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Biochemical Genetics (v.46, #7-8)

Chromosome Location and Association of Haplotypes of Insulin-like Growth Factor Binding Protein-2 with Production Performance in Swine by Wenjun Wang; Qinyong Meng; Xiaoxiang Hu; Jin Fei; Jidong Feng; Weidong Liu; Ning Li (pp. 381-391).

Insulin-like growth factor binding protein-2 is a member of the insulin-like growth factor families. Using a porcine RH panel, the gene was mapped on chromosome 15q22-23. Meanwhile, using polymerase chain reaction single strand conformation polymorphism, genotypic and allelic frequencies were analyzed in 17 pig breeds (total animals 570), together with a chi-square test of Hardy–Weinberg equilibrium. Also the association between haplotypes and production performance was analyzed in a Lantang × Landrace population family (n = 133, total 43 traits). At each locus we investigated, all the breeds showed different genotypic and allelic frequency distributions. In general, the Chinese native pig breeds carried a higher allele A frequency (over 50%) than the European pigs. For production performance, pigs with the CAG haplotype had higher fore-body and rear-body weight than those with the TGT and TAG haplotypes (P < 0.05). Also, pigs with the CAG haplotype had higher bone weight of the rear-body than those with the CAT haplotype (P < 0.05); pigs with the TGT and CAG haplotypes had higher forelimb and rearlimb weight than those with the CAT haplotype (P < 0.01 and P < 0.05, respectively); pigs with the TGG haplotype had higher leaf fat weight than those with the TGT and CAG haplotypes (P < 0.05); and pigs with the CAG haplotype had more stomach weight than those with the CAT and CGT haplotypes (P < 0.01); pigs with the TGT and CAG haplotypes had more ribs and longer body than those with the CGT–TGG, and CAT–TAG haplotypes (P < 0.05). These results suggest that IGFBP-2 is associated with production performance, but our population family was small. More studies with large samples are needed before the IGFBP-2 locus will be useful for a selection program.

Keywords: Insulin-like growth factor binding protein-2; Chromosome location; RH panel; Haplotype; Production performance; Swine

Isolation and Characterization of Polymorphic Microsatellite Markers for the Masked Palm Civet (Paguma larvata) by J. P. Chen; D. H. Andersen; G. Veron; E. Randi; S. Y. Zhang (pp. 392-397).

The masked palm civet (Paguma larvata) has been suspected to be the host of a SARS-like CoV virus that causes severe acute respiratory syndrome in humans. In China, the palm civet lives wild and is farmed, but even though the species is a potential carrier of the virus, its geographic distribution and genetic diversity have never been studied. We report the isolation and characterization of six polymorphic microsatellite markers for P. larvata. To characterize each locus, two farmed masked palm civet populations from Shanxi and Guangxi provinces in China were genotyped. The number of alleles per locus ranged from 3 to 15, and the observed heterozygosity for these populations was 47.1 and 68.7%, respectively.

Keywords: Masked palm civet; Paguma larvata ; Microsatellite marker

Cloning, Expression Pattern, Chromosomal Localization, and Evolution Analysis of Porcine Gnaq, Gna11, and Gna14 by Huaping Chen; Wenshu Yao; Dan Jin; Tao Xia; Xiaodong Chen; Ting Lei; Lei Zhou; Zaiqing Yang (pp. 398-405).

The Gq class is one subfamily of the G protein α subunits multigene family. It comprises four genes: Gnaq, Gna11, Gna14, and Gna15. In mice and humans, the α subunit is an essential component of G protein interaction with receptors and effectors. We report here the cloning and characterization of porcine Gnaq, Gna11, and Gna14. We have cloned the full-length coding sequences of porcine Gnaq, Gna11, and Gna14 (1,080, 1,080, and 1,068 bp, respectively) and then mapped them chromosomally to regions 1q21-27, 2q21-24, and 1q21-27 by radiation hybrid mapping. Tissue distribution analysis indicated that Gnaq and Gna11 were coexpressed in liver, heart, muscle, spleen, adipose tissue, brain, and uterus, but Gna14 mRNA was detected only in kidney and lung. The phylogenetic trees reveal that porcine Gnaq, Gna11, and Gna14 are evolutionarily closer to their human homologs. This is the first report of molecular cloning and characterization of porcine Gnaq, Gna11, and Gna14, which will be helpful for further understanding of the physiological role of Gq class genes in pigs.

