Pub Date : 2016-04-01DOI: 10.21082/ijas.v17n1.2016.p35-40
I. Riyadi, S. Sumaryono
The application of gamma irradiation on plant materials may increase the genetic variation of the offspring with useful traits. The experiment was conducted to determine the effect of irradiation dosage of gamma ray on growth and development of sago palm (Metroxylon sagu) calli. Friable calli of sago palm derived from suspension culture were used as a material source. The primary calli were initiated from apical meristematic tissues of sago palm suckers of Alitir variety from Merauke, Papua. The treatments used were dosage of gamma ray irradiation at 0, 5, 10, 15, 20 and 25 Gy. The treated calli were then subcultured on modified Murashige and Skoog (MMS) solid medium containing 3% sucrose and 0.1% activated charcoal and added with 1 mg l-1 2,4-D and 0.1 mg l-1 kinetin. The results showed that at all irradiation dosages, calli biomass increased significantly. The highest proliferation of calli biomass of 5.33 folds from the initial culture after 4 weeks was achieved at gamma irradiation of 25 Gy, whereas the lowest proliferation of calli biomass of 3.4 folds was achieved at control. The best development of embryogenic calli was obtained at 10 Gy that produced 100% somatic embryos, whereas the lowest somatic embryo formation at 0% was obtained at 0 and 25 Gy after one subculture. High response of somatic embryo induction to gamma irradiation at 10 Gy may increase production of somatic embryos. These results can be used in in vitro breeding of sago palm via mutagenesis to create new elite varieties.
{"title":"EFFECT OF GAMMA IRRADIATION ON THE GROWTH AND DEVELOPMENT OF SAGO PALM (Metroxylon sagu Rottb.) CALLI","authors":"I. Riyadi, S. Sumaryono","doi":"10.21082/ijas.v17n1.2016.p35-40","DOIUrl":"https://doi.org/10.21082/ijas.v17n1.2016.p35-40","url":null,"abstract":"The application of gamma irradiation on plant materials may increase the genetic variation of the offspring with useful traits. The experiment was conducted to determine the effect of irradiation dosage of gamma ray on growth and development of sago palm (Metroxylon sagu) calli. Friable calli of sago palm derived from suspension culture were used as a material source. The primary calli were initiated from apical meristematic tissues of sago palm suckers of Alitir variety from Merauke, Papua. The treatments used were dosage of gamma ray irradiation at 0, 5, 10, 15, 20 and 25 Gy. The treated calli were then subcultured on modified Murashige and Skoog (MMS) solid medium containing 3% sucrose and 0.1% activated charcoal and added with 1 mg l-1 2,4-D and 0.1 mg l-1 kinetin. The results showed that at all irradiation dosages, calli biomass increased significantly. The highest proliferation of calli biomass of 5.33 folds from the initial culture after 4 weeks was achieved at gamma irradiation of 25 Gy, whereas the lowest proliferation of calli biomass of 3.4 folds was achieved at control. The best development of embryogenic calli was obtained at 10 Gy that produced 100% somatic embryos, whereas the lowest somatic embryo formation at 0% was obtained at 0 and 25 Gy after one subculture. High response of somatic embryo induction to gamma irradiation at 10 Gy may increase production of somatic embryos. These results can be used in in vitro breeding of sago palm via mutagenesis to create new elite varieties.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-04-01DOI: 10.21082/ijas.v17n1.2016.p17-26
N. Izzah, R. Reflinur, Tae-Jin Yang
Development of Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) markers derived from public database is known to be more efficient, faster and low cost. The objective of this study was to generate a new set of EST-SSR markers for broccoli and its related species and their usefulness for assessing their genetic diversity. A total of 202 Brassica oleracea ESTs were retrieved from NCBI and then assembled into 172 unigenes by means of CAP3 program. Identification of SSRs was carried out using web-based tool, RepeatMasker software. Afterwards, EST-SSR markers were developed using Primer3 program. Among the identified SSRs, trinucleotide repeats were the most common repeat types, which accounted for about 50%. A total of eight primer pairs were successfully designed and yielded amplification products. Among them, five markers were polymorphic and displayed a total of 30 alleles with an average number of six alleles per locus. The polymorphic markers were subsequently used for analyzing genetic diversity of 36 B. oleracea cultivars including 22 broccoli, five cauliflower and nine kohlrabi cultivars based on genetic similarity matrix as implemented in NTSYS program. At similarity coefficient of 61%, a UPGMA clustering dendrogram effectively separated 36 genotypes into three main groups, where 30 out of 36 genotypes were clearly discriminated. The result obtained in the present study would help breeders in selecting parental lines for crossing. Moreover, the novel EST-SSR markers developed in the study could be a valuable tool for differentiating cultivars of broccoli and related species.
