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Pengembangan Identitas Spesifik Berbasis Marka SSR pada 29 Varietas Kedelai Lokal Indonesia Lestari, Puji; Risliawati, Andari; Utami, Dwinita Wikan; Hidayatun, Nurul; Santoso, Tri Joko; Chaerani, Chaerani
JURNAL BIOLOGI INDONESIA Vol 12, No 2 (2016): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

ABSTRACTSoybean is an important legume crop in Indonesia and local varieties from different regions are diversed. Accurate identification of local varieties is needed to determine the genetic identity in order to protect them to indicate the geographical origin and registration purpose. This study aimed to analyze DNA fingerprints of local varieties of soybean in Indonesia to develop a specific identity using SSR markers along with the marker set. A total of 29 local varieties/accessions was analyzed using 9 selected SSR markers with semi automated genetic analyzer on the basis of capillary electrophoresis. Total markers successfully detected 50 alleles in all varieties, with the average polymorphism information content (PIC) of each locus (0.579) and the genetic diversity index (0.629) were quite high as a reflection of diversity of the local varieties. Based on the analysis of the genetic diversity index, PIC, rare alleles, dominant allele frequency, analysis of genetic distance, 6 SSRs (Satt009, Satt038, Satt177, Satt242, Satt308 and Satt114) were selected as a set of markers for variety identification. Although three varieties can not be distinguished because of their close genetic relationship, but the digital coding indicates that local varieties of soybeans have possessed specific identities (ID) representing variation of SSR alleles. The selected SSR loci with additional identifier can be used to develop ID of Indonesian local soybean in the germplasm collection. Overall, the marker set is a powerful tool to complement morphological markers for the protection of local soybean varieties that contribute in accelerating local varieties improvement in the future agriculture.Keywords: specific identity, SSR, Indonesian local soybean variety, DNA fingerprint.

IDENTIFIKASI GEN / QTL (Quantitative Trait Loci) SIFAT TOLERAN CEKAMAN ALUMINIUM PADA GALUR-GALUR PADI GOGO [Identification of Gene/QTL (Quantitative Trait Loci) for Aluminium Stress Tolerant in Upland Rice Lines] Utami, Dwinita Wikan; Rosdianti, I; Yuriyah, S; Ambarwati, AD; Hanarida, I; Suwarno, Suwarno; Miftahudin, Miftahudin
BERITA BIOLOGI Vol 15, No 2 (2016)
Publisher : Research Center for Biology-Indonesian Institute of Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/beritabiologi.v15i2.2276

Program on the ability of agriculture to provide rice as a staple food tends to decrease with the reduced land area used for rice cultivation. improvement rice production should be directed to use Â marginal land Â as dry and acid land, where poisoning aluminium was seen as a constrain factor. Development of Aluminium (Al) tolerant variety is needed to increase rice production. This technology was environmentally friendly, cheaper and also easier for farmers adopted. The rice lines with broad genetics background which tolerant to Al toxicity has been produced by breeding program. The diversity of Indonesian local rice germplasm is a basic foundation on development of Al toxicity tolerant rice varieties. The purpose of this research was to analyze the genotype variety using 384 SNPs markers on selected Al tolerant rice lines based on bioinformatics approach. Based on the 384 SNPs markers, the total 26 selected Â genotypes were clustered into 5 groups. Each group was having varied Relative Root Length (RRL), which was an Al tolerant parameter of phenotype. These groups were indicated for having different genes or QTL that were related to the Al tolerant character. The association analysis obtained 9 significant SNPs markers that can be applied as the molecular markers for assisting selection in breeding Â program.

SELEKSI BERBANTUKAN MARKA MOLEKULER UNTUK PEMBENTUKAN CALON VARIETAS PADI TURUNAN ESENSIAL SITU PATENGGANG Yuriyah, Siti; Utami, Dwinita Wikan; Nurani, Siti; Nasution, Anggiani; Lestari, Puji; Dadang, Ahmad; Suwarno, Suwarno
BERITA BIOLOGI Vol 18, No 1 (2019)
Publisher : Research Center for Biology-Indonesian Institute of Sciences

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 derived from Situ Patenggang/IRBLta and Situ Patenggang/IRBLkp, 21 plants for crossing Situ Patenggang/IRBLi, and 22 plants for Situ Patenggang/IRBLa-A. The results of field experiment revealed that blast resistance response of the selected lines was varied from 0 to 5. Lines of foreground were successfully selected using STS markers specified for Pii, Pita, Pikp and Pia genes. As for the background selection by SNPs markers, some lines carried the recurrent parent genetic background, Situ Patenggang. Overall, 20 resistance lines that harbored the target genes and Situ Patenggang background were obtained. Further observation was entailed to these twenty selected lines in order to attain promising lines candidate for blast resistance.