Keywords: Gnaq ; Gna11 ; Gna14 ; Molecular cloning; Porcine

High-Throughput Multiplex Single-Nucleotide Polymorphism (SNP) Analysis in Genes Involved in Methionine Metabolism by Betti Giusti; Ilaria Sestini; Claudia Saracini; Elena Sticchi; Paola Bolli; Alberto Magi; Anna Maria Gori; Rossella Marcucci; Gian Franco Gensini; Rosanna Abbate (pp. 406-423).

Hyperhomocysteinemia is a well-known independent marker factor for atherothrombotic diseases and may result from acquired and genetic influences. Several polymorphisms are suspected to be associated with hyperhomocysteinemia, but data are limited and inconsistent. High-throughput genotyping technologies, such as GenomeLab SNPStream, are now available. Moreover, an appropriate selection of SNPs to be analyzed could represent a strong resource to define the role of genetic risk factors. We developed a multiplex PCR-oligonucleotide extension approach by GenomeLab platform. We selected 72 SNPs based on their putative function and frequency in the candidate genes AHCY, BHMT, BHMT2, CBS, ENOSF1, FOLH1, MTHFD1, MTHFR, MTR, MTRR, NNMT, PON1, PON2, SLC19A1, SHMT1, TCN2, and TYMS. We were able to analyze 57 of the SNPs (79%). For MTHFR C677T and A1298C and MTR A2756G SNPs, we compared data obtained with an electronic microchip technology and found 99.2% concordance. We also performed a haplotype analysis. This approach could represent a useful tool to investigate the genotype–phenotype correlation and the association of these genes with hyperhomocysteinemia and correlated diseases.

Keywords: Hyperhomocysteinemia; High-throughput technologies; Genotyping; Primer extension; Single-nucleotide polymorphism (SNP); Homocysteine

A TaqI PCR-RFLP Detecting a Novel SNP in Exon 2 of the Bovine POU1F1 Gene by Chuanying Pan; Xianyong Lan; Hong Chen; Yikun Guo; Jianhong Shu; Chuzhao Lei; Xinzhuang Wang (pp. 424-432).

PCR-SSCP and DNA sequencing methods were applied to reveal three novel single nucleotide polymorphisms (SNPs) in exon 2 of the POU1F1 gene in 963 Chinese cattle belonging to eight breeds. Among them, a silent SNP (NM_174579:c.545G > A) detected by TaqI endonuclease is described. Frequencies of the POU1F1-G allele varied from 0.685 to 1.000. The association of TaqI polymorphism with growth traits was analyzed in 251 Nanyang cattle. No significant associations of the TaqI polymorphism with body weight and average daily gain for different growth periods (6, 12, 18, and 24 months old) were observed (P > 0.05), as well as for body sizes (P > 0.05).

Keywords: Cattle; POU1F1 gene; Single nucleotide polymorphism (SNP); PCR-RFLP; Growth traits

No Correlation Between Heterozygosity and Vegetative Fitness in the Narrow Endemic and Critically Endangered Clematis acerifolia (Ranunculaceae) by Jordi López-Pujol; Fu-Min Zhang; Song Ge (pp. 433-445).

The relationship between heretozygosity and vegetative fitness was explored in the narrow endemic and threatened Clematis acerifolia (Ranunculaceae), both at individual and population levels. The relationships between fitness, habitat factors, and population size were also analyzed. Allozyme electrophoresis was used to quantify the levels of heterozygosity of nearly 200 surveyed individuals belonging to the nine extant populations of this species. Six parameters of vegetative fitness were measured: plant height, shrub diameter, length of the largest leaf, width of the largest leaf, mean number of leaves/stem, and total number of stems. The percentage of tree cover (light availability) was measured as an indicator of habitat quality. A principal component analysis reduced the original fitness variables to two uncorrelated principal components. None of these correlated significantly with both heterozygosity and population size, in contrast to the expected result. Nevertheless, one of the principal components showed a positive relationship with light availability, which may indicate that habitat quality may have significant effects on the performance of this species. Thus, to ensure the viability of this endangered species, maintenance of adequate habitat quality (by avoiding further fragmentation) may be more important than maximizing genetic diversity within populations.

