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Biochemical Genetics (v.48, #9-10)

Genetic Diversity of Aedes vexans (Diptera, Culicidae) from New Orleans: Pre- and Post-Katrina by Cesar D. Solorzano; Allen L. Szalanski; Carrie B. Owens; C. Dayton Steelman (pp. 711-726).

The floodwater mosquito Aedes vexans, a potential vector of West Nile virus, has a worldwide distribution that includes the continental United States and southern Canada. In order to determine the effect that Hurricane Katrina had on the temporal genetic variation of Ae. vexans from New Orleans, we compared genetic diversity of a portion of the mtDNA ND5 gene of mosquito specimens collected during 2005 (n = 99) with specimens from 2006 (n = 103), after the hurricane. Average haplotype diversity (Hd) was high (>0.88) in 2005 and 2006 for both the parishes studied. It does not appear that Hurricane Katrina had any impact on genetic diversity, and despite the intense efforts to control mosquitoes in New Orleans, Ae. vexans has not undergone a population bottleneck. A bottleneck effect may be lacking because this species breeds outside the city and the adults migrate into the city.

Keywords: Aedes vexans ; Mosquito mtDNA; Genetic diversity; Haplotype; Hurricane Katrina

Assessment of Genetic Relatedness of Crossbred Chicken Populations Using Microsatellite Markers by Rudra Nath Chatterjee; Tarun K. Bhattacharya; Meenakshi Dange; U. Rajkumar (pp. 727-736).

To measure genetic relatedness between populations, for breeding purposes, we analyzed 170 birds from six crossbred populations of three pure lines of White Leghorn chickens, using 14 microsatellite markers. All the microsatellites were polymorphic, with 2–6 alleles. The mean number of alleles per locus was 3.21. The effective number of alleles varied from 1.14 to 3.94. The observed heterozygosity varied from 0.133 to 1.00, with a mean of 0.748. The F _IS values were mostly negative, with an average of −0.345. The mean F _ST value was 0.056. The Nm values ranged from 1.91 to 42.17. The highest genetic identity was observed between IWI × IWK and IWK × IWI. The relation between any two groups of crosses was more than 85%. The results suggest that the crossbred populations were very closely related.

Keywords: Genetic closeness; Microsatellites; Crossbred population; Diallel crosses

Identification of Four SUMO Paralogs in the Medaka Fish, Oryzias latipes, and Their Classification into Two Subfamilies by Daisuke Seki; Shinpei Obata; Tsuyoshi Shirozu; Takeshi Kitano; Hisato Saitoh (pp. 737-750).

At least four paralogs of the small ubiquitin-related modifier (SUMO) exist in humans, but there is limited information about SUMO paralogs from other vertebrate species. We isolated the four cDNA encoding proteins, similar to human SUMOs, from the medaka fish, Oryzias latipes: OlSUMO-1, OlSUMO-2, OlSUMO-3, and OlSUMO-4. The amino acid sequences of OlSUMO-2, -3, and -4 are 89–94% identical, but they share only 45% identity with OlSUMO-1. Phylogenetic analysis, transient expression of OlSUMOs in cultured cells, and in vitro binding of OlSUMOs with two SUMO-interacting proteins demonstrated that the medaka SUMO paralogs can be grouped into two subfamilies, OlSUMO-1 and OlSUMO-2/3/4. Furthermore, this is the first report of all four OlSUMO transcripts being expressed in medaka embryos, implying that they have a role in fish development. This study will improve understanding of the relationship between structural and functional diversity of SUMO paralogs during vertebrate evolution.

Keywords: Post-translational modification; Small ubiquitin-related modifier (SUMO); Medaka fish

Genetic Polymorphisms of the CACNA2D1 Gene and Their Association with Carcass and Meat Quality Traits in Cattle by Guan-Yu Hou; Zheng-Rong Yuan; Xue Gao; Jun-Ya Li; Hui-Jiang Gao; Jin-Bao Chen; Shang-Zhong Xu (pp. 751-759).

The objective of this study was to identify genetic polymorphisms of the CACNA2D1 gene and to analyze associations between SNPs and carcass and meat quality traits in cattle. Through PCR-RFLP and DNA sequencing methods, a new allelic variant corresponding to the A → G mutation (aspartic to glycine amino acid replacement) of the bovine CACNA2D1 gene was detected. Two alleles and three genotypes (AA, AG, and GG) were defined. Genetic character indicated that the A526745G locus showed moderate polymorphism and was in Hardy–Weinberg equilibrium. Gene-specific SNP marker association analysis showed that the A526745G mutant was significantly associated with carcass weight, dressing percentage, meat percentage, and backfat thickness. The results add new evidence that CACNA2D1 is an important candidate gene for the selection of carcass and meat quality traits in the cattle industry.

