Phosphorus sorption, supply potential and availability in soils with contrasting parent material and soil chemical properties

Soil phosphorus (P) management requires a more targeted and soil-specific approach than is currently applied for agronomic recommendations and environmental evaluation. Phosphorus buffering capacities control the supply of P in the soil solution and were measured across Irish soils with contrasting parent material and chemical properties. Langmuir sorption buffer capacities (MBCs) and binding energies (b) were strongly correlated with soil pH and extractable aluminium (Al). A broken-line regression fitted to the relationship between MBC and Al derived a change-point value for Al above which MBC increased linearly. Soils above the change point were predominantly acidic to neutral with non-calcareous parent material, with larger buffering capacities and binding energies than calcareous soils. Ratios of Mehlich3-Al and P (Al:P) were used to relate buffering capacity to supply potential in non-calcareous soils. Large ratios of Al:P were associated with poor P availability, characteristic of strongly P-fixing soils. Threshold values of iron-oxide paper strip P (FeO-P) and Morgan's P revealed Al:P ratios where soils began to supply P in available form. The change-point for Morgan's P fell within the current target index for P availability; however, the confidence interval was more compatible with previous agronomic P indices used in Ireland. Relationships between Morgan's P and measures of extractable P, M3-P and Olsen P, deviated in calcareous soils at large soil P contents, indicative of P precipitation processes dominating in these soils. Identifying differences in soil P buffering capacity at the laboratory scale would improve agronomic and environmental assessment at field and catchment scales

The use of mid-infrared spectrometry to predict body energy status of Holstein cows

Energy balance, especially in early lactation, is known to be associated with subsequent health and fertility in dairy cows. However, its inclusion in routine management decisions or breeding programs is hindered by the lack of quick, easy, and inexpensive measures of energy balance. The objective of this study was to evaluate the potential of mid-infrared (MIR) analysis of milk, routinely available from all milk samples taken as part of large-scale milk recording and milk payment operations, to predict body energy status and related traits in lactating dairy cows. The body energy status traits investigated included energy balance and body energy content. The related traits of body condition score and energy intake were also considered. Measurements on these traits along with milk MIR spectral data were available on 17 different test days from 268 cows (418 lactations) and were used to develop the prediction equations using partial least squares regression. Predictions were externally validated on different independent subsets of the data and the results averaged. The average accuracy of predicting body energy status from MIR spectral data was as high as 75% when energy balance was measured across lactation. These predictions of body energy status were considerably more accurate than predictions obtained from the sometimes proposed fat-to-protein ratio in milk. It is not known whether the prediction generated from MIR data are a better reflection of the true (unknown) energy status than the actual energy status measures used in this study. However, results indicate that the approach described may be a viable method of predicting individual cow energy status for a large scale of application

Considerable potential exists to improve lambing performance traits in sheep through breeding

peer-reviewedThe high demand for resources at lambing necessitates strategies to reduce such requirements; one such strategy is breeding programs that enable selection for fewer lambing events requiring assistance as well as less perinatal mortality. The objective of the present study was to estimate the genetic (co)variances for a range of lambing traits in sheep, based on alternative trait definitions that considered differences in mating type and litter size. A total of 158,561 lambing events from both crossbred and purebred Irish sheep were available. Four lambing traits were considered in the analysis: lambing difficulty score, lambing dystocia, lamb perinatal mortality and birth weight. Variance components for each trait were estimated using animal linear mixed models either in the entire data as a whole, or within sub-populations stratified by litter size (i.e., single versus multiple) or stratified by mating type (i.e., crossbred versus purebred animals). The presence of significant re-scaling and re-ranking across population strata were investigated to determine if genotype-by-environmental interactions existed. Considerable genetic variation existed for all lambing traits investigated. Irrespective of the dataset analysed, direct heritability estimates for lambing difficulty score (0.04 ± 0.02 to 0.12 ± 0.03), lambing dystocia (0.04 ± 0.01 to 0.09 ± 0.03), and lamb mortality (0.01 ± 0.01 to 0.09 ± 0.02) were all low. In contrast, lamb birth weight (0.11 ± 0.02 to 0.20 ± 0.04) exhibited a low to moderate direct heritability. Using the entire dataset, the maternal heritability ranged from 0.01 ± 0.005 (lamb mortality) to 0.15 ± 0.02 (birth weight). All direct genetic effects for the lambing traits were positively correlated with each other, except between lamb birth weight and perinatal mortality (-0.15; SE=0.16). Significantly different genetic variances in different environments and significant re-ranking between environments was detected for lamb mortality (across different mating types and litter sizes), and for lambing difficulty score (only across different litter sizes). Results clearly indicate that ample genetic variation exists for the lambing-related traits investigated

