无叶假木贼叶绿体基因组特征系统发育及密码子偏好性分析

目的 分析无叶假木贼叶绿体基因组结构特征,阐明假木贼属在藜科中的分类地位,进一步探究其密码子偏好性和确定最优密码子。 方法 基于CTAB法从无叶假木贼幼嫩同化枝中提取总DNA;通过Illumina Genome Analyzer HiSeq 2000高通量测序平台进行测序;使用GetOrganelle和Plann对叶绿体基因组序列进行组装和注释;利用MISA对叶绿体基因组中简单重复序列（SSR）进行分析;使用MAFFT v. 7. 450和IQ-TREE v. 2. 1. 1软件进行多序列比对、构建最大似然法（Maximum likelihood,ML）系统进化树;使用DnaSP 6. 0软件计算核苷酸多态性值;通过CUSP和Codon W 1. 4. 2软件进行密码子偏好性研究。 结果 无叶假木贼叶绿体基因组全长为154 084 bp,包括1个大单拷贝区（LSC,85 124 bp）、1个小单拷贝区（SSC,18 934 bp）、1对反向重复序列（IRa和IRb,25 013 bp）。共注释到132个基因,包含83个蛋白编码基因,8个rRNA基因,37个tRNA基因和4个假基因。SSR位于基因间区的数量最多（70.4%）,单碱基（A/T）重复类型SSR数量最多。系统发育树的最优构树模型为TVM + F + R3,藜科划分为4个聚类组,其中,无叶假木贼与梭梭属和猪毛菜属亲缘关系最近。trnS-trnG(exon1)、ndhF-rpl32、rpl32-trnL、rps16(exon1)-trnQ和ycf1是高核苷酸多态性区域。共确定20个最优密码子（UUU、UAU、UGU、CAU、UCU、UCA、UUA、CUU、CCU、AGA、GAA、ACU、ACA、AAU、GAU、AAA、GUU、GCU、GGU、CAA）,均以A/U结尾,密码子使用偏好性主要受自然选择影响,突变等影响因素对其影响较弱。 结论 无叶假木贼叶绿体基因组结构保守,呈典型的四分体结构。在藜科的系统发育中,无叶假木贼与梭梭属和猪毛菜属亲缘关系最近。鉴定的高变区和SSR位点可用于藜科属间物种的分子鉴定。无叶假木贼叶绿体基因组密码子偏好以A/U结尾,确定的20个最优密码子有助于其外源密码子的优化。研究结果可为无叶假木贼分子标记开发、系统进化及叶绿体基因工程研究提供参考。     

Hierarchical models for white mould in snap bean

Limitations on the acceptable proportion (incidence) of pods with white mould may lead to the rejection of entire fields of processing snap bean. The low tolerances (no more than 2% to 6% of pods with white mould) are difficult to estimate with sufficient precision in the field when time is limited. These constraints motivated this study of white mould across three spatial hierarchical levels: pods, plants and quadrats consisting of two adjacent plants within rows. Hierarchical relationships are required when designing formal rules for estimating the incidence of pods with white mould from units higher in the spatial hierarchy. Disease assessments were made on all pods from 38 within‐row transects of 40 plants each of the snap bean cultivar Hystyle. Using probability‐based principles, equations were derived and fitted to data on the incidence of white mould on pods (i_pod), plants (i_pad) and quadrats (i_q(2)), which led to a function directly linking i_pod to i_q(2). The variance of i_pod increased with i_q(2), but that may be of little consequence at the lower values of i_q(2) likely to be associated with i_pod values at processor‐set tolerances. For example, at i_q(2) = 0.1 there was a 92% probability that i_pod was less than 0.02. Assessing i_q(2) may be more efficient than directly estimating i_pod because i_q(2) was about an order of magnitude higher than i_pod. Results suggest it may be feasible to design sampling plans for estimating the proportion of pods with white mould from an assessment of the proportion of diseased quadrats.     

