Assessing the options for upland livestock systems under CAP reform: Developing and applying a livestock systems model within whole-farm systems analysis

This paper presents a scenario-based analysis of the impacts of Common Agricultural Policy (CAP) reform for upland agriculture using a Welsh case-study. Specifically the paper examines the impacts of the introduction of the single-farm payment (SFP), the modulation of direct payments under Pillar I of the CAP and the increase in agri-environment payments under Pillar II. Three enterprises are examined, upland sheep rearing with lamb finishing, spring- and autumn-calving suckler-cattle with calf rearing. These enterprises are modelled under conditions in 2002/3, 2004/5 and for the reformed CAP in 2005/6. To support this analysis a livestock system model (LSM) was implemented. The model assesses alternative management regimen using a flexible state-transition approach. This simplifies the realisation and parameterisation of potentially complex management regimen. The model tracks fodder requirements to achieve targets based on defined diets. The LSM underpins whole-farm analyses of stocking-rates, labour and other resource requirements and net-farm income. From the case study the paper concludes that the impacts of the introduction of the CAP reform on the financial performance of the systems are small but negative (a net reduction of around 5% in support). The larger reduction in direct payments (15–18%) is partially offset by agri-environment measures. The paper concludes that while SFP encourages a more market-oriented outlook, the adaptive capacity within systems as they stand is very limited. There are a range of possible adaptation strategies, but for the uplands the extensification of cattle systems by reducing stock numbers and cutting back on labour seems most probable.     

The effect of irrigation and nitrogen fertilizer on rapeseed (Brassica napes) production in South-Eastern Australia

Summary A field trial was conducted to determine the response of rapeseed (Brassica napus cv. Marnoo) to two irrigation treatments and six nitrogen fertilizer treatments. Dry matter accumulation, leaf area development and seed yield were measured. The dry matter and seed yield response to applied nitrogen was greater under irrigated compared to rainfed conditions. Maximum seed yield (approx. 3.8 t ha^–1) was obtained from the irrigated treatment receiving 100 kg N ha^–1 applied at sowing. This high rate of N application at sowing led to more rapid leaf area development and higher maximum LAI compared to treatments supplied with split application of the same amount of N at sowing and rosette stages. Greater partitioning of dry matter into the leaf component and higher specific leaf areas under the higher N regime were largely responsible for this increase. Higher maximum LAI's were associated with greater numbers of pods per plant, which combined with longer leaf area duration led to higher final seed yields.     

The future of tropical species in secondary forests: A quantitative review

Deforestation and degradation of tropical old-growth forests has the potential to cause catastrophic species extinctions. In this review, we assess whether regenerating secondary forests (SF) can support species typically found in old-growth forest (OG) and so prevent extinctions. We review 65 studies that compare faunal diversity in SF and corresponding OG, and compare the similarity of species composition both within and between these two forest types using the Sorensen, Morisita-Horn and Sorensen-Chao indices. Comparisons between traditional similarity indices and Sorensen-Chao, which minimizes sampling biases, indicated that limited sampling effort consistently reduced apparent similarity between SF and OG and that similarity between SF and OG is actually higher than previously appreciated. Similarity, which ranges from 0 to 1, varied from 0.49 to 0.92 between replicate OG sites and was correlated with similarity between SF and OG. This correlation might be an artefact of variation among studies in sampling effort, especially for vertebrates where small samples reduce apparent similarity across all comparisons, as well as a real effect of variation among studies in landscape heterogeneity and the presence of species with patchy distributions. Therefore, similarity between SF and OG cannot be interpreted without an understanding of background variation in OG. Similarity between different SF sites provided no evidence that disturbance specialists dominate SF. Similarity to OG increased rapidly with SF age; when SF was contiguous with OG; when SF was growing in small clearings; and after low intensity land uses including clearing only, shifting agriculture and tree plantations. This describes the most frequently observed tropical SF; isolated from roads and on hilly terrain unsuitable for mechanized agriculture. Thus, our analyses indicate that tropical SF can play an important role in biodiversity conservation particularly when OG forests are nearby. An important caveat remains, however. Abundance, geographic range and levels of habitat specialization are often related. Widespread, abundant, habitat generalists might dominate similarity analyses even when relatively rare OG specialists are present. Additional species-level analyses of habitat specialization will be needed before the conservation value of tropical SF is fully understood.     

