Partial-genome evaluation of postweaning feed intake and efficiency of crossbred beef cattle

The effects of individual SNP and the variation explained by sets of SNP associated with DMI, metabolic midtest BW, BW gain, and feed efficiency, expressed as phenotypic and genetic residual feed intake, were estimated from BW and the individual feed intake of 1,159 steers on dry lot offered a 3.0 Mcal/kg ration for at least 119 d before slaughter. Parents of these F(1) × F(1) (F(1)(2)) steers were AI-sired F(1) progeny of Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, and Simmental bulls mated to US Meat Animal Research Center Angus, Hereford, and MARC III composite females. Steers were genotyped with the BovineSNP50 BeadChip assay (Illumina Inc., San Diego, CA). Effects of 44,163 SNP having minor allele frequencies >0.05 in the F(1)(2) generation were estimated with a mixed model that included genotype, breed composition, heterosis, age of dam, and slaughter date contemporary groups as fixed effects, and a random additive genetic effect with recorded pedigree relationships among animals. Variance in this population attributable to sets of SNP was estimated with models that partitioned the additive genetic effect into a polygenic component attributable to pedigree relationships and a genotypic component attributable to genotypic relationships. The sets of SNP evaluated were the full set of 44,163 SNP and subsets containing 6 to 40,000 SNP selected according to association with phenotype. Ninety SNP were strongly associated (P < 0.0001) with at least 1 efficiency or component trait; these 90 accounted for 28 to 46% of the total additive genetic variance of each trait. Trait-specific sets containing 96 SNP having the strongest associations with each trait explained 50 to 87% of additive variance for that trait. Expected accuracy of steer breeding values predicted with pedigree and genotypic relationships exceeded the accuracy of their sires predicted without genotypic information, although gains in accuracy were not sufficient to encourage that performance testing be replaced by genotyping and genomic evaluations.     

Effects of weaning and syndyphalin-33 on expression of melanocortinergic appetite-regulating genes in swine

Syndyphalin-33 (SD-33) increases feed intake in sheep and recently weaned pigs. To assess the effects of SD-33 on hypothalamic gene expression, hypothalami were collected from unweaned pigs (n=19; 21±3 d of age) on day 0. Remaining pigs received an intramuscular injection of 0.5 μmole/kg SD-33 (SD) or saline (VEH) and weaned into individual pens. On days 1, 4, and 7 after weaning, hypothalami were collected from subsets of pigs (n=8 or 9) within each treatment group. Expression of μ-opioid receptor (MOR) was less in SD pigs than in VEH pigs on day 1 and day 4, suggesting down-regulation of the receptor by SD-33. Expression of hypothalamic melanocortin 4 receptor (MC4R) at 1 d after weaning was increased in VEH pigs (but not SD pigs) relative to levels before weaning. Expression of AGRP was not significantly altered by weaning or treatment at 1 d after weaning. At 4 d after weaning, expression of AGRP was greater in SD pigs than in VEH pigs, but at day 7 expression was less in SD pigs than in VEH pigs. A strong positive correlation was noted between expression levels of MOR and MC4R across treatment and time. Treatment with SD-33 appeared to partially abrogate the effects of weaning on expression of two key appetite-regulating genes within 24 h. Effects of SD-33 appear to be mediated at least in part by the μ-opioid receptor and include actions on the melanocortinergic pathway.     

Extending ideas about animal welfare assessment to include ‘quality of life’ and related concepts

