Genotyping by sequencing for the construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield related quantitative trait loci.

Background: Oil palm (Elaeis guineensis Jacq.) is one of the major oil-producing crops. Improving the quality and increasing the production yield of oil palm have been the primary focuses of both conventional and modern breeding approaches. However, the conventional breeding approach for oil palm is very challenging due to its longevity, which results in a long breeding cycle. Thus, the establishment of marker assisted selection (MAS) for oil palm breeding programs would speed up the breeding pipeline by generating new oil palm varieties that possess high commercial traits. With the decreasing cost of sequencing, Genotyping-by-sequencing (GBS) is currently feasible to many researchers and it provides a platform to accelerate the discovery of single nucleotide polymorphism (SNP) as well as insertion and deletion (InDel) markers for the construction of a genetic linkage map. A genetic linkage map facilitates the identification of significant DNA regions associated with the trait of interest via quantitative trait loci (QTL) analysis. Methods: A mapping population of 112 F1 individuals from a cross of Deli dura and Serdang pisifera was used in this study. GBS libraries were constructed using the double digestion method with HindIII and TaqI enzymes. Reduced representation libraries (RRL) of 112 F1 progeny and their parents were sequenced and the reads were mapped against the E. guineensis reference genome. To construct the oil palm genetic linkage map, informative SNP and InDel markers were used to discover significant DNA regions associated with the traits of interest. The nine traits of interest in this study were fresh fruit bunch (FFB) yield, oil yield (OY), oil to bunch ratio (O/B), oil to dry mesocarp ratio (O/DM) ratio, oil to wet mesocarp ratio (O/WM), mesocarp to fruit ratio (M/F), kernel to fruit ratio (K/F), shell to fruit ratio (S/F), and fruit to bunch ratio (F/B). Results: A total of 2.5 million SNP and 153,547 InDel markers were identified. However, only a subset of 5,278 markers comprising of 4,838 SNPs and 440 InDels were informative for the construction of a genetic linkage map. Sixteen linkage groups were produced, spanning 2,737.6 cM for the maternal map and 4,571.6 cM for the paternal map, with average marker densities of one marker per 2.9 cM and one per 2.0 cM respectively, were produced. A QTL analysis was performed on nine traits; however, only QTL regions linked to M/F, K/F and S/F were declared to be significant. Of those QTLs were detected: two for M/F, four for K/F and one for S/F. These QTLs explained 18.1-25.6% of the phenotypic variance and were located near putative genes, such as casein kinase II and the zinc finger CCCH domain, which are involved in seed germination and growth. The identified QTL regions for M/F, K/F and S/F from this study could be applied in an oil palm breeding program and used to screen palms with desired traits via marker assisted selection (MAS).

Recent developments, applications and challenges for carbon quantum dots as a photosynthesis enhancer in agriculture.

Since the world's population is expanding, mankind may be faced with a huge dilemma in the future, which is food scarcity. The situation can be mitigated by employing sustainable cutting-edge agricultural methods to maintain the food supply chain. In recent years, carbon quantum dots (CQD), a member of the well-known carbon-based nanomaterials family, have given rise to a new generation of technologies that have the potential to revolutionise horticulture and agriculture research. CQD has drawn much attention from the research community in agriculture owing to their remarkable properties such as good photoluminescence behaviour, high biocompatibility, photo-induced electron transfer, low cost, and low toxicity. These unique properties have led CQD to become a promising material to increase plant growth and yield in the agriculture field. This review paper highlights the recent advances of CQD application in plant growth and photosynthesis rate at different concentrations, with a focus on CQD uptake and translocation, as well as electron transfer mechanism. The toxicity and biocompatibility studies of CQD, as well as industrial scale applications of CQD for agriculture are discussed. Finally, the current challenges of the present and future perspectives in this agriculture research are presented.

Influence of Climatic Factors and Nest Tree Characteristics on the Nest Structures of the Baya Weaver (Ploceus philippinus) in Peninsular Malaysia.

