Journal of Genetics and Genomics

Yiming Sun, Tao Yang, Zhiheng Xu

2007, 34(11): 957-965. doi: 10.1016/S1673-8527(07)60108-8

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Abstract:
The c-Jun N-terminal kinases (JNKs) are important regulators of a variety of physiological and pathological processes both in the central and in the peripheral nervous systems. JNKs are considered as crucial mediators of neuronal cell death in response to stress and injury. However, recent studies have provided substantial evidence that the JNK pathway plays an important role in neuronal migration. Here, we will give a brief introduction of the JNK signaling pathway and put more emphasis on its role in neuronal migration.

Identification of Differentially Expressed MicroRNAs During the Development of Chinese Murine Mammary Gland

Chunmei Wang, Qingzhang Li

2007, 34(11): 966-973. doi: 10.1016/S1673-8527(07)60109-X

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Abstract:
MicroRNAs (miRNAs) are endogenous ∼22 nucleotide-long noncoding RNAs. In this study, to investigate miRNA expression profiles and their functions in mammary gland development, we have used microarray as well as qRT-PCR, to analyze the miRNA expression changes along the murine mammary cycle during pregnancy, particularly on transition from pregnancy to lactation. It shows that every developmental stage of the mammary gland has its own miRNA expression pattern. Compared with virgin and involution, some miRNAs such as miR-138 and miR-431 are downregulated, whereas, some miRNAs such as miR-133 and miR-133a-133b are upregulated during pregnancy and lactation. These results indicate that miRNAs are functionally involved in mammary gland development.

Microsatellite DNA Marker Analysis of Genetic Diversity in Wild Common Carp (Cyprinus carpio L.) Populations

Dayu Li, Dahai Kang, Qianqian Yin, Xiaowen Sun, Liqun Liang

2007, 34(11): 984-993. doi: 10.1016/S1673-8527(07)60111-8

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Abstract:
Thirty microsatellite loci were used for analyzing six wild populations of common carp (Cyprinus carpio L.). Observed () and expected () heterozygosity values, polymorphic information content (PIC), and number of effective alleles () were all detected. Genetic similarity index and genetic distance were computed based on the allele frequency. The Hardy-Weinberg Equilibrium was checked according to the test of χ². Genetic differentiation and hierarchical partition of genetic diversity were evaluated by and . A clustering dendrogram was made based on the results of UPGMA methods using the PHYLIP software package (version 3.63). There were totally 8,136 fragments ranging from 125 bp to 414 bp in length. Three to thirteen alleles were amplified in 30 loci and 210 alleles in all six populations. The average number of alleles in each locus was seven. The result showed that 1) the level of genetic variability was moderate in the six populations. Polymorphic information contents of the six wild common carp populations were 0.44, 0.52, 0.53, 0.57, 0.63, and 0.64 respectively. Effective alleles were from 1.04 to 4.72, the average numbers in each population were 2.19, 2.60, 2.42, 2.43, 2.45, and 2.33. The average expected heterozygosity values were 0.50, 0.59, 0.56, 0.56, 0.57, and 0.54 respectively; 2) the highest genetic similarity index that came from the populations of BR and ZL was 0.8511 and the lowest index was 0.6688, and it came from the populations of BR and HN. There was a correlation between the clustering result and the geographical distribution.

In Silico Cloning, Expression and Phylogenetic Analysis of Pig GATA-3 Gene

Hao Yu, Jingfen Li, Li Li, Yuefen Song, Xiuqin Yang, Linlin Ding, Di Liu

2007, 34(11): 994-1000. doi: 10.1016/S1673-8527(07)60112-X

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Abstract:
Pig GATA-3 cDNA was obtained by reverse transcription polymerase chain reaction (RT-PCR), using in silico cloning strategy based on pig dbEST. The length of pig GATA-3 cDNA is 1,760 bp containing a 1,335 bp open reading frame (ORF), which encodes a 444 amino acid protein. Semi-quantitative RT-PCR analysis of GATA-3 mRNA expression was done using the total RNAs from different normal tissues of a large white pig. The GATA-binding family of transcription factors comprised of a subgroup of DNA-binding proteins that both bound the consensus GATA motif and contained the class ? zinc finger motif. The molecular evolution tree was constructed based on the GATA-3 amino acid sequence and class ? zinc finger motif using mega 3.1. Phylogeny analysis of GATA factors isolated from vertebrates suggested that the six distinct vertebrate GATAs had descended from a common ancestral sequence, and the topology also suggested multiple modes of evolution including gene duplication and class ? zinc finger motif recombination. These data helped the authors in illuminating the pathways of divergent and convergent evolution of the GATA-binding family of transcription factors.

