Journal of Genetics and Genomics

Identification of a Novel VEGFR-3 Missense Mutation in a Chinese Family with Hereditary Lymphedema Type I

Zhengya Yu, Jingjing Wang, Shuling Peng, Bing Dong, Yang Li

2007, 34(10): 861-867. doi: 10.1016/S1673-8527(07)60097-6

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A novel mutation of vascular endothelial growth factor receptor gene (VEGFR-3), was identified in a four-generation Chinese family with hereditary lymphedema type I (HL-I). Genetic linkage analysis was performed on the known genetic locus for HL-I with a panel of polymorphic markers, and then mutations were screened out by direct sequencing. By genotyping, the family showed the linkage to HL-I locus on 5q35.3. Mutation screening analysis of the exons encoding the intracellular kinase domains of VEGFR-3, revealed a novel missense mutation D1055V. This mutation cosegregated with the disease phenotype in the family and was not found in 100 normal controls. This finding has expanded the spectrum of the VEGFR-3 gene mutations causing HL-I, and will be useful for further genetic consultation and genetic diagnosis.

Association of CA Repeat Polymorphism in Estrogen Receptor β Gene with Postmenopausal Osteoporosis in Chinese

Li Geng, Zhenwei Yao, Hongchang Yang, Jianyun Luo, Lili Han, Qi Lu

2007, 34(10): 868-876. doi: 10.1016/S1673-8527(07)60098-8

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Postmenopausal osteoporosis (PMO) is considered a polygenic disease. The estrogen receptor β (ESR2) gene is a candidate mediating the genetic influence on bone mass and the risk of osteoporosis. The aim of this study is to investigate the association of a cytosine-adenine (CA) repeat polymorphism in the fifth intron of the ESR2 gene with PMO in Chinese Han population. The CA repeat polymorphism was genotyped in a case-control study, involving 78 femoral neck PMO patients vs. 122 controls and 108 lumbar spine (L2-4) PMO patients vs. 92 controls. The (CA)_n < 22 and (CA) _n ≥ 22 alleles were designated short (S) and long (L), respectively. ESR2 genotype was categorically defined as SS (2 S alleles), SL (having the mixed S and L alleles), and LL (2 L alleles). At both the femoral neck and the L2-4 region, LL genotype and L allele frequencies of the PMO group were significantly higher than those of the control group ( P < 0.01). The subjects with the SL, the LL, and the combined SL and LL genotype had a significant increased risk of PMO when compared with those with the SS genotype ( P < 0.05). After adjustments for age, years since menopause, menopausal age, and body mass index, logistic regression analysis showed that the subjects with the combined SL and LL genotype had increased risk of PMO when compared with those with the SS genotype both at the femoral neck (adjusted OR 4.923, 95% CI 1.986–12.203, P=0.001) and the L2-4 (adjusted OR 2.267, 95% CI 1.121–4.598, P=0.023). This extensive association study has identified the ESR2 CA repeat polymorphism to be independently associated with PMO at the femoral neck and the L2-4 in Chinese Han population. The data also suggested that the presence of the L allele may dominantly increase the risk of PMO at the two regions.

Molecular Genetic Diagnostics of Prader-Willi Syndrome: a Validation of Linkage Analysis for the Chinese Population

Hongyi Li, Shu Meng, Zheng Chen, Haifei Li, Minlian Du, Huamei Ma, Haiyun Wei, Honglei Duan, Hui Zheng, Qing Wenren, Xinming Song

