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Biochemical Genetics (v.46, #1-2)

Polymorphisms of Two Indels at the PRNP Gene in Three Beef Cattle Herds by Alexandre R. Kerber; Diego Hepp; Daniel T. Passos; Tania de Azevedo Weimer (pp. 1-7).

Bovine spongiform encephalopathy (BSE) is a transmissible fatal neurodegenerative disorder, presenting a characteristic spongiform degeneration of cattle brain due to the accumulation of a pathogenic and protease-resistant infectious protein (prion). Two deletion/insertion polymorphisms of the prion protein gene (23 bp at the promoter region and 12 bp at intron 1) were analyzed in three beef cattle herds (Aberdeen Angus, Charolais, and Franqueiro) to verify allele frequencies for possible use in selection of resistant animals. High frequencies of susceptibility alleles (23 and 12 bp deletion) and haplotype (23 del/12 del) were observed in the Aberdeen Angus and Charolais herds, but Franqueiro presented one of the highest frequencies of resistant alleles so far described. These data indicate the need for selection in Aberdeen Angus and Charolais breeds to increase the frequency of resistant animals in order to reduce the probabilities of BSE outbreaks in these populations.

Keywords: Transmissible spongiform encephalopathy; Bovine; Prion disease; Insertion/deletion polymorphism

Genetic Screening of the Canine Connexin 40 Gene in Dogs with Inherited Cardiac Conduction Defects by Shin-Aeh Lee; Joon-Seok Lee; Seung-Gon Lee; Lopeti Lavulo; Kyoung-Oh Cho; Changbaig Hyun (pp. 8-17).

Connexin 40 (Cx40) is a gap-junction protein expressed in the heart where it mediates the coordinated electrical activation of the atria and ventricular conduction tissues, facilitates cell-to-cell adhesion, and provides pathways for direct intercellular communication. Recent studies have shown that Cx40 null mice have cardiac conduction abnormalities with a very high incidence of cardiac malformations in heterozygous (18%) and homozygous (33%) animals, indicating that Cx40 plays a vital role in cardiomorphogenesis. Since several inherited cardiac conduction defects have also been found in dogs, we hypothesized that the clinical findings are genetically linked to a tissue-specific mutation or mutations in the canine Cx40 gene. We therefore screened the Cx40 gene in dogs with inherited cardiac conduction defects for mutations. In this study, we have identified three heterozygous base changes (C384G, C402T, C837T) in the dogs screened and determined them to be synonymous mutations. These mutations, however, have recently been found in an unrelated group of normal dogs.

Keywords: Dog; Cx40; Congenital heart disease; Conduction defect; Heart disease

Sequence Characterization, Polymorphism, and Chromosomal Localizations of the Porcine Capz Genes by E. Yang; H. Wang; X. X. Wu; Z. L. Tang; S. L. Yang; K. Li (pp. 18-28).

CapZ is a widely distributed and highly conserved actin-binding protein that caps the barbed end of actin filaments and nucleates actin polymerization in a Ca²⁺-independent manner. In myofibrils, it is localized in the Z-lines. In this study, we cloned and characterized Capz subunit genes from the pig muscle. The nucleotide sequences and the predicted protein sequences share high sequence identity with other mammalian orthologs. The reverse transcriptase polymerase chain reaction (RT-PCR) revealed that porcine Capzβ, Capzα1, and Capzα2 genes are expressed in all 11 tissues studied (liver, spleen, small intestine, large intestine, lymph node, kidney, heart, skeletal muscle, brain, fat, and lung) but in variable amounts. Radiation hybrid mapping data indicated that Capzβ, Capzα1, and Capzα2 map to q2.1–2.6 of pig chromosome 6 (SSC6), q1.6–q2.2 of pig chromosome 4 (SSC4), and q1.3–2.3 of pig chromosome 18 (SSC18), respectively. An A/C single nucleotide polymorphism in Capzβ intron 4 was identified with a HhaI PCR restriction fragment length polymorphism, which showed great allele frequency differences between Guizhou Xiang, Guangxi Bama, Wuzhishan, Tongcheng, Landrace, and Yorkshire pigs. The association analysis suggested that the Capzβ genotype was associated with leaf fat (P < 0.05) in our experimental population.

Keywords: Porcine; Physical mapping; Polymorphism; Association analysis; Capz

Evaluation of FORS-D Analysis: A Comparison with the Statistically Significant Stem-loop Potential by Chi-Yu Zhang; Ji-Fu Wei; Jian-Sheng Wu; Wen-Rong Xu; Xiao Sun; Shao-Heng He (pp. 29-40).

