IOP Conference Series: Earth and Environmental Science, 2021
Local rice varieties often carry useful genes related to yield component traits that can be utili... more Local rice varieties often carry useful genes related to yield component traits that can be utilized to develop high-yielding rice varieties. This study aimed to identify quantitative trait loci (QTLs) for yield component traits in Untup Rajab, an Indonesian local rice variety. QTL mapping was conducted using Inclusive Composite Interval Mapping (ICIM) method on a F2 population from a cross between TN-1 and Untup Rajab, which was genotyped using SNP markers and phenotyped for several yield component traits. A total of eight QTLs were detected. Two QTLs for spikelet number per panicle were found in chromosome 6 and 9 with PVE values of 13.01% and 15.57%, respectively. Three QTLs were identified for the number of filled spikelets per panicle in chromosome 4, 6, and 12 with PVE values of 7.73%, 9.19%, and 19.51%, respectively. Two QTLs were identified for the ratio of filled spikelets to total spikelet number per panicle in chromosome 3 and 12 with PVE values of 9.73% and 10.71%, respe...
THE SECOND INTERNATIONAL CONFERENCE ON GENETIC RESOURCES AND BIOTECHNOLOGY: Harnessing Technology for Conservation and Sustainable Use of Genetic Resources for Food and Agriculture, 2022
Hybrid purity assessment in F 1 hybrids segregating for phytophthora root rot resistance genes of... more Hybrid purity assessment in F 1 hybrids segregating for phytophthora root rot resistance genes of chili pepper (Capsicum annuum L.
Resistance screening of promising rice lines in Indonesia requires the use of brown planthopper (... more Resistance screening of promising rice lines in Indonesia requires the use of brown planthopper (BPH) biotypes 1, 2, and 3. Three BPH populations have been raised as biotypes 1, 2, and 3 on differential rice host of improved varieties Pelita I-1 (no Bph gene), IR26 (Bph1), and IR42 (bph2), respectively. Three alternative populations have also been developed on the respective traditional varieties TN1 (no Bph gene), Mudgo (Bph1), and ASD7 (bph2). Although these populations displayed two virulent patterns other than biotype 1 to 3 phenotypes, they were expected to be discriminated into two virulence groups by SSR analysis. The study aimed to investigate the level of genetic variation among the six BPH populations using SSR markers and to relate it with the observed virulence patterns. Genotyping of 30 females with 29 polymorphic SSR markers revealed higher genetic parameter values in populations reared on improved varieties than those on traditional varieties. This difference was mark...
Brown planthopper is the most important rice pest in Indonesia. Its high adaptability to feed and... more Brown planthopper is the most important rice pest in Indonesia. Its high adaptability to feed and reproduce on previously introduced resistant varieties to form more virulent population often causes BPH outbreak and hopperburn that lead to total crop yield loss. Rice breeding for resistant to BPH requires information on the current status of BPH virulences in the fields to anticipate the virulence adaptation on new varieties. The objectives of this study were to investigate the degree of virulence of BPH populations and to cluster the BPH virulence to form BPH core collection. Thirteen BPH populations collected from paddy fields in six provinces (Banten, West Java, Central Java, East Java, South Kalimantan, and South Sulawesi) in 2011 and 2013 were tested on 10 differential rice varieties and seven host varieties of BPH populations, using the standard seedbox screening technique. Based on resistance reaction of four differential varieties (TN1, Mudgo, ASD7, and Rathu Heenathi), most...
The improvement of rice (Oryza sativa L.) Ciherang variety for early maturity and high production... more The improvement of rice (Oryza sativa L.) Ciherang variety for early maturity and high production traits was carried out by Marker Assisted Backcrossing (MAB) method using Nipponbare as donor parent. The foreground selection of Hd2 gene was laid on flanking markers of RM1362 and RM7601 in QTL region. The selection process of F1 to BC2F2 plants were based on molecular markers and agronomic characters. The BC2F3 plants were challenged to bacterial leaf blight to know their resistance in this hybridization. The results indicated that the foreground and background selection were not sufficient as selection tools therefore they would be more accurate if assosiated with agronomic characters. Four selected lines derived from Ciherang x Nipponbare crossed (BC2F3 plant # 283, 307, 373, and 462) could be promising lines with early maturity and high productioncompared to Ciherang. Selected BC2F3 lines flowered earlier than original Ciherang up to 7-10 days, while the yield increasing was 3.55 ...
