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All Journal Pelita Perkebunan AGRIVITA, Journal of Agricultural Science
Erwin Prastowo
Indonesian Coffee and Cocoa Research Insitute
Agriculture, Biological Sciences & Forestry

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In silico study of RKD4 gene function in Coffea arabica L. and various cultivated plants related to embryo formation initiation Arimarsetiowati, Rina; Semiarti, Endang; Daryono, Budi Setiadi; Astuti, Yohana Theresia Maria; Prastowo, Erwin
Pelita Perkebunan (a Coffee and Cocoa Research Journal) Vol. 40 No. 2 (2024)
Publisher : Indonesian Coffee and Cocoa Research Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iccri.jur.pelitaperkebunan.v40i2.600

Abstract

Arabica coffee supplies 60% of world coffee production because has a unique taste as superior quality beverage. Arabica coffee micropropagation can be conducted by somatic embryogenesis technique which produce clonal, fast dan uniform plant. The somatic embryogenesis (SE) process describes the integration of endogenous signals and gene reprogramming, which releases signals to initiate embryogenic processes. The use of endogenous auxin, either alone or in combination with other PGRs or stress, induces differential gene expression, which modifies the genetic program of somatic cells and regulates the transition to each stage during SE development. The RKD4 gene (RWP-RK DOMAIN-4) is a gene that plays a role in early initiation embryo formation and development. The characterization of RKD4 genes in C. arabica is still limited and under explored. The objective of this research is to explore the characteristics of RKD4 gene by comparing the difference and similarity of RKD4 gene in C. arabica and other cultivated plants. The method was initiate by identifying nucleotide sequences from the National Center for Biotechnology Information (NCBI) database. Furthermore, consists of analysis of nucletide alignment, alignment of amino acid sequences, protein analysis, protein motif functions discovery, analysis of phylogenetic tree, protein 2D and 3D-modelling and physiochemical properties. According to the analysis, there were 100 polymorphism points with a total number of mutations of 211 points. The phylogenetic tree show C. arabica L. has a very close relationship with grapes (Vitis vinivera) based on the RKD4 protein, gene structures and protein motifs. There are nine highly conserved motifs found in the protein alignment. C. arabica L. had more methyl jasmonate element responses than A. thaliana. The findings are useful to understand the intitiation of embryo formation mechanisms of C. arabica L and other cultivate plants during propagation through somatic embryogenesis in the long run.
Responses of Two Cocoa Varieties to Environmental Stress Conditions Fuadati, Ayu Zahrotul; Prastowo, Erwin; Munawarti, Aminatun; Arimarsetiowati, Rina
AGRIVITA Journal of Agricultural Science Vol 47, No 2 (2025)
Publisher : Faculty of Agriculture University of Brawijaya in collaboration with PERAGI

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.17503/agrivita.v47i2.4425

Abstract

Environmental changes resulting from climate anomalies may have significant implications for the future of global cocoa sustainability. A study was conducted to investigate the responses of two different cocoa varieties, i.e., ICCRI 06H and ICCRI 08H, to various environmental conditions at the greenhouse scale. Two distinct factors, i.e., green-house microclimate and soil moisture level, were simulated in a split-split plot design. A glass box equipped with artificial light was installed to modify the ambient temperature and air humidity, providing two different conditions: inside (IB) and outside (OB) the glass box, assigned as the main plot. The performance of cocoa seedlings was tested as a subplot, and they were exposed to different soil moisture levels, i.e., 100% soil moisture (ETa1), 50% soil moisture (ETa2), and 25% soil moisture (ETa3), defined as sub-subplot. Data suggested a slight difference in daily air temperature and relative humidity fluctuations, in both plots, observed as a function of time. A higher response of the stomatal index and density, up to 20%, was found in the ETa3 treatment for ICCRI 08H. The stress simulation increased the ICCRI 08H proline by up to 36% and guaiacol peroxidase by 27% higher than ICCRI 06H.
Co-Authors Aminatun Munawarti, Aminatun Arimarsetiowati, Rina BUDI SETIADI DARYONO Endang Semiarti Fuadati, Ayu Zahrotul Yohana Theresia Maria Astuti, Yohana Theresia Maria