Morphological and Molecular Dissection of Leaf Development in Wild-Type and Various Morphogenetic Mutants in Rice

Dechkrong, Punyavee; Yoshikawa, Takanori; Itoh, Jun-Ichi

doi:10.4236/ajps.2015.68125

Cited by 5 publications

(6 citation statements)

References 39 publications

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“…Moreover, samples derived from the P4 leaf exhibited large transcriptomic variations, whereas all P4-stage leaf samples including sheath samples were aligned along the arrow. This result indicates that the shift in the transcriptome associated with leaf maturation is found throughout the leaf during P4, coinciding with intensive basipetal tissue differentiation at stage P4 [30].…”

Section: Transcriptome Dynamics During Rice Leaf Developmentmentioning

confidence: 78%

Genome-Wide Analysis of Spatiotemporal Expression Patterns During Rice Leaf Development

Miya

Yoshikawa

Satō

et al. 2020

Preprint

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Background: Rice leaves consist of three distinct regions along a proximal-distal axis, namely the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, but the genetic programs underlying the development of each region are poorly understood. To fully elucidate rice leaf development and discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions.Results: In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages. The dynamics in each region revealed that the transcriptomes changed dramatically throughout the progress of tissue differentiation, and those of the leaf blade and sheath differed greatly at the mature stage. Cluster analysis of expression patterns among leaf parts revealed groups of genes that may be involved in specific biological processes related to rice leaf development. Moreover, we found novel genes potentially involved in rice leaf development using a combination of transcriptome data and in situ hybridization, and analyzed their spatial expression patterns at high resolution. We successfully identified multiple genes that exhibit localized expression in tissues characteristic of rice or grass leaves.Conclusions: Although the genetic mechanisms of leaf development have been elucidated in several eudicots, direct application of that information to rice and grasses is not appropriate due to the morphological and developmental differences between them. Our analysis provides not only insights into the development of rice leaves but also expression profiles that serve as a valuable resource for gene discovery. The genes and gene clusters identified in this study may facilitate future research on the unique developmental mechanisms of rice leaves.

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Section: Transcriptome Dynamics During Rice Leaf Developmentmentioning

confidence: 78%

Genome-Wide Analysis of Spatiotemporal Expression Patterns During Rice Leaf Development

Miya

Yoshikawa

Satō

et al. 2020

Preprint

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Section: Resultsmentioning

confidence: 99%

“…Quantitative RT- PCR was performed with the StepOne™ Real-Time PCR System (Life Technologies, Carlsbad, CA) using the TaqMan Fast Universal PCR Master Mix and FAM-labeled TaqMan probes for each gene. OsRAD6 ( Os03g0791800 ) was used as an internal standard [ 31 ]. Three technical replicates were performed for each sample.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide analysis of spatiotemporal expression patterns during rice leaf development

et al. 2021

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Background Rice leaves consist of three distinct regions along a proximal-distal axis, namely the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, but the genetic programs underlying the development of each region are poorly understood. To fully elucidate rice leaf development and discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions. Results In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages. The dynamics in each region revealed that the transcriptomes changed dramatically throughout the progress of tissue differentiation, and those of the leaf blade and sheath differed greatly at the mature stage. Cluster analysis of expression patterns among leaf parts revealed groups of genes that may be involved in specific biological processes related to rice leaf development. Moreover, we found novel genes potentially involved in rice leaf development using a combination of transcriptome data and in situ hybridization, and analyzed their spatial expression patterns at high resolution. We successfully identified multiple genes that exhibit localized expression in tissues characteristic of rice or grass leaves. Conclusions Although the genetic mechanisms of leaf development have been elucidated in several eudicots, direct application of that information to rice and grasses is not appropriate due to the morphological and developmental differences between them. Our analysis provides not only insights into the development of rice leaves but also expression profiles that serve as a valuable resource for gene discovery. The genes and gene clusters identified in this study may facilitate future research on the unique developmental mechanisms of rice leaves.