Keywords: Cattle; CACNA2D1 gene; Carcass and meat quality traits; SNPs; Association analysis

Assessing Genetic Differentiation in Geographic Populations of Labeo calbasu Using Allozyme Markers by Rajeev K. Singh; Kuldeep K. Lal; Vindhya Mohindra; Peyush Punia; Rama S. Sah; Akhilesh K. Mishra; Rajesh Kumar; B. N. Mishra; W. S. Lakra (pp. 760-778).

The population structure of Labeo calbasu from 11 rivers belonging to the Indus, Ganges, Bhima, Mahanadi, and Godavari basins was investigated using allozyme marker systems. Seven out of 20 allozyme loci (35%) were polymorphic (P < 0.99). Both probability and score tests indicated significant deviation of genotype proportions from Hardy–Weinberg expectations at two loci, XDH* (Mahanadi, Bhima, and Godavari) and G6PDH* (Mahanadi). A pairwise genetic homogeneity test and F _ST values indicated a low-to-moderate level (0.0515) of genetic structuring in the wild population of L. calbasu. AMOVA analysis also indicated moderate differentiation among the samples from different river basins. Analysis for genetic bottleneck was performed under the infinite allele model. The study revealed nine genetic stocks of L. calbasu from the natural population across Indian rivers. Evidence of genetic bottlenecks in some rivers was also revealed.

Keywords: Labeo calbasu ; Allozyme; Electrophoresis; Genetic differentiation

Novel Single Nucleotide Polymorphisms of the Caprine PC1 Gene and Association with Growth Traits by Jiajie Sun; Chunlei Zhang; Xingtang Fang; Chuzhao Lei; Xianyong Lan; Hong Chen (pp. 779-788).

Proprotein convertase 1 (PC1) is an endopeptidase involved in proteolytic processing of peptide hormone precursors in granules of the regulated secretory pathway in endocrine cells. Mutations in the PC1 gene are thought to cause obesity, and multiple alternatively spliced transcript variants have been described for this gene. In this study, based on PCR–SSCP and DNA sequencing methods, polymorphisms of the PC1 gene were detected in 447 individuals from three breeds. Only the P₁, P₂, P₃, P₉, and P₁₀ loci showed polymorphisms, and 12 SNPs in the PC1 gene were identified. Additionally, an association analysis between mutations in the 5′-UTR and four growth traits indicated that the polymorphisms were significantly associated with caprine body height (P < 0.05) and chest circumference (P < 0.01).

Keywords: Growth traits; Goat; PC1 ; PCR–SSCP; SNP

Development of Molecular Tools for Characterization and Genetic Diversity Analysis in Tunisian Fig (Ficus carica) Cultivars by Khaled Chatti; Ghada Baraket; Ahmed Ben Abdelkrim; Olfa Saddoud; Messaoud Mars; Mokhtar Trifi; Amel Salhi Hannachi (pp. 789-806).

Fig, Ficus carica L., is a useful genetic resource for commercial cultivation. In this study, RAPD (60), ISSR (48), RAMPO (63), and SSR (34) markers were compared to detect polymorphism and to establish genetic relationships among Tunisian fig tree cultivars. The statistical procedures conducted on the combined data show considerable genetic diversity, and the tested markers discriminated all fig genotypes studied. The identification key established on the basis of SSR permitted the unambiguous discrimination of cultivars and confirmed the reliability of SSR for fingerprinting fig genotypes. The study findings are discussed in relation to the establishment of a national reference collection that will aid in the conservation of Tunisian fig resources.

Keywords: Ficus carica L.; ISSR; RAMPO; RAPD; SSR

LDL-R AvaII and NcoI Polymorphisms: An Indirect Risk Factor for Coronary Heart Disease Among a Mendelian Population of Delhi, India by Ekata Sinha; Gagandeep Kaur Walia; Budh Prakash Gupta; Pradeep Kumar Ghosh; Kallur Nava Saraswathy (pp. 807-815).

AvaII and NcoI polymorphisms in the low-density lipoprotein receptor (LDL-R) gene are reported to alter cholesterol levels. Although found to be highly polymorphic worldwide, these mutations have not been validated in any Indian population. This case–control association study was conducted in an endogamous business community of Delhi. Blood samples from 100 cases and 100 age- and sex-matched controls belonging to the same ethnic group were subjected to biochemical and molecular analyses. Medical history and anthropometric measurements were taken from all the enrolled subjects. Linkage disequilibrium between the two polymorphisms was found to be significant (P = 0.0016). Significant variability was observed for the AvaII polymorphism among cases concerning waist–hip ratio, serum triglyceride, and low-density lipoprotein, which in turn was found to be associated with coronary heart disease.

