

Genetic Diversity and Genetic Structure Analysis of the Natural Populations of Lilium brownii from Guangdong, China by Yong-fang Huang; Mao-xun Yang; Hao Zhang; Xue-ying Zhuang; Xue-hui Wu; Wan Xie (pp. 503-510).

Relationships Between Single Nucleotide Polymorphisms of the H-FABP Gene and Slaughter and Meat Quality Traits in Chicken by Xiaoyan You; Yiping Liu; Xiaosong Jiang; Huarui Du; Zuohua Liu; Qing Zhu (pp. 511-520).

Using PCR-SSCP with five primer pairs, we detected six single nucleotide polymorphisms of the H-FABP gene: 332G → A, 534G → A, 783C → T, 835C → T, 1198T → C, and 2329C → T. Chi-square results showed significant differences (P < 0.05) in genotype frequency among breeds in Fragment 1 and extremely significant differences (P < 0.01) in Fragments 2–4. We found a significant association between Fragment 2 genotype and muscle fiber number, Arg and Thr (P < 0.05); between Fragment 3 genotype and living weight, carcass weight, breast muscle weight, abdominal fat weight, and abdominal fat percentage (P < 0.05); between Fragment 4 genotype and Thr, Phe, and inosinic acid (P < 0.05). It was concluded that H-FABP was the major gene influencing slaughter performance and meat quality or was linked with the major gene in these strains and that the C783T mutation could be used as a candidate molecular genetic marker for breeding selection. The combination M1C2–B2B2–D1D1 is an ideal model for breeding in these strains because it can improve slaughter and meat quality traits.

Keywords: H-FABP ; PCR-SSCP; Slaughter; Meat quality traits

Genetic Diversity and Population Structure of Celosia argentea and Related Species Revealed by SRAP by Na Feng; Qie Xue; Qinghua Guo; Ru Zhao; Meili Guo (pp. 521-532).

Genetic diversity of 16 populations of Celosia argentea L. and 6 populations of Celosia cristata L. in China was investigated using sequence-related amplified polymorphism (SRAP). Ten SRAP primer combinations generated 507 scorable amplification bands ranging from 50 to 2000 bp, among which 274 were polymorphic, with an average of 54 polymorphic bands per primer combination. The unweighted pair group method of arithmetic averages (UPGMA) cluster analysis enabled construction of a phylogenetic tree for estimating genetic distance among populations, which agreed well with the geographic origin information. Twenty-two populations were distinctly separated into two major genetic groups. One typical representative fragment, M1E6 in C. argentea, provided an alternative approach to distinguish C. argentea from C. cristata. Also, great genetic diversity found in C. argentea populations by significant geographic difference was confirmed by a high level of population genetics parameters. The information may be beneficial to future breeding selection and conservation management for populations of C. argentea.

Keywords: Celosia argentea L.; Celosia cristata L.; SRAP; Genetic diversity

Genetic Stability of Progeny from an Artificial Allotetraploid Carp Using Sperm from Five Fish Species by Yuzhen Ye; Zhongwei Wang; Jianfeng Zhou; Qingjiang Wu (pp. 533-539).

Microsatellite markers and D-loop sequences of mtDNA from a female allotetraploid parent carp and her progenies of generations 1 and 2 induced by sperm of five distant fish species were analyzed. Eleven microsatellite markers were used to identify 48 alleles from the allotetraploid female. The same number of alleles (48) appeared in the first and second generations of the gynogenetic offspring, regardless of the source of the sperm used as an activator. The mtDNA D-loop analysis was performed on the female tetraploid parent, 25 gynogenetic offspring, and 5 sperm-donor species. Fourteen variable sites from the 1,018 bp sequences were observed in the offspring as compared to the female tetraploid parent. Results from D-loop sequence and microsatellite marker analysis showed exclusive maternal transmission, and no genetic information was derived from the father. Our study suggests that progenies of artificial tetraploid carp are genetically stable, which is important for genetic breeding of this tetraploid fish.

Keywords: Genetic stability; Allotetraploid carp; Gynogenetic offspring; Microsatellite markers; mtDNA D-loop

Allele Frequency of VNTR Locus D1S80 Observed in Denizli Province of Turkey by Aylin Köseler; Ayfer Atalay; Erol Ömer Atalay (pp. 540-546).