2007, 34(10): 885-891. doi: 10.1016/S1673-8527(07)60100-3

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Prader-Willi Syndrome (PWS) is a genetic disorder that is difficult to detect, particularly at an early age. PWS is caused by disruption of normal, epigenetically controlled gene function in the chromosome 15q11-q13 region. Clinical symptoms are difficult to diagnose in infants and only become clearer at later ages as the patients develop hyperphagia and morbid obesity. Molecular genetic tests are able to definitively diagnose PWS and allow early diagnosis of the syndrome. High resolution cytogenetic testing, methylation-specific PCR (MS-PCR), and linkage analysis are routinely used to diagnose PWS. To establish a linkage analysis method for Chinese patients, this study identified a useful set of STR markers in the typical PWS deletion and adjacent area, for linkage analysis in two Chinese families with PWS offspring. Using this method, the authors confirmed that one patient had a paternal deletion in chromosome 15q11-q13 and the other patient had maternal uniparental heterodisomy of chromosome 15. MS-PCR and high resolution chromosome G-banding also confirmed this diagnosis. This linkage analysis method can detect both deletion and uniparental disomy, thus providing valuable information for genetic counseling and the opportunity to analyze the relationship between the genotype and phenotype of PWS.

Adiponectin Gene Variation −4522C/T Is Associated with Type 2 Diabetic Obesity and Insulin Resistance in Chinese

Hekun Liu, Suyun Chen, Sizhong Zhang, Cuiying Xiao, Yan Ren, Haoming Tian, Xuefei Li

2007, 34(10): 877-884. doi: 10.1016/S1673-8527(07)60099-X

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The authors investigated the possible association of −4522C/T variation of adiponectin gene with coronary heart disease (CHD) and type 2 diabetes mellitus (T2DM). Genotyping of SNP −4522C/T in 304 patients with CHD, 389 patients with T2DM, and 405 age and sex-matched healthy control subjects was carried out by means of PCR-RFLP approach. No significant difference in the genotype or allele frequencies was found, either between patients with CHD and control subjects, or between patients with T2DM and control subjects. However, in the subgroup analysis, an association of the T/T genotype and T allele with type 2 diabetes combined with obesity (BMI ≥ 25 kg/m²) was found (P = 0.014 and P = 0.034, respectively). Also the homeostasis model assessment of insulin resistance (HOMA-IR) in T2DM patients with T/T genotype was significantly higher than that in T2DM patients carrying C allele (P = 0.0069). The authors' findings for the first time demonstrated that SNP −4522 in the adiponectin gene was associated with T2DM that combined with obesity and higher insulin resistance index in patients with T2DM. This indicated that the variation might associate with an increased susceptibility to type 2 diabetic obesity and insulin resistance. But −4522C/T polymorphism did not contribute to the susceptibility of CHD.

Expression Patterns of the Cell Junction-associated Genes During Rat Liver Regeneration

Honglei Li, Xiaoguang Chen, Fuchun Zhang, Ji Ma, Cunshuan Xu

2007, 34(10): 892-908. doi: 10.1016/S1673-8527(07)60101-5

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To study actions of the genes associated with tight junction, adherent junction, focal adhesion, and gap junction during liver regeneration (LR), these genes were obtained by collecting data from databases and thesis, and their expression profiles in rat regenerating liver were detected employing Rat Genome 230 2.0 array. Next the LR-associated genes were identified by comparing the difference between sham operation (SO) and partial hepatectomy (PH) groups. 79, 53, 109, 53 genes involved in the above four junctions were found to be LR-associated. The initial and total expression numbers of these genes occurring in the initial phase of LR, G0/G1, cell proliferation, cell differentiation, and structure-functional rebuilding were 124, 43, 122, 10, and 249, 145, 957, 306, respectively, illustrating that genes were initially expressed mainly in the initiation stage, and functioned in different phases. Up-regulation and down-regulation to a total of 972 and 540 times, as well as, 41 types of expression patterns showed that the physiological and biochemical activities were diverse and complicated in LR. According to the data, there was an increase in the forepart and prophase, but a decrease in late-metaphase and anaphase for gap junction assembly. Focal adhesion formation displayed an enhancement in forepart, prophase, and anaphase; and formation of tight junctions and adherent junctions last throughout the LR.