The baya weaver (Ploceus philippinus: Ploceidae), found across South and Southeast Asia, is known for its oblique-shaped overhanging nests. During the breeding season, females select from partially built ('helmet'-stage) nests constructed by the males, after which nests are completed and used by the birds. Reproductive success is linked to an optimal microclimate within these nest structures. We recorded nest tree and nest structure characteristics of 66 fully completed nests for 22 colonies located in two climatically dissimilar sites in Peninsular Malaysia and examined how these factors affected the microclimate within six nests that were randomly selected at each location. Total vertical length of the nests, the height of nests from the ground, and the diameter at breast height of the nest trees recorded for the Selangor and Perlis colonies (in the southwest and north, respectively), were significantly different. The climatic variables inside and outside the nests correlated significantly in both sites. Our findings indicate that nest structures differed in Selangor and Perlis and were linked to nest microclimate, possibly being influenced by the surrounding temperature.

Potentially Toxic Metals in the High-Biomass Non-Hyperaccumulating Plant Amaranthus viridis: Human Health Risks and Phytoremediation Potentials.

Human health risk and phytoremediation of potentially toxic metals (PTMs) in the edible vegetables have been widely discussed recently. This study aimed to determine the concentrations of four PTMs, namely Cd, Fe, Ni, and Zn) in Amaranthus viridis (leaves, stems, and roots) collected from 11 sampling sites in Peninsular Malaysia and to assess their human health risk (HHR). In general, the metal levels followed the order: roots > stems > leaves. The metal concentrations (µg/g) in the leaves of A. viridis ranged from 0.45 to 2.18 dry weight (dw) (0.05−0.26 wet weight (ww)), 74.8 to 535 dw (8.97−64.2 ww), 2.02 to 7.45 dw (0.24−0.89 ww), and 65.2 to 521 dw (7.83−62.6 ww), for Cd, Fe, Ni, and Zn, respectively. The positive relationships between the metals, the plant parts, and the geochemical factions of their habitat topsoils indicated the potential of A. viridis as a good biomonitor of Cd, Fe, and Ni pollution. With most of the values of the bioconcentration factor (BCF) > 1.0 and the transfer factor (TF) > 1.0, A. viridis was a very promising phytoextraction agent of Ni and Zn. Additionally, with most of the values of BCF > 1.0 and TF < 1.0, A. viridis was a very promising phytostabiliser of Cd and Fe. With respect to HHR, the target hazard quotients (THQ) for Cd, Fe, Pb, and Zn in the leaves of A. viridis were all below 1.00, indicating there were no non-carcinogenic risks of the four metals to consumers, including children and adults. Nevertheless, routine monitoring of PTMs in Amaranthus farms is much needed.

Invasive Weed Asystasia gangetica as a Potential Biomonitor and a Phytoremediator of Potentially Toxic Metals: A Case Study in Peninsular Malaysia.

The invasive weed Asystasia gangetica was investigated for its potential as a biomonitor and as a phytoremediator of potentially toxic metals (PTMs) (Cd, Cu, Ni, Pb, and Zn) in Peninsular Malaysia owing to its ecological resistance towards unfavourable environments. The biomonitoring potential of PTMs was determined based on the correlation analysis of the metals in the different parts of the plant (leaves, stems, and roots) and its habitat topsoils. In the roots, the concentrations (mg/kg dry weight) of Cd, Cu, Ni, Pb, and Zn ranged from 0.03 to 2.18, 9.22 to 139, 0.63 to 5.47, 2.43 to 10.5, and 50.7 to 300, respectively. In the leaves, the concentrations (mg/kg dry weight) of Cd, Cu, Ni, Pb, and Zn ranged from 0.03 to 1.16, 7.94 to 20.2, 0.03 to 6.13, 2.10 to 21.8, and 18.8 to 160, respectively. In the stems, the concentrations (mg/kg dry weight) of Cd, Cu, Ni, Pb, and Zn ranged from 0.03 to 1.25, 5.57 to 11.8, 0.23 to 3.69, 0.01 to 7.79, and 26.4 to 246, respectively. On the other hand, the phytoremediation potential of the five metals was estimated based on the bioconcentration factor (BCF) and the translocation factor (TF) values. Correlation analysis revealed that the roots and stems could be used as biomonitors of Cu, the stems as biomonitors of Ni, the roots and leaves as biomonitors of Pb, and all three parts of the plant as biomonitors of Zn. According to the BCF values, in the topsoil, the "easily, freely, leachable, or exchangeable" geochemical fractions of the five metals could be more easily transferred to the roots, leaves, and stems when compared with total concentrations. Based on the TF values of Cd, Ni, and Pb, the metal transfer to the stems (or leaves) from the roots was efficient (>1.0) at most sampling sites. The results of BCF and TF showed that A. gangetica was a good phytoextractor for Cd and Ni, and a good phytostabilizer for Cu, Pb, and Zn. Therefore, A. gangetica is a good candidate as a biomonitor and a phytoremediator of Ni, Pb, and Zn for sustainable contaminant remediation subject to suitable field management strategies.

