In-depth analysis of ambient air pollution changes due to the COVID-19 pandemic in the Asian Monsoon region.

The COVID-19 pandemic has given a chance for researchers and policymakers all over the world to study the impact of lockdowns on air quality in each country. This review aims to investigate the impact of the restriction of activities during the lockdowns in the Asian Monsoon region on the main criteria air pollutants. The various types of lockdowns implemented in each country were based on the severity of the COVID-19 pandemic. The concentrations of major air pollutants, especially particulate matter (PM) and nitrogen dioxide (NO2), reduced significantly in all countries, especially in South Asia (India and Bangladesh), during periods of full lockdown. There were also indications of a significant reduction of sulfur dioxide (SO2) and carbon monoxide (CO). At the same time, there were indications of increasing trends in surface ozone (O3), presumably due to nonlinear chemistry associated with the reduction of oxides of nitrogens (NOX). The reduction in the concentration of air pollutants can also be seen in satellite images. The results of aerosol optical depth (AOD) values followed the PM concentrations in many cities. A significant reduction of NO2 was recorded by satellite images in almost all cities in the Asian Monsoon region. The major reductions in air pollutants were associated with reductions in mobility. Pakistan, India, Bangladesh, Myanmar, Vietnam, and Taiwan had comparatively positive gross domestic product growth indices in comparison to other Asian Monsoon nations during the COVID-19 pandemic. A positive outcome suggests that the economy of these nations, particularly in terms of industrial activity, persisted during the COVID-19 pandemic. Overall, the lockdowns implemented during COVID-19 suggest that air quality in the Asian Monsoon region can be improved by the reduction of emissions, especially those due to mobility as an indicator of traffic in major cities.

Elemental Characterization of Ambient Particulate Matter for a Globally Distributed Monitoring Network: Methodology and Implications.

Global ground-level measurements of elements in ambient particulate matter (PM) can provide valuable information to understand the distribution of dust and trace elements, assess health impacts, and investigate emission sources. We use X-ray fluorescence spectroscopy to characterize the elemental composition of PM samples collected from 27 globally distributed sites in the Surface PARTiculate mAtter Network (SPARTAN) over 2019-2023. Consistent protocols are applied to collect all samples and analyze them at one central laboratory, which facilitates comparison across different sites. Multiple quality assurance measures are performed, including applying reference materials that resemble typical PM samples, acceptance testing, and routine quality control. Method detection limits and uncertainties are estimated. Concentrations of dust and trace element oxides (TEO) are determined from the elemental dataset. In addition to sites in arid regions, a moderately high mean dust concentration (6 µg/m3) in PM2.5 is also found in Dhaka (Bangladesh) along with a high average TEO level (6 µg/m3). High carcinogenic risk (>1 cancer case per 100000 adults) from airborne arsenic is observed in Dhaka (Bangladesh), Kanpur (India), and Hanoi (Vietnam). Industries of informal lead-acid battery and e-waste recycling as well as coal-fired brick kilns likely contribute to the elevated trace element concentrations found in Dhaka.

Comprehensive analysis of long-term trends, meteorological influences, and ozone formation sensitivity in the Jakarta Greater Area.

Jakarta Greater Area (JGA) has encountered recurrent challenges of air pollution, notably, high ozone levels. We investigate the trends of surface ozone (O3) changes from the air quality monitoring stations and resolve the contribution of meteorological drivers in urban Jakarta (2010-2019) and rural Bogor sites (2017-2019) using stepwise Multi Linear Regression. During 10 years of measurement, 41% of 1-h O3 concentrations exceeded Indonesia' s national threshold in Jakarta. In Bogor, 0.1% surpassed the threshold during 3 years of available data records. The monthly average of maximum daily 8-h average (MDA8) O3 anomalies exhibited a downward trend at Jakarta sites while increasing at the rural site of Bogor. Meteorological and anthropogenic drivers contribute 30% and 70%, respectively, to the interannual O3 anomalies in Jakarta. Ozone formation sensitivity with satellite demonstrates that a slight decrease in NO2 and an increase in HCHO contributed to declining O3 in Jakarta with 10 years average of HCHO to NO2 ratio (FNR) of 3.7. Conversely, O3 increases in rural areas with a higher FNR of 4.4, likely due to the contribution from the natural emission of O3 precursors and the influence of meteorological factors that magnify the concentration.

