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.

     

Purification of xylitol obtained by fermentation of corncob hydrolysates

Hydrolysates obtained by autohydrolysis-posthydrolysis of corncobs were detoxified with charcoal, concentrated, supplemented with nutrients, and fermented with Debaryomyces hansenii. After biomass removal, the fermented media contained 0.1137 kg of nonvolatile components (NVC)/kg of liquor, which corresponded mainly to xylitol (0.6249 kg/kg of NVC) but also to minor amounts of inorganic components (measured as ashes), proteins, nonfermented sugars (xylose and arabinose), uronic acids, arabitol, and other nonvolatile components (ONVC). The media were subjected to further processing (sequential stages of adsorption, concentration, ethanol precipitation, concentration, and crystallization) to obtain food-grade xylitol. Adsorption experiments were carried out at various solid-to-liquor ratios. Under selected conditions (1 kg of charcoal/15 kg of liquors), the xylitol content increased to 0.6873 kg/kg of NVC, and almost total decoloration was achieved. The resulting liquor was concentrated by evaporation to increase its NVC content to 0.4032 kg/kg of liquor (corresponding to a xylitol concentration of 0.280 kg/kg of liquor), and ethanol was added to precipitate a part of the NVC (mainly proteins, but also uronic acids, ashes, and other nonvolatile compounds). Refined liquors (containing 0.7303 kg of xylitol/kg of NVC) were concentrated again, and ethanol was added (to reach 40-60% volume of the stream) to allow crystallization at -10 or -5 degrees C. Under selected conditions, 43.7% of xylitol contained in the initial fermentation broth was recovered in well-formed, homogeneous crystals, in which xylitol accounted for 98.9% of the total oven-dry weight. Material balances are presented for the whole processing scheme considered in this work.     

Enzyme Bioprospection of Marine-Derived Actinobacteria from the Chilean Coast and New Insight in the Mechanism of Keratin Degradation in Streptomyces sp. G11C

Marine actinobacteria are viewed as a promising source of enzymes with potential technological applications. They contribute to the turnover of complex biopolymers, such as pectin, lignocellulose, chitin, and keratin, being able to secrete a wide variety of extracellular enzymes. Among these, keratinases are a valuable alternative for recycling keratin-rich waste, which is generated in large quantities by the poultry industry. In this work, we explored the biocatalytic potential of 75 marine-derived actinobacterial strains, focusing mainly on the search for keratinases. A major part of the strains secreted industrially important enzymes, such as proteases, lipases, cellulases, amylases, and keratinases. Among these, we identified two streptomycete strains that presented great potential for recycling keratin wastes—Streptomyces sp. CHA1 and Streptomyces sp. G11C. Substrate concentration, incubation temperature, and, to a lesser extent, inoculum size were found to be important parameters that influenced the production of keratinolytic enzymes in both strains. In addition, proteomic analysis of culture broths from Streptomyces sp. G11C on turkey feathers showed a high abundance and diversity of peptidases, belonging mainly to the serine and metallo-superfamilies. Two proteases from families S08 and M06 were highly expressed. These results contributed to elucidate the mechanism of keratin degradation mediated by streptomycetes.     

Landscape drivers of connectivity for a forest rodent in a coffee agroecosystem

Landscape Ecology - The majority of remaining tropical forests exist as fragments embedded in a matrix of agricultural production. Understanding the effects of these agricultural landscapes on...     

Genetic Structure of Peruvian Populations of Phytophthora infestans

ABSTRACT Isolates of the late blight pathogen Phytophthora infestans (n = 327) from the central to southern Peruvian Andes were systematically collected in 1997 to 1999 and analyzed to determine the pathogen's population structure at its host's center of diversity. No isolates of the A2 mating type were detected. Cluster analysis of DNA fingerprinting data indicated that the collection consisted of five major groups that were interpreted to be clonal lineages. Two of the lineages (US-1 and EC-1) have been previously described, and three (PE-3, 5, and 6) are described here for the first time. Collections from three areas in the central Peruvian Andes, including two key sites used in an international potato breeding program, consisted of isolates of the EC-1 lineage, which has been reported to dominate the pathogen population in Andean countries to the north of Peru. The collections from Cusco and Puno were more diverse. More than one lineage was detected in 10 of the 20 fields sampled in Cusco. Data on virulence, metalaxyl sensitivity, and band data for allozymes, mitochondrial DNA, and ipiB1 suggested that PE-3 may have been produced through recombination events between US-1 and EC-1. Restriction fragment length polymorphism and amplified fragment length polymorphism marker data were not consistent with this hypothesis.     