Bioaccumulation of zinc in edible tropical vegetables in Peninsular Malaysia and its human health risk assessment based on various ethnicities in Malaysia.

Along with the growing utilization of zinc (Zn) and Zn-containing nanoparticles in various industries, Zn ecotoxicological evaluation on human food supply is necessary even though Zn is generally considered safe and rarely concentrated ecotoxicologically. This study aimed to investigate the bioaccumulation of Zn in 18 species of vegetables (seven leafy, nine fruity vegetables and one species each of tuber and legume) collected from two farming sites in the west coast of Peninsular Malaysia. A human health risk assessment (HHRA) was also conducted. In addition to HHRA based on the general population, HHRA based on each major ethnic group of the Malaysian society was also determined considering that the food consumption pattern would definitely be varied across ethnicities and age groups (children and adults). The study results showed that Zn concentrations were significantly higher (p < 0.05) in leafy vegetables than in other types of vegetables. However, the target hazard quotient (THQ) values were all found to be < 1.0. Therefore, based on the Malaysian ethnicities and age groups with their respective vegetable consumption patterns, the results indicated insignificant noncarcinogenic human health risk of Zn via oral consumption of vegetables by the Malaysian population. As a metric of measurement of HHRA, a comparison of THQ values could yield previously unreported insights into HHRA differences among the compared populations. A comparison of THQ values among the consumer groups indicated higher HHR for Chinese Malaysians and children due to their higher vegetable consumption and lower body weight, respectively. A comparison the Zn intakes of all the consumer groups with the recommended nutrient intakes indicated that the oral consumption of the vegetable species collected in this study would not result in Zn-related hazards and would not be able to fulfil the Zn dietary need of the individual consumer.

Efficacy of KNO3, SiO2 and SA priming for improving emergence, seedling growth and antioxidant enzymes of rice (Oryza sativa), under drought.

Rice is an important staple crop produced and consumed worldwide. However, poor seed emergence is one of the main impediments to obtaining higher yield of rice especially in hot and dry ecosystems of the world that are ravaged by drought. Therefore, this study was carried out to evaluate the effects of potassium nitrate (KNO3), salicylic acid (SA) and silicon dioxide (SiO2) priming in improving emergence, seedling growth, biochemical attributes and antioxidant activities of FARO44 rice under drought conditions. Rice seedlings primed with 2.5% and 5% KNO3, 3% and 3.5% SiO2, and 1 mM and 2.5 mM SA were subjected to three drought levels of low, moderate and severe under the greenhouse. Seed emergence, seedling growth, biochemical attributes and antioxidant activities were thereafter evaluated. Seed priming experiments were laid in a completely randomized design with five replicates per treatment. The results found that rice seedlings responded differently to different priming treatments. However, all primed rice seedlings had significantly (P ≤ 0.05) improved emergence percentage (72-92%), seedling growth, seedling vigor, seedling fresh and dry biomass and shorter emergence time compared with controls. Likewise, total soluble protein content, activities of catalase, ascorbate peroxidase and superoxide dismutase, carbohydrate, soluble sugar and total chlorophyll contents of rice seedlings were increased by more than two-folds by seed priming compared with control. Salicylic acid showed less effect in increasing emergence, seedling growth, antioxidant activities and biochemical attributes of rice. Thus, this study established that seed priming with KNO3 (2.5% and 5%) and SiO2 (3% and 3.5%) were more effective in improving emergence, seedling growth, biochemical attributes and antioxidant activities of FARO44. Thus, priming of FARO44 rice with this chemical is recommended for fast emergence, seedling growth and drought resistance in dry ecosystems.

Assessments of the Ecological and Health Risks of Potentially Toxic Metals in the Topsoils of Different Land Uses: A Case Study in Peninsular Malaysia.

