Journal of Genetics and Genomics

The contribution of distant hybridization with decaploid Agropyron elongatum to wheat improvement in China

Zhensheng Li, Bin Li, Yiping Tong

2008, 35(8): 451-456. doi: 10.1016/S1673-8527(08)60062-4

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Abstract:
Wheat is a staple food crop in the world as well as in China. Because of the progress of wheat breeding and other agricultural scitechnologies, the wheat grain yield per unit area has increased more than five folds from 1952 to 2006 in China. The first part of this article briefly reviews the history of wheat breeding in China. Second, the establishment of “Triticum aestivum-Agropyron” distant hybridization system and its contribution to wheat production and breeding in China are summarized. Finally, the future challenges of wheat breeding are discussed, which include how to increase the utilization efficiencies of water, soil nutrient and light energy through breeding. As an example, our research progress on how to increase light use efficiency in wheat through breeding is introduced and discussed.

Transgenic analyses of TGIF family proteins in Drosophila imply their role in cell growth

Yonghua Wang, Lixia Wang, Zhaohui Wang

2008, 35(8): 457-465. doi: 10.1016/S1673-8527(08)60063-6

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Abstract:
TG-interacting factors (TGIFs) belong to a family of TALE-homeodomain proteins including TGIF, TGIF2, and TGIF2LX/Y (TGIF2 like on X or Y chromosome) in human. They potentially play important functions in various tissues during development. Mutations in TGIF are frequently associated with malformation of forebrain and facial structures; TGIF2 proteins are over-expressed in many ovarian cancer cell lines; and TGIF2LX/Y are specifically expressed in adult testis. The molecular functions of these proteins have been investigated mostly in cultured cells. TGIF and TGIF2 have been found as transcriptional repressors that modulate TGF-beta signaling. However, these findings are far from sufficient to explain their mutant phenotypes or expression patterns, and the functions of TGIF2LX/Y have never been reported. Here we use Drosophila as a model system to explore the functions of TGIF family proteins in vivo. We observed in fly tissues such as fat body, epithelia, and neuronal cells, that expressing human TGIF2 or human TGIF2LX generally inhibited cell growth in size and number. Co-expressing Drosophila Myc, Cyclin E, or human c-MycS partially rescued the growth inhibition induced by human TGIFs, whereas activated insulin pathway signaling did not. Taken together, we provide in vivo evidence for the potential functions of human TGIF2 and TGIF2LX in growth control. Additionally, we confirmed thatDrosophila TGIFs are transcriptional activators by assaying their activities in spermatogenesis.

A nuclear localized protein ZCCHC9 is expressed in cerebral cortex and suppresses the MAPK signal pathway

Aidong Zhou, Jianlin Zhou, Liping Yang, Mingjun Liu, Hong Li, Su Xu, Mei Han, Jian Zhang

2008, 35(8): 467-472. doi: 10.1016/S1673-8527(08)60064-8

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Abstract:
The CCHC-type zinc finger motif has numerous biological activities (such as DNA binding and RNA binding) and can also mediate protein-protein interaction. This article gives a primary report about the human ZCCHC9 gene. Protein ZCCHC9 contains four CCHC motifs and is highly conserved in humans, mice, and rats. The whole cDNA sequence of the ZCCHC9 gene has been amplified by PCR and a number of plasmids have been constructed for further study. The results show that ZCCHC9 is localized in the nucleus, and especially concentrated in the nucleolus. It is highly expressed in the brain and testicles of the mouse. This has been confirmed by real-time reverse transcription polymerase chain reaction (RT-PCR). In situ hybridization of the mouse brain indicates that ZCCHC9 is mainly expressed in the cerebral cortex. Reporter gene assay shows that ZCCHC9 suppresses the transcription activities of NF-kappa B and SRE, and may play roles in the Mitogen-Activated Protein Kinase (MAPK) signaling transduction pathway.

