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Biochemical Genetics (v.45, #11-12)

Development of a Species-diagnostic SCAR Marker of the Blue Swimming Crab (Portunus pelagicus) by Sirawut Klinbunga; Kannika Khetpu; Bavornlak Khamnamtong; Piamsak Menasveta (pp. 755-760).

Encoding PCR Products with Batch-stamps and Barcodes by Megan L. McCloskey; Reinhard Stöger; R. Scott Hansen; Charles D. Laird (pp. 761-767).

Polymerase chain reaction (PCR) has become the mainstay of DNA sequence analysis. Yet there is always uncertainty concerning the source of the template DNA that gave rise to a particular PCR product. The risks of contamination, biased amplification, and product redundancy are especially high when limited amounts of template DNA are used. We have developed and applied molecular encoding principles to solve this source-uncertainty problem for DNA sequences generated by standard PCR. Batch-stamps specify the date and sample identity, and barcodes detect template redundancy. Our approach thus enables classification of each PCR-derived sequence as valid, contaminant, or redundant, and provides a measure of sequence diversity. We recommend that batch-stamps and barcodes be used when amplifying irreplaceable DNAs and cDNAs available for forensic, clinical, single cell, and ancient DNA analyses.

Keywords: PCR; Contamination; Redundancy; Batch-stamp; Barcode; Source DNA; Populations of molecules

Rapid Genotyping Using Real-time Fluorescent PCR of the Trp64Arg Polymorphism of the β3-adrenergic Receptor Gene and the −3826 A to G Variant of the Uncoupling Protein-1 Gene by Arizumi Kikuchi; Yuko Kuramoto; Nobuyasu Noritake; Hiroshi Murase; Osami Daimaru; Takeo Nakakita; Shinichi Itoh (pp. 769-773).

Microsatellite Analysis of Genetic Variation and Population Subdivision for the Black Muntjac, Muntiacus crinifrons by Hai-Long Wu; Qiu-Hong Wan; Sheng-Guo Fang (pp. 775-788).

The black muntjac (Muntiacus crinifrons) is a rare deer found only in a restricted region in east China. Recent studies of mitochondrial DNA diversity have shown a markedly low level of nucleotide diversity for the species, and the Suichang population was genetically differentiated from the two other populations, in Huangshan and Tianmushan mountains. In this study, we extended the analysis of genetic diversity and population subdivision for the black muntjac using data from 11 highly polymorphic nuclear DNA microsatellite loci. Contrary to the results based on mtDNA data, the microsatellite loci revealed that the black muntjac retained a rather high nuclear genetic diversity (overall average H _E = 0.78). Nevertheless, both types of markers supported the idea that the extant black muntjac population is genetically disrupted (overall ϕ _ST = 0.16 for mtDNA and overall F _ST = 0.053 for microsatellite, both P < 0.001). The correlation between genetic differentiation and geographic distance was not significant (Mantel test; P > 0.05), implying that the patterns of genetic differentiation observed in this study might result from recent habitat fragmentation or loss. Based on the results from the mtDNA and nuclear DNA data sets, two management units were defined for the species, Huangshan/Tianmushan and Suichang. We also recommend that a new captive population be established with individuals from the Suichang region as a founder source.

Keywords: Microsatellite; Muntiacus crinifrons ; Conservation; Management units; Genetic diversity; Population subdivision

Abundant Within-varietal Genetic Diversity in Rice Germplasm from Yunnan Province of China Revealed by SSR Fingerprints by Min Tu; Bao-Rong Lu; Youyong Zhu; Yunyue Wang (pp. 789-801).

In order to estimate genetic diversity of rice (Oryza sativa L.) germplasm in Yunnan Province of China, 60 varieties from different regions were analyzed by microsatellite (SSR) fingerprints. Nine selected SSR primer pairs amplified a total of 55 alleles from these varieties, and high genetic diversity (0.706) was found, although it was not evenly distributed across the regions. Marked genetic variation was detected within the traditional varieties. A UPGMA dendrogram based on SSR polymorphism indicated a great variation among the rice varieties, with coefficients ranging between 0.229 and 1.000. The formation of the rice diversity pattern in Yunnan is associated with natural conditions and especially with diverse cultural demands and farming styles. Strategic conservation of rice germplasm in Yunnan is important, and this could be implemented by collecting varieties across geographic regions with sufficient individuals within the same varieties. Effective rice conservation should also consider cultural aspects during collection.

