Agrocampus Ouest

About: Agrocampus Ouest is a education organization based out in Rennes, France. It is known for research contribution in the topics: Population & Soil water. The organization has 2160 authors who have published 3219 publications receiving 75606 citations. The organization is also known as: Institut supérieur des sciences agronomiques, agroalimentaires, horticoles et du paysage & Higher Institute for agricultural sciences, food industry, horticulture and landscape management.

Fast sequence-based microsatellite genotyping development workflow.

Abstract: Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20-40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.

Response of organic matter to reduced tillage and animal manure in a temperate loamy soil

Abstract: The impacts of tillage and organic fertilization on soil organic matter (SOM) are highly variable and still unpredictable, and their interactions need to be investigated under various soil, climate and cropping system conditions. Our work examined the effect of reduced tillage and animal manure on SOM stocks and quality in the 0―40 cm layer of a loamy soil under mixed cropping system and humid temperate climate. The soil organic carbon (SOC) and N stocks, particulate organic matter (POM), and C and N mineralization potential (301 days at 15 °C) were measured in a 8-yr-old split-plot field trial, including three tillage treatments [mouldboard ploughing (MP), shallow tillage (ST), no tillage (NT)] and two fertilization treatments [mineral (M), poultry manure 2.2 t/ha/yr C (O)]. No statistically significant interactive effects of tillage and fertilization were measured except on C mineralization. NT and ST showed greater SOC stocks (41.2 and 39.7 t/ha C) than MP (37.1 t/ha C) in the 0-15 cm increment, while no statistical differences were observed at a greater depth. N stocks exhibited similar distribution patterns with regard to tillage effect. Animal manure, applied at a rate representative of typical field application rates, had a smaller impact on SOC and N stocks than tillage. The mean SOC and N stocks were higher under O than M, but the differences were statistically significant only in the 0―5 cm increment. MP showed lower C-POM stocks than NT and ST in the 0-5 cm increment, whereas greater C-POM stocks were measured under MP than under NT or under ST in the 20-25 cm increment. Organic fertilization had no impact on C-POM or N-POM stocks. In the 0-25 cm increment, NT showed a lower C and N mineralization potential than MP. Our work shows that the sensitivity of SOM to reduced tillage for the whole soil profile can be relatively small in a loamy soil, under humid-temperate climate. However, POM was particularly sensitive to the differential effects of tillage practices with depth, and indicative of differentiation in total SOM distribution in the soil profile.

Meta-analysis on the effects of the physical environment, animal traits, feeder and feed characteristics on the feeding behaviour and performance of growing-finishing pigs

Abstract: A meta-analysis, using information from 45 experiments on growing-finishing pigs published in 39 manuscripts, was carried out to determine the simultaneous effects of the physical environment (space allowance, group size, flooring conditions, temperature, presence of enrichment), pig traits (initial body weight (BW) for each studied time interval, sex, genetics), feeder characteristics (water provision within the feeder, feeder design (individual/collective), feeder places/pig, presence of feeder protection) and feed characteristics (feed allowance (ad libitum/restricted), net energy content, crude protein (CP) content), as well as their potential interactions, on the feeding behaviour and performance of growing-finishing pigs. The detrimental effect of low temperature on performance was particularly evident for restricted-fed pigs (P < 0.05). At reduced feeder space allowance, a reduction in the percentage of time spent eating was predicted when increasing initial BW, whereas the opposite was predicted for larger feeder space allowances (P < 0.001). The reduction in visit duration to the feeder in higher BW groups became gradually more important with increasing feeder space allowance (P < 0.01), whereas the increase in the ingestion rate and average daily feed intake (ADFI) with increasing initial BW became smaller with increasing feeder space (P < 0.05). The model predicted a reduction in feed conversion ratio (FCR) with increasing group size (P < 0.05) and floor space allowance (P < 0.01) and on solid floors with or without bedding (P < 0.05). In comparison with other feeders, wet/dry feeders were associated with more frequent but shorter feeder visits (P < 0.05), higher ingestion rates (P < 0.001) and higher ADFI (P < 0.10). The use of protection within individual feeders increased the time spent feeding (P < 0.001), reduced the number of visits per day (P < 0.01), the ingestion rate (P < 0.001) and FCR (P < 0.01) in comparison with other feeder types. Sex modulated the effect of the number of feeder places/pig on FCR (P < 0.05), with a gradual reduction of FCR in entire males and females when increasing feeder space allowance. Genetics tended to modulate the effect of diets' CP content on FCR (P < 0.10). Overall, these results may contribute to the improvement of the welfare and performance of growing-finishing pigs by a better knowledge of the influence of the rearing environment and may help optimize the feeding strategies in current production systems.