Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L

We studied the dynamics of hopi, Retrosat1, and RIRE3, three gypsy-like long terminal repeat (LTR) retrotransposons, in Oryza sativa L. genome. For each family, we assessed the phenetic relationships of the copies and estimated the date of insertion of the complete copies through the evaluation of their LTR divergence. We show that within each family, distinct phenetic groups have inserted at significantly different times, within the past 5 Myr and that two major amplification events may have occurred during this period. We show that solo-LTR formation through homologous unequal recombination has occurred in rice within the past 5 Myr for the three elements. We thus propose an increase/decrease model for rice genome evolution, in which both amplification and recombination processes drive variations in genome size.     

Isolation and annotation of 10828 putative full length cDNAs from indica rice

Rice has become a model plant for genomic studies of monocot species, because of its relative small ge-nome size (430 Mb), high synteny with other impor-tant crop species such as maize, barley and wheat, the release of draft sequences of both indica[1] and japon-ica[2] genomes, and the near completion of the map-based sequencing of rice genome by the Interna-tional Rice Genome Sequencing Project. Currently, more than 340 Mb of non-overlapping genomic se-quences including completely sequenced…     

Evolution of Tom, 297, 17.6 and rover retrotransposons in Drosophilidae species

LTR retrotransposons are the most abundant transposable elements in Drosophila and are believed to have contributed significantly to genome evolution. Different reports have shown that many LTR retrotransposon families in Drosophila melanogaster emerged from recent evolutionary episodes of transpositional activity. To contribute to the knowledge of the evolutionary history of Drosophila LTR retrotransposons and the mechanisms that control their abundance, distribution and diversity, we conducted analyses of four related families of LTR retrotransposons, 297, 17.6, rover and Tom. Our results show that these elements seem to be restricted to species from the D. melanogaster group, except for 17.6, which is also present in D. virilis and D. mojavensis. Genetic divergences and phylogenetic analyses of a 1-kb fragment region of the pol gene illustrate that the evolutionary dynamics of Tom, 297, 17.6 and rover retrotransposons are similar in several aspects, such as low codon bias, the action of purifying selection and phylogenies that are incongruent with those of the host species. We found an extremely complex association among the retrotransposon sequences, indicating that different processes shaped the evolutionary history of these elements, and we detected a very high number of possible horizontal transfer events, corroborating the importance of lateral transmission in the evolution and maintenance of LTR retrotransposons.     

Analysis of genes associated with retrotransposons in the rice genome

Retrotransposons comprise a significant fraction of the rice genome. Despite their prevalence, the effects of retrotransposon insertions are not well understood, especially with regard to how they affect the expression of genes. In this study, we identified one-sixth of rice genes as being associated with retrotransposons, with insertions either in the gene itself or within its putative promoter region. Among genes with insertions in the promoter region, the likelihood of the gene being expressed was shown to be directly proportional to the distance of the retrotransposon from the translation start site. In addition, retrotransposon insertions in the transcribed region of the gene were found to be positively correlated with the presence of alternative splicing forms. Furthermore, preferential association of retrotransposon insertions with genes in several functional classes was identified. Some of the retrotransposons that are part of full-length cDNA (fl-cDNA) contribute splice sites and give rise to novel exons. Several interesting trends concerning the effects of retrotransposon insertions on gene expression were identified. Taken together, our data suggests that retrotransposon association with genes have a role in gene regulation. The data presented in this study provides a foundation for experimental studies to determine the role of retrotransposons in gene regulation.     

Identification of novel LTR retrotransposons in the genome of Aedes aegypti

We have detected seventy-six novel LTR retrotransposons in the genome of the mosquito Aedes aegypti by a genome wide analysis using the LTR_STRUC program. We have performed a phylogenetic classification of these novel elements and a distribution analysis in the genome of A. aegypti. These mobile elements belong either to the Ty3/gypsy or to the Bel family of retrotransposons and were not annotated in the mosquito LTR retrotransposon database (TEfam). We have found that  1.8% of the genome is occupied by these newly detected retrotransposons that are distributed predominantly in intergenic genomic sequences and introns. The potential role of retrotransposon insertions linked to host genes is described and discussed. We show that a retrotransposon family belonging to the Osvaldo lineage has peculiar structural features, and its presence is likely to be restricted to the A. aegypti and to the Culex pipiens quinquefasciatus genomes. Furthermore we show that the ninja-like group of elements lacks the Primer Binding Site (PBS) sequence necessary for the replication of retrotransposons. These results integrate the knowledge on the complicate genomic structure of an important disease vector.     

Genetic analysis and gene mapping of a rice few-tillering mutant in early backcross populations ( Oryza sativa L.)

A rice mutant,G069, characteristic of few tiller numbers, was found in anther culture progeny from theF ₁ hybrid between anindica-japonica cross, Gui630×02428. The mutant has another two major features: delayed tillering development and yellowing apex and margin on the mature leaves. As a donor parent,G069 was further backcrossed with the recurrent parent,02428, for two turns to develop aBC ₂F₂ population. Genetic analysis in theBC ₂F₂ population showed that the traits of few-tillering and yellowing apex and margin on the mature leaves were controlled by one recessive gene. A pool of equally mixed genomic DNA, from few-tillering individual plants inBC ₂F₂, was constructed to screen polymorphism with simple sequence repeat (SSR) markers in comparison with the02428 genome. One SSR marker and three restriction fragment length polymorphism (RFLP) markers were found possibly linked with the recessive gene. By using these markers, the gene of few-tillering was mapped on chromosome 2 between RFLP marker C424 and S13984 with a genetic distance of 2.4 cM and 0.6 cM, respectively. The gene is designatedft1.     

