Prevalence of and intrinsic risk factors for appendicular osteosarcoma in dogs: 179 cases (1996-2005)

OBJECTIVE: To determine the prevalence of appendicular osteosarcoma (OSA) in Greyhounds compared with other breeds and identify potential intrinsic risk factors associated with development of OSA. DESIGN: Retrospective case series. ANIMALS: 179 dogs with primary appendicular OSA. PROCEDURES: Medical records of dogs in which primary appendicular OSA had been diagnosed between 1996 and 2005 were reviewed. Prevalence and crude odds ratios for OSA were calculated for various breeds by comparison with a reference population of mixed-breed dogs. Age and sex were examined as potential risk factors for the 3 breeds with highest prevalence. RESULTS: Breed period prevalence of OSA was highest for Greyhounds (21/339 [6.2%]), followed by Rottweilers (51/969 [5.3%]) and Great Danes (13/297 [4.4%]); all 21 Greyhounds with OSA were identified as having retired from racing. Sex was not identified as a risk factor for OSA in these breeds, but in all 3 breeds, risk of OSA increased with age. Greyhounds were significantly older at the time of OSA diagnosis (mean, 9.9 years) than were Rottweilers (8.3 years) and Great Danes (7.8 years). Rottweilers and Great Danes were more likely to have OSA involving the forelimbs than the hind limbs. The most frequent lesion sites for all 3 breeds were the proximal end of the humerus and distal end of the radius. The proximal end of the femur was also a common site for the Greyhounds. CONCLUSIONS AND CLINICAL RELEVANCE: Results of the present study suggested that Greyhounds, Rottweilers, and Great Danes had an increased risk of developing OSA, compared with mixed-breed dogs.     

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.     

Fertilizer location modifies root zone salinity,root morphology,and water‐stress resistance of tree seedlings according to the watering regime in a dryland reforestation

There is a direct relationship between soil nutrient concentration in localized zones and root proliferation and elongation under well‐watered conditions. However, in field studies under semiarid conditions this relationship can change due to higher salt accumulation and soil dryness that affect root growth, water stress resistance, and seedling survival. We assessed the effect of different locations of fertilizer placement in the soil profile and water availability on root zone salinity, root development and ecophysiological responses of Quillaja saponaria Mol. after outplanting. A single dose (6 g L^?1) of controlled‐release nitrogen fertilizer (CRF_N) was placed at 0 cm (top layer), 15 cm (middle layer), or 30 cm (bottom layer) depth in the containers in a greenhouse, in addition to an unfertilized treatment (control). After 6 months, seedlings were transplanted to the field and subjected to weekly watering regimes (2 L plant^?1 and unwatered). Morphological and ecophysiological parameters were periodically measured on seedlings, as well as soil electrical conductivity (EC). After 1 year, the shoot : root ratio of unwatered seedlings decreased as a function of CRF_N placement depth, which was attributed to lower shoot growth and not to greater root growth. The root morphology of the bottom layer treatment was negatively affected by high EC in unwatered seedlings. Greater total root length and root volume of the middle layer treatment was found only when well‐watered; however, this did not contribute to improve physiological responses against water stress. The lowest EC and the highest photochemical efficiency, net photosynthesis, and stomatal conductance were shown by unfertilized seedlings, independent of water availability. Our findings suggest that varying depth of CRF_N placement does not contribute significantly to improve root growth under water restriction. Water supplements, independently of the CRF_N location in the substrate, contribute to decrease root zone salinity, and consequently, improve root volume growth.     

Identification of QTLs related to sugar and organic acid composition in melon using near-isogenic lines

The soluble sugar and organic acid composition of melon (Cucumis melo L.) fruit flesh has become a major focus of plant breeding worldwide in an attempt to improve taste. Thus, sugar and organic acid profiles were characterized using near-isogenic lines (NILs) derived from the Spanish cultivar Piel de Sapo (PS) and the exotic Korean accession Shongwan Charmi (PI 161375). Fruits were cultivated in only one environment. These data were used to map 60 quantitative trait loci (QTLs): 18 for individual sugars, eight for sucrose equivalents, five for the glucose-to-fructose ratio, seven for the total sugar content and 21 for organic acids. Within the QTLs that were associated with the sugar profile, 27 defined the sugar content: eight for fructose, six for glucose, four for sucrose, and nine for sucrose equivalents. Although increased sweetness of selected NILs compared with the parental PS was achieved by an increased glucose or fructose content, only glucose heritability was above 0.5. A total of 21 QTLs (two with positive effects and nineteen with detrimental effects compared with the PS levels) controlled the organic acid profile: l-glutamic, ascorbic and succinic acids (the principal ones) and fumaric, citric, oxalacetic, and isocitric acids. The levels of sugars imparted by the PI 161375 introgression frequently decreased the score grades given to NILs by consumers. Within the 32 QTLs mapped for sensory traits, 27 were associated with lower scores in taste (nine QTLs), sweetness (eight QTLs) or global quality appreciation (nine QTLs); two with increased fruit sourness or sweetness and three with increased fruit bitterness. The QTLs defined herein may assist breeders to understand the overall organoleptic balance (sweetness, sourness, and umami taste) in melon fruit, particularly those located within linkage groups III, V, VI, and VIII to XI.     