{"title":"Development Of Est-ssr Markers To Assess Genetic Diversity Of Broccoli And Its Related Species","authors":"N. Izzah, R. Reflinur, Tae-Jin Yang","doi":"10.21082/ijas.v17n1.2016.p17-26","DOIUrl":"https://doi.org/10.21082/ijas.v17n1.2016.p17-26","url":null,"abstract":"Development of Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) markers derived from public database is known to be more efficient, faster and low cost. The objective of this study was to generate a new set of EST-SSR markers for broccoli and its related species and their usefulness for assessing their genetic diversity. A total of 202 Brassica oleracea ESTs were retrieved from NCBI and then assembled into 172 unigenes by means of CAP3 program. Identification of SSRs was carried out using web-based tool, RepeatMasker software. Afterwards, EST-SSR markers were developed using Primer3 program. Among the identified SSRs, trinucleotide repeats were the most common repeat types, which accounted for about 50%. A total of eight primer pairs were successfully designed and yielded amplification products. Among them, five markers were polymorphic and displayed a total of 30 alleles with an average number of six alleles per locus. The polymorphic markers were subsequently used for analyzing genetic diversity of 36 B. oleracea cultivars including 22 broccoli, five cauliflower and nine kohlrabi cultivars based on genetic similarity matrix as implemented in NTSYS program. At similarity coefficient of 61%, a UPGMA clustering dendrogram effectively separated 36 genotypes into three main groups, where 30 out of 36 genotypes were clearly discriminated. The result obtained in the present study would help breeders in selecting parental lines for crossing. Moreover, the novel EST-SSR markers developed in the study could be a valuable tool for differentiating cultivars of broccoli and related species.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-10-13DOI: 10.21082/IJAS.V15N2.2014.P79-85
S. D. Indrasari, S. D. Ardhiyanti, B. Abdullah
Rice is an important source of vitamin B1 and folic acid, but cultivated rice cultivars contain low of these nutrient. Breeding program had been conducted and several advanced lines with a high vitamin B and folic acid contents were found. This research aimed to study the contents of vitamin B1 and folic acid in the brown rice and milled rice of fifteen promising lowland rice lines. Dried paddy (14% moisture content) were husked in the mini husker (Satake THU 35A) to obtain brown rice and milled rice by using abrasive-type mini polisher (Satake TM-05, 1,450 RPM for 2 minutes). Vitamin B1 and folic acid in the brown rice and milled rice were determined by using HPLC equipped with fluorescence detector for vitamin B1 and UV detector for folic acid. Four out of fifteen rice lines studied showed a unique characteristic of vitamin B1 content in the brown rice and milled rice. Rice lines which have highest vitamin B1 in the brown rice were B10267-4-PN-6-2-3-2-2-2-3-3-2 (3.03 mg 100 g-1), B10876H-MR-2 (2.13 mg 100 g-1), B10531E-KN-1-2-PN-1-4-2 (1.33 mg 100 g-1) and B12411E-RS*-1-2-1 (1.21 mg 100 g-1). However after milling, 43-92% of their vitamin B1 were lost; the least loss was observed in B12411E-RS*-1-2-1 (1.21 mg 100 g-1) which was only 4%. Three out of fifteen rice lines studied has highest folic acid in brown rice, i.e. BP400G-PN-12-3-6 (158.5 µg 100 g-1), B10876H-MR-2 (152.0 µg 100 g-1), and B11742-RS*-2-3-MR-5-5-1-Si-1-3 (100.0 µg 100 g-1). After milling the line B10876H-MR-2 had the highest folic acid content (52.0 µg 100 g-1), much higher than that of Ciherang variety as a control. This study indicates the importance of having a suitable milling instrument to minimize loss of vitamin B1 and folic acid. The study also suggests the importance of creating new rice cultivars that have high nutrient and resistant to milling process.