Biodiversitas Journal of Biological Diversity, 2021
Brown planthopper (Nilaparvata lugens Stål) biotypes differ in virulence to rice varieties carryi... more Brown planthopper (Nilaparvata lugens Stål) biotypes differ in virulence to rice varieties carrying different Bph resistance genes. These biotypes are reported can be genetically discriminated against using DNA markers. Four brown planthoppers (BPH) populations, which displayed two virulence phenotypes, have been produced by selection and adaptation on four differential host varieties. Sequence-related amplified polymorphism (SRAP) marker preferentially amplifies the coding regions in the genome and, thus, can discriminate the observed virulence variations among those populations. This study aimed to analyze the genetic variation of four developed BPH populations using SRAP markers. Genetic analysis of a total of 40 BPH females with 18 polymorphic primers revealed equal genetic diversity parameter values among populations (Na: 1.1 to 1.4, Ne: 1.2 to 1.3, I: 0.22 to 0.29, He: 0.14 to 0.18, and UHe: 0.15 to 0.19). Analysis of population structure by AMOVA indicated low genetic variation among populations (9%). Still, pairwise PhiPT population values between all pairs of the population revealed the presence of moderate genetic differentiations (PhiPT ranged from 0.57 to 0.133, P<0.01). Two partial clusters in plots of PCoA were corresponded to two virulence groups, indicating the ability of SRAP markers to discriminate virulence phenotype. Further selection and adaptation are expected can form four desired virulence patterns with complete genetic separation among the population before its application as resistance screening agents of rice lines.
Brown planthopper biotype 1, 2, 3 and a representative field population are required for resistan... more Brown planthopper biotype 1, 2, 3 and a representative field population are required for resistance screening of promising rice lines in Indonesia, but the current biotype stocks has shown deviation in virulence patterns. The objectives of this study were to develop a set of brown planthopper populations with differential virulence and to investigate their genetic variability using SSR marker. Females originated from two field populations were selected on variety Mudgo (carries Bph1 gene) or ASD7 (bph2 gene) using honeydew excretion as the virulence parameter. Selection cycles resulted in population T, M, A, and R, which was raised and adapted on variety TN1 (carries no Bph gene), Mudgo, ASD7, and Rathu Heenathi (Bph3, Bph17), respectively. Population R was the most virulent as expected and can be used to represent a field population, but the remaining populations still showed high virulence level. AMOVA and PCoA results based on analysis with 38 SSR primer pairs revealed partial ge...
International Journal on Advanced Science, Engineering and Information Technology, 2021
DNA markers can detect DNA sequence variations in the genome, and they are useful for genetic stu... more DNA markers can detect DNA sequence variations in the genome, and they are useful for genetic studies, DNA fingerprinting, and genotype-based selection in breeding programs. Rice, as one of the model plants for genetic and genomic studies, has abundant DNA markers stored in various online databases. Selecting markers in rice is not limited by marker availability but rather by their polymorphism in the target population. We developed a computational method to screen millions of single nucleotide polymorphism (SNP) markers listed in IRRI 3000 rice genome database in order to find a subset of markers that are polymorphic in an F2 mapping population created from a cross between a parental line with a known genome sequence and a local Indonesian variety with no genome sequence data. The parental lines were genotyped using an affordable medium-density SNP array. The genotype data was cross-referenced with the rice genome database to perform phylogenetic analysis and identify accessions clusters with the highest genetic similarities to each parental line. The cluster data was then used to identify monomorphic SNP candidates within the cluster but exhibit consistent polymorphism between the two clusters. Using this method, we obtained a SNP marker set for a segment in rice chromosome 8 with 76.19% polymorphism rate, which is much higher than the expected 1.06% polymorphism rate if the SNP markers were chosen randomly. The improved polymorphism rate was also observed when the method was applied to other random chromosome segments and randomly chosen parental candidates.
Heading date is one of key traits in rice adaptation to different environments. Rice with early m... more Heading date is one of key traits in rice adaptation to different environments. Rice with early maturity is very useful for increasing rice production extensively especially in Indonesia. The improvement of rice variety Conde for heading date and resistance to bacterial leaf blight (BLB) was developed through Marker Assisted Backcrossing approach (MAB). Xa7 derived from Conde as recipient parents for resistance to BLB and Hd2 gene derived from Nipponbare as a donor parent for heading date. The aim of this research was to evaluate the performance of heading date and agronomic traits of 85 BC2F4 lines in two field stations, Sukamandi (West Java) and Maros (South Sulawesi). Molecular analysis of Xa7 on chromosome 6 and Hd2 gene on chromosome 7 and agronomic performance was evaluated. Foreground analysis resulted 41% for Xa7 and 66.7% for Hd2 gene in homozygous condition. The majority of lines have similar heading date and yield with Conde and more resistance to bacterial leaf blight (B...
Improving Ciherang rice variety for earliness and higher productivity was obtained using Marker A... more Improving Ciherang rice variety for earliness and higher productivity was obtained using Marker Assisted Backcrossing (MAB). Among 78 lines of BC2F4 generation of Ciherang x Nipponbare were obtained from greenhouse and molekuler analysis selection. Field evaluations were conducted at two locations, namely field station of Sukamandi (Indonesian Center for Rice Research, West Java), and field station of Maros (Indonesian Cereals Research Institute, South Sulawesi). Molecular analysis was performed using markers RM1362 and RM7601 which are flanking markers for the QTL region for Hd2 gene, located on chromosome 7. Flowering time and grain yield were evaluated among BC2 F4 lines. Five lines flowered earlier and yielded higher than Ciherang were selected for background analysis using microsatellites covering the rice chromosomes. The earliest flowering line was BC2F4 CihNip-60 (at 74 days, 4 days earlier than that of Ciherang), and the highest yield (which flowered earlier than Ciherang) ...
