Identification of genomic regions that exhibit sexual dimorphism for size and muscularity in cattle

Sexual dimorphism, the phenomenon whereby males and females of the same species are distinctive in some aspect of appearance or size, has previously been documented in cattle for traits such as growth rate and carcass merit using a quantitative genetics approach. No previous study in cattle has attempted to document sexual dimorphism at a genome level; therefore, the objective of the present study was to determine whether genomic regions associated with size and muscularity in cattle exhibited signs of sexual dimorphism. Analyses were undertaken on 10 linear-type traits that describe the muscular and skeletal characteristics of both males and females of five beef cattle breeds: 1,444 Angus (AA), 6,433 Charolais (CH), 1,129 Hereford, 8,745 Limousin (LM), and 1,698 Simmental. Genome-wide association analyses were undertaken using imputed whole-genome sequence data for each sex separately by breed. For each single-nucleotide polymorphism (SNP) that was segregating in both sexes, the difference between the allele substitution effect sizes for each sex, in each breed separately, was calculated. Suggestively (P ≤ 1 × 10⁻⁵) sexually dimorphic SNPs that were segregating in both males and females were detected for all traits in all breeds, although the location of these SNPs differed by both trait and breed. Significantly (P ≤ 1 × 10⁻⁸) dimorphic SNPs were detected in just three traits in the AA, seven traits in the CH, and three traits in the LM. The vast majority of all segregating autosomal SNPs (86% in AA to 94% in LM) had the same minor allele in both males and females. Differences (P ≤ 0.05) in allele frequencies between the sexes were observed for between 36% (LM) and 66% (AA) of the total autosomal SNPs that were segregating in both sexes. Dimorphic SNPs were located within a number of genes related to muscularity and/or size including the NAB1, COL5A2, and IWS1 genes on BTA2 that are located close to, and thought to be co-inherited with, the MSTN gene. Overall, sexual dimorphism exists in cattle at the genome level, but it is not consistent by either trait or breed.     

Factors affecting the field performance of an attracticide against the codling moth Cydia pomonella

Factors affecting the efficacy of an attracticide strategy for the control of the codling moth Cydia pomonella L (Lepidoptera: Tortricidae) were investigated using laboratory and field experiments. The sex-pheromone-based insect-control strategy utilises 100-microliters droplets of a sticky, paste-like formulation containing 1 mg g-1 (E,E)-8,10-dodecadien-1-ol (codlemone) as an attractant for male moths and 40 mg g-1 cyfluthrin, a contact insecticide, applied to branches in the upper parts of the tree crown. The longevity of the treatment under field conditions was assessed in the laboratory by biological testing of variously aged samples of the attracticide formulation which had been applied to the bark of apple trees growing in commercial orchards. Electroantennogram responses of male moth antennae were used to compare codlemone release from the attracticide after different lengths of environmental exposure. Changes in insecticidal efficacy of the same samples were assessed with reference to the speed of knockdown (KT50) and the mortalities after 48 h among populations of male moths confined in cages containing samples of fresh and field-aged formulations. Gradual declines in both the amount of pheromone released and insecticidal activity were observed over the 10-week period of the experiments. Various factors associated with the behaviour of codling moths in the field which might influence the attracticide strategy were also investigated. Although the vertical position of attracticide sources within apple trees had a strong influence on their attractiveness, their horizontal position had none. Results of field trials showed that efficacy of the attracticide depends on the population density of the pest. Under the conditions of the current study a density of three or more sources per tree (= 4500 sources per ha) was required to attain satisfactory levels of codling moth control.     

Determinants of annual fluxes of CO2 and N2O in long-term no-tillage and conventional tillage systems in northern France