Keywords: Heterozygosity; Fitness; Allozymes; Endangered; Clematis acerifolia

Selection Against Glycosylation in Ruminant Pancreatic Ribonucleases by Replacements in the Ancestral Carbohydrate Attachment Site by Matthias Gautschi; Jaap J. Beintema (pp. 446-450).

A hypothesis, proposed 25 years ago, that there is selection against glycosylation in ruminant pancreatic ribonucleases by replacement of methionine to leucine in the ancestral carbohydrate attachment site Asn–Met–Thr at residues 34–36, was experimentally confirmed. The replacement of leucine at position 35 by methionine in bovine ribonuclease resulted in a three-fold relative increase in glycosylation when expressed in Chinese hamster ovary cells.

Keywords: Bovine; Glycoprotein; Molecular evolution; Ribonuclease; Ruminants

The Genetic Aspects of Pre-eclampsia: Achievements and Limitations by Azim Nejatizadeh; Tsering Stobdan; Neena Malhotra; M. A. Qadar Pasha (pp. 451-479).

Pre-eclampsia, a life-threatening disease during pregnancy, is a leading cause of global maternal mortality. Although there is substantial evidence of a genetic background, the complexity of the processes involved and nature of the maternal–fetal phenomenon do not make the search for the causative genes easy. Recent retrospective studies on the subject suggest the heritable allelic variations, particularly the utero-placental renin–angiotensin system with defective placental vascular development, could become the cornerstone for the genetics of pre-eclampsia and hence might well be associated with such defective development. Moreover, the role of immune mechanisms (immune maladaptation) deserves not to be ignored. Large-scale studies entailing genomewide scanning, sib-pair linkage analysis, and family-based association studies with appropriate power to detect genes with a lower relative risk are necessary to understand the puzzle of the disease. Moreover, recently, the importance of epigenetic features and the effect of imprinted genes related to trophoblast growth as well as fetal development on hypertension in pregnancy have been highlighted. All these possibilities are intuitively attractive and are supported by some circumstantial evidence. Although the consistent tenor of a series of papers instills some confidence, we need meticulously designed larger-scale investigations including large numbers of affected women and their babies to provide the analytic stringency essential to study the polygenic multifactorial basis of pre-eclampsia.

Keywords: Pre-eclampsia; Pregnancy; Genetics; Polymorphism; Association studies; Linkage analysis

Genetic Diversity Among Turkish Native Chickens, Denizli and Gerze, Estimated by Microsatellite Markers by Muhammet Kaya; Mehmet Ali Yıldız (pp. 480-491).

The genetic diversity of the Turkish native chicken breeds Denizli and Gerze was evaluated with 10 microsatellite markers. We genotyped a total of 125 individuals from five subpopulations. Among loci, the mean number of alleles was 7.5, expected heterozygosity (H _e) was 0.665, PIC value was 0.610, and Wright’s fixation index was 0.301. H _e was higher in the Denizli breed (0.656) than in the Gerze breed (0.475). The PIC values were 0.599 and 0.426 for Denizli and Gerze, respectively. A phylogenetic tree was constructed using genetic distance and the neighbor-joining method. Its topology reflects the general pattern of genetic differentiation among the Denizli and Gerze breeds. The present study suggests that Denizli and Gerze subpopulations have a rich genetic diversity. The information about Denizli and Gerze breeds estimated by microsatellite analysis may also be useful as an initial guide in defining objectives for designing future investigations of genetic variation and developing conservation strategies.

Keywords: Turkish native chickens; Denizli; Gerze; Genetic diversity; Microsatellites

Population Genetic Study of Mitochondrial DNA in Roseate Spoonbill (Aves; Platalea ajaja) Breeding Colonies from the Pantanal Wetlands, Brazil by Mateus Henrique Santos; Iara Freitas Lopes; Silvia Nassif Del Lama (pp. 492-505).