The stem-loop potential of a nucleic acid segment (expressed as a FONS value), decomposes into base composition-dependent and base order-dependent components. The latter, expressed as a FORS-D value, is derived by subtracting the value of the base composition-dependent component (FORS-M) from the FONS value. FORS-D analysis is the use of FORS-D values to estimate the potential of local base order to contribute to a stem-loop structure, and it has been used to investigate the relationship between stem-loop structure and other selective pressures on genomes. In the present study, we evaluated the reliability of FORS-D analysis by comparing it with statistically significant stem-loop potential, another robust method developed by Le and Maizel for examining stem-loop structure. We found that FORS-M values calculated using 10 randomized sequences are as reliable as those calculated using 100 randomized sequences. The resulting FORS-D values have a similar trend and distribution as statistically significant stem-loop potential, implying that FORS-D analysis is as reliable as the latter in measuring the distribution of base order-dependent stem-loop potential. Since the calculation of the FORS-M values is time consuming, the integrated program Bodslp developed by us will become a convenient tool for large-scale FORS-D analysis. The results also suggest that for some purposes the online program SigStb developed by Le and Maizel may be used as an alternative tool for FORS-D analysis.

Keywords: FORS-D analysis; Base order-dependent stem-loop potential; Significance score; FORS-M; Randomized sequences

Biochemical, ECF18R, and RYR1 Gene Polymorphisms and Their Associations with Osteochondral Diseases and Production Traits in Pigs by Haja N. Kadarmideen (pp. 41-53).

This study reports the association of five blood types, three enzymes, two proteins, Escherichia coli F18 receptor gene (ECF18R), and the Ryanodin receptor (RYR1) gene with six production traits, four meat quality traits, and two osteochondral diseases in Swiss pig populations. Data on on-farm traits (daily weight gain, percent premium cuts, and backfat) and on station-tested traits (daily weight gain, feed conversion ratio, meat quality, and osteochondral lesions) were available on 3,918 and 303 animals, respectively. A mixed linear model with allele substitution effects was used for each trait by marker analysis (144 analyses). Significant marker-trait associations and allele substitution effects are presented. In general, heritability estimates for production and meat quality traits were higher than those for osteochondral lesions. Blood types lack significant associations with many traits except H and S types. Enzymes (mainly, glucose phosphate isomerase) and protein polymorphisms show significant associations with daily weight gain, premium cuts, and backfat as well as osteochondral lesions. The RYR and ECF18R genes significantly affected all growth, production, and lean meat content traits and osteochondral lesions; RYR also affected pH values. This study reports many novel marker-trait associations, particularly between the incidence of osteochondral lesions and polymorphisms at glucose phosphate isomerase, 6-phosphogluconate dehydrogenase, postalbumin 1A, RYR, and ECF18R loci. These results should be useful in selection and for further functional genomics and proteomics investigations.

Keywords: RYR1 gene; ECF18R gene; Production traits; Osteochondrosis; Pigs

Substitutions of Three Amino Acids in Human Heart/Muscle Type Carnitine Palmitoyltransferase I Caused by Single Nucleotide Polymorphisms by Naoshi Yamazaki; Taisuke Matsuo; Miho Kurata; Makiko Suzuki; Takehisa Fujiwaki; Seiji Yamaguchi; Hiroshi Terada; Yasuo Shinohara (pp. 54-63).

Heart/muscle type carnitine palmitoyltransferase I (M-CPTI) catalyzes the rate-limiting step of mitochondrial long-chain fatty acid (LCFA) oxidation in muscle and adipose tissue. Three replacements of nucleotides resulting in missense mutations of I66V, S427C, and E531K were observed in the M-CPTI gene of patients showing abnormal fatty acid metabolism. These nucleotide replacements were found to be common single nucleotide polymorphisms (SNPs) of this gene and not specific to patients. The question of whether these missense mutations caused by SNPs alter the functional properties of M-CPTI remains unanswered. Thus, we examined whether these missense mutations are associated with any changes in the enzymatic properties of M-CPTI. None of these mutations was found to cause remarkable alteration of its enzymatic properties. Based on the comparison of amino acid sequences of M-CPTI among different animal species, the roles of these amino acids in the enzyme are discussed.

Keywords: Carnitine palmitoyltransferase; Enzyme activity; Mitochondria; Single nucleotide polymorphism

Association of Interleukin-6, Interleukin-12, and Interleukin-10 Gene Polymorphisms with Essential Hypertension in Tatars from Russia by Y. R. Timasheva; T. R. Nasibullin; A. N. Zakirova; O. E. Mustafina (pp. 64-74).

