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.

     

Assessing seed desiccation responses of native trees in the Caribbean

New Forests - Native trees from the Caribbean were tested for seed desiccation responses, by adapting the “100-seed test” protocol. Ninety-seven seed lots of 91 species were collected...     

Chitosan-Based Films with 2-Aminothiophene Derivative: Formulation,Characterization and Potential Antifungal Activity

In this study, films of chitosan and 2-amino-4,5,6,7-tetrahydrobenzo[b]thiophene-3-carbonitrile (6CN), a 2-aminothiophene derivative with great pharmacological potential, were prepared as a system for a topical formulation. 6CN-chitosan films were characterized by physicochemical analyses, such as Fourier-transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), X-ray diffraction (XRD), and scanning electronic microscopy (SEM). Additionally, the antifungal potential of the films was evaluated in vitro against three species of Candida (C. albicans, C. tropicalis, and C. parapsilosis). The results of the FTIR and thermal analysis showed the incorporation of 6CN in the polymer matrix. In the diffractogram, the 6CN-chitosan films exhibited diffraction halos that were characteristic of amorphous structures, while the micrographs showed that 6CN particles were dispersed in the chitosan matrix, exhibiting pores and cracks on the film surface. In addition, the results of antifungal investigation demonstrated that 6CN-chitosan films were effective against Candida species showing potential for application as a new antifungal drug.     

Effect of Fucoidan on the Mitochondrial Membrane Potential (ΔΨm) of Leukocytes from Patients with Active COVID-19 and Subjects That Recovered from SARS-CoV-2 Infection

Fucoidan is a polysaccharide obtained from marine brown algae, with anti-inflammatory, anti-viral, and immune-enhancing properties, thus, fucoidan may be used as an alternative treatment (complementary to prescribed medical therapy) for COVID-19 recovery. This work aimed to determine the ex-vivo effects of treatment with fucoidan (20 µg/mL) on mitochondrial membrane potential (ΔΨm, using a cationic cyanine dye, 3,3′-dihexyloxacarbocyanine iodide (DiOC₆(3)) on human peripheral blood mononuclear cells (HPBMC) isolated from healthy control (HC) subjects, COVID-19 patients (C-19), and subjects that recently recovered from COVID-19 (R1, 40 ± 13 days after infection). In addition, ex-vivo treatment with fucoidan (20 and 50 µg/mL) was evaluated on ΔΨm loss induced by carbonyl cyanide 3-chlorophenylhydrazone (CCCP, 150 µM) in HPBMC isolated from healthy subjects (H) and recovered subjects at 11 months post-COVID-19 (R2, 335 ± 20 days after infection). Data indicate that SARS-CoV-2 infection induces HPBMC loss of ΔΨm, even 11 months after infection, however, fucoidan promotes recovery of ΔΨm in PBMCs from COVID-19 recovered subjects. Therefore, fucoidan may be a potential treatment to diminish long-term sequelae from COVID-19, using mitochondria as a therapeutic target for the recovery of cellular homeostasis.     

Effect of Density at Harvest on the Growth Performance and Profitability of Hatchery‐reared Spotted Rose Snapper,Lutjanus guttatus,Cultured in Floating Net Cages

This study evaluated the effect of the density at harvest on the performance and profitability of hatchery‐reared spotted rose snapper cultured in cages. The fish were stocked at harvest densities of 15, 20, and 22 kg/m³ in cages of 222 and 286 m³. More than 39,000 snapper fingerlings with an initial weight of 14 g were stocked. The fish were fed an extruded diet and cultured over a 360 d period. The thermal growth coefficient ranged from 0.04 to 0.05 and survival was 95% for all treatments, with the highest final weight (436.8 g) observed for fish reared at a density of 20 kg/m³. The allometric value b indicated that hatchery‐raised, cage‐cultured snapper were heavier than their wild counterparts. The major costs were feed (ranging from 44.7–45.9%), labor (22.4–32.6%), and seed costs (20.2–26.1%). The total production cost ranged from US$ 6.5 to US$ 7.5/kg. The baseline scenario was not economically feasible. However, a 10% increase in the sales price resulted in increases in the internal rate of return (183%) and net present value (US$ 97,628.9). These results suggest that L. guttatus has the potential for commercial production in cages.     

An in vitro study of hematopoietic progenitor cells from peripheral blood of rabbits

The purpose of this study was to isolate and cultivate a subpopulation of pluripotent stem cells (PSCs) from the peripheral blood of rabbits, which are frequently used in veterinary research as an animal model. Pluripotent stem cells, as described in human beings, are fibroblast-like cells that exhibit a CD34 marker, specific from other hematopoietic stem cells. Commonly used human commercial media has been researched for culturing rabbit PSCs. These findings allow us to contemplate the direct application of this simple and standardized methodology in several areas of study, such as of the pharmacological effect of many drugs on hematopoietic cells, veterinary practice, and even the study of new strategies in cellular therapy for some human diseases.     