Abstract

Ideas within the animal welfare science arena have evolved continuously throughout the last 30 years, and will continue to do so. This paper outlines some of these developments. These included reformulation of the five freedoms concept into the five domains of potential welfare compromise. This accommodated weaknesses in the former by distinguishing between the physical/functional and the mental factors that contribute to an animal's welfare state. This development reflected a rising scientific acceptance that the mental experiences of animals were legitimate foci for study and highlighted that what the animal itself experiences represents its welfare status. Initially, most concepts of animal welfare emphasised predominantly negative subjective experiences, such as thirst, hunger and pain, and negative affective states or feelings including anxiety, fear and boredom, but today positive experiences or emotions such as satiety, vitality, reward, contentment, curiosity and playfulness are also considered to be important. During the same period, the focus shifted from evaluating the impacts of individual mental subjective experiences or emotions towards seeking a more comprehensive, multifactorial understanding. The five domains concept was specifically designed to achieve this. Subsequent notions about quality of life (QoL) had the same objective, and emphasised the importance of positive experiences. However, some approaches to QoL assessment relied heavily on empathetic speculation about what animals may experience subjectively and this raised concerns about inappropriate anthropomorphic projections. Such pitfalls may be minimised when informed personnel rigorously apply objectively based methodologies to QoL assessments limited to a short time frame. It is clear that both formal and somewhat less formal QoL assessments of this type are already used to guide decision-making about the ongoing care and therapeutic management of animals on a daily basis. However, application of the recently introduced concepts of ‘a life not worth living’, ‘a life worth avoiding’, ‘a life worth living’ and ‘a good life’ is problematical, because extending the assessment time scale to the whole of life is attended by a number of as yet unresolved difficulties. Accordingly, their value in the practical management of animals is limited so that, at present, reliance on the minimum standards and recommendations for best practice outlined in codes of practice or welfare will continue to be necessary and worthwhile. Nevertheless, these concepts have value in providing a contextual theme that strongly focuses attention on the promotion of a lifelong QoL with an overall balance that is positive.     

Utility of inline milk fat and protein ratio to diagnose subclinical ketosis and to assign propylene glycol treatment in lactating dairy cows

The objective was to identify a fat-to-protein ratio (FPR) cut-off to diagnose subclinical ketosis (SCK) and to evaluate the effect of propylene glycol (PPG) treatment of cows with high FPR. The optimized cut-off was > 1.42; sensitivity (Se) = 92%; specificity (Sp) = 65%. A cut-off > 1.5 was selected for the PPG trial for balanced Se-Sp. Fat-to-protein ratio cut-offs > 1.25, 1.35, 1.50, 1.60, and 1.70 resulted in Se-Sp of 100% to 49%, 96% to 59%, 75% to 78%, 33% to 90%, and 8% to 96%, respectively. The proportions of cows with FPR > 1.25, 1.35, 1.42, 1.50, 1.60, and 1.70 were 60%, 50%, 44%, 30%, 14%, and 6%, respectively. Incidences of clinical ketosis and milk yield were similar between cows that received 400 mL of PPG (n = 34) and control cows (n = 38). Prevalence of SCK at enrollment was 29.2%; therefore, FPR > 1.5 is not indicated for treatment. Lower cut-offs should be used for screening.     

Depth of root symbiont occurrence in soil

Summary The woody legume Prosopis glandulosa (mesquite) growing in the California Sonoran Desert develops functional root symbiotic associations (N₂-fixing nodules, vesicular-arbuscular mycorrhizal fungi) at depths greater than 4 m in moist soil above a seasonally stable water table. Population densities of symbiotic microorganisms are substantially greater at depth than near the surface. Inferences of plant symbiotic dependence based upon examination of surface roots and soil may be incorrect since deep roots can support the symbioses which are critical for plants utilizing deep water.     

Forest disturbance and river proximity influence chameleon abundance in Madagascar

Many chameleon species are thought to be restricted to primary rainforest where they are threatened by the continued fragmentation and degradation of natural vegetation. We surveyed chameleon abundance in forest subject to high disturbance, low disturbance and in a riparian zone in Madagascar. Four Calumma species and Brookesia thieli were present in all habitats, but B. minima was not recorded from the high-disturbance forest. Chameleons were more abundant in rainforest subject to low-disturbance (e.g. selective timber extraction) than in patches of high-disturbance forest that was recovering from burning. Riparian zones within low-disturbance forest provided linear patches of high chameleon abundance and are therefore an important conservation resource because they also protect a range of other endemic and threatened species. Carefully designed management plans are needed to conserve biodiversity and allow the sustainable use of forest products by people in Madagascar.     