First report of Ageratum yellow vein virus infecting papaya in Lampung, Indonesia.

BACKGROUND: Papaya (Carica papaya) is a tropical fruit of great economic and nutritional importance, loved for its sweet and delicious flesh. However, papaya cultivation faces serious challenges in the form of Begomovirus attacks. Begomoviruses are a group of viruses that pose a serious threat to plants worldwide. Including papaya, Begomovirus has become a significant threat to papaya production in various parts of the world and has been identified in several regions in Indonesia. METHODS: DNA was extracted from seven samples representing different papaya growing areas using a Plant Genomic DNA Mini Kit. Genomic DNA from the samples was subjected to PCR using universal primers of AC2, AC1, SPG1 and SPG2. The PCR products then sequenced using the dideoxy (Sanger) approach. The obtained sequence then compared to the gene bank using BLAST software available at NCBI. Multiple sequence alignment and phylogenetic tree construction were analyzed using the MEGA11 program. RESULTS: Detection based on viral nucleic acid in papaya plants in Pesawaran, Lampung Province with seven sampling points using universal primers SPG1/SPG2 showed positive results for Begomovirus infection with visible DNA bands measuring ± 900 bp. Direct nucleotide sequencing using SPG1/SPG2 primers for the AC2 and AC1 genes of the Begomovirus and confirmed by the BLAST program showed that papaya samples were infected with Ageratum yellow vein virus (AYVV). The phylogenetic results show that AYVV from papaya samples has a close relationship with the AYVV group from several other countries, with 98% homology. CONCLUSION: In the papaya cultivation area in Pesawaran, Lampung province, it was identified as Begomovirus, Ageratum yellow vein virus (AYVV) species and is closely related to the AYVV group from several other countries. Overall, our study further suggests that Ageratum acts as an alternative host and reservoir for Begomovirus.

Unlocking gut microbiota potential of dairy cows in varied environmental conditions using shotgun metagenomic approach.

Food security and environmental pollution are major concerns for the expanding world population, where farm animals are the largest source of dietary proteins and are responsible for producing anthropogenic gases, including methane, especially by cows. We sampled the fecal microbiomes of cows from varying environmental regions of Pakistan to determine the better-performing microbiomes for higher yields and lower methane emissions by applying the shotgun metagenomic approach. We selected managed dairy farms in the Chakwal, Salt Range, and Patoki regions of Pakistan, and also incorporated animals from local farmers. Milk yield and milk fat, and protein contents were measured and correlated with microbiome diversity and function. The average milk protein content from the Salt Range farms was 2.68%, with an average peak milk yield of 45 litters/head/day, compared to 3.68% in Patoki farms with an average peak milk yield of 18 litters/head/day. Salt-range dairy cows prefer S-adenosyl-L-methionine (SAMe) to S-adenosyl-L-homocysteine (SAH) conversion reactions and are responsible for low milk protein content. It is linked to Bacteroides fragilles which account for 10% of the total Bacteroides, compared to 3% in the Patoki region. The solid Non-Fat in the salt range was 8.29%, whereas that in patoki was 6.34%. Moreover, Lactobacillus plantarum high abundance in Salt Range provided propionate as alternate sink to [H], and overcoming a Methanobrevibacter ruminantium high methane emissions in the Salt Range. Furthermore, our results identified ruminant fecal microbiomes that can be used as fecal microbiota transplants (FMT) to high-methane emitters and low-performing herds to increase farm output and reduce the environmental damage caused by anthropogenic gases emitted by dairy cows.

The infiltration of wildfire smoke and its potential dose on pregnant women: Lessons learned from Indonesia wildfires in 2019.