PENGEMBANGAN IDENTITAS SPESIFIK BERBASIS MARKA SSR PADA 29 VARIETAS KEDELAI LOKAL INDONESIA Lestari, Puji; Risliawati, Andari; Utami, Dwinita Wikan; Hidayatun, Nurul; Santoso, Tri Joko; Chaerani, Chaerani
JURNAL BIOLOGI INDONESIA Vol 12, No 2 (2016): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v12i2.2888

ABSTRACTSoybean is an important legume crop in Indonesia and local varieties from different regions are diversed. Accurate identification of local varieties is needed to determine the genetic identity in order to protect them to indicate the geographical origin and registration purpose. This study aimed to analyze DNA fingerprints of local varieties of soybean in Indonesia to develop a specific identity using SSR markers along with the marker set. A total of 29 local varieties/accessions was analyzed using 9 selected SSR markers with semi automated genetic analyzer on the basis of capillary electrophoresis. Total markers successfully detected 50 alleles in all varieties, with the average polymorphism information content (PIC) of each locus (0.579) and the genetic diversity index (0.629) were quite high as a reflection of diversity of the local varieties. Based on the analysis of the genetic diversity index, PIC, rare alleles, dominant allele frequency, analysis of genetic distance, 6 SSRs (Satt009, Satt038, Satt177, Satt242, Satt308 and Satt114) were selected as a set of markers for variety identification. Although three varieties can not be distinguished because of their close genetic relationship, but the digital coding indicates that local varieties of soybeans have possessed specific identities (ID) representing variation of SSR alleles. The selected SSR loci with additional identifier can be used to develop ID of Indonesian local soybean in the germplasm collection. Overall, the marker set is a powerful tool to complement morphological markers for the protection of local soybean varieties that contribute in accelerating local varieties improvement in the future agriculture.Keywords: specific identity, SSR, Indonesian local soybean variety, DNA fingerprint.

Molecular Marker-Assisted Selection of Rice Grain Quality on Rice (Oryza sativa L.) Lines Tolerant to Fe Toxicity Stress Utami, Silvia; Widyastuti, Utut; Utami, Dwinita Wikan; Rosdianti, Ida; Lestari, Puji
Journal of Tropical Life Science Vol 7, No 3 (2017)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.07.03.13

The elite rice has been produced, including iron (Fe) tolerant varieties. To get the appropriate rice lines which superior not only Fe tolerant but also have good grain quality needs to be developed selection system, especially in the use of molecular markers. This study was aimed to develop molecular markers for selection the rice grain quality characters of selected rice lines Fe tolerant. A total of 30 selected Fe tolerant rice lines and 5 parents as control lines were used in this research. Characterization of grain quality were quantitatively using the standard. While for genotyping analysis used 19 molecular markers of STS, SSR, Indel and SNP. This study showed that 14 of 19 markers result polymorphic DNA band (DNA markers). Association analysis of genotype and phenotype showed that 10 of 14 markers were significantly (p < 0.05) related to high quality of rice grain. Among four types of markers used in this study, STS was the most widely associated significantly with four characters of rice quality. The phenotyping analysis showed that the physical grain and palatability quality which obtained from the total mean of 30 rice lines tested tend to nearly with the parentâ€™s value as controls lines. The most of these lines were included in the group IV of National Rice Grain Quality Standard (SNI). The amylose content (AC) showed that the texture was varied from firm and dry (high AC) to soft and sticky (low AC). The association results showed that there were significant (p â‰¤ 0.05) markers related with the biosynthesis starch genes, i.e: SBE1, SS1, SSIIa, GPA, PUL and S3cl which contributed on the character of rice palatability. These selected significant markers could be useful for screening of other population with Fe tolerant and/ or other desired morpho-agronomical traits in support of rice breeding program in Indonesia.

Genetic Diversity of Indonesian Bacterial Leaf Blight Isolate (Xanthomonas oryzae pv. oryzae) Core Collection based on the VNTR and avrXa7 Molecular Markers Yuriyah, Siti; Utami, Dwinita Wikan
Makara Journal of Science
Publisher : UI Scholars Hub

Show Abstract | Download Original | Original Source | Check in Google Scholar

Bacterial leaf blight (BLB) is one of the major diseases in rice caused by Xanthomonas oryzae pv. oryzae. This study aimed to identify and analyze the genetic diversity of 18 BLB isolates that consist of 7 races and 11 haplotypes from various locations in Indonesia. The genetic diversity analysis was conducted on the basis of the VNTR (Variable Number of Tandem Repeat) markers and the avrxa7 gene marker. The banding pattern of the amplification product was made into binary data as input for the construction of a dendogram. Based on the dendogram, three X. oryzae pv. oryzae genotype groups with different virulence levels were formed. The VII (IXO80_021) race of X. oryzae pv. oryzae genotype group I and the VIII-A (IXO 80_024) race of genotype group II were avirulent, whereas the races and haplotypes of genotype group III were virulent.

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