Estimating farmworker population size in New York State using a minimum labor demand method

Assessment of health needs and services for hand-harvest farmworkers requires reliable population estimates. In New York State, the only publicly available source for these is the Department of Labor (DOL). However, published production data exist that may enable estimation of minimum labor demand (MLD) for hand-harvest labor. Our objective was to develop an estimation process for minimum labor demand (MLD) for hand-harvested crops in NYS and contrast the results with DOL estimates. Four crop strata (below ground, ground, bush/vine, and orchard) were identified. MLD (measured in worker-seasons) was estimated by dividing the total annual harvest hours required for each crop stratum by the total hours worked by one worker in a season for that crop stratum. The MLD estimate of the total number of worker seasons combined for all strata (14,121) was higher than that of the DOL (8,230). Harvest acreage was unavailable for 21% of the 991 county-crop combinations studied; therefore, data were imputed from other sources. Within these strata, the greatest difference was found for ground crops, where the DOL count was 28% of the size of the MLD estimate. DOL and MLD estimates were closest in orchard crops (DOL 109% of MLD). Publicly available data provide a potentially valuable source of informationfor estimation of the MLD. Use of these methods implies that the DOL may substantially underestimate the size of this population. Differences seen between the two methods were sensitive to the crop type. County-level farm surveys to verify MLD estimation factors would enhance the method's accuracy.     

A comparison of soil and water properties in organic and conventional farming systems in England

Organic farming and improvements to agricultural sustainability are often seen as synonymous. However, an extensive European review demonstrated that in practice this is not always true. This study aims to compare the status of soil and water properties between separate fields managed in either an organic or a conventional manner. Soil samples were collected from 16 pairs of farms, throughout England, with both arable and grass fields within each pair on similar soil type. Chemical (nutrients, pesticides, herbicides) and physical (aggregate stability, field capacity, shear strength, soil organic matter, infiltration rates) soil properties were measured in four main soil texture classes in organic and conventional fields. The physical soil properties varied significantly between the different classes of texture and land use. The heavier textured soils have significantly higher soil organic carbon (SOC), aggregate stability and shear strength. The coarse‐textured soils have significantly lower field capacity moisture contents. The grassland has a significantly higher level of SOC, field capacity moisture content, aggregate stability and soil shear strength. However, there were no significant differences between organic and conventional treatments for any of the soil physical properties measured. There were fewer traces of agrochemicals in the soil water from the organic fields compared with the conventionally managed fields. The conventional arable fields had higher levels of total inorganic nitrogen than the other land uses and treatments. There was evidence to show that infiltration rates were significantly higher on organically managed grassland soils (7.6 mm/h) than conventionally managed grassland (2.5 mm/h) with lower stocking rates. The results suggest that improved grassland management, whether organic or conventional, could reduce predicted runoff by 28%.     

Genotypic comparisons of chromosomes 01, 04, and 18 from three tetraploid species of <Emphasis Type="Italic">Gossypium</Emphasis> in topcrosses with five elite cultivars of <Emphasis Type="Italic">G. hirsutum</Emphasis> L.

Upland cotton, Gossypium hirsutum L. is the most widely planted cultivated cotton in the United States and the world. The other cultivated tetraploid species G. barbadense L. is planted on considerable less area; however, it produces extra long, strong, and fine fibers which spins into superior yarn. The wild cotton tetraploid species G. tomentosum Nuttall ex Seemann, native to the Hawaiian Archipelago also exhibits traits, such as drought tolerance, that would also be desirable to transfer to Upland cotton. Long-term breeding efforts using whole genome crosses between Upland and these species have not been successful in transferring very many desirable alleles into Upland cotton. Our chromosome substitution lines (CSL) have one chromosome or chromosome arm from an alien species backcrossed into the Upland cotton line,TM-1, via aneuploid technology. Five Upland cultivars were crossed with CS-B01, CS-T01, CS-B04, CS-T04, CS-B18 and CS-T18 and TM-1 the recurrent parent of the CSLs. This provided an opportunity to determine the effects of chromosomes 01, 04, and 18 from the three species in crosses with the five cultivars. Predicted genotypic mean effects of the parents, F₂, and F₃ generations for eight agronomic and fiber traits of importance were compared. The predicted hybrid mean effects for the three chromosomes from each species were different for several of the traits across cultivars. There was no single chromosome or species that was superior for all traits in crosses. Parental and hybrid lines often differed in the effect of a particular chromosome among the three species. The predicted genotypic mean effects for F₂ and F₃, with a few exceptions, generally agree with our previous results for additive and dominance genetic effects of these CSL.