The occurrence of wildfires in Indonesia is prevalent during drought seasons. Multiple toxic pollutants emitted from wildfires have deleterious effects on pregnant women. However, the evidence for these on pregnant women was underreported. The study conducted 24-h monitoring of fine particulate matter (PM2.5) concentrations indoors and outdoors in 9 low-income homes in Palangka Raya during the 2019 wildfire season and 6 low-income homes during the 2019 non-wildfire season. A hundred and seventy pregnant women had their PM exposure assessed between July and October 2019 using personal monitors. It was observed that outdoor air pollutant levels were greater than those found indoors without indoor sources. The findings indicate that indoor PM2.5 concentrations were modestly increased by 1.2 times higher than outdoor, suggesting that buildings only partially protected people from exposure during wildfires. The concentrations of PM2.5 were found to be comparatively higher indoors in residential buildings with wood material than in brick houses. The study findings indicate that 8 out of 12 brick houses exhibited a notable RI/O24 h of less than 1 during the wildfires, whereas all I/O24 h ratios during the non-wildfire season were >1, suggesting the influence of indoor sources. Based on the estimation of daily PM2.5 dose, pregnant women received around 21% of their total daily dose during sedentary activity involving cooking. The present research offers empirical support for the view that indoor air quality in low-income households is affected by a complex combination of factors, including wildfire smoke, air tightness, and occupant behaviour. Also, this situation is more likely a potential risk to pregnant women being exposed to wildfire smoke.

Lysinabacillus fusiformis and Paenibacillus alvei Obtained from the Internal of Nasutitermes Termites Revealed Their Ability as Antagonist of Plant Pathogenic Fungi.

This study was performed to reveal phenotypic characters and identity of symbiont bacteria of Nasutitermes as well as investigate their potential as antagonist of plant pathogenic fungi. Isolation of the symbiont bacteria was carried out from inside the heads and the bodies of soldier and worker termite which were collected from 3 locations of nests. Identification was performed using phenotypic test and sequence of 16S ribosomal DNA (16S rDNA). Antagonistic capability was investigated in the laboratory against 3 phytopathogenic fungi i.e., Phytophthora capsici, Ganoderma boninense, and Rigidoporus microporus. Totally, 39 bacterial isolates were obtained from inside the heads and the bodies of Nasutitermes. All the isolates showed capability to inhibit growth of P. capsici, however, 34 isolates showed capability to inhibit growth of G. boninense and 32 isolates showed capability to inhibit growth of R. microporus. Two bacterial strains (IK3.1P and 1B1.2P) which showed the highest percentage of inhibition were further identified based on their sequence of 16S rDNA. The result showed that 1K3.1P strain was placed in the group of type strain and reference strains of Lysinibacillus fusiformis meanwhile 1B1.2P strain was grouped within type strain and reference strains Paenibacillus alvei. The result of this study supply valuable information on the role of symbiont bacteria of Nasutitermes, which may support the development of the control method of the three above-mentioned phytopathogenic fungi.

One-pot alkanolamines-assisted synthesis of magnetic mesoporous silica for synthetic dye adsorption.

Magnetic mesoporous silica (MMS) was synthesized in a one-pot system using various alkanolamines (triethanolamine, diethanolamine, tris (hydroxymethyl)aminomethane) as a basic catalyst. The characterization of the composites was conducted using scanning electron microscope, transmission electron microscope, X-ray diffractometer, surface area analyzer, and X-ray photoelectros spectroscopy. The MMS synthesized with tris(hydroxymethyl)aminomethane (MMSTRIS) showed the highest specific surface area, pore volume, and average pore diameter. However, when the composites were applied as adsorbents for brilliant green (BG) dye, MMS synthesized with diethanolamine (MMSDEA) showed the highest maximum adsorption capacity of 339.7 mg g-1. The fastest adsorption rate constant of 1.57 × 10-2 g mg-1 min-1 was obtained for MMSTRIS, which has the largest average pore size among all composites. The adsorption kinetic study suggested that the adsorption of BG onto the prepared MMS composites was mainly chemisorption process, which most likely involves electrostatic interaction and hydrogen bonding between BG molecule and the surface of the composites.

Potential plasma biomarkers: miRNA-29c, miRNA-21, and miRNA-155 in clinical progression of Hepatocellular Carcinoma patients.

