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All Journal Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Jurnal Biologi Tropis ANNALES BOGORIENSES
Mia Kosmiatin
Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian, Jalan Tentara Pelajar 3A, Bogor 16111
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Economics, Econometrics & Finance Immunology & microbiology Medicine & Pharmacology

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Characterization Of Zygotic And Nucellar Embryo Of Six Indonesian Mango Cultivars Using Molecular Markers Fatimah, Fatimah; Husni, Ali; Kosmiatin, Mia; Karsinah, Karsinah; Baroya, Mushlihatun
ANNALES BOGORIENSES Vol 20, No 2 (2016): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (458.762 KB) | DOI: 10.14203/ann.bogor.2016.v20.n2.69-75

Abstract

Breeding mangoes is a long term activity and complicated. One of difficulties is polyembryonic seeds. These factors make genetic improvement through conventional parental selection and breeding slow and unpredictable. Adoption of molecular markers and genomics-based breeding strategies will likely improve predictability and breeding efficiency. The objective of this study was to evaluate the occurrence of zygotic or nucellar in polyembryony mango cultivars Garifta Merah, Lalijiwo, Manalagi, Madu, Saigon Kuning, and Saigon Merah using RAPD and SSR markers. The type of embryo (zygotic or nucellar) was evaluated by comparing the exhibiting amplification patterns, if different from the mother plant considered as zygotic and identified as nucellar if they exhibited the same banding pattern as the mother plant. Out of the 16 SSR and 16 RAPD primers evaluated, 9 primers each amplified the largest number of allele and sharply defined band. Dendogram of the SSR primers divide into three groups while RAPD primers distinguish clearly into two major groups, zygotic group and nucellar group. Based on zygotic and nucellar size, number and position, indicating no relationship between the type of embryo and embryo size, number and the position. 
Molecular diversity of citrus genotypes using callose synthase 7 gene markers linked to Huanglongbing resistance Nugroho, Kristianto; Purwito, Agus; Sukma, Dewi; Kosmiatin, Mia; Santoso, Tri Joko; Husni, Ali; Martasari, Chaireni; Lestari, Puji
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol. 53 No. 2 (2025): Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy)
Publisher : Indonesia Society of Agronomy (PERAGI) and Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24831/jai.v53i2.64952

Abstract

Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus, is a notable disease affecting citrus plantations globally. Several studies showed that the callose synthase 7 gene is crucial for the citrus defense system against this pathogen. The study aimed to analyze the nucleotide variations and genetic diversity among several citrus genotypes using specific gene primers designed from the callose synthase 7 gene sequence. Genomic DNA from eleven citrus genotypes was amplified using the specific primers, and Sanger sequencing was employed to identify the nucleotide sequence of the PCR products. The results revealed a total of 66 single-nucleotide polymorphisms (SNPs), 10 insertions, and 11 deletions were detected in callose synthase 7 gene fragment sequences. Of these, one out of five noteworthy SNPs identified at a position of 200 bp downstream of the START codon showed distinguishing features between susceptible and resistant/tolerant genotypes. Phylogenetic analysis clearly discriminated the eleven citrus genotypes into two clusters at a dissimilarity coefficient of 0.05, with all genotypes grouped in the first cluster, except for the Chinese box orange and orange jasmine. The identification of notable SNPs in this study can aid in developing new markers for the rapid selection of genotypes with enhanced HLB resistance in citrus breeding programs.   Keywords: Candidatus Liberibacter asiaticus; nucleotide variations; Sanger sequencing; phylogenetic analysis; SNP
Nucleotide variations of WRKY70 gene sequence related to Huanglongbing resistance in citrus Nugroho, Kristianto; Purwito, Agus; Sukma, Dewi; Kosmiatin, Mia; Santoso, Tri Joko; Reflinur, Reflinur; Mastur, Mastur
Jurnal Biologi Tropis Vol. 25 No. 4 (2025): in Progress
Publisher : Biology Education Study Program, Faculty of Teacher Training and Education, University of Mataram, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29303/jbt.v25i4.10092

Abstract

Huanglongbing, inflicted by Candidatus Liberibacter asiaticus in Asia region, is a destructive disease affecting citrus productions worlwide. Several studies have identified resistance genes that play essential roles in the citrus defense system against this pathogen. The goals of this study were to design the specific gene primers from the WRKY70 gene sequence and analyze the nucleotide variations and genetic diversity among several citrus genotypes. Genomic DNA from nine citrus genotypes were amplified using WRKY70-specific gene primers and the products of PCR were sent to Sanger sequencing, while the sequences of the other 12 genotypes were collected from Citrus Genome Database. The results revealed a total of 282 nucleotide variations which consisted of 157 SNPs, 28 insertions, and 97 deletions, were identified in the WRKY70 gene fragment sequence. There were three notable SNPs detected, with only one SNP [C/T] in first intron area at the position of 524 bp downstream from START codon that showed its ability to distinguish between susceptible and tolerant/resistant citrus genotypes. The phylogenetic analysis also revealed the clearly separation among citrus genotypes in two main clusters. The discovery of this SNP is useful for designing a functional marker as a screening tool in citrus breeding program in the future.
Co-Authors Agus Purwito Ali Husni Baroya, Mushlihatun Chaireni Martasari Desyandri Desyandri Dewi Sukma fatimah Fatimah KRISTIANTO NUGROHO, KRISTIANTO Mastur Mastur PUJI LESTARI REFLINUR REFLINUR TRI JOKO SANTOSO