{"title":"STUDY OF MILLING PROCESS AND ITS EFFECT ON VITAMIN B1 AND FOLIC ACID CONTENTS ON LOWLAND RICE PROMISING LINES","authors":"S. D. Indrasari, S. D. Ardhiyanti, B. Abdullah","doi":"10.21082/IJAS.V15N2.2014.P79-85","DOIUrl":"https://doi.org/10.21082/IJAS.V15N2.2014.P79-85","url":null,"abstract":"Rice is an important source of vitamin B1 and folic acid, but cultivated rice cultivars contain low of these nutrient. Breeding program had been conducted and several advanced lines with a high vitamin B and folic acid contents were found. This research aimed to study the contents of vitamin B1 and folic acid in the brown rice and milled rice of fifteen promising lowland rice lines. Dried paddy (14% moisture content) were husked in the mini husker (Satake THU 35A) to obtain brown rice and milled rice by using abrasive-type mini polisher (Satake TM-05, 1,450 RPM for 2 minutes). Vitamin B1 and folic acid in the brown rice and milled rice were determined by using HPLC equipped with fluorescence detector for vitamin B1 and UV detector for folic acid. Four out of fifteen rice lines studied showed a unique characteristic of vitamin B1 content in the brown rice and milled rice. Rice lines which have highest vitamin B1 in the brown rice were B10267-4-PN-6-2-3-2-2-2-3-3-2 (3.03 mg 100 g-1), B10876H-MR-2 (2.13 mg 100 g-1), B10531E-KN-1-2-PN-1-4-2 (1.33 mg 100 g-1) and B12411E-RS*-1-2-1 (1.21 mg 100 g-1). However after milling, 43-92% of their vitamin B1 were lost; the least loss was observed in B12411E-RS*-1-2-1 (1.21 mg 100 g-1) which was only 4%. Three out of fifteen rice lines studied has highest folic acid in brown rice, i.e. BP400G-PN-12-3-6 (158.5 µg 100 g-1), B10876H-MR-2 (152.0 µg 100 g-1), and B11742-RS*-2-3-MR-5-5-1-Si-1-3 (100.0 µg 100 g-1). After milling the line B10876H-MR-2 had the highest folic acid content (52.0 µg 100 g-1), much higher than that of Ciherang variety as a control. This study indicates the importance of having a suitable milling instrument to minimize loss of vitamin B1 and folic acid. The study also suggests the importance of creating new rice cultivars that have high nutrient and resistant to milling process.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-10-01DOI: 10.21082/ijas.v16n2.2015.pp.59-70
P. Lestari, H. Rijzaani, D. Satyawan, A. Anggraeni, D. Utami, I. Rosdianti, Muchamad Lutfi, I. M. Tasma
Single nucleotide polymorphisms (SNPs) abundant in bovine genome influence genetic variation in biological mechanism. The study aimed to identify SNPs on Indonesian cattle breeds and analyze their genetic diversity using Bovine 50K SNP chip. Twenty eight "Ongole Grade" (OG) beef cattle and 20 "Holstein Friesian" (HF) dairy cattle were used for the Infinium II assay test. This assay included amplification of genomic DNA, fragmenta-tion, precipitation, resuspension, hybridization, processing bead chip for single-base extension, and imaging at iScan. Data and clusters were analyzed using GenomeStudio software. The Bovine 50K SNP chip containing 54,609 SNPs was observed spanning all chromosomes of bovine genome. Genotyping for the total SNPs was successfull based on Call Rate, GeneCall and GeneTrain scores. Most SNP markers had alleles that shared among the individuals or breeds, or had specific alleles at distinctive frequencies. Minor allele frequency (MAF) spreads equally with intervals of 0-0.5. The breeds of OG and HF tended to be separated in different clusters without considering their genetic history and twin or normal. This result suggests that most individuals are closely related to one another, regardless of the same breed. Some genes identified on chromosomes 3, 4, 5, 7, 13, 17 and 18 were located in the loci/regions that contained SNPs with specific alleles of either HF or OG breed. These SNPs were more powerful for differentiation of beef cattle and dairy cattle than among individuals in the same breed. These SNP variations and genetic relatedness among individuals and breeds serve basic information for cattle breeding in Indonesia.