Essential hypertension is a common disease with fatal clinical complications. Epidemiological and family studies have confirmed the role of genetic predisposition in its development. Hypertensive patients have been shown to have an altered profile of pro- and anti-inflammatory cytokines. The aim of our investigation was to reveal the association of interleukin-6, interleukin-12, and interleukin-10 gene polymorphisms with essential hypertension and its clinical complications in a Tatar ethnic group from Bashkortostan, Russia. The study involved 362 hypertensive patients and 244 healthy subjects from this Tatar ethnic group (Bashkortostan, Russia). DNA was isolated from whole venous blood using phenol–chloroform extraction by the standard method. IL6 −572 G/C, IL12B 1159 C/A, and IL10 –627 C/A genotypes were typed using polymerase chain reaction followed by restriction enzyme digestion. We found that the IL10 −627 *C/*C genotype was associated with decreased risk of hypertension (OR = 0.64, P = 0.035). IL6 genotypes and allele distribution did not differ significantly between subjects with and without hypertension, but the IL6 −572 *G/*G genotype frequency was found to be significantly higher among those patients who had stroke, compared with normotensive control subjects (P = 0.036). Carriers of the IL12B 1159 *A/*A genotype had a lower risk of stroke (OR = 0.38, P = 0.028). Our study has shown the association between IL10 −627 C/A polymorphism and essential hypertension in the Tatar ethnic group from Bashkortostan, Russia. The IL10 −627*C/*C genotype was found to be protective against hypertension. We also demonstrated that hypertensive patients with the IL12B *A/*A and IL6 *G/*G genotypes had increased risk of stroke. Our results suggest a role for cytokines in cardiovascular disease development in the Tatar ethnic group, but further investigation is needed.

Keywords: Essential hypertension; Interleukin; Polymorphism; Association study

Strong Genetic Differentiation of Primula sikkimensis in the East Himalaya–Hengduan Mountains by Feng-Ying Wang; Xue-Jun Ge; Xun Gong; Chi-Ming Hu; Gang Hao (pp. 75-87).

The East Himalaya-Hengduan Mountains region is the center of diversity of the genus Primula, and P. sikkimensis is one of the most common members of the genus in the region. In this study, the genetic diversity and structure of P. sikkimensis populations in China were assessed using inter-simple sequence repeat (ISSR) and chloroplast microsatellite markers. The 254 individuals analyzed represented 13 populations. High levels of genetic diversity were revealed by ISSR markers. At the species level, the expected heterozygosity and Shannon’s index were 0.4032 and 0.5576, respectively. AMOVA analysis showed that 50.3% of the total genetic diversity was partitioned among populations. Three pairs of chloroplast microsatellite primers tested yielded a total of 12 size variants and 15 chloroplast haplotypes. Strong cpDNA genetic differentiation (G _ST = 0.697) and evidence for phylogeographic structure were detected (N _ST= 0.788, significantly higher than G _ST). Estimated rates of pollen-mediated gene flow are approximately 27% greater than estimated rates of seed-mediated gene flow in P. sikkimensis. Both seed and pollen dispersal, however, are limited, and gene flow among populations appears to be hindered by the patchiness of the species’ habitats and their geographic isolation. These features may have played important roles in shaping the genetic structure of P. sikkimensis. A minimum-spanning tree of chloroplast DNA haplotypes was constructed, and possible glacial refugia of P. sikkimensis were identified.

Keywords: Chloroplast microsatellite; East Himalaya–Hengduan Mountains; ISSR; Primula sikkimensis

Mating Systems of Psychotria tenuinervis (Rubiaceae): Distance from Anthropogenic and Natural Edges of Atlantic Forest Fragment by Flavio Nunes Ramos; Maria Imaculada Zucchi; Vera Nisaka Solferini; Flavio A. M. Santos (pp. 88-100).

The aim of this study was to determine and compare the mating systems among Psychotria tenuinervis populations at anthropogenic edges, natural edges, and the forest interior using allozyme electrophoresis of naturally pollinated progeny arrays. P. tenuinervis showed low outcrossing rates, varying from 37% to 50% of the mating attributable to outcrossing and 50% to 63% attributable to self-fertilization, in the three habitats. The forest interior had the highest outcrossing rate (t _m = 0.50 and t _s = 0.43) among the three habitats. However, there were no differences in either multilocus or single-locus rates among the three habitats, indicating that the contribution of biparental inbreeding to the apparent selfing rate in these populations was very low. The multilocus (t _m) and single-locus (t _s) outcrossing rates for the P. tenuinervis in the sample plots within each habitat showed great heterogeneity. In conclusion, edge creation seems not to influence its mating systems. Additionally, although P. tenuinervis is a distylous species, the population’s inbreeding can be attributed almost entirely to self-fertilization.

Keywords: Edge; Fragmentation; Isozymes; Mating systems; Seeds

Molecular Analysis Using Mitochondrial DNA and Microsatellites to Infer the Formation Process of Japanese Native Horse Populations by Hironaga Kakoi; Teruaki Tozaki; Hitoshi Gawahara (pp. 101-104).

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Biochemical Genetics (v.46, #1-2)

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Biochemical Genetics (v.46, #1-2)