Journal of Genetics and Genomics

Yingying Zhang, Xiaowei Zhou, Peitang Huang

2007, 34(7): 573-580. doi: 10.1016/S1673-8527(07)60065-4

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Abstract:
Fanconi anemia (FA) is a rare recessive hereditary disease characterized clinically by congenital defects, progressive bone-marrow failure, and cancer predisposition. Cells from FA patients exhibit hypersensitivity to DNA cross-linking agents, such as mitomycin C (MMC). To date, at least 12 FA genes have been found deleted or mutated in FA cells, and 10 FA gene products form a core complex involved in FA/BRCA2 DNA repair pathway?FA pathway. The ubiquitin E3 ligase FANCL, an important factor of FA core complex, co-functions with a new ubiquitin conjugating enzyme UBE2T to catalyze the monoubiquitination of FANCD2. FANCD2-Ub binds BRCA2 to form a new complex located in chromatin foci and then take part in DNA repair process. The deubiquitylating enzyme USP1 removes the mono-ubiquitin from FANCD2-Ub following completion of the repair process, then restores the blocked cell cycle to normal order by shutting off the FA pathway. In a word, the FANCD2 activity adjusted exquisitely by ubiquitination and/or deubiquitination in vivo may co-regulate the FA pathway involving in variant DNA repair pathway.

Screening of the Metastasis-Associated Genes by Gene Chip in High Metastatic Human Ovarian Cancer Cell Lines

Shenhua Xu, Hangzhou Mou, Linhuei Gu, Dan Su, Chihong Zhu, Xianglin Liu

2007, 34(7): 581-590. doi: 10.1016/S1673-8527(07)60066-6

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Affymetrix U133A oligonucleotide microarrays were used to study the differences of gene expressions between high (H) metastatic ovarian cancer cell line, HO-8910PM, and normal ovarian tissues (C), bioinformatics was used to identify their chromosomal localizations. A total of 1,237 genes were found to have a difference in expression levels more than eight times. Among them 597 were upregulated (Signal Log Ratio[SLR] ≥ 3), and 640 genes were downregulated (SLR≤3). Except one gene, whose location was unknown, all these genes were randomly distributed on all the chromosomes. However, chromosome 1 contained the most differentially expressed genes (115 genes, 9.3%), followed by chromosome 2 (94 genes, 7.6%), chromosome 12 (88 genes, 7.1%), chromosome 11 (76 genes, 6.1%), chromosomes X (71 genes, 5.7%), and chromosomes17 (69 genes, 5.6%). These genes were localized on short-arm of chromosome (q), which had 805 (65.1%) genes, and the short arms of No.13, 14, 15, 21, and 22 chromosomes were the only parts of the chromosomes where the differentially expressed genes were localized. Functional classification showed that most of the genes (306 genes, 24.7%) belonged to the enzymes and their regulator groups. The subsequent group was the nucleic acid binding genes (144 genes, 11.6%). The rest of the top two groups were signal transduction genes (137 genes, 11.1%) and proteins binding genes (116 genes, 9.4%). These comprised 56.8% of all the differentially expressed genes. There were also 207 genes whose functions were unknown (16.7 %). Therefore it was concluded that differentially expressed genes in high metastatic ovarian cancer cell were supposed to be randomly distributed across the genome, but the majority were found on chromosomes 1, 2, 12, 11, 17, and X. Abnormality in four groups of genes, including in enzyme and its regulator, nucleic acid binding, signal transduction and protein binding associated genes, might play important roles in ovarian cancer metastasis. Those genes need to be further studied.

Adhesive Patterns of Escherichia coli F4 in Piglets of Three Breeds

Yuhua Li, Xiaotian Qiu, Hejun Li, Qin Zhang

2007, 34(7): 591-599. doi: 10.1016/S1673-8527(07)60067-8

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Abstract:
Escherichia coli expressing F4 fimbriae is the major pathogenic bacteria that causes diarrhea in piglets before weaning. The adhesion of E. coli to the brush borders of the epithelial cells of piglets is the precondition leading to diarrhea, which in turn is due to the presence of the F4 receptors determined by an autosomal recessive gene on the brush borders of the epithelial cells. In order to clarify the genetic mechanism of the adhesion, an in vitro adhesion experiment was carried out for three variants of E. coli F4 (ab, ac, and ad) in 366 piglets of three pig breeds [Landrace (LR), Large White (LW), and Songliao Black (SB)]. The results showed that there existed significant differences (P<0.001) in the adhesion percentage among the three breeds. Most SB piglets were nonadhesive for all the three variants, whereas most LR piglets were adhesive. Within each breed except for LR, the proportions of the three F4 variants adhering to the brush borders differed significantly. According to the patterns of the adhesion of the three F4 variants in the three breeds, it is very likely that the three F4 variants F4ab, F4ac, and F4ad have different receptors that are controlled by three different loci.

