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Biochemical Genetics (v.44, #5-6)

The Loss of Genetic Diversity in Sichuan Taimen as Revealed by DNA Fingerprinting by Xue-Chang Wu (pp. 177-185).

Species endangerment often derives from the “endangerment” of genetic diversity, thus loss of genetic diversity is an important cause of species extinction. Since historical specimens were unavailable, previous studies mainly described the genetic diversity status in the current population rather than the loss of genetic variation over time. In this study, we collected samples during1998–1999 and obtained historical specimens from 1957 to 1958. Based on the two sets of fish, we determined the changes in genetic diversity of Sichuan taimen using DNA fingerprinting. The differences in genetic parameters between the present samples and historical taimens revealed their loss of genetic variation. As a result, the existing populations have lower viability, and proper management has to be implemented to preserve genetic diversity.

Keywords: DNA fingerprinting; loss of genetic variation; endangered fishes

Genetic Variation in Hippophae rhamnoides ssp. sinensis (Elaeagnaceae) Revealed by RAPD Markers by Kun Sun; Wen Chen; Ruijun Ma; Xuelin Chen; Ang Li; Song Ge (pp. 186-197).

Hippophae rhamnoides ssp. sinensis is endemic to China, and it is a dioecious, outcrossing plant. Although many studies have been undertaken mainly on its agricultural, nutritional, medical, and ornamental value, little is known about its population genetics. This study uses random amplified polymorphic DNA to investigate the genetic diversity and population genetic structure of 13 natural populations of the subspecies sinensis. Fifteen primers amplified 107 reproducible bands, with 95 (88.79%) being polymorphic. The gene diversity within population was 0.168, considerably lower than that of tree species and most perennial, outcrossing species, but higher than that of annual or short-lived, selfing species. The Gst value showed that 18.3% of the total genetic variation resided among populations, a little lower than that of outcrossing species. The present results are quite similar to those previously reported in another subspecies, H ssp. . rhamnoides rhamnoides. The low genetic differentiation among populations in ssp. sinensis may be attributed to the long-distance dispersal of seeds facilitated by birds, in addition to its characteristics of outcrossing, wind pollination, and widespread distribution. No association between genetic distance and geographical distribution was found. The population relationships revealed by the UPGMA dendrogram parallel this result, in that genetic distance did not increase with geographic separation. This pattern of population differentiation may imply the adaptation of ssp. s populations to the local environment, given that its habitats vary greatly across its distribution.

Keywords: Hippophae rhamnoides ssp. sinensis ; RAPD; genetic diversity; population differentiation.

Phylogenetic Relationships and Possible Hybrid Origin of Lycoris Species (Amaryllidaceae) Revealed by ITS Sequences by Shude Shi; Yingxiong Qiu; Enxiang Li; Ling Wu; Chengxin Fu (pp. 198-208).

To examine interspecific relationships and test the hypothesis of hybrid origin within Lycoris species, this study used data from parsimony analyses with nuclear ITS sequences for 19 taxa representing 14 species of Lycoris and two outgroup taxa. The ITS sequences resolved three infrageneric clades. One clade included L. chinensis, L. longituba, L. longituba var. flava, L. anhuiensis, and L. aurea; the second one consisted of L. sprengeri, L. radiata, L. radiata var. radiata, L. radiata var. pumila, L. haywardii, L. rosea, L. sanguinea var. sanguinea, and L. sanguinea var. koreana; and the third included L. caldwellii, L. straminea, L. albiflora, L. flavescens, and two hybrids. The results strongly support the hypothesis that L. straminea originated from hybridization between L. chinensis and L. radiata var. pumila, and the allotriploid L. caldwellii and L. albiflora derived from hybridization between L. chinensis and L. sprengeri. As nucleotide additivity was observed in the artificial hybrids and several presumed hybrids, the likelihood of hybrid origin of Lycoris species is supported.

Keywords: Lycoris ; ITS; interspecific hybridization; phylogenetic relationships

Genetic Structure of Przewalski’s Rock Partridge (Alectoris magna) Populations in the Longzhong Loess Plateau, China by Yanke Chen; Zhongliang Zhao; Naifa Liu (pp. 209-221).