Analysis on Genetic Diversity and Isolation Mechanism by Distance of Different Ecological Type Sheep Breeds in Mongolia Sheep Group

Wei Sun, Hong Chang, Dejun Ji, Xinjun Liao, Lei Du, Shengxia Lu, Tsunoda Kenji

2007, 34(11): 1001-1009. doi: 10.1016/S1673-8527(07)60113-1

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Abstract:
In the present study with Tan sheep, small-tailed Han sheep, Hu sheep, Tong sheep, and Wadi sheep, we detected the distribution of gene frequency of several microsatellite sites in different chromosomes, the result showed that: 1) Hu sheep was in the status of Hardy-Weinberg extreme disequilibrium (P < 0.01), while populations including Tong sheep, small-tailed Han sheep, Tan sheep, and Wadi sheep were in Hardy-Weinberg equilibrium ( P > 0.05). 2) Variance analysis of the heterozygosity and polymorphic information content at microsatellite makers showed that there were not significant differences among populations as to heterozygosity and PIC ( P > 0.05), as to effective number of alleles there were not significant differences both among Tan sheep, Hu sheep, Tong sheep, and Wadi sheep, and between Wadi sheep and small-tailed sheep ( P > 0.05), but between the former three populations and the latter two populations, there were significant differences (0.01< P < 0.05). The variation levels of small-tailed Han sheep was the highest in the five populations based on microsatellite maker data, subsequently followed by Wadi sheep, Tong sheep, Tan sheep, and then Hu sheep. 3) The phylogenetic relationships of the five sheep populations in this study did not meet the mechanism of isolation by distance, and the genetic differentiation relationships among five sheep populations were not closely linearly correlative with their geography distribution. Our findings supported related records in literature:The five populations originated on different time stage from the primogenitor population and communicated genetically with each other thereafter in the process of natural and artificial selection and on different ecological environment.

Genetic Analysis of Six Endangered Local Duck Populations in China Based on Microsatellite Markers

Ying Su, Ruijun Long, Guohong Chen, Xinsheng Wu, Kaizhou Xie, Jianghong Wan

2007, 34(11): 1010-1018. doi: 10.1016/S1673-8527(07)60114-3

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Abstract:
Seventeen microsatellite loci were used to assess the genetic variation and population structure of six endangered duck populations in China. PIC, heterozygosity with two estimators of genetic differentiation ( and ), and Nei's standard genetic distance were evaluated. The results showed that these six endangered duck populations showed high polymorphism. The proportion of inter-population subdivision among the six duck populations ranged between 17.0 and 14.7%. The average heterozygosity was 0.706, 0.702, 0.691, 0.676, 0.604, and 0.660 in the Gaoyou, Liancheng, Jinding, Beijing, Shaoxing, and Jianchang ducks, respectively. The averagePIC ranged from 0.561 to 0.663. Finally, the results showed higher genetic diversity and difference above the levels of genetic variation among all the populations.

Fine Mapping and Isolation of Bc7(t), Allelic to OsCesA4

Changjie Yan, Song Yan, Xiuhong Zeng, Zhengqiu Zhang, Minghong Gu

2007, 34(11): 1019-1027. doi: 10.1016/S1673-8527(07)60115-5

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Abstract:
Several brittle culm mutants of rice were identified and characterized. In this study, we characterized a brittle mutant (bc7(t)) identified from japonica variety Zhonghua 11 by means of ⁶⁰Co-γ radiation. This mutant displays normal phenotype similar to its wild type plants except for the fragility of all plant body, with ∼10% decrease in the cellulose content. The genetic analysis and gene fine mapping showed that the bc7(t) mutant was controlled by a recessive gene, residing on an 8.4 kb region of the long arm of chromosome 1. The gene annotation indicated that there was only one putative gene encoding cellulose synthase catalytic subunit (CesA) in this region, which was allelic to OsCesA4. Furthermore, the sequence analysis was carried out and 7 bases deletion in the junction of exon 10 and intron 10 was done in bc7(t) mutant, resulting in the change of reading frame and the consequent failure to generate functional protein. In addition, the result of RNA interference experiment showed that when theBc7(t) was knocked down, the transplants exhibited fragility, similar to bc7(t) mutant. The finding of novel allele of OsCesA4 locus will facilitate the understanding of the mechanism of cell wall biosynthesis. The potential utilization of the bc7(t) mutant in animal food was discussed as well.

Studies on the Inheritance of Locule Formation in Tomatoes (Lycopersicon esculentum Mill.)

