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SUSUMU SHIRAISHI
Laboratory of Silviculture, Faculty of Agriculture, Kyushu University, Fukuoka
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Immunology & microbiology Materials Science & Nanotechnology

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GEOGRAPHIC VARIATION OF CHLOROPLAST DNA HAPLOTYPES IN Acacia aulacocarpa A. Cunn. ex Benth Widyatmoko, Anthonius Y.P.B.C.; Shiraishi, Susumu
Indonesian Journal of Forestry Research Vol 10, No 1 (2013): Journal of Forestry Research
Publisher : Secretariat of Forestry Research and Development Agency

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Abstract

The geographic  variation  of chloroplast  DNA (cpDNA)  haplotypes  of Acacia aulacocar pa was investigated among 18 natural populations. These populations represent the geographical range of the species in New Guinea Island and Queensland. Single strand conformation polymorphism (SSCP) was used for the analysis. Two non-coding regions of cpDNA, the intron region of the trnL gene and the intergenic spacer region between the trnP and trnW genes, were analyzed, and four haplotypes (A, B, C, and D) were recognized. The haplotype distribution corresponded with the geographic distribution of the populations.  Based on four cpDNA haplotypes, the eighteen populations were divided into three groups: New Guinea Island, Northern  Queensland  and Southern Queensland.  Haplotype  C was observed only in the New Guinean populations, while the other three haplotypes (A, B, and D) were found in Queensland only. All of these three haplotypes were observed in Southern Queensland, whereas haplotype B was found only in the Northern Queensland populations. The cpDNA haplotype diversity of this species seemed to be highest in southern Queensland.
STUDY ON GENETIC VARIATION AND RELATIONSHIPS AMONG FOUR ACACIA SPECIES USING RAPD AND SSCP MARKER Widyatmoko, Anthonius Y.P.B.C.; Watanabe, Atsushi; Shiraishi, Susumu
Indonesian Journal of Forestry Research Vol 7, No 2 (2010): Journal of Forestry Research
Publisher : Secretariat of Forestry Research and Development Agency

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Abstract

Genetic diversity and relationship of four Acacia species, Acacia aulacocarpa, A. Cunn. ex Benth., A. auriculiformis Cunn. ex Benth., A. crassicarpa Cunn. ex Benth. and A. mangium Willd. were investigated using DNA molecular markers. Using RAPD analysis, a total of 20 arbitrar y primers successfully gave 127 polymorphic fragments. These RAPD data were used to estimate genetic distance and construct dendrograms using the unweighted pair-group with the arithmetic mean average (UPGMA) method. The four species were divided into two major clusters. A. auriculiformis and A. mangium were in one cluster, and the other cluster contained both A. aulacocarpa and A. crassicarpa. The divergence time of the two species (A. auriculiformis and A. mangium) in the former cluster appeared to be relatively early in comparison to in the latter (A. aulacocarpa and A. crassicarpa) based on RAPD data. This result was also supported by Principal Component Analysis (PCA). Among the four species, A. aulacocarpa showed the highest divergence in nuclear DNA (ncDNA), followed by A. auriculiformis. SSCP analysis also revealed that these two species possessed a haplotypic variation of the trnL-trnF intergenic spacer region of chloroplast DNA. In A. aulacocarpa, a large difference in the composition of both nuclear and chloroplast genomes was obser ved between populations distributed in Queensland, Australia and those in New Guinea Island. In contrast, compared to the other species, A. mangium showed the lowest genetic diversity and less genetic differentiation among populations.
SEQUENCE POLYMORPHISMS OF FOUR CHLOROPLAST GENES IN FOUR ACACIA SPECIES Widyatmoko, Anthonius Y.P.B.C.; Shiraishi, Susumu
Indonesian Journal of Forestry Research Vol 8, No 1 (2011): Journal of Forestry Research
Publisher : Secretariat of Forestry Research and Development Agency

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Abstract

Sequence polymorphisms among and within four Acacia species,  A. aulacocarpa, A. auriculiformis, A. crassicarpa, and A. mangium, were investigated using four chloroplast DNA genes (atpA, petA, rbcL, and rpoA). The phylogenetic relationship among these species is discussed in light of the results of the sequence information. No intraspecific sequence variation was found in the four genes of the four species, and a conservative rate of mutation of the chloroplast DNA genes was also confirmed in the Acacia species. In the atpA and petA of the four genes, all four species possessed identical sequences, and no sequence variation was found among the four Acacia species. In the rbcL and rpoA genes, however, sequence polymorphisms were revealed among these species. Acacia aulacocarpa and A. crassicarpa shared an identical sequence, and A. auriculiformis and A. mangium also showed no sequence variation.  The fact that A. mangium and A. auriculiformis shared identical sequences as did A. aulacocarpa and A. crassicarpa indicated that the two respective species were extremely closely related. Although a putative natural hybrid of A. aulacocarpa and A. auriculiformis has been reported, our results suggested that natural hybridization should be further verified using molecular markers.
EVALUATION FOR THE EFFICIENCY OF EARLY SELECTION IN Acacia mangium SEEDLING SEED ORCHARDS BASED ON AGE TRENDS IN GENETIC PARAMETER Nirsatmanto, Arif; Kurinobu, Susumu; Shiraishi, Susumu
Indonesian Journal of Forestry Research Vol 9, No 1 (2012): Journal of Forestry Research
Publisher : Secretariat of Forestry Research and Development Agency

