Chromosome mapping, molecular cloning and expression analysis of a novel gene response for leaf width in rice

Wu, Yejun; Luo, Lixin; Chen, Likai; Tao, Xingxing; Huang, Ming; Wang, Hui; Chen, Zhiqiang; Xiao, Wuming

doi:10.1016/j.bbrc.2016.10.061

Cited by 11 publications

(6 citation statements)

References 29 publications

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“…OsDjA7 and OsGrp94 were common genes in both genotypes. OsDjA7 , the first characterized DnaJ gene, is involved in DNA replication and repair through the interaction with the proliferating cell nuclear antigen (PCNA) gene, and also functions in the chloroplast development of rice [ 52 , 53 , 54 , 55 ]. OsGrp94 belongs to the HSP90 family protein.…”

Section: Discussionmentioning

confidence: 99%

WGCNA Analysis Identifies the Hub Genes Related to Heat Stress in Seedling of Rice (Oryza sativa L.)

Wang

Liu

et al. 2022

Genes

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Frequent high temperature weather affects the growth and development of rice, resulting in the decline of seed–setting rate, deterioration of rice quality and reduction of yield. Although some high temperature tolerance genes have been cloned, there is still little success in solving the effects of high temperature stress in rice (Oryza sativa L.). Based on the transcriptional data of seven time points, the weighted correlation network analysis (WGCNA) method was used to construct a co–expression network of differentially expressed genes (DEGs) between the rice genotypes IR64 (tolerant to heat stress) and Koshihikari (susceptible to heat stress). There were four modules in both genotypes that were highly correlated with the time points after heat stress in the seedling. We further identified candidate hub genes through clustering and analysis of protein interaction network with known–core genes. The results showed that the ribosome and protein processing in the endoplasmic reticulum were the common pathways in response to heat stress between the two genotypes. The changes of starch and sucrose metabolism and the biosynthesis of secondary metabolites pathways are possible reasons for the sensitivity to heat stress for Koshihikari. Our findings provide an important reference for the understanding of high temperature response mechanisms and the cultivation of high temperature resistant materials.

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Section: Discussionmentioning

confidence: 99%

WGCNA Analysis Identifies the Hub Genes Related to Heat Stress in Seedling of Rice (Oryza sativa L.)

Wang

Liu

et al. 2022

Genes

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“…Finally, we included only 42 RL genes in our analysis for which locus IDs were available. As a result, we confined all of our analyses with only those 42 RL genes: OsACL1 (Li et al ., 2010), OsADL1 (Hibara et al ., 2009), OsAGO1a (Li et al ., 2013a), OsAGO7 (Shi et al ., 2007), OsARF18 (Huang et al ., 2016), OsARVL4 (Wang et al ., 2016), OsAS2 (Ma et al ., 2009), OsCFL1 (Wu et al ., 2011), OsDCL1 (Liu et al ., 2005), OsHB4 (Zhang et al ., 2018), OsI_14279 (Wang et al ., 2017), OsLBD3-7 (Li et al ., 2016), OsLC2 (Zhao et al ., 2010), OsLRRK1 (Zhou et al ., 2018), OsMYB103L (Yang et al ., 2014), OsNAL1 (Qi et al ., 2008), OsNAL11 (Wu et al ., 2016; Zhao et al ., 2017), OsNAL2 (Cho et al ., 2013), OsNAL3 (Cho et al ., 2013), OsNAL7 (Fujino et al ., 2008), OsNAL9 (Li et al ., 2013b), OsNRL1 (Hu et al ., 2010; Wu et al ., 2010), OsNRL4 (Liang et al ., 2016), OsREL1 (Chen et al ., 2015), OsREL2 (Yang et al ., 2016), OsRFS (Cho et al ., 2018; Yoshimura et al ., 1997), OsRL14 (Fang et al ., 2012), OsRL15 (Lee et al ., 2016), OsRL16 (Liu et al ., 2015), OsRL9 (Yan et al ., 2008), OsRRK1 (Ma et al ., 2017), OsRoc5 (Zou et al ., 2011), OsSCL1 (Shen, 2011), OsSFL1 (Alamin et al ., 2017), OsSLL2 (Zhang et al ., 2015), OsSND2 (Ye et al ., 2018), OsSRL1 (Xiang et al ., 2012), OsSRL2 (Liu et al ., 2016), OsSRS5 (Segami et al ., 2012), OsYABBY1 (Dai et al ., 2007), OsYABBY6 (Xia et al ., 2017) and OsZHD1 (Xu et al ., 2014). Then we downloaded the genomic sequence, coding sequence (CDS) and protein sequence from the Rice Genome Annotation Project database () for each of the 42 RL genes included in our study.…”

