Journal of Genetics and Genomics

Progress in gene transfer by germ cells in mammals

Yidong Niu, Shulong Liang

2008, 35(12): 701-714. doi: 10.1016/S1673-8527(08)60225-8

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Abstract:
Use of germ cells as vectors for transgenesis in mammals has been well developed and offers exciting prospects for experimental and applied biology, agricultural and medical sciences. Such approach is referred to as either male germ cell mediated gene transfer (MGCMGT) or female germ cell mediated gene transfer (FGCMGT) technique. Sperm-mediated gene transfer (SMGT), including its alternative method, testis-mediated gene transfer (TMGT), becomes an established and reliable method for transgenesis. They have been extensively used for producing transgenic animals. The newly developed approach of FGCMGT, ovary-mediated gene transfer (OMGT) is also a novel and useful tool for efficient transgenesis. This review highlights an overview of the recent progress in germ cell mediated gene transfer techniques, methods developed and mechanisms of nucleic acid uptake by germ cells.

Genetic analysis and fine-mapping of a dwarfing with withered leaf-tip mutant in rice

Liang Jiang, Longbiao Guo, Hua Jiang, Dali Zeng, Jiang Hu, Liwen Wu, Jian Liu, Zhenyu Gao, Qian Qian

2008, 35(12): 715-721. doi: 10.1016/S1673-8527(08)60226-X

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Abstract:
A dwarf mutant of rice (Oryza sativa L.) by mutagenesis of ethylene methylsulfonate (EMS) treatment from Nipponbare was identified. The mutant exhibited phenotypes of dwarfism and withered leaf tip (dwl1). Based on the internode length of dwl1, this mutant belongs to the dm type of dwarfing. Analysis of elongation of the second sheath and α-amylase activity in endosperm showed that the phenotype caused by dwl1 was insensitive to gibberellin acid treatment. Using a large F₂ population derived from a cross between the dwl1 and an indica rice variety, TN1, the DWL1 gene was mapped to the terminal region of the long arm of chromosome 3. Fine-mapping delimited it into a 46 kb physical distance between two STS markers, HL921 and HL944, where 6 open reading frames were predicted. Cloning of DWL1 will contribute to dissecting molecular mechanism that regulates plant height in rice, which will be beneficial to molecular assisted selection of this important trait.

Identification of karyopherin-alpha 2 as an Oct4 associated protein

Xiangqun Li, Lei Sun, Ying Jin

2008, 35(12): 723-728. doi: 10.1016/S1673-8527(08)60227-1

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Abstract:
The POU domain transcription factor Oct4 is a master regulator in maintaining self-renewal and pluripotency of embryonic stem (ES) cells. To further explore the functional network of Oct4, the yeast two-hybrid system was used to search for Oct4 interacting proteins. PH domain (containing POU domain and homeodomain) of human OCT4 was used as a bait. From the human testis cDNA library, we identified a strong interaction between OCT4 and karyopherin-alpha 2 (KPNA-2). KPNA2 is involved in active nuclear import of proteins. This finding was confirmed by glutathione S-transferase pull-down and co-immunoprecipitation assays. The interaction between OCT4 and KPNA-2 was further mapped to multiple regions of the two proteins. In addition, we studied nuclear localization signal (NLS) of mouse Oct4 and demonstrated that it is essential for Oct4 nuclear localization. Thus, our data suggest that Oct4 nuclear localization may be mediated by its interaction with KPNA-2.

Factors affecting mito-nuclear codon usage interactions in the OXPHOS system of Drosophila melanogaster

Zheng Sun, Liang Ma, Robert W. Murphy, Xiansheng Zhang, Dawei Huang

2008, 35(12): 729-735. doi: 10.1016/S1673-8527(08)60228-3

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Abstract:
Codon usage bias varies considerably among genomes and even within the genes of the same genome. In eukaryotic organisms, energy production in the form of oxidative phosphorylation (OXPHOS) is the only process under control of both nuclear and mitochondrial genomes. Although factors affecting codon usage in a single genome have been studied, this has not occurred when both interactional genomes are involved. Consequently, we investigated whether or not other factors influence codon usage of coevolved genes. We used Drosophila melanogaster as a model organism. Our χ² test on the number of codons of nuclear and mitochondrial genes involved in the OXPHOS system was significantly different (χ² = 7945.16, P < 0.01). A plot of effective number of codons against GC3s content of nuclear genes showed that few genes lie on the expected curve, indicating that codon usage was random. Correspondence analysis indicated a significant correlation between axis 1 and codon adaptation index ( R = 0.947, P < 0.01) in every nuclear gene sequence. Thus, codon usage bias of nuclear genes appeared to be affected by translational selection. Correlation between axis 1 coordinates and GC content ( R = 0.814, P < 0.01) indicated that the codon usage of nuclear genes was also affected by GC composition. Analysis of mitochondrial genes did not reveal a significant correlation between axis 1 and any parameter. Statistical analyses indicated that codon usages of both nDNA and mtDNA were subjected to context-dependent mutations.

