Exploring wheat landraces for rust resistance using a single marker scan

Marker-trait associations identified in diverse germplasm can be exploited in crop improvement programs. An attempt to establish such associations was made by evaluating 205 wheat landraces for stripe rust, leaf rust and stem rust responses in the field over three crop seasons. Diversity arrays technology was used to genotype the landraces and associations were identified using a single-marker scan. Sixty-eight markers were significantly associated with rust resistance. Several significantly associated loci coincided with the presence of known major genes or QTL for rust resistance. In contrast, many marker-rust response associations identified in this analysis for each of the three rust diseases uncovered new loci. Dual associations; stripe rust-leaf rust (1AL, 2BS, 2BL, 3DL, 5BS, 6BS and 7DL), leaf rust-stem rust (5BL) and stripe rust-stem rust (4BL and 6AS) resistance were also observed. These associations could enable a cost-effective targeted mapping of dual rust resistance. Some marker-trait associations identified in this study have been validated through genetic analyses and formal naming of resistance loci.     

Ligno-Cellulose Composting: Case Study on Monitoring Oil Palm Residuals

Oil palm empty fruit bunches (EFB) composting is increasingly being considered by tropical farmers as a worthwhile alternative to direct spreading in the field. EFB are ligno-cellulose residues comprising 46% cellulose and 16.5% lignin with a high C:N ratio ranging from 45 to 70. In hot regions, it is essential to control variations in the water content of the substrate. This case study set out to optimize the EFB composting procedure by monitoring two key factors, namely the nutritional balance of the biomass and its water content. The trial was conducted on a composting platform belonging to the PT SMART Tbk company (Indonesia) in windrows comprising shredded EFB watered weekly with oil mill effluents. The quantity of effluent to be added was calculated so as to systematically top up to 60% humidity. The initial C:N ratio of the EFB was reduced by urea and/or ripe compost applications (seeding). Application times and rates were studied on two windrows, one in an open area, the other in an area sheltered by a roof to prevent over-rapid drying. After ten weeks the compost could be considered ripe for all the treatments; at that stage, composting had reduced the volume and initial weight of the fresh EFB by 85% and 50% respectively. The combined action of a temperature rise and windrow turning led to substantial water losses through evaporation, resulting in a sudden drop in windrow humidity at the start of composting. When rainfall was insufficient, effluent applications became essential. The total amount of effluent to be applied during composting (without rainfall) was around 3 m³ per initial tonne of EFB. This amount approximately corresponded to the standard effluents : EFB ratio in the oil mill. Inoculation of the mass of EFB to be composted with ripe compost had a significant effect on the speed with which the mixture was reduced. A urea application a fortnight after the start of fermentation seemed to be beneficial. The resulting compost had a good agronomic value. However, the mineral balance was considerably affected, as the nutrients provided by the effluents were poorly retained by the substrate, and partially lost in percolation water following the weekly watering operations. For instance, almost 50% of the phosphorus, 70% of the potassium, 45% of the magnesium and between 10% and 20% of the calcium theoretically applied were lost ten weeks into the trial. Better distribution of the effluent applications, combined with a system to recover the leachings, should substantially reduce these losses, while maintaining suitable humidity for microbial degradation.     

Effect of feed intake and dietary vitamin A levels on sheep performance.

A study was conducted on 20 "Rahmani" male lambs of 16 kg body weight fed on normal feed level and high vitamin A level (NF-HV); normal feed level and normal vitamin A level (NF-NV); low feed level and high vitamin A level (LF-HV) or low feed level and normal vitamin A level (LF-NV) till slaughter weight of 35-40 kg. Average daily gains of lambs were 211, 148, 117 and 87 g for the NF-HV, NF-NV, LF-HV and LF-NV groups, respectively. The corresponding feed conversions were 4.3, 5.9, 5.0 and 6.4 kg DM/kg gain. Raising feed intake and vitamin A level enhanced nutrients digestibility and nitrogen balance. Rumen liquor reflected higher pH value in animals fed higher intake (NF) in the first two diets. Both feed intake and vitamin A levels enhanced volatile fatty acids and ammonia concentrations in the rumen liquor. Feed intake and vitamin A levels positively affected haemoglobin content, packed cell volume, glucose, urea, total protein, vitamin A, insulin, cholesterol, phospholipids, glutamate oxaloacetate and glutamate pyruvate transaminases and alkaline phosphatase in blood Vitamin A, insulin, cholesterol and phospholipids in blood increased gradually over the experimental period. Dressing percentages were 56.2, 49.6, 49.1 and 44.6% for the experimental groups, respectively. Liver content of glycogen and vitamin A increased with increasing feed intake and vitamin A levels. It is concluded that higher levels of vitamin A supplementation (than usually recommended) is required during fattening of lambs. Low energy and normal vitamin A levels are not recommended in lambs feeding.     