Situ Patenggang is an elite upland rice variety well-accepted by farmers, but recently this varie... more Situ Patenggang is an elite upland rice variety well-accepted by farmers, but recently this variety started to be attacked by blast disease (Pyricularia grisea) that causes yield loss up to 50%. To overcome this problem, Bio Patenggang variety has been developed through molecular breeding using blast-resistant monogenic lines as donor parents. The aim of this research was to present molecular breeding approach of Bio Patenggang development, including steps from the phenotypic selection on candidate lines to the genotypic analysis assisted by molecular markers. The phenotypic performances were assessed using Distinctness, Uniformity, and Stability (DUS) testing by following the standard method stated in the rice test guidelines. The genotypic analyses were performed using foreground and background markers. Four BC3F7 lines were selected as the candidates of the Situ Patenggang-derived variety. Based on ANOVA and Principal Component Analysis (PCA), phenotypic performances of the four ...
Brown planthopper (BPH) is a major rice pest in Indonesia. The most economical and effective appr... more Brown planthopper (BPH) is a major rice pest in Indonesia. The most economical and effective approach to control the insect pest is by using resistant varieties. Exploring for resistance genes is, therefore, a prerequisite for effective breeding program for BPH resistance. This study aimed to map BPH resistance genes in Untup Rajab, an Indonesian local rice variety. Genetic map was constructed using an F 2 population from a cross between TN-1 and Untup Rajab, and SNP markers from RiceLD SNP Chip. Phenotyping was performed using bulk seedling test on F 2:3 seedlings against two BPH populations, i.e. X1 and S1. Four QTLs were identified on chromosomes 5, 6, 8, and 11 with PVE values of 7.63%, 9.40%, 17.66%, and 3.05%, respectively. Relatively normal distribution of resistance phenotype and the relatively low PVE values indicate that Untup Rajab has a quantitative resistance to BPH with two different resistance loci identified for each BPH test population. The QTL on chromosome 8 overlaps with OsHI-LOX gene, which is associated with resistance to BPH, and adjacent to another QTL for resistance to green leafhopper. The QTL on chromosome 6 was found near OsPLDα4 and OsPLDα5 genes which are related to BPH resistance. Meanwhile, the QTL intervals on chromosome 5 and 11 did not overlap with any known BPH QTLs or genes, which make them attractive candidates for novel BPH resistance gene discovery.
Selection and Confirmation Allele of Hd Genes on Rice with Early Maturity and High Productivity o... more Selection and Confirmation Allele of Hd Genes on Rice with Early Maturity and High Productivity on Code x Nipponbare Crossed. Ahmad Dadang, Tasliah, and Joko Prasetiyono. To support the IP 300 program rice varieties with both early maturity and high productivity are needed. The objective of the research was to improve those traits in Code variety using RIL (recombinant inbreed line) methods. The research was conducted in the year 2009-2011 at the greenhouse and laboratory of Molecular Biology, Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development. Materials consisted of 600 individuals of F 2 derived from one of F 1 Code x Nipponbare crossed plants and they were planted up to F 4 with seed-to-seed, then confirmed by 8 microsatelite markers linked to loci of Hd genes. The molecular analysis showed that 84 of 600 F 2 plants produced. The F 4 plants have 50% of flowering time shorter than F 2 and F 3 plants. Two lines (CdNb_388 and CdNb_270) have higher productivity compared to Code by the number of productive tillers (20) and the number of tiller grains (2240 and 1740) and have closely 50% of 60 days flowering time of Nipponbare. Three lines of F 4 plants (CdNb_270, 364, and 388) were predicted to have allele of Hd7 gene, and CdNb_472 was predicted to have alelle of Hd14 gene.
Early-maturing and high-yielding rice variety is very useful for increasing rice production in In... more Early-maturing and high-yielding rice variety is very useful for increasing rice production in Indonesia. The aim of this research was to develop new lines of Indonesian rice containing Hd2 gene using Code variety as a recipient parent and Nipponbare variety as a donor parent through targetted MAB approach using RM1362 and RM7601 in chromosom 7 for foreground selection. After two generations of backcrossing, the positive alleles of Hd2 gene from Nipponbare had successfully trans-ferred into Code. The plant number CdNp_29 in BC2F2 popula-tion had the highest genome recovery of 82.7%. The twelve BC2F3 plants were selected for self-pollination to generate BC2F4. These selected lines that carried the Hd2 gene were screened in the greenhouse for the evaluation of heading date and agronomic traits. All improved lines had Hd2 gene similar to the donor parent Nipponbare. The heading date of the breeding lines ranged from 73 to 89 days (Code 85 days) or fill the third criterion of rice matur...