{"title":"IDENTIFICATION OF SINGLE NUCLEOTIDE POLYMORPHISMS ON CATTLE BREEDS IN INDONESIA USING BOVINE 50K","authors":"P. Lestari, H. Rijzaani, D. Satyawan, A. Anggraeni, D. Utami, I. Rosdianti, Muchamad Lutfi, I. M. Tasma","doi":"10.21082/ijas.v16n2.2015.pp.59-70","DOIUrl":"https://doi.org/10.21082/ijas.v16n2.2015.pp.59-70","url":null,"abstract":"Single nucleotide polymorphisms (SNPs) abundant in bovine genome influence genetic variation in biological mechanism. The study aimed to identify SNPs on Indonesian cattle breeds and analyze their genetic diversity using Bovine 50K SNP chip. Twenty eight \"Ongole Grade\" (OG) beef cattle and 20 \"Holstein Friesian\" (HF) dairy cattle were used for the Infinium II assay test. This assay included amplification of genomic DNA, fragmenta-tion, precipitation, resuspension, hybridization, processing bead chip for single-base extension, and imaging at iScan. Data and clusters were analyzed using GenomeStudio software. The Bovine 50K SNP chip containing 54,609 SNPs was observed spanning all chromosomes of bovine genome. Genotyping for the total SNPs was successfull based on Call Rate, GeneCall and GeneTrain scores. Most SNP markers had alleles that shared among the individuals or breeds, or had specific alleles at distinctive frequencies. Minor allele frequency (MAF) spreads equally with intervals of 0-0.5. The breeds of OG and HF tended to be separated in different clusters without considering their genetic history and twin or normal. This result suggests that most individuals are closely related to one another, regardless of the same breed. Some genes identified on chromosomes 3, 4, 5, 7, 13, 17 and 18 were located in the loci/regions that contained SNPs with specific alleles of either HF or OG breed. These SNPs were more powerful for differentiation of beef cattle and dairy cattle than among individuals in the same breed. These SNP variations and genetic relatedness among individuals and breeds serve basic information for cattle breeding in Indonesia.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-10-01DOI: 10.21082/ijas.v16n2.2015.pp.51-58
E. Listanto, E. I. Riyanti, T. Santoso, T. Hadiarto, A. D. Ambarwati
Development of potato cultivars with high levels of broad spectrum resistance is a key long-term management strategy against late blight disease caused by Phytophthora infestans. Six progeny lines of hybridization between transgenic potato Katahdin SP951 with non-transgenic Granola and Atlantic were selected based on agronomical characteristics and resistance to late blight disease. The study aimed to analyze the number of insertions and stability of inserted RB gene in the transgenic potato lines. The research was carried out through plant DNA extraction, southern blot analysis and polymerase chain reaction (PCR). Southern blot analysis was used to detect the number of inserts integrated into potato genome, while PCR analysis was used to detect stability of RB gene from generation to generation. The results showed that the progenies obtained from hybridization between Atlantic and transgenic Katahdin SP951 (lines No. 20 and 27) and between Granola and transgenic Katahdin SP951 (line No. 69) contained one copy number of RB gene, according to the probing of nptII. The result is similar to that of inserted RB gene found in the parental transgenic Katahdin SP951. The presence of RB gene in four different generations (G0, G1, G2 and G3) showed stable integration of the gene into the plant genome. The single copy number of RB gene will repress the occurrence of silencing gene expression. The stability analysis of RB gene can determine that the gene is still present in plant genome after several generations.
