Advances in crop phenotyping and multi-environment trials

Efficient evaluation of crop phenotypes is a prerequisite for breeding, cultivar adoption, genomics and phenomics study. Plant genotyping is developing rapidly through the use of high-throughput sequencing techniques,while plant phenotyping has lagged far behind and it has become the rate-limiting factor in genetics, large-scale breeding and development of new cultivars. In this paper,we consider crop phenotyping technology under three categories. The first is high-throughput phenotyping techniques in controlled environments such as greenhouses or specifically designed platforms. The second is a phenotypic strengthening test in semi-controlled environments, especially for traits that are difficult to be tested in multi-environment trials(MET), such as lodging, drought and disease resistance. The third is MET in uncontrolled environments, in which crop plants are managed according to farmer's cultural practices. Research and application of these phenotyping techniques are reviewed and methods for MET improvement proposed.     

基于Multi-probe LSH的菊花花型相似性计算

针对海量高维菊花图像相似性计算带来的挑战,研究了基于多探测局部位置敏感哈希技术的菊花表型相似性计算方法。针对菊花图像,采用SIFT技术提取菊花图像特征,并采用BoVW模型进行建模。由于图像特征的高维性质,海量的菊花表型相似性计算效率不高,为了提高计算效率,提出采用近似相似性技术中的多探测局部位置敏感哈希技术,用此方法构建菊花图像数据的哈希数据结构,在菊花相似性查询方面提高了计算效率,并确保了计算结果的质量。在菊花数据集上进行了计算效率和查询质量两方面的测试,并与典型的方法进行了试验对比和分析。结果表明,相比线性式扫描,平均查询成功概率达到0. 90以上,平均加速比为3. 3～19. 8。本文方法能够在查询质量和计算效率两方面通过参数设置提供灵活的优化选择,并对参数的选择提供了参考范围,可为海量菊花花型相似性计算提供参考。     

Recovery from mild Escherichia coli O157:H7 infection in young and aged C57BL/6 mice with intact flora estimated by fecal shedding,locomotor activity and grip strength

Escherichia coli 0157:H7 is a food-borne pathogen that can cause severe complications in vulnerable populations. Mouse infection models of E. coli 0157:H7 are usually developed under severe animal suffering classification by depleting the normal flora, in which age plays a role.ObjectiveTo develop a refined method for longitudinal monitoring of E. coli 0157:H7 in young and old mice with intact flora.MethodsWe applied discriminant analysis and computed composite standardized scores from 19 variables obtained from physiological parameters, analysis of locomotor activity, grip strength measurement and fecal shedding in 16 aged and 16 young C57BL/6 mice after two mild oral challenges of E. coli 0157:H7. The resulting scores were validated in another experiment performed in 24 aged and 24 young mice including a group (8 aged and 8 young mice) treated with oxytetracycline.ResultsWe show that our scores are significantly affected in the post-infection period and that can be used to measure and compare the recovery time after a treatment. The scores are most sensitive when separately developed in young and aged mice.ConclusionsWe developed a method that minimizes the level of animal suffering and that can be applied in preclinical testing of new therapies.     

A strategy of ideotype development for heat-tolerant wheat

Heat stress significantly limits yield in many wheat-growing areas globally including north-western NSW. While various traits linked to high-temperature tolerance have been identified, the combination of traits that optimize the heat tolerance of wheat has not been established in most environments. A total of 554 genotypes were evaluated in the field at different times of sowing in north-western NSW for three consecutive years to develop a heat-tolerant wheat ideotype for this environment. The later sown experiments were exposed to higher temperatures at the critical reproductive and grain-filling stages of development. The impact of high temperature was greatest at anthesis, and eventual grain yield was reduced by between 4% and 7% with every 1°C rise in average maximum temperature above the optimum of 25°C. High temperature reduced yield, plant height, grain weight and days to anthesis and maturity, and increased the percentage of screenings and grain protein content. Genotypes that produced higher yield under heat stress had shorter days to flowering and maturity, higher NDVI during grain filling, greater chlorophyll content at the milk stage of grain fill, taller plants, greater grain weight and number, and lower screenings compared with the benchmark cultivar Suntop. The genotype closest to the predicted heat-tolerant wheat ideotype identified from trait ranges had 79.6% similarity.     

