Genetic Diversity Analysis of Jatropha Curcas Provenances Using Randomly Amplified Polymorphic DNA Markers

Genetic Diversity Analysis of Jatropha CurcasProvenances Using Randomly Amplified PolymorphicDNA Markers. Dani Satyawan and I Made Tasma.Jatropha curcas nuts are rich in oil that is higly suitable forHak Cipta © 2011, BB-Biogenthe production of bio-diesel or to be used directly inmodified diesel engines. The objective of this study was toassess the extent of genetic diversity among 50 J. curcasprovenances and one accession of J. integerrima usingRAPD markers. The fifty J. curcas provenances werecollected from ecologically diverse regions of Indonesia, andplanted in the Pakuwon Experimental Station (Sukabumi,West Java). Fourteen RAPD primers with 60-80% G+Ccontent were used in this genetic diversity analysis andproduced 64 bands with 95.7% polymorphism level. ThePolymerase Chain Reactions used to generate the RAPDbands sometimes produced inconsistent and nonreproducibleresults, necessitating the duplication of eachreaction to prevent scoring errors. Sixty one validated bandswere subsequently used for genetic diversity analysis usingUnweighted Pair Group Method Arithmetic (UPGMA)method and Dice coefficients. It was shown that thesimilarity coefficients among the provenances ranged from0.2 to 0.98 with an average similarity of 0.75. Dendrogramanalysis produced two major groups of provenances, withone outlier from South Lampung. There was no tendency forprovenances originated from nearby regions to clustertogether in each group, and several provenances showedmore similarities with provenances originated from distantregions. This pattern lent credence to reports that Jatrophawas introduced to Indonesia around four centuries ago andwas mainly spread by humans. Based on the meansimilarities among the accessions and their clusteringpattern, the genetic diversity of the Jatropha collectionappeared to be fairly low. Future additions of geneticmaterials from more diverse genetic background will benecessary to maintain the current progress of Jatrophaimprovement program

Pembentukan Pustaka Genom, Resekuensing, Dan Identifikasi SNP Berdasarkan Sekuen Genom Total Genotipe Kedelai Indonesia

Resequencing of the soybean genome facilitates SNP marker discoveries useful for supporting the national soybean breedingprograms. The objectives of the present study were to construct soybean genomic libraries, to resequence the whole genome offive Indonesian soybean genotypes, and to identify SNPs based on the resequence data. The studies consisted of genomiclibrary construction and quality analysis, resequencing the whole-genome of five soybean genotypes, and genome-wide SNPidentification based on alignment of the resequence data with reference sequence, Williams 82. The five Indonesian soybeangenotypes were Tambora, Grobogan, B3293, Malabar, and Davros. The results showed that soybean genomic library wassuccessfully constructed having the size of 400 bp with library concentrations range from 21.2–64.5 ng/μl. Resequencing of thelibraries resulted in 50.1 x 109 bp total genomic sequence. The quality of genomic library and sequence data resulted from thisstudy was high as indicated by Q score of 88.6% with low sequencing error of only 0.97%. Bioinformatic analysis resulted in atotal of 2,597,286 SNPs, 257,598 insertions, and 202,157 deletions. Of the total SNPs identified, only 95,207 SNPs (2.15%) werelocated within exons. Among those, 49,926 SNPs caused missense mutation and 1,535 SNPs caused nonsense mutation. SNPsresulted from this study upon verification will be very useful for genome-wide SNP chip development of the soybean genome toaccelerate breeding program of the soybean

Konstruksi Pustaka Genom Kakao (Theobroma Cacao L.) Untuk Sekuensing Genom Total Menggunakan Next Generation Sequencing HiSeq2000