Humoral response (IgG) of goats experimentally infected with Fasciola hepatica against cysteine proteinases of adult fluke

The use of cysteine proteinases from Fasciola hepatica adult flukes for the serodiagnosis of caprine fasciolosis by means of an indirect ELISA test was studied. Two proteolytic fractions from adult fluke homogenates, with apparent molecular weights of 28 and 34 kDa (P28 and P34 respectively), were characterised as cysteine proteinases using azocasein assays and gelatin gel analysis. Both P28 and P34 fractions were electroluted and used as antigens in two different indirect ELISA tests. Serum IgG levels against P28 and P34 in goats given an experimental primary infection with 200 metacercariae or in goats given two experimental infections with 200 metacercariae were determined and compared with those observed in an uninfected control group. ELISA tests using both cysteine proteases showed a rapid and consistent detection of specific IgG in all experimentally infected goats. The IgG response to P28 was the first to be detected as early as 2-3 weeks post-infection and remained elevated throughout the experiment. The response to P34 was detected later (4-6 wpi) and disappeared in some animals at 18 wpi, while flukes were still present in the bile ducts. No significant differences were observed between the anti-P28 and anti-P34 IgG responses between animals receiving a primary or a challenge infection. The results of our study, although preliminary, are promising since the P28 ELISA described here may be a reliable method for the immunodiagnosis of F. hepatica infection in goats.     

SDS-PAGE and Western blot of urinary proteins in dogs with leishmaniasis

Canine leishmaniasis is an endemic disease in the Mediterranean area caused by the protozoan Leishmania infantum, which usually produces renal failure. Sodium dodecyl sulphate polyacrylamide gel electrophoresis and Western blot using antibodies to IgG and IgA from dogs were carried out in the urine of 22 dogs with leishmaniasis diagnosed by ELISA and confirmed by PCR, and 20 healthy dogs. The results were compared to renal function laboratory tests and to those from a histopathological study of the kidneys from sick animals that died naturally or were euthanized. Five different bands with molecular weights ranging from 10 to 110 kDa were obtained from the electrophoresis of the urine of healthy dogs. 33.5% of total proteins corresponded to low molecular weight proteins and the other proteins had middle and high molecular weights. However, in the group with leishmaniasis, a maximum of 11 different bands with molecular weights ranging from 10 kDa to 150 kDa were displayed in the electrophoresis of the urine. The urine electrophoretic pattern in the sick dogs was classified as mixed (proteins with high and low molecular weights) because low molecular weight proteins made up 57.9% and the rest of the proteins had middle and high molecular weights. In Western blot, none of the healthy dogs showed excretion of IgG and/or IgA, whereas IgG and IgA were detected in the Western blot of urine of 68% and 55% respectively of dogs with leishmaniasis. The results obtained in the leishmaniasis group agreed with glomerular and tubular damage, which were confirmed by the histopathological findings.     

Chemical restraint of peccaries with tiletamine/zolazepam and xylazine or tiletamine/zolazepam and butorphanol

Objective To evaluate the use of a combination of tiletamine/zolazepam and xylazine (TZX) in collared and white‐lipped peccaries and to compare its efficacy as an anesthetic technique with that of tiletamine/zolazepam and butorphanol (TZB). Study design Prospective experimental trial. Animals Seven white‐lipped peccaries (Tayassu pecari) (four females and three males) and four collared peccaries (Tayasu tajacu) (two males and two females). Methods Animal immobilization was attempted with TZX and TZB (IM) on two different occasions. Heart and respiratory rates (HR, RR), rectal temperature (RT), sedation, muscle relaxation, posture, auditory response and analgesia were evaluated every 15 minutes during immobilization. Induction, anesthesia, standing and walking time were determined after drug administration. Results Doses for white‐lipped peccaries were 1.23 ± 0.26 mg kg^?1 (mean ± SD) of TZ and 1.23 ± 0.26 mg kg^?1 of X, and 1.46 ± 0.09 mg kg^?1 of TZ and 0.14 ± 0.008 mg kg^?1 of B; doses for collared peccaries were 1.51 ± 0.29 mg kg^?1 of TZ and 1.51 ± 0.29 mg kg^?1 of X and 1.68 ± 0.02 mg kg^?1 of TZ and 0.17 ± 0.002 mg kg^?1 of B. In white‐lipped peccaries, both drug combinations provided a smooth induction and good immobilization for more than an hour. Anesthesia and standing times were significantly longer in animals given TZB, whereas walking time was significantly longer in animals given TZX. A significant decrease in HR was observed with both treatments. Respiratory rate decreased significantly with TZX, but the rate remained higher than with TZB. Induction and recovery quality in white‐lipped peccaries was better with TZB than with TZX. Neither protocol provided adequate immobilization in collared peccaries. Conclusion and clinical relevance At the doses described, TZB is effective in providing a long period of immobilization, whereas TZX is adequate for short to medium immobilization in white‐lipped peccaries. Neither drug combination was effective in collared peccaries at the doses given.