Non‐random distribution of T‐DNA insertions at various levels of the genome hierarchy as revealed by analyzing 13 804 T‐DNA flanking sequences from an enhancer‐trap mutant library

Zhang, Jian; Guo, Dong; Chang, Yuxiao; You, Changjun; Li, Xingwang; Dai, Xiaoxia; Weng, Qijun; Zhang, Jianwei; Chen, Guoxing; Li, Xianghua; Liu, Huifang; Han, Bin; Zhang, Qifa; Wu, Changyin

doi:10.1111/j.1365-313x.2006.03001.x

Cited by 105 publications

(83 citation statements)

References 51 publications

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“…Our study showed that the distribution of T-DNA insertions was correlated with the chromosome size, which is consistent with previous reports that T-DNA insertions are not randomly distributed on the chromosomes [57,58]. The larger chromosomes contain more T-DNA insertions and also show higher insertion density (Table 1; Supplementary information, Figure S1).…”

Section: Distribution Of T-dna Insertions On Chromosomessupporting

confidence: 81%

Studies on rice seed quality through analysis of a large-scale T-DNA insertion population

et al. 2009

Cell Res

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A rice (Oryza sativa) T-DNA insertion population, which included more than 63 000 independent transgenic lines and 8 840 identified flanking sequence tags (FSTs) that were mapped onto the rice genome, was developed to systemically study the rice seed quality control. Genome-wide analysis of the FST distribution showed that T-DNA insertions were positively correlated with expressed genes, but negatively with transposable elements and small RNAs. In addition, the recovered T-DNAs were preferentially located at the untranslated region of the expressed genes. More than 11 000 putative homozygous lines were obtained through multi-generations of planting and resistance screening, and measurement of seed quality of around half of them, including the contents of starch, amylose, protein and fat, with a nondestructive near-infrared spectroscopy method, identified 551 mutants with unique or multiple altered parameters of seed quality. Analysis of the corresponding FSTs showed that genes participating in diverse functions, including metabolic processes and transcriptional regulation, were involved, indicating that seed quality is regulated by a complex network. IntroductionRice (Oryza sativa), as a wholesome and nutritious cereal grain, provides the staple food for more than half of the world's population [1]. Along with the growth of economies and population throughout the world, there is an increasing demand for high-yield and high-quality rice. The grain quality of rice, including that of milling, appearance, cooking and eating, and nutrition, is determined by multiple physicochemical properties [2], and studies on the involved key genes and relevant regulatory mechanisms will help to illustrate the regulatory networks of rice quality control and benefit for the breeding efforts.Starch, which is composed of amylose and amylopectin, comprises ∼90% of dry endosperm of rice seed.The apparent amylose content (AAC) is recognized as an important determinant of the appearance and texture of grain [3]. Thai jasmine rice (KDML 105), one of the best-quality rice with good cooking and eating qualities, has low amylose content (AC) and medium gel consistency (GC) [4].The nutritional quality includes the proportions of protein, fat, mineral and other substances [5]. The rice protein is rich in methionine and cysteine, and compares favorably with proteins of other cereals, but is poor in lysine and threonine, making it an incomplete protein source for human infants [6]. Storage triacylglycerols are stored in oil bodies containing phospholipids and oleosins at the surface [7], and oil bodies are abundant in embryo and aleurone layer of rice seed. However, the aleurone layer is usually removed by milling because it turns rancid upon storage [8]. In addition, oil also influences other aspects of seed quality, and a recent report showed that the quality and viability of Arabidopsis seeds can be enhanced by suppressing phospholipase D [9].The near-infrared spectroscopy (NIRS) technology, which is based on the fact that several natural pr...