Developmental Changes of the FAS and HSL mRNA Expression and Their Effects on the Content of Intramuscular Fat in Kazak and Xinjiang Sheep

Yong Qiao, Zhiguo Huang, Qifa Li, Zhenshan Liu, Chengli Hao, Guoqing Shi, Rong Dai, Zhuang Xie

2007, 34(10): 909-917. doi: 10.1016/S1673-8527(07)60102-7

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Twenty-four male Kazak sheep and 30 Xinjiang fine wool sheep at different ages were selected to investigate the development-dependent expression levels of fatty acid synthase (FAS) gene and hormone-sensitive lipase (HSL) gene in muscle and their effects on the contents of intramuscular fat (IMF). Longissimus dorsal muscle was sampled to measure IMF and total RNA was extracted to determine FAS and HSL mRNA expression levels by real-time PCR. The results showed that: 1) The IMF content increased continuously with growth and showed significant differences (P < 0.05) between different age groups in male Kazak sheep, but in Xinjiang fine wool sheep there was no such difference observed. Furthermore, the IMF contents in Kazak were much higher ( P < 0.01) than that of the other breed from day 30 to 90. 2) FAS mRNA expression level was the highest (P < 0.05) on day 0 in Kazak sheep and then declined with growth, in the other breed the gene showed a ‘decline-rise-decline-rise’ expression manner as the animals grew. HSL mRNA expression level had a similar model in two breeds, in Kazak sheep it was the highest on day 0 (P < 0.05) and in Xinjiang fine wool sheep on day 30 ( P < 0.01), then both decreased after this term. 3) In male Kazak sheep, FAS and HSL mRNA expression level were both negatively related to IMF content (r = −0.485 (P = 0.02), r = −0.423 (P = 0.05)), and the ratio ofFAS/HSL expression exhibited significantly negatively related IMF contents. In male Xinjiang sheep, there were no obvious relationship between FAS and HSL expression and IMF content (P > 0.05).

Polymorphism of Exon 3 of MHC Class II B Gene in Chinese Alligator (Alligator sinensis)

Hui Liu, Xiaobing Wu, Peng Yan, Zhigang Jiang

2007, 34(10): 918-929. doi: 10.1016/S1673-8527(07)60103-9

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The polymorphism of MHC class II B gene in 14 Chinese alligators was analyzed, which came from three different areas: a wild population from Xuancheng, Anhui, a captive population from Changxing, Zhejiang, and a captive population from Anhui Research Center for Reproduction of Chinese Alligators. The gene fragment was amplified using a pair of specific primers designed from the MHC gene sequence of the spectacled caiman. A total of 34 sequence haplotypes of exon 3 were detected in the sampled Chinese alligators. The numbers of haplotypes of the 3 Chinese alligator populations were 15, 10, and 9, respectively. The overall estimation of the MHC polymorphism in the Chinese alligator population was higher than those in mammals and in cyprinid fish. The rates of nonsynonymous substitutions (d_N) occurred at a significantly lower frequency than that of synonymous substitutions (d_S), which were not consistent with the common rule. This result might suggest that the polymorphism of exon 3 seemed not to be maintained by the balancing selection. The neutrality test of Tajima excluded the null hypothesis that the polymorphism of exon 3 was generated by a random drift, and the fact that D = −0.401 indicated an excess of rare mutations in the Chinese alligator. The nucleotide diversity of the sequences and the phylogenetic relations were also analyzed, and the results suggested that there was no significant difference in genetic diversity among the 3 populations of Chinese alligator.

The Phylogeny and Expression Pattern of APETALA2-like Genes in Rice

Meifang Tang, Guisheng Li, Mingsheng Chen

2007, 34(10): 930-938. doi: 10.1016/S1673-8527(07)60104-0

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The multigene families undergo birth-and-death evolution and thus contribute to biological innovations. The APETALA2-like genes belong to the euAP2 group of the AP2 gene family. These genes are characterized by several distinct motifs and exist in ferns, gymnosperms, and angiosperms. The phylogenetic analysis indicated that these genes have undergone the birth-and-death evolution. The five APETALA2-like genes in rice (Oryza sativa L.) display redundant but distinct expression patterns as demonstrated by RT-PCR and in situ hybridization. The potential functions of these genes were discussed on the basis of phylogenetic and expression pattern.