Pemuliaan kakao secara konvensional memerlukan waktu panjang (10-15 tahun). Pemanfaatan marka DNA akan memperpendek siklus pemuliaan kakao. Tujuan penelitian ini adalah mengkonstruksi pustaka genom tiga genotipe kakao yang dapat digunakan untuk sekuensing genom total kakao menggunakan NGS HiSeq2000 dan mendapatkan data resekuen genom total tiga genotipe kakao. Bahan tanaman terdiri dari tiga klon unggul kakao (ICCR02, ICCR04, dan SUL02) diperoleh dari Balittri, Pakuwon. DNA genomik diisolasi dari daun muda sebagai bahan konstruksi pustaka genom total. Sekuensing pustaka dilakukan pada mesin HiSeq2000 mengikuti protokol dari Illumina. Pustaka genom yang telah berhasil dikonstruksi berukuran 300 pasang basa (bp) masing-masing dengan konsentrasi 14,70 ng/µL (ICCR02), 15,20 ng/µL (ICCR04), dan 12,90 ng/µL (SUL02). Ukuran dan konsentrasi pustaka genom yang dihasilkan sangat ideal untuk sekuensing menggunakan HiSeq2000. Sekuensing ketiga genom menghasilkan data sekuen 52,9 x 109 bp. Klaster DNA pustaka genom memiliki nilai Q scores>30 (75,0%) dengan tingkat kesalahan pembacaan basa rendah (1,47%). Nilai densitas klaster, persen klaster PF, intensitas basa, persen phasing, dan persen prephasing menunjukkan kualitas klaster pustaka genom ketiga genotipe kakao termasuk kategori pustaka ideal. Data sekuen yang dihasilkan juga sangat ideal untuk identifikasi marka SNP genom kakao. Koleksi marka SNP digunakan untuk identifikasi gen pengendali karakter penting kakao dan pemuliaan berbasis marka DNA untuk memperpendek siklus pemuliaan kakao. Genomic Library Construction Of Cocoa (Theobroma Cacao L.) For Whole Genome Sequensing Using A Next Generation Sequencer Hiseq2000Conventional cocoa breeding is slow and takes about 10-15 years to complete a breeding cycle. Applying genomic technology using DNA markers will significantly decrease cocoa breeding cycle. The objectives of this study were to construct cocoa whole genome genomic libraries to be used for resequencing the whole genome of cocoa and obtain whole genome resequence data of three cocoa genotypes. Three Indonesian cocoa genotypes (ICCR02, ICRR04, and SUL02) were used. DNA genomic was isolated from young leaf and used to construct genomic DNA libraries and generate DNA clusters. DNA clusters were sequenced using a HiSeq2000 platform. The whole genome libraries of the cocoa genotypes were successfully constructed. The library size was 300 bp with concentrations of 14.70 ng/µL (ICCR02), 15.20 ng/µL (ICCR04), and 12.90 ng/µL (SUL02), respectively. The genomic library size and concentrations are suitable for sequencing study using the NGS HiSeq2000. Total sequencing output obtained was 52.9 x 109 bp. The genomic library clusters resulted during the sequencing process demonstrated the Q scores > 30 of 75.0% with low error sequencing rate of 1.47%. Cluster densities, percentage of cluster PF, base intensity, and percentage of phasing and prephasing indicated the cluster quality of the genomic libraries is classified as an ideal one to be used for resequencing study using NGS HiSeq2000. The resequence data were ideal for SNP marker discovery. SNP markers are used to identify economically important genes of cocoa and marker-aided cocoa breeding to decrase the cocoa breeding cycle

Genomic Variation of Five Indonesian Cacao (Theobroma Cacao L.) Varieties Based on Analysis Using Next Generation Sequencing

Indonesian cacao productivity is still low mainly due to the lack availability of superior cacao planting materials. A new breeding method is necessary to expedite cacao yield improvement programs. To date, no study has yet been done to characterize Indonesian cacao varieties at the whole genome level. The objective of this study was to characterize genomic variation of five superior Indonesian cacao varieties using next-generation sequencing. Genetic materials used were five Indonesian cacao varieties, i.e. ICCRI2, ICCRI3, ICCRI4, SUL2 and ICS13. Genome sequences were mapped to the cacao reference genome sequence of Criollo variety. Sequence alignment and genomic variation discovery were done using Bowtie2 and mpileup software of Samtools, respectively. A total of 2,326,088 single nucleotide polymorphisms (SNPs) and 362,081 insertions and deletions (Indels) were obtained from this study. In average, a DNA variant was identified in every 121 nucleotides of the genome sequence. Most of the DNA variants were located outside the genes. Only 347,907 SNPs and Indels (13.18%) were located within protein coding region (exon). Among the DNA variations within exon, 188,949 SNPs caused missense mutation and 1,535 SNPs induced nonsense mutation. Unique gene-based SNPs were also discovered from this study that can be used as fingerprints for the particular cacao variety. The DNA variants obtained were excellent DNA marker resources to support cacao breeding programs. The SNPs discovered are useful as materials for genome-wide SNP chip development to be used for gene and QTL tagging of important traits for expediting national cacao breeding program

Identification of Single Nucleotide Polymorphisms on Cattle Breeds in Indonesia Using Bovine 50k

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

Genetic Diversity Analysis and F2 Population Development for Breeding of Long Juvenile Trait in Soybean

