Global Identification of Significantly Expressed Genes in Developing Endosperm of Rice by Expression Sequence Tags and cDNA Array Approaches

Tu, Qichao; Dong, Hua; Yao, Haigen; Fang, Yongqi; Dai, Chengen; Luo, Hongmei; Yao, Jian; Zhang, Dong; Li, Debao

doi:10.1111/j.1744-7909.2008.00714.x

Cited by 6 publications

(9 citation statements)

References 37 publications

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“…The homogenate was centrifuged at 10,000 g at 4°C for 20 min, and the supernatant was used as the crude enzyme extract. Ten μl of each extract was applied onto a native-polyacrylamide gel and native PAGE/staining of BE isozyme activity was performed as described previously ( Yamanouchi and Nakamura, 1992 ). Native PAGE was performed on a slab gel prepared of 7.5% (w/v) resolving gel with 3.3% (w/v) stacking gel using a modified version of the method described by Davis (1964) .…”

Section: Methodsmentioning

confidence: 99%

“…The roles of individual BE isozymes in starch biosynthesis in rice endosperm have been examined by many groups worldwide using mutants and transformants prepared from both japonica -type and indica -type rice cultivars. It has been reported that although the relative activities of BEI, BEIIa, and BEIIb in both cultivars are reported approximately 60–80%, 10–20%, and 10–20%, respectively ( Yamanouchi and Nakamura, 1992 ), the impacts of the three BE isozymes on the starch synthesis and structure greatly differ among them ( Nakamura, 2002 ). Mutations in the BEIIb gene resulted in the amylose-extender ( ae ) phenotype of the caryopses, which had a floury appearance and reduced weight ( Mizuno et al, 1993 ; Nishi et al, 2001 ).…”

Section: Introductionmentioning

confidence: 99%

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Contributions of Three Starch Branching Enzyme Isozymes to the Fine Structure of Amylopectin in Rice Endosperm

2018

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Three starch branching enzyme (BE) isozymes, BEI, BEIIa, and BEIIb, are involved in starch biosynthesis in rice endosperm. Past in vivo and in vitro studies have suggested that each BE isozyme plays a distinct role in forming the fine structure of amylopectin. To elucidate more details of their roles, we prepared DNA constructs in which all the possible combinations of the expressions of these three isozymes were suppressed in developing rice endosperm. Analysis of the chain-length distributions of amylopectin produced under these various conditions confirmed the contributions of the individual BE isozymes to the fine structure of amylopectin in rice endosperm. Among these isozymes, the impact of loss of BEIIb activity on amylopectin fine structure was most remarkable and indicated that it plays a specific role in the synthesis of short chains with a 6–13 degree of polymerization (DP). The contribution of BEI to the amylopectin synthesis was unclear when only BEI activity was reduced. It was clear, however, when both BEI and BEIIb activities were substantially inhibited. The DP11-22 intermediate chains were markedly reduced in the ΔBEI/BEIIb line compared with the ΔBEIIb line, indicating that BEI plays a distinct role in the synthesis of these intermediate chains. Although no substantial change in amylopectin chain profile was detected in the ΔBEIIa line, the role of BEIIa could be deciphered by analyzing amylopectin fine structure from the ΔBEI/BEIIa/BEIIb line in comparison to that from ΔBEI/BEIIb line. This strongly suggests that BEIIa compensates for the role of BEI, rather than that of BEIIb, by forming intermediate chains of DP11-22. In addition, the new possibility that BEIIa is involved in the formation of starch granules in rice endosperm was suggested because the onset temperature for gelatinization of starch granules in the ΔBEIIa/BEIIb line was significantly higher than that in the ΔBEIIb line. In summary, the present study highlights the distinct roles of BEI, BEIIa, and BEIIb in the synthesis of amylopectin in developing rice endosperm.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Contributions of Three Starch Branching Enzyme Isozymes to the Fine Structure of Amylopectin in Rice Endosperm

2018

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“…SBEIIa and SBEIIb share ∼80% sequence identity (Mizuno et al, 1992; Nakamura et al, 1992). SBEIIa is prodominantly expressed in leaves, while SBEIIb is mainly expressed in the rice grains (Yamanouchi and Nakamura, 1992; Ohdan et al, 2005; Yamakawa et al, 2007). SBEIIb is a major SBEII isoform in the rice endosperm (Yamanouchi and Nakamura, 1992).…”

