Floristic Diversity And Conservation Importance of Bukit Bauk (Terengganu) in Peninsular Malaysia

Bukit Bauk is an isolated, coastal small hilly range which is part of the Terengganu hills situated in the low hills at the southern end of the East Range in the east coast of Terengganu in Peninsular Malaysia. These hills have been deemed to be extremely interesting botanically because they were surmissed to contain a high number of species and endemic plant'). However to date, a satisfactory inventory of plant species in the east coast have yet to be taken (are under-collected) and studied botanically. This study was therefore carried out to determine the floristic diversity of Bukit Bauk and subsequently compile a floristic checklist by checking relevant literature and through fieldwork; to assess the conservation importance of Bukit Bauk; to evaluate the conservation status of important species, where sampling plots and size were site and species specific and to determine threats to the flora of Bukit Bauk. The flora of Bukit Bauk was found to comprise 638 species (7.7% of the total flora of the Malay Peninsula) belonging to 285 genera and 103 families. Of these, 14.3% were endemic taxa (91 taxa) which constituted about 3.6% of the total number of endemic species in the Malay Peninsula. Bukit Bauk also contained 17.6% of the total number of tree species and 8.0% of endemic tree species in Peninsular Malaysia. The most speciose families on Bukit Bauk were Euphorbiaceae (59 species), Dipterocarpaceae (43 species), Rubiaceae (36 species) Palmae and Guttiferae (31 species respectively). Several specific types of vegetation could be distinguished on Bukit Bauk and it'> nearby lowland forest according to habitat, altitude zonation and floristic composition. The vegetation types were lowland dipterocarp forest (flatland, foothills and valley bottoms), vegetation on the seaward front, hill dipterocarp forest (steep slopes and hill ridges), vegetation on the summit, vegetation of disturbed areas and peat swamp forest. A total of 385 species (60.3%) of species found on Bukit Bauk provide one or more usage to humankind with 58.7% contributing more than one type of usage. Edible wild plants, products and medicinal plants are important to the local community in Terengganu

Utilizing a discovery learning, real-world based fruit juice clarification experiment to enhance teaching and learning of biological enzyme concepts

Discovery learning is an approach that encourages students to become active participants in the learning process by exploring concepts and answering questions through experience. It is one of several inquiry-based learning techniques that seems particularly suited to the instruction of science since performing experiments is one of the key methods in discovery learning. However, the efficacy of discovery learning projects have not been explored much in Malaysia. In this study, an experiment integrated with real-world biotechnology industry example focusing on the function of the enzyme pectinase in the clarification of fruit (apple) juice was adapted and introduced to a group of urban, international secondary school science students who had undergone prior direct instructional guidance on the biological role and function of enzymes. The students were asked to complete a set of pre-experiment and post-experiment questions in order to analyse the impact of the experiment on their understanding of this topic. Results suggest that this discovery learning project do strengthen the learners’ prior knowledge and understanding of the function of biological enzymes through application of concept based on real world practice. High level of positive feedback was received (86.2%), with the students commenting on the “fun aspect”, being excited about being able to perform the experiment and expanding their understanding by linking their findings with a real-world, industrial application. Given the reported steady decline of Malaysian students enrolled in STEM (Science, Technology, Engineering and Mathematics) courses at secondary and tertiary levels, our findings suggest that developing and including more real-world, discovery type projects in secondary schools may help to effectively raise student interests in science subjects such as biology through new learning approaches. &nbsp

Selection and validation of reference genes for qRT-PCR expression analyses of leaf, flower and capsules of Impatiens balsamina (Balsaminaceae)

Impatiens balsamina (Balsaminaceae) is both an ornamental and medicinal plant featured in many Asian traditional remedies due to an abundance of selected secondary metabolites with beneficial pharmacological properties. Attempts to improve production of biocompounds have led to characterization of genes, gene expression and pathways involved in secondary metabolites biosynthesis in I. balsamina. Gene expression analysis by quantitative reverse transcription PCR (qRT-PCR) technique has been well-established but its reliability is heavily dependent on the selection of suitable reference genes, which information is currently lacking for I. balsamina, and other Impatiens species. In this study, six typical housekeeping genes including actin-like protein (ACT), polyubiquitin-A (UBQ), ubiquitin-conjugated enzyme E2 (UBC), fructose-bisphosphate aldolase (FBA), elongation factor 1-alpha (EF1-α), and clathrin light chain 1 (CLC) were evaluated as candidate reference genes. Expression stability was tested in four tissue types (leaf, flower, early- and mature stage capsules) of I. balsamina. FBA, CLC, and EF1-α were observed to be the most stable reference genes across the tested tissue types. When expression data were normalised by the most stable FBA gene, the target secondary metabolite biosynthesis pathway genes showed significant different expression pattern compared to the least stable UBQ gene. The use of multiple reference genes in the combination of either FBA + EF1-α or FBA + CLC + EF1-α was observed to give more reliable results compared with a single gene. This study provides a resource for selection of suitable reference gene(s) for future gene expression normalisation experiments in I. balsamina

Characterization and comparative sequence analysis of the DNA mismatch repair MSH2 and MSH7 genes from tomato

