Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications

Background

Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit “sweet spot” for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice.

Results

Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina’s production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material.

Conclusions

The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.

     

Can carbon sequestration markets benefit low-income producers in semi-arid Africa? Potentials and challenges

The Clean Development Mechanism (CDM) of the Kyoto Protocol of the United Nations Framework Convention on Climate Change allows a country that emits C above agreed-upon limits to purchase C offsets from an entity that uses biological means to absorb or reduce greenhouse emissions. The CDM is currently offered for afforestation and reforestation projects, but may apply subsequently to sequestration in agricultural soils. Additionally, markets outside of the Protocol are developing for soil C sequestration.     

Quantitative structure-antifungal activity relationships of some benzohydrazides against Botrytis cinerea

Fourteen benzohydrazides have been synthesized and evaluated for their in vitro antifungal activity against the phytopathogenic fungus Botrytis cinerea. The best antifungal activity was observed for the N',N'-dibenzylbenzohydrazides 3b-d and for the N-aminoisoindoline-derived benzohydrazide 5. A quantitative structure-activity relationship (QSAR) study has been developed using a topological substructural molecular design (TOPS-MODE) approach to interpret the antifungal activity of these synthetic compounds. The model described 98.3% of the experimental variance, with a standard deviation of 4.02. The influence of an ortho substituent on the conformation of the benzohydrazides was investigated by X-ray crystallography and supported by QSAR study. Several aspects of the structure-activity relationships are discussed in terms of the contribution of different bonds to the antifungal activity, thereby making the relationships between structure and biological activity more transparent.     

Preparation of soybean oil-based greases: effect of composition and structure on physical properties

Vegetable oils have significant potential as a base fluid and a substitute for mineral oil in grease formulation. Preparation of soybean oil-based lithium greases using a variety of fatty acids in the soap structure is discussed in this paper. Soy greases with lithium-fatty acid soap having C12-C18 chain lengths and different metal to fatty acid ratios were synthesized. Grease hardness was determined using a standard test method, and their oxidative stabilities were measured using pressurized differential scanning calorimetry. Results indicate that lithium soap composition, fatty acid types, and base oil content significantly affect grease hardness and oxidative stability. Lithium soaps prepared with short-chain fatty acids resulted in softer grease. Oxidative stability and other performance properties will deteriorate if oil is released from the grease matrix due to overloading of soap with base oil. Performance characteristics are largely dependent on the hardness and oxidative stability of grease used as industrial and automotive lubricant. Therefore, this paper discusses the preparation methods, optimization of soap components, and antioxidant additive for making soy-based grease.     

Indole acetic acid production by Rhizobium: Effect of 2-ketoglutaric acid

I ndole acetic acid (IAA) production from tryptophan by cell suspensions of Rhizobium trifolii, R. leguminosarum, R. phaseoli and R. lupini was studied in the presence or in the absence of 2-ketoglutaric acid. In R. lupini, production of IAA was strongly enhanced by the ketoacid, but in fast growing rhizobia it was less enhanced or unaffected. On the other hand, glutamic acid inhibits IAA production by R. meliloti, but stimulates IAA production in both R. leguminosarum and R. phaseoli. A hypothesis is proposed to explain these results.     

Direct aqueous injection liquid chromatography/electrospray ionization-mass spectrometry/mass spectrometry analysis of water for atrazine, simazine, and their chlorotriazine metabolites

A method is reported for the determination of atrazine, simazine, and their respective dealkylated chlorotriazine metabolites in ground, surface, and finished drinking water. Water samples are diluted 1:4 in an injection vial prior to analysis using liquid chromatography/electrospray ionization-mass spectrometry/mass spectrometry (LC/ESI-MS/MS). The lower limit of method validation is 0.10 microg/L (ppb) for 2-chloro-4-(ethylamino)-6-isopropylamino)-s-triazine (atrazine, G-30027), 2-chloro-4, 6-(diethylamino)-s-triazine (simazine, G-27692), 2-amino-4-chloro-6-(isopropylamino)-s-triazine (deethylatrazine, DEA, or G-30033), 2-amino-4-chloro-6-(ethylamino)-s-triazine (deisopropylatrazine, DIA, or G-28279), and 2,4-diamino-6-chloro-s-triazine (didealkylatrazine, DDA, or G-28273). The overall mean procedural recoveries (and % relative standard deviations) for atrazine, simazine, DEA, DIA, and DDA are 98 (4.4), 102 (3.6), 99 (4.8), 103 (4.0), and 109% (4.8%), respectively, in finished drinking water; 108 (2.7), 104 (5.4), 113 (4.5), 111 (5.2), and 105% (5.3%), respectively, in groundwater; and 96 (6.9), 103 (4.2), 102 (4.4), 102 (5.2), and 102% (8.2%), respectively, in surface water. The method validation was conducted under U.S. EPA FIFRA Good Laboratory Practice Guidelines 40 CFR 160.     

Culture of juvenile European lobster (<Emphasis Type="Italic">Homarus gammarus</Emphasis> L.) in submerged cages

A bottleneck for re-establishment or enhancement of lobster (Homarus gammarus L.) populations through release of hatchery-produced juveniles is ineffective and expensive juvenile production. In this study, we cultured lobster juveniles from stage V to a size being suitable for re-establishment or enhancement purposes (40–50 mm total length) in cages submerged under existing facilities for culture of bivalves. The lobsters were not feed or tended during the culture period (6–14 months). The survival and growth rates were similar or higher compared to what has been achieved with other methods used for culture of lobster juveniles in the past. The highest survival (82–89%) and fastest growth (4–5 cm total length over 190–250 days) were achieved using commercial oyster baskets. It is believed that the juveniles fed on naturally occurring plankton and organisms growing inside the cages. Thus, the current study shows that it is possible to culture lobster juveniles for reestablishment or enhancement purposes in a way that would involve less investments and operational costs than earlier used methods as there would be no need for artificial heating of water, for large buildings or for continuous feeding and tending of large numbers of juveniles.     

Disodium-fosfomycin pharmacokinetics and bioavailability in post weaning piglets

Disodium-fosfomycin pharmacokinetics has been studied in different species after oral, intravenous, intramuscular and subcutaneous administration. At present there are neither documented clinical experiences of the use of fosfomycin in pigs nor any published studies in weaning piglets, although it is a period of high incidence of infectious diseases. The pharmacokinetics and the bioavailability of sodium fosfomycin were studied in post weaning piglets after intravenous and intramuscular administration of 15 mg/kg of body weight. Plasma concentrations were measured by a high-performance liquid ms/ms. After IV administration the area under the fosfomycin concentration:time curve in plasma was AUC_(0–12) of 120.00 ± 23.12 μg h/ml and the volume of distribution (Vd) of 273.00 ± 40.70 ml/kg. The elimination was rapid with a plasma clearance of 131.50 ± 30.07 ml/kg/h and a T_1/2 of 1.54 ± 0.40 h. Peak serum concentration (C_max), T_max, AUC_(0–12) and bioavailability for the IM administration were 43.00 ± 4.10 μg/ml, 0.75 ± 0.00 h, 99.00 ± 0.70 μg h/ml and 85.5 ± 9.90% respectively. Different authors have determined a minimum inhibitory concentration (MIC₉₀) ranging from 0.25 μg/ml for Streptococcus sp. and 0.5 μg/ml for Escherichia coli. Considering the above, and according to the values of plasma concentration vs time profiles observed in this study, effective plasma concentrations of fosfomycin for sensitive bacteria can be obtained following IV and IM administration of 15 mg/kg in piglets.