The greenhouse gases CO₂ and N₂O emissions were quantified in a long-term experiment in northern France, in which no-till (NT) and conventional tillage (CT) had been differentiated during 32 years in plots under a maize–wheat rotation. Continuous CO₂ and periodical N₂O soil emission measurements were performed during two periods: under maize cultivation (April 2003–July 2003) and during the fallow period after wheat harvest (August 2003–March 2004). In order to document the dynamics and importance of these emissions, soil organic C and mineral N, residue decomposition, soil potential for CO₂ emission and climatic data were measured. CO₂ emissions were significantly larger in NT on 53% and in CT on 6% of the days. From April to July 2003 and from November 2003 to March 2004, the cumulated CO₂ emissions did not differ significantly between CT and NT. However, the cumulated CO₂ emissions from August to November 2003 were considerably larger for NT than for CT. Over the entire 331 days of measurement, CT and NT emitted 3160 ± 269 and 4064 ± 138 kg CO₂-C ha⁻¹, respectively. The differences in CO₂ emissions in the two tillage systems resulted from the soil climatic conditions and the amounts and location of crop residues and SOM. A large proportion of the CO₂ emissions in NT over the entire measurement period was probably due to the decomposition of old weathered residues. NT tended to emit more N₂O than CT over the entire measurement period. However differences were statistically significant in only half of the cases due to important variability. N₂O emissions were generally less than 5 g N ha⁻¹ day⁻¹, except for a few dates where emission increased up to 21 g N ha⁻¹ day⁻¹. These N₂O fluxes represented 0.80 ± 0.15 and 1.32 ± 0.52 kg N₂O-N ha⁻¹ year⁻¹ for CT and NT, respectively. Depending on the periods, a large part of the N₂O emissions occurred was probably induced by nitrification, since soil conditions were not favorable for denitrification. Finally, for the period of measurement after 32 years of tillage treatments, the NT system emitted more greenhouses gases (CO₂ and N₂O) to the atmosphere on an annual basis than the CT system.     

Coupling hysteresis analysis with sediment and hydrological connectivity in three agricultural catchments in Navarre,Spain

Purpose

Rain storm events mobilise large proportions of fine sediments in catchment systems. Sediments from agricultural catchments are often adsorbed by nutrients, heavy metals and other (in)organic pollutants that may impact downstream environments. To mitigate erosion, sediment transport and associated pollutant transport, it is crucial to know the origin of the sediment that is found in the drainage system, and therefore, it is important to understand catchment sediment dynamics throughout the continuity of runoff events.

Materials and methods

To assess the impact of the state of a catchment on the transport of fine suspended sediment to catchment outlets, an algorithm has been developed which classifies rain storm events into simple (clockwise, counter-clockwise) and compound (figure-of-eight; complex) events. This algorithm is the first tool that uses all available discharge and suspended sediment data and analyses these data automatically. A total of 797 runoff events from three experimental watersheds in Navarre (Spain) were analysed with the help of long-term, high-resolution discharge and sediment data that was collected between 2000 and 2014.

Results and discussion

Morphological complexity and in-stream vegetation structures acted as disconnecting landscape features which caused storage of sediment along the transport cascade. The occurrence of sediment storage along transport paths was therefore responsible for clockwise hysteresis due to the availability of in-stream sediment which could cause the “first flush” affect. Conversely, the catchment with steeper channel gradients and a lower stream density showed much more counter-clockwise hysteresis due to better downstream and lateral surface hydrological connectivity. In this research, hydrological connectivity is defined as the actual and potential transfer paths in a catchment. The classification of event SSC-Q hysteresis provided a seasonal benchmark value to which catchment managers can compare runoff events in order to understand the origin and locations of suspended sediment in the catchment.

Conclusions

A new algorithm uses all available discharge and suspended sediment data to assess catchment sediment dynamics. From these analyses, the catchment connectivity can be assessed which is useful to develop catchment land management.

     

Impacts of urbanization on Florida Key deer behavior and population dynamics

Rapid human population growth and urbanization have had a negative impact on species biodiversity. As competition for resources between man and wildlife continues, it is important to understand the effects of urbanization on species. Endangered Key deer (Odocoileus virginianus clavium) are endemic to the Florida Keys which have undergone rapid human population growth and development over the past 30 years. Our study objectives were to evaluate the impacts of urban development on Key deer habitat use, population dynamics, behavior, and body mass. We used data from two comprehensive studies on Key deer spanning 30 years to evaluate these changes. Our results suggest that Key deer have become more urbanized, using urban areas more today than they did 30 years ago. Contrary to our predictions, survival was higher for more urban deer than for less urban deer. Problems still exist with mortality factors heavily impacting some portions of the deer population including lower survival associated with less urban male deer. Analysis of Key deer body mass also was converse to our predictions as deer weights appear to have increased over time. Collectively, our results suggest that over the past 30 years Key deer have become more urbanized and that deer plasticity has allowed them to adapt and persist in an urbanizing environment. However, the future ability of Key deer to persist in an environment with continued urban development is unknown. At some threshold, urban development would become unsustainable and unlike other forms of habitat change or environmental disturbances, urban development is in most cases irreversible requiring careful planning in habitat conservation strategies.     