Section: Methodsmentioning

confidence: 99%

Bioinformatics studies on structures, functions and diversifications of rolling leaf related genes in rice (Oryza sativaL.)

Alam

Al-Amin

Sultana

et al. 2020

Plant Genet. Resour.

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Leaf morphology of crop plants has significant value in agronomy. Leaf rolling in rice plays a vital role to increase grain yield. However, collective information on the rolling leaf (RL) genes reported to date and different comparative bioinformatics studies of their sequences are still incomplete. This bioinformatics study was designed to investigate structures, functions and diversifications of the RL related genes reported till now through several studies. We performed different comparative and functional analyses of the selected 42 RL genes among 103 RL genes using different bioinformatics techniques including gene structure, conserved domain, phylogenetic, gene ontology (GO), transcription factor (TF), Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein–protein network. Exon-intron organization and conserved domain analysis showed diversity in structures and conserved domains of RL genes. Phylogenetic analysis classified the proteins into five major groups. GO and TF analyses revealed that regulation-related genes were remarkably enriched in biological process and 10 different TF families were involved in rice leaf rolling. KEGG analysis demonstrated that 14 RL genes were involved in the KEGG pathways, among which 50% were involved in the metabolism pathways. Of the selected RL proteins, 55% proteins were non-interacting with other RL proteins and OsRL9 was the most interacting RL protein. These results provide important information regarding structures, conserved domains, phylogenetic revolution, protein–protein interactions and other genetic bases of RL genes which might be helpful to the researchers for functional analysis of new candidate RL genes to explore their characteristics and molecular mechanisms for high yield rice breeding.

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“…Nal11 encodes the small molecule heat shock protein HSP40. The disruption of the DNAJ domain in mutant nal11 affects the mRNA splicing pattern and leads to premature termination of translation, which affects agronomic traits such as the tiller, leaf width, and panicle length in rice ( Wu et al., 2016 ). Meanwhile, Nal11 has been confirmed to have a negative regulatory effect on the drought resistance of rice seedlings in terms of morphology, physiology and biochemistry, and gene expression ( Wang et al., 2020 ).…”

Section: The Functional Mechanism Of Heat Shock Proteins In Rice Plan...mentioning

confidence: 99%

The coordinated regulation mechanism of rice plant architecture and its tolerance to stress

et al. 2022

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Rice plant architecture and stress tolerance have historically been primary concerns for rice breeders. The “Green Revolution” and super-rice breeding practices have demonstrated that ideal plant architecture can effectively improve both stress tolerance and yield. The synergistic selection and breeding of rice varieties with ideal architecture and stress tolerance can increase and stabilize yield. While rice plant plant architecture and stress tolerance are separately regulated by complicated genetic networks, the molecular mechanisms underlying their relationships and synergism have not yet been explored. In this paper, we review the regulatory mechanism between plant architecture, stress tolerance, and biological defense at the different level to provide a theoretical basis for the genetic network of the synergistic regulation and improvement of multiple traits.

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Chromosome mapping, molecular cloning and expression analysis of a novel gene response for leaf width in rice

Cited by 11 publications

References 29 publications

WGCNA Analysis Identifies the Hub Genes Related to Heat Stress in Seedling of Rice (Oryza sativa L.)

WGCNA Analysis Identifies the Hub Genes Related to Heat Stress in Seedling of Rice (Oryza sativa L.)

Bioinformatics studies on structures, functions and diversifications of rolling leaf related genes in rice (Oryza sativaL.)

The coordinated regulation mechanism of rice plant architecture and its tolerance to stress

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