Comparison of QTLs for rice seedling morphology under different water supply conditions

Bingsong Zheng, Ling Yang, Chuanzao Mao, Youjun Huang, Ping Wu

2008, 35(8): 473-484. doi: 10.1016/S1673-8527(08)60065-X

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Abstract:
The variation of seedling characteristics under different water supply conditions is strongly associated with drought resistance in rice (Oryza sativa L.) and a better elucidation of its genetics is helpful for improving rice drought resistance. Ninetysix doubled-haploid (DH) rice lines of an indica and japonica cross were grown in both flooding and upland conditions and QTLs for morphological traits at seedling stage were examined using 208 restriction fragment length polymorphism (RFLP) and 76 microsatellite (SSR) markers. A total of 32 putative QTLs were associated with the four seedling traits: average of three adventitious root lengths (ARL), shoot height (SH), shoot biomass (SW), and root to shoot dry weight ratio (RSR). Five QTLs detected were the same under control and upland conditions. The ratio between the mean value of the seedling trait under upland and flooding conditions was used for assessing drought tolerance. A total of six QTLs for drought tolerance were detected. Comparative analysis was performed for the QTLs detected in this case and those reported from two other populations with the same upland rice variety Azucena as parent. Several identical QTLs for seedling elongation across the three populations with the positive alleles from the upland rice Azucena were detected, which suggests that the alleles of Azucena might be involved in water stress-accelerated elongation of rice under different genetic backgrounds. Five cell wall-related candidate genes forOsEXP1, OsEXP2, OsEXP4, EXT, and EGase were mapped on the intervals carrying the QTLs for seedling traits.

Comparative analysis of mitochondrial fragments transferred to the nucleus in vertebrate

Hongying Qu, Fei Ma, Qingwei Li

2008, 35(8): 485-490. doi: 10.1016/S1673-8527(08)60066-1

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Mitochondrial DNA sequences transferred to the nucleus give rise to the socalled nuclear mitochondrial DNA (numt). In the GenBank database, 244 numts have been found in six orders of birds (Anseriformes, Columbiformes, Falconiformes, Charadriiformes, Galliformes and Passeriformes). Sequences alignment (NCBI-BLASTN) was carried out with mitochondrial and corresponding nuclear genome sequences in nine vertebrate species. The sequences with high homology were considered as numts. The number of numts ranged from 15 in chicken to 159 in chimpanzee. The sequences of numts in macaque, chimpanzee, and human spanned 100% of the entire mammalian mitochondrial genome. The reconstructed frequency of the mitochondrial gene transferred to the nucleus demonstrated that the rRNA genes had high frequencies than other mitochondrial genes. Using the RepeatMasker program, the transposable elements were detected in the flanking regions of each numt. The results showed that less than 5% of the flanking sequences were made up of repetitive elements in chicken. The GC content of 5′- and 3′-flanking regions of numts in nine species was less than 44%. The analysis of the flanking sequences provided a valuable understanding for future study on mechanism of mitochondrial gene transfer to the nucleus and the site of numt integration.

A preliminary investigation on genetic diversity of Sousa chinensis in the Pearl River Estuary and Xiamen of Chinese waters

Hongshan Chen, Kan Zhai, Jialin Chen, Yulong Chen, Haijun Wen, Sufang Chen, Yuping Wu

2008, 35(8): 491-497. doi: 10.1016/S1673-8527(08)60067-3

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Abstract:
In this study, the mitochondrial DNA (mtDNA) control region and the mitochondrial cytochromeb gene of stranded Indo-Pacific humpback dolphin (Sousa chinensis) samples from the Pearl River Estuary and Xiamen waters were sequenced and analyzed. The result of mtDNA control region revealed 34 variable sites and four unique haplotypes (named as A, B, C and D) identified among the total samples from these two water areas, and the most common haplotype (A) was shared by 75% of the dolphins sampled from the two water areas. The haplotypic diversity (h) was 0.455 and the nucleotide diversity (π) was 0.0088. The phylogenetic analysis showed that the haplotype A, C, and D were closely related, but the haplotype B (unique for XM01 from Xiamen) was far from the other three. By scanning cytochrome b fragments, two haplotypes (A and B) were identified in these two water areas, and the most common haplotype (A) was shared by 91.67% individuals, while XM01 from Xiamen as the only exception. The data suggest that there is a possibility of gene exchange between the two populations in the Pearl River Estuary and Xiamen waters, and there possibly exists a unique maternal lineage in Xiamen waters.