‘Genetic Diversity of Microsatellite DNA Loci of Tibetan Antelope (Chiru, Pantholops hodgsonii) in Hoh Xil National Nature Reserve, Qinghai, China

Hui Zhou, Diqiang Li, Yuguang Zhang, Tao Yang, Yi Liu

2007, 34(7): 600-607. doi: 10.1016/S1673-8527(07)60068-X

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Abstract:
The Tibetan antelope (Pantholops hodgsonii), indigenous to China, became an endangered species because of considerable reduction both in number and distribution during the 20th century. Presently, it is listed as an Appendix?species by CITES and as Category? by the Key Protected Wildlife List of China. Understanding the genetic diversity and population structure of the Tibetan antelope is significant for the development of effective conservation plans that will ensure the recovery and future persistence of this species. Twenty-five microsatellites were selected to obtain loci with sufficient levels of polymorphism that can provide information for the analysis of population structure. Among the 25 loci that were examined, nine of them showed high levels of genetic diversity. The nine variable loci (MCM38, MNS64, IOBT395, MCMAI, TGLA68, BM1329, BMS1341, BM3501, and MB066) were used to examine the genetic diversity of the Tibetan antelope (n = 75) in Hoh Xil National Nature Reserve (HXNNR), Qinghai, China. The results obtained by estimating the number of population suggested that all the 75 Tibetan antelope samples were from the same population. The mean number of alleles per locus was 9.4 ? 0.5300 (range, 7-12) and the mean effective number of alleles was 6.519 ? 0.5271 (range, 4.676-9.169). The observed mean and expected heterozygosity were 0.844 ? 0.0133 (range, 0.791-0.897) and 0.838 ? 0.0132 (range, 0.786-0.891), respectively. Mean Polymorphism Information Content (PIC) was 0.818 ? 0.0158 (range, 0.753-0.881). The value of Fixation index (Fis) ranged from ?0.269 to ?0.097 with the mean of ?0.163 ? 0.0197. Mean Shannon's information index was 1.990 ? 0.0719 among nine loci (range, 1.660-2.315). These results provide baseline data for the evaluation of the level of genetic variation in Tibetan antelope, which will be important for the development of conservation strategies in future.

Genetic Analysis and Mapping of Genes Involved in Fertility of Pingxiang Dominant Genic Male Sterile Rice

Tingyou Huang, Yuping Wang, Bingtian Ma, Yuqing Ma, Shigui Li

2007, 34(7): 616-622. doi: 10.1016/S1673-8527(07)60070-8

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Pingxiang dominant genic male sterile rice (PDGMSR) was the first dominant genic male sterile mutant identified in rice (Oryza sativa L.), and the corresponding dominant genic male sterile gene was designated as Ms-p. The fertility of PDGMSR can be restored by introduction of a dominant epistatic fertility restoring gene in some rice varieties. In the present study, E823, an indica inbred rice variety, restored the fertility of PDGMSR, and the genetic pattern was found to be consistent with a dominant epistatic model, therefore, the dominant epistatic fertility restorer gene was designated asRfe. The F2 population from the cross of PDGMSR/E823 was developed to map gene Rfe. The F2 plants with the genotypes Ms-pMs-pRferfe or Ms-pms-pRferfe were used to construct a fertile pool, and the corresponding sterile plants with genotypes Ms-pMs-prferfe or Ms-pms-prferfe were used to construct a sterile pool. The fertility restoring gene Rfe was mapped to one side of the microsatellite markers RM311 and RM3152 on rice chromosome 10, with genetic distances of 7.9 cM and 3.6 cM, respectively. The microsatellite markers around the location of the Ms-p gene were used to finely map the Ms-p gene. The findings of this study indicated that the microsatellite markers RM171 and RM6745 flanked the Ms-p gene, and the distances were 0.3 cM and 3.0 cM, respectively. On the basis of the sequence of rice chromosome 10, the physical distance between the two markers is approximately 730 kb. These findings facilitates molecular marker-assisted selection (MAS) of genes Ms-p and Rfe in rice breeding programs, and cloning them in the future.