Responses of Chilean forest birds to anthropogenic habitat fragmentation across spatial scales

Although it is recognized that anthropogenic forest fragmentation affects habitat use by organisms across multiple spatial scales, there is uncertainty about these effects. We used a hierarchical sampling design spanning three spatial scales of habitat variability (landscape > patch > within-patch) and generalized mixed-effect models to assess the scale-dependent responses of bird species to fragmentation in temperate forests of southern Chile. The abundances of nine of 20 bird species were affected by interactions across spatial scales. These interactions resulted in a limited effect of within-patch habitat structure on the abundance of birds in landscapes with low forest cover, suggesting that suitable local habitats, such as sites with dense understory cover or large trees, are underutilized or remain unused in highly fragmented landscapes. Habitat specialists and cavity-nesters, such as tree-trunk foragers and tapaculos, were most likely to exhibit interactions across spatial scales. Because providing additional sites with dense understory vegetation or large habitat trees does not compensate the negative effect of the loss of forest area on bird species, conservation strategies should ensure the retention of native forest patches in the mixed-use landscapes.     

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.

     

QTL mapping and analysis of epistatic interactions for grain yield and yield-related traits in <Emphasis Type="Italic">Triticum turgidum</Emphasis> L. var. <Emphasis Type="Italic">durum</Emphasis>

A quantitative trait loci (QTL) analysis of grain yield and yield-related traits was performed on 93 durum wheat recombinant inbred lines derived from the cross UC1113 × Kofa. The mapping population and parental lines were analyzed considering 19 traits assessed in different Argentine environments, namely grain yield, heading date, flowering time, plant height, biomass per plant, and spikelet number per ear, among others. A total of 224 QTL with logarithm of odds ratio (LOD) ≥ 3 and 47 additional QTL with LOD > 2.0 were detected. These QTL were clustered in 35 regions with overlapping QTL, and 12 genomic regions were associated with only one phenotypic trait. The regions with the highest number of multi-trait and stable QTL were 3BS.1, 3BS.2, 2BS.1, 1BL.1, 3AL.1, 1AS, and 4AL.3. The effects of epistatic QTL and QTL × environment interactions were also analyzed. QTL putatively located at major gene loci (Rht, Vrn, Eps, and Ppd) as well as additional major/minor QTL involved in the complex genetic basis of yield-related traits expressed in Argentine environments were identified. Interestingly, the 3AL.1 region was found to increase yield without altering grain quality or crop phenology.     

Occupancy pattern of a long-horned beetle in a variegated forest landscape: linkages between tree quality and forest cover across spatial scales

Context

Interactions between landscape-scale processes and fine-grained habitat heterogeneity are usually invoked to explain species occupancy in fragmented landscapes. In variegated landscapes, however, organisms face continuous variation in micro-habitat features, which makes necessary to consider ecologically meaningful estimates of habitat quality at different spatial scales.

Objectives

We evaluated the spatial scales at which forest cover and tree quality make the greatest contribution to the occupancy of the long-horned beetle Microplophorus magellanicus (Coleoptera: Cerambycidae) in a variegated forest landscape.

Methods

We used averaged data of tree quality (as derived from remote sensing estimates of the decay stage of single trees) and spatially independent pheromone-baited traps to model the occurrence probability as a function of multiple cross-scale combinations between forest cover and tree quality (with scales ranging between 50 and 400 m).

Results

Model support and performance increased monotonically with the increasing scale at which tree quality was measured. Forest cover was not significant, and did not exhibit scale-specific effects on the occurrence probability of M. magellanicus. The interactive effect between tree quality and forest cover was stronger than the independent (additive) effects of tree quality and particularly forest cover. Significant interactions included tree quality measured at spatial scales ≥200 m, but cross-scale interactions occurred only in four of the seven best-supported models.

Conclusions

M. magellanicus respond to the high-quality trees available in the landscape rather than to the amount of forest per se. Conservation of viable metapopulations of M. magellanicus should consider the quality of trees at spatial scales >200 m.