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Ida Rosdianti
Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development
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GENOMIC VARIATION OF FIVE INDONESIAN CACAO (Theobroma cacao L.) VARIETIES BASED ON ANALYSIS USING NEXT GENERATION SEQUENCING I Made Tasma; Dani Satyawan; Habib Rijzaani; Ida Rosdianti; Puji Lestari; Rubiyo Rubiyo
Indonesian Journal of Agricultural Science Vol 17, No 2 (2016): October 2016
Publisher : Indonesian Agency for Agricultural Research and Development

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21082/ijas.v17n2.2016.p57-64

Abstract

Indonesian cacao productivity is still low mainly due to the lack availability of superior cacao planting materials. A new breeding method is necessary to expedite cacao yield improvement programs. To date, no study has yet been done to characterize Indonesian cacao varieties at the whole genome level. The objective of this study was to characterize genomic variation of five superior Indonesian cacao varieties using next-generation sequencing. Genetic materials used were five Indonesian cacao varieties, i.e. ICCRI2, ICCRI3, ICCRI4, SUL2 and ICS13. Genome sequences were mapped to the cacao reference genome sequence of Criollo variety. Sequence alignment and genomic variation discovery were done using Bowtie2 and mpileup software of Samtools, respectively. A total of 2,326,088 single nucleotide polymorphisms (SNPs) and 362,081 insertions and deletions (Indels) were obtained from this study. In average, a DNA variant was identified in every 121 nucleotides of the genome sequence. Most of the DNA variants were located outside the genes. Only 347,907 SNPs and Indels (13.18%) were located within protein coding region (exon).  Among the DNA variations within exon, 188,949 SNPs caused missense mutation and 1,535 SNPs induced nonsense mutation.  Unique gene-based SNPs were also discovered from this study that can be used as fingerprints for the particular cacao variety. The DNA variants obtained were excellent DNA marker resources to support cacao breeding programs. The SNPs discovered are useful as materials for genome-wide SNP chip development to be used for gene and QTL tagging of important traits for expediting national cacao breeding program.
IDENTIFICATION OF IRON TOLERANT CANDIDATE LOCI IN RICE DETERMINED THROUGH GENOME-WIDE ASSOCIATION STUDY Dwinita Wikan Utami, M.Si.; Ida Rosdianti; Lili Chrisnawati; Subardi Subardi; Siti Nurani; Suwarno Suwarno
Indonesian Journal of Agricultural Science Vol 21, No 1 (2020): June 2020
Publisher : Indonesian Agency for Agricultural Research and Development

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21082/ijas.v21n1.2020.p17-29

Abstract

Iron (Fe) toxicity is a significant abiotic stress in swamp land. The study aimed to identify the candidate loci related to Fe toxicity tolerance through Genome-Wide Association Study (GWAS) approach.  The study used 288 rice accessions consisting of 192 breeding lines and 50 local landraces, and custom-designed 384 rice SNPs-chips. A field evaluation was conducted in inland swamp for two season periods (2014 and 2015). Phenotypic data and association mapping were analyzed using XLSTAT and TASSEL 3.0. The candidate loci were analyzed by functional gene detection of the significant SNPs aligned to the Rice Annotation Project and the Institute for Genomic Research databases. Three linkage disequilibrium (LD) blocks were detected in the Fe tolerant population around the significant SNPs. The first LD block was mapped in chromosome 1 (the AtIRT gene and qFETOX1; qFETOX1-3 QTLs loci) resembled partitioning of Fe-toxicity tolerant mechanism. The second LD blocks located in chromosome 2 (qFE-TOX-2-1 and qFETOX-2 QTLs loci) and chromosome 3 (qFETOX-3 QTL, OsNAS1 and OsNAS2 loci), probably contributed to Fe exclusion mechanism. The third LD blocks located in chromosome 4 (OsFRO2 and qFETOX-4 QTL loci) and chromosome 7 (OsIRT2 and NAS3 loci). The third LD block found on tolerant genotypes both on vegetative and generative stages. This condition indicated that these loci were presumed playing a role for Fe toxicity tolerance in rice. Result of the study are beneficial for determining the strategy on developing Fe-toxicity tolerant rice for specific swamp land type through breeding programs.
Co-Authors Dani Satyawan Dwinita Wikan Utami, M.Si. Habib Rijzaani I Made Tasma Lili Chrisnawati PUJI LESTARI Rubiyo Rubiyo Siti Nurani Subardi Subardi Suwarno Suwarno