Journal of Genetics and Genomics

DNA cytosine methylation in plant development

Meishan Zhang, Josphert N. Kimatu, Kezhang Xu, Bao Liu

2010, 37(1): 1-12. doi: 10.1016/S1673-8527(09)60020-5

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Abstract:
Cytosine bases of the nuclear genome in higher plants are often extensively methylated. Cytosine methylation has been implicated in the silencing of both transposable elements (TEs) and endogenous genes, and loss of methylation may have severe functional consequences. The recent methylation profiling of the entire Arabidopsis genome has provided novel insights into the extent and pattern of cytosine methylation and its relationships with gene activity. In addition, the fresh studies also revealed the more dynamic nature of this epigenetic modification across plant development than previously believed. Cytosine methylation of gene promoter regions usually inhibits transcription, but methylation in coding regions (gene-body methylation) does not generally affect gene expression. Active demethylation (though probably act synergistically with passive loss of methylation) of promoters by the 5-methyl cytosine DNA glycosylase or DEMETER (DME) is required for the uni-parental expression of imprinting genes in endosperm, which is essential for seed viability. The opinion that cytosine methylation is indispensible for normal plant development has been reinforced by using single or combinations of diverse loss-of-function mutants for DNA methyltransferases, DNA glycosylases, components involved in siRNA biogenesis and chromatin remodeling factors. Patterns of cytosine methylation in plants are usually faithfully maintained across organismal generations by the concerted action of epigenetic inheritance and progressive correction of strayed patterns. However, some variant methylation patterns may escape from being corrected and hence produce novel epialleles in the affected somatic cells. This, coupled with the unique property of plants to produce germline cells late during development, may enable the newly acquired epialleles to be inherited to future generations, which if visible to selection may contribute to adaptation and evolution.

The many roles of small RNAs in leaf development

Catherine A. Kidner

2010, 37(1): 13-21. doi: 10.1016/S1673-8527(09)60021-7

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Leaf development involves many complex genetic interactions, signals between adjacent cells or between more distant tissues and consequent changes in cell fate. This review describes three stages in leaf development where regulation by small RNAs have been used to modulate gene expression patterns.

Activation of gibberellin 2-oxidase 6 decreases active gibberellin levels and creates a dominant semi-dwarf phenotype in rice (Oryza sativa L.)

Jian Huang, Ding Tang, Yi Shen, Baoxiang Qin, Lilan Hong, Aiqing You, Ming Li, Xin Wang, Hengxiu Yu, Minghong Gu, Zhukuan Cheng

2010, 37(1): 23-36. doi: 10.1016/S1673-8527(09)60022-9

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Gibberellin (GA) 2-oxidase plays a key role in the GA catabolic pathway through 2β-hydroxylation. In the present study, we isolated a CaMV 35S-enhancer activation tagged mutant, H032. This mutant exhibited a dominant dwarf and GA-deficient phenotype, with a final stature that was less than half of its wild-type counterpart. The endogenous bioactive GAs are markedly decreased in the H032 mutant, and application of bioactive GAs (GA₃ or GA₄) can reverse the dwarf phenotype. The integrated T-DNA was detected 12.8 kb upstream of the OsGA2ox6 in the H032 genome by TAIL-PCR. An increased level of OsGA2ox6 mRNA was detected at a high level in the H032 mutant, which might be due to the enhancer role of the CaMV 35S promoter. RNAi and ectopic expression analysis of OsGA2ox6 indicated that the dwarf trait and the decreased levels of bioactive GAs in the H032 mutant were a result of the up-regulation of the OsGA2ox6 gene. BLASTP analysis revealed that OsGA2ox6 belongs to the class III of GA 2-oxidases, which is a novel type of GA2ox that uses C20-GAs (GA₁₂ and/or GA₅₃) as the substrates. Interestingly, we found that a GA biosynthesis inhibitor, paclobutrazol, positively regulated the OsGA2ox6 gene. Unlike the over-expression of OsGA2ox1, which led to a high rate of seed abortion, the H032 mutant retained normal flowering and seed production. These results indicate that OsGA2ox6 mainly affects plant stature, and the dominant dwarf trait of the H032 mutant can be used as an efficient dwarf resource in rice breeding.

