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.

     

Global Dryland Ecosystem Programme (Global-DEP): Australasian consultation report

Journal of Soils and Sediments -     

Changes in phosphorus fractions in three tropical soils amended with corn cob and rice husk biochars

ABSTRACT

The formation of phosphorus (P) compounds including iron-P, aluminum-P and calcium-P in highly weathered tropical soils can be altered upon biochar addition. We investigated the effect of corn cob biochar (CC) and rice husk biochar (RH) pyrolyzed at three temperatures (300°C, 450°C and 650°C) on phosphorus (P) fractions of three contrasting soils. A 90d incubation study was conducted by mixing biochar with soil at a rate of 1% w/w and at 70% field capacity. Sequential P fraction was performed on biochar, soil and soil-biochar mixtures. Increase in most labile P (resin-P_i, NaHCO₃-P_i) and organic P fraction (NaHCO₃-P_o + NaOH-P_o) in CC and RH biochars were inversely related to increasing temperature. HCl-P_i and residual P increased with increasing temperature. Interaction of CC and RH with soils resulted in an increase in most labile P as well as moderately labile P (NaOH-P_i) fractions in the soils. CC increased most labile P in the soils more than RH. The increase in most labile P fraction in soils was more significant at relatively lower temperatures (300°C and 450°C) than 650°C. However, the increase in HCl-P_i and residual P of the soils was more predominant at high temperature (650°C). The study suggested that biochar pyrolyzed at 300–450°C could be used to increase P bioavailability in tropical soils.     

Transendoscopic biopsy of the horse's airway mucosa

Transtracheal wash and bronchoalveolar lavage are diagnostic techniques that have been adopted from human medicine for monitoring inflammatory changes in the airway of the horse. Transendoscopic biopsy has also proven to be a valuable tool for obtaining samples of the airway mucosa in human patients. A transendoscopic technique was developed in this study for obtaining a respiratory mucosal biopsy from standing, sedated horses. Six normal adult horses were sampled at eight-week intervals for a total of three sample periods. Horses were monitored for adverse effects of the technique and none were noted. Sample sites were completely healed after eight weeks with no gross or histologic abnormalities. Biopsy samples were 3 to 4 millimeters in diameter, and 17 of 18 samples provided interpretable histological sections. Methods for handling, staining and evaluating tissue were also developed. The results of this study demonstrated that airway mucosal biopsy is a safe, repeatable technique that can be performed in the sedated, standing horse.     

Volatile chemical cues guide host location and host selection by parasitic plants

The importance of plant volatiles in mediating interactions between plant species is much debated. Here, we demonstrate that the parasitic plant Cuscuta pentagona (dodder) uses volatile cues for host location. Cuscuta pentagona seedlings exhibit directed growth toward nearby tomato plants (Lycopersicon esculentum) and toward extracted tomato-plant volatiles presented in the absence of other cues. Impatiens (Impatiens wallerana) and wheat plants (Triticum aestivum) also elicit directed growth. Moreover, seedlings can distinguish tomato and wheat volatiles and preferentially grow toward the former. Several individual compounds from tomato and wheat elicit directed growth by C. pentagona, whereas one compound from wheat is repellent. These findings provide compelling evidence that volatiles mediate important ecological interactions among plant species.     

Planktonic foraminifera of the California Current reflect 20th-century warming

It is currently unclear whether observed pelagic ecosystem responses to ocean warming, such as a mid-1970s change in the eastern North Pacific, depart from typical ocean variability. We report variations in planktonic foraminifera from varved sediments off southern California spanning the past 1400 years. Increasing abundances of tropical/subtropical species throughout the 20th century reflect a warming trend superimposed on decadal-scale fluctuations. Decreasing abundances of temperate/subpolar species in the late 20th century indicate a deep, penetrative warming not observed in previous centuries. These results imply that 20th-century warming, apparently anthropogenic, has already affected lower trophic levels of the California Current.     

Transformation of the nitrogen cycle: recent trends, questions, and potential solutions

Humans continue to transform the global nitrogen cycle at a record pace, reflecting an increased combustion of fossil fuels, growing demand for nitrogen in agriculture and industry, and pervasive inefficiencies in its use. Much anthropogenic nitrogen is lost to air, water, and land to cause a cascade of environmental and human health problems. Simultaneously, food production in some parts of the world is nitrogen-deficient, highlighting inequities in the distribution of nitrogen-containing fertilizers. Optimizing the need for a key human resource while minimizing its negative consequences requires an integrated interdisciplinary approach and the development of strategies to decrease nitrogen-containing waste.     

Fear of predation slows plant-litter decomposition

Aboveground consumers are believed to affect ecosystem functioning by regulating the quantity and quality of plant litter entering the soil. We uncovered a pathway whereby terrestrial predators regulate ecosystem processes via indirect control over soil community function. Grasshopper herbivores stressed by spider predators have a higher body carbon-to-nitrogen ratio than do grasshoppers raised without spiders. This change in elemental content does not slow grasshopper decomposition but perturbs belowground community function, decelerating the subsequent decomposition of plant litter. This legacy effect of predation on soil community function appears to be regulated by the amount of herbivore protein entering the soil.     

Compatibility of Beauveria bassiana with Neoseiulus barkeri for Control of Frankliniella occidentalis

The entomopathogenic fungus Beauveria bassiana(Balsamo) Vuillemin and predatory mite Neoseiulus barkeri Hughes are effective biological control agents of F rankliniella occidentalis Pergande(Thysanoptera: Thripidae), one of the most important pests of ornamentals and vegetables world-wide. Combined application of both may enhance control efficiency. T he functional response for N. barkeri on the first instar larvae of western flower thrips which were infected by B. bassiana for 1 2 and 24 h in the laboratory((25±1)°C,(70±5)% RH, L:D=16 h:8 h) was determined. The virulence of B. bassiana against the secon d instar and pupae of the thrips attacked by N. barkeri were also tested. The re sults showed that N. barkeri exhibited a Hollin g type II fu n ctional response on treated thrips. After having been treated with the fungus for 12 h and then offered to the predator, thrips were more vulnerable to be killed by N. barkeri. The second instar larvae and pupae of the thrips which had been attacked by predatory mites were m arkedly more susceptible to B. bassiana infection than normal thrips; the cu mulative corrected mortality of B. bassiana of the second instar and pupae which were attacked by N. barkeri were 57 and 94%, respectively, compared to 35 and 80% in controls on the day 8. These findings highlight the potential use of B. bas siana in combination with N. barkeri to control F. occidentalis.