Identification of potential genomic regions for egg weight by a haplotype-based genome-wide association study using Bayesian methods

ABSTRACT

1. Theoretically, haplotype blocks might be a more suitable alternative to SNP genotypes as they are usually better at capturing multi-allelic QTL effects, compared to individual SNP genotypes in genome-wide association studies. The objectives of this study were to identify genomic regions related to egg weight traits by Bayesian methods (BayesA, BayesB, and BayesN) that fit fixed-length haplotypes using GenSel software.

2. Genotypes at 294,705 SNPs, that were common on a 600K Affymetrix chip, were phased for an egg-laying hen population of 1,063 birds. Recorded traits included first egg weight (FEW) and average egg weight at 28, 36, 56, 66, 72 and 80 weeks of age.

2. Fitting 1Mb haplotypes from BayesB resulted in the highest proportion of genetic variance explained for the egg weight traits. Based on the trait, the genetic variance explained by each marker ranged from 27% to 76%.

3. Different haplotype windows associated with egg weight traits only explained a small percentage of the genetic variance.

4. The top one 1-Mb window on GGA1 explained approximately 4.05% of total genetic variance for the FEW. Candidate genes, including PRKAR2B, HMGA2, LEMD3, GRIP1, EHBP1, MAP3K7, and MYH were identified for egg weight traits.

5. Several genomic regions, potentially associated with egg weight traits, were identified, some of which overlapped with known genes and previously reported QTL regions for egg production traits.     

Agrocenosis Stability during Long-Term Application of Fertilizers on Soddy-Podzolic Soil

Eurasian Soil Science - In a long-term field experiment in the western part of the nonchernozemic zone of Russia (Smolensk oblast) on sandy loamy soddy-podzolic soil (Albic Glossic Retisol...     

Death of a neonatal lamb due to Clostridium perfringens type B in New Zealand

ABSTRACT

Case history and clinical findings: A flock of 20 sheep was kept within three paddocks on a single property. None of the animals in the flock had been vaccinated against any disease for at least three years. Abdominal bloating and haemorrhagic diarrhoea were observed in Lamb 1 at 24 hours-of-age. The lamb subsequently died within an hour of the onset of clinical signs. Lamb 2 was 3-days-old when observed to be recumbent with opisthotonus. The lamb was treated with dextrose, vitamins B1 and B12, and penicillin G, but died 4 hours later.

Pathological findings: Examination of Lamb 1 revealed markedly increased gas within the peritoneum and within dilated loops of intestine. The intestines were dark red and contained large quantities of haemorrhagic fluid. Histology of the intestines revealed peracute mucosal necrosis with minimal accompanying inflammation. The intestinal lumen contained cell debris, haemorrhage, and myriad large Gram-positive bacilli. The intestines of Lamb 2 did not appear bloated or reddened. However, multiple fibrin clots were visible within the pericardial sac. Histopathological examination revealed small foci of necrosis within the mucosa of the distal intestine. The necrotic foci were often associated with large numbers of large Gram-positive bacilli.

Immunohistochemsitry and molecular biology: Intestinal samples from Lamb 1 were processed for Clostridium perfringens immunohistochemistry, which revealed large numbers of intralesional, positively immunostained rods. Fragments corresponding to the expected sizes for genes encoding alpha, beta, and epsilon C. perfringens typing toxins were amplified by PCR from DNA extracted from formalin-fixed sections of intestine.

Diagnosis: Lamb dysentery due to C. perfringens type B.

Clinical relevance: C. perfringens bacteria have a worldwide distribution, but disease due to C. perfringens type B has only been diagnosed in a small number of countries and has never been reported in New Zealand or Australia. C. perfringens type B produce both beta toxin and epsilon toxins, therefore both haemorrhagic enteritis and systemic vascular damage can develop. As many animals are exposed to C. perfringens without developing disease, there must be additional unknown factors that resulted in disease in these particular sheep. Vaccines that specifically protect against C. perfringens type B are available and may be recommended for use in smaller non-commercial flocks, as in the present case.     