Changes in mineral nitrogen, phosphorus availability and salt-extractable aluminium following the application of green manure residues in two weathered soils of South Vietnam

Phosphorus deficiency and aluminium toxicity in weathered soils can be amended by applying organic residues. Nitrogen mineralization, changes in P-availability and changes in salt-extractable Al following the incorporation of residues of various green manures (Flemingia congesta, Mucuna pruriens, Pueraria phaseoloides, Tithonia diversifolia) were quantified in a field core incubation experiment. Dried residues were added at an application rate of 45 kg P ha⁻¹ to two soils representative for the main soil groups of the South Vietnamese uplands, set up in incubation cores in an experimental field near Ho Chi Minh City, Vietnam.Decomposition of the residues proceeded at high rates. Mineralized nitrogen from the residues was recovered mainly as ammonium during the first 2 weeks of incubation. Nitrogen release from Tithonia residues with the highest lignin content and lignin:N ratio occurred more gradually compared to the three legumes. Resin-extractable P was significantly increased by residue treatments. Largest and sustained increases in resin-extractable P (0.67 and 2.06 mg P kg⁻¹ in the two soils) were observed in samples amended with Tithonia, which was related to the large P-content (0.37%) and small C:P ratio (110) of the residues. The P-concentration in the residues, rather than the total amount of P applied through the residues, affected the increase in P-availability. The increase in resin-extractable P was correlated to the P-content (R=0.64) and C:P ratio (R=−0.65) of the residues. Salt-extractable Al-concentrations were considerably reduced by the organic amendments, up to 70 and 50% in the two soils. At the rate of 45 kg P ha⁻¹, no significant differences between the residue treatments to reduce soil acidity were observed.As such, the application of high quality residues that are rich in P, in particular T. diversifolia, may enhance crop production by creating favourable soil conditions during the initial stages of plant development of the main crop.     

Factors controlling aggregation in a minimum and a conventionally tilled undulating field

Wind and water erosion induce breakdown of soil aggregates and loss of soil organic matter. Whereas most of the relations between aggregation and its driving factors have been established on a plot scale, these relations might be very different within an undulating landscape where both erosion (by wind or water) and deposition occur. The aim of this study was to investigate to what degree spatial patterns in soil variables influence spatial patterns in aggregation under different tillage intensities. We studied an agricultural field of about 3 ha in the silty region of Belgium. The site was split into a conventional tillage (CT) and a minimum tillage (MT) system. Within the field, 396 geo‐referenced surface soil samples (0–5 cm) were taken and analyzed for organic matter content, quantity of aggregates and a number of other soil properties. Under CT, 28.5% of the total sample variation was explained by the occurrence of depositional areas, 20.8% by the amount of soil organic matter, and 13.8% by the presence of a clay‐rich B horizon which surfaced due to progressive water and tillage erosion. Regression analysis revealed that 27% of the variation in the quantity of macroaggregates (>0.25 mm) was accounted for by these three factors. Under MT, 27.1% of the total sample variation was related to the surface cover of Tertiary sand, 22.6% to the amount of soil organic matter, and 13% to erodibility. These three factors explained 53% of the variation in the quantity of macroaggregates. In the CT system, the correlation between grass‐ or maize‐ carbon and the quantity of macroaggregates was strongly linked to erodibility, while this was not the case in the MT system. We concluded that at this site, macroaggregation is dominated by landscape‐scale processes (such as water or tillage erosion) rather than determined by the commonly considered local variables (such as small variations in texture or organic matter content).     

