Gene expression analysis revealed Hbr-miR396b as a key piece participating in reaction wood formation of Hevea brasiliensis (rubber tree)

2022 ◽  
Vol 177 ◽  
pp. 114460
Author(s):  
Xiangxu Meng ◽  
Lingshan Kong ◽  
Yuanyuan Zhang ◽  
Mengjia Wu ◽  
Yue Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Hevea Brasiliensis ◽  
Gene Expression Analysis ◽  
Rubber Tree ◽  
Wood Formation ◽  
Reaction Wood

scholarly journals Respons molekuler Hevea brasiliensis ethylene response factors (HbERFs) sebagai marka ekspresi gen terhadap stimulasi ethephon pada klon-klon tanaman karet Moleculer response of Hevea brasiliensis ethylene response factors (HbERFs) as expression marker genes in response to ethephon stimulation in rubber tree clones

2016 ◽  
Vol 82 (2) ◽  
Author(s):  
Riza Arief PUTRANTO ◽  
. KUSWANHADI ◽  
Pascal MONTORO
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Hevea Brasiliensis ◽  
Gene Expression Analysis ◽  
Rubber Tree ◽  
Rt Pcr ◽  
Response Factors ◽  
Ethylene Response ◽  
Ethylene Response Factors ◽  
Expression Marker

Abstract Real-Time quantitative RT-PCR technique is a sensitive method for measuring the accumulation of gene transcripts. This widely used technique in a variety of plant species; including rubber tree (Hevea brasiliensis) must meet basic criteria in order to produce accurate gene expression markers. Gene expression markers associated to the response of ethephon stimulation such as the Hevea brasiliensis Ethylene Response Factors (HbERFs) family has been characterized in a single rubber clone. It is known that the effect of genotype on rubber tree clones can give different expression of the same gene. This difference can be converted into a profile that characterizes clones to a certain trait. This study aimed to identify gene expression profile in response to ethephon stimulation using six HbERFs (HbORA47, HbRAP2.3, HbERF12, HbERF3, HbABR1, HbRRTF1) in three rubber tree clones having contrasted latex metabolism (PB 260, SP 217, and RRIM 600). Total RNA was isolated from 18 samples and used for cDNA synthesis. The quality of cDNAs was examined by PCR using HbActin primer. HbRH2b was selected among the 11 housekeeping genes to be used as an internal control in gene expression analysis. Gene expression analysis resulted to an induction and inhibition of  HbERFs by ethephon stimulation which are specific to a particular clone. Expression profile of three Hevea clones showed distinct characteristics. The high latex metabolism clone PB 260 was characterized by the upregulated expression of  HbRAP2.3 and HbERF12. The low latex metabolism clone SP 217 was characterized by the upregulated expression of HbRAP2.3 and HbRRTF1. Meanwhile, the profile of intermediate latex metabolism clone RRIM 600 was shown by downregulated expression of HbORA47 and up-regulated expression of HbABR1. This study shows that HbERFs gene family is an important expression marker because it can inform physiological conditions of rubber clones associated in response to ethephon. AbstrakTeknik Real-Time quantitative RT-PCR merupakan metode sensitif untuk mengukur akumulasi transkrip dari gen. Teknik yang telah banyak digunakan pada berbagai spesies tanaman, termasuk tanaman karet (Hevea brasiliensis) ini harus memenuhi kriteria dasar agar meng-hasilkan marka ekspresi gen yang akurat. Beberapa marka ekspresi gen terkait respons terhadap stimulasi ethephon seperti famili gen Hevea brasiliensis Ethylene Response Factors (HbERFs) telah dikarakterisasi pada satu klon tanaman karet. Sebagaimana diketahui, efek genotip pada klon tanaman karet dapat memberikan ekspresi yang berbeda dari gen yang sama. Perbedaan ekspresi tersebut dapat dikonversi menjadi sebuah profil yang menjadi karakteristik klon karet terhadap perlakuan tertentu. Penelitian ini bertujuan untuk mengidentifikasi profil ekspresi gen HbERFs pada tiga klon tanaman karet (PB 260, SP 217, dan RRIM 600) yang memiliki metabolisme lateks yang berbeda terhadap respons stimulasi ethephon dengan menggunakan enam gen HbERFs (HbORA47, HbRAP2.3, HbERF12, HbERF3, HbABR1, HbRRTF1). RNA total diisolasi dari 18 sampel dan digunakan untuk sintesis cDNA. Kualitas cDNA diperiksa dengan PCR menggunakan primer HbActin. Gen HbRH2b terseleksi diantara 11 gen housekeeping digunakan sebagai kontrol internal pada analisis ekspresi gen. Hasil dari analisis ekspresi gen menunjukkan bahwa stimulasi ethephon memiliki efek induksi dan inhibisi gen yang spesifik untuk klon tertentu. Profil ekspresi dari tiga klon tanaman karet yang diuji memperlihatkan perbedaan karakteristik. Klon metabolisme tinggi PB 260 ditunjukkan dengan ekspresi positif dari gen HbRAP2.3 dan HbERF12. Klon meta-bolisme rendah SP 217 ditunjukkan oleh ekspresi positif gen HbRAP2.3 dan HbRRTF1. Sedangkan klon metabo-lisme intermedier RRIM 600 memiliki profil ekspresi negatif dari HbORA47 dan ekspresi positif dari HbABR1. Penelitian ini memperlihatkan bahwa famili gen HbERFs merupakan marka ekspresi yang penting karena dapat menginformasikan kondisi fisiologis klon tanaman karet terkait respons terhadap ethephon.