Evaluation and analysis of reduction of late blight disease in a diploid potato progeny

The rate of late blight disease was analysed for individuals of a diploid Solanum phureja – Solanum tuberosum dihaploid hybrid population (PD), using three different assessment techniques, in the laboratory, screenhouse, and field. These hybrids expressed low disease rates in the field, comparable to resistance based on intact R genes. However, none of the parents of PD expressed any R genes and the pattern of segregation within the PD population was not indicative of R-gene inheritance. The foliage (or leaflet) area diseased had the largest broad-sense heritability of all criteria analysed, in all tests performed. In the field evaluations, the PD population showed intermediate levels of broad-sense heritability for foliage area diseased, relative to the much larger heritability detected for the group of controls possessing R genes. Resistance in the field of the PD hybrids had very little genotype-environment (G × E) interaction, indicating stability of its expression. All genotypes without R genes exhibited heritable, reduced rates of late blight disease in the field, but they were susceptible with low heritability in screenhouse and laboratory tests. This differential expression of disease indicates that the plants' indirect response to unknown environmental stress in the field may have been measured. The value of the PD hybrids for breeding of late blight resistant potato and the use of the disease rate data for detection of the underlying quantitative trait loci are discussed.     

Albendazole sulphoxide enantiomers in pregnant rats' embryo concentrations and developmental toxicity

Three single oral doses (8.5, 10, and 14 mg/kg) of a racemic formulation of albendazole sulphoxide (ABZSO) were administered to pregnant rats on day 10 of gestation. Mother plasma and embryo concentrations of ABZSO enantiomers and albendazole sulphone (ABZSO(2)) were determined 9 h after administration. The (-)-ABZSO enantiomer showed higher peak concentrations in both maternal plasma and embryo than the (+) enantiomer. An increase in embryo concentrations of ABZSO enantiomers and ABZSO(2) was only observed when dose rose to 14 mg/kg. There was an increase in resorption when the dose increased, but significant differences were only found in the higher dose group when compared with the other groups. The incidence of external and skeletal malformations (mostly of the tail, vertebrae and ribs) rose significantly in the 10 mg/kg group, producing almost 20% and 90% of malformed fetuses, respectively, and gross external and skeletal abnormalities in the thoracic region and limbs were also found.     

Antigens from Rhipicephalus sanguineus ticks elicit potent cell-mediated immune responses in resistant but not in susceptible animals

In the present study we compared the immunological reactions between Rhipicephalus sanguineus tick-infested susceptible (dogs and mice) and tick-resistant hosts (guinea pigs), elucidating some of the components of efficient protective responses against ticks. We found that T-cells from guinea pigs infested with adult ticks proliferate vigorously in the presence of concanavalin A (ConA), whereas ConA-induced cell proliferation of tick-infested mice and dogs was significantly decreased at 43.1 and 94.0%, respectively, compared to non-infested controls. Moreover, cells from mice and dogs submitted to one or three successive infestations did not exhibit a T-cell proliferative response to tick antigens, whilst cells from thrice tick-infested guinea pigs, when cultured with either a tick extract or tick saliva, displayed a significant increase in cell proliferation. Also, we evaluated the response of tick-infested mice to a cutaneous hypersensitivity test induced by a tick extract. Tick-infested mice developed a significant immediate reaction, whereby a 29.9% increase in the footpad thickness was observed. No delayed-type hypersensitivity (DTH) reaction was detected. Finally, the differential cell count at the tick attachment site in repeatedly infested mice exhibited a 6.6- and 4.1-fold increase in the percentage of eosinophils and neutrophils, respectively, compared to non-infested animals, while a decrease of 77.0-40.9 in the percentage of mononuclear cells was observed. The results of the cutaneous hypersensitivity test and the cellular counts at the tick feeding site for mice support the view that tick-infested mice develop an immune response to R. sanguineus ticks very similar to dogs, the natural host of this species of tick, but very different from guinea pigs (resistant host), which develop a DTH reaction in addition to a basophil and mononuclear cell infiltration at the tick-attachment site. In conclusion, saliva introduced during tick infestations reduces the ability of a susceptible animal host to respond to tick antigens that could stimulate a protective immune response. As a consequence, the animals present a lack of DTH response and disturbed cellular migration to tick feeding site, which can represent a deficient response against ticks.     