Human activities due to different land uses are being studied widely in many countries. This study aimed to determine the ecological risks and human health risk assessments (HHRA) of Cd, Pb, Ni, Cu, and Zn in the topsoils of six land uses in Peninsular Malaysia. The ranges of the potentially toxic metals (PTMs) in the soils (mg/kg, dry weight) of this study were 0.24-12.43 for Cd (mean: 1.94), 4.66-2363 for Cu (mean: 228), 2576-116,344 for Fe (mean: 32,618), 2.38-75.67 for Ni (mean: 16.04), 7.22-969 for Pb (mean: 115) and 11.03-3820 for Zn (mean: 512). For the ecological risk assessments, the potential ecological risk index (PERI) for single metals indicated that the severity of pollution of the five metals decreased in the following sequence: Cd > Cu > Pb > Zn > Ni. It was found that industry, landfill, rubbish heap, and mining areas were categorized as "very high ecological risk". For HHRA, the land uses of industry, landfill and rubbish heap were found to have higher hazard quotient (HQ) values for the three pathways (with the order: ingestion > dermal contact > inhalation ingestion) of the five metals for children and adults, when compared to the mining, plantation, and residential areas. The values for both the non-carcinogenic (Cd, Cu, Ni, and Zn), and carcinogenic risks (CR) for inhalation (Cd and Ni) obtained for children and adults in this study showed no serious adverse health impacts on their health. However, of public concern, the hazard index (HI), for Pb of children at the landfill (L-3) and the rubbish heap (RH-3) sites exceeded 1.0, indicating non-carcinogenic risk (NCR) for children. Therefore, these PERI and HHRA results provided fundamental data for PTMs pollution mitigation and environmental management in areas of different land uses in Peninsular Malaysia.

Assessment of Water Mimosa (Neptunia oleracea Lour.) Morphological, Physiological, and Removal Efficiency for Phytoremediation of Arsenic-Polluted Water.

Arsenic is considered to be a toxic and heavy metal that exists in drinking water and can lead to acute biotoxicity. Water mimosa (Neptunia oleracea) has been widely identified as a feasible phytoremediator to clean up aquatic systems. In the current study, the phytoremediation potential of water mimosa exposed to different concentrations of sodium heptahydrate arsenate (Na2HAsO4·7H2O) was tested. A number of plant physiological and growth responses such as height of frond, existence of green leaves, relative growth rate, relative water content, tolerance index, decrease in ratio of biomass and ratio of dry weight, chlorophyll content, photosynthesis rate, intercellular CO2 concentrations, stomatal conductance, air pressure deficit, transpiration rate, proline and lipid peroxidation, as well as arsenic accumulation and removal efficacy were analyzed. The micromorphological analysis results confirmed water mimosa's tolerance of up to 30 ppm of arsenic treatment. The results obtained from the chlorophyll and gas exchange content also showed severe damage by arsenic at doses higher than 30 ppm. In addition, the highest arsenic accumulation and arsenic removal efficacy were observed at the range of 30-60 ppm. An analysis of proline and lipid peroxidation content confirmed water mimosa's tolerance of up to 30 ppm of arsenic. The scanning electron microscopy (SEM) and X-ray spectroscopy (EDX) and analysis also confirmed the accumulation of arsenic as shown by the deformation of water mimosa tissues. The results showed that water mimosa is a reliable bioremediator for removing arsenic from aquatic systems.

Human Health Risk Assessments of Trace Metals on the Clam Corbicula javanica in a Tropical River in Peninsular Malaysia.

This study aimed to analyse ten trace metal concentrations in the edible part of the freshwater clam Corbicula javanica and to provide a critical assessment of the potential risks to human health through consumption of this clam as food based on well-established indices and food safety guidelines. The clams were captured from a pristine original site and transplanted to other sites with different environmental qualities. The trace metal levels in the edible total soft tissue (TST) of the clam were below those of the food safety guidelines referred to except for Pb, which exceeded the permissible limit set by the European Commission (2006) and the US Food and Drug Administration/ Center for Food Safety and Applied Nutrition); Interstate Shellfish Sanitation Conference. (USFDA/CFSAN; ISSC) (2007). The estimated daily intake (EDI) values of the clam were found to be lower than the oral reference dose and the calculated target hazard quotient (THQ) and total THQ were found to be less than 1. Therefore, in conclusion, the human health risk for consumption of TST of C. javanica at both average and high-level were insignificant regardless of the environment it was exposed to.

