Epigenetic Regulation on Plant Stress Memory

Plants are sessile organisms; they cannot move like animals when the environment is not favorable. Therefore, plants need a mechanism to cope with environmental changes. For example, when a plant experiences stress, like water deficit, it will employ a certain mechanism that allows the plant to survive the next exposure (see Fig. 1), often referred to as “Epigenetic” regulation. By application, epigenetics deals with the changes of the level of the gene expression without change in the DNA sequence, by DNA methylation, histone modifications, and or small RNA regulation. Plant epigenetic regulation is related to the Lamarckian theory of evolution. Lamarck’s (1744 – 1829) discredited theory of how transgenerational memory could be passed down through generations became one possible explanation for how plants become more resistant to future stress through acquisition of memory (see Fig. 2). Basically, an unnecessary gene (stress gene) is turned off. However, during stress, plant cells need to reactivate the genes by removing silencing marks, but the longer it is activated, the more prone the plant is to stress. The learning process can be induced and referred as priming. In the basic mechanism of priming, the histone demethylase enzyme unwinds the specific DNA regions that contain stress genes and remove the silent marks; thus it can be expressed more rapidly to tackle unfavorable condition compare to unprimed plants (consult the Figure 3). Remarkably, this working model of epigenetic transgenerational memory has also been applied for generating resistant plants with the same epigenetic mark by tissue culture propagation technique, which had been impossible to achieve previously (see Figure 4)

Hd3a Florigen Recruits Different Proteins to Reveal Its Function in Plant Growth and Development

The nature of Hd3a protein in rice and its ortholog FT in Arabidopsis as a florigen has been proposed. However, molecular mechanism of its function still remains to be investigated. Therefore, it is important to search their interaction partners to better understand their signaling in flowering. As a long-distance signal that moves along leaf cells and the vascular system of leaves and stem and exerts its action in apical buds, it is important to determine the possible mediators of such common responses activated by Hd3a. To search Hd3a interactor, yeast two-hybrid screening have performed by using a cDNA library. A wide range of Hd3a interacting proteins involved in signaling were identified, including GF14c, OsKANADI and the BRI1 kinase domain interacting protein 116b (BIP116b). To reveal its function, Hd3a recruits different protein in plant developmental stage. It is possible that Hd3a and its partner(s) may form a platform for cross-talk between signal transduction pathways. Another homolog of Hd3a in many plants was identified and sugessted that Hd3a/FT has versatile role in plant development. This role depend on its partner and interaction to achieve its function. Our understanding in floral transition in rice would make for better crop management in future

NMR metabolite comparison of local pigmented rice in Yogyakarta

Pigmented rice may have a black or red color due to higher anthocyanin content in its grain. A natural antioxidant, many studies on anthocyanin have reported its positive effects on human health. This fact has spurred the development of pigmented rice as a functional food. This study aimed to compare the metabolite profiles of black and red rice. Three black rice cultivars, namely Melik, Pari Ireng, and Cempo Ireng Sleman, and two red rice cultivars, Inpari 24 and RC 204, were used. After husk removal, grain samples were ground in liquid nitrogen and dried with a freeze dryer. The dried samples were extracted using 50% MeOD4 (in a D2O phosphate buffer pH 6 containing 0.01% TSP as an internal standard). Metabolomic analysis was performed using 500 MHz NMR followed by multivariate data analysis. An orthogonal partial least squares-discriminant analysis (OPLS-DA) model ađer PCA was constructed to discriminate between the five different cultivars. The resulting OPLS-DA score plot revealed a clear separation between black rice and red rice. The metabolites that could influence the separation of red rice and black rice were valine, threonine, alanine, glutamate, galactinol, β-glucose, α-glucose, raffinose, and fumaric acid

MORFOLOGI POLEN DAN PEMBERIAN SUKROSA PADA STIGMA KAITANNYA DENGAN INKOMPATIBILITAS UBIJALAR [Ipomoea batatas (L.) L.]

