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All Journal Jurnal Hortikultura Indonesia (JHI) Jurnal Ilmu Komputer dan Informasi Communication in Biomathematical Sciences
Adi Pancoro
Sekolah Ilmu Teknologi dan Hayati, Institut Teknologi Bandung, Jalan Ganesha No. 10, Bandung 40132
Agriculture, Biological Sciences & Forestry Computer Science & IT Library & Information Science Social Sciences

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Linear Mixed Model for Oil Palm Parents Selection Sonhaji, Abdullah; Pasaribu, Udjianna Sekteria; Indratno, Sapto Wahyu; Pancoro, Adi
Communication in Biomathematical Sciences Vol. 8 No. 1 (2025)
Publisher : The Indonesian Bio-Mathematical Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/cbms.2025.8.1.3

Abstract

The objective of plant breeding is to obtain superior seeds. These seeds originated from parents that can pass their superior traits to their progeny. The observed characteristics of the progeny (phenotype) determined the traits of these seeds. Therefore, we performed a progeny analysis. In this analysis, the data samples were collected from Riau in Sumatera and Kumai in Kalimantan (two locations). The main objective is to find superior parents from these two locations. The superiority of the selected parents lies not only in passing high production traits but also in adaptability (fit) to the diversity or variability of the environment or locations. This analysis calculates the General Combining Ability (GCA) values for both male and female parents using the Linear Mixed Model (LMM). The experimental design, as the source of data, was an alpha lattice design, so the LMM contains locations, replicas, blocks, male and female parents, and the progeny factors. The analyzed phenotype is Fresh Fruit Bunches of third-year production. Since the data sets of the two locations were nonintersect, the model uses the coefficient of parentage (additive relationship matrix) to link both. The results of the GCA analysis showed that selected female parents were 137, 155, 126, 147, and 159 (Dura), and 101, 113, 109, and 117 for male parents. They are among the parents with highly productive progenies. There are also new potential crossings not currently available on the plantation - for example, the crossing 137 x 101 with the additive genetic value of 35.37.
The Effect of Drought Stress on Phyllanthin and Quercetin Contents of Green Meniran Plant (Phyllanthus niruri L.): Pengaruh Cekaman Kekeringan terhadap Kandungan Filantin dan Kuersetin Tanaman Meniran Hijau (Phyllanthus niruri L.) Nailulkamal Djamas; Pancoro, Adi; Devy, Lukita; E
Jurnal Hortikultura Indonesia (JHI) Vol. 15 No. 2 (2024): Jurnal Hortikultura Indonesia (JHI)
Publisher : Indonesian Society for Horticulture / Department of Agronomy and Horticulture

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jhi.15.2.112-118

Abstract

Penelitian tentang pengaruh cekaman kekeringan terhadap produksi filantin dan kuersetin pada meniran hijau (Phyllanthus niruri L.) telah dilakukan. Tujuan penelitian yaitu: Menentukan dampak cekaman kekeringan terhadap pertumbuhan vegetatif tanaman meniran hijau dan menentukan taraf kapasitas lapang serta waktu panen yang optimal untuk memperoleh konsentrasi optimal filantin dan kuersetin. Penelitian dilakukan dari September 2021 hingga September 2022 di Laptiab BRIN menggunakan tiga taraf Kapasitas Lapang (KL) (30, 60 dan 100%) dan dua waktu panen (2 dan 4 minggu). Parameter yang diamati adalah parameter morfologi serta kandungan filantin dan kuersetin. Hasil penelitian menunjukkan bahwa cekaman kekeringan dan waktu panen memberikan perbedaan yang nyata pada kandungan filantin dan tidak berbeda nyata pada kandungan kuersetin. Kandungan filantin tertinggi diperoleh pada 100% KL dan waktu panen 4 minggu setelah tanam (MST). Kesimpulan dari penelitian ini adalah: Cekaman kekeringan dapat mengurangi pertumbuhan vegetatif dari tanaman meniran hijau dan untuk memperoleh pertumbuhan vegetatif yang optimal, meniran hijau sebaiknya tidak diberikan cekaman kekeringan; Untuk memperoleh kandungan filantin dari tanaman meniran hijau dengan tingkat kandungan yang paling tinggi, taraf kapasitas lapang dan waktu panen yang optimal adalah pada 100% KL dan waktu panen empat minggu; Kandungan kuersetin dari meniran hijau tidak dipengaruhi secara signifikan oleh perbedaan taraf cekaman kekeringan dan waktu panen. Kata kunci : rekayasa irigasi, pertumbuhan vegetatif tanaman, rekayasa metabolit sekunder, teknik budidaya tanaman obat, waktu panen
Detecting Type and Index Mutation in Cancer DNA Sequence Based on Needleman–Wunsch Algorithm Wisesty, Untari Novia; Mengko, Tati Rajab; Purwarianti, Ayu; Pancoro, Adi
Jurnal Ilmu Komputer dan Informasi Vol. 17 No. 2 (2024): Jurnal Ilmu Komputer dan Informasi (Journal of Computer Science and Informatio
Publisher : Faculty of Computer Science - Universitas Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21609/jiki.v17i2.1273

Abstract

Detecting DNA sequence mutations in cancer patients contributes to early identification and treatment of the disease, which ultimately enhances the effectiveness of treatment. Bioinformatics utilizes sequence alignment as a powerful tool for identifying mutations in DNA sequences. We used the Needleman-Wunsch algorithm to identify mutations in DNA sequence data from cancer patients. The cancer sequence dataset used includes breast, cervix uteri, lung, colon, liver and prostate cancer. Various types of mutations were identified, such as Single Nucleotide Variant (SNV)/substitution, insertion, and deletion, locate by the nucleotide index. The Needleman Wunch algorithm can detect type and index mutation with the average F1-scores 0.9507 for all types of mutations, 0.9919 for SNV, 0.7554 for insertion, and 0.8658 for deletion with a tolerance of 5 bp. The F1-scores obtained are not correlated with gene length. The time required ranges from 1.03 seconds for a 290 base pair gene to 3211.45 seconds for a gene with 16613 base pairs.
Co-Authors Ayu Purwarianti E Indratno, Sapto Wahyu Lukita Devy Mengko, Tati Rajab Nailulkamal Djamas Pasaribu, Udjianna Sekteria Sonhaji, Abdullah Untari Novia Wisesty