Genetic variability and pathogenicity of Rhizoctonia solani associated with black scurf of potato in New Zealand

Isolates (a total of 129) of Rhizoctonia solani were collected from black scurf on potato tubers from different potato‐growing regions in New Zealand. Sequence analysis of the nuclear ribosomal DNA internal transcribed spacer (rDNA–ITS) regions from these isolates identified three anastomosis groups (AGs), AG‐3PT, AG‐2‐1 and AG‐5. Isolates classified as AG‐3PT were widely distributed, whereas AG‐2‐1 and AG‐5 were confined to distinct locations. Sequence heterogeneity was identified in the ITS regions of 100 AG‐3PT and AG‐2‐1 isolates. Variation in the sequence and length of the rDNA–IGS1 region was also observed for selected isolates of AG‐3PT and AG‐2‐1. Phylogenetic studies found all AG‐2‐1 isolates belong to AG‐2Nt, a subset of AG‐2‐1 previously associated with solanaceous crops in other countries. AG‐2‐1 isolates were consistently more aggressive than those of AG‐3PT. Delayed emergence, severe infection on stolons, formation of aerial tubers and considerable yield losses were associated with AG‐2‐1, but they caused negligible black scurf. In contrast, AG‐3PT caused black scurf on progeny tubers but variable effects on stem emergence and stolons. Furthermore, AG‐2‐1 isolates caused severe tuber malformation, but isolates of other AGs did not. This is the first report on the AG composition, genetic variability and pathogenicity of R. solani isolates associated with black scurf of New Zealand potatoes.     

Health and mineral nutrition status of yaks in southern Mustang,Nepal

Biochemical values and mineral concentrations in blood plasma were investigated to evaluate the statuses of health and mineral nutrition among yaks in Mustang District, Nepal. In total, 118 plasma samples of female yaks collected in April and September/October of 2013–2015 were offered. Seventy‐four percent of yaks showed lower plasma total‐cholesterol concentrations than the lowest limit of reference range (100 mg/dL) and the values in spring (83.41 mg/dL) were lower (P < 0.05) than those in autumn (95.05 mg/dL). All the yaks had lower plasma albumin concentrations than the lowest limit of reference range (3.0 g/dL) and 66% of yaks showed lower plasma inorganic phosphorus concentrations than the critical level of phosphorus deficiency (4.5 mg/dL). Thirty‐five percent of yaks showed lower plasma calcium concentrations than the lowest limit of normal range (8 mg/dL) and the concentrations were lower in spring than in autumn (P < 0.01). Seventy‐five percent of yaks presented lower copper concentrations than the critical level (0.65 mg/L) and the concentrations were lower in spring than in autumn (P < 0.01). Since the low plasma total‐cholesterol might have indicated shortage of dry matter and energy intake, attention should be paid to the nutritional statuses of energy, phosphorus, calcium and copper in winter and early spring.     

Dietary supplementation with glutamine and γ‐aminobutyric acid improves growth performance and serum parameters in 22‐ to 35‐day‐old broilers exposed to hot environment