The utilization of molecular marker technology for Blast (Pyricularia grisea) resistance in rice ... more The utilization of molecular marker technology for Blast (Pyricularia grisea) resistance in rice breeding could accelerate and improve the precision of selection. This study aimed to identify and to select the BC3F2 progenies from Situ Patenggang and the opted Blast Monogenic Lines based on their resistance to blast disease in green house and field using molecular characterization. A total of 200-300 BC3F2 population strains resulted in 4 crosses between Situ Patenggang varieties and Monogenic Varieties IRBLta2-Re, IRBLkp-k60, IRBLi-F5 and IRBLa-A were used as total genetic material in the study. Blast resistance assay was initially carried out in a greenhouse and further selection was conducted in the endemic blast area, Sukabumi. The selected Molecular marker was STS (Sequence Taq Sites) marker for foreground selection and 384-SNPs (Single Nucleotide Polymorphism) chip for background selection. The number of lines from each cross was selected by greenhouse assay i.e: 25 lines der...
Availability of fertile land on the island of Java in Indonesia decreases due to the shifting fro... more Availability of fertile land on the island of Java in Indonesia decreases due to the shifting from agricultural land to non-agricultural land. Hence, an extensification of soybean culture to outer Java suboptimal land areas is needed, such as tidal swamp which occupies approximately 20.192 million hectares. The main limitations in this soil are soil acidity, Fe toxicity and excess water. To develop soybean varieties tolerant to acid tidal swamp, tolerant soybean gene resources are needed. Hence, glasshouse and field experiments were carried out to identify tolerant gene resources. The glasshouse experiment has been conducted using 185 genotypes of germplasm at the Indonesian Legume and Tuber Crops Research Institute, Malang, East Java. Selection was carried out by using a selection index method. The glasshouse experiment was followed by field experiment at the Belandean research station, Banjarbaru, South Kalimantan, using the best 17 genotypes selected from the glasshouse trial. R...
Swampland is a prospective marginal land to be developed for rice cultivation. Rice plants that a... more Swampland is a prospective marginal land to be developed for rice cultivation. Rice plants that are adaptive to swampland usually have good tolerance to Fe. Previously, we obtained several rice lines tolerant to Fe toxicity in the field. This study aimed to analyze the swampy rice genotypes using STS molecular markers linked to bacterial leaf blight (BLB)-resistant genes and evaluate the resistance level of the genotypes against three BLB races under the greenhouse condition. This research was conducted in the Molecular Biology Laboratory and Greenhouse of the Indonesian Center for Agricultural Biotechnology andGenetic Resources Research and Development from January to May 2021. Eighteen swampy rice varieties/lines and two check varieties for Fe toxicity and BLB, respectively, were used in this research. The eight STS molecular markers linked to BLB resistance genes were used for genotyping analysis. The results showed that all rice plants tested contained xa5 allele gene, 19 genoty...
Program pemuliaan untuk peningkatan produksi minyak kelapa sawit dapat dilakukan dengan cara mela... more Program pemuliaan untuk peningkatan produksi minyak kelapa sawit dapat dilakukan dengan cara melakukan seleksi plasma nutfah, observasi/eksplorasi lapang, maupun introduksi aksesi baru dari luar negeri. Teknologi seleksi kelapa sawit dapat dilakukan secara konvensional dan non-konvensional. Penelitian ini bertujuan untuk memperoleh informasi keragaman genetik aksesi kelapa sawit asal Kamerun berdasarkan keragaman karakter morfologi, produksi awal, dengan menggunakan marka molekuler SSR. Penelitian dilakukan di KP Sitiung dan BB Biogen. Sampel yang dipilih adalah aksesi yang memiliki produksi awal tandan buah segar (TBS) minimal 4 kg. Sebanyak 35 aksesi kelapa sawit asal Kamerun dan 20 primer SSR digunakan dalam penelitian ini. Hasil pengamatan karakter morfologi menunjukkan bahwa tidak terdapat perbedaan karakter morfologi diantara 35 tanaman kelapa sawit yang produksi awalnya ≥ 4 kg TBS. Produksi awal kelapa sawit berkisar antara 4-9,5 kg TBS per tandan dengan koefisien keragaman rendah, yaitu < 20%. Berdasarkan analisis 20 primer SSR dihasilkan enam pita dengan kisaran 4−12 alel. Jumlah alel dominan sangat mendominasi dibanding dengan alel jarang maupun alel sedang. Nilai Polymorphism Information Content (PIC) yang diperoleh sebagian bernilai negatif, 11 primer (55%) bernilai positif. Primer MEgcl3639 menghasilkan nilai PIC tertinggi (0,65), sedangkan nilai PIC terendah pada primer MEgcl0046 (-0,48). Berdasarkan analisis UPGMA aksesi 35 kelapa sawit terbagi ke dalam dua kelompok, yaitu kelompok I terdiri dari 34 aksesi pada tingkat kesamaan genetik 42,5-67,5%, dan kelompok II, yaitu satu aksesi (D91.4). Aksesi D91.4 memiliki komposisi genetik yang sangat berbeda dengan kelompok I, dapat digunakan sebagai calon tetua persilangan. Perlu penelitian lebih detail pada aksesi D91.4 ini untuk pengamatan karakter kadar minyak, ketebalan cangkang, daging buah, dll.