scholarly journals Respons molekuler Hevea brasiliensis ethylene response factors (HbERFs) sebagai marka ekspresi gen terhadap stimulasi ethephon pada klon-klon tanaman karet Moleculer response of Hevea brasiliensis ethylene response factors (HbERFs) as expression marker genes in response to ethephon stimulation in rubber tree clones

2016 ◽  
Vol 82 (2) ◽  
Author(s):  
Riza Arief PUTRANTO ◽  
. KUSWANHADI ◽  
Pascal MONTORO
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Hevea Brasiliensis ◽  
Gene Expression Analysis ◽  
Rubber Tree ◽  
Rt Pcr ◽  
Response Factors ◽  
Ethylene Response ◽  
Ethylene Response Factors ◽  
Expression Marker

Abstract Real-Time quantitative RT-PCR technique is a sensitive method for measuring the accumulation of gene transcripts. This widely used technique in a variety of plant species; including rubber tree (Hevea brasiliensis) must meet basic criteria in order to produce accurate gene expression markers. Gene expression markers associated to the response of ethephon stimulation such as the Hevea brasiliensis Ethylene Response Factors (HbERFs) family has been characterized in a single rubber clone. It is known that the effect of genotype on rubber tree clones can give different expression of the same gene. This difference can be converted into a profile that characterizes clones to a certain trait. This study aimed to identify gene expression profile in response to ethephon stimulation using six HbERFs (HbORA47, HbRAP2.3, HbERF12, HbERF3, HbABR1, HbRRTF1) in three rubber tree clones having contrasted latex metabolism (PB 260, SP 217, and RRIM 600). Total RNA was isolated from 18 samples and used for cDNA synthesis. The quality of cDNAs was examined by PCR using HbActin primer. HbRH2b was selected among the 11 housekeeping genes to be used as an internal control in gene expression analysis. Gene expression analysis resulted to an induction and inhibition of  HbERFs by ethephon stimulation which are specific to a particular clone. Expression profile of three Hevea clones showed distinct characteristics. The high latex metabolism clone PB 260 was characterized by the upregulated expression of  HbRAP2.3 and HbERF12. The low latex metabolism clone SP 217 was characterized by the upregulated expression of HbRAP2.3 and HbRRTF1. Meanwhile, the profile of intermediate latex metabolism clone RRIM 600 was shown by downregulated expression of HbORA47 and up-regulated expression of HbABR1. This study shows that HbERFs gene family is an important expression marker because it can inform physiological conditions of rubber clones associated in response to ethephon. AbstrakTeknik Real-Time quantitative RT-PCR merupakan metode sensitif untuk mengukur akumulasi transkrip dari gen. Teknik yang telah banyak digunakan pada berbagai spesies tanaman, termasuk tanaman karet (Hevea brasiliensis) ini harus memenuhi kriteria dasar agar meng-hasilkan marka ekspresi gen yang akurat. Beberapa marka ekspresi gen terkait respons terhadap stimulasi ethephon seperti famili gen Hevea brasiliensis Ethylene Response Factors (HbERFs) telah dikarakterisasi pada satu klon tanaman karet. Sebagaimana diketahui, efek genotip pada klon tanaman karet dapat memberikan ekspresi yang berbeda dari gen yang sama. Perbedaan ekspresi tersebut dapat dikonversi menjadi sebuah profil yang menjadi karakteristik klon karet terhadap perlakuan tertentu. Penelitian ini bertujuan untuk mengidentifikasi profil ekspresi gen HbERFs pada tiga klon tanaman karet (PB 260, SP 217, dan RRIM 600) yang memiliki metabolisme lateks yang berbeda terhadap respons stimulasi ethephon dengan menggunakan enam gen HbERFs (HbORA47, HbRAP2.3, HbERF12, HbERF3, HbABR1, HbRRTF1). RNA total diisolasi dari 18 sampel dan digunakan untuk sintesis cDNA. Kualitas cDNA diperiksa dengan PCR menggunakan primer HbActin. Gen HbRH2b terseleksi diantara 11 gen housekeeping digunakan sebagai kontrol internal pada analisis ekspresi gen. Hasil dari analisis ekspresi gen menunjukkan bahwa stimulasi ethephon memiliki efek induksi dan inhibisi gen yang spesifik untuk klon tertentu. Profil ekspresi dari tiga klon tanaman karet yang diuji memperlihatkan perbedaan karakteristik. Klon metabolisme tinggi PB 260 ditunjukkan dengan ekspresi positif dari gen HbRAP2.3 dan HbERF12. Klon meta-bolisme rendah SP 217 ditunjukkan oleh ekspresi positif gen HbRAP2.3 dan HbRRTF1. Sedangkan klon metabo-lisme intermedier RRIM 600 memiliki profil ekspresi negatif dari HbORA47 dan ekspresi positif dari HbABR1. Penelitian ini memperlihatkan bahwa famili gen HbERFs merupakan marka ekspresi yang penting karena dapat menginformasikan kondisi fisiologis klon tanaman karet terkait respons terhadap ethephon.