Keywords: LDL-R polymorphism; Endogamous population; Linkage disequilibrium; Case–control association study

Expression of Glutathione Reductase Splice Variants in Human Tissues by Nana Satoh; Nobuko Watanabe; Ayato Kanda; Maki Sugaya-Fukasawa; Hisashi Hisatomi (pp. 816-821).

Stearoyl-CoA Desaturase (SCD) Gene Polymorphism in Goat Breeds by Chun-Lei Zhang; Xue-Yuan Gao; Ru-Ying Shao; Yan-Hong Wang; Xing-Tang Fang; Hong Chen (pp. 822-828).

There is evidence that stearoyl-CoA desaturase (SCD) is a key enzyme for lipid metabolism. Changes in enzyme activity that depends on SCD gene polymorphism and regulation could cause variations of fatty acid composition of meat and milk. We investigated genetic variability in caprine SCD, analyzing 335 animals belonging to three goat breeds by single-strand conformation polymorphism and DNA sequencing. Six single nucleotide polymorphism were identified, in intron 3 (585T→A and 601A→G; Ref. AF422168), intron 4 (719T→A; AF422169), and exon 6 (690 A→G, 718 C→G, and 802 A→C; AF422171). The less polymorphic SNP 601A→G displayed variability only in Xuhuai and Boer breeds. Across breeds, the average frequency for the least frequent alleles ranged from 0.1158 to 0.2532. The three SNPs in exon 6 resulted in variations of amino acids 313 tyr → cys, 322 phe → leu, and 350 arg → ser. The allelic distribution in exon 6 of Xuhuai was significantly different from Boer and Haimen.

Keywords: Stearoyl CoA desaturase gene; Lipid metabolism, SNPs; Meat quality; SSCP

Allele Distributions and Frequencies of the Six Prion Protein Gene (PRNP) Polymorphisms in Asian Native Cattle, Japanese Breeds, and Mythun (Bos frontalis) by Takeshi Shimogiri; George Msalya; Si Lhyam Myint; Shin Okamoto; Kotaro Kawabe; Kazuaki Tanaka; Hideyuki Mannen; Mitsuru Minezawa; Takao Namikawa; Takashi Amano; Yoshio Yamamoto; Yoshizane Maeda (pp. 829-839).

Six polymorphic sites of the bovine prion protein gene (PRNP) were genotyped in 569 animals of Asian native cattle, Japanese breeds, purebred mythun (Bos frontalis), and mythun × cattle composite animals. At the 23-bp indel site, a deletion (23−) allele was a major allele in all populations except mythun. At the 12-bp indel site, an insertion (12+) allele was a major allele in all populations. The 14-bp indel site was polymorphic in all Asian native cattle. In the octapeptide repeat region, a six-repeat allele was a major allele in all populations, and 5/5 and 4/6 genotypes were detected in Japanese Black and Mongolian cattle and in mythun, respectively. Two nonsynonymous single nucleotide polymorphisms (SNPs) (K3T and S154N) were detected in Asian native cattle and mythun. Haplotype analysis using the genotypes of the six sites estimated 33 different haplotypes. The haplotype 23− 12− K 6 S 14+ was found in all populations.

Keywords: Asian native cattle; Mythun; Polymorphism; PRNP ; Variability

Positive Selection of the Bat Interferon Alpha Gene Family by Guimei He; Beibei He; Paul A. Racey; Jie Cui (pp. 840-846).

Type I interferons (IFNs) are produced by leukocytes in reaction to pathogenic infection and function as positive mediators in antiviral pathways. Among IFNs, IFN alpha (IFNA) has the largest number of family members and plays an important role against the invasion of pathogens. Bats are putative and proven vectors for numerous viruses; however, the evolution of the IFNA family in bats has not been addressed. Here, we construct a phylogeny of IFNA families, including one fruit bat (Dobsonia viridis), with other vertebrates as references. Site-model estimation reveals that positive selection has shaped bat IFNA genes, showing that positive selection drives the evolution of bat IFNA genes.

Keywords: Positive selection; Bat; Interferon alpha; Gene family

Novel SNPs of the Caprine Growth Hormone Secretagogue Receptor (GHSR) Gene and Their Association with Growth Traits in Goats by Qijiang Jin; Xing Tang Fang; Liu Yang; Chun Lei Zhang; Jia Jie Sun; Dan Xia Chen; X. Y. Shi; Yu Du; Chuchao Lei; Hong Chen (pp. 847-856).