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“…Teknologi ini memberikan hasil yang cepat, efektif, akurat, dan telah banyak diaplikasikan pada komoditas padi, di antaranya keragaman 330 varietas tradisional Indonesia (Thomson et al, 2007), keragaman genetik padi lokal (landrace) Brasil berdasarkan marka SSR putatif (Borba et al, 2009), keragaman 96 aksesi plasma nutfah padi terkait umur genjah (Utami et al, 2011), kekerabatan 26 varietas unggul baru asal Indonesia (Susanto et al, 2014), dan keragaman genetik beras berwarna berdasarkan marka terkait sifat warna beras (Kristamtini et al, 2014;Patel et al, 2014;Suzuki et al, 2004;Utami et al, 2009), serta keragaman daun padi liar (Dechkrong et al, 2015). Penelitian ini bertujuan mengetahui kekerabatan dan jarak genetik beberapa plasma nutfah padi lokal yang telah teridentifikasi secara fenotipik tahan terhadap beberapa jenis HPT berdasarkan analisis polimorfisme beberapa marka SSR.…”

Section: Pendahuluanunclassified

Kekerabatan Beberapa Aksesi Padi Lokal Tahan Hama Penyakit Berdasarkan Analisis Polimorfisme Marka SSR

Susanto¹,

Satoto²

2018

J. AgroBiogen

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The level of phylogeny among local rice that has identified the resistances to plant pests and diseases needs to be studied to determine the genetic distance, so that information can be used for a recommendation parental crosses. Simple sequence repeat (SSR) markers could be used as one tool to know the degree of phylogeny and the genetic distance between genotypes. The aim of this study was to determine phylogenetic tree and the coefficient of genetic distance of several local rice resistant to host and pest based polymorphic analysis of SSR markers. Fifteen host and pest resistant local rice and one popular variety (Ciherang) were used. Molecular analysis was carried out using eighteen SSR markers. The banding patterns of DNA amplification resulted from PCR on polyacrylamide electrophoresis gel was documented by using UV Transilluminator. The phylogenetic tree showed three clearly separated clusters. Cluster 1 consisted of indica accessions resistant to blast and BLB: Gadis Langsat, Kebo, Bandang Si Gadis, Ciherang, Jawa Wangi Sleman, Marahmay, Takong, Ampek Panjang, Benoraja, and Siawak. Cluster 2 consisted of javanica and indica accessions resistant to BPH, tungro, blast, and BLB: Ase Balucung, Ase Bukne, Pare Lottong, Pare Pulu, and Jadul. Cluster 3 consisted of japonica accession resistant to blast: Kapas. The farthest genetic distance was between Pare Pulu and Ampek Panjang (DA = 0.816). The closest genetic distance was between Pare Pulu dan Pare Lottong (DA = 0.098). This research data can be used as a reference in determining the crossing parents that will be used in plant breeding program for varieties improvement of Indonesian local rice.Keywords: Genetic distance, local rice, kinship, SSR markers. ABSTRAKTingkat kekerabatan antarpadi lokal dengan keunggulan tahan terhadap hama dan penyakit tanaman (HPT) perlu dipelajari untuk mengetahui seberapa jauh kekerabatannya, sehingga informasi yang diperoleh dapat digunakan untuk kebutuhan pemilihan tetua persilangan. Marka simple sequence repeat (SSR) dapat dijadikan salah satu alat bantu untuk mengetahui tingkat kekerabatan antargenotipe. Penelitian ini bertujuan mengetahui tingkat kekerabatan dan jarak genetik beberapa aksesi padi lokal unggul tahan HPT berdasarkan analisis polimorfisme marka SSR. Materi genetik yang digunakan adalah lima belas padi lokal tahan HPT dan varietas Ciherang. Analisis molekuler dilakukan menggunakan delapan belas marka SSR. Pola pita DNA hasil amplifikasi PCR pada elektroforesis gel poliakrilamida didokumentasi dengan visualisasi gel doc/UV transilluminator. Pohon kekerabatan menunjukkan tiga klaster yang terpisah jelas. Klaster 1 terdiri atas aksesi-aksesi subspesies indica tahan blas dan HDB, yaitu Gadis Langsat, Kebo, Bandang Si Gadis, Ciherang, Jawa Wangi Sleman, Marahmay, Takong, Ampek Panjang, Benoraja, dan Siawak. Klaster 2 terdiri atas aksesi-aksesi subspesies javanica dan japonica tahan WBC, tungro, blas, dan HDB, yaitu Ase Balucung, Ase Bukne, Pare Lottong, Pare Pulu, dan Jadul. Klaster 3 berisi aksesi subsp...

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Morphological and Molecular Dissection of Leaf Development in Wild-Type and Various Morphogenetic Mutants in Rice

Cited by 5 publications

References 39 publications

Genome-Wide Analysis of Spatiotemporal Expression Patterns During Rice Leaf Development

Genome-Wide Analysis of Spatiotemporal Expression Patterns During Rice Leaf Development

Genome-wide analysis of spatiotemporal expression patterns during rice leaf development

Kekerabatan Beberapa Aksesi Padi Lokal Tahan Hama Penyakit Berdasarkan Analisis Polimorfisme Marka SSR

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