Antibody response to a fragment of the protein G of VHS rhabdovirus in immunised trout

A fragment (called frg#11, amino acids, aa 56-110) of the protein G (pG) of viral haemorrhagic septicaemia virus (VHSV) was designed after previous results showed it to be recognised by approximately 40% of the trout immunised to VHSV [Dis. Aquat. Organ. 34 (1999) 167]. frg#11 was then cloned, expressed, purified and used to study the production of antibodies to its epitopes in trout immunised to VHSV. Anti-frg#11 trout antibodies could be detected in serum from individual trout surviving VHSV exposure, immunised by injection with purified VHSV or DNA-immunised with its pG gene whereas it was not detected in non-infected and non-immunised trout. The trout serum antibodies which reacted more strongly by ELISA using solid-phase frg#11 (continuous or linear epitopes on the sequence of the pG) had the lowest VHSV-neutralising activity (epitopes which are pG conformation-dependent). Because antibodies recognising continuous as well as conformation-dependent epitopes of the pG seem to be involved in protective trout immunological responses to VHSV, the estimation of anti-frg#11 antibodies could help to the dissection of the complex trout antibody response to VHSV infections. In addition, these preliminary results suggest that the determination of anti-frg#11 antibodies might also be used to complement in vitro viral neutralising assays which seem to be restricted to pG conformation-dependent epitopes.     

Use of spatial statistics and monitoring data to identify clustering of bovine tuberculosis in Argentina

The spatial distribution of endemic bovine tuberculosis (TB) in Argentine cattle herds was described using recorded information on the detection of TB-like lesions in cattle slaughtered between March 1995 and 1997 at 126 slaughterhouses with federal inspection. Approximately, 47% (9472396 cattle) of the estimated total number of cattle slaughtered in Argentina during this period was included in the study. Information on the number of cattle per source herd consigned to slaughter, number of cattle with TB-like lesions per herd and the geographical location of counties from which cattle originated was used to investigate spatial clustering of TB. Overall, no evidence of clustering of TB prevalence by county was detected (Moran's autocorrelation statistic I=0.009, P=0.089). However, first- (Cuzick and Edwards' test statistic, T(k)=87, P=0.036) and second-order (T(k)=170, P=0.038) nearest-neighbor case-counties (TB prevalence>median prevalence of all counties, 6.7%) were clustered. Using the spatial scan test based on a Bernoulli model, the most-likely cluster (P=0.001) identified during the study period included 5793 cases of TB (5.2 per 1000 km(2)) in five counties. This cluster coincided with Santa Fe Province, which contains 21% of all dairy cows in Argentina and accounts for 34% of the country's milk production. Several secondary clusters of TB-also located in dairy districts-were identified. Study results demonstrate that bovine TB is clustered in Argentina, and these clusters coincide with dairy cattle production. Identification of clustering can assist efforts to eradicate bovine TB from Argentina. Further spatial investigations need to focus on the reasons why TB is clustered in Argentina. In particular, the relationship between TB clustering and management practices-such as grazing density and production systems-need to be described to assist in the development of disease-control programs. The use of spatial statistics and geographical information systems could meet these needs.