The variable numbers of tandem repeats (VNTR) locus D1S80, located on chromosome 1 (1p35-36), has a repeat unit 16 bp in length, and different numbers of these repeat units have been observed for populations of different origins and ethnicity. We used a molecular identification method based on capillary electrophoresis separation to analyze D1S80 locus polymorphism among 74 subjects from Denizli province, Turkey, finding an amplified fragment length size of 379–635 bp. Allele repeat numbers were deduced from these sizes and sequence comparison. The most common alleles were repeat units 24 (34.3%) and 18 (22.4%), with frequencies of 0.414 and 0.207, respectively. Other alleles were 25 (7.86%), 28 (5.71%), 22 (4.25%), and 29 (2.86%). The allele with 23 repeat units was not observed. Results were in Hardy–Weinberg linkage disequilibrium. Observed heterozygosity was 0.614, and expected heterozygosity was 0.787. Theta(k) value was 4.86 (95% confidence interval limits). Capillary electrophoresis is a powerful approach for accurate identification of VNTR loci, especially for low base pair units like D1S80, for prenatal diagnosis, linkage analysis, forensic identification, paternity testing, anthropological research, and phylogenetic studies.

Keywords: VNTR; D1S80; Polymorphism; Prenatal diagnosis; Capillary electrophoresis

Cloning and Expression of a Novel Chitinase chi58 from Chaetomium cupreum in Pichia pastoris by Yan-Jun Wang; Qian Yang (pp. 547-558).

A gene encoding a novel chitinase chi58 was cloned from the fungus Chaetomium cupreum by using inverse PCR. The DNA sequence of chi58 contains a 1,602 bp open reading frame and two introns that are 52 and 201 bp in length. Regarding our in silico analysis, chi58 is a modular enzyme composed of a family-18 catalytic domain, which is responsible for chitinase activity, and a chitin-binding domain containing several cysteines. Apparently, the function of these domains is to anchor the enzyme tightly onto the large insoluble polymeric substrate. Chi58 has a pI of 4.47 and a deduced molecular mass of 58 kDa. The optimal pH and temperature conditions were determined to be 5.8 and 45°C, respectively, when colloidal chitin was used as the substrate. SDS-PAGE and zymogram analyses indicated the presence of a single active chitinase. Cells with pPIC9K-chi58 produced an extracellular chitinase that had an activity of 39 U/ml protein. Metal ions such as Ba²⁺, Mg²⁺, K⁺, Cu²⁺, Fe³⁺, Zn²⁺, and Co²⁺ also influenced the activity of the recombinant enzyme.

Keywords: Chitinase; Inverse-PCR; Chitin-binding domain; Pichia pastoris

FAS and FAS Ligand Polymorphisms in the Promoter Regions and Risk of Gastric Cancer in Southern China by Meilin Wang; Dongmei Wu; Ming Tan; Weida Gong; Hengchuan Xue; Hongbin Shen; Zhengdong Zhang (pp. 559-568).

The FAS and FAS ligand (FASLG) system plays a key role in regulating apoptotic cell death, and corruption of this signaling pathway has been shown to participate in tumorigenesis. Functional promoter polymorphisms of the FAS and FASLG genes can alter transcriptional activities and thus alter risk of cancer. We hypothesized that the FAS −1377G>A, FAS −670A>G, and FASLG −844T>C polymorphisms in the promoter regions are associated with risk of gastric cancer. In a population-based case-control study of 332 gastric cancer cases and 324 controls, we genotyped these three polymorphisms and evaluated their association with risk of gastric cancer. We found that the FAS and FASL genotypes and the FAS haplotypes had no significant associations with risk of gastric cancer. In addition, there was no significant interaction between the FAS and FASL polymorphisms in the development of gastric cancer. The FAS and FASLG polymorphisms may not contribute to risk of gastric cancer in the southern Chinese population.

Keywords: FAS ; FAS ligand; Gastric cancer; Susceptibility; Molecular epidemiology

STR Polymorphisms of the Henan Population and Investigation of the Central Plains Han Origin of Chaoshanese by Li-Na Xu; Sheng-Ping Hu; Guo-Ying Feng (pp. 569-581).

Allele frequencies for 15 short tandem repeat (STR) loci were obtained from a Chinese Han population in Henan province of middle China. No deviation from Hardy–Weinberg equilibrium was observed for the STR loci except for D3S1358. The 15 STR loci are potentially useful for paternity testing and forensic casework in the Henan population. A phylogenetic tree based on CODIS STR allele frequencies of 25 Han populations revealed noticeable but far less clear distinctions between southern and northern Chinese populations; the Henan Han population was located at an intermediate position between south and north Chinese Han populations, relatively closer to Chaoshan and Minnan Han. Moreover, admixture analysis showed a large proportion of Central Plains Han origin in Chaoshanese and Minnanese. Admixture and phylogenetic analysis also reflected the genetic similarity shared by these two groups.