{"title":"GENETIC STABILITY ANALYSIS OF RB GENE IN GENETICALLY MODIFIED POTATO LINES TOLERANT TO Phytophthora infestans","authors":"E. Listanto, E. I. Riyanti, T. Santoso, T. Hadiarto, A. D. Ambarwati","doi":"10.21082/ijas.v16n2.2015.pp.51-58","DOIUrl":"https://doi.org/10.21082/ijas.v16n2.2015.pp.51-58","url":null,"abstract":"Development of potato cultivars with high levels of broad spectrum resistance is a key long-term management strategy against late blight disease caused by Phytophthora infestans. Six progeny lines of hybridization between transgenic potato Katahdin SP951 with non-transgenic Granola and Atlantic were selected based on agronomical characteristics and resistance to late blight disease. The study aimed to analyze the number of insertions and stability of inserted RB gene in the transgenic potato lines. The research was carried out through plant DNA extraction, southern blot analysis and polymerase chain reaction (PCR). Southern blot analysis was used to detect the number of inserts integrated into potato genome, while PCR analysis was used to detect stability of RB gene from generation to generation. The results showed that the progenies obtained from hybridization between Atlantic and transgenic Katahdin SP951 (lines No. 20 and 27) and between Granola and transgenic Katahdin SP951 (line No. 69) contained one copy number of RB gene, according to the probing of nptII. The result is similar to that of inserted RB gene found in the parental transgenic Katahdin SP951. The presence of RB gene in four different generations (G0, G1, G2 and G3) showed stable integration of the gene into the plant genome. The single copy number of RB gene will repress the occurrence of silencing gene expression. The stability analysis of RB gene can determine that the gene is still present in plant genome after several generations.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-10-01DOI: 10.21082/ijas.v16n2.2015.pp.71-78
Rubiyo Rubiyo, N. Izzah, I. Sulistiyorini, C. Tresniawati
Kolaka, which is located in Southeast Sulawesi, has long been known as one of cacao production centers in Indonesia. Therefore, many different cacao germplasms can be found in this region. The study aimed to evaluate genetic diversity and relationships of 12 cacao genotypes collected from Kolaka. Genomic DNA was extracted by using a modified CTAB method. Meanwhile, genetic diversity was analyzed based on 16 SSR markers, which then separated by 6% non-denaturing polyacryl-amide gel electrophoresis. The result showed that all of those markers, 14 markers exhibited polymorphism and subsequently used for data analysis using NTSYS and PowerMarker program. About 70 different alleles were generated from 12 cacao genotypes analyzed with an average of 5 alleles per locus. Average value of polymorphism information content (PIC) resulted in this study was 0.59. The cluster analysis using UPGMA method based on the genetic similarity coefficient revealed that all cacao genotypes were separated into three major groups. The first group consisted of five cacao genotypes, the second one held four cacao genotypes, whereas the third group contained three genotypes. This result indicates that three genotypes that clustered separately from the others could be used as a good clonal candidate for cacao breeding program. The information resulted from this present study would be useful for future cacao breeding program, especially in efforts to release a new variety.
{"title":"EVALUATION OF GENETIC DIVERSITY IN CACAO COLLECTED FROM KOLAKA, SOUTHEAST SULAWESI, USING SSR MARKERS","authors":"Rubiyo Rubiyo, N. Izzah, I. Sulistiyorini, C. Tresniawati","doi":"10.21082/ijas.v16n2.2015.pp.71-78","DOIUrl":"https://doi.org/10.21082/ijas.v16n2.2015.pp.71-78","url":null,"abstract":"Kolaka, which is located in Southeast Sulawesi, has long been known as one of cacao production centers in Indonesia. Therefore, many different cacao germplasms can be found in this region. The study aimed to evaluate genetic diversity and relationships of 12 cacao genotypes collected from Kolaka. Genomic DNA was extracted by using a modified CTAB method. Meanwhile, genetic diversity was analyzed based on 16 SSR markers, which then separated by 6% non-denaturing polyacryl-amide gel electrophoresis. The result showed that all of those markers, 14 markers exhibited polymorphism and subsequently used for data analysis using NTSYS and PowerMarker program. About 70 different alleles were generated from 12 cacao genotypes analyzed with an average of 5 alleles per locus. Average value of polymorphism information content (PIC) resulted in this study was 0.59. The cluster analysis using UPGMA method based on the genetic similarity coefficient revealed that all cacao genotypes were separated into three major groups. The first group consisted of five cacao genotypes, the second one held four cacao genotypes, whereas the third group contained three genotypes. This result indicates that three genotypes that clustered separately from the others could be used as a good clonal candidate for cacao breeding program. The information resulted from this present study would be useful for future cacao breeding program, especially in efforts to release a new variety.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-10-01DOI: 10.21082/ijas.v16n2.2015.pp.79-86
A. Muis, N. Nonci, M. Pabendon
The compulsory requirement for releasing new high yielding maize varieties is resistance to downy mildew. The study aimed to determine the level of homozygosity, genetic diversity, and genetic distance of 30 S3 genotypes of maize. Number of primers to be used were 30 polymorphic SSR loci which are distributed over the entire maize genomes. The S3 genotypes used were resistant to downy mildew with homozygosity level of >80%, genetic distance between the test and tester strains >0.7, and anthesis silking interval (ASI) between inbred lines and tester lines was maximum 3 days. The results showed that 30 SSR primers used were spread evenly across the maize genomes which were manifested in the representation of SSR loci on each chromosome of a total of 10 chromosomes. The levels of polymorphism ranged from 0.13 to 0.78, an average of 0.51, and the number of alleles ranged from 2 to 8 alleles per SSR locus, an average of 4 alleles per SSR locus. The size of nucleotides in each locus also varied from 70 to 553 bp. Cophenetic correlation value (r) at 0.67 indicated that the Unweighted Pair-Group Method Using Arithmetic Averages (UPGMA) was less reliable for differentiating genotypes in five groups. Of the total of 30 genotypes analyzed, 17 genotypes had homozygosity level of >80% so it can be included in the hybrid assembly program.