This study evaluated differences in the clinical appearance of patients with hepatocellular carcinoma (HCC) based on plasma level and regulation of microRNAs (miRNA-29c, miRNA-21, and miRNA-155). The observational-analytical study with a cross-sectional design was conducted on 36 HCC patients and 36 healthy controls. The blood samples were collected from 2 Province Hospitals (Dr. Sardjito Hospital and Prof. Dr. Margono Soekarjo Hospital) for HCC and the Blood Bank Donor of the Indonesian Red Cross for 36 healthy controls. These blood samples were treated as follows: plasma isolation, RNA isolation, cDNA synthesis, quantification by qRT-PCR using a sequence-specific forward primer, and normalization of miRNA using housekeeping-stably miRNA-16. There were only 27 HCC patients with complete clinical variables (neutrophil to lymphocyte ratio (NLR), platelet to lymphocyte ratio (PLR), platelet count, albumin, C-reactive protein (CRP), and cholinesterase (ChE)) that were able to analyses for regulation miRNAs based on its fold change expression miRNA target. All 27 HCC subjects were follow-up until 3-years of monitoring for their overall survival. The miRNA plasma expression was analyzed by Bio-Rad CFX 96 Manager software to determine the cycle of quantification, followed by the calculation of expression levels using Livak's methods. Data were analyzed using STATA 11.0, with a significant value of p<0.05. The miRNAs expression of HCC subjects were lower than that healthy control subjects in miRNA-29c (down-regulation 1.83-fold), higher than that healthy control subjects in miRNA 21 and miRNA-155 (up-regulation, 1.74-fold; 1.55-fold) respectively. NLR, CRP, ChE, and platelet count showed a significant difference in miRNA-29c regulation, though neutrophil count showed a significant difference in miRNA-21 and miRNA-155 regulation (p<0.05). Conclusion: Plasma biomarkers: miRNA-21 and miRNA-155 might be potential biomarkers as onco-miR in HCC subjects, while miRNA-29c might act as a tumor suppressor. Significant evidence was identified with clinical progression based on the regulation of miRNAs, which was consistent with miRNA -29c.

Research Priorities of Applying Low-Cost PM2.5 Sensors in Southeast Asian Countries.

The low-cost and easy-to-use nature of rapidly developed PM2.5 sensors provide an opportunity to bring breakthroughs in PM2.5 research to resource-limited countries in Southeast Asia (SEA). This review provides an evaluation of the currently available literature and identifies research priorities in applying low-cost sensors (LCS) in PM2.5 environmental and health research in SEA. The research priority is an outcome of a series of participatory workshops under the umbrella of the International Global Atmospheric Chemistry Project-Monsoon Asia and Oceania Networking Group (IGAC-MANGO). A literature review and research prioritization are conducted with a transdisciplinary perspective of providing useful scientific evidence in assisting authorities in formulating targeted strategies to reduce severe PM2.5 pollution and health risks in this region. The PM2.5 research gaps that could be filled by LCS application are identified in five categories: source evaluation, especially for the distinctive sources in the SEA countries; hot spot investigation; peak exposure assessment; exposure-health evaluation on acute health impacts; and short-term standards. The affordability of LCS, methodology transferability, international collaboration, and stakeholder engagement are keys to success in such transdisciplinary PM2.5 research. Unique contributions to the international science community and challenges with LCS application in PM2.5 research in SEA are also discussed.

Large global variations in measured airborne metal concentrations driven by anthropogenic sources.

Globally consistent measurements of airborne metal concentrations in fine particulate matter (PM2.5) are important for understanding potential health impacts, prioritizing air pollution mitigation strategies, and enabling global chemical transport model development. PM2.5 filter samples (N ~ 800 from 19 locations) collected from a globally distributed surface particulate matter sampling network (SPARTAN) between January 2013 and April 2019 were analyzed for particulate mass and trace metals content. Metal concentrations exhibited pronounced spatial variation, primarily driven by anthropogenic activities. PM2.5 levels of lead, arsenic, chromium, and zinc were significantly enriched at some locations by factors of 100-3000 compared to crustal concentrations. Levels of metals in PM2.5 and PM10 exceeded health guidelines at multiple sites. For example, Dhaka and Kanpur sites exceeded the US National Ambient Air 3-month Quality Standard for lead (150 ng m-3). Kanpur, Hanoi, Beijing and Dhaka sites had annual mean arsenic concentrations that approached or exceeded the World Health Organization's risk level for arsenic (6.6 ng m-3). The high concentrations of several potentially harmful metals in densely populated cites worldwide motivates expanded measurements and analyses.