Keywords: Short tandem repeat (STR); Henan Han population; Allele frequency; Population genetics; Central Plains

The Polymorphism of DNA Repair Gene ERCC2/XPD Arg156Arg and Susceptibility to Breast Cancer in a Chinese Population by Jiaoyang Yin; Duohong Liang; Ulla Vogel; Yaping Chang; Zhengrong Liu; Li Yue; Xiaoling Sun; Rong Qi; Tiehua Song (pp. 582-590).

Polymorphisms in DNA repair genes are good candidates for modifying cancer risk. ERCC2/XPD, a gene involved in nucleotide excision repair and basal transcription, may influence individual DNA repair capacity, particularly of bulky adducts. This is implicated in cancer susceptibility. To detect the association between ERCC2/XPD Arg156Arg and susceptibility to breast cancer in a Chinese population, we conducted a hospital-based case–control study consisting of 129 patients with breast cancer and 205 controls matched by age, gender, and ethnicity. PCR-RFLP was used for genotyping. No associations were found between ERCC2/XPD Arg156Arg and risk of breast cancer (AA/AC versus CC: OR = 0.79, 95% CI = 0.49–1.28, P = 0.33; AA versus CC: OR = 0.89, 95% CI = 0.49–1.63, P = 0.72; AC versus CC: OR = 0.74, 95% CI = 0.44–1.24, P = 0.25). Breast cancer cases with the variant AA genotype were marginally younger (mean age 45 years) than cases with the wild CC genotype (mean age 50 years) (P = 0.05). There were no differences in risk estimates in relation to menopause and occurrence of breast cancer. Our findings do not suggest that ERCC2/XPD Arg156Arg contributes to breast cancer susceptibility in a Chinese population.

Keywords: ERCC2/XPD Arg156Arg; Breast cancer; Susceptibility; Chinese population

Genetic Polymorphisms of Cytochrome P450 and Matrix Metalloproteinase in Chronic Obstructive Pulmonary Disease by Shih-Lung Cheng; Chong-Jen Yu; Pan-Chyr Yang (pp. 591-601).

We investigated whether polymorphisms of cytochrome P450 (CYP) and matrix metalloproteinase (MMP) are associated with the development and severity of chronic obstructive pulmonary disease (COPD). Genotypes of 184 patients with COPD and 212 controls were determined by polymerase chain reaction, followed by restriction fragment length polymorphism. The homozygous T allele of MMP-9 was significantly higher in patients with COPD than in controls (14.7% vs. 7.5%). The odds ratio was 2.4 (95% CI 1.1–5.9). No differences were observed in the frequency of polymorphic genotypes in CYP1A1, 1A2, MMP-1 and -3. During combined analysis of these candidate genes, we found strong indicators for susceptibility to COPD (combined with homozygotes *2A for CYP1A1 and T alleles of MMP-9 versus others = 3.3, 95% CI 1.2–8.6). The frequency of the homozygous *2A allele of CYP1A1 was significantly higher in very severe COPD (P < 0.01). Combinations of genetic variants including *2A homozygotes of CYP1A1 and T alleles in MMP-9 are significant indicators for susceptibility to COPD. The homozygous *2A allele of CYP1A1 is an independent risk factor for very severe COPD.

Keywords: Polymorphism; Cytochrome P-450; Matrix metalloproteinase; Pulmonary disease; Chronic obstructive

Over-Seasonal and Sex-Independent Expression of Kappa Casein Gene (CSN3) in Mammalian Blood Lymphocytes by Małgorzata Tokarska; Iwona Ruczyńska; Hanna Zalewska; Anna M. Wójcik (pp. 602-608).

After observing the nonspecific expression of the alpha S1 casein gene in peripheral blood mononuclear cells of goats, we continued to trace illegitimate gene-expression patterns in mammals. Six mammalian species (Bos taurus, Capra hircus, Ovis aries, Equus caballus, Sus scrofa, and Bison bonasus) were analyzed for the presence of kappa casein in peripheral blood mononuclear cells and Ficoll-isolated lymphocytes. To detect potential relationships between the expression pattern and reproductive status of the individual, the animals within species represented different sex, age, and physiological status (immature and reproducing males; immature, pregnant, lactating, and sterile females). Species-specific primers were designed for the two-step post reverse transcriptional-polymerase chain reaction. The products were sequenced and a Blast search performed. Transcripts of kappa casein were successfully detected in the peripheral blood mononuclear cells and lymphocytes of three of the species (goat, cow, and European bison). The presence of the transcripts was unrelated to sex, physiological status, or age of the animals.

Keywords: Nontissue-specific expression; Milk protein genes; Gene expression; Illegitimate gene expression; Kappa casein

Sections

Personal tools

Biochemical Genetics (v.47, #7-8)

Sections

Personal tools

Local resources

Biochemical Genetics (v.47, #7-8)