Efficient and High-Quality RNA Isolation from Metabolite-Rich Tissues of Stevia rebaudiana, an Important Commercial Crop.

Stevia rebaudiana, a perennial herb native to northeastern Paraguay, has gained immense attention globally over the recent decades due to the natural sweetness of its leaves. Like in most plants, this particular species contains high amount of secondary metabolites, thus rendering the isolation of high quality and quantity RNA extract for molecular applications rather challenging. An effective, high-yield and high-quality RNA isolation protocol for this economically important plant species was devised here based on the cetyltrimethylammonium bromide (CTAB) extraction method, with an additional genomic DNA (gDNA) removal step. DNA and other contaminants that may affect downstream applications were effectively removed. Our results exhibited that RNA samples isolated from the leaves and stems of Stevia rebaudiana using this improvised method are high in integrity and quality with RNA integrity number (RIN) of more than 8 and low in contaminants.

Effects of anthropogenic activities on the heavy metal levels in the clams and sediments in a tropical river.

The present study aimed to assess the effects of anthropogenic activities on the heavy metal levels in the Langat River by transplantation of Corbicula javanica. In addition, potential ecological risk indexes (PERI) of heavy metals in the surface sediments of the river were also investigated. The correlation analysis revealed that eight metals (As, Co, Cr, Fe, Mn, Ni, Pb and Zn) in total soft tissue (TST) while five metals (As, Cd, Cr, Fe and Mn) in shell have positively and significantly correlation with respective metal concentration in sediment, indicating the clams is a good biomonitor of the metal levels. Based on clustering patterns, the discharge of dam impoundment, agricultural activities and urban domestic waste were identified as three major contributors of the metals in Pangsun, Semenyih and Dusun Tua, and Kajang, respectively. Various geochemical indexes for a single metal pollutant (geoaccumulation index (I geo), enrichment factors (EF), contamination factor (C f) and ecological risk (Er)) all agreed that Cd, Co, Cr, Cu, Fe, Mn, Ni and Zn are not likely to cause adverse effect to the river ecosystem, but As and Pb could pose a potential ecological risk to the river ecosystem. All indexes (degree of contamination (C d), combined pollution index (CPI) and PERI) showed that overall metal concentrations in the tropical river are still within safe limit. River metal pollution was investigated. Anthropogenic activities were contributors of the metal pollution. Geochemical indexes showed that metals are within the safe limit.

Inhibitory effect of allicin and garlic extracts on growth of cultured hyphae.

OBJECTIVE(S): Trichophyton rubrum (T. rubrum) is one of the most common dermatophytes worldwide. This fungus invaded skin appendages of humans and animals. Recently, resistance to antifungal drugs as well as appearance of side effects due to indication of these kinds of antibiotics has been reported. Besides, using some plant extracts have been indicated in herbal medicine as an alternative treatment of these fungal infections. The aim of this study was to investigate the effects of Garlic (Allium sativum) and pure allicin on the growth of hypha in T. rubrum using Electron miscroscopy. MATERIALS AND METHODS: This study was carried out to observe the morphological changes of T. rubrum treated with allicin as well as aqueous garlic extract using scanning electron microscopy (SEM) and transmission electron microscopy (TEM). RESULTS: SEM surveys, showed that hypha treated with allicin has rough and granular like surface, abnormal and irregularly-shape. However, hypha treated with garlic extract had rough and fluffy surface and also irregularly-shape. TEM studies also found that hypha treated with allicin displays disintegration of cytoplasm, breaking down in cell membrane and the cell wall, and collapsing of hypha, meanwhile hypha treated with garlic extract exhibiting degradation and dissolution of cytoplasm components, demolition of cell wall and cell membrane, and hypha appeared to break. CONCLUSION: The present study revealed that pure allicin (6.25 µg/ml and 12.5 µg/ml) is more efficient in inhibition of the growth in hyphal cells compare to the garlic extract (2 mg/ml and 4 mg/ml) and they could be used as alternatives in treatment of dermatophytosis.