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
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 ...
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...
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 ...
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...
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
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 ...
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...
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 ...
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...
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