Keywords: Oryza sativa ; Varietal diversity; Conservation; Similarity coefficient; SSR

Sequence Variations and Haplotype Identification of Wheat Dimeric α-Amylase Inhibitor Genes in Einkorn Wheats by Ji-Rui Wang; Yu-Ming Wei; Ze-Hong Yan; You-Liang Zheng (pp. 803-814).

This study characterizes 80 dimeric α-amylase inhibitor genes from 68 accessions of the einkorn wheats Triticum urartu, T. boeoticum, and T. monococcum. The mature protein coding sequences of WDAI genes were analyzed. Nucleotide sequence variations in these regions resulted from base substitution and/or indel mutations. Most of the WDAI gene sequences from T. boeoticum and all sequences from T. monococcum had one nucleotide insertion in the coding region, such that these α-amylase inhibitor sequences could not encode the correct mature proteins. We identified 21 distinct haplotypes from the diploid wheat WDAI gene sequences. A main haplotype was found in 15 gene samples from the A^u genome and 35 gene samples from the A^m genome. The T. monococcum and T. boeoticum accessions shared the same main haplotype, with 25 samples from T. monococcum and 10 from T. boeoticum. The WDAI gene sequences from the A^u and A^m genomes could be obviously clustered into two clades, but the sequences from the A^m genome of T. boeoticum and T. monococcum could not be clearly distinguished. The phylogenetic analysis revealed that the WDAI gene sequences from the A^m genome had accumulated fewer variations and evolved at a slower rate than the sequences from the A^u genome. Although some accessions from only one or two areas had unique mutations at the same position, the diversity of WDAI gene sequences in diploid wheat showed little relationship to the origin of the accessions.

Keywords: Diploid wheat; Phylogenetic analysis; Haplotype; Single nucleotide polymorphism

Genetic Polymorphisms of DNA Repair Gene: XRCC1 Pro206Pro and Gln632Gln in a Chinese Han Population by Jiaoyang Yin; Rong Qi; Yegang Ma; Zhongfu Sun; Huiwen Wang (pp. 815-821).

DNA repair genes are increasingly studied because of their critical role in maintaining genome integrity. The base excision repair (BER) pathway is a DNA repair pathway that operates on small lesions, such as oxidized or reduced bases, fragmented or nonbulky adducts, or those produced by methylating agents. The XRCC1 polymorphic system is the key gene of the BER pathway. In this study, polymorphisms of XRCC1 Pro206Pro on exon 7 and Gln632Gln on exon 17 were analyzed in a northeastern Chinese Han population. Genomic DNA extracted from 303 unrelated individuals and the PCR-RFLP technique were used to identify variants. The allele frequencies were 0.90 (A) and 0.10 (G) for XRCC1 Pro206Pro and 0.88 (G) and 0.12 (A) for XRCC1 Gln632Gln. The genotype frequencies were 0.797 (AA), 0.203 (AG), and 0 (GG) for XRCC1 Pro206Pro and 0.007 (AA), 0.222 (AG), and 0.771 (GG) for XRCC1 Gln632Gln. The expected heterozygosity and PIC were 18 and 16.38% for Pro206Pro and 21.12 and 18.89% for Gln632Gln. The two polymorphisms were in strong linkage disequilibrium (D′ = 0.921, r ² = 0.735). The results are compared with those of other reported populations. They showed marked ethnic group differences. This study provides the first analysis of the distribution of allele frequency for XRCC1 Pro206Pro and Gln632Gln in a Chinese population.

Keywords: DAN repair gene; XRCC1 Pro206Pro and Gln632Gln; Genetic polymorphisms; Chinese population

Genetic Diversity and Systematic Evolution of Chinese Domestic Ducks Along the Yangtze-Huai River by Tang-jie Zhang; Hui-fang Li; Kuan-wei Chen; Hong Chang; Qing-ping Tang; Jing-xin Zhang (pp. 823-837).