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Section: Distribution Of T-dna Insertions On Chromosomessupporting

confidence: 81%

Studies on rice seed quality through analysis of a large-scale T-DNA insertion population

et al. 2009

Cell Res

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“…The osbc1l4 mutant exhibited a dwarf and less tiller phenotype The osbc1l4 mutant line was identified from our T-DNA insertion Rice Mutant Database (RMD; http://rmd.ncpgr.cn/; Wu et al 2003;Zhang et al 2007). The mutant exhibited a d Wild type (left) and OsBC1L5/osbc1l5 (right) heterozygous plants at maturity stage.…”

Section: Identification and Characterization Of Osbc1l Insertion Mutantsmentioning

confidence: 99%

Molecular characterization, expression pattern, and function analysis of the OsBC1L family in rice

et al. 2009

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COBRA-like proteins play important roles in cell expansion and cell wall biosynthesis in Arabidopsis. In rice, a COBRA-like gene, BRITTLE CULM1 (BC1), has been identified as a regulator controlling the culm mechanical strength. Analysis of the rice genome indicated that BC1 belongs to an 11-member multigene family, termed the OsBC1L family in this study. Based on sequence comparisons and phylogenetic analysis, the OsBC1L family comprises two main subgroups. Expression patterns examined by microarray and reverse transcription polymerase chain reaction revealed that OsBC1L genes exhibit universal or specific expression patterns. Through T-DNA or Tos17 insertion mutant lines, the functions of six OsBC1L family members have been examined by investigating the phenotype variations of knockout mutants under normal growth conditions. Results suggest that the OsBC1L genes perform a range of functions and participate in various developmental processes in rice.

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“…A BLASTn search of the T-DNA flanking sequence isolated by thermal asymmetric interlaced PCR (Zhang et al, 2007) against the rice genomic sequence database (http://rice.plantbiology.msu.edu) showed that the T-DNA was inserted into the intron of OsRPA1a (LOC_Os02g53680; Fig. 2A), which encodes RPA1a, one of the isoforms of RPA1 subunit in rice (Ishibashi et al, 2006).…”

Section: Isolation and Characterization Of The Osrpa1a Genementioning

confidence: 99%

Replication Protein A (RPA1a) Is Required for Meiotic and Somatic DNA Repair But Is Dispensable for DNA Replication and Homologous Recombination in Rice

et al. 2009

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Replication protein A (RPA), a highly conserved single-stranded DNA-binding protein in eukaryotes, is a stable complex comprising three subunits termed RPA1, RPA2, and RPA3. RPA is required for multiple processes in DNA metabolism such as replication, repair, and homologous recombination in yeast (Saccharomyces cerevisiae) and human. Most eukaryotic organisms, including fungi, insects, and vertebrates, have only a single RPA gene that encodes each RPA subunit. Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), however, possess multiple copies of an RPA gene. Rice has three paralogs each of RPA1 and RPA2, and one for RPA3. Previous studies have established their biochemical interactions in vitro and in vivo, but little is known about their exact function in rice. We examined the function of OsRPA1a in rice using a T-DNA insertional mutant. The osrpa1a mutants had a normal phenotype during vegetative growth but were sterile at the reproductive stage. Cytological examination confirmed that no embryo sac formed in female meiocytes and that abnormal chromosomal fragmentation occurred in male meiocytes after anaphase I. Compared with wild type, the osrpa1a mutant showed no visible defects in mitosis and chromosome pairing and synapsis during meiosis. In addition, the osrpa1a mutant was hypersensitive to ultraviolet-C irradiation and the DNA-damaging agents mitomycin C and methyl methanesulfonate. Thus, our data suggest that OsRPA1a plays an essential role in DNA repair but may not participate in, or at least is dispensable for, DNA replication and homologous recombination in rice.

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Non‐random distribution of T‐DNA insertions at various levels of the genome hierarchy as revealed by analyzing 13 804 T‐DNA flanking sequences from an enhancer‐trap mutant library

Cited by 105 publications

References 51 publications

Studies on rice seed quality through analysis of a large-scale T-DNA insertion population

Studies on rice seed quality through analysis of a large-scale T-DNA insertion population

Molecular characterization, expression pattern, and function analysis of the OsBC1L family in rice

Replication Protein A (RPA1a) Is Required for Meiotic and Somatic DNA Repair But Is Dispensable for DNA Replication and Homologous Recombination in Rice

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