一个新的水稻叶绿素缺失黄叶突变体的特征及基因分子定位

从粳稻"嘉花1号"60Coγ射线辐照的后代中筛选到一个叶绿素缺失黄叶突变体(yl11),与野生型"嘉花1号"相比该突变体表现为全生育期植株叶片呈黄色,叶绿素含量以及净光合速率明显下降,叶绿体发育不完善,并且伴随着株高等主要农艺性状的变化。遗传分析表明,该突变性状受一对隐性核基因(yl11)控制。该突变体与籼稻"培矮64S"杂交生产的F2、F3群体中的分离出突变体型920个单株作为定位群体,利用SSR和InDel分子标记将yl11基因定位在水稻第11染色体长臂上的MM2199和ID21039分子标记之间,其物理距离约为110kb,目前该区域内没有发现与水稻叶绿素合成/叶绿体发育相关已知功能基因。研究结果为今后对该基因的克隆和功能分析奠定了基础。     

Identification of the regeneration potential of embryo derived calluses from various Indica rice varieties

The regeneration response of mature and immature rice embryos from 15 rice varieties (Oryza sativa L. var. indica) was separately measured in terms of regeneration per cent and total number of regenerated plantlets obtained for a fixed sample size per variety, when cultured on standard MS media. The response of the rice varieties was classed as high, medium or poor, based on the above criteria. The regeneration per cent of genotypes showing high, medium and poor response ranged from 67 to 97, 38 to 63 and 0 to 36 respectively. The variation in the regeneration response amongst the defined groups was found to be statistically significant in terms of regeneration per cent and total plantlets for a constant sample size when subjected to one way analysis of variance and Duncan's multiple range test. Only small influences on regeneration frequency were found when the most and least responsive genotypes, Binnatoa and BR-23 were cultured on N6 and MS media with additional or different supplements.     

Origins and population genetics of weedy red rice in the USA

Weedy red rice (Oryza sativa spontonea) is a persistent and problematic weed of rice culture worldwide. A major hypothesis for the mechanism of production of this weed in South and Southeast Asia is hybridization between cultivated rice (Oryza sativa) and wild rice (Oryza rufipogon). However, weedy red rice can often be found outside the range of O. rufipogon leaving questions on the origin and process behind weedy rice infestations. In the USA, weedy red rice was first documented as early as 1846 and has continued to affect rice production areas. In this study, we attempt to identify the origin and population structure of weedy red rice sampled from the USA using both DNA sequence data from a neutral nuclear locus as well as microsatellite genotype data. Results suggest that two major accessions of weedy rice exist, strawhull and blackhull, and these forms may both hybridize with the cultivated rice of the USA, O. sativa japonica. Using population assignment of multilocus genotype signatures with principal component analysis and structure, an Asian origin is supported for US weedy rice. Additionally, hybridization between strawhull and blackhull varieties was inferred and may present the opportunity for the production of new weedy forms in the future.     

水稻Ds插入淡绿叶突变体的鉴定和遗传分析

Ac/Ds插入突变是水稻基因功能鉴定的有力工具之一。文章从水稻中花11 Ds-T-DNA转化纯合体与Ac-T-DNA 转化纯合体的杂交群体中筛选到一个淡绿叶突变体。该突变体在三叶期由绿苗转为淡绿叶苗, 自然光照下突变体迅速焦枯, 但是在弱光照条件下, 突变体能缓慢生长至开花结实; 突变体光合作用特性研究表明该突变是典型的光抑制突变体。遗传分析表明该突变为Ds插入导致的隐性突变。     

一个新的水稻叶绿素缺失黄叶突变体的特征及基因分子定位

从粳稻“嘉花1号”⁶⁰Coγ射线辐照的后代中筛选到一个叶绿素缺失黄叶突变体(yl11), 与野生型“嘉花1号”相比该突变体表现为全生育期植株叶片呈黄色, 叶绿素含量以及净光合速率明显下降, 叶绿体发育不完善, 并且伴随着株高等主要农艺性状的变化。遗传分析表明, 该突变性状受一对隐性核基因(yl11)控制。该突变体与籼稻“培矮64S”杂交生产的F₂、F₃群体中的分离出突变体型920个单株作为定位群体, 利用SSR和InDel分子标记将yl11基因定位在水稻第11染色体长臂上的MM2199和ID21039分子标记之间, 其物理距离约为110 kb, 目前该区域内没有发现与水稻叶绿素合成/叶绿体发育相关已知功能基因。研究结果为今后对该基因的克隆和功能分析奠定了基础。     

Stress-induced rearrangement of Fusarium retrotransposon sequences

 Rearrangement of Fusarium oxysporum retro- transposon skippy was induced by growth in the presence of potassium chlorate. Three fungal strains, one sensitive to chlorate (Co60) and two resistant to chlorate and deficient for nitrate reductase (Co65 and Co94), were studied by Southern analysis of their genomic DNA. Polymorphism was detected in their hybridization banding pattern, relative to the wild type grown in the absence of chlorate, using various enzymes with or without restriction sites within the retrotransposon. Results were consistent with the assumption that three different events had occurred in strain Co60: genomic amplification of skippy yielding tandem arrays of the element, generation of new skippy sequences, and deletion of skippy sequences. Amplification of Co60 genomic DNA using the polymerase chain reaction and divergent primers derived from the retrotransposon generated a new band, corresponding to one long terminal repeat plus flanking sequences, that was not present in the wild-type strain. Molecular analysis of nitrate reductase-deficient mutants showed that generation and deletion of skippy sequences, but not genomic amplification in tandem repeats, had occurred in their genomes. Received: 29 March 1996 / Accepted: 29 June 1996