Growth of lucerne (Medicago sativa,L.) in response to frequency of irrigation and gypsum application on a heavy clay soil

Summary Effects of weekly (W) and fortnightly (F) irrigation schedules on established stands of lucerne (Medicago sativa L.) grown on gypsum treated (G) and untreated (C) heavy clay soil were investigated. Two irrigations were applied under the fortnightly regime and four under the weekly schedule during a single cutting cycle. Growth and light interception were measured during both the vegetative and mature phases of growth.Leaf expansion, light interception and dry matter production were greater under treatments W _G and W _C, with yield increasing from 3.4 t ha^–1 under the fortnightly schedule to 5.0 t ha-1 with weekly irrigation. Gypsum treatment was effective under the more frequent irrigation schedule. Specific leaf area and the proportion of stem were both increased by treatments W _G and W _C. The responses to irrigation were therefore characteristic of those elicited by a more favourable plant moisture status. Growth was analysed in terms of light interception, the efficiency of utilisation of intercepted light, the proportion of the daily dry matter gain retained by the leaves and leaf expansion. The analysis demonstrated that impaired leaf expansion contributed to a decline of approximately 15% in yield, and that impaired efficiencies of utilisation of intercepted light contributed to losses of approximately 30% under the less frequent irrigation schedule.A comparison of growth rates and efficiencies of energy conversion with published data showed that satisfactory rates of growth and levels of productivity were achieved on the heavy soils of the local region using gypsum treatment and the more frequent irrigation schedule.     

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.

     

Genome-wide detection of genetic loci associated with soybean aphid resistance in soybean germplasm PI 603712

Soybean aphid (Aphis glycines Matsumura) has become one of the major pests of soybean [Glycine max (L.) Merr.] in North America since 2000. At least four biotypes of soybean aphid have been confirmed in the United States. Genetic characterization of new sources of soybean aphid resistance will facilitate the expansion of soybean gene pool for soybean aphid resistance and thus will help to develop soybean aphid resistant cultivars. To characterize the genetic basis of soybean aphid resistance in PI 603712, a newly identified resistant germplasm line, 142 F₂ plants derived from the cross ‘Roberts’ × PI 603712 and their parents were evaluated for soybean aphid resistance in the greenhouse, and were genotyped with BARCSoySNP6K Illumina Infinium II BeadChip. A genome-wide molecular linkage map was constructed with 1495 polymorphic SNP markers. QTL analysis revealed that PI 603712 possessed two major loci associated with soybean aphid resistance, located on chromosome 7 and 16, respectively. The locus on chromosome 7 was dominantly expressed and positioned about one Mega-base-pair distant from the previously identified resistance locus Rag1. The locus on chromosome 16 was positioned near the previously identified resistance locus Rag3 and expressed partially dominance or additive effect. Interestingly, two minor loci were also detected on chromosomes 13 and 17 but the alleles from PI 603712 decreased the resistance. In developing soybean aphid resistant cultivars through marker-assisted selection, an appropriate combination of resistance loci should be selected when PI 603712 is used as a donor parent of resistance.     

Glomalin in aggregate size classes from three different farming systems

Glomalin was measured in soil from farming systems managed for 8 years by chisel tillage (CT), more intensive tillage for organic (ORG) production, and no tillage (NT) on Acrisols (FAO Soil Units) in the Mid-Atlantic region of the U.S. Whole soil and aggregate size classes of >2.00, 0.50–2.00 and 0.21–0.50 mm (macroaggregates), 0.05–0.21 mm (microaggregates), and <0.05 mm (fine material) were examined. Glomalin-related soil protein (GRSP) was extracted from 1-g samples (four plots per treatment) with 100 mM sodium pyrophosphate, pH 9.0, at 121 °C in three extraction cycles. Extracts were pooled and quantified by using the Bradford protein assay. Concentrations of GRSP and total carbon (C) in aggregates were linearly related across aggregate size classes for all treatments (GRSP = 0.101C + 0.56, r² = 0.95). No tillage had significantly greater whole soil GRSP than did CT or ORG (P = 0.01). Mean values for GRSP in aggregates of NT were higher than for CT or ORG aggregates by 0.53 and 0.66 mg g⁻¹ aggregates, respectively. There were no differences among treatments in GRSP concentrations in fine material. In NT the concentration of GRSP increased as aggregate size increased in contrast to the disturbed treatments, CT or ORG, where there were no differences in GRSP concentration across aggregate size fractions. Larger proportions of GRSP were distributed in macroaggregates of NT compared to CT and ORG in contrast to larger proportions in microaggregates of CT and ORG than in NT. Although soil disturbance in ORG farming is greater than for CT farming, both treatments had similar GRSP concentrations and distributions.     