ABSTRAK   Susanto, Febri Adi. 2012. Morfologi Polen dan Pemberian Sukrosa pada Stigma Kaitannya dengan Inkompatibilitas Ubijalar [Ipomoea batatas (L.) L.]. Skripsi, Jurusan Biologi, Fakultas Matematika dan Ilmu Pengetahuan Alam, Universitas Negeri Malang. Pembimbing: (I) Dra. Eko Sri Sulasmi, M.S., (II) Ir. St. A. Rahayuningsih, M.S.   Kata Kunci: morfologi polen, pemberian sukrosa, inkompatibilitas ubijalar. Terbatasnya pilihan varietas unggul ubijalar [Ipomoea batatas (L.) L.] bagi petani merupakan permasalahan yang harus diatasi. Upaya dalam program pemuliaan untuk menghasilkan varietas baru terus dilakukan. Adanya inkompatibilitas pada ubijalar dapat manghambat program tersebut. Penelitian ini bertujuan untuk meningkatkan keberhasilan persilangan dengan menanggulangi mekanisme inkompatibilitas melalui pemberian sukrosa pada stigma dan pemeriksaan morfologi polen. Varietas Papua Solosa dan klon harapan MSU 03028-10 dipilih sebagai tetua persilangan. Penelitian deskriptif kuantitatif dengan mengamati jumlah inti polen, jarak antera stigma, viabilitas polen, reseptivitas putik, dan pengukuran kadar sukrosa putik. Penelitian eksperimen menggunakan rancangan acak kelompok (RAK). Perlakuan berupa konsentrasi sukrosa, yaitu 0 ppm (S0) kontrol, 50 ppm (S1), 100 ppm (S2), dan 150 ppm (S3) pada persilangan ubijalar. Parameter yang diamati adalah persentase (%) terbentuknya buah. Setiap perlakuan dilakukan pada 10 bunga yang diulang sebanyak 3 kali. Persilangan dengan metode soda straw. Persilangan yang dilakukan, yaitu persilangan sendiri Papua Solosa, persilangan sendiri MSU 03028-10, dan persilangan Papua Solosa

MORFOLOGI POLEN DAN PEMBERIAN SUKROSA PADA STIGMA KAITANNYA DENGAN INKOMPATIBILITAS UBIJALAR [Ipomoea batatas (L.) L.]

ABSTRAK   Susanto, Febri Adi. 2012. Morfologi Polen dan Pemberian Sukrosa pada Stigma Kaitannya dengan Inkompatibilitas Ubijalar [Ipomoea batatas (L.) L.]. Skripsi, Jurusan Biologi, Fakultas Matematika dan Ilmu Pengetahuan Alam, Universitas Negeri Malang. Pembimbing: (I) Dra. Eko Sri Sulasmi, M.S., (II) Ir. St. A. Rahayuningsih, M.S.   Kata Kunci: morfologi polen, pemberian sukrosa, inkompatibilitas ubijalar. Terbatasnya pilihan varietas unggul ubijalar [Ipomoea batatas (L.) L.] bagi petani merupakan permasalahan yang harus diatasi. Upaya dalam program pemuliaan untuk menghasilkan varietas baru terus dilakukan. Adanya inkompatibilitas pada ubijalar dapat manghambat program tersebut. Penelitian ini bertujuan untuk meningkatkan keberhasilan persilangan dengan menanggulangi mekanisme inkompatibilitas melalui pemberian sukrosa pada stigma dan pemeriksaan morfologi polen. Varietas Papua Solosa dan klon harapan MSU 03028-10 dipilih sebagai tetua persilangan. Penelitian deskriptif kuantitatif dengan mengamati jumlah inti polen, jarak antera stigma, viabilitas polen, reseptivitas putik, dan pengukuran kadar sukrosa putik. Penelitian eksperimen menggunakan rancangan acak kelompok (RAK). Perlakuan berupa konsentrasi sukrosa, yaitu 0 ppm (S0) kontrol, 50 ppm (S1), 100 ppm (S2), dan 150 ppm (S3) pada persilangan ubijalar. Parameter yang diamati adalah persentase (%) terbentuknya buah. Setiap perlakuan dilakukan pada 10 bunga yang diulang sebanyak 3 kali. Persilangan dengan metode soda straw. Persilangan yang dilakukan, yaitu persilangan sendiri Papua Solosa, persilangan sendiri MSU 03028-10, dan persilangan Papua Solosa>i varietas Papua Solosa/span, MSU 03028-10, dan persilangan Papua Solosa

