Journal of Genetics and Genomics

Recent progress in the study of Hedgehog signaling

Gang Ma, Yue Xiao, Lin He

2008, 35(3): 129-137. doi: 10.1016/S1673-8527(08)60019-3

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Abstract:
The Hedgehog (Hh) family of secreted signaling proteins plays a critical role in regulating the development of several tissues and organ systems. The ability of Hh proteins to exert their biological effects is regulated by a series of post-translational processes. These processes include an intramolecular cleavage, covalent addition of cholesterol and/or palmitate, and conversion into a multimeric freely diffusible form. The processing of Hh proteins affects their trafficking, potency, and ability to signal over several cell diameters. Here we review the current understanding of the Hh signaling mechanisms that govern the establishment of the Hh gradient and the transduction of the Hh signal in the light of recent data.

Prepulse inhibition (PPI) of tactile startle response in recombinant congenic strains of mice: QTL mapping and comparison with acoustic PPI

Adam Torkamanzehi, Patricia Boksa, Ridha Joober

2008, 35(3): 139-151. doi: 10.1016/S1673-8527(08)60020-X

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Abstract:
Prepulse inhibition (PPI) of the startle response is a psychophysiological measure of sensorimotor gating believed to be cross-modal between different sensory systems. We analyzed the tactile startle response (TSR) and PPI of TSR (tPPI), using light as a prepulse stimulus, in the mouse strains A/J and C57BL/6J and 36 recombinant congenic strains derived from them. Parental strains were significantly different for TSR, but were comparable for tPPI. Among the congenic strains, variation for TSR was significant in both genetic backgrounds, but that of tPPI was significant only for the C57BL/6J background. Provisional mapping for loci modulating TSR and tPPI was carried out. Using mapping data from our previous study on acoustic startle responses (ASR) and PPI of ASR (aPPI), no common markers for aPPI and tPPI were identified. However, some markers were significantly associated with both ASR and TSR, at least in one genetic background. These results indicate cross-modal genetic regulation for the startle response but not for PPI, in these mouse strains.

The ethanol response gene Cab45 can modulate the impairment elicited by ethanol and ultraviolet in PC12 cells

Yunfeng Zhu, Quanli Wang, Wangru Xu, Sha Li

2008, 35(3): 153-161. doi: 10.1016/S1673-8527(08)60021-1

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Abstract:
High consumption of ethanolic beverages facilitates neurodegeneration, but the mechanism of this process still remained elusive. Suppression subtractive hybridization (SSH) is a technique for detection of rare transcripts. With SSH approach, we identified one ethanol response gene Cab45, which was down-regulated by ethanol with time-dependent manner in B104 cells. The full-length sequence of Cab45 gene was obtained by 5′ -RACE (5′ Rapid Amplification of cDNA Ends) for the first time in rat. Based on the sequence of deduced amino acid of rat Cab45, the alignment was conducted with its counterparts in different species and displayed a high conservation. Using different tissues in rat and cell lines, Cab45 was characterized by a ubiquitous expression and differentiation dependent down-regulation. Given that ethanol facilitates some cell differentiation, we hypothesize that Cab45 is involved in ethanol-mediated differentiation. With transient transfection, the function of Cab45 was investigated by up-regulation and down-regulation in PC12 cells. Ethanol treatment and UV exposure were conducted subsequently and cell proliferations were detected by MTT (Methyl Thiazolyl Tetrazolium) approach. It revealed that the up-regulation of Cab45 modulated the impairment elicited by ethanol and UV in transfected cells. As a member of new calcium binding protein family, the exact role of Cab45 still remains unclear.

Porcine growth differentiation factor 9 gene polymorphisms and their associations with litter size

Yushan Zhang, Hongli Du, Jing Chen, Guanfu Yang, Xiquan Zhang

2008, 35(3): 163-169. doi: 10.1016/S1673-8527(08)60022-3

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Abstract:
Growth differentiation factor 9 (GDF9) is expressed in oocytes and is thought to be required for ovarian folliculogenesis. Given this function, GDF9 may be considered as a candidate gene controlling pig ovulate rate. In this study, the complete coding sequence was cloned (encoding a 444 amino acid), intron sequence and partial 5′ -UTR of pig GDF9. RT-PCR results showed that GDF9 mRNA is expressed in a wide range of tissues of the ruttish Erhualian pig. The expression levels of GDF9 mRNA in pituitary, ovary, uterus and oviduct are higher in the Erhualian pigs than those in Duroc pigs, especially in pituitary with a significant difference (P < 0.05). Comparative sequencing revealed 12 polymorphisms, including 8 single nucleotide polymorphisms (SNPs) and one 314 bp indel in noncoding regions, and the other 3 SNPs in coding regions. Four polymorphisms, G359C, C1801T, T1806C and 314 bp indel, were developed as markers for further use in population variation and association studies. The G359C polymorphism segregates only in Chinese native pigs, Erhualian and Dahuabai, on the contrary, 314 bp indel segregates only in Duroc and Landrace. C1801T and T1806C sites seem to be completely linked and segregate in Erhualian, Dahuabai and Landrace. In a word, GDF9 may be not associated with pig litter size in extensive populations as per the studies of allele distributions of the four polymorphisms and pilot association in four breeds.

