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.

     

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.     

Diversity of the calabash tree (<Emphasis Type="Italic">Crescentia cujete</Emphasis> L.) in Colombia

Germplasm of the calabash tree (Crescentia cujete L.) was collected in five major regions of Colombia, i.e. the Andes, Caribbean, Amazon, Orinoco, and Pacific regions. Collecting this multipurpose tree was guided by the indigenous knowledge of farmers and artisans in each region. Large variation in fruit shapes and sizes was found, of which some forms were typical for certain regions. Overall 56 accessions were collected and roughly classified into 22 types by eight fruit shapes and eight sizes. Molecular markers (Amplified fragment length polymorphisms) were applied to leaf tip tissue originating from vegetatively propagated plants in order to assess the diversity available in the germplasm collected as well as to detect patterns of geographical or morphological similarity. One accession each of C. alata H.B.&K. and C. amazonica Ducke were used as outgroups. Overall, genetic diversity was high (mean Nei and Li’s coefficient of 0.43). No relations could be established between either geographical provenance or fruit morphology and patterns of genetic diversity. Concerning the outgroups, the C. amazonica accession appeared to be a distinct species. The C. alata accession, however, did not seem to be sufficiently distinct from C. cujete to merit species status. The latter material may in fact be a hybrid or serve to challenge the validity of interspecific organization of the genus Crescentia.

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.     

Determination of anthocyanins from camu-camu (Myrciaria dubia) by HPLC-PDA, HPLC-MS, and NMR

Camu-camu [Myrciaria dubia (HBK) McVaugh] is a small fruit native to the Amazonian rain forest. Its anthocyanin profile has now been investigated for the first time. Fruits from two different regions of the S?o Paulo state, Brazil, were analyzed. The major anthocyanins were isolated by high-speed countercurrent chromatography. HPLC-PDA, HPLC-MS/MS, and 1H NMR were used to confirm the identity of the main anthocyanins of camu-camu. Cyanidin-3-glucoside was identified as the major pigment in the fruits from both regions, representing 89.5% in the fruits produced in Iguape and 88.0% in those from Mirandópolis, followed by the delphinidin-3-glucoside, ranging between 4.2 and 5.1%, respectively. Higher total anthocyanin contents were detected in the fruits from Iguape (54.0 +/- 25.9 mg/100 g) compared to those from Mirandópolis (30.3 +/- 6.8 mg/100 g), most likely because of the lower temperatures in the Iguape region.     

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.     

Coriander essential oil composition from two genotypes grown in different environmental conditions

The objective was to study the essential oil composition of coriander fruits in plants growing in environments differing in soil conditions and weediness level. Factorial field experiments were conducted in two locations from the Rolling Pampas, Argentina, and two coriander landraces (European and Argentinean) were tested under two levels of nitrogen fertilization and weediness. Data were evaluated with uni- and multivariate techniques. The variation in the oil composition was related to the relative proportion of the constituents and not to the presence/absence of a particular component. Weather conditions in 1997 favored linalool and camphor in both landraces. Location, fertilization, and weediness also affected the chemical profile. The European landrace showed a more stable concentration of the major components than the Argentinean landrace. These results, which show the relationships between some environmental conditions and the essential oil composition, are useful in the development of innovative strategies aimed to improve oil composition and to manage crop pests.