Section: Introductionmentioning

confidence: 99%

“…SBEIIa is prodominantly expressed in leaves, while SBEIIb is mainly expressed in the rice grains (Yamanouchi and Nakamura, 1992; Ohdan et al, 2005; Yamakawa et al, 2007). SBEIIb is a major SBEII isoform in the rice endosperm (Yamanouchi and Nakamura, 1992). To further increase the AC, one can direct the starch synthesis toward amylose production through either overexpressing a suitable GBSS ( Waxy ) allele (Hanashiro et al, 1996; Itoh et al, 2003), or suppressing the expression of enzymes involved in amylopectin biosynthesis (Morell and Myers, 2005; Regina et al, 2006; Rahman et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Generation of High-Amylose Rice through CRISPR/Cas9-Mediated Targeted Mutagenesis of Starch Branching Enzymes

et al. 2017

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Cereals high in amylose content (AC) and resistant starch (RS) offer potential health benefits. Previous studies using chemical mutagenesis or RNA interference have demonstrated that starch branching enzyme (SBE) plays a major role in determining the fine structure and physical properties of starch. However, it remains a challenge to control starch branching in commercial lines. Here, we use CRISPR/Cas9 technology to generate targeted mutagenesis in SBEI and SBEIIb in rice. The frequencies of obtained homozygous or bi-allelic mutant lines with indels in SBEI and SBEIIb in T0 generation were from 26.7 to 40%. Mutations in the homozygous T0 lines stably transmitted to the T1 generation and those in the bi-allelic lines segregated in a Mendelian fashion. Transgene-free plants carrying only the frame-shifted mutagenesis were recovered in T1 generation following segregation. Whereas no obvious differences were observed between the sbeI mutants and wild type, sbeII mutants showed higher proportion of long chains presented in debranched amylopectin, significantly increased AC and RS content to as higher as 25.0 and 9.8%, respectively, and thus altered fine structure and nutritional properties of starch. Taken together, our results demonstrated for the first time the feasibility to create high-amylose rice through CRISPR/Cas9-mediated editing of SBEIIb.

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“…However, most of the studies focused on various metabolic pathways such as nutrient partitioning. In rice, different technologies including EST [15], [16], cDNA [16] and DNA microarray [14], [17], [18], and deep sequencing [19] have been applied to analyze the transcriptional profiles in seeds. In most of these studies (except in 14), RNAs were collected from seed tissues at single time point of multiple genotypes/cultivars.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of the Complex Transcriptional Networks of Rice Developing Seeds

2012

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BackgroundThe development of rice (Oryza sativa) seed is closely associated with assimilates storage and plant yield, and is fine controlled by complex regulatory networks. Exhaustive transcriptome analysis of developing rice embryo and endosperm will help to characterize the genes possibly involved in the regulation of seed development and provide clues of yield and quality improvement.Principal FindingsOur analysis showed that genes involved in metabolism regulation, hormone response and cellular organization processes are predominantly expressed during rice development. Interestingly, 191 transcription factor (TF)-encoding genes are predominantly expressed in seed and 59 TFs are regulated during seed development, some of which are homologs of seed-specific TFs or regulators of Arabidopsis seed development. Gene co-expression network analysis showed these TFs associated with multiple cellular and metabolism pathways, indicating a complex regulation of rice seed development. Further, by employing a cold-resistant cultivar Hanfeng (HF), genome-wide analyses of seed transcriptome at normal and low temperature reveal that rice seed is sensitive to low temperature at early stage and many genes associated with seed development are down-regulated by low temperature, indicating that the delayed development of rice seed by low temperature is mainly caused by the inhibition of the development-related genes. The transcriptional response of seed and seedling to low temperature is different, and the differential expressions of genes in signaling and metabolism pathways may contribute to the chilling tolerance of HF during seed development.ConclusionsThese results provide informative clues and will significantly improve the understanding of rice seed development regulation and the mechanism of cold response in rice seed.

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Global Identification of Significantly Expressed Genes in Developing Endosperm of Rice by Expression Sequence Tags and cDNA Array Approaches

Cited by 6 publications

References 37 publications

Contributions of Three Starch Branching Enzyme Isozymes to the Fine Structure of Amylopectin in Rice Endosperm

Contributions of Three Starch Branching Enzyme Isozymes to the Fine Structure of Amylopectin in Rice Endosperm

Generation of High-Amylose Rice through CRISPR/Cas9-Mediated Targeted Mutagenesis of Starch Branching Enzymes

Genome-Wide Analysis of the Complex Transcriptional Networks of Rice Developing Seeds

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