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Edamame is a vegetable-typed soybean with a large pod size that is very popular as a snack-type food with a sweeter taste. DNA fingerprinting analysis of edamame lines will produce specific identities that are useful for digital registration and protecting superior edamame genotypes. The objective of this study was to analyse DNA fingerprints of edamame advanced lines using SSR markers to obtain fingerprints and construct barcodes on edamame advanced lines. Eight edamame superior advanced lines and 17 SSR markers were used in this study. The SSR markers used were those that are well distributed across soybean chromosomes and were previously well characterised for genetic diversity analysis purposes. Results showed that the total SSR alleles detected in this study were 149 with the average alleles per marker locus being 8.76, an average of gene diversity of 0.83, and an average Polymorphic Information content (PIC) value of 0.81. The PIC values observed ranged from 0.51 (Satt063) to 0.91 (Satt009). Phylogenetic analysis demonstrated that the eight edamame genotypes analysed were divided into two main clusters and are considered closely related to each other having genetic distance values ranging from 3% to 23%. Out of 17 SSR markers analysed, five markers (Satt030, Satt045, Satt147, Satt431, and Satt463) were informative and were very appropriate to be used as DNA fingerprints and the five markers were then used to construct barcodes for edamame genotypes tested in this study. The barcodes should be useful for protection purposes of the superior edamame genotypes analysed in this study. [ABSTRACT FROM AUTHOR]

Oil palm is the most productive oil crop in the world but breeding a new oil palm variety is a costly and time-consuming activity due to its long reproductive cycle and large plant size. Genomic selection technology utilizes whole-genome genotypic data to predict the best-performing breeding lines and enable the selection of breeding lines from the seedling stage while maximizing genetic gains in each selection cycle. We explored the utility of genomic selection implemented using the rrBLUP package in predicting the best breeding lines in a population comprising 499 F1, BC1, and parental generations from crosses between various Elaeis guineensis and Elaeis oleifera accessions. Phenotypic scores for 29 traits were collected from each line and combined with genotypic data from 3908 SNP markers to calculate the marker effects for trait predictions. When all lines were treated as a single population, and 60% of the population was selected randomly as the training population, high prediction accuracy was observed in some traits, and 19 traits had prediction accuracy between 0.406 to 0.709. However, the prediction accuracy dropped significantly in most traits when we simulated intergenerational prediction by using only the F1 and parental lines as the training population and used the calculated marker effects to predict the phenotypes of BC1 lines. Only two traits (mesocarp per fruit and leaflet width) retained accuracy values larger than 0.400. Thus, further investigations and optimizations are still required to improve the utility of rrBLUP for intergenerational genomic selection in pseudo-backcross populations. [ABSTRACT FROM AUTHOR]

Ciherang is an Indonesian rice mega variety that was developed from IR64. To study the extent of genetic exchange on IR64 genome during Ciherang development and to identify the effects of those genomic changes, whole-genome sequencing and analyses were conducted on Ciherang and IR64. Ciherang genome sequencing generated reads that are >24 times the size of rice genome and 98.6% of those sequences could be mapped to the Nipponbare reference genome. Variant calling showed that IR64 and Ciherang had 3,015,867 (0.8%) and 2,954,801 (0.79%) sequence differences to Nipponbare, respectively, while Ciherang and IR64 only differed by 0.13%. There were 493,298 sequence variations between Ciherang and IR64, and 434,890 of them were single nucleotide polymorphisms (SNPs) while the remaining 58,408 were insertions/deletions (indels). Sequence differences are prominent in chromosomes 8, 10, and 12, indicating that many introgressions from the donor parents were retained in those chromosomes. There are 1,007 high impact mutations in Ciherang that are polymorphic to IR64, and some of them were found in genes affecting panicle and seed characteristics like Os01g0588900 and Os02g0154200. These discoveries will aid breeding programs that utilize IR64 or Ciherang and can serve as the basis for intellectual property rights management for future varieties. [ABSTRACT FROM AUTHOR]

Oil palm is an important estate crop and Indonesia is the largest palm oil producer in the world. Since the average yield is relatively low, a more efficient breeding program that utilizes the latest technological developments in DNA analysis is necessary. The objectives of this study were to (1) characterize genomic variations of three Indonesian oil palm genotypes based on whole genome sequencing using next-generation sequencing (NGS) HiSeq; (2) provide genomic data resources for future oil palm breeding program. Whole genome sequencing was performed on three Indonesian oil palm genotypes (Dura, Pisifera, and Elaeis oleifera from Brazil). Sequence data were aligned with that of the Eg5 genome reference sequences. The average sequence coverage depth for all loci was 34 and more than 95% of the genome was sequenced at least ten times. Comparison of the sequences revealed 3,735,311 sequence changes, an average of one sequence change per 197 bases. Among these changes, 3,371,088 were SNPs and 364,233 were insertions and deletions (indels). DNA variations found within exons total 329,087. Of these, 214,068 SNPs variations were capable of causing modification in the amino acid composition of the encoded proteins (nonsynonymous mutations). A genomic database was constructed to manage DNA variations resulted from this study. The SNPs collected from this study should be useful for constructing high density oil palm SNP chip to expedite future national oil palm breeding program. [ABSTRACT FROM AUTHOR]

Root rot caused by Phytophthora capsici is the most devastating disease in Indonesia causing up to 100% yield loss. Breeding resistant cultivars is the most effective strategy to reduce losses caused by this disease. This study aimed to (1) determine the parentage confirmation and genetic relatedness of the parents, (2) genotype two F1 populations using a subset of six markers, and (3) measure the horticultural characteristics of two F1 populations. Tanjung-2 and Ciko varieties were used as recurrent parent (RP) in a cross with donor parent (DP) CM334 having Phytophthora root rot resistance gene. Molecular analysis of the parents was done using 33 markers linked to the resistance genes of which 17 markers demonstrated clear polymorphism. The phylogenetic tree classified the parents into two groups, i.e. group 1 consisted of two RPs (Ciko and Tanjung-2) and group 2 consisted of CM334. Clustering analysis clearly revealed that genetic materials used in this study were not closely related. Genotyping using six polymorphic markers showed that the marker-hybrid purity index ranged from 47.17 to 100% for F1 Tanjung-2/CM334 and 80 to 100% for F1 Ciko/CM334. The selected F1 was self-hybridized to develop F2 population. Horticulture characterization showed that branch number per plant, fruit diameter, fruit weight, and total fruit weight per plant of F1 Ciko/CM334 were higher than F1 Tanjung- 2/CM334. Meanwhile, for plant height, canopy diameter, flowering time, and harvesting time the F1 Tanjung-2/CM334 demonstrated better performances than the F1 Ciko/CM334. The populations developed from this study can be used in genetic linkage mapping of genes conferring resistance to P. capsici. [ABSTRACT FROM AUTHOR]