Field scale phosphorus balances and legacy soil pressures in mixed-land use catchments

peer-reviewedReducing legacy soil phosphorus (P) is recognised as an effective measure to mitigate diffuse P losses from agricultural landscapes and alleviate trophic pressure to freshwaters systems. Accounting for the distribution of P within farms is critical in identifying fields of agronomic underperformance and/or environmental risk to water as a consequence of inadequately managed re-cycling of P. There is also a need to understand how P use and legacy soil P evolves under the Nitrates Action Programme (NAP) regulations from the European Union (EU) Nitrates Directive. In an Irish case study the aim was to provide a systematic and detailed audit of P balance and soil P responses and trends in two mixed land use agricultural catchments (Arable A and B) across a four year study period. Driven by increased mineral P inputs the field balances in the Arable A catchment had an average surplus P, ranging from 1.9 to 7.5 kg ha−1 yr−1. However, between the study period 2010 to 2013, the average soil test P (STP) levels declined, with the area of excessive soil P concentrations decreasing by 8%. Similarly, in the Arable B catchment the average annual P inputs increased the surplus field P from -0.42 to 25.5 kg ha−1 yr−1, but the area of excessive soil P concentrations increased by 4%. In part, this increase is attributed to some fields receiving excess applications of organic nutrient forms above crop requirements. Whilst, the legacy soil P declined in the Arable A catchment indicating a response to NAP, for both catchments it is evident that the distribution of P sources within farms was poor and P inputs often did not match crop and soil P requirements at the field scale. This study highlights the need for improved support to knowledge transfer mechanisms that can deliver better farm and soil specific nutrient management planning strategies. Without this consideration, achieving the dual benefits of improvement to water quality and increased crop output from agricultural landscapes will be restricted.Department of Agricultural, Food and the Marine in Irelan

Mean difference in live-weight per incremental difference in body condition score estimated in multiple sheep breeds and crossbreds

peer-reviewedBody condition score (BCS) is a subjective assessment of the proportion of body fat an animal possesses and is independent of frame size. There is a growing awareness of the importance of mature animal live-weight given its contribution to the overall costs of production of a sector. Because of the known relationship between BCS and live-weight, strategies to reduce live-weight could contribute to the favouring of animals with lesser body condition. The objective of the present study was to estimate the average difference in live-weight per incremental change in BCS, measured subjectively on a scale of 1 to 5. The data used consisted of 19 033 BCS and live-weight observations recorded on the same day from 7556 ewes on commercial and research flocks; the breeds represented included purebred Belclare (540 ewes), Charollais (1484 ewes), Suffolk (885 ewes), Texel (1695 ewes), Vendeen (140 ewes), as well as, crossbreds (2812 ewes). All associations were quantified using linear mixed models with the dependent variable of live-weight; ewe parity was included as a random effect. The independent variables were BCS, breed (n=6), stage of the inter-lambing interval (n=6; pregnancy, lambing, pre-weaning, at weaning, post-weaning and mating) and parity (1, 2, 3, 4 and 5+). In addition, two-way interactions were used to investigate whether the association between BCS and live-weight differed by parity, a period of the inter-lambing interval or breed. The association between BCS and live-weight differed by parity, by a period of the inter-lambing interval and by breed. Across all data, a one-unit difference in BCS was associated with 4.82 (SE=0.08) kg live-weight, but this differed by parity from 4.23 kg in parity 1 ewes to 5.82 kg in parity 5+ ewes. The correlation between BCS and live-weight across all data was 0.48 (0.47 when adjusted for nuisance factors in the statistical model), but this varied from 0.48 to 0.53 by parity, from 0.36 to 0.63 by stage of the inter-lambing interval and from 0.41 to 0.62 by breed. Results demonstrate that consideration should be taken of differences in BCS when comparing ewes on live-weight as differences in BCS contribute quite substantially to differences in live-weight; moreover, adjustments for differences in BCS should consider the population stratum, especially breed