To investigate the population structure and systematic evolution of the domestic duck in China, we sequenced the 667 bp mitochondrial DNA (mtDNA) D-loop control region of 106 ducks from nine breeds along the Yangtze-Huai River. Of the total analyzed sites, 34 (5.1%) were polymorphic due to transitions, transversions, insertions, and deletions. Nucleotide content was 25.6% A, 33.3% C, 15.2% G, and 25.9% T. In total, 31 haplotypes were identified in the target region; of these, the major haplotype was A7, and nine haplotypes were shared by the tested ducks. The haplotype diversity (Hd) and average nucleotide diversity (Pi) were 0.798% and 0.28%, respectively. Hd was highest in the Jingjiang shelduck, followed by the Youxian and Enshi shelducks, and it was lowest in the Wendeng black duck. Nucleotide diversity (Dxy) among the nine breeds ranged from 0.139 to 0.433%, and the Kimura 2-parameter distances were 0.0013–0.0044. Molecular variance indicated that a very high proportion of the insignificant genetic variance was attributable to variations within breeds. Phylogenetic analysis of 31 haplotypes revealed only one distinct maternal lineage in the tested ducks, and no evidence was found of a contribution of the Anas zonorhyncha group B haplotype to the maternal origin of Chinese domestic duck breeds along the Yangtze-Huai.

Keywords: Chinese domestic duck; Mitochondrial DNA; Haplotype; Genetic distance

Geographic Patterns of Genetic Variation and Conservation Consequences in Three South American Rodents by Gustavo B. Miranda; Jaqueline Andrades-Miranda; Luiz F. B. Oliveira; Alfredo Langguth; Margarete S. Mattevi (pp. 839-856).

In this study, the geographic patterns of genetic variation of three rodent species belonging to the tribe Oryzomyini were investigated using the mitochondrial cytochrome b and nuclear IRBP genes in biomes that are undergoing degradation processes to a greater or lesser degree. The samples are from 25 collecting localities distributed throughout the Amazon, Cerrado, Atlantic Forest, and Pampa biomes. The results show that the three species have a population and geographic structure, besides being in demographic equilibrium. The phylogenetic analyses performed on Euryoryzomys russatus and Hylaeamys megacephalus showed these specimens grouped in three distinct clades forming geographic gradients (North–South direction in H. megacephalus). Intraspecific genetic divergence was higher in H. megacephalus (4.53%), followed by E. russatus (1.79%), and lowest in Sooretamys angouya (0.88%). The results obtained indicate that, necessarily, the management strategies to preserve genetic diversity should be different for each species, since each of them presented specific population parameters.

Keywords: Euryoryzomys russatus ; Hylaeamys megacephalus ; Sooretamys angouya ; Cytochrome b ; IRBP

The Porcine Nuclear Receptor Co-repressor 1 (NCOR1) Gene: Chromosome Location, Expression Profile, and Polymorphism by Kaixuan Yang; Jun Ren; Junwu Ma; Xueming Yan; Lusheng Huang (pp. 857-862).

NCOR1 (nuclear receptor co-repressor1) encodes a protein that represses the expression of the targeted genes by promoting chromatin condensation and disabling access to the transcription machinery. So far, only a few NCOR1 EST sequences are available, and the chromosomal location of NCOR1 is unknown in the porcine genome. In this study, we have localized NCOR1 to the end of pig chromosome (SSC) 12 by a porcine radiation hybrid panel. The expression profile of NCOR1 was clarified using RNA from 18 tissues, and it is expressed ubiquitously in pigs. We did not identify any missense mutation in the exonic region encoding the first SANT domain of the NCOR1 protein, although we found six SNPs and two deletions in intron 12, and three SNPs and one deletion in intron 13, using DNA of 10 founder animals in a White Duroc × Erhualian intercross. These polymorphic markers can be integrated into a genome scan for identifying the QTL affecting economically important traits in pigs.

Keywords: Pig; NCOR1 ; Chromosomal location; Expression profile; Polymorphism

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Biochemical Genetics (v.45, #11-12)

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Biochemical Genetics (v.45, #11-12)