{"title":"GENETIC DIVERSITY OF S3 MAIZE GENOTYPES RESISTANT TO DOWNY MILDEW BASED ON SSR MARKERS","authors":"A. Muis, N. Nonci, M. Pabendon","doi":"10.21082/ijas.v16n2.2015.pp.79-86","DOIUrl":"https://doi.org/10.21082/ijas.v16n2.2015.pp.79-86","url":null,"abstract":"The compulsory requirement for releasing new high yielding maize varieties is resistance to downy mildew. The study aimed to determine the level of homozygosity, genetic diversity, and genetic distance of 30 S3 genotypes of maize. Number of primers to be used were 30 polymorphic SSR loci which are distributed over the entire maize genomes. The S3 genotypes used were resistant to downy mildew with homozygosity level of >80%, genetic distance between the test and tester strains >0.7, and anthesis silking interval (ASI) between inbred lines and tester lines was maximum 3 days. The results showed that 30 SSR primers used were spread evenly across the maize genomes which were manifested in the representation of SSR loci on each chromosome of a total of 10 chromosomes. The levels of polymorphism ranged from 0.13 to 0.78, an average of 0.51, and the number of alleles ranged from 2 to 8 alleles per SSR locus, an average of 4 alleles per SSR locus. The size of nucleotides in each locus also varied from 70 to 553 bp. Cophenetic correlation value (r) at 0.67 indicated that the Unweighted Pair-Group Method Using Arithmetic Averages (UPGMA) was less reliable for differentiating genotypes in five groups. Of the total of 30 genotypes analyzed, 17 genotypes had homozygosity level of >80% so it can be included in the hybrid assembly program.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-10-01DOI: 10.21082/ijas.v16n2.2015.pp.87-96
N. Dharmayanti, Risza Hartawan
Epidemiological studies on H5N1 avian influenza viruses indi-cated that the viruses do not transmit efficiently from human to human. Transmissibility of viruses among human population is very complex and polygenic. Studies on molecular determinants facilitating interspecies transmission of the viruses suggested that two polymerase complex proteins such as PB2 and PB1-F2 are important. PB2 is critical in determining the host specificity, whereas mutations in PB1-F2 increase the viral virulence. The study aimed to characterize the polymerase complex of PB2 and PB1-F2 proteins of H5N1 avian influenza viruses isolated from Indonesia. The DNA samples encoding the PB2 and PB1-F2 complex proteins of several H5N1 isolates were sequenced and analyzed. Pathogenicity of the viruses was studied in both avian and mammal models. The sequencing results showed that there was no mutation in both proteins of PB2 and PB1-F2 of the avian influenza virus isolates. The molecular character for host specificity was consistent with the animal experiment results. The H5N1 virus isolates were only infectious and pathogenic in chickens, but not in BALB/C mice as the mammal model. The study suggests that host range of H5N1 virus isolates of Indonesia is restricted to poultry and not transmisible to mammal model used in this study.