Imputation of non-genotyped sheep from the genotypes of their mates and resulting progeny

peer-reviewedAccurate genomic analyses are predicated on access to a large quantity of accurately genotyped and phenotyped animals. Because the cost of genotyping is often less than the cost of phenotyping, interest is increasing in generating genotypes for phenotyped animals. In some instances this may imply the requirement to genotype older animals with greater phenotypic information content. Biological material for these older informative animals may, however, no longer exist. The objective of the present study was to quantify the ability to impute 11 129 single nucleotide polymorphism (SNP) genotypes of non-genotyped animals (in this instance sires) from the genotypes of their progeny with or without including the genotypes of the progenys’ dams (i.e. mates of the sire to be imputed). The impact on the accuracy of genotype imputation by including more progeny (and their dams’) genotypes in the imputation reference population was also quantified. When genotypes of the dams were not available, genotypes of 41 sires with at least 15 genotyped progeny were used for the imputation; when genotypes of the dams were available, genotypes of 21 sires with at least 10 genotyped progeny were used for the imputation. Imputation was undertaken exploiting family and population level information. The mean and variability in the proportion of genotypes per individual that could not be imputed reduced as the number of progeny genotypes used per individual increased. Little improvement in the proportion of genotypes that could not be imputed was achieved once genotypes of seven progeny and their dams were used or genotypes of 11 progeny without their respective dam’s genotypes were used. Mean imputation accuracy per individual (depicted by both concordance rates and correlation between true and imputed) increased with increasing progeny group size. Moreover, the range in mean imputation accuracy per individual reduced as more progeny genotypes were used in the imputation. If the genotype of the mate of the sire was also used, high accuracy of imputation (mean genotype concordance rate per individual of 0.988), with little additional benefit thereafter, was achieved with seven genotyped progeny. In the absence of genotypes on the dam, similar imputation accuracy could not be achieved even using genotypes on up to 15 progeny. Results therefore suggest, at least for the SNP density used in the present study, that it is possible to accurately impute the genotypes of a non-genotyped parent from the genotypes of its progeny and there is a benefit of also including the genotype of the sire’s mate (i.e. dam of the progeny)

Genetic parameters for lameness, mastitis and dagginess in a multi-breed sheep population

peer-reviewedThe objective of the present study was to quantify the extent of genetic variation in three health-related traits namely dagginess, lameness and mastitis, in an Irish sheep population. Each of the health traits investigated pose substantial welfare implications as well as considerable economic costs to producers. Data were also available on four body-related traits, namely body condition score (BCS), live weight, muscle depth and fat depth. Animals were categorised as lambs (<365 days old) or ewes (⩾365 days old) and were analysed both separately and combined. After edits, 39 315 records from 264 flocks between the years 2009 and 2015 inclusive were analysed. Variance components were estimated using animal linear mixed models. Fixed effects included contemporary group, represented as a three-way interaction between flock, date of inspection and animal type (i.e. lamb, yearling ewe (i.e. females ⩾365 days but <730 days old that have not yet had a recorded lambing) or ewe), animal breed proportion, coefficients of heterosis and recombination, animal gender (lambs only), animal parity (ewes only; lambs were assigned a separate ‘parity’) and the difference in age of the animal from the median of the respective parity/age group. An additive genetic effect and residual effect were both fitted as random terms with maternal genetic and non-genetic components also considered for traits of the lambs. The direct heritability of dagginess was similar across age groups (0.14 to 0.15), whereas the direct heritability of lameness ranged from 0.06 (ewes) to 0.12 (lambs). The direct heritability of mastitis was 0.04. For dagginess, 13% of the phenotypic variation was explained by dam litter, whereas the maternal heritability of dagginess was 0.05. The genetic correlation between ewe and lamb dagginess was 0.38; the correlation between ewe and lamb lameness was close to zero but was associated with a large standard error. Direct genetic correlations were evident between dagginess and BCS in ewes and between lameness and BCS in lambs. The present study has demonstrated that ample genetic variation exists for all three health traits investigated indicating that genetic improvement is indeed possible