Maize harvest index and water use efficiency can be improved by inhibition of gibberellin biosynthesis

Possibilities to improve maize harvest index and nutrient utilization efficiency by application of plant growth regulators were investigated. In container experiments, the effects of different growth regulators on the development of the maize (Zea mays L.) cultivars Pioneer 3906 and Fabregas were tested. Paclobutrazol (PAC) and chlorocholine chloride (CCC), two inhibitors of gibberellin biosynthesis, as well as gibberellic acid (GA₃) were applied at growth stage V5. Three weeks after application of PAC, shoot growth of both maize cultivars was strongly affected with a significant decrease in plant height in the PAC treatment by 44% and 36% for Pioneer 3906 and Fabregas, respectively. The growth‐retarded plants had higher leaf areas and reduced transpiration rates. The higher shoot growth after GA₃ application was accompanied by a reduction in leaf area and an increase in transpiration rate during 1 week before anthesis. CCC treatment showed no significant effects on plant height, leaf area and transpiration rate. The PAC‐treated cultivar Pioneer 3906 produced several cobs per plant, which were mainly barren at maturity. However, PAC application to Fabregas resulted in just one cob per plant with good kernel development and a grain yield, which was not significantly reduced in comparison with the control. With this similar grain yield in combination with a straw yield decrease of 32%, the harvest index was significantly improved by 12%. In addition, with PAC‐treated Fabregas plants, a 19% increased water use efficiency of the grain (WUE_grain) during the critical period of kernel setting was achieved. In this maize cultivar, CCC application also improved harvest index by 5%, but no effect on WUE_grain occurred. GA₃ treatment decreased harvest index of both maize cultivars, and it either reduced WUE_grain (Pioneer 3906) or showed no effect (Fabregas). Utilization efficiencies of N, P and K were not increased with growth regulator application, even in the PAC‐treated Fabregas plants with a significantly improved allocation of assimilates to the grain, mirrored by the higher harvest index. The results indicate that fertilizer applications must be adjusted to the reduced demand of growth‐retarded plants, most likely leading to higher nutrient utilization efficiencies.     

Summer drought decreases Leymus chinensis productivity through constraining the bud,tiller and shoot production

Extreme drought events can directly decrease productivity in perennial grasslands. However, for rhizomatous perennial grasses it remains unknown how drought events influence the belowground bud bank which determines future productivity. Ninety‐day‐long drought events imposed on Leymus chinensis, a rhizomatous perennial grass, caused a 41% decrease in the aboveground biomass and a 28% decrease in belowground biomass. Aboveground biomass decreased due to decrease in both the parent and the daughter shoot biomass. The decreases in daughter shoot biomass were due to reductions in both the shoot number and each individual shoot weight. Most importantly, drought decreased the bud bank density by 56%. In addition, drought induced a bud allocation change that decreased by 41% the proportion of buds that developed into shoots and a 41% increase in the buds that developed into rhizomes. Above results were supported by our field experiment with watering treatments. Thus, a 90‐day‐long summer drought event decreases not only current productivity but also future productivity, because the drought reduces the absolute bud number. However, plasticity in plant development does partly compensate for this reduction in bud number by increasing bud development into rhizomes, which increases the relative allocation of buds into future shoots, at the cost of a decrease in current shoots.     

Cross‐linked polyacrylates in post‐mining substrates: persistence and effects on plant growth

Application of hydrophilic polymers composed of cross‐linked polyacrylate can improve soil water‐holding capacity and accelerate the restoration of post‐mining substrates. In this work, we studied the persistence of a polyacrylate polymer incorporated into a soil and its impact on plant nutrients at a reclamation site of former lignite mining in Lusatia (Germany). In contrast to autumn application, the incorporation of the polymer enhanced the sequestration of plant‐derived carbon in the soil, which was reflected by a significant increase in the concentration of a lignin marker. Attenuated total reflexion–Fourier transform infrared spectra (ATR‐FTIR) and total elemental contents in the applied polymer suggested an intensive cation exchange between the polymer framework and the soil‐forming substrate. In addition, there was an enrichment of carbonaceous material, which seems to reduce the swelling and thus the water‐holding capacity of the cross‐linked polyacrylate. Conversely, this process protected the polymer structure from rapid decomposition.     