Top-Down Estimation of Particulate Matter Emissions from Extreme Tropical Peatland Fires Using Geostationary Satellite Fire Radiative Power Observations.

Extreme fires in the peatlands of South East (SE) Asia are arguably the world's greatest biomass burning events, resulting in some of the worst ambient air pollution ever recorded (PM10 > 3000 µg·m-3). The worst of these fires coincide with El Niño related droughts, and include huge areas of smouldering combustion that can persist for months. However, areas of flaming surface vegetation combustion atop peat are also seen, and we show that the largest of these latter fires appear to be the most radiant and intensely smoke-emitting areas of combustion present in such extreme fire episodes. Fire emissions inventories and early warning of the air quality impacts of landscape fire are increasingly based on the fire radiative power (FRP) approach to fire emissions estimation, including for these SE Asia peatland fires. "Top-down" methods estimate total particulate matter emissions directly from FRP observations using so-called "smoke emission coefficients" [Ce; g·MJ-1], but currently no discrimination is made between fire types during such calculations. We show that for a subset of some of the most thermally radiant peatland fires seen during the 2015 El Niño, the most appropriate Ce is around a factor of three lower than currently assumed (~16.8 ± 1.6 g·MJ-1 vs. 52.4 g·MJ-1). Analysis indicates that this difference stems from these highly radiant fires containing areas of substantial flaming combustion, which changes the amount of particulate matter emitted per unit of observable fire radiative heat release in comparison to more smouldering dominated events. We also show that even a single one of these most radiant fires is responsible for almost 10% of the overall particulate matter released during the 2015 fire event, highlighting the importance of this fire type to overall emission totals. Discriminating these different fires types in ways demonstrated herein should thus ultimately improve the accuracy of SE Asian fire emissions estimates derived using the FRP approach, and the air quality modelling which they support.

Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits.

Jatropha curcas (physic nut), a non-edible oilseed crop, represents one of the most promising alternative energy sources due to its high seed oil content, rapid growth and adaptability to various environments. We report ~339 Mbp draft whole genome sequence of J. curcas var. Chai Nat using both the PacBio and Illumina sequencing platforms. We identified and categorized differentially expressed genes related to biosynthesis of lipid and toxic compound among four stages of seed development. Triacylglycerol (TAG), the major component of seed storage oil, is mainly synthesized by phospholipid:diacylglycerol acyltransferase in Jatropha, and continuous high expression of homologs of oleosin over seed development contributes to accumulation of high level of oil in kernels by preventing the breakdown of TAG. A physical cluster of genes for diterpenoid biosynthetic enzymes, including casbene synthases highly responsible for a toxic compound, phorbol ester, in seed cake, was syntenically highly conserved between Jatropha and castor bean. Transcriptomic analysis of female and male flowers revealed the up-regulation of a dozen family of TFs in female flower. Additionally, we constructed a robust species tree enabling estimation of divergence times among nine Jatropha species and five commercial crops in Malpighiales order. Our results will help researchers and breeders increase energy efficiency of this important oil seed crop by improving yield and oil content, and eliminating toxic compound in seed cake for animal feed.

Global Sources of Fine Particulate Matter: Interpretation of PM2.5 Chemical Composition Observed by SPARTAN using a Global Chemical Transport Model.

