A draft sequence of the rice (Oryza sativa ssp.indica) genome

Yu, Jun; Hu, Songnian; Wang, Jun; Li, Songgang; Wong, Ka-Shu Gane; Liu, Bin; Deng, Yajun; Dai, Li; Zhou, Yan; Zhang, Xiuqing; Cao, Mengliang; Liu, Jing; Sun, Jie; Tang, Jiabin; Chen, Yanjiong; Huang, Xiande; Lin, Wei Yu; Wang, Hongzhi; Tong, Wei; Cong, Lijuan; Geng, Jianing; Han, Yujun; Lin, Li; Wei, Li; Hu, Guangqiang; Huang, Xiangang; Li, Wenjie; Li, Jian; Liu, Zhanwei; Li, Long; Liu, Jianping; Qi, Qiuhui; Liu, Jinsong; Li, Li; Wang, Xuegang; Liang, Hong; Wu, Tingting; Zhu, Mengting; Ni, Peixiang; Han, Hua; Dong, Wei; Ren, Xiaoyu; Feng, Xiaoli; Cui, Peng; Li, Xianran; Wang, Hao; Xu, Xin; Zhai, Wenxue; Zhang, Jinsong; He, Shiying; Zhang, Jianguo; Zhang, Kunlin; Zheng, Xingwei; Dong, Jianhai; Zeng, Wanyong; Lin, Tao; Chen, Xuewei; He, Jun; Liu, Daofeng; Tian, Chaoguang; Xia, Hongai; Li, Gang; Gao, Hui; Li, Ping; Chen, Wei; Wang, Xudong; Hu, Jianfei; Wang, Jing; Liu, Song; Yang, Jian; Zhang, Guangyu; Xiong, Yuqing; Li, Zhijie; Mao, Long; Zhou, Chengshu; Zhu, Zhenfeng; Chen, Runsheng; Hao, Bailin; Zheng, Wei-Mou; Chen, Shouyi; Guo, Wei; Li, Guojie; Liu, Siqi; Huang, Guyang Matthew; Tao, Ming; Wang, Jian; Zhu, Lihuang; Yuan, Longping; Yang, Huanming

doi:10.1007/bf02901901

Cited by 482 publications

(587 citation statements)

References 16 publications

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“…Construction of a BAC ®ngerprint-based physical map of the japonica rice variety Nipponbare led to a size prediction of about 400 Mbp for its euchromatic region (Chen et al, 2002). Analysis of a draft sequence derived by whole-genome shotgun sequencing furthermore indicated the genome size of an indica rice variety to be 466 Mbp (Yu et al, 2002). By adding the predicted physical lengths of all gaps derived from the FISH experiment and YAC or genetic maps, we predict a total length of 198.7 Mbp for the six rice chromosomes studied, excluding the nuclear organizing region (NOR) on chromosome 9 (Table 1).…”

Section: Discussionmentioning

confidence: 99%

“…The International Rice Genome Sequencing Project (IRGSP) was established in 1998 with the aim of decoding the sequence of the entire genome using a single variety of rice (Oryza sativa L., japonica cultivar Nipponbare). In 2002, a private company and an academic institute reported draft sequences of the rice genome from the japonica and indica varieties, respectively (Goff et al, 2002;Yu et al, 2002). These two draft sequences, both obtained from whole-genome shotgun sequencing, are of immense scienti®c value to our general understanding of the rice genome.…”

Section: Introductionmentioning

confidence: 99%

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Physical maps and recombination frequency of six rice chromosomes

Wu¹,

Mizuno²,

et al. 2003

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These authors contributed equally to this work. SummaryWe constructed physical maps of rice chromosomes 1, 2, and 6±9 with P1-derived arti®cial chromosome (PAC) and bacterial arti®cial chromosome (BAC) clones. These maps, with only 20 gaps, cover more than 97% of the predicted length of the six chromosomes. We submitted a total of 193 Mbp of non-overlapping sequences to public databases. We analyzed the DNA sequences of 1316 genetic markers and six centromere-speci®c repeats to facilitate characterization of chromosomal recombination frequency and of the genomic composition and structure of the centromeric regions. We found marked changes in the relative recombination rate along the length of each chromosome. Chromosomal recombination at the centromere core and surrounding regions on the six chromosomes was completely suppressed. These regions have a total physical length of about 23 Mbp, corresponding to 11.4% of the entire size of the six chromosomes. Chromosome 6 has the longest quiescent region, with about 5.6 Mbp, followed by chromosome 8, with quiescent region about half this size. Repetitive sequences accounted for at least 40% of the total genomic sequence on the partly sequenced centromeric region of chromosome 1. Rice CentO satellite DNA is arrayed in clusters and is closely associated with the presence of Centromeric Retrotransposon of Rice (CRR )-and RIce RetroElement 7 (RIRE7 )-like retroelement sequences. We also detected relatively small coldspot regions outside the centromeric region; their repetitive content and gene density were similar to those of regions with normal recombination rates. Sequence analysis of these regions suggests that either the amount or the organization patterns of repetitive sequences may play a role in the inactivation of recombination.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Physical maps and recombination frequency of six rice chromosomes