This study was designed using 360 21‐day‐old chicks to determine the influences of diet supplementation with glutamine (5 g/kg), γ‐aminobutyric acid (GABA, 100 mg/kg) or their combinations on performance and serum parameters exposed to cycling high temperatures. From 22 to 35 days, the experimental groups (2 × 2) were subjected to circular heat stress by exposing them to 30–34 °C cycling, while the positive control group was exposed to 23 °C constant. The blood of broilers was collected to detect serum parameters on days 28 and 35. Compared with the positive control group, the cycling high temperature decreased (p < 0.05) the feed consumption, weight gain and serum total protein (TP), glucose, thyroxine (T4), insulin, alkaline phosphatase (ALP), glutamine, GABA and glutamate levels, while increased (p < 0.05) the serum triglyceride (TG), corticosterone (CS), glucagon (GN), creatine kinase (CK), glutamic oxaloacetic transaminase (GOT), nitric oxide synthase (NOS), glutamate pyruvate transaminase (GPT) and lactate dehydrogenase (LDH) levels during 22–35 days. However, dietary glutamine (5 g/kg) increased (p < 0.05) the feed consumption, weight gain and serum levels of glutamine, TP, insulin and ALP, but decreased (p < 0.05) the serum TG, CK, GOT, NOS and GPT levels. Diet supplemented with GABA also increased (p < 0.05) weight gain and the serum levels of TP, T4, ALP, GABA and glutamine. In addition, the significant interactions (p < 0.05) between glutamine and GABA were found in the feed consumption, weight gain and the serum ALP, CK, LDH, GABA, T3 and T4 levels of heat‐stressed chickens. This research indicated that dietary glutamine and GABA improved the antistress ability in performance and serum parameters of broilers under hot environment.     

Recycling gamma irradiated sewage sludge as fertilizer: A case study using onion (Alium cepa)

Recycling sewage sludge into fertilizer for agricultural purposes may improve soil fertility by influencing the physical, chemical, and biological properties of the land. However, there is concern regarding elevated levels of heavy metals and pathogenic microorganisms, which may result from the use of untreated sewage sludge. Gamma radiation is found to be an efficient tool in the hygienization of municipal sewage sludge. In order to evaluate the agricultural potential of gamma irradiated sewage sludge and to assess the safety of this fertilizer, field experiments were performed in a root crop, onion (Alium cepa), during the 2003–2004 and 2004–2005 winter months. The influence over major nutrients, metallic micronutrients, and heavy metals in soil and crop plant were key factors to be analyzed. Treatments consisted of three source of fertilizers {S₁: farmyard manure (FYM); S₂: gamma irradiated sewage sludge (GISS); and S₃: non-irradiated sewage sludge (NISS)}, each at three separate levels (L₁: 5 t ha^?1; L₂: 10 t ha^?1; and L₃: 15 t ha^?1), which were evaluated and compared. The growth parameters and onion yield were not significantly influenced by the different sources of fertilizer, or the different application levels. Values of pH, organic carbon, organic N, available P and K, metallic micronutrients (Zn, Mn, Fe, Cu) and heavy metals (Ni, Cd, Pb, Co) indicate no negative effects on either soil or plant properties. Concentrations of heavy metals in soil and plant were slightly higher in NISS treatment in compare to GISS; however, the concentrations did remain within the prescribed limit, and no significant increase was consistently noted. The results prove that the gamma irradiated sludge material was of equal quality compared to the conventional FYM.     

Influence of crop residue management, cropping system and N fertilizer on soil N and C dynamics and sustainable wheat (Triticum aestivum L.) production

Management of N is the key for sustainable and profitable wheat production in a low N soil. We report results of irrigated crop rotation experiment, conducted in the North West Frontier Province (NWFP), Pakistan, during 1999–2002 to evaluate effects of residue retention, fertilizer N application and mung bean (Vigna radiata) on crop and N yields of wheat and soil organic fertility in a mung bean–wheat sequence. Treatments were (a) crop residue retained (+residue) or (b) removed (−residue), (c) 120 kg N ha⁻¹ applied to wheat, (d) 160 kg N ha⁻¹ to maize or (e) no nitrogen applied. The cropping system was rotation of wheat with maize or wheat with mung bean. The experiment was laid out in a spit plot design. Postharvest incorporation of crop residues significantly (p < 0.05) increased the grain and straw yields of wheat during both years. On average, crop residues incorporation increased the wheat grain yield by 1.31 times and straw yield by 1.39 times. The wheat crop also responded strongly to the previous legume (mung bean) in terms of enhanced grain yield by 2.09 times and straw yield by 2.16 times over the previous cereal (maize) treatment. Application of fertilizer N to previous maize exerted strong carry over effect on grain (1.32 times) and straw yield (1.38 times) of the following wheat. Application of N fertilizer to current wheat produced on average 1.59 times more grain and 1.77 times more straw yield over the 0 N kg ha⁻¹ treatment. The N uptake in wheat grain and straw was increased 1.31 and 1.64 times by residues treatment, 2.08 and 2.49 times by mung bean and 1.71 and 1.86 times by fertilizer N applied to wheat, respectively. The soil mineral N was increased 1.23 times by residues, 1.34 times by mung bean and 2.49 times by the application of fertilizer N to wheat. Similarly, the soil organic C was increased 1.04-fold by residues, 1.08 times by mung bean and 1.00 times by the application of fertilizer N. We concluded that retention of residues, application of fertilizer N and involvement of legumes in crop rotation greatly improves the N economy of the cropping system and enhances crop productivity in low N soils.     