IOP Conference Series: Earth and Environmental Science, 2021
Local rice varieties often carry useful genes related to yield component traits that can be utili... more Local rice varieties often carry useful genes related to yield component traits that can be utilized to develop high-yielding rice varieties. This study aimed to identify quantitative trait loci (QTLs) for yield component traits in Untup Rajab, an Indonesian local rice variety. QTL mapping was conducted using Inclusive Composite Interval Mapping (ICIM) method on a F2 population from a cross between TN-1 and Untup Rajab, which was genotyped using SNP markers and phenotyped for several yield component traits. A total of eight QTLs were detected. Two QTLs for spikelet number per panicle were found in chromosome 6 and 9 with PVE values of 13.01% and 15.57%, respectively. Three QTLs were identified for the number of filled spikelets per panicle in chromosome 4, 6, and 12 with PVE values of 7.73%, 9.19%, and 19.51%, respectively. Two QTLs were identified for the ratio of filled spikelets to total spikelet number per panicle in chromosome 3 and 12 with PVE values of 9.73% and 10.71%, respe...
THE SECOND INTERNATIONAL CONFERENCE ON GENETIC RESOURCES AND BIOTECHNOLOGY: Harnessing Technology for Conservation and Sustainable Use of Genetic Resources for Food and Agriculture, 2022
Hybrid purity assessment in F 1 hybrids segregating for phytophthora root rot resistance genes of... more Hybrid purity assessment in F 1 hybrids segregating for phytophthora root rot resistance genes of chili pepper (Capsicum annuum L.
Resistance screening of promising rice lines in Indonesia requires the use of brown planthopper (... more Resistance screening of promising rice lines in Indonesia requires the use of brown planthopper (BPH) biotypes 1, 2, and 3. Three BPH populations have been raised as biotypes 1, 2, and 3 on differential rice host of improved varieties Pelita I-1 (no Bph gene), IR26 (Bph1), and IR42 (bph2), respectively. Three alternative populations have also been developed on the respective traditional varieties TN1 (no Bph gene), Mudgo (Bph1), and ASD7 (bph2). Although these populations displayed two virulent patterns other than biotype 1 to 3 phenotypes, they were expected to be discriminated into two virulence groups by SSR analysis. The study aimed to investigate the level of genetic variation among the six BPH populations using SSR markers and to relate it with the observed virulence patterns. Genotyping of 30 females with 29 polymorphic SSR markers revealed higher genetic parameter values in populations reared on improved varieties than those on traditional varieties. This difference was mark...
Brown planthopper is the most important rice pest in Indonesia. Its high adaptability to feed and... more Brown planthopper is the most important rice pest in Indonesia. Its high adaptability to feed and reproduce on previously introduced resistant varieties to form more virulent population often causes BPH outbreak and hopperburn that lead to total crop yield loss. Rice breeding for resistant to BPH requires information on the current status of BPH virulences in the fields to anticipate the virulence adaptation on new varieties. The objectives of this study were to investigate the degree of virulence of BPH populations and to cluster the BPH virulence to form BPH core collection. Thirteen BPH populations collected from paddy fields in six provinces (Banten, West Java, Central Java, East Java, South Kalimantan, and South Sulawesi) in 2011 and 2013 were tested on 10 differential rice varieties and seven host varieties of BPH populations, using the standard seedbox screening technique. Based on resistance reaction of four differential varieties (TN1, Mudgo, ASD7, and Rathu Heenathi), most...
The improvement of rice (Oryza sativa L.) Ciherang variety for early maturity and high production... more The improvement of rice (Oryza sativa L.) Ciherang variety for early maturity and high production traits was carried out by Marker Assisted Backcrossing (MAB) method using Nipponbare as donor parent. The foreground selection of Hd2 gene was laid on flanking markers of RM1362 and RM7601 in QTL region. The selection process of F1 to BC2F2 plants were based on molecular markers and agronomic characters. The BC2F3 plants were challenged to bacterial leaf blight to know their resistance in this hybridization. The results indicated that the foreground and background selection were not sufficient as selection tools therefore they would be more accurate if assosiated with agronomic characters. Four selected lines derived from Ciherang x Nipponbare crossed (BC2F3 plant # 283, 307, 373, and 462) could be promising lines with early maturity and high productioncompared to Ciherang. Selected BC2F3 lines flowered earlier than original Ciherang up to 7-10 days, while the yield increasing was 3.55 ...