{"title":"HOST-RESTRICTED RANGE OF H5N1 AVIAN INFLUENZA VIRUSES ASSOCIATED WITH CHARACTERS OF POLYMERASE COMPLEX OF PB2 AND PB1-F2 PROTEINS","authors":"N. Dharmayanti, Risza Hartawan","doi":"10.21082/ijas.v16n2.2015.pp.87-96","DOIUrl":"https://doi.org/10.21082/ijas.v16n2.2015.pp.87-96","url":null,"abstract":"Epidemiological studies on H5N1 avian influenza viruses indi-cated that the viruses do not transmit efficiently from human to human. Transmissibility of viruses among human population is very complex and polygenic. Studies on molecular determinants facilitating interspecies transmission of the viruses suggested that two polymerase complex proteins such as PB2 and PB1-F2 are important. PB2 is critical in determining the host specificity, whereas mutations in PB1-F2 increase the viral virulence. The study aimed to characterize the polymerase complex of PB2 and PB1-F2 proteins of H5N1 avian influenza viruses isolated from Indonesia. The DNA samples encoding the PB2 and PB1-F2 complex proteins of several H5N1 isolates were sequenced and analyzed. Pathogenicity of the viruses was studied in both avian and mammal models. The sequencing results showed that there was no mutation in both proteins of PB2 and PB1-F2 of the avian influenza virus isolates. The molecular character for host specificity was consistent with the animal experiment results. The H5N1 virus isolates were only infectious and pathogenic in chickens, but not in BALB/C mice as the mammal model. The study suggests that host range of H5N1 virus isolates of Indonesia is restricted to poultry and not transmisible to mammal model used in this study.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-04-01DOI: 10.21082/ijas.v16n1.2015.p1-10
Sutoro Sutoro, P. Lestari, H. Kurniawan
Java Island is one of origins of a large number of indigenous upland rice accessions, which may serve as valuable plant genetic resources for future crop improvement in Indonesia. However, these landraces especially non-glutinous and glutinous rice are rapidly being lost because of land-use, agricultural practices and other factors. A better understanding of genetic diversity of local upland rice is important for crop improvement program, crop management and conservation strategy. This study aimed to evaluate the genetic diversity of upland rice landraces originating from Java Island. A total of 82 upland rice accessions comprising of 55 non-glutinous rice and 27 glutinous type were genotyped using the 16 simple sequence repeat (SSR) markers. The result showed that a total of 74 alleles were found with major allele frequency found on RM431 (0.96). Most of the SSR markers (56.3%) showed high discriminating power as represented by polymorphic informa-tion content (PIC) value higher than 0.5. A moderate genetic diversity index was detected in all landraces, which was 0.55. Genetic diversity index of non-glutinous and glutinous rice were 0.54 and 0.53, respectively. Their genetic distance was about 0.057. The phylogenetic tree generated two main clusters that demonstrated discrimination among landraces according to the individual genetic properties rather than their geographical origins and grain types (non-glutinous and glutinous type). The levels of genetic diversity were varied across rice types and geographical origins. According to the regions, the closest genetic distance was found between upland rice landraces from Central Java and West Java (0.040). The information derived from this study is important, in combination with phenotypic data, to identify desired useful traits came from different origins of the gene pool to be used for breeding purposes.
{"title":"GENETIC DIVERSITY OF UPLAND RICE LANDRACES FROM JAVA ISLAND AS REVEALED BY SSR MARKERS","authors":"Sutoro Sutoro, P. Lestari, H. Kurniawan","doi":"10.21082/ijas.v16n1.2015.p1-10","DOIUrl":"https://doi.org/10.21082/ijas.v16n1.2015.p1-10","url":null,"abstract":"Java Island is one of origins of a large number of indigenous upland rice accessions, which may serve as valuable plant genetic resources for future crop improvement in Indonesia. However, these landraces especially non-glutinous and glutinous rice are rapidly being lost because of land-use, agricultural practices and other factors. A better understanding of genetic diversity of local upland rice is important for crop improvement program, crop management and conservation strategy. This study aimed to evaluate the genetic diversity of upland rice landraces originating from Java Island. A total of 82 upland rice accessions comprising of 55 non-glutinous rice and 27 glutinous type were genotyped using the 16 simple sequence repeat (SSR) markers. The result showed that a total of 74 alleles were found with major allele frequency found on RM431 (0.96). Most of the SSR markers (56.3%) showed high discriminating power as represented by polymorphic informa-tion content (PIC) value higher than 0.5. A moderate genetic diversity index was detected in all landraces, which was 0.55. Genetic diversity index of non-glutinous and glutinous rice were 0.54 and 0.53, respectively. Their genetic distance was about 0.057. The phylogenetic tree generated two main clusters that demonstrated discrimination among landraces according to the individual genetic properties rather than their geographical origins and grain types (non-glutinous and glutinous type). The levels of genetic diversity were varied across rice types and geographical origins. According to the regions, the closest genetic distance was found between upland rice landraces from Central Java and West Java (0.040). The information derived from this study is important, in combination with phenotypic data, to identify desired useful traits came from different origins of the gene pool to be used for breeding purposes.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2015-04-01DOI: 10.21082/ijas.v16n1.2015.p11-20
