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Expression of TAD1 (Tillering & Dwarf1) Gene in Hawara Bunar and IR64 Rice Cultivars: Expression of TAD1 (Tillering & Dwarf1) Gene in Hawara Bunar and IR64 Sindiya, Vita; Fendiyanto, Miftahul Huda; Hamim, Hamim; Miftahudin , Miftahudin
Journal of Tropical Life Science Vol. 14 No. 3 (2024): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.03.11

Rice cv. Hawara Bunar is a local rice cultivar tolerant to aluminum (Al) and drought stress. However, the cultivar has inferior characteristics, such as a tall habitus and a small number of tillers, making the cultivar agronomically unattractive. Many genes control plant height and tiller number; one is the TAD1 gene. Analysis of gene expression in two contrasting rice cultivars for both characters is a prerequisite for selecting certain genes for gene editing targets. This study aimed to analyze the gene expression of the TAD1 in rice cv. IR64 and Hawara Bunar, and to construct a phylogenetic tree of genes that regulate rice plant height and tiller number. Gene expression analysis was conducted using the qRT-PCR technique, while the phylogenetic tree was constructed based on the Neighbor-Joining method using PAUP4 software. The results showed TAD1 gene expression in the tillering phase of rice cv. Hawara Bunar is higher than the cv. IR64. The gene expression level in both cultivars corresponds to the plant height and tiller number characters in both rice cultivars. Phylogenetic analysis showed that the TAD1 gene clustered with genes that cause the rice to have a tall habitus with few tillers. The results of a transcriptome meta-analysis reinforced the phylogenetic tree, which shows that the TAD1 gene was found in a group of downregulated genes based on the volcano plots. Therefore, the TAD1 gene can be selected as a target gene for editing in rice cv. Hawara Bunar to obtain superior characters.

KARAKTERISTIK PERTUMBUHAN BIBIT BATANG BAWAH KARET YANG DIAPLIKASIKAN CENDAWAN DSE (DARK SEPTATE ENDOPHYTE) Andriyanto, Mochlisin; HANUM, Chairani; HASANUDDIN, HASANUDDIN; FENDIYANTO, Miftahul Huda; DALIMUNTHE, Cici Indriani
Jurnal Penelitian Karet JPK : Volume 42, Nomor 2, Tahun 2024
Publisher : Pusat Penelitian Karet - PT. Riset Perkebunan Nusantara

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/ppk.jpk.v42i2.998

Pembibitan batang bawah karet seringkali terkendala oleh adanya penyakit jamur akar putih (JAP), morfologi akar pendek dan kerdil. Salah satu upaya untuk menekan hal tersebut dilakukan dengan inokulasi cendawan DSE. Banyak penelitian menunjukkan respon pertumbuhan tanaman tahunan dan musiman meningkat setelah diaplikasikan DSE. Keragaman cendawan DSE lokal perakaran karet asal Sumatera Utara belum banyak dieksplorasi dan diketahui efektivitas dalam pertumbuhan tanaman. Penelitian ini bertujuan untuk mendapatkan informasi pengaruh DSE terhadap pertumbuhan dan fisiologi tanaman batang bawah karet. Rancangan percobaan menggunakan Rancangan Acak Lengkap (RAK) non faktorial dengan perlakuan aplikasi DSE isolat KHPSG, KLAJI, KRPPT dan kontrol (non isolat). Parameter pengamatan yaitu tinggi, diameter, panjang tangkai daun, jumlah daun, kadar IAA daun, gula total, dan total klorofil. Hasil penelitian diketahui bahwa DSE mempengaruhi karakter pertumbuhan tinggi, diameter batang, panjang tangkai daun, jumlah munculnya daun, kadar IAA daun, gula total dan total klorofil. Pengaruh DSE pada tanaman di pembibitan batang bawah polibeg diketahui terjadi saat fase awal pertumbuhan. Isolat KHPSG dan KLAJI merupakan isolat terbaik dan berpotensi dapat dijadikan sebagai stimulan hayati tanaman.

Expression of TAD1 (Tillering & Dwarf1) Gene in Hawara Bunar and IR64 Rice Cultivars: Expression of TAD1 (Tillering & Dwarf1) Gene in Hawara Bunar and IR64 Sindiya, Vita; Fendiyanto, Miftahul Huda; Hamim, Hamim; Miftahudin , Miftahudin
Journal of Tropical Life Science Vol. 14 No. 3 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.03.11

Rice cv. Hawara Bunar is a local rice cultivar tolerant to aluminum (Al) and drought stress. However, the cultivar has inferior characteristics, such as a tall habitus and a small number of tillers, making the cultivar agronomically unattractive. Many genes control plant height and tiller number; one is the TAD1 gene. Analysis of gene expression in two contrasting rice cultivars for both characters is a prerequisite for selecting certain genes for gene editing targets. This study aimed to analyze the gene expression of the TAD1 in rice cv. IR64 and Hawara Bunar, and to construct a phylogenetic tree of genes that regulate rice plant height and tiller number. Gene expression analysis was conducted using the qRT-PCR technique, while the phylogenetic tree was constructed based on the Neighbor-Joining method using PAUP4 software. The results showed TAD1 gene expression in the tillering phase of rice cv. Hawara Bunar is higher than the cv. IR64. The gene expression level in both cultivars corresponds to the plant height and tiller number characters in both rice cultivars. Phylogenetic analysis showed that the TAD1 gene clustered with genes that cause the rice to have a tall habitus with few tillers. The results of a transcriptome meta-analysis reinforced the phylogenetic tree, which shows that the TAD1 gene was found in a group of downregulated genes based on the volcano plots. Therefore, the TAD1 gene can be selected as a target gene for editing in rice cv. Hawara Bunar to obtain superior characters.

Genome-Wide SNP Discovery and Population Structure Analysis of 244 Indonesian Local Rice Accessions Satrio, Rizky Dwi; Fendiyanto, Miftahul Huda; Nugroho, Satya; Hairmansis, Aris; Miftahudin
HAYATI Journal of Biosciences Vol. 33 No. 1 (2026): January 2026
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.33.1.142-152

Single Nucleotide Polymorphism (SNP) markers are essential tools for the genetic management and breeding of rice, enabling precise characterization of genetic diversity. However, SNP datasets specifically developed for analyzing the population structure of Indonesian local rice remain limited. This study aimed to identify polymorphic SNP markers and analyze the lineage and population structure of 244 Indonesian local rice accessions. BAM files of these accessions were obtained from the 3K Rice Genome Project via the International Rice Informatics Consortium. High-quality SNPs were generated through variant calling and stringent filtering, followed by annotation and population analyses using IR64, DJ123, and Nipponbare as references. A total of 3,839,961 high-quality SNP loci were identified across the 12 rice chromosomes. Hierarchical clustering and principal coordinate analysis consistently grouped the accessions into three major clusters, corresponding to Indica, Japonica, and admixed groups. Population structure analysis confirmed two main subpopulations: Indica and Japonica, with Japonica further divided into Temperate and Tropical subgroups. Eleven accessions showed admixed ancestry. This study provides essential insights into the genetic diversity and population structure of Indonesian local rice, supporting genetic resource conservation, trait discovery, and breeding efforts.

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