Journal of Genetics and Genomics

Toward understanding genetic mechanisms of complex traits in rice

Wei Hao, Hong-Xuan Lin

2010, 37(10): 653-666. doi: 10.1016/S1673-8527(09)60084-9

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Abstract:
Rice is the primary carbohydrate staple cereal feeding the world population. Many genes, known as quantitative trait loci (QTLs), control most of the agronomically important traits in rice. The identification of QTLs controlling agricultural traits is vital to increase yield and meet the needs of the increasing human population, but the progress met with challenges due to complex QTL inheritance. To date, many QTLs have been detected in rice, including those responsible for yield and grain quality; salt, drought and submergence tolerance; disease and insect resistance; and nutrient utilization efficiency. Map-based cloning techniques have enabled scientists to successfully fine map and clone approximately seventeen QTLs for several traits. Additional in-depth functional analyses and characterizations of these genes will provide valuable assistance in rice molecular breeding.

A nuclear-encoded mitochondrial gene AtCIB22 is essential for plant development in Arabidopsis

Lihua Han, Genji Qin, Dingming Kang, Zhangliang Chen, Hongya Gu, Li-Jia Qu

2010, 37(10): 667-683. doi: 10.1016/S1673-8527(09)60085-0

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Abstract:
Complex I (the NADH:ubiquinone oxidoreductase) of the mitochondrial respiratory chain is a complicated, multi-subunit, membrane-bound assembly and contains more than 40 different proteins in higher plants. In this paper, we characterize the Arabidopsis homologue (designated as AtCIB22) of the B22 subunit of eukaryotic mitochondrial Complex I. AtCIB22 is a single-copy gene and is highly conserved throughout eukaryotes. AtCIB22 protein is located in mitochondria and theAtCIB22 gene is widely expressed in different tissues. Mutant Arabidopsis plants with a disrupted AtCIB22 gene display pleiotropic phenotypes including shorter roots, smaller plants and delayed flowering. Stress analysis indicates that the AtCIB22 mutants' seed germination and early seedling growth are severely inhibited by sucrose deprivation stress but more tolerant to ethanol stress. Molecular analysis reveals that in moderate knockdown AtCIB22 mutants, genes including cell redox proteins and stress related proteins are significantly up-regulated, and that in severe knockdown AtCIB22 mutants, the alternative respiratory pathways including NDA1, NDB2, AOX1a and AtPUMP1 are remarkably elevated. These data demonstrate that AtCIB22 is essential for plant development and mitochondrial electron transport chains in Arabidopsis. Our findings also enhance our understanding about the physiological role of Complex I in plants.

Identification and expression analysis of mical family genes in zebrafish

Yulin Xue, Chikin Kuok, An Xiao, Zuoyan Zhu, Shuo Lin, Bo Zhang

2010, 37(10): 685-693. doi: 10.1016/S1673-8527(09)60086-2

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Abstract:
Mical (molecule interacting with CasL) represent a conserved family of cytosolic multidomain proteins that has been shown to be associated with a variety of cellular processes, including axon guidance, cell movement, cell-cell junction formation, vesicle trafficking and cancer cell metastasis. However, the expression and function of these genes during embryonic development have not been comprehensively characterized, especially in vertebrate species, although some limited in vivo studies have been carried out in neural and musculature systems of Drosophila and in neural systems of vertebrates. So far, no mical family homologs have been reported in zebrafish, an ideal vertebrate model for the study of developmental processes. Here we report eight homologs of mical family genes in zebrafish and their expression profiles during embryonic development. Consistent with the findings in Drosophila and mammals, most zebrafish mical family genes display expression in neural and musculature systems. In addition, five mical homologs are detected in heart, and one, micall2a, in blood vessels. Our data established an important basis for further functional studies of mical family genes in zebrafish, and suggest a possible role for mical genes in cardiovascular development.

Faster evolution of Z-linked duplicate genes in chicken

Li Yan, Zhang Liqing, Zhang Dexiang, Zhang Xiquan, Lu Xuemei

2010, 37(10): 695-702. doi: 10.1016/S1673-8527(09)60087-4

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Abstract:
It has been shown that duplicate genes on the X chromosome evolve much faster than duplicate genes on autosomes inDrosophila melanogaster. However, whether this phenomenon is general and can be applied to other species is not known. Here we examined this issue in chicken that have heterogametic females (females have ZW sex chromosome). We compared sequence divergence of duplicate genes on the Z chromosome with those on autosomes. We found that duplications on the Z chromosome indeed evolved faster than those on autosomes and show distinct patterns of molecular evolution from autosomal duplications. Examination of the expression of duplicate genes revealed an enrichment of duplications on the Z chromosome having male-biased expression and an enrichment of duplications on the autosomes having female-biased expression. These results suggest an evolutionary trend of the recruitment of duplicate genes towards reproduction-specific function. The faster evolution of duplications on Z than on the autosomes is most likely contributed by the selective forces driving the fixation of adaptive mutations on Z. Therefore, the common phenomena observed in both flies and chicken suggest that duplicate genes on sex chromosomes have distinct dynamics and are more influenced by natural selection than autosomal duplications, regardless of the kind of sex determination systems.

Expression of CENH3 alleles in synthesized allopolyploid Oryza species

Li Hui, Li Lu, Yanfang Heng, Rui Qin, Yongzhong Xing, Weiwei Jin

2010, 37(10): 703-711. doi: 10.1016/S1673-8527(09)60088-6

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Abstract:
Synthesized allopolyploids are valuable materials for comparative analyses of two or more distinct genomes, such as the expression changes (activation, inactivation or differential expression) of orthologous genes following allopolyploidization. CENH3 is a centromere- specific histone H3 variant and has been regarded as a central component in kinetochore formation and centromere function. In this study, interspecific hybrids ofOryza genus (AA × CC, AA × CCDD) and their backcross progenies were produced, and the genome constitutions were identified as AC, ACC, ACD, AACD, or AA(CD) by Genomic in situ hybridization (GISH). We further cloned and sequenced the CENH3 genes from O. sativa (AA), O. officinalis (CC) and O. latifolia (CCDD). Sequencing of RT-PCR products revealed that CENH3_C2 and CENH3_D, the two CENH3 alleles from O. latifolia, showed polymophism in several sites, while CENH3_C2 and CENH3_C1 from O. officinalis were different at only two amino acids positions. Moreover, we found that the CENH3 genes from both parents are expressed in interspecific hybrids and their progenies. Specifically, based on our cDNA sequencing data, the ratio of expression level between CENH3_A and CENH3_C1 was approximately 1 in AC and 0.5 in ACC genomes, respectively. As a result, the CENH3 expression patterns shed more light on the inter-coordination between varied centromeric DNA sequences and highly conserved kinetochore protein in synthesized allopolyploids of Oryza genus.

2010 Vol. 37, No. 10