DNA mismatch repair proteins play an essential role in maintaining genomic integrity during replication and genetic recombination. We successfully isolated a full length MSH2 and partial MSH7 cDNAs from tomato, based on sequence similarity between MutS and plant MSH homologues. Semi-quantitative RT-PCR reveals higher levels of mRNA expression of both genes in young leaves and floral buds. Genetic mapping placed MSH2 and MSH7 on chromosomes 6 and 7, respectively, and indicates that these genes exist as single copies in the tomato genome. Analysis of protein sequences and phylogeny of the plant MSH gene family show that these proteins are evolutionarily conserved, and follow the classical model of asymmetric protein evolution. Genetic manipulation of the expression of these MSH genes in tomato will provide a potentially useful tool for modifying genetic recombination and hybrid fertility between wide crosses

A modified ctab-based protocol for total RNA extraction from the medicinal plant Impatiens balsamina (Balsaminaceae) for next-generation sequencing studies

High RNA quality, integrity and reproducibility are essential for functional genomics study involving library preparation and sequencing using next generation sequencing (NGS) technologies. The medicinal herbaceous plant, Impatiens balsamina, possess a rich source of diverse bioactive compounds including polysaccharides and phenolic compounds, hindering the extraction of high quality total RNAs. Four existing RNA extraction protocols were performed using fresh leaf material of I. balsamina, namely the CTAB method, the TRI reagent® method, modified TRI reagent® method and a commercial kit but the results were unsatisfactory. This led to the development of a modified CTAB protocol by combining CTAB/ polyvinylpyrrolidone (PVP) extraction with using commercial spin column purification for successful isolation of high quality total RNA from the leaf material of I. balsamina, that is suitable for NGS applications (RIN values > 7). This new method also successfully extracted total RNA from flower buds and capsules of I. balsamina

Begonia yenyeniae (Begoniaceae), a new species from Endau Rompin National Park, Johor, Malaysia

Begonia yenyeniae is a new species of horticultural value known only from the Endau Rompin National Park, Peninsular Malaysia. It is similar to Begonia rajah with which it had previously been confused in the number of tepals and leaf characters. The new species is compared with three similar species, B. foxworthyi, B. rajah and B. reginula and photographs of all four species and descriptions of B. yenyeniae and B. rajah are provided. Molecular analysis using the ndhF-rpl132 chloroplast marker confirms the four species as distinct. Amongst native species, the three variegated species, B. yenyeniae, B. rajah and B. reginula, are some of the most popular Malaysian begonias in cultivation. Based on its restricted distribution, Begonia yenyeniae, under the IUCN Red List Categories and Criteria, is assessed as Critically Endangered

Characterisation of AmCCR1 and pseudoCOMTAm promoters in Acacia mangium

Acacia mangium is one of the most important species in forest plantation industry in Southeast Asia. Lignin is a complex polymer found in plant which has to be removed using harsh and toxic chemicals for the production of high quality paper. Understanding the complex pathway that underlies the regulation of lignin biosynthetic genes requires in depth knowledge of the genes involved and it’s regulatory elements. Using Thermal Asymmetric Interlaced PCR, a 770bp promoter of pseudoCOMTAm and 619bp of AmCCR1 promoter were isolated. Bioinformatics analysis revealed the presence of cis acting elements commonly found in lignin biosynthetic genes such as TATA box, CAAT box, W box, AC-I and AC-11 elements on both promoters

Data from: Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia

Weedy rice is a close relative of domesticated rice (Oryza sativa) that competes aggressively with the crop and limits rice productivity worldwide. Most genetic studies of weedy rice have focused on populations in regions where no reproductively compatible wild Oryza species occur (North America, Europe, northern Asia). Here we examined the population genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be found growing in close proximity to cultivated and weedy rice. Using 375 accessions and a combined analysis of 24 neutral SSR loci and two rice domestication genes (sh4, controlling seed shattering, and Bh4, controlling hull color), we addressed the following questions: 1) What is the relationship of Malaysian weedy rice to domesticated and wild rice, and to weedy rice strains in the US? 2) To what extent does the presence of O. rufipogon influence the genetic and phenotypic diversity of Malaysian weeds? 3) What do the distributions of sh4 and Bh4 alleles and associated phenotypes reveal about the origin and contemporary evolution of Malaysian weedy rice? Our results reveal: independent evolutionary origins for Malaysian weeds and US strains, despite their very close phenotypic resemblance; wild-to-weed gene flow in Malaysian weed populations, including apparent adaptive introgression of seed-shattering alleles; and a prominent role for modern Malaysian cultivars in the origin and recent proliferation of Malaysian weeds. These findings suggest that the genetic complexity and adaptability of weedy crop relatives can be profoundly influenced by proximity to reproductively compatible wild and domesticated populations

##Song12_Suppl_RiceInfo+sh4+Bh4+sample_code_140910

This file contains sample naming for sh4 multiple sequence alignment

Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR

The retrotransposon-based sequence-specific amplification polymorphism (SSAP) marker system was used to assess the genetic diversities of collections of tomato and pepper industrial lines. The utility of SSAP markers was compared to that of amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. On the basis of our results, SSAP is most informative of the three systems for studying genetic diversity in tomato and pepper, with a significant correlation of genetic relationships between different SSAP datasets and between SSAP, AFLP and SSR markers. SSAP showed about four- to ninefold more diversity than AFLP and had the highest number of polymorphic bands per assay ratio and the highest marker index. For tomato, SSAP is more suitable for inferring overall genetic variation and relationships, while SSR has the ability to detect specific genetic relationships. All three marker results for pepper showed general agreement with pepper types. Additionally, retrotransposon sequences isolated from one species can be used in related Solanaceae genera. These results suggest that different marker systems are suited for studying genetic diversity in different contexts depending on the group studied, where discordance between different marker systems can be very informative for understanding genetic relationships within the study group