Growth hormone secretagogue receptor (GHSR), a G protein-coupled receptor that binds ghrelin, plays an important role in the central regulation of pituitary growth hormone secretion, food intake, and energy homeostasis. This study analyzed polymorphism of the caprine GHSR gene as a genetic marker candidate for growth traits in goats. Two single nucleotide polymorphisms (GU014697:g.165G→A and GU014697:g.548T→C) were identified in exon 2 of the caprine GHSR gene by PCR-single-strand conformation polymorphism and DNA sequencing methods. Their associations with growth traits were analyzed in 313 Xuhuai goats. The results indicated that GU014697:g.548T→C had significant effects on growth traits. Body length and body length index were significantly higher in individuals with genotype TT than CC and CT in (P < 0.05). TT individuals also tended to have better performance in other traits, such as body height and chest circumference, although there were no statistical differences (P > 0.05). This suggests that GHSR is a strong candidate gene that affects growth traits in goats.

Keywords: Caprine GHSR gene; Single-strand conformation polymorphism; Single nucleotide polymorphism; Growth traits

Genetic Variation in Natural Populations of Stipa tenacissima from Algeria by Mohamed Boussaid; Cesar Benito; Mériem Kaid Harche; Tomás Naranjo; Mohamed Zedek (pp. 857-872).

Intermicrosatellite PCR [inter-simple sequence repeat (ISSR)-PCR] markers and cytogenetics criteria were used to assess the level of genetic diversity and genetic structure in 17 populations of Stipa tenacissima (Gramineae) from Algeria. All populations sampled in the steppe area were diploids (2n = 2x = 24), and those sampled in the dry area were hexaploids (2n = 6x = 72). The dendrogram based on ISSR-PCR showed homogeneity within populations and large variability among populations. All individuals of the same population were gathered and formed groups clearly separated in all populations. These groups were separated into two clusters related to biotope, one from the steppe area and the other from the dry area. AMOVA indicated low genetic diversity among populations (30% of variation) and high within populations (70%). This variation pattern would constitute an adaptive strategy to grow in various ecological conditions.

Keywords: Stipa tenacissima ; Algeria; ISSR; Genetic diversity; Genetic differentiation

Genetic Relationships Among Some Hawthorn (Crataegus spp.) Species and Genotypes by Kadir Ugurtan Yilmaz; Makbule Yanar; Sezai Ercisli; Hatice Sahiner; Tuncer Taskin; Yasar Zengin (pp. 873-878).

The genus Crataegus is well distributed in Turkey as a wild plant, with numerous, inherently variable species and genotypes. RAPD markers were used to study 17 hawthorn genotypes belonging to Crataegus monogyna ssp. monogyna Jacq (2 genotypes), C. monogyna ssp. azarella Jacq (1), Crataegus pontica K.Koch (3), Crataegus orientalis var. orientalis Pallas Ex Bieb (3), Crataegus pseudoheterophylla Pojark (1), Crataegus aronia var. dentata Browicz (1), C. aronia var. aronia Browicz (4), and Crateagus × bornmuelleri Zabel (2). The 10 RAPD primers produced 72 polymorphic bands (88% polymorphism). A dendrogram based on Jaccard’s index included four major groups and one outgroup according to taxa. The lowest genetic variability was observed within C. aronia var. aronia genotypes. The study demonstrated that RAPD analysis is efficient for genotyping wild-grown hawthorns.

Keywords: Wild hawthorn; Crataegus ; RAPD; Genetic diversity

Microsatellite Polymorphisms in Cassava Landraces from the Cerrado Biome, Mato Grosso do Sul, Brazil by M. V. B. M. Siqueira; T. T. Pinheiro; A. Borges; T. L. Valle; M. Zatarim; E. A. Veasey (pp. 879-895).

Using nine microsatellite loci, we investigated genetic structure and diversity in 83 Brazilian cassava accessions, including several landraces, in the Cerrado biome in Mato Grosso do Sul, Brazil. All nine loci were polymorphic, averaging 6.00 alleles per locus. Treating each of seven municipalities as a cassava group or population, they averaged 3.5 alleles per locus, with 97% polymorphic loci, high values for observed heterozygosity (0.32) and gene diversity (0.56). Total genetic variability was high (0.668), and most of this genetic variability was concentrated within municipalities (0.577). Cluster and structure analyses divided accessions into two major clusters or populations (K = 2). Also, a significant genetic versus geographic correlation was found (r = 0.4567; P < 0.0260). Migratory routes in the Cerrado are considered main contributors to the region’s high cassava diversity and spatial genetic structure, amplifying interactions between traditional farmers and the evolutionary dynamics of this crop.

Keywords: Manihot esculenta ; SSR; Genetic variability; Traditional agriculture; Cerrado

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Biochemical Genetics (v.48, #9-10)

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Biochemical Genetics (v.48, #9-10)