The Post-meiotic Deficicent Anther1 (PDA1) gene is required for post-meiotic anther development in rice

Lifang Hu, Hexin Tan, Wanqi Liang, Dabing Zhang

2010, 37(1): 37-46. doi: 10.1016/S1673-8527(09)60023-0

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To understand the molecular mechanism of male reproductive development in the model crop rice, we isolated a complete male sterile mutant post-meiotic deficient anther1 (pda1) from a γ-ray-treated rice mutant library. Genetic analysis revealed that the pda1 mutant was controlled by a recessive nucleus gene. The pda1 mutant anther seemed smaller with white appearance. Histological analysis demonstrated that the pda1 mutant anther undergoes normal early tapetum development without obvious altered meiosis. However, the pda1 mutant displayed obvious defects in postmeiotic tapetal development, abnormal degeneration occurred in the tapetal cells at stage 9 of anther development. Also we observed abnormal lipidic Ubisch bodies from the tapetal layer of the pda1 mutant, causing no obvious pollen exine formation. RT-PCR analysis indicated that the expression of genes involved in anther development including GAMYB, OsC4 and Wax-deficient anther1 (WDA1) was greatly reduced in the pda1 mutant anther. Using map-based cloning approach, the PDA1 gene was finely mapped between two markers HLF610 and HLF627 on chromosome 6 using 3,883 individuals of F₂ population. The physical distance between HLF610 and HLF627 was about 194 kb. This work suggests that PDA1 is required for post-meiotic tapetal development and pollen/microspore formation in rice.

Characterization and mapping of a novel mutant sms1 (senescence and male sterility 1) in rice

Wenyi Yan, Shenghai Ye, Qingsheng Jin, Longjun Zeng, Yu Peng, Dawei Yan, Weibing Yang, Donglei Yang, Zuhua He, Yanjun Dong, Xiaoming Zhang

2010, 37(1): 47-55. doi: 10.1016/S1673-8527(09)60024-2

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Plant senescence plays diverse important roles in development and environmental responses. However, the molecular basis of plant senescence is remained largely unknown. A rice spontaneous mutant with the character of early senescence and male sterility (sms) was found in the breeding line NT10-748. In order to identify the gene SMS1 and the underlying mechanism, we preliminarily analyzed physiological and biochemical phenotypes of the mutant. The mutant contained lower chlorophyll content compared with the wild type control and was severe male sterile with lower pollen viability. Genetic analysis showed that the mutant was controlled by a single recessive gene. By the map-based cloning approach, we fine-mapped SMS1 to a 67 kb region between the markers Z3-4 and Z1-1 on chromo-some 8 using 1,074 F₂ recessive plants derived from the cross between the mutant sms1 (japonica) × Zhenshan 97 (indica), where no known gene involved in senescence or male sterility has been identified. Therefore the SMS1 gene will be a novel gene that regulates the two developmental processes. The further cloning and functional analysis of the SMS1 gene is under way.

Two sequence alterations, a 136 bp InDel and an A/C polymorphic site, in the S5 locus are associated with spikelet fertility of indica-japonica hybrid in rice

Qing Ji, Jufei Lu, Qing Chao, Yan Zhang, Meijing Zhang, Minghong Gu, Mingliang Xu

2010, 37(1): 57-68. doi: 10.1016/S1673-8527(09)60025-4

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The rice indica/japonica hybrid shows strong heterosis. However, such inter-subspecific hybrid can't be directly used in rice production due to its low spikelet fertility. The S5 locus was proved to be associated with fertility of indica/japonica hybrid and its S5n allele from wide-compatibility variety (WCV) is capable to overcome fertility barrier. In the present study, we reported the causal sites in the S5 locus responsible for compatibility of indica/japonica hybrid. Fine-mapping of the S5 locus using the 11 test-cross families pinpoints a candidate S5 locus encoding aspartic protease (Asp). Intragenic recombination within the Asp gene happened in a number of recombinants, resulting in chimeric S5j-S5n alleles. Just like S5n, the chimeric S5j-S5n allele displayed higher spikelet fertility when combined with the S5i allele. In the complementary test, however, the S5n allele from WCVs failed to enhance fertilities of the indica/japonica hybrids. Compared to both indica and japonica varieties, all nine WCVs from different resources are characterized with a 136 bp deletion in the Asp N-terminus, which probably renders the S5n allele non-functional. Furthermore, an A/C polymorphic site is detected 1,233 bp downstream of the Asp start codon. The heterozygous A/C site of the Asp gene in indica/japonica hybrid is believed to be the casual factor to cause partial sterility. The functional makers based on the two polymorphic sites will be broadly used in developing wide-compatibility rice varieties.