Assessment of Genetic Diversity of Yunnan, Tibetan, and Xinjiang Wheat Using SSR Markers

Haiyan Wang, Xiu'e Wang, Peidu Chen, Dajun Liu

2007, 34(7): 623-633. doi: 10.1016/S1673-8527(07)60071-X

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Abstract:
A total of 206 SSR (Simple Sequence Repeats) primer pairs were used to detect genetic diversity in 52 accessions of three unique wheat varieties of western China. A total of 488, 472, and 308 allelic variants were detected in 31 Yunnan, 15 Tibetan and 6 Xinjiang wheat accessions with an average of PIC values 0.2764, 0.3082, and 0.1944, respectively. Substantial differences in allelic polymorphisms were detected by SSR markers in all the 21 chromosomes, the 7 homoeologous groups, and the three genomes (A, B, and D) in Yunnan, Tibetan, and Xinjiang wheat. The highest and lowest allelic polymorphisms in all the 21 chromosomes were observed in 3B and 1D chromosomes, respectively. The lowest and highest allelic polymorphisms among the seven homoeologous groups was observed in 6 and 3 homoeologous groups, respectively. Among the three genomes, B genome showed the highest, A the intermediate, and D the lowest allelic polymorphism. The genetic distance (GD) indexes within Yunnan, Tibetan, and Xinjiang wheat, and between different wheat types were calculated. The GD value was found to be much higher within Yunnan and Tibetan wheat than within Xinjiang wheat, but the GD value between Yunnan and Tibetan wheat was lower than those between Yunnan and Xinjiang wheat, and between Tibetan and Xinjiang wheat. The cluster analysis indicated a closer relationship between Yunnan and Tibetan wheat than that between Yunnan and Xinjiang wheat or between Tibetan and Xinjiang wheat.

A Novel Segregation Distortion in Intraspecific Population of Asian Cotton (Gossypium arboretum L.) Detected by Molecular Markers

Wu Li, Zhongxu Lin, Xianlong Zhang

2007, 34(7): 634-640. doi: 10.1016/S1673-8527(07)60072-1

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The segregation ratio of markers in an F2 population derived from Rudongjijiaoyaguo (Rdjjyg) and Zhongmian971 (Zm971) was studied using 3 morphological markers, 20 SSR markers, and 11 SRAP markers. Totally, 24 markers (77.42%) showed a distorted segregation and all of them skewed toward the female genotype, which was peculiar in recent cotton research. All the three types of SSR markers and SRAP marker showed distorted segregation, but the morphological markers (Purple stem, Okra leaf, and Red spot color) were normally segregated. this indicated that such a novel segregation distortion phenomenon resulted from interior genetic factors. The allele frequency and the distribution of different genotype frequencies in the F2 population were analyzed in codominant markers, to find out factors attributed to distorted segregation. Most of them implied distorted allele frequency, but it was normal genotype frequency, which showed that these markers were influenced at the gamete level.

Function and Chromosomal Localization of Differentially Expressed Genes Induced by Marssonina brunnea f. sp. multigermtubi in Populus deltoides

Yanmei Zhang, Xinye Zhang, Yuchen Chen, Qi Wang, Mingxiu Wang, Minren Huang

2007, 34(7): 641-648. doi: 10.1016/S1673-8527(07)60073-3

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A total of 1,160 differentially expressed genes induced by Marssonina brunnea f. sp. multigermtubi were identified in Populus deltoides cv. ‘Lux’ (I-69/55) with two-colour cDNA microarray including 2,952 cDNAs from two cDNA libraries constructed with 72 h inoculated poplar leaves. Functional analysis showed that 1,160 genes were classified into 11 functional categories that are involved in metabolism (15.9%), signal transduction (9.5%), transcription and replication (8.7%), and cell rescue and defense (7.8%). Among them, 926 genes were sporadically localized on 19 linkage groups. Chromosome 2 contained 102 (11%) differentially expressed genes, followed by chromosome 1 which contains 93 genes (10%), and chromosome 17 had the least number of differentially expressed genes. Clustering of expressed sequence tags (ESTs) in poplar genome was observed at the terminal regions of several chromosomes. The relationship between cluster of genes and plant defense response would be further studied.