Prospect of the QTL-qSB-9Tq utilized in molecular breeding program of japonica rice against sheath blight

Shimin Zuo, Li Zhang, Hui Wang, Yuejun Yin, Yafang Zhang, Zongxiang Chen, Yuyin Ma, Xuebiao Pan

2008, 35(8): 499-505. doi: 10.1016/S1673-8527(08)60068-5

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Abstract:
The major QTL-qSB-9^Tq conferring partial resistance to rice (Oryza sativa L.) sheath blight (Rhizoctonia solani Kühn) has been verified on chromosome 9 of the indica rice cultivar, Teqing. In this study, the prospect of this QTL utilized in molecular breeding program of japonica rice for sheath blight resistance was investigated. Most of the japonica rice cultivars showed lower level of sheath blight resistance than the indica rice cultivars. At the corresponding site of qSB-9^Tq, nine typical japonica rice cultivars from different ecological regions or countries proved to possess the susceptible allele(s). Introgression of qSB-9^Tq into these cultivars enhanced their resistance level by decreasing sheath blight score of 1.0 (0.5-1.3), which indicated that qSB-9^Tq had a large potential in strengthening the resistance of japonica rice to sheath blight. The use of the three molecular markers, which were polymorphic between Teqing and many japonica rice cultivars, promotes the application of qSB-9^Tq in a concrete molecular breeding program.

Characterization of Ser73 in Arabidopsis thaliana Glutathione S-transferase zeta class

Sudan Tao, Xiwen Chen, Jia Liu, Ming Ming, Namsu Chong, Defu Chen

2008, 35(8): 507-512. doi: 10.1016/S1673-8527(08)60069-7

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Abstract:
Glutathione S-transferases (GSTs) are ubiquitous detoxifying superfamily enzymes. The zeta class GST from Arabidopsis thaliana (AtGSTZ) can efficiently degrade dichloroacetic acid (DCA), which is a common carcinogenic contaminant in drinking water. Ser73 in AtGSTZ is a conserved residue at Glutathione binding site (G-site). Compared with the equivalent residues in other GSTs, the catalytic and structural properties of Ser73 were poorly investigated. In this article, site-saturation mutagenesis was performed to characterize the detailed role of Ser73. The DCA dechlorinating (DCA-DC) activity showed that most of the mutants had less than 3% of the wild-type activity, except S73T and S73A showing 43.48% and 21.62% of the wild-type activity, respectively, indicating that position 73 inAtGSTZ showed low mutational substitutability. Kinetic experiments revealed that mutants S73T, S73A, and S73G showed low binding affinity and catalytic efficiency toward DCA, 1.8-, 3.1-, and 10.7-fold increases in K_m^DCA values and 4.0-, 9.6-, and 34.1-fold decreases in K_cat-^DCA/K_m^DCA values, respectively, compared to the wild type. Thermostability and refolding experiments showed that the wild type maintained more thermostability and recovered activity. These results demonstrated the important role of Ser73 in catalytic activity and structural stability of the enzyme. Such properties of Ser73 could be particularly crucial to the molecular evolution of AtGSTZ and might, therefore, help explain why Ser73 is conserved in all GSTs. This conclusion might provide insights into the directed evolution of the DCA-DC activity of AtGSTZ.

Instructions for authors

2008, 35(8): 513-516. doi: 10.1016/S1673-8527(08)60070-3

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Abstract:

2008 Vol. 35, No. 8