Evaluation of nitrogen status of agricultural soils in Java,Indonesia

Abstract

To evaluate the content of nitrogen (N) fractions of agricultural soils in Java, Indonesia, in relation to soil type and land use, 46 surface soil samples, 23 from paddy and 23 from upland, were collected throughout Java to include various types of soils. Soil N was separated into four fractions according to form and availability: inorganic extractable nitrogen (Iex-N), fixed ammonium nitrogen (Ifix-N), organic mineralizable nitrogen (Omin-N) and organic stable nitrogen (Osta-N). The total-N content was determined by the dry combustion method. The Iex-N content was determined by extraction with a 2 mol L^?1 potassium chloride (KCl) solution and the Ifix-N content by extraction with an hydrofluoric and hydrochloric acid (HF-HCl) solution after removal of organic-N. The Omin-N content was evaluated as the potentially mineralizable N based on a long-term incubation method. The Osta-N content was calculated as the difference between the contents of total-N and the three other fractions. The total-N content was 2.06 g kg^?1 on average. The contents of Iex-N, Ifix-N, Omin-N and Osta-N were 25.8, 99.1, 103 and 1,832 mg kg^?1, respectively, and corresponded to 1.3, 4.8, 5.0 and 88.9% of the total-N. Hence, available (Iex-N and Omin-N) and stable (Ifix-N and Osta-N) fractions accounted for 6.3% and 93.7% of the total-N, respectively. Correlation analysis indicated that the contents of total-N and Osta-N had positive correlation with (Alo + 1/2Feo) as an index of amorphous minerals (p < 0.01), suggesting strong influence of volcanic materials for the accumulation of organic matter in Java soils. The content of Ifix-N had a positive correlation with nonexchangeable potassium (K) content (p < 0.01), suggesting the contribution of 2:1 clay minerals which can fix both ammonium (NH₄⁺) and K⁺ in their interlayer sites. On the contrary, Omin-N did not have any significant correlation with soil properties, implying the importance of management for the improvement of the available N level in soils, rather than intrinsic soil properties. Soil N status further showed strong topographical trends depending on the elevation where soil developed. The contents of total N, Iex-N, Ifix-N, Omin-N and Osta-N in Java soils were on average 80, 69, 90, 65 and 80% of those in Japanese soils, respectively, suggesting that the soil N level in Java was lower than that in Japan, probably due to accelerated decomposition of organic matter, especially degradable fractions, reflecting high temperature, but that the level was relatively high for tropical soils due to the effect of volcanic materials. In conclusion, these results should be taken into account for the sustainable management of soil N in agricultural fields in Java, Indonesia.     

Retrieval of forest attributes in complex successional forests of Central Indonesia: Modeling and estimation of bitemporal data

Quantification of forest parameters in different successional stages is required because of its importance as a source of global emissions and ecosystem changes. This study focuses on a successional tropical forest under logging practices in East Kalimantan province, Indonesia. We modeled the forest attributes using both a parametric multiple linear regression analysis and neural networks approach, with Landsat ETM data acquired in 2000 (ETM00). We compiled sample plot data using forest inventory data collected from 1997 to 1998. A total of 226 plots were used to train the models and 112 plots were used for the validation. The remote sensing data (spectral values, vegetation indices, texture, etc.) coupled with digital elevation model (DEM) were experimented with and selectively used to model basal area, stem volume and above ground biomass (AGB). We investigated the possibility to estimate the forest attributes from bitemporal ETM data by calibrating radiometric properties of the ETM image from 2003 (ETM03) using the multivariate alteration detection method. The Pearson correlations showed that the mean texture index is strongly correlated with the forest attributes. We show that neural networks resulted in a higher coefficient of determination (r²) and lower RMSE than multiple regressions for predicting the forest attributes. The estimated forest properties increased with the forest succession advancement (i.e. from the open forest to advanced secondary forest classes). The modeled basal area, stem volume and AGB varied from 10.7–15.1 m² ha⁻¹, 123.2–181.9 m³ ha⁻¹, and 132.7–185.3 Mg ha⁻¹, respectively. The RMSE_r values of model fitting ranged from 11.2% to 13.3%, and the test dataset estimated slightly higher RMSE_r which varied from 12% to 14.1%. The ETM03 forest attributes revealed favorable estimates, showing considerably higher estimates than the ETM00. The estimation of forest properties using neural networks makes Landsat data a valuable source of information for forest management, mainly with the recent free access to its historical dataset.     