Turnover of root-derived material and related microbial biomass formation in soils of different texture

Wheat plants were grown on two soils of different texture, a sandy soil and a silty clay loam, in an atmosphere containing ¹⁴CO₂. The ¹⁴C and total C content of the shoots, roots, soil rhizosphere CO₂ and soil microbial biomass were measured 21, 28, 35 and 42 days after germination. There was a pronounced effect of soil texture on the turnover of root-derived C through the microbial biomass. Turnover was relatively fast and at a constant rate in the sandy soil but slowed down in the clay soil, following an initial high assimilation of root products into the microbial biomass.Four percent of the total fixed ¹⁴C was retained in the clay loam after 6 weeks compared with a corresponding value of 1.2% for the sandy soil. The proportion of fixed ¹⁴C recovered as rhizosphere CO₂ at each of the sampling times was relatively constant for the sandy soil (ca 19%) but decreased from 17% at day 28 to 11% at day 42 in the clay soil. The proportion of total fixed ¹⁴C in the soil biomass as measured by a fumigation technique increased to a maximum value of 20% after 6 weeks in the sandy soil but decreased in the clay soil from 86% at day 21 to 26% after 42 days plant growth.     

Resistance to potato cyst nematodes,Globodera spp., in wild and primitiveSolanum species

Summary This paper summarizes the results, up to June 1986, of screening the Dutch-German potato collection at Braunschweig Genetic Resources Centre (BGRC) for resistance toGlobodera pallida andG. rostochiensis virulence groups. Resistance toG. pallida was detected in 4.1 of the 78Solanum species tested. The number of accessions with a pathotype-specific high-level resistance was high but accessions with resistance to allG. pallida andG. rostochiensis virulence groups were rare. Four accessions had a high level of resistance to all virulence groups and 26 had partial resistance. The partially resistant genotypes differed in the average number of larvae per root and of eggs per cyst.

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Zusammenfassung Die Suche nach Quellen für Resistenz gegen Zystennematoden der Kartoffel,Globodera pallida undG. rostochiensis, wird bei der Stiftung für landwirtschaftliche Pflanzenzüchtung (SVP) durchgeführt. In einem kooperativen Programm werden die Neuzug?nge bei der ‘Niederl?ndisch-Deutschen Abteilung Kartoffeln der Genbank in Braunschweig’ (BGRC) in S?mlingstests intensiv auf Resistenz gegenG. pallida undG. rostochiensis in Münster (Institut für Nematologie) und in Wageningen (SVP) geprüft. Die Ergebnisse sind in den Tabellen 1, 2 und 3 zusammengefasst. Insgesamt 699 Neuzug?nge von 78Solanum-Spezies wurden auf Resistenz gegen die Virulenzgruppe Pa3 untersucht. In 260 Zug?ngen von 41Solanum-Spezies wurden resistente Genotypen beobachtet, Genotypen mit m?ssiger Resistenz (RS) in 65 Zug?ngen. Die Frequenz von Spezies mit Resistenz gegen Pa2 war ebenfalls hoch (28 von 58 Spezies). Resistenz gegen Virulenzgruppen vonG. rostochiensis wurde weniger h?ufig gefunden (Tabellen 1 und 2). Die Zahl der Zug?nge mit Resistenz gegen eine, zwei oder drei Virulenzgruppen zeigt Tabelle 3. Die H?ufigkeit von Zug?ngen mit Resistenz sowohl gegen Pa2 als auch Pa3 war hoch. Zug?nge mit kombinierter Resistenz gegen Pa2, Pa3 und Ro5 ergaben sich beiS. acaule, S. gourlayi, S. leptophyes, S. megistacrolobum, S. multidissectum, S. oplocense, S. spegazzinii, S. sucrense undS. vernei. SVP-Genotypen unter den Zug?ngen mit kombinierter Resistenz gegen die Virulenzgruppen Pa2 und Pa3 wurden zus?tzlich mit Isolaten von Pa2, Pa3, Ro1.4, Ro2.3 und Ro5 getestet. Genotypen mit Resistenz gegen eine oder mehrere Virulenzgruppen waren gegen andere Virulenzgruppen oft anf?llig. Dies deutet auf Gen-für-Gen-Verh?ltnisse hin. Nur vier Zug?nge konnten gefunden werden, die in hohem Ma?e gegen alle Virulenzgruppen Resistenz aufwiesen. Zug?nge mit partieller Resistenz gegen alle Virulenzgruppen wurden ebenfalls untersucht. Genotypen mit partieller Resistenz unterschieden sich in der durchschnittlichen Zahl von Larven pro Wurzel und von Eiern pro Zyste (Tabelle 4).