In this paper, we have analyzed the nuclear DNA of Alectoris magna samples, collected from the Longzhong Loess Plateau. We used allelic variation at eight microsatellite markers to describe the genetic structure of A. magna populations. The primary goal of this study was to examine the population genetic structure and determine the extent of population differentiation among populations of A. magna. The average value of H E (0.455) was smaller than H O (0.477), and there was a heterozygote deficit at the MCW135 locus in the Lanzhou population and the Beidao population. The AB063167 locus in each population (except that of Jingyuan) was not in equilibrium (P < 0.05). The Lixian edge population had a lower proportion of genetic diversity than the central geographic populations; the Haiyuan and Jingyuan populations had higher genetic diversity than the central geographic populations. Analysis of population structure revealed clear differentiation among the eight populations of A. magna, suggesting strong isolation of these populations and correspondingly low levels of migration or gene flow. The A. magna populations of Longzhong Loess Plateau are separated into eastern and western populations by a clustering chart. Genetic data indeed suggest that patterns of speciation and population diversification of A. magna in the Longzhong Plateau have been affected by the stability of the climate, natural selection, and human intervention.

Keywords: Przewalski’s rock partridge (Alectoris magna); microsatellite DNA; genetic structure of population; Longzhong Loess Plateau

Genetic Diversity of the Giant Tiger Shrimp (Penaeus monodon) in Thailand Revealed by PCR-SSCP of Polymorphic EST-Derived Markers by Sirawut Klinbunga; Rachanimuk Preechaphol; Supaporn Thumrungtanakit; Rungnapa Leelatanawit; Takashi Aoki; Padermsak Jarayabhand; Piamsak Menasveta (pp. 222-236).

A total of 90 ESTs from normal and 157 from subtractive ovarian cDNA libraries of the giant tiger shrimp (Penaeus monodon) were sequenced. SSCP analysis of disulfide isomerase (DSl), zinc finger protein (ZFP), PMO920, and PMT1700 was carried out for population genetic studies of P. monodon in Thai waters. The number of codominant alleles per locus for overall samples was 6 for PMO920, 5 for PMT1700, and 12 for ZFP, and there were 19 dominant alleles for DSI. The observed heterozygosity of each geographic sample was 0.3043–0.5128 for PMO920, 0.3462–0.4643 for PMT1700, and 0.5000–0.8108 for ZFP. Linkage disequilibrium analysis indicated that genotypes of these loci segregate randomly (P > 0.05). Low genetic distance was found between pairs of geographic samples (0.0077–0.0178). The neighbor-joining tree constructed from the average genetic distance of overall loci allocated the Andaman samples (Satun, Trang, and Phangnga) into one cluster, and Chumphon and Trat into other clusters. Geographic differentiation between Satun-Trat and Satun-Phangnga was found only at the ZFP locus (P < 0.05), suggesting low degrees of genetic subdivision of Thai P. monodon.

Keywords: genetic diversity; SSCP; EST; Penaeus monodon ; shrimp

Mitochondrial DNA Cleavage Patterns Distinguish Independent Origin of Chinese Domestic Geese and Western Domestic Geese by X-W. Shi; J-W. Wang; F-T. Zeng; X-P Qiu (pp. 237-245).

It has generally been assumed, based on morphology, that Chinese domestic goose breeds were derived from the swan goose (Anser cygnoides) and that European and American breeds were derived from the graylag goose (Anser anser). To test the validity of this assumption, we investigated the mtDNA cleavage patterns of 16 Chinese breeds and 2 European breeds as well as hybrids produced between a Chinese breed and a European breed. After 224 mtDNAs, isolated from the Chinese and European breeds, were digested by 19 restriction endonucleases, variations of the cleavage patterns were observed for four enzymes (EcoRV, HaeII, HincII, and KpnI). All Chinese breeds and their maternal hybrids except the Yili breed showed an identical haplotype, named haplotype I or the Chinese haplotype; the European breeds and the Yili breed showed another haplotype, named haplotype II or the western haplotype. None of the haplotype found in the Chinese type was detectable in the western type and vice versa. The two haplotypes were found to differ from each other at 8.0% of the sites surveyed and with a 0.72% sequence divergence. Using 2% substitution per million years calibrated from the genera Anser and Branta, the two domestic geese haplotypes were estimated to have diverged approximately 360,000 years ago, well outside the 3000–6000 years in domestic history. Our findings provide the first molecular genetic evidence to support the dual origin assumption of domestic geese in the world. Meanwhile, the four mtDNA restriction fragment length polymorphisms can be used as maternal genetic markers to distinguish the two types of domestic geese.

Keywords: domestic geese; origin; mtDNA; RFLP

Genetic Polymorphism of Interferon-γ, Interferon-γ Receptor, and Interferon Regulatory Factor-1 Genes in Patients with Hepatitis B Virus Infection by Jae Youn Cheong; Sung Won Cho; Soon Gee Chung; Jung A. Lee; Marie Yeo; Hee Jung Wang; Jong Eun Lee; Ki Baik Hahm; Jin Hong Kim (pp. 246-255).