Evidence for Positive Darwinian Selection of Vip Gene in Bacillus thuringiensis

Jinyu Wu, Fangqing Zhao, Jie Bai, Gang Deng, Song Qin, Qiyu Bao

2007, 34(7): 649-660. doi: 10.1016/S1673-8527(07)60074-5

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Vegetative insecticidal proteins (VIPs), produced during the vegetative stage of their growth in Bacillus thuringiensis, are a group of insecticidal proteins and represent the second generation of insecticidal trans-genes that will complement the novel d-endotoxins in future. Fewer structural and functional relationships of Vip proteins are known in comparison with those of d-endotoxins. In this study, both the maximum-likelihood methods and the maximum parsimony based sliding window analysis were used to evaluate the molecular evolution of Vip proteins. As a result, strong evidence was found that Vip proteins are subject to the high rates of positive selection, and 16 sites are identified to be under positive selection using the Bayes Empirical Bayesian method. Interestingly, all these positively selected sites are located from site-705 to site-809 in the C-terminus of the Vip proteins. Most of these sites are exposed and clustered in the loop regions when mapped onto its computational predicted secondary tertiary and a part of the tertiary structure. It has been postulated that the high divergence in the C-terminal of Vip proteins may not result from the lack of functional constraints, but rather from the rapid mutation to adapt their targeted insects, driven by positive selection. The potential positive selection pressures may be an attempt to adapt for the “arm race” between Vip proteins and the targeted insects, or to enlarge their target's host range. Sites identified to be under positive selection may be related to the insect host range, which may shed a light on the investigation of the Vip proteins’ structural and functional relationships.

An Entropy-based Index for Fine-scale Mapping of Disease Genes

Yumei Li, Yang Xiang, Hongwen Deng, Zhenqiu Sun

2007, 34(7): 661-668. doi: 10.1016/S1673-8527(07)60075-7

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Abstract:
By comparing the entropy and the conditional entropy in a marker, an entropy-based index has been presented for fine-scale linkage disequilibrium gene mapping using high-density marker maps for human disease genes. The index can quantify the level of linkage disequilibrium (LD) between the marker and the disease susceptibility locus (DSL) of genes. The advantage of using the index is attributed to the fact that it does not depend on marker allele frequencies across loci. Moreover, it is parallel to Hardy-Weinberg disequilibrium (HWD) measure for DSL fine mapping. Through various simulations, the fine mapping performances of the proposed entropy-based index was extensively investigated under various genetic parameters. The results show that the index presented is both robust and powerful for DSL mapping in genes.

Influence of Epistasis and QTL × Environment Interaction on Heading Date of Rice (Oryza sativa L.)

Guifu Liu, Jian Yang, Haiming Xu, Jun Zhu

2007, 34(7): 608-615. doi: 10.1016/S1673-8527(07)60069-1

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QTLs for heading date of rice (Oryza sativa L.) with additive, epistatic, and QTL × environment (QE) interaction effects were studied using a mixed-model-based composite interval mapping (MCIM) method and a double haploid (DH) population derived from IR64/Azucena in two crop seasons. Fourteen QTLs conferring heading date in rice, which were distributed on ten chromosomes except for chromosomes 5 and 9, were detected. Among these QTLs, eight had single-locus effects, five pairs had double-locus interaction effects, and two single-loci and one pair of double-loci showed QTL × environment interaction effects. All predicted values of QTL effects varied from 1.179 days to 2.549 days, with corresponding contribution ratios of 1.04%?4.84%. On the basis of the effects of the QTLs, the total genetic effects on rice heading date for the two parents and the two superior lines were predicted, and the putative reasons for discrepancies between predicted values and observed values, and the genetic potentiality in the DH population for improvement of heading date were discussed. These results are in agreement with previous results for heading date in rice, and the results provide further information, which indicate that both epistasis and QE interaction are important genetic basis for determining heading date in rice.

2007 Vol. 34, No. 7