Simulation of gene pyramiding in Drosophila melanogaster

Li Jiang, Fuping Zhao, Qin Zhang

2008, 35(12): 737-742. doi: 10.1016/S1673-8527(08)60229-5

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Abstract:
Gene pyramiding has been successfully practiced in plant breeding for developing new breeds or lines in which favorable genes from several different lines were integrated. But it has not been used in animal breeding, and some theoretical investigation and simulation analysis with respect to its strategies, feasibility and efficiency are needed before it can be implemented in animals. In this study, we used four different pure lines of Drosophila melanogaster, each of which is homozygous at a specific mutant gene with a visible effect on phenotype, to simulate the gene pyramiding process and analyze the duration and population size required in different pyramiding strategies. We finally got the ideal individuals, which are homozygous at the four target genes simultaneously. This study demonstrates that gene pyramiding is feasible in animal breeding and the interaction between genes may affect the final results.

Molecular characterization of LMW-GS genes from a somatic hybrid introgression line II-12 between Triticum aestivum and Agropyron elongatum in relation to quick evolution

Fanguo Chen, Feng Zhao, Chunhui Xu, Guangmin Xia

2008, 35(12): 743-749. doi: 10.1016/S1673-8527(08)60230-1

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Abstract:
In order to exploit the evolution and find novel low-molecular-weight glutenin subunit (LMW-GS) for improvement of common wheat quality, thirteen variants from a somatic hybrid introgression line II-12 between Triticum aestivum cv. Jinan 177 (JN177) and Agropyron elongatum were characterized via genomic PCR. Four clones were pseudogenes because they contained an internal stop codon. The remaining nine variants contained intact open reading frames (ORFs). Sequence alignment indicates that the proteins deduced from the nine ORFs have similar primary structure with LMW-GS cloned from its parents previously. However, they have some unique modifications in the structures. For example, EU292737 contains not only an extra Cys residue in the C-terminal domain but also a long repetitive domain. Both EU159511 and EU292738 start their first Cys residue in the N-terminal repetitive domain, but not in the N-conserved domain traditionally. These structural alterations may have positive contributions to wheat flour quality. The results of phylogeny showed that most LMW-GS variances from II-12 were homologous to those from parent JN177 and other wheat lines. The reason for quick evolution of LMW-GS in II-12 was discussed.

QTL mapping in A-genome diploid Asiatic cotton and their congruence analysis with AD-genome tetraploid cotton in genus Gossypium

Xuexia Ma, Yezhang Ding, Baoliang Zhou, Wangzhen Guo, Yanhui Lv, Xiefei Zhu, Tianzhen Zhang

2008, 35(12): 751-762. doi: 10.1016/S1673-8527(08)60231-3

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Abstract:
Asiatic cotton (Gossypium arboreum L.) is an Old World cultivated cotton species. The sinense race was planted extensively in China. Due to the advances in spinning technology during the last century, the species was replaced by the New World allotetraploid cotton G. hirsutum L. Gossypium arboreum is still grown in India and Pakistan and also used as an elite in current cotton breeding programs. In addition, G. arboreum serves as a model for genomic research in Gossypium. In the present study, we generated an A-genome diploid cotton intraspecific genetic map including 264 SSR loci with three morphological markers mapped to 13 linkage groups. The map spans 2,508.71 cM with an average distance of 9.4 cM between adjacent loci. A population containing 176 F_2:3 families was used to perform quantitative trait loci (QTL) mapping for 17 phenotypes using Multiple QTL Model (MQM) of MapQTL ver 5.0. Overall, 108 QTLs were detected on 13 chromosomes. Thirty-one QTLs for yield and its components were detected in the F₂ population. Forty-one QTLs for yield and its components were detected in the F_2:3 families with a total of 43 QTLs for fiber qualities. Two QTLs for seed cotton weight/plant and lint index and three QTLs for seed index were consistently detected both in F₂ and F_2:3. Most QTLs for fiber qualities and yields were located at the same interval or neighboring intervals. These results indicated that the negative correlation between fiber qualities and yield traits may result from either pleiotropic effect of one gene or linkage effects of multiple closely linked genes.

2008 Vol. 35, No. 12