Exposure to ambient fine particulate matter (PM2.5) is a leading risk factor for the global burden of disease. However, uncertainty remains about PM2.5 sources. We use a global chemical transport model (GEOS-Chem) simulation for 2014, constrained by satellite-based estimates of PM2.5 to interpret globally dispersed PM2.5 mass and composition measurements from the ground-based surface particulate matter network (SPARTAN). Measured site mean PM2.5 composition varies substantially for secondary inorganic aerosols (2.4-19.7 µg/m3), mineral dust (1.9-14.7 µg/m3), residual/organic matter (2.1-40.2 µg/m3), and black carbon (1.0-7.3 µg/m3). Interpretation of these measurements with the GEOS-Chem model yields insight into sources affecting each site. Globally, combustion sectors such as residential energy use (7.9 µg/m3), industry (6.5 µg/m3), and power generation (5.6 µg/m3) are leading sources of outdoor global population-weighted PM2.5 concentrations. Global population-weighted organic mass is driven by the residential energy sector (64%) whereas population-weighted secondary inorganic concentrations arise primarily from industry (33%) and power generation (32%). Simulation-measurement biases for ammonium nitrate and dust identify uncertainty in agricultural and crustal sources. Interpretation of initial PM2.5 mass and composition measurements from SPARTAN with the GEOS-Chem model constrained by satellite-based PM2.5 provides insight into sources and processes that influence the global spatial variation in PM2.5 composition.

A quantitative assessment of distributions and sources of tropospheric halocarbons measured in Singapore.

This work reports the first ground-based atmospheric measurements of 26 halocarbons in Singapore, an urban-industrial city-state in Southeast (SE) Asia. A total of 166 whole air canister samples collected during two intensive 7 Southeast Asian Studies (7SEAS) campaigns (August-October 2011 and 2012) were analyzed for C1-C2 halocarbons using gas chromatography-electron capture/mass spectrometric detection. The halocarbon dataset was supplemented with measurements of selected non-methane hydrocarbons (NMHCs), C1-C5 alkyl nitrates, sulfur gases and carbon monoxide to better understand sources and atmospheric processes. The median observed atmospheric mixing ratios of CFCs, halons, CCl4 and CH3CCl3 were close to global tropospheric background levels, with enhancements in the 1-17% range. This provided the first measurement evidence from SE Asia of the effectiveness of Montreal Protocol and related national-scale regulations instituted in the 1990s to phase-out ozone depleting substances (ODS). First- and second-generation CFC replacements (HCFCs and HFCs) dominated the atmospheric halocarbon burden with HFC-134a, HCFC-22 and HCFC-141b exhibiting enhancements of 39-67%. By combining near-source measurements in Indonesia with receptor data in Singapore, regionally transported peat-forest burning smoke was found to impact levels of several NMHCs (ethane, ethyne, benzene, and propane) and short-lived halocarbons (CH3I, CH3Cl, and CH3Br) in a subset of the receptor samples. The strong signatures of these species near peat-forest fires were potentially affected by atmospheric dilution/mixing during transport and by mixing with substantial urban/regional backgrounds at the receptor. Quantitative source apportionment was carried out using positive matrix factorization (PMF), which identified industrial emissions related to refrigeration, foam blowing, and solvent use in chemical, pharmaceutical and electronics industries as the major source of halocarbons (34%) in Singapore. This was followed by marine and terrestrial biogenic activity (28%), residual levels of ODS from pre-Montreal Protocol operations (16%), seasonal incidences of peat-forest smoke (13%), and fumigation related to quarantine and pre-shipment (QPS) applications (7%).

Draft genome sequence of adzuki bean, Vigna angularis.

Adzuki bean (Vigna angularis var. angularis) is a dietary legume crop in East Asia. The presumed progenitor (Vigna angularis var. nipponensis) is widely found in East Asia, suggesting speciation and domestication in these temperate climate regions. Here, we report a draft genome sequence of adzuki bean. The genome assembly covers 75% of the estimated genome and was mapped to 11 pseudo-chromosomes. Gene prediction revealed 26,857 high confidence protein-coding genes evidenced by RNAseq of different tissues. Comparative gene expression analysis with V. radiata showed that the tissue specificity of orthologous genes was highly conserved. Additional re-sequencing of wild adzuki bean, V. angularis var. nipponensis, and V. nepalensis, was performed to analyze the variations between cultivated and wild adzuki bean. The determined divergence time of adzuki bean and the wild species predated archaeology-based domestication time. The present genome assembly will accelerate the genomics-assisted breeding of adzuki bean.

Genome sequence of mungbean and insights into evolution within Vigna species.