Seed Halopriming Improves Salinity Tolerance of Some Rice Cultivars During Seedling Stage

ackground: Saline land in coastal areas has great potential for crop cultivation. Improving salt tolerance in rice is a key to expanding the available area for its growth and thus improving global food security. Seed priming with salt (halopriming) can enhance plant growth and decrease saline intolerance under salt stress conditions during the subsequent seedling stage. However, there is little known about rice defense mechanisms against salinity at seedling stages after seed halopriming treatment. This study focused on the effect of seed halopriming treatment on salinity tolerance in a susceptible cultivar, IR 64, a resistant cultivar, Pokkali, and two pigmented rice cultivars, Merah Kalimantan Selatan (Merah Kalsel) and Cempo Ireng Pendek (CI Pendek). We grew these cultivars in hydroponic culture, with and without halopriming at the seed stage, under either non-salt or salt stress conditions during the seedling stage. Results: The SES scoring assessment showed that the level of salinity tolerance in susceptible cultivar, IR 64, and moderate cultivar, Merah Kalsel, improved after seed halopriming treatment. Furthermore, seed halopriming improved the growth performance of IR 64 and Merah Kalsel rice seedlings. Quantitative PCR revealed that seed halopriming induced expression of the OsNHX1 and OsHKT1 genes in susceptible rice cultivar, IR 64 and Merah Kalsel thereby increasing the level of resistance to salinity. The expression levels of OsSOS1 and OsHKT1 genes in resistant cultivar, Pokkali, also increased but there was no affect on the level of salinity tolerance. On the contrary, seed halopriming decreased the expression level of OsSOS1 genes in pigmented rice cultivar, CI Pendek, but did not affect the level of salinity tolerance. The transporter gene expression induction significantly improved salinity tolerance in salinity-susceptible rice, IR 64, and moderately tolerant rice cultivar, Merah Kalsel. Induction of expression of the OsNHX1 and OsHKT1 genes in susceptible rice, IR 64, after halopriming seed treatment balances the osmotic pressure and prevents the accumulation of toxic concentrations of Na+, resulting in tolerance to salinity stress. Conclusion: These results suggest that seed halopriming can improve salinity tolerance of salinity-susceptible and moderately tolerant rice cultivars. © 2022, The Author(s)

Metabolite Profiling of Black Rice (Oryza sativa L.) Following Xanthomonas oryzae pv. oryzae Infection

Black rice as a functional food contains a high anthocyanin content, which functions as an antioxidant. However, bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) has resulted in a reduction in yield. Black rice has been reported to have a higher resistance to BLB than white rice cultivars. This study aimed to determine the metabolite responses of two black rice cultivars, �Melik' and �Pari Ireng', compared to two white rice cultivars, �IR64' and �Java14', after infection with Xoo pathotype IV and mock negative control. Gas Chromatography-Mass Spectrometer (GC-MS) was used for the metabolite profiling analysis, followed by the quantification of total phenolic concentration (TPC) and total flavonoid concentration (TFC). Across all cultivars, the results revealed that following Xoo infection, there were significantly higher concentrations of primary metabolites including sugars, sugar alcohols, fatty acids, glycerol, and some organic acids. In �Pari Ireng' and �Melik' cultivars, sugars including fructose, and gluco-hexodialdose were significantly higher than the white cultivars following the infection. The infection significantly increased the TPC of all cultivars. �Java 14� contained the highest TPC while �Pari Ireng� was observed as cultivars with the highest TFC. These results suggested that pigmented rice cultivars possess a different chemical defense strategy from the white ones to respond to Xoo infection. © 2021 Jordan Journal of Biological Sciences. All Rights Reserved