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Résumé La Fondation pour l'Amélioration des Plantes Cultivées (SVP) a entrepris des recherches de sources de résistance àGlobodera pallida et àG. rostochiensis dans la collection germanonéerlandaise du centre de Ressources Génétiques de Braunschweig (BGRC). En collaboration, l'Institut für Nematologie de Münster et le SVP de Wageningen ont réalisés des tests de résistance à ces deux nématodes sur des plantules issues de graines provenant de diverses introductions. On trouvera la synthèse des résultats en tableaux 1, 2 et 3, 699 introductions appartenant à 78 espèces deSolanum ont été testées vis-à-vis de Pa3: des génotypes résistants ont été trouvés dans 260 introductions de 41 espèces deSolanum et des génotypes modérément résistants (RS) ont été trouvés dans 65 introductions. La fréquence d'espèces possédant une résistance à Pa2 est également élevéc (28 sur 58 espèces). La résistance àG. rostochiensis est trouvée plus rarement (tableaux 1 et 2). Le tableau 3 indique le nombre d'introductions possédant une résistance à un, deux ou trois groupes' de virulence. La fréquence des introductions possédant une résistance à la fois à Pa2 et à Pa3 est élevée. Des résistances à la fois à Pa2, Pa3 et Ro5 sont trouvées dans des introductions appartenant àS. acaule, S. gourlayi, S. leptophyes, S. megistacrolobum, S. multidissectum, S. oplocense, S. spegazzinii, S. sucrense etS. vernei. Ultérieurement, les génotypes combinant la résistance à Pa2 et Pa3 ont été testés au SVP vis-à vis de différentes populations de Pa2, Pa3, Ro1,4, Ro2,3 et Ro5. Souvent, les génotypes résistant au moins un groupe de virulence ne sont pas résistans aux autres groupes de virulence. Ceci montre que la résistance est basée sur une réaction gène pour gène. Un haut niveau de résistance à tous les groupes de virulence n'a été trouvé que dans quatre introductions. Des introductions possédant une résistance partielle à tous les groupes de virulence ont été trouvées. Les génotypes partiellement résistants diffèrent entre eux par le nombre moyen de larves par racine et d'oeufs par kyste.

     

Taxonomy and new collections of wild potato species in Central and Southern Peru in 1999

Peru contains about half of the described wild potato taxa, and many of these are not yet preserved in genebanks. This paper reports results of the second of a series of five planned collecting expeditions to Peru. Collections were made in the central Peruvian departments of Ancash, Huancavelica, La Libertad, and Lima, from March 8 to April 25,1999. They follow collections in 1998 in the southern Peruvian departments of Apurimac, Arequipa, Cusco, Moquegua, Puno, and Tacna. We collected 101 germplasm accessions, including first germplasm collections of the following 22Solanum taxa:Solanum amayanum, S. anamatophilum, S. arahuayum (lost in germplasm increase),S. augustii, S. bill- hookeri, S. cantense, S. chavinense, S. chomatophilum var. subnivale, S. chrysoflorum, S. gracilifrons, S. hapalos um, S. huarochiriense, S. hypacrarthrum, S.jalcae, S. moniliforme, S. multiinterruptum f. longipilosum, S. multiinterruptum var. machaytambinum, S. peloquinianum, S. rhombilanceolatum, S. simplicissimum, S. taulisense (lost in germplasm increase), andS. wittmackii. In addition, new collections were made of the under-collected speciesS. hastiforme (three collections). The above taxonomy is that used in planning our expedition, that we compare to a new treatment of Peruvian wild potatoes published by C. Ochoa in 1999. This paper reports the collection and new species identifications of the 1999 collections, and germplasm conservation and survival of the 1998 and 1999 collections. In addition, chromosome counts are provided for 134 accessions from the 1998 and 1999 expeditions, including first reports forS. chomatophilum var. subnivale (2n = 2x = 24),S. megistacrolobum subsp.purpureum (2n = 2x = 24), andS. multiinterruptum var.multiinterruptum f.albiflorum (2n = 2x = 24); we also report the first triploid count of an accession ofS. immite.