Yue Li, Tianlai Li, Dan Wang

2007, 34(11): 1028-1036. doi: 10.1016/S1673-8527(07)60116-7

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Abstract:
To fully understand the tomato ovary locule formation of inheritance, two varieties, ovary multi-locule (MLK1) and few-locule (FL1), were used in these studies. Using reciprocal cross, self-cross, and backcross, we have constructed various groups to seek the genetic law and mechanisms of tomato locule formation, for modifying the tomato breeding theory. The parental and the resulting F₁ and F₂ generations have been used to examine the heredity of the locule number. The results showed that few-locule was incompletely dominant. The data from backcross demonstrated a significant effect on the locule number, whereas, the reciprocal cross showed an insignificant effect. Not surprisingly, the locule number was controlled by nuclear genomes, not by exogenous substances. The model that inherited the locule number belonged to the additive-dominant model: additive effects played a very important role and were partially dominant. In addition, the results revealed that the locule number in tomato was mainly controlled by a single gene, whereas, it was modulated by a number of other genes. Finally, the general inheritability and narrow inheritability of the locule number were 69.44% and 52.98%, respectively.

Population Genetic Structure in Apricot (Prunus armeniaca L.) Cultivars Revealed by Fluorescent-AFLP Markers in Southern Xinjiang, China

Zhaohe Yuan, Xuesen Chen, Tianming He, Jianrong Feng, Tao Feng, Chunyu Zhang

2007, 34(11): 1037-1047. doi: 10.1016/S1673-8527(07)60117-9

Abstract (91) HTML PDF (0)

Abstract:
Population-wide genetic structure was studied using fluorescent-AFLP markers on 85 apricot (Prunus armeniaca L.) cultivars collected from Kuche, Kashi, Hetian in the Tarim Basin, southern Xinjiang Uygur Autonomous Region of China. The purpose of this study was to determine the genetic structure and genotypic diversity among the different eco-geographical populations. Based on the results from this study, 8 pairs of fluorescent-AFLP primers showed clear electrophoregram and high polymorphism amongst the 64 pairs of EcoR|/Mse|(Mse|- a FAM fluorescent marked primer) primers screened. There was a significant polymorphic difference for the same primer pair in different populations and for the same population with different primer pairs. The percentage of polymorphic loci (P) at species level was higher than Kuche, Hetian, Kashi population levels, respectively. The Nei's gene diversity index (H) and Shannon's information index (I) at species level were higher than those of Kuche, Hetian, and Kashi at population level, respectively. H and I of Kuche population were the highest amongst the three populations. Apricot population genetic diversity was found mainly within the population. Genetic differentiation coefficient between populations () was 0.0882. Gene flow Nm between the populations was 5.1689. Population genetic identity was between 0.9772–0.9811 and genetic distance was between 0.0191–0.0232. These results further indicated that the similarity between populations was higher and the genetic distance between populations was smaller. The UPGMA cluster analysis indicates that the geographical populations at Kuche, Kashi, Hetian were relatively independent Mendelian populations. Concurrently, there was also partial gene exchange between the populations. All the evidences indicated that the genetic diversity in Kuche population was the highest, suggesting that it could be a transition population from wild apricot to cultivated apricot. There were abundant genetic diversities in apricot cultivar populations in southern Xinjiang, China, which provide promising germplasm for further breeding and theoretical basis for biodiversity conservation and utilization for apricot population in this area.

Effect of Menopause on Gene Expression Profiles of Circulating Monocytes: A Pilot in vivo Microarray Study

Volodymyr Dvornyk, Yaozhong Liu, Yan Lu, Hui Shen, Joan M Lappe, Robert R Recker, Hongwen Deng, Shufeng Lei

2007, 34(11): 974-983. doi: 10.1016/S1673-8527(07)60110-6

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Abstract:
Menopause is one of the key physiological events in the female life and can increase the risk for a number of complex autoimmune, neurodegenerative, metabolic, and cardiovascular disorders. Circulating monocytes can differentiate into various cell types and play an important role in tissue morphogenesis and immune response. We studied gene expression profiles of peripheral blood monocytes in healthy pre- and postmenopausal women using Affymetrix Human U133A GeneChip array that contains probes for ∼14,500 genes. Comparative analyses between the samples showed that 20 genes were up- and 20 were down-regulated. Of these genes, 28 were classified into six major GO categories relevant to such biological processes as the cell proliferation, immune response, cellular metabolism, and the others. The remaining 12 genes have yet unidentified biological functions. Our results support the hypothesis that functional state of circulating monocytes is indeed affected by menopause, and resulting changes may be determined through the genomewide gene expression profiling. Several differentially expressed genes identified in this study may be candidates for further studies of menopause-associated systemic autoimmune, neurodegenerative, and cardiovascular disorders. Our study is only the first attempt in this direction, but it lays a basis for further research.

2007 Vol. 34, No. 11