Microsatellite analysis of genetic diversity and population structure of Chinese mitten crab (Eriocheir sinensis)

Yumei Chang, Liqun Liang, Haitao Ma, Jianguo He, Xiaowen Sun

2008, 35(3): 171-176. doi: 10.1016/S1673-8527(08)60023-5

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Abstract:
Chinese mitten crab (Eriocheir sinensis) has higher commercial value as food source than any other species of Eriocheir in China. To evaluate the germplasm resources and characterize the genetic diversity and population structure of the crabs in different water systems, two stocks and two farming populations were assessed with 25 polymorphic microsallite loci available in public GenBank. Basic statistics showed that the average observed heterozygosity (Ho) amongst populations ranged from 0.5789 to 0.6824. However, a remarkable presence of inbreeding and heterozygote deficiencies were observed. To analyze population structure, pairwise coefficients explained only ∼ 10.3% variability from the subdivision of mitten crab populations, the remaining variability stems from the subdivision within subpopulations. Although the four populations had slight differentiation, different allelic frequencies resulted in distinct population structures. Two stocks and one farming population were clustered together to the phylogenetic branch of Yangtze crab, with an approximate membership of 95%. Whereas, another farming population was clustered singly to the phylogenetic branch of the Liaohe crab, with a membership of 97.1%. The tests for individual admixture showed that Yangtze crab had probably been contaminated with individuals from other water systems. Genetic relationships between populations also supported the conclusion that Yangtze crab and Liaohe crab had different gene pools in spite of the origins of the same species.

Characterization and mapping of a new male sterility mutant of anther advanced dehiscence (t) in rice

Yi Zhang, Yunfeng Li, Jian Zhang, Fucheng Shen, Yuanxin Huang, Zhiwei Wu

2008, 35(3): 177-182. doi: 10.1016/S1673-8527(08)60024-7

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Abstract:
Anther dehiscence is very important for pollen maturation and release. The mutants of anther dehiscence in rice (Oryza sativa L.) are few, and related research remains poor. A male sterility mutant of anther dehiscence in advance, add(t), has been found in Minghui 63 and its sterility is not sensitive to thermo-photo. To learn the character of sterilization and the function of the add(t) gene, the morphological and cytological studies on the anther and pollen, the ability of the pistil being fertilized, inheritance of the mutant, and mapping of add(t) gene have been conducted. The anther size is normal but the color is white in the mutant against the natural yellow in the wild-type. The pollen is malformed, unstained, and small in the KI-I₂ solution. The anther dehiscence is in advance at the bicellular pollen stage. A crossing test indicated that the grain setting ratio of the add(t) is significantly lower than that of the CMS line 2085A. The ability of the pistil being fertilized is most probably decreased by the add(t) gene. The male sterility is controlled by a single recessive gene of add(t). This gene is mapped between the markers of R02004 (InDel) and RM300 (SSR) on chromosome 2, and the genetic distance from the add(t) gene to these markers is 0.78 cM and 4.66 cM, respectively.

The application of the entropy-based statistic for genomic association study of QTL

Yang Xiang, Yumei Li, Zaiming Liu, Zhenqiu Sun

2008, 35(3): 183-188. doi: 10.1016/S1673-8527(08)60025-9

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An entropy-based statistic has been proposed for genomic association study for disease-susceptibility locus. The statistic may be directly adopted and/or extended to quantitative-trait locus (QTL) mapping for quantitative traits. In this article, the statistic was extended and applied to quantitative trait for association analysis of QTL by means of selective genotyping. The statistical properties (the type I error rate and the power) were examined under a range of parameters and population-sampling strategies (e.g., various genetic models, various heritabilities, and various sample-selection threshold values) by simulation studies. The results indicated that the statistic is robust and powerful for genomic association study of QTL. A simulation study based on the haplotype frequencies of 10 single nucleotide polymorphisms (SNPs) of angiotensin-I converting enzyme genes was conducted to evaluate the performance of the statistic for genetic association study.

Instructions for authors

2008, 35(3): 189-192. doi: 10.1016/S1673-8527(08)60026-0

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Abstract:

2008 Vol. 35, No. 3