The natural history of hepatitis B virus (HBV) infection is probably related to host immune factors. Interferon-γ (IFN-γ) plays significant roles in immune defense. This study was undertaken to investigate the association between HBV infection and single nucleotide polymorphisms (SNPs) of IFN-γ, IFN-γ receptor (IFNGR)-1 and 2, and interferon regulatory factor (IRF)-1 genes. Between March 2002 and December 2002, 614 Korean patients were enrolled in two different groups: an HBV clearance group (n = 201), who were hepatitis B surface antigen (HBsAg) negative with antibodies to HBsAg and hepatitis B core antigen, and an HBV persistence group (n = 413), who were repeatedly HBsAg positive. We assessed polymorphisms in the IFN-γ gene at position +874, in the IFNGR-1 gene at positions −56 and +95, in the IFNGR-2 gene at the second position of codon 64 (Gln64Arg), and in the IRF-1 gene promoter (−410, −388), and the genotype distributions of the HBV clearance and persistence groups were compared. On the basis of unconditional logistic regression analysis with adjustment for age and sex, no statistically significant association with susceptibility to persistent HBV infection was observed with the IFN-γ, IFNGR-1 and 2, and IRF-1 gene polymorphisms under the codominant, dominant, and recessive models.

Keywords: hepatitis B; single nucleotide polymorphism (SNP); interferon-γ (IFN-γ); interferon regulatory factor (IRF)

Mitochondrial DNA Diversity and Genetic Differentiation of the Honeybee (Apis cerana) in Thailand by Onuma Songram; Siriporn Sittipraneed; Sirawut Klinbunga (pp. 256-269).

Genetic diversity of the honeybee (Apis cerana) in Thailand collected from north, northeast, the central region, peninsular Thailand, and Samui Island (n = 181) was examined by PCR–RFLP of ATPase6–ATPase8. Interestingly, 78 individuals (43.09%) of the southern-latitude bees exhibited length heteroplasmy of the PCR product. The gel-eluted ATPase6–ATPase8 (825 bp) of each bee was restricted with TaqI, SspI, and VspI, respectively. Eight mitotypes were generated and revealed biogeographic differentiation between conspecific samples of A. cerana. AAA, ACA, AAD, BAA, ADA, and ABA were found only in the north-to-central samples (north, northeast, and central region); BBB and BBC were found in the southern-latitude bees; and BBC was restrictively found in the Samui sample. Large genetic distances were observed between each of the north-to-central samples and peninsular Thailand and Samui samples, but lower levels of genetic distance were found within each region. Geographic heterogeneity and phylogenetic analyses indicated that Thai A. cerana could be genetically differentiated into northern Thailand, peninsular Thailand, and Samui Island populations.

Keywords: heteroplasmy; ATPase; PCR–RFLP; Apis cerana ; honeybee

Mitochondrial cytochrome b Sequence Variation and Phylogenetics of the Highly Specialized Schizothoracine Fishes (Teleostei: Cyprinidae) in the Qinghai-Tibet Plateau by Delin Qi; Taiping Li; Xinquan Zhao; Songchang Guo; Junxiang Li (pp. 270-285).

The complete 1140 bp mitochondrial cytochrome b sequences were obtained from 39 individuals representing five species of all four genera of highly specialized schizothoracine fishes distributed in the Qinghai-Tibet plateau. Sequence variation of the cytochrome b gene was surveyed among the 39 individuals as well as three primitive schizothoracines and one outgroup. Phylogenetic analysis suggested that the group assignment based on 1140 bp of the cytochrome b sequence is obviously different from previous assignments, and the highly specialized schizothoracine fishes (Schizopygopsis pylzovi, Gymnocypris przewalskii, G. eckloni, Chuanchia labiosa, and Platypharodon extremus) form a monophyletic group that is sister to the clade formed by the primitive schizothoracine fishes (Schizothorax prenanti, S. pseudaksaiensis, and S. argentatus). The haplotypes of Schizopygopsis pylzovi and G. przewalskii were paraphyletic based on cytochrome b data, which most likely reflected incomplete sorting of mitochondrial DNA lineages. The diploid chromosome numbers of Schizothoracinae were considered in phylogenetic analysis and provided a clear pattern of relationships. Molecular dating estimated for highly specialized schizothoracine fishes suggested that the highly specialized schizothoracine fishes diverged in the late Miocene Pliocene to Pleistocene (4.5 × 10⁴–4.05 × 10⁶years BP). The relationship between the cladogenesis of highly specialized schizothoracine fishes and geographical events of the Qinghai-Tibet plateau is discussed.

Keywords: Schizothoracinae; mtDNA; cytochrome b ; biogeography; diploid chromosome numbers

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Biochemical Genetics (v.44, #5-6)

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Biochemical Genetics (v.44, #5-6)