Biodiversitas Journal of Biological Diversity, 2021
Brown planthopper (Nilaparvata lugens Stål) biotypes differ in virulence to rice varieties carryi... more Brown planthopper (Nilaparvata lugens Stål) biotypes differ in virulence to rice varieties carrying different Bph resistance genes. These biotypes are reported can be genetically discriminated against using DNA markers. Four brown planthoppers (BPH) populations, which displayed two virulence phenotypes, have been produced by selection and adaptation on four differential host varieties. Sequence-related amplified polymorphism (SRAP) marker preferentially amplifies the coding regions in the genome and, thus, can discriminate the observed virulence variations among those populations. This study aimed to analyze the genetic variation of four developed BPH populations using SRAP markers. Genetic analysis of a total of 40 BPH females with 18 polymorphic primers revealed equal genetic diversity parameter values among populations (Na: 1.1 to 1.4, Ne: 1.2 to 1.3, I: 0.22 to 0.29, He: 0.14 to 0.18, and UHe: 0.15 to 0.19). Analysis of population structure by AMOVA indicated low genetic variation among populations (9%). Still, pairwise PhiPT population values between all pairs of the population revealed the presence of moderate genetic differentiations (PhiPT ranged from 0.57 to 0.133, P<0.01). Two partial clusters in plots of PCoA were corresponded to two virulence groups, indicating the ability of SRAP markers to discriminate virulence phenotype. Further selection and adaptation are expected can form four desired virulence patterns with complete genetic separation among the population before its application as resistance screening agents of rice lines.
Brown planthopper biotype 1, 2, 3 and a representative field population are required for resistan... more Brown planthopper biotype 1, 2, 3 and a representative field population are required for resistance screening of promising rice lines in Indonesia, but the current biotype stocks has shown deviation in virulence patterns. The objectives of this study were to develop a set of brown planthopper populations with differential virulence and to investigate their genetic variability using SSR marker. Females originated from two field populations were selected on variety Mudgo (carries Bph1 gene) or ASD7 (bph2 gene) using honeydew excretion as the virulence parameter. Selection cycles resulted in population T, M, A, and R, which was raised and adapted on variety TN1 (carries no Bph gene), Mudgo, ASD7, and Rathu Heenathi (Bph3, Bph17), respectively. Population R was the most virulent as expected and can be used to represent a field population, but the remaining populations still showed high virulence level. AMOVA and PCoA results based on analysis with 38 SSR primer pairs revealed partial ge...
International Journal on Advanced Science, Engineering and Information Technology, 2021
DNA markers can detect DNA sequence variations in the genome, and they are useful for genetic stu... more DNA markers can detect DNA sequence variations in the genome, and they are useful for genetic studies, DNA fingerprinting, and genotype-based selection in breeding programs. Rice, as one of the model plants for genetic and genomic studies, has abundant DNA markers stored in various online databases. Selecting markers in rice is not limited by marker availability but rather by their polymorphism in the target population. We developed a computational method to screen millions of single nucleotide polymorphism (SNP) markers listed in IRRI 3000 rice genome database in order to find a subset of markers that are polymorphic in an F2 mapping population created from a cross between a parental line with a known genome sequence and a local Indonesian variety with no genome sequence data. The parental lines were genotyped using an affordable medium-density SNP array. The genotype data was cross-referenced with the rice genome database to perform phylogenetic analysis and identify accessions clusters with the highest genetic similarities to each parental line. The cluster data was then used to identify monomorphic SNP candidates within the cluster but exhibit consistent polymorphism between the two clusters. Using this method, we obtained a SNP marker set for a segment in rice chromosome 8 with 76.19% polymorphism rate, which is much higher than the expected 1.06% polymorphism rate if the SNP markers were chosen randomly. The improved polymorphism rate was also observed when the method was applied to other random chromosome segments and randomly chosen parental candidates.
Heading date is one of key traits in rice adaptation to different environments. Rice with early m... more Heading date is one of key traits in rice adaptation to different environments. Rice with early maturity is very useful for increasing rice production extensively especially in Indonesia. The improvement of rice variety Conde for heading date and resistance to bacterial leaf blight (BLB) was developed through Marker Assisted Backcrossing approach (MAB). Xa7 derived from Conde as recipient parents for resistance to BLB and Hd2 gene derived from Nipponbare as a donor parent for heading date. The aim of this research was to evaluate the performance of heading date and agronomic traits of 85 BC2F4 lines in two field stations, Sukamandi (West Java) and Maros (South Sulawesi). Molecular analysis of Xa7 on chromosome 6 and Hd2 gene on chromosome 7 and agronomic performance was evaluated. Foreground analysis resulted 41% for Xa7 and 66.7% for Hd2 gene in homozygous condition. The majority of lines have similar heading date and yield with Conde and more resistance to bacterial leaf blight (B...
Improving Ciherang rice variety for earliness and higher productivity was obtained using Marker A... more Improving Ciherang rice variety for earliness and higher productivity was obtained using Marker Assisted Backcrossing (MAB). Among 78 lines of BC2F4 generation of Ciherang x Nipponbare were obtained from greenhouse and molekuler analysis selection. Field evaluations were conducted at two locations, namely field station of Sukamandi (Indonesian Center for Rice Research, West Java), and field station of Maros (Indonesian Cereals Research Institute, South Sulawesi). Molecular analysis was performed using markers RM1362 and RM7601 which are flanking markers for the QTL region for Hd2 gene, located on chromosome 7. Flowering time and grain yield were evaluated among BC2 F4 lines. Five lines flowered earlier and yielded higher than Ciherang were selected for background analysis using microsatellites covering the rice chromosomes. The earliest flowering line was BC2F4 CihNip-60 (at 74 days, 4 days earlier than that of Ciherang), and the highest yield (which flowered earlier than Ciherang) ...