Wu¹,

Mizuno²,

et al. 2003

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“…To understand the pattern and dynamics of DNA elimination in the context of the age distribution of elements, we performed comparative analysis of two O. sativa subspecies, japonica (cultivar, Nipponbare) and indica (cultivar, 93-11; Yu et al 2002) (see Methods). Of the 14,924 solo, truncated, and complete LTR-RTs identified in the japonica genome, 10,052 were shared between japonica and indica, indicating that their presence at these locations in the common ancestor of the two subspecies .…”

Section: Patterns Of Recent Accumulation and Distribution Of Ltr-rtsmentioning

confidence: 99%

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

Tian

Rizzon²,

Du³

et al. 2009

Genome Res.

146

176

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In flowering plants, the accumulation of small deletions through unequal homologous recombination (UR) and illegitimate recombination (IR) is proposed to be the major process counteracting genome expansion, which is caused primarily by the periodic amplification of long terminal repeat retrotransposons (LTR-RTs). However, the full suite of evolutionary forces that govern the gain or loss of transposable elements (TEs) and their distribution within a genome remains unclear. Here, we investigated the distribution and structural variation of LTR-RTs in relation to the rates of local genetic recombination (GR) and gene densities in the rice (Oryza sativa) genome. Our data revealed a positive correlation between GR rates and gene densities and negative correlations between LTR-RT densities and both GR and gene densities. The data also indicate a tendency for LTR-RT elements and fragments to be shorter in regions with higher GR rates; the size reduction of LTR-RTs appears to be achieved primarily through solo LTR formation by UR. Comparison of indica and japonica rice revealed patterns and frequencies of LTR-RT gain and loss within different evolutionary timeframes. Different LTR-RT families exhibited variable distribution patterns and structural changes, but overall LTR-RT compositions and genes were organized according to the GR gradients of the genome. Further investigation of non-LTR-RTs and DNA transposons revealed a negative correlation between gene densities and the abundance of DNA transposons and a weak correlation between GR rates and the abundance of long interspersed nuclear elements (LINEs)/short interspersed nuclear elements (SINEs). Together, these observations suggest that GR and gene density play important roles in shaping the dynamic structure of the rice genome.

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“…The paternal parent 93-11 is a typical indica variety, and its whole genome has been sequenced (Yu et al, 2002). The F 1 (Pei′ai64S/93-11) and F 2 populations were planted in the field under LD/HT conditions on the experimental farm at Zhejiang University, Hangzhou, China in 2005.…”

Section: Plant Materials and Mapping Populationmentioning

confidence: 99%

Fine mapping and candidate gene prediction of the photoperiod and thermo-sensitive genic male sterile gene pms1(t) in rice

Zhou

Xianyin

Xue

2011

J. Zhejiang Univ. Sci. B

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Pei′ai64S, an indica sterile variety with photoperiod and thermo-sensitive genic male sterile (PTGMS) genes, has been widely exploited for commercial seed production for "two-line" hybrid rice in China. One PTGMS gene from Pei′ai64S, pms1(t), was mapped by a strategy of bulked-extreme and recessive-class approach with simple sequence repeat (SSR) and insert and deletion (In-Del) markers. Using linkage analysis for the F 2 mapping population consisting of 320 completely male sterile individuals derived from a cross between Pei′ai64S and 93-11 (indica restorer) lines, the pms1(t) gene was delimited to the region between the RM21242 (0.2 cM) and YF11 (0.2 cM) markers on the short arm of chromosome 7. The interval containing the pms1(t) locus, which was co-segregated with RM6776, is a 101.1 kb region based on the Nipponbare rice genome. Fourteen predicted loci were found in this region by the Institute for Genomic Research (TIGR) Genomic Annotation. Based on the function of the locus LOC_Os07g12130 by bioinformatics analysis, it is predicted to encode a protein containing a Myb-like DNA-binding domain, and may process the transcript with thermosensory response. The reverse transcription-polymerase chain reaction (RT-PCR) results revealed that the mRNA levels of LOC_Os07g12130 were altered in different photoperiod and temperature treatments. Thus, the LOC_Os07g12130 locus is the most likely candidate gene for pms1(t). These results may facilitate not only using the molecular marker assisted selection of PTGMS genes, but also cloning of the pms1(t) gene itself.

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A draft sequence of the rice (Oryza sativa ssp.indica) genome

Cited by 482 publications

References 16 publications

Physical maps and recombination frequency of six rice chromosomes

Physical maps and recombination frequency of six rice chromosomes

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

Fine mapping and candidate gene prediction of the photoperiod and thermo-sensitive genic male sterile gene pms1(t) in rice

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