应用中分辨率遥感数据和地理信息系统改进森林材积和生物量评估策略(英文)

应用遥感技术、地理信息系统和野外观测数据,评估了热带森林环境下地上生物量和木材蓄积量。用于模拟森林属性的这些数据具有地理特异性和高度的不确定性,因此,这方面需要开展更多的研究工作。选取了16个试样地带1460个样地,测定树木胸径及其他用于评估生物量的其他森林属性。本实验在印尼加里曼丹东部的热带雨林开展。应用现有的胸径-生物量公式来评估地上生物量密度。估测值在研究区修正的GIS地图上重叠显示,计算各种地被物的生物量密度。用样品数据子集表达遥感方法来形成地上生物量和材积线性方程模型。皮尔森相关统计检验采用ETM条带反射率、植被指数、图像变化图层、主成分分析条带、缨帽变换、灰度共生矩阵纹理特征和DEM数据作为预报值。在显著的遥感数据中形成了两个线性模型。为了分析每块地被物总的生物量和材积量,对2000年到2003年卫星ETM图进行了预处理、最大似然估计法分类和主体分析过滤。遥感方法获得的结果表明:材积量为(158±16)m3·hm-2,地上生物量为(168±15)t·hm-2;而野外测定和地理信息系统估计的结果分别是材积量为(157±92)m3·hm-2、地上生物量为(167±94)t·hm-2。用多个瞬间ETM数据评估了从2000年到2003年间的生物量丰富度动态,结果发现这一时期总生物量呈略微的下降趋势。遥感技术评估的生物量丰富度低于地理信息系统和野外测定的结果。前一种测定方法估计2000年和2003年总生物量分别是10.47Gt和10.3Gt,而后一种则估计11.9Gt和11.6Gt。还发现,灰度共生矩阵纹理特征与材积量和生物量之间存在较强的相关性。图7表9参43。     

Application of a dendrogram seriation algorithm to extract pattern from plant breeding data

A dendrogram is often used to display the results from hierarchical clustering; however, the order of objects in a standard dendrogram is arbitrary and so similarity cannot be readily interpreted. An optimized dendrogram, a dendrogram produced by re-ordering the objects using a seriation method, has a customized ordering that reflects the similarity among objects with most similar objects located closest together. Hierarchical clustering has been applied to the analysis of data from plant breeding programs to identify the patterns in breeding populations and to study genotype by environment interactions. In this paper we demonstrate the advantage of an optimized dendrogram for interpretation of plant breeding data and, given this advantage, argue that an optimized dendrogram should be used as the default whenever hierarchical clustering is used.     

Grain dormancy QTL identified in a doubled haploid barley population derived from two non-dormant parents

Grain dormancy provides protection against pre-harvest sprouting (PHS) in cereals. Composite interval mapping and association analyses were performed to identify quantitative trait loci (QTL) contributing grain dormancy in a doubled haploid (DH) barley population (ND24260?×?Flagship) consisting of 321 lines genotyped with DArT markers. Harvest-ripe grain collected from three field experiments was germinated over a 7-day period to determine a weighted germination index for each line. DH lines displaying moderate to high levels of grain dormancy were identified; however, both parental lines were non-dormant and displayed rapid germination within the first two?days of testing. Genetic analysis identified two QTL on chromosome 5H that were expressed consistently in each of the three environments. One QTL (donated by Flagship) was located close to the centromeric region of chromosome 5H (qSDFlag), accounting for up to 15% of the phenotypic variation. A second QTL with a larger effect (from ND24260) was detected on chromosome 5HL (qSDND), accounting for up to 35% of the phenotypic variation. qSDFlag and qSDND displayed an epistatic interaction and DH lines that had the highest levels of grain dormancy carried both genes. We demonstrate that qSDND in the ND24260?×?Flagship DH population is positioned proximal and independent to the well-characterised SD2 region that is associated with both high levels of dormancy and inferior malt quality. This indicates that it should be possible to develop cultivars that combine acceptable malting quality and adequate levels of grain dormancy for protection against PHS by utilizing these alternate QTL.