Situ Patenggang is an elite upland rice variety well-accepted by farmers, but recently this varie... more Situ Patenggang is an elite upland rice variety well-accepted by farmers, but recently this variety started to be attacked by blast disease (Pyricularia grisea) that causes yield loss up to 50%. To overcome this problem, Bio Patenggang variety has been developed through molecular breeding using blast-resistant monogenic lines as donor parents. The aim of this research was to present molecular breeding approach of Bio Patenggang development, including steps from the phenotypic selection on candidate lines to the genotypic analysis assisted by molecular markers. The phenotypic performances were assessed using Distinctness, Uniformity, and Stability (DUS) testing by following the standard method stated in the rice test guidelines. The genotypic analyses were performed using foreground and background markers. Four BC3F7 lines were selected as the candidates of the Situ Patenggang-derived variety. Based on ANOVA and Principal Component Analysis (PCA), phenotypic performances of the four ...
Brown planthopper (BPH) is a major rice pest in Indonesia. The most economical and effective appr... more Brown planthopper (BPH) is a major rice pest in Indonesia. The most economical and effective approach to control the insect pest is by using resistant varieties. Exploring for resistance genes is, therefore, a prerequisite for effective breeding program for BPH resistance. This study aimed to map BPH resistance genes in Untup Rajab, an Indonesian local rice variety. Genetic map was constructed using an F 2 population from a cross between TN-1 and Untup Rajab, and SNP markers from RiceLD SNP Chip. Phenotyping was performed using bulk seedling test on F 2:3 seedlings against two BPH populations, i.e. X1 and S1. Four QTLs were identified on chromosomes 5, 6, 8, and 11 with PVE values of 7.63%, 9.40%, 17.66%, and 3.05%, respectively. Relatively normal distribution of resistance phenotype and the relatively low PVE values indicate that Untup Rajab has a quantitative resistance to BPH with two different resistance loci identified for each BPH test population. The QTL on chromosome 8 overlaps with OsHI-LOX gene, which is associated with resistance to BPH, and adjacent to another QTL for resistance to green leafhopper. The QTL on chromosome 6 was found near OsPLDα4 and OsPLDα5 genes which are related to BPH resistance. Meanwhile, the QTL intervals on chromosome 5 and 11 did not overlap with any known BPH QTLs or genes, which make them attractive candidates for novel BPH resistance gene discovery.
Selection and Confirmation Allele of Hd Genes on Rice with Early Maturity and High Productivity o... more Selection and Confirmation Allele of Hd Genes on Rice with Early Maturity and High Productivity on Code x Nipponbare Crossed. Ahmad Dadang, Tasliah, and Joko Prasetiyono. To support the IP 300 program rice varieties with both early maturity and high productivity are needed. The objective of the research was to improve those traits in Code variety using RIL (recombinant inbreed line) methods. The research was conducted in the year 2009-2011 at the greenhouse and laboratory of Molecular Biology, Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development. Materials consisted of 600 individuals of F 2 derived from one of F 1 Code x Nipponbare crossed plants and they were planted up to F 4 with seed-to-seed, then confirmed by 8 microsatelite markers linked to loci of Hd genes. The molecular analysis showed that 84 of 600 F 2 plants produced. The F 4 plants have 50% of flowering time shorter than F 2 and F 3 plants. Two lines (CdNb_388 and CdNb_270) have higher productivity compared to Code by the number of productive tillers (20) and the number of tiller grains (2240 and 1740) and have closely 50% of 60 days flowering time of Nipponbare. Three lines of F 4 plants (CdNb_270, 364, and 388) were predicted to have allele of Hd7 gene, and CdNb_472 was predicted to have alelle of Hd14 gene.
Early-maturing and high-yielding rice variety is very useful for increasing rice production in In... more Early-maturing and high-yielding rice variety is very useful for increasing rice production in Indonesia. The aim of this research was to develop new lines of Indonesian rice containing Hd2 gene using Code variety as a recipient parent and Nipponbare variety as a donor parent through targetted MAB approach using RM1362 and RM7601 in chromosom 7 for foreground selection. After two generations of backcrossing, the positive alleles of Hd2 gene from Nipponbare had successfully trans-ferred into Code. The plant number CdNp_29 in BC2F2 popula-tion had the highest genome recovery of 82.7%. The twelve BC2F3 plants were selected for self-pollination to generate BC2F4. These selected lines that carried the Hd2 gene were screened in the greenhouse for the evaluation of heading date and agronomic traits. All improved lines had Hd2 gene similar to the donor parent Nipponbare. The heading date of the breeding lines ranged from 73 to 89 days (Code 85 days) or fill the third criterion of rice matur...