Comparison of Salt and Drought‐Stress Effects on Maize Growth and Yield Formation with Regard to Acid Invertase Activity in the Kernels

The long‐term effects of salt stress (11 dS m^?1) and drought stress (35 % WHC) were investigated for two maize genotypes, focusing on the relation between metabolic changes around the time of pollination and the impact on yield determinants at maturity. The relatively salt‐resistant hybrid Pioneer 3906 and the relatively drought‐resistant hybrid Fabregas were compared. The experiments were conducted in large plastic containers in a vegetation hall in two consecutive years (2011 and 2012). Plant height and leaf area were significantly reduced under both stress conditions. The transpiration rate was only slightly reduced under drought stress; but under salt stress, a significant reduction occurred 40–53 days after sowing. As a significant increase in sucrose concentrations was observed in the salt‐treated maize kernels 2 days after pollination, the availability of assimilates was not limiting and the plants could afford to save water by reduced stomatal opening. Although under both stress conditions the soluble acid invertase activity was reduced 2 days after pollination, concomitantly, an increase in hexose concentrations was observed. Thus, in these experiments, the delivery of hexoses by acid invertase activity did not limit kernel development. Differences in grain yield at maturity between salt and drought stress were most likely caused by salt‐specific effects (Na⁺ toxicity), Fabregas being more affected than Pioneer 3906.     

How to characterize ‘good’ and ‘greening’ in the EU Common Agricultural Policy (CAP): the case of clay soils in the Netherlands

The change in the Common Agricultural Policy (CAP) of the European Union from product to producer support, including requirements for ‘good agricultural and environmental conditions’ and ‘greening’, is excellent. However, these requirements are now defined in rather general terms. Questions can be raised about suitable indicators, and there is a recognized need for effective management recommendations to support farmers in achieving the required ‘good’ conditions. These recommendations are bound to be quite different for different soils in different countries. A study of Dutch clay soils was based on a storyline describing current problems and management options for improvement, which were quantified using a soil–water–crop simulation model. Indicators were defined for agricultural conditions and suggestions made for the use of the model in a predictive mode to help farmers improve their soil management. Environmental conditions were judged by current environmental guidelines for water and air. When modelling, implicit assumptions that soils are homogeneous were shown to be unrealistic for these clay soils, requiring development of innovative methods and procedures, presenting a challenge for soil research.     

Use of geoinformation and neurotechnology to assess and to forecast the humus content variations in the steppe soils

This paper reports the results obtained using the systemic basin approach, geoinformation, and neurotechnology for modeling and forecasting of the humus spatial inhomogeneity and content variations in the steppe and dry steppe zones (Kherson oblast, Ukraine). The general trend of such variations has been determined in the 0–40 cm layer for 42 years. The intensive use of irrigation and drainage activities in 1970–1989 resulted in a significant humus depletion by 0.36% on average (from 2.56% to 2.2%). The analysis in 4450 observation points has yielded a decrease in the variability, the rising polynomial dependence of the humus enrichment from the west to the east, and the logarithmic dependence from the south to the north. The neurotechnological modeling has made it possible to develop the artificial neural network for the spatiotemporal modeling of the humus content in the soils. The humus is predicted to be subject to the irreversible process of gradual depletion in the 0–40 layer until 2025 upon the use of the existing agrotechnologies: rainfed land by 0.01%/year and irrigated land by 0.03%/year. This result defines the territorial priorities of the regional policy and suggests the differentiated efficiency evaluation of the soil-protective unit of the farming systems.