Comparison of Newly Synthetic Hexaploid Wheat with Its Donors on SSR Products

Lianquan Zhang, Genlou Sun, Zehong Yan, Qijiao Chen, Zhongwei Yuan, Xiujin Lan, Youliang Zheng, Dengcai Liu

2007, 34(10): 939-946. doi: 10.1016/S1673-8527(07)60105-2

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Microsatellites or SSRs as powerful genetic markers have widely been used in genetics and evolutionary biology in common wheat. Because of the high polymorphism, newly synthesized hexaploid wheat has been used in the construction of genetic segregation population for SSR markers. However, data on the evolution of microsatellites during the polyploidization event of hexaploid wheat are limited. In this study, 66 pairs of specific to A/B genome SSR patterns among newly synthesized hexaploid wheat, the donor tetraploid wheat and Aegilops tauschii were compared. The results indicated that most SSR markers were conserved during the polyploidization events of newly synthetic hexaploid wheat, from Triticum turgidum and Ae. tauschii. Over 70% A/B genome specific SSR markers could amplify the SSR sequences from the D genome of Ae. tauschii. Most amplified fragments from Ae. tauschii were detected in synthetic hexaploid at corresponding positions with the same sizes and patterns as in its parental Ae. tauschii. This suggested that these SSR markers, specific for A/B genome in common wheat, could amplify SSR products of D genome besides A/B genome in the newly synthesized hexaploid wheat, that is, these SSR primers specific for A/B genome in common wheat were nonspecific for the A/B genome in the synthetic hexaploid wheat. In addition, one amplified Ae. tauschii product was not detected in the newly synthetic hexaploid wheat. An extra-amplified product was found in the newly synthetic hexaploid wheat. These results suggested that caution should be taken when using SSR marker to genotype newly synthetic hexaploid wheat.

Genetic Structure of Malus sieversii Population from Xinjiang, China, Revealed by SSR Markers

Chunyu Zhang, Xuesen Chen, Tianming He, Xiaoli Liu, Tao Feng, Zhaohe Yuan

2007, 34(10): 947-955. doi: 10.1016/S1673-8527(07)60106-4

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One hundred and nine Malus sieversii accessions from four geographical populations located at Kuerdening in Mohe town, Gongliu County, Jiaowutuohai, in Xinyuan County, Daxigou in Houcheng County of Ily State, and Baerluke Mountain in Yumin County of Tacheng State, Xinjiang Uygur Autonomous Region of China were studied by SSR markers. The purpose of the study was to determine the genetic structure and diversity in these eco-geographical populations with eight pair SSR primers of apple. The results indicated that: an average of 16 bands was detected in the four populations. The percentage of polymorphic bands in Gongliu population (89.06%) was the highest in the four populations. The average Nei's gene diversity index was 0.257 for all the loci. Totally, 128 polymorphic loci were detected and the percentage of polymorphic loci (P) was 100%, 88.28%, 84.83%, 87.50%, and 87.12%, respectively, at the species level and Gongliu, Xinyuan, Huocheng, and Yumin population levels. The Nei's gene diversity index (H = 0.2619) and Shannon's information index (I = 0.4082) in the species level were higher than in the population level. The Nei's gene diversity index and Shannon's information index in the four populations were Gongliu > Huocheng > Xinyuan > Yumin. Gongliu population and Xinyuan population were the highest in genetic identity and the closest in genetic distance. Gene flow between the populations was 7.265 based on genetic differentiation coefficient ( G_ST = 0.064). The UPGMA cluster analysis indicated that the genetic relationships between the Gongliu and Xinyuan population were the closest, and the Yumin population were the farthest with the other three populations. The UPGMA cluster analysis indicated that the four geographical populations located in Gongliu, Xinyuan, Huocheng, and Yumin were relatively independent populations. Concurrently, there was also mild gene exchange between the populations. On the basis of the study of population genetic structure and the highest genetic diversity, Gongliu population should be given a high priority consideration in Malus sieversii population's in situ germplasm conservation.

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2007, 34(10) doi: 10.1016/S1673-8527(07)60107-6

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2007 Vol. 34, No. 10