Characterization of rubber tree microRNA in phytohormone response using large genomic DNA libraries, promoter sequence and gene expression analysis

2014 ◽  
Vol 289 (5) ◽  
pp. 921-933 ◽  
Author(s):  
Supanath Kanjanawattanawong ◽  
Sithichoke Tangphatsornruang ◽  
Kanokporn Triwitayakorn ◽  
Panthita Ruang-areerate ◽  
Duangjai Sangsrakru ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Genomic Dna ◽  
Gene Expression Analysis ◽  
Rubber Tree ◽  
Promoter Sequence ◽  
Dna Libraries

scholarly journals Gene expression analysis and SNP/InDel discovery to investigate yield heterosis of two rubber tree F1 hybrids

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Dejun Li ◽  
Rizhong Zeng ◽  
Yan Li ◽  
Manman Zhao ◽  
Jinquan Chao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Rubber Tree ◽  
F1 Hybrids

scholarly journals Identification and evaluation of suitable reference genes for gene expression analysis in rubber tree leaf

2020 ◽  
Vol 47 (3) ◽  
pp. 1921-1933
Author(s):  
Xiangyu Long ◽  
Jilai Lu ◽  
Nat N. V. Kav ◽  
Yunxia Qin ◽  
Yongjun Fang
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Reference Genes ◽  
Gene Expression Analysis ◽  
Rubber Tree ◽  
Suitable Reference ◽  
Tree Leaf

scholarly journals RNA Sequencing Reveals Phenylpropanoid Biosynthesis Genes and Transcription Factors for Hevea brasiliensis Reaction Wood Formation

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiangxu Meng ◽  
Yue Wang ◽  
Jia Li ◽  
Nanbo Jiao ◽  
Xiujie Zhang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Rna Sequencing ◽  
Hevea Brasiliensis ◽  
Rubber Tree ◽  
Lignin Biosynthesis ◽  
Wood Formation ◽  
Industrial Applications ◽  
Normal Wood ◽  
Reaction Wood ◽  
Phenylpropanoid Biosynthesis

Given the importance of wood in many industrial applications, much research has focused on wood formation, especially lignin biosynthesis. However, the mechanisms governing the regulation of lignin biosynthesis in the rubber tree (Hevea brasiliensis) remain to be elucidated. Here, we gained insight into the mechanisms of rubber tree lignin biosynthesis using reaction wood (wood with abnormal tissue structure induced by gravity or artificial mechanical treatment) as an experimental model. We performed transcriptome analysis of rubber tree mature xylem from tension wood (TW), opposite wood (OW), and normal wood (NW) using RNA sequencing (RNA-seq). A total of 214, 1,280, and 32 differentially expressed genes (DEGs) were identified in TW vs. NW, OW vs. NW, and TW vs. OW, respectively. GO and KEGG enrichment analysis of DEGs from different comparison groups showed that zeatin biosynthesis, plant hormone signal transduction, phenylpropanoid biosynthesis, and plant–pathogen interaction pathways may play important roles in reaction wood formation. Sixteen transcripts involved in phenylpropanoid biosynthesis and 129 transcripts encoding transcription factors (TFs) were used to construct a TF–gene regulatory network for rubber tree lignin biosynthesis. Among them, MYB, C2H2, and NAC TFs could regulate all the DEGs involved in phenylpropanoid biosynthesis. Overall, this study identified candidate genes and TFs likely involved in phenylpropanoid biosynthesis and provides novel insights into the mechanisms regulating rubber tree lignin biosynthesis.

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