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Abstract

The efficiency of early selection was evaluated based on age trend in genetic parameters using tree height data that was measured periodically repeatedly up to age 3 years of age in four seedling seed orchards of Acacia mangium at South Kalimantan, Indonesia. The four orchards were grouped into two populations based upon their provenances, namely: Papua New Guinea (PNG) and Far North Queensland-Australia (FNQ). A model for time trend of genetic parameters was developed by fitting regression equation to the estimates of variances and correlations using tree height data as an independent variable. In both populations, genetic variances and total phenotypic variances increased along with the mean height. Trend of individual heritability along the rotation ages were almost stable at around 0.19 for PNG, and gradually increased from 0.36 to 0.40 for FNQ. Trend of genetic correlations between selection age and rotation age increased rapidly starting at around 0.5 for PNG and 0.6 for FNQ, then exceeding 0.9 at age four years in both populations. Genetic gains due to indirect selection increased with age, in which the gains in FNQ were generally larger than those in PNG. Selection efficiency based on gain per year as a ratio of the gains from indirect selection to direct selection may conclude resulted the optimum age for selection at age two years old in both of PNG and FNQ population.
Micro - minisatellite marker for Acacia Widyatmoko, AYPC; Shiraishi, Susumu
Indonesian Journal of Biotechnology Vol 19, No 1 (2014)
Publisher : Universitas Gadjah Mada

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Abstract

Indonesian Journal of Biotechnology.
Inter- and intraspecifi c variation of chloroplast mini- and microsatellites DNA in the four closed related Acacia species Widyatmoko, AYPBC; Shiraishi, Susumu
Indonesian Journal of Biotechnology Vol 19, No 1 (2014)
Publisher : Universitas Gadjah Mada

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Abstract

Mini- and microsatellites of four Acacia species, A. aulacocarpa, A. auriculiformis, A. crassicarpa and A.mangium were investigated on four non-coding regions of cpDNA, the intron of trnL, and the intergenicspacers of trnL - trnP, trnD - trnY, and trnP – trnW. Nine single base substitutions and six informative miniandmicrosatellites were detected in the the four cpDNA non-coding regions. Based on the substitutionsand mini- and microsatellites, ten cpDNA haplotypes (A - J) could be distinguished. Acacia auriculiformispossessed fi ve haplotypes, A. aulacocarpa, four haplotypes, and A. crassicarpa, three haplotypes. All samplesof A. mangium possessed the same haplotype. Mini- and microsatellites recognized in this study can beused for species identifi cation of the four Acacia species. The ten haplotypes could divided the four speciesinto 2 groups, A. aulacocarpa-A.crassicarpa group and A. auriculiformis-A. mangium group. By developing thePCR-based markers based on the sequence information, many experiments can be carried out for the Acaciaimprovement programs.
EVALUATION FOR THE EFFICIENCY OF EARLY SELECTION IN Acacia mangium SEEDLING SEED ORCHARDS BASED ON AGE TRENDS IN GENETIC PARAMETER Nirsatmanto, Arif; Kurinobu, Susumu; Shiraishi, Susumu
Indonesian Journal of Forestry Research Vol 9, No 1 (2012): Journal of Forestry Research
Publisher : Secretariat of Forestry Research and Development Agency

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20886/ijfr.2012.9.1.16-24

Abstract

The efficiency of early selection was evaluated based on age trend in genetic parameters using tree height data that was measured periodically repeatedly up to age 3 years of age in four seedling seed orchards of Acacia mangium at South Kalimantan, Indonesia. The four orchards were grouped into two populations based upon their provenances, namely: Papua New Guinea (PNG) and Far North Queensland-Australia (FNQ). A model for time trend of genetic parameters was developed by fitting regression equation to the estimates of variances and correlations using tree height data as an independent variable. In both populations, genetic variances and total phenotypic variances increased along with the mean height. Trend of individual heritability along the rotation ages were almost stable at around 0.19 for PNG, and gradually increased from 0.36 to 0.40 for FNQ. Trend of genetic correlations between selection age and rotation age increased rapidly starting at around 0.5 for PNG and 0.6 for FNQ, then exceeding 0.9 at age four years in both populations. Genetic gains due to indirect selection increased with age, in which the gains in FNQ were generally larger than those in PNG. Selection efficiency based on gain per year as a ratio of the gains from indirect selection to direct selection may conclude resulted the optimum age for selection at age two years old in both of PNG and FNQ population.
GEOGRAPHIC VARIATION OF CHLOROPLAST DNA HAPLOTYPES IN Acacia aulacocarpa A. Cunn. ex Benth Widyatmoko, Anthonius Y.P.B.C.; Shiraishi, Susumu
Indonesian Journal of Forestry Research Vol 10, No 1 (2013): Journal of Forestry Research
Publisher : Secretariat of Forestry Research and Development Agency