U. Chavan, S. Patil, B. D. Rao, J. Patil
The present study was undertaken with the objective to standardise procedures for preparation of semolina (rava) from sorghum, to identify the best genotype for preparation of semolina and to study the nutritional quality parameters of semolina. For processing of sorghum, ten varieties and five hybrids were used for preparation of semolina and their products. A process has been standardized for semolina preparation using ultra grinding mill from sorghum grain. The semolina yield ranged from 46.51% to 54.29%. Hybrid CSH-15R gave the highest yield of semolina (54.29%). Starch content in semolina ranged from 59.93% to 66.43%. The new genotypes Phule Vasudha, Phule Yashoda and M 35-1 showed higher levels of starch content as compared to the other genotypes. The Phule Vasudha and Selection-3 showed higher levels of total soluble sugars in grains, as well as in semolina than the other genotypes. Phule Maulee gave higher level of crude fibre content (3.12%). The amino acid profile of sorghum grain and semolina showed very minor differences in the content due to the processing of sorghum grains into various products like semolina. The new genotypes of rabi sorghum showed comparable results for the mineral with that of hybrids. The organoleptic properties of the sweet (shira), upama and idali prepared from semolina were judged on the basis of colour, texture and appearance, flavour, taste and overall acceptability of the products using semi-trained judges and 1 to 9 hedonic scales. All products prepared from semolina were like very much and gave highest rating of more than 8 hedonic scales. While considering the yield of semolina from sorghum grains as well as their nutritional composition and organoleptic properties of the niche products (shira, upama, idali) prepared from them, the varieties Phule Vasudha and Phule Yashoda were the best one as compared to the other varieties and hybrids and overall varieties were better than the hybrids.
{"title":"PROCESSING OF SORGHUM FROM DIFFERENT VARIETIES AND HYBRIDS FOR SEMOLINA AND THEIR PRODUCTS","authors":"U. Chavan, S. Patil, B. D. Rao, J. Patil","doi":"10.21082/ijas.v16n1.2015.p11-20","DOIUrl":"https://doi.org/10.21082/ijas.v16n1.2015.p11-20","url":null,"abstract":"The present study was undertaken with the objective to standardise procedures for preparation of semolina (rava) from sorghum, to identify the best genotype for preparation of semolina and to study the nutritional quality parameters of semolina. For processing of sorghum, ten varieties and five hybrids were used for preparation of semolina and their products. A process has been standardized for semolina preparation using ultra grinding mill from sorghum grain. The semolina yield ranged from 46.51% to 54.29%. Hybrid CSH-15R gave the highest yield of semolina (54.29%). Starch content in semolina ranged from 59.93% to 66.43%. The new genotypes Phule Vasudha, Phule Yashoda and M 35-1 showed higher levels of starch content as compared to the other genotypes. The Phule Vasudha and Selection-3 showed higher levels of total soluble sugars in grains, as well as in semolina than the other genotypes. Phule Maulee gave higher level of crude fibre content (3.12%). The amino acid profile of sorghum grain and semolina showed very minor differences in the content due to the processing of sorghum grains into various products like semolina. The new genotypes of rabi sorghum showed comparable results for the mineral with that of hybrids. The organoleptic properties of the sweet (shira), upama and idali prepared from semolina were judged on the basis of colour, texture and appearance, flavour, taste and overall acceptability of the products using semi-trained judges and 1 to 9 hedonic scales. All products prepared from semolina were like very much and gave highest rating of more than 8 hedonic scales. While considering the yield of semolina from sorghum grains as well as their nutritional composition and organoleptic properties of the niche products (shira, upama, idali) prepared from them, the varieties Phule Vasudha and Phule Yashoda were the best one as compared to the other varieties and hybrids and overall varieties were better than the hybrids.","PeriodicalId":13456,"journal":{"name":"Indonesian Journal of Agricultural Science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67800442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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