Characterization and Fine Mapping of SFL1, a Gene Controlling Screw Flag Leaf in Rice

Alamin, Md.; Zeng, Dongdong; Qin, Ran; Sultana, Most. Humaira; Jin, Xiaogang; Shi, Chao

doi:10.1007/s11105-017-1039-x

Cited by 13 publications

(12 citation statements)

References 45 publications

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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%

“…Leaf is the major photosynthetic organ in rice which is directly related to biomass accumulation and grain yield production (Alamin et al ., 2017). It has been proved that appropriate leaf shape improves photosynthesis rate resulting in the higher grain yield in rice (Wu et al ., 2010).…”

Section: Introductionmentioning

confidence: 99%

“…Thus, identifying moderately RL rice mutants and isolating the responsible genes for controlling leaf rolling will be advantageous for rice breeding with the desired traits (e.g. high yield) and architecture (Zhang et al ., 2009; Xu et al ., 2014; Alamin et al ., 2017).…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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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“…qRT- PCR was carried out using the LightCycler ® 96 System (Roche, Indianapolis, IN, USA). The qRT-PCR was setup following the protocol described previously [47]. Three biological replicates were used, and the values shown are the mean ± SD, where the statistical significance evaluated using the Student’s t -test.…”

Section: Methodsmentioning

confidence: 99%

Gene Modules Co-regulated with Biosynthetic Gene Clusters for Allelopathy between Rice and Barnyardgrass

Sultana

Liu

Alamin

et al. 2019

IJMS

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Allelopathy is a central process in crop–weed interactions and is mediated by the release of allelochemicals that result in adverse growth effects on one or the other plant in the interaction. The genomic mechanism for the biosynthesis of many critical allelochemicals is unknown but may involve the clustering of non-homologous biosynthetic genes involved in their formation and regulatory gene modules involved in controlling the coordinated expression within these gene clusters. In this study, we used the transcriptomes from mono- or co-cultured rice and barnyardgrass to investigate the nature of the gene clusters and their regulatory gene modules involved in the allelopathic interactions of these two plants. In addition to the already known biosynthetic gene clusters in barnyardgrass we identified three potential new clusters including one for quercetin biosynthesis and potentially involved in allelopathic interaction with rice. Based on the construction of gene networks, we identified one gene regulatory module containing hub transcription factors, significantly positively co-regulated with both the momilactone A and phytocassane clusters in rice. In barnyardgrass, gene modules and hub genes co-expressed with the gene clusters responsible for 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) biosynthesis were also identified. In addition, we found three genes in barnyardgrass encoding indole-3-glycerolphosphate synthase that regulate the expression of the DIMBOA cluster. Our findings offer new insights into the regulatory mechanisms of biosynthetic gene clusters involved in allelopathic interactions between rice and barnyardgrass, and have potential implications in controlling weeds for crop protection.

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“…Paraffin section analysis was conducted as previously reported by Alamin et al [ 27 ]. Briefly, the leaves were soaked overnight in FAA (10% formaldehyde, 50% ethanol, and 5% glacial acetic acid) at 4 °C, thereafter dehydrated in a 50–100% ethanol series, and finally set in paraplast.…”

Section: Methodsmentioning

confidence: 99%

The Brown Midrib Leaf (bml) Mutation in Rice (Oryza sativa L.) Causes Premature Leaf Senescence and the Induction of Defense Responses

Akhter

Qin

Nath

et al. 2018

Genes

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Isolating and characterizing mutants with altered senescence phenotypes is one of the ways to understand the molecular basis of leaf aging. Using ethyl methane sulfonate mutagenesis, a new rice (Oryza sativa) mutant, brown midrib leaf (bml), was isolated from the indica cultivar ‘Zhenong34’. The bml mutants had brown midribs in their leaves and initiated senescence prematurely, at the onset of heading. The mutants had abnormal cells with degraded chloroplasts and contained less chlorophyll compared to the wild type (WT). The bml mutant showed excessive accumulation of reactive oxygen species (ROS), increased activities of superoxide dismutase, catalase, and malondialdehyde, upregulation of senescence-induced STAY-GREEN genes and senescence-related transcription factors, and down regulation of photosynthesis-related genes. The levels of abscisic acid (ABA) and jasmonic acid (JA) were increased in bml with the upregulation of some ABA and JA biosynthetic genes. In pathogen response, bml demonstrated higher resistance against Xanthomonas oryzae pv. oryzae and upregulation of four pathogenesis-related genes compared to the WT. A genetic study confirmed that the bml trait was caused by a single recessive nuclear gene (BML). A map-based cloning using insertion/deletion markers confirmed that BML was located in the 57.32kb interval between the L5IS7 and L5IS11 markers on the short arm of chromosome 5. A sequence analysis of the candidate region identified a 1 bp substitution (G to A) in the 5′-UTR (+98) of bml. BML is a candidate gene associated with leaf senescence, ROS regulation, and disease response, also involved in hormone signaling in rice. Therefore, this gene might be useful in marker-assisted backcrossing/gene editing to improve rice cultivars.

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Characterization and Fine Mapping of SFL1, a Gene Controlling Screw Flag Leaf in Rice

Cited by 13 publications

References 45 publications

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

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

Gene Modules Co-regulated with Biosynthetic Gene Clusters for Allelopathy between Rice and Barnyardgrass

The Brown Midrib Leaf (bml) Mutation in Rice (Oryza sativa L.) Causes Premature Leaf Senescence and the Induction of Defense Responses

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