BackgroundAutomated genotype calling in tetraploid species was until recently not possible, which hampered genetic analysis. Modern genotyping assays often produce two signals, one for each allele of a bi-allelic marker. While ample software is available to obtain genotypes (homozygous for either allele, or heterozygous) for diploid species from these signals, such software is not available for tetraploid species which may be scored as five alternative genotypes (aaaa, baaa, bbaa, bbba and bbbb; nulliplex to quadruplex).ResultsWe present a novel algorithm, implemented in the R package fitTetra, to assign genotypes for bi-allelic markers to tetraploid samples from genotyping assays that produce intensity signals for both alleles. The algorithm is based on the fitting of several mixture models with five components, one for each of the five possible genotypes. The models have different numbers of parameters specifying the relation between the five component means, and some of them impose a constraint on the mixing proportions to conform to Hardy-Weinberg equilibrium (HWE) ratios. The software rejects markers that do not allow a reliable genotyping for the majority of the samples, and it assigns a missing score to samples that cannot be scored into one of the five possible genotypes with sufficient confidence.ConclusionsWe have validated the software with data of a collection of 224 potato varieties assayed with an Illumina GoldenGate™ 384 SNP array and shown that all SNPs with informative ratio distributions are fitted. Almost all fitted models appear to be correct based on visual inspection and comparison with diploid samples. When the collection of potato varieties is analyzed as if it were a population, almost all markers seem to be in Hardy-Weinberg equilibrium. The R package fitTetra is freely available under the GNU Public License from http://www.plantbreeding.wur.nl/UK/software_fitTetra.html and as Additional files with this article.

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Diffuse light enhanced crop photosynthesis. A more uniform horizontal PPFD distribution played the most important role in this enhancement, and a more uniform vertical PPFD distribution and higher leaf photosynthetic capacity contributed more to the enhancement of crop photosynthesis than did higher values of LAI.

Background and aims Organic inputs have a positive effect on the soil organic matter balance. They are therefore an important asset for soil fertility and crop growth. This study quantifies the additional yield effect due to organic inputs for arable crops in Europe when macronutrients are not a limiting factor. Methods A meta-analysis was performed using data from 20 long-term experiments in Europe. Maxima of yield response curves to nitrogen were compared, with and without organic inputs, under abundant P and K supply. Results We were surprised to find that, across all experiments, the mean additional yield effect of organic inputs was not significant (+ 1.4 % ± 1.6 (95 % confidence interval)). In specific cases however, especially for root and tuber crops, spring sown cereals, or for very sandy soils or wet climates, organic inputs did increase attainable yields. A significant correlation was found between increase in attainable yields and increase in soil organic matter content. Conclusions Aggregating data from 20 long-term experiments in Europe, this study shows that organic inputs and/ or soil organic matter do not necessarily increase yields, given sufficient nutrients are supplied by mineral fertilisers. Results show the relevance of some environmental factors for additional yield effect of organic inputs, but no simple relation between organic inputs and crop growth.

Knowledge of the morphological adaptation of rumen papilla, which plays an important role in volatile fatty acid absorption, in dry and early lactation dairy cattle is limited. Therefore, macro- and microscopic changes in papilla morphology during the dry period and lactation and the effect of rate of increase of concentrate allowance were studied. Samples were collected from 12 rumen-cannulated Holstein Friesian dairy cows during a pretreatment period, 50, 30, and 10 d antepartum (the dry period) and 3 d postpartum (pp), and a treatment period, 9, 16, 30, 44, 60, and 80 d pp. Cows had free access to either a dry period ration [27% grass silage, 27% corn silage, 35% wheat straw, and 11% soybean meal on a dry matter (DM) basis] or a basal lactation ration (42% grass silage, 41% corn silage, and 17% soybean meal on a DM basis, and 0.9 kg of DM/d concentrate). Treatment consisted of either a rapid (1.0 kg of DM/d; RAP; n=6) or gradual (0.25 kg of DM/d; GRAD; n=6) increase of concentrate allowance (up to 10.9 kg of DM/d), starting at d 4 pp, aimed at creating a contrast in rumen-fermentable organic matter (FOM) intake. Papillae were collected from the ventral, ventral blind, and dorsal blind rumen sacs and measured digitally. Intake of DM (11.9 kg/d) and FOM (5.7 kg/d) did not change during the pretreatment period, but increased during the treatment period to 24.5 and 15.0 kg/d at 80 d pp, respectively. Concentrate treatment and sampling day interacted for FOM intake, which was 22% greater in RAP at 16 d pp compared with GRAD. Papilla surface area decreased during the pretreatment period by 19% to 28.0mm(2) at 3 d pp, thereafter increasing to 63.0mm(2) at 80 d pp. Concentrate treatment and sampling day interacted for surface area, which was greater in RAP compared with GRAD at 16 (46.0 vs. 33.2mm(2)), 30 (55.4 vs. 41.2mm(2)), and 44 (60.5 vs. 49.7 mm(2)) days pp, showing that papillae can respond to a rapid rate of increase of FOM intake by increasing growth rate. Microscopic morphology was affected by sampling day, but neither by concentrate treatment nor by their interaction, with a decrease in papilla and epithelium thickness during the lactation. In conclusion, the rumen papillae respond to changes in FOM intake and the magnitude of this response depends on the rate of increase of FOM intake. This response in surface area of the rumen papillae potentially facilitates the absorption of the volatile fatty acids.