日粮精粗比、能量和酵母培养物添补对体外干物质降解的影响

本试验采集泌乳期奶牛的瘤胃液,按2×4×2因子设计,用体外尼龙袋发酵技术研究了60:40和50:50两种精粗比日粮,棉籽油作为能源在奶牛日粮中分别添补0%、2.5%、5%、10%和在日粮中分别添加0%、0.5%的酵母培养物及其互作对体外干物质降解率的影响。体外实验结果表明,对于高产泌乳期奶牛而言,精粗比为60:40的奶牛日粮其干物质降解率高于50:50的精粗比日粮;奶牛日粮中添补植物油和酵母培养物均能显著提高体外干物质降解率(P<0.05);日粮精粗比与能量的互作对6小时的干物质降解率有显著影响(P<0.01);日粮能量添补与酵母培养物添补亦对体外干物质降解率有显著互作影响(P<0.05);而日粮精粗比与酵母培养物添补的互作影响则不明显;植物油作为奶牛日粮能源其添补量不宜超过10%。     

Relationship of Phosphorus Fractions with Soil Properties in Mothbean Growing Acid Soils of North Western Indian Himalayas

Phosphorus (P) availability in acid soils is affected and hence it is important to monitor the distribution of P in acid soils. Here, the relationship was investigated taking 81 surface (0–0.20 m) soil samples into consideration collected from 21 mothbean cultivated areas and were analyzed for different phosphorus fractions in relation to their physical and chemical properties. Results revealed that available P ranged from 8.19 to 15.46 kg ha^–1 which lies in a slightly low-to-medium range. Available P was significantly positively correlated with organic carbon and cation exchange capacity (CEC). The content of soil total P increased significantly with organic carbon and was found in range between 201.00 and 596.11 mg kg^–1 which was in suffice category. Various phosphorus fractions under study viz., Al–P, Fe–P and Ca–P ranged between 20.23–32.28, 34.80–51.44 and 8.57–15.00 mg kg^?1, respectively. Among the various P fractions, organic carbon was positively correlated with Fe–P and Ca–P.     

NDVI-Based Lacunarity Texture for Improving Identification of Torreya Using Object-Oriented Method

Normalized Difference Vegetation Index (NDVI) is a very useful feature for differentiating vegetation and non-vegetation in remote sensed imagery. In the light of the function of NDVI and the spatial patterns of the vegetation landscapes, we proposed the lacunarity texture derived from NDVI to characterize the spatial patterns of vegetation landscapes concerning the “gappiness” or “emptiness” characteristics. The NDVI-based lacunarity texture was incorporated into object-oriented classification for improving the identification of vegetation categories, especially Torreya which was the targeted tree species in the present research. A three-level hierarchical network of image objects was defined and the proposed texture was integrated as potential sources of information in the rules base. A knowledge base of rules created by classifier C5.0 indicated that the texture could potentially be applied in object-oriented classification. It was found that the addition of such texture improved the identification of every vegetation category. The results demonstrated that the texture could characterize the spatial patterns of vegetation structures, which could be a promising approach for vegetation identification.