Mungbean (Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. Here we construct a draft genome sequence of mungbean to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species. Based on the de novo assembly of additional wild mungbean species, the divergence of what was eventually domesticated and the sampled wild mungbean species appears to have predated domestication. Moreover, the de novo assembly of a tetraploid Vigna species (V. reflexo-pilosa var. glabra) provides genomic evidence of a recent allopolyploid event. The species tree is constructed using de novo RNA-seq assemblies of 22 accessions of 18 Vigna species and protein sets of Glycine max. The present assembly of V. radiata var. radiata will facilitate genome research and accelerate molecular breeding of the subgenus Ceratotropis.

Gene divergence of homeologous regions associated with a major seed protein content QTL in soybean.

Understanding several modes of duplication contributing on the present genome structure is getting an attention because it could be related to numerous agronomically important traits. Since soybean serves as a rich protein source for animal feeds and human consumption, breeding efforts in soybean have been directed toward enhancing seed protein content. The publicly available soybean sequences and its genomically featured elements facilitate comprehending of quantitative trait loci (QTL) for seed protein content in concordance with homeologous regions in soybean genome. Although parts of chromosome (Chr) 20 and Chr 10 showed synteny, QTLs for seed protein content present only on Chr 20. Using comparative analysis of gene contents in recently duplicated genomic regions harboring QTL for protein/oil content on Chrs 20 and 10, a total of 27 genes are present in duplicated regions of both Chrs. Notably, 4 tandem duplicates of the putative homeobox protein 22 (HB22) are present only on Chr 20 and this Medicago truncatula homolog expressed in endosperm at seed filling stage. These tandem duplicates could contribute on the protein/oil QTL of Chr 20. Our study suggests that non-shared gene contents within the duplicated genomic regions might lead to absence/presence of QTL related to protein/oil content.

Identification of quantitative trait loci for cadmium accumulation and distribution in rice (Oryza sativa).

Cadmium (Cd) poses a serious risk to human health due to its biological concentration through the food chain. To date, information on genetic and molecular mechanisms of Cd accumulation and distribution in rice remains to be elucidated. We developed an independent F7 RIL population derived from a cross between two japonica cultivars with contrasting Cd levels, 'Suwon490' and 'SNU-SG1', for QTLs identification of Cd accumulation and distribution. 'Suwon490' accumulated five times higher Cd in grain than 'SNU-SG1'. Large genotypic variations in Cd accumulation (17-fold) and concentration (12-fold) in grain were found among RILs. Significant positive correlations between Cd accumulation in grain with shoot Cd accumulation and shoot to grain distribution ratio of Cd signify that both shoot Cd accumulation and shoot to grain Cd distribution regulate Cd accumulation in japonica rice grain. A total of five main effect QTLs (scc10 for shoot Cd accumulation; gcc3, gcc9, gcc11 for grain Cd accumulation; and sgr5 for shoot to grain distribution ratio) were detected in chromosomes 10, 3, 9, 11, and 5, respectively. Of these, the novel potential QTL sgr5 has the strongest effect on shoot to grain Cd distribution. In addition, two digenic epistatic interaction QTLs were identified, suggesting the substantial contribution of nonallelic genes in genetic control of these Cd-related traits.

Single nucleotide polymorphisms and haplotype diversity in rice sucrose synthase 3.

Rice sucrose synthase 3 (RSUS3) is expressed predominantly in rice seed endosperm and is thought to play an important role in starch filling during the milky stage of rice seed ripening. Because the genetic diversity of this locus is not known yet, the full sequence of RSUS3 from 43 rice varieties was amplified to examine the distribution of DNA polymorphisms. A total of 254 sequence variants, including SNPs and insertion/deletions, were successfully identified in the 7733 bp sequence that comprises the promoter, exons and introns, and 3' downstream nontranscribed region (NTR). Eleven haplotypes were distinguished among the 43 rice varieties based on nucleotide variation in the 3 defined regions (5' NTR, transcript, and 3' NTR). The promoter region showed evidence of a base change on a cis-element that might influence the functional role of the motif in seed-specific expression. The genetic diversity of the RSUS3 gene sequences in the rice germplasm used in this study appears to be the result of nonrandom processes. Analysis of polymorphism sites indicated that at least 11 recombinations have occurred, primarily in the transcribed region. This finding provides insight into the development of a cladistic approach for establishing future genetic association studies of the RSUS3 locus.