Identification and functional analysis of the MOC1 interacting protein 1

Fengli Sun, Weiping Zhang, Guosheng Xiong, Meixian Yan, Qian Qian, Jiayang Li, Yonghong Wang

2010, 37(1): 69-77. doi: 10.1016/S1673-8527(09)60026-6

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Rice tillering is one of the most important agronomic traits that determine grain yields. Our previous study has demonstrated that the MONOCULM1 (MOC1) gene is a key component that controls the formation of rice tiller buds. To further elucidate the molecular mechanism of MOC1 involved in the regulation of rice tillering, we performed a yeast-two-hybrid screening to identify MOC1 interacting proteins (MIPs). Here we reported that MIP1 interacted with MOC1 both in vitro and in vivo. The overexpression of MIP1 resulted in enhanced tillering and reduced plant height. In-depth characterization of the context of MIP1 and MOC1 would further our understanding of molecular regulatory mechanisms of rice tillering.

Sporophytic nondisjunction of the maize B chromosome at high copy numbers

Rick E. Masonbrink, James A. Birchler

2010, 37(1): 79-84. doi: 10.1016/S1673-8527(09)60027-8

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It has been known for decades that the maize B chromosome undergoes nondisjunction at the second pollen mitosis. Fluorescence in-situ hybridization (FISH) was used to undertake a quantitative study of maize plants with differing numbers of B chromosomes to observe if instability increases by increasing B dosage in root tip tissue. B chromosome nondisjunction was basically absent at low copy number, but increased at higher B numbers. Thus, B nondisjunction rates are dependent on the dosage of B's in the sporophyte. Differences in nondisjunction were also documented between odd and even doses of the B. In plants that have inherited odd numbered doses of the B chromosome, B loss is nearly twice as likely as B gain in a somatic division. When comparing plants with even doses of B's to plants with odd doses of B's, plants with even numbers had a significantly higher chance to increase in number. Therefore, the B's non-disjunctive capacity, previously thought to be primarily restricted to the gametophyte, is present in sporophytic cells.

A conserved unusual posttranscriptional processing mediated by short, direct repeated (SDR) sequences in plants

Xiangli Niu, Di Luo, Shaopei Gao, Guangjun Ren, Lijuan Chang, Yuke Zhou, Xiaoli Luo, Yuxiang Li, Pei Hou, Wei Tang, Bao-Rong Lu, Yongsheng Liu

2010, 37(1): 85-99. doi: 10.1016/S1673-8527(09)60028-X

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In several stress responsive gene loci of monocot cereal crops, we have previously identified an unusual posttranscriptional processing mediated by paired presence of short direct repeated (SDR) sequences at 5′ and 3′ splicing junctions that are distinct from conventional (U2/U12-type) splicing boundaries. By using the known SDR-containing sequences as probes, 24 plant candidate genes involved in diverse functional pathways from both monocots and dicots that potentially possess SDR-mediated posttranscriptional processing were predicted in the GenBank database. The SDRs-mediated posttranscriptional processing events including cis- and trans-actions were experimentally detected in majority of the predicted candidates. Extensive sequence analysis demonstrates several types of SDR-associated splicing peculiarities including partial exon deletion, exon fragment repetition, exon fragment scrambling and trans-splicing that result in either loss of partial exon or unusual exonic sequence rearrangements within or between RNA molecules. In addition, we show that the paired presence of SDR is necessary but not sufficient in SDR-mediated splicing in transient expression and stable transformation systems. We also show prokaryote is incapable of SDR-mediated premRNA splicing.

Reviewer acknowledgements

2010, 37(1) doi: 10.1016/S1673-8527(10)60001-X

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2010 Vol. 37, No. 1