Distribution and metabolism of abamectin in larval stages of Spodoptera littoralis boisduval and Heliothis armigera hübner (Lepidoptera: Noctuidae)

Comparisons were made between the amounts of abamectin and total radioactivity recovered from Spodoptera littoralis and Heliothis armigera larvae after topical application of [³H]abamectin. Penetration (as shown by wash-off experiments) did not differ significantly between the Spodoptera instars. Significantly more abamectin was recovered from ventral nerve cord samples of larvae showing symptoms of poisoning than from larvae not showing these symptoms. Fifth-instar S. littoralis larvae had a significantly lower proportion of radioactivity as abamectin in the ventral nerve cord than in sixth-instar S. littoralis or fifth- and sixth-instar H. armigera. The proportion of radioactivity present as abamectin (but not total radioactivity) was significantly increased when the fifth-instar S. littoralis larvae were pre-treated with piperonyl butoxide (PB) suggesting that the relative insensitivity of fifth-instar S. littoralis larvae to abamectin is due at least in part to greater metabolism, particularly by microsomal oxidases. Fat body samples consistently had a greater proportion of radioactivity as abamectin than the nerve cord and the former may act as storage sites for abamectin.     

Clinical features of dilated cardiomyopathy in Great Danes and results of a pedigree analysis: 17 cases (1990-2000)

OBJECTIVE: To determine clinical features of dilated cardiomyopathy (DCM) in Great Danes and to determine whether DCM is familial in this breed. DESIGN: Retrospective study. ANIMALS: 17 Great Danes with DCM. PROCEDURE: Medical records of Great Danes in which DCM was diagnosed on the basis of results of echocardiography (fractional shortening < 25%, end-systolic volume index > 30 ml/m2 of body surface area) were reviewed. Pedigrees were obtained for affected animals, as well as for other Great Danes in which DCM had been diagnosed. RESULTS: Dilated cardiomyopathy appeared to be familial and was characterized by ventricular dilatation, congestive heart failure (left-sided or biventricular), and atrial fibrillation. Pedigree analysis suggested that DCM was inherited as an X-linked recessive trait, but the mode of inheritance could not be definitively identified. CONCLUSIONS AND CLINICAL RELEVANCE: Results suggest that DCM may be an X-linked recessive trait in Great Danes. Thus, dogs with DCM probably should not be used for breeding, and female offspring of affected dogs should be used cautiously. Male offspring of affected females are at an increased risk of developing DCM and should be evaluated periodically for early signs of disease. Results of pedigree analysis were preliminary and should be used only as a guide for counseling breeders, rather than as a basis for making breeding decisions.     

Ovulation rate and litter size in gilts immunized against androstenedione and 17alpha-hydroxyprogesterone

Two experiments were conducted to evaluate the effects of the immunization of gilts against ovarian steroids on ovulation rate and litter size. In Exp. 1, gilts (n = five gilts/treatment) at 165+/-1.6 d of age were immunized against either carrier (Control), androstenedione, or 17alpha-hydroxyprogesterone. Age at puberty and estrous cycle length averaged 208+/-5.5 (P = 0.67) and 20.3+/-2.8 d (P = 0.41), respectively, and were not affected by treatment. The androstenedione- and 17alpha-hydroxyprogesterone immunized gilts had higher (P < 0.02) ovulation rates than Controls (14.2, 14.2, and 11.4+/-0.8, respectively). Total pigs born (P = 0.66) and pigs born live (P = 0.65) for the androstenedione-treated group were not different from Controls. Gestation length was not different (P = 0.36) between any of the treatments and the Controls (115+/-0.9 d). Procedures used in Exp. 2 were similar to those in Exp. 1, except that only Control (n= 18) and 17alpha-hydroxyprogesterone (n = 16) treatments were included and only litter size at farrowing was measured. Total pigs and pigs born live were higher in the 17a-hydroxyprogesterone-treated gilts than in the Controls (12.6 vs 10.5+/-0.6, P < 0.02; and 11.4 vs 9.2+/-0.6; P < 0.01, respectively). Data from this study indicate that litter size in gilts can be increased by immunization against 17alpha-hydroxyprogesterone.