RWP-RK Domain 3 (OsRKD3) induces somatic embryogenesis in black rice

Background: Plants have the unique capability to form embryos from both gametes and somatic cells, with the latter process known as somatic embryogenesis. Somatic embryogenesis (SE) can be induced by exposing plant tissues to exogenous growth regulators or by the ectopic activation of embryogenic transcription factors. Recent studies have revealed that a discrete group of RWP-RK DOMAIN-CONTAINING PROTEIN (RKD) transcription factors act as key regulators of germ cell differentiation and embryo development in land plants. The ectopic overexpression of reproductive RKDs is associated with increased cellular proliferation and the formation of somatic embryo-like structures that bypass the need for exogenous growth regulators. However, the precise molecular mechanisms implicated in the induction of somatic embryogenesis by RKD transcription factors remains unknown. Results: In silico analyses have identified a rice RWP-RK transcription factor, named Oryza sativa RKD3 (OsRKD3), which is closely related to Arabidopsis thaliana RKD4 (AtRKD4) and Marchantia polymorpha RKD (MpRKD) proteins. Our study demonstrates that the ectopic overexpression of OsRKD3, which is expressed preferentially in reproductive tissues, can trigger the formation of somatic embryos in an Indonesian black rice landrace (Cempo Ireng) that is normally resistant to somatic embryogenesis. By analyzing the transcriptome of induced tissue, we identified 5,991 genes that exhibit differential expression in response to OsRKD3 induction. Among these genes, 50 were up-regulated while the other half were down-regulated. Notably, approximately 37.5 of the up-regulated genes contained a sequence motif in their promoter region, which was also observed in RKD targets from Arabidopsis. Furthermore, OsRKD3 was shown to mediate the transcriptional activation of a discrete gene network, which includes several transcription factors such as APETALA 2-like (AP2-like)/ETHYLENE RESPONSE FACTOR (ERF), MYB and CONSTANS-like (COL), and chromatin remodeling factors associated with hormone signal transduction, stress responses and post-embryonic pathways. Conclusions: Our data show that OsRKD3 modulates an extensive gene network and its activation is associated with the initiation of a somatic embryonic program that facilitates genetic transformation in black rice. These findings hold substantial promise for improving crop productivity and advancing agricultural practices in black rice. © 2023, The Author(s)

RWP-RK Domain 3 (OsRKD3) induces somatic embryogenesis in black rice

Abstract Background Plants have the unique capability to form embryos from both gametes and somatic cells, with the latter process known as somatic embryogenesis. Somatic embryogenesis (SE) can be induced by exposing plant tissues to exogenous growth regulators or by the ectopic activation of embryogenic transcription factors. Recent studies have revealed that a discrete group of RWP-RK DOMAIN-CONTAINING PROTEIN (RKD) transcription factors act as key regulators of germ cell differentiation and embryo development in land plants. The ectopic overexpression of reproductive RKDs is associated with increased cellular proliferation and the formation of somatic embryo-like structures that bypass the need for exogenous growth regulators. However, the precise molecular mechanisms implicated in the induction of somatic embryogenesis by RKD transcription factors remains unknown. Results In silico analyses have identified a rice RWP-RK transcription factor, named Oryza sativa RKD3 (OsRKD3), which is closely related to Arabidopsis thaliana RKD4 (AtRKD4) and Marchantia polymorpha RKD (MpRKD) proteins. Our study demonstrates that the ectopic overexpression of OsRKD3, which is expressed preferentially in reproductive tissues, can trigger the formation of somatic embryos in an Indonesian black rice landrace (Cempo Ireng) that is normally resistant to somatic embryogenesis. By analyzing the transcriptome of induced tissue, we identified 5,991 genes that exhibit differential expression in response to OsRKD3 induction. Among these genes, 50% were up-regulated while the other half were down-regulated. Notably, approximately 37.5% of the up-regulated genes contained a sequence motif in their promoter region, which was also observed in RKD targets from Arabidopsis. Furthermore, OsRKD3 was shown to mediate the transcriptional activation of a discrete gene network, which includes several transcription factors such as APETALA 2-like (AP2-like)/ETHYLENE RESPONSE FACTOR (ERF), MYB and CONSTANS-like (COL), and chromatin remodeling factors associated with hormone signal transduction, stress responses and post-embryonic pathways. Conclusions Our data show that OsRKD3 modulates an extensive gene network and its activation is associated with the initiation of a somatic embryonic program that facilitates genetic transformation in black rice. These findings hold substantial promise for improving crop productivity and advancing agricultural practices in black rice

Additional file 6 of RWP-RK Domain 3 (OsRKD3) induces somatic embryogenesis in black rice

Additional file 6: Unprocessed gel images