Genetic diversity analysis using molecular markers is an important step for selecting appropriate parents in a soybean breeding program. The aims of this study were to (1) analyze genetic diversity of 29 soybean genotypes assessed with 27 SSR markers for selecting appropriate parents and (2) develop F2 populations to be used for breeding long juvenile (LJ) trait in soybean tobe cultivated in short photoperiod condition. The soybean genotypes used consisted of 11 Indonesian soybean genotypes and 18 genotypes introduced from the USA. F2 populations were developed by crossing Grobogan with three introduced genotypes carrying LJ character. The PIC values of the 27 SSR markers ranged from 0.87 to 0.96. Cluster analysis resulted in three mainclusters at coefficient similarity of 0.76. The five LJ introduced accessions and the nine Indonesian genotypes showed high genetic distances and are useful as parent pairs for developing breeding populations. The F1 progeny phenotypicperformances of the cross far exceeded the performaces of both parents. Three F2 populations were developed by crossing the distantly related soybean genotypes. The F2 populations were verified by using SSR markers and it was found that they segregated in a 1:2:1 ratio confirming the segregation ratio of codominant SSR markers. The F2 populations should be useful for breeding LJ characters to improve soybean productivity in low latitude tropical countries such as Indonesia, which has day length of approximately 12 h all year round

Genetic Mapping of SSR Markers in Eight Soybean Chromosomes Based on F2 Population B3462 X B3293

Genetic Mapping of SSR Markers in Eight SoybeanChromosomes Based on F2 Population B3462 x B3293. IMade Tasma, Ahmad Warsun, Dani Satyawan, SaptowoJ. Pardal, and Slamet. Aluminum toxicity is one of the maincontrains for cultivating soybean in acid soils. GeneticHak Cipta © 2011, BB-Biogenmapping of SSR markers is one step for detecting aluminumtoxicitytolerant QTLs in soybean. Another step is tophenotype the same population at various aluminum-toxicityenvironments. The objectives of this study were to analyzethe segregation of SSR markers in progenies of an F2population and map the markers in 8 soybean chromosomes.The F2 population was previously developed bycrossing the Al-tolerant parent B3462 and the Al-sensitiveparent B3293. Polymorphic SSR markers in the parents wereused to PCR amplify DNA of the 100 F2 progenies. PCRproducts were separated using agarose or polyacrylamidegels. A Chi-Square test was done with a null hypothesis thatprogenies segregated in a 1 : 2 : 1 ratio. Results showed that125 SSR markers were polymorphics in the parents. Out of125 polymorphic markers, 122 were segregated in theprogenies of the F2 population. Among the segregatingmarkers, 114 were segregated in a 1 : 2 : 1 ratio. Only 8markers (5.6%) did not follow the 1 : 2 : 1 ratio. One hundredand nineteen SSR markers were mapped in 8 soybeanchromosomes. These include 18 markers in chromosomeA2, 10 in B1, 16 (C1), 16 (F), 10 (G), 23 (J), 16 (L), and 10 (N).Total genetic maps covered was 1,194.8 cM with averagemap distances between two adjacent markers of 10.7 cM.Further SSR marker enrichment is required to fill in the gapsof several chromosomal regions. Genetic maps presented inthis study should be useful for detection of Al-toxicitytolerant QTLs in soybean

Research data supporting "Local Nanoscale Phase Impurities are Degradation Sites in Halide Perovskites"

Understanding the nanoscopic chemical and structural changes that drive instabilities in emerging energy materials is essential for mitigating device degradation. The power conversion efficiency of halide perovskite photovoltaic devices has reached 25.7% in single junction and 29.8% in tandem perovskite/silicon cells1,2, yet retaining such performance under continuous operation has remained elusive3. Here, we develop a multimodal microscopy toolkit to reveal that in leading formamidinium-rich perovskite absorbers, nanoscale phase impurities including hexagonal polytype and lead iodide inclusions are not only traps for photo-excited carriers which themselves reduce performance4,5, but via the same trapping process are sites at which photochemical degradation of the absorber layer is seeded. We visualise illumination-induced structural changes at phase impurities associated with trap clusters, revealing that even trace amounts of these phases, otherwise undetected with bulk measurements, compromise device longevity. The type and distribution of these unwanted phase inclusions depends on film composition and processing, with the presence of polytypes being most detrimental for film photo-stability. Importantly, we reveal that performance losses and intrinsic degradation processes can both be mitigated by modulating these defective phase impurities, and demonstrate that this requires careful tuning of local structural and chemical properties. This multimodal workflow to correlate the nanoscopic landscape of beam sensitive energy materials will be applicable to a wide range of semiconductors for which a local picture of performance and operational stability has yet to be established.Royal Society (UF150033) European Research Council (756962) European Commission Horizon 2020 (H2020) Marie Sklodowska-Curie actions (841136) European Commission Horizon 2020 (H2020) Marie Sklodowska-Curie actions (841386) Engineering and Physical Sciences Research Council (EP/S030638/1) EPSRC (EP/T02030X/1) EPSRC (2127077) EPSRC (EP/V012932/1) Engineering and Physical Sciences Research Council (EP/R023980/1