Five breeding colonies of the Roseate spoonbill (Aves: Platalea ajaja) from two Brazilian wetland areas (Pantanal and Taim marshes) were sampled, and domain I of the mitochondrial DNA control region (483 bp) was sequenced in 50 birds. The average haplotype diversity (h = 0.75, s = 0.071) and average nucleotide diversity (π = 0.004, s = 0.003) were evaluated, and nonsignificant differences were found among the colonies studied. The lack of differentiation among breeding colonies revealed by AMOVA analysis was explained either as a consequence of high gene flow or recent expansion. The significantly negative results of the neutrality tests (Fu's F s = −23.271, P < 0.01; Tajima's D = −1.941, P < 0.01) associated with the star shape of the haplotype tree and mismatch distribution data are evidence supporting the idea that these populations underwent a recent demographic expansion in the Pantanal region. The average time since the expansion is estimated to be 25,773 years, and this agrees with a period of increased moisture that occurred during the last glacial period.

Keywords: Population genetics; Mitochondrial DNA; Population expansion; Waterbirds; Roseate spoonbill

SLC11A1 Polymorphisms Are Associated with the Risk of Chronic Obstructive Pulmonary Disease in a Korean Population by Eun Jin Kim; Kyung Mee Kim; Sun Ha Park; Jong Sik Kim; Won Kee Lee; Sung Ick Cha; Chang Ho Kim; Young Mo Kang; Sung Beom Han; Tae Hoon Jung; Jae Yong Park (pp. 506-519).

The solute carrier family 11 member 1 (SLC11A1) protein plays important roles in macrophage activation and displays pleiotropic effects on various macrophage functions, including the regulation of tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and oxidative burst. Considering the important roles of macrophage in the pathogenesis of chronic obstructive pulmonary disease (COPD), we hypothesized that the SLC11A1 gene may act as a low-penetrance susceptibility gene for COPD. To test this hypothesis, we first examined the frequencies of 12 candidate polymorphisms in the SLC11A1 gene in 27 healthy Korean individuals, and then genotyped 3 haplotype-tagging polymorphisms [IVS4 + 14G > C (rs3731865), D543 N (rs17235409), and ^*86A > G (rs1059823)] in 83 COPD patients and 203 healthy controls. Individuals with at least one variant allele of the D543 N and ^*86A > G polymorphisms were at a significantly increased risk for COPD compared with carriers with each homozygous wild-type allele [adjusted odds ratio (OR) = 2.23, 95% confidence interval (CI) = 1.24–4.02, P = 0.007; and adjusted OR = 1.92, 95% CI = 1.10–3.35, P = 0.022, respectively]. Consistent with the findings of the genotyping analysis, the 122 haplotype carrying both the 543 N and ^*86G alleles was associated with a significantly increased risk for COPD compared with the 111 haplotype with the 542D and ^*86A alleles (adjusted OR = 2.05, 95% CI = 1.19–3.51, P = 0.009 and Bonferroni corrected P = 0.027). These findings suggest that the SLC11A1 polymorphisms could be used as markers for genetic susceptibility to COPD. However, further studies with large numbers of subjects are needed to confirm our findings.

Keywords: SLC11A1 ; Polymorphism; COPD; Genetic susceptibility

Evidence of Sibling Species in the Brown Planthopper Complex (Nilaparvata lugens) Detected from Short and Long Primer Random Amplified Polymorphic DNA Fingerprints by M. A. Latif; Tan Soon Guan; Omar Mohd. Yusoh; Siti Shapor Siraj (pp. 520-537).

The inheritance of 31 amplicons from short and long primer RAPD was tested for segregating ratios in two families of the brown planthopper, Nilaparvata lugens, and they were found to be inherited in a simple Mendelian fashion. These markers could now be used in population genetics studies of N. lugens. Ten populations of N. lugens were collected from five locations in Malaysia. Each location had two sympatric populations. Cluster and principal coordinate analyses based on genetic distance along with AMOVA revealed that the rice-infesting populations (with high esterase activity) at five localities clustered together as a group, and Leersia-infesting populations (with low esterase activity) at the same localities formed another distinct cluster. Two amplicons from primers OPD03 (0.65 kb) and peh#6 (1.0 kb) could be considered diagnostic bands, which were fixed in the Leersia-infesting populations. These results represent evidence of a sibling species in the N. lugens complex.

Keywords: Rice brown planthopper; Nilaparvata lugens ; Short and long primer RAPD-PCR; Sibling species

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