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20886/ijfr.2013.10.1.43-56

Abstract

The geographic  variation  of chloroplast  DNA (cpDNA)  haplotypes  of Acacia aulacocar pa was investigated among 18 natural populations. These populations represent the geographical range of the species in New Guinea Island and Queensland. Single strand conformation polymorphism (SSCP) was used for the analysis. Two non-coding regions of cpDNA, the intron region of the trnL gene and the intergenic spacer region between the trnP and trnW genes, were analyzed, and four haplotypes (A, B, C, and D) were recognized. The haplotype distribution corresponded with the geographic distribution of the populations.  Based on four cpDNA haplotypes, the eighteen populations were divided into three groups: New Guinea Island, Northern  Queensland  and Southern Queensland.  Haplotype  C was observed only in the New Guinean populations, while the other three haplotypes (A, B, and D) were found in Queensland only. All of these three haplotypes were observed in Southern Queensland, whereas haplotype B was found only in the Northern Queensland populations. The cpDNA haplotype diversity of this species seemed to be highest in southern Queensland.
STUDY ON GENETIC VARIATION AND RELATIONSHIPS AMONG FOUR ACACIA SPECIES USING RAPD AND SSCP MARKER Widyatmoko, Anthonius Y.P.B.C.; Watanabe, Atsushi; Shiraishi, Susumu
Indonesian Journal of Forestry Research Vol 7, No 2 (2010): Journal of Forestry Research
Publisher : Secretariat of Forestry Research and Development Agency

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20886/ijfr.2010.7.2.125-143

Abstract

Genetic diversity and relationship of four Acacia species, Acacia aulacocarpa, A. Cunn. ex Benth., A. auriculiformis Cunn. ex Benth., A. crassicarpa Cunn. ex Benth. and A. mangium Willd. were investigated using DNA molecular markers. Using RAPD analysis, a total of 20 arbitrar y primers successfully gave 127 polymorphic fragments. These RAPD data were used to estimate genetic distance and construct dendrograms using the unweighted pair-group with the arithmetic mean average (UPGMA) method. The four species were divided into two major clusters. A. auriculiformis and A. mangium were in one cluster, and the other cluster contained both A. aulacocarpa and A. crassicarpa. The divergence time of the two species (A. auriculiformis and A. mangium) in the former cluster appeared to be relatively early in comparison to in the latter (A. aulacocarpa and A. crassicarpa) based on RAPD data. This result was also supported by Principal Component Analysis (PCA). Among the four species, A. aulacocarpa showed the highest divergence in nuclear DNA (ncDNA), followed by A. auriculiformis. SSCP analysis also revealed that these two species possessed a haplotypic variation of the trnL-trnF intergenic spacer region of chloroplast DNA. In A. aulacocarpa, a large difference in the composition of both nuclear and chloroplast genomes was obser ved between populations distributed in Queensland, Australia and those in New Guinea Island. In contrast, compared to the other species, A. mangium showed the lowest genetic diversity and less genetic differentiation among populations.
SEQUENCE POLYMORPHISMS OF FOUR CHLOROPLAST GENES IN FOUR ACACIA SPECIES Widyatmoko, Anthonius Y.P.B.C.; Shiraishi, Susumu
Indonesian Journal of Forestry Research Vol 8, No 1 (2011): Journal of Forestry Research
Publisher : Secretariat of Forestry Research and Development Agency

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20886/ijfr.2011.8.1.79-89

Abstract

Sequence polymorphisms among and within four Acacia species,  A. aulacocarpa, A. auriculiformis, A. crassicarpa, and A. mangium, were investigated using four chloroplast DNA genes (atpA, petA, rbcL, and rpoA). The phylogenetic relationship among these species is discussed in light of the results of the sequence information. No intraspecific sequence variation was found in the four genes of the four species, and a conservative rate of mutation of the chloroplast DNA genes was also confirmed in the Acacia species. In the atpA and petA of the four genes, all four species possessed identical sequences, and no sequence variation was found among the four Acacia species. In the rbcL and rpoA genes, however, sequence polymorphisms were revealed among these species. Acacia aulacocarpa and A. crassicarpa shared an identical sequence, and A. auriculiformis and A. mangium also showed no sequence variation.  The fact that A. mangium and A. auriculiformis shared identical sequences as did A. aulacocarpa and A. crassicarpa indicated that the two respective species were extremely closely related. Although a putative natural hybrid of A. aulacocarpa and A. auriculiformis has been reported, our results suggested that natural hybridization should be further verified using molecular markers.
Co-Authors Anthonius Y.P.B.C. Widyatmoko Arif Nirsatmanto Atsushi Watanabe AYPBC Widyatmoko, AYPBC AYPC Widyatmoko, AYPC Susumu Kurinobu VIVI YUSKIANTI