Recloning of regenerated plantlets from elite oil palm (Elaeis guineensis Jacq.) cv. Tenera

Plant regeneration in oil palm cv. Tenera via somatic embryogenesis was conducted using regenerated plantlets as an explant source. Explants from different positions – apex, middle and basal segments of regenerated plantlets – were cultured in N6 medium supplemented with 100, 120 and 140 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D) in the presence of activated charcoal. The production of embryogenic calli was affected by 2,4-D concentration and explant position; 2,4-D 120 mg/L was the most effective (62.53%) in inducing embryogenic calli from the basal segment 5 months after inoculation. After 3 months of culture in embryo maturation medium, an average of 36 ± 8 somatic embryos per embryogenic callus was obtained. When transferred to plant regeneration medium for 3 to 4 months, these somatic embryos differentiated into shoots, with ranges of 6 to 40 and 4 to 32 shoots on the medium with and without 2-isopentyladenine (6-dimethylaminopurine) (2iP), respectively. Plantlets (6 to 8 cm height) with balanced shoots and roots were obtained after 12 to 14 months. Histological analysis confirmed the initiation, development and germination of somatic embryos from explants of regenerated plantlets. Simple sequence repeat (SSR) analysis showed the genetic identity and uniformity between the first and second regenerated plantlets at five SSR loci.Key words: Elaeis guineensis Jacq., genetic identity, regenerated plantlets, somatic embryogenesis, SSR marker

Sequence Variation and Haplotype Structure in the Lox3 Gene of Oryza sativa L

ABSTRACT For 24 rice (Oryza sativa L.) varieties, genetic variation was studied of the Lox3 gene in samples of the two subspecies, japonica and indica. The genomic DNA was amplified, followed by DNA sequencing to detect sequence variation. A total of 13 single nucleotide polymorphisms (SNPs) was detected in the exon 4 containing lipoxygenase domain. The nucleotide diversity in the Lox3 region of O. sativa was 0.00112, which could be classified into ten haplotypes. Phylogenetic relationships among varieties were inferred using neighbor-joining methods. Cluster analysis showed that all populations could be clustered into five groups. The results also revealed that the haplotype of Oryza sativa ssp.japonica rice is distinctively separated from that of Oryza sativa ssp.indica rice

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ~32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene

Developing know-how for the improvement and sustainable management of teak genetic resources

The project had the following objectives: To trace and quantify genetic diversity of teak within its natural range, DNA markers were used to assay the current distribution of genetic diversity within and between populations, investigate its mating system and establish historical migration patterns. To evaluate the amount of contemporary gene flow through pollen and seed, hypervariable microsatellite DNA markers have been developed for parentage analysis. The molecular work was complemented by field observations of teak flower insect pollinators. To assess the influence of human disturbance, the genetic diversity in teak forests that have been undisturbed, lightly or heavily disturbed have been assessed and compared for both population genetic diversity and contemporary gene flow processes