The utilization of molecular marker technology for Blast (Pyricularia grisea) resistance in rice ... more The utilization of molecular marker technology for Blast (Pyricularia grisea) resistance in rice breeding could accelerate and improve the precision of selection. This study aimed to identify and to select the BC3F2 progenies from Situ Patenggang and the opted Blast Monogenic Lines based on their resistance to blast disease in green house and field using molecular characterization. A total of 200-300 BC3F2 population strains resulted in 4 crosses between Situ Patenggang varieties and Monogenic Varieties IRBLta2-Re, IRBLkp-k60, IRBLi-F5 and IRBLa-A were used as total genetic material in the study. Blast resistance assay was initially carried out in a greenhouse and further selection was conducted in the endemic blast area, Sukabumi. The selected Molecular marker was STS (Sequence Taq Sites) marker for foreground selection and 384-SNPs (Single Nucleotide Polymorphism) chip for background selection. The number of lines from each cross was selected by greenhouse assay i.e: 25 lines der...
Availability of fertile land on the island of Java in Indonesia decreases due to the shifting fro... more Availability of fertile land on the island of Java in Indonesia decreases due to the shifting from agricultural land to non-agricultural land. Hence, an extensification of soybean culture to outer Java suboptimal land areas is needed, such as tidal swamp which occupies approximately 20.192 million hectares. The main limitations in this soil are soil acidity, Fe toxicity and excess water. To develop soybean varieties tolerant to acid tidal swamp, tolerant soybean gene resources are needed. Hence, glasshouse and field experiments were carried out to identify tolerant gene resources. The glasshouse experiment has been conducted using 185 genotypes of germplasm at the Indonesian Legume and Tuber Crops Research Institute, Malang, East Java. Selection was carried out by using a selection index method. The glasshouse experiment was followed by field experiment at the Belandean research station, Banjarbaru, South Kalimantan, using the best 17 genotypes selected from the glasshouse trial. R...
Swampland is a prospective marginal land to be developed for rice cultivation. Rice plants that a... more Swampland is a prospective marginal land to be developed for rice cultivation. Rice plants that are adaptive to swampland usually have good tolerance to Fe. Previously, we obtained several rice lines tolerant to Fe toxicity in the field. This study aimed to analyze the swampy rice genotypes using STS molecular markers linked to bacterial leaf blight (BLB)-resistant genes and evaluate the resistance level of the genotypes against three BLB races under the greenhouse condition. This research was conducted in the Molecular Biology Laboratory and Greenhouse of the Indonesian Center for Agricultural Biotechnology andGenetic Resources Research and Development from January to May 2021. Eighteen swampy rice varieties/lines and two check varieties for Fe toxicity and BLB, respectively, were used in this research. The eight STS molecular markers linked to BLB resistance genes were used for genotyping analysis. The results showed that all rice plants tested contained xa5 allele gene, 19 genoty...
Program pemuliaan untuk peningkatan produksi minyak kelapa sawit dapat dilakukan dengan cara mela... more Program pemuliaan untuk peningkatan produksi minyak kelapa sawit dapat dilakukan dengan cara melakukan seleksi plasma nutfah, observasi/eksplorasi lapang, maupun introduksi aksesi baru dari luar negeri. Teknologi seleksi kelapa sawit dapat dilakukan secara konvensional dan non-konvensional. Penelitian ini bertujuan untuk memperoleh informasi keragaman genetik aksesi kelapa sawit asal Kamerun berdasarkan keragaman karakter morfologi, produksi awal, dengan menggunakan marka molekuler SSR. Penelitian dilakukan di KP Sitiung dan BB Biogen. Sampel yang dipilih adalah aksesi yang memiliki produksi awal tandan buah segar (TBS) minimal 4 kg. Sebanyak 35 aksesi kelapa sawit asal Kamerun dan 20 primer SSR digunakan dalam penelitian ini. Hasil pengamatan karakter morfologi menunjukkan bahwa tidak terdapat perbedaan karakter morfologi diantara 35 tanaman kelapa sawit yang produksi awalnya ≥ 4 kg TBS. Produksi awal kelapa sawit berkisar antara 4-9,5 kg TBS per tandan dengan koefisien keragaman rendah, yaitu < 20%. Berdasarkan analisis 20 primer SSR dihasilkan enam pita dengan kisaran 4−12 alel. Jumlah alel dominan sangat mendominasi dibanding dengan alel jarang maupun alel sedang. Nilai Polymorphism Information Content (PIC) yang diperoleh sebagian bernilai negatif, 11 primer (55%) bernilai positif. Primer MEgcl3639 menghasilkan nilai PIC tertinggi (0,65), sedangkan nilai PIC terendah pada primer MEgcl0046 (-0,48). Berdasarkan analisis UPGMA aksesi 35 kelapa sawit terbagi ke dalam dua kelompok, yaitu kelompok I terdiri dari 34 aksesi pada tingkat kesamaan genetik 42,5-67,5%, dan kelompok II, yaitu satu aksesi (D91.4). Aksesi D91.4 memiliki komposisi genetik yang sangat berbeda dengan kelompok I, dapat digunakan sebagai calon tetua persilangan. Perlu penelitian lebih detail pada aksesi D91.4 ini untuk pengamatan karakter kadar minyak, ketebalan cangkang, daging buah, dll.
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