群体小麦条锈病发病动态无人机遥感监测方法

针对当前育种群体小麦条锈病表型分析手段单一、效率低下等问题,该研究提出了一种基于无人机低空遥感和多光谱成像技术的群体小麦田间条锈病高通量表型动态分析方法.该方法利用无人机采集自然发病的育种群体小麦(共600个样本,516个基因型)冠层多时相的光谱图像,并提取22个植被指数作为后续分析的表型,同时按照发病后的时间顺序与传...     

Chinese Box turtle (Cuora flavomarginata) with lymphoid leukemia characterized by immunohistochemical and cytochemical phenotyping

Lymphoid leukemia of T‐cell origin was diagnosed in a male Chinese Box turtle, Cuora flavomarginata, of approximately 25 years of age. The turtle presented with a history of anorexia, open‐mouth breathing, and lethargy for one week. The CBC findings included a mildly increased PCV, and severe leukocytosis due to high numbers of atypical cells interpreted to be blasts. The blasts were medium‐sized cells with round to pleomorphic nuclei, slightly clumped chromatin, indistinct nucleoli, and scant moderate‐to‐dark blue cytoplasm with occasional red‐to‐purple cytoplasmic granulation. Cytochemical and immunohistochemical staining indicated that the neoplastic cells were positive for CD3 and α‐naphthyl butyrate esterase (ANBE), leading to the diagnosis of T‐cell lymphoid leukemia. Histology of tissues collected at necropsy showed multifocal infiltrations of neoplastic round cells in the liver, spleen, kidneys, testicles, pancreas, thyroid, duodenum, bone marrow, epicardium, and myocardium. Transmission electron microscopy failed to identify viral particles within the neoplastic cells. This article describes the hematologic, histologic, and ultrastructural abnormalities associated with lymphoid leukemia in this turtle, and advanced diagnostic methods used for phenotyping the T‐cell origin.     

High-throughput phenotyping identifies plant growth differences under well-watered and drought treatments

The ability to screen larger populations with fewer replicates and non-destructive measurements is one advantage of highthroughput phenotyping(HTP) over traditional phenotyping techniques. In this study, two wheat accessions were grown in a controlled-environment with a moderate drought imposed from stem elongation to post-anthesis. Red-green-blue(RGB) imaging was performed on 17 of the 22 d following the start of drought imposition. Destructive measurements from all plants were performed at the conclusion of the experiment. The effect of line was significant for shoot dry matter, spike dry matter, root dry matter, and tiller number, while the water treatment was significant on shoot dry matter and root dry matter. The temporal, non-destructive nature of HTP allowed the drought treatment to be significantly differentiated from the well-watered treatment after 6 d in a line from Argentina and 9 d in a line from Chile. This difference of 3 d indicated an increased degree of drought tolerance in the line from Chile. Furthermore, HTP from the final day of imaging accurately predicted reference plant height(r=1), shoot dry matter(r=0.95) and tiller number(r=0.91). This experiment illustrates the potential of HTP and its use in modeling plant growth and development.     

Molecular phenotyping of malignant canine mammary tumours: Detection of high-risk group and its relationship with clinicomolecular characteristics

Canine mammary gland tumours (CMTs) constitute the most common cancer in female dogs and comprise approximately 50% of all canine cancers. With the advent of high-throughput technologies such as microarray and next-generation sequencing, the molecular phenotyping (classification) of various cancers has been extensively developed. The present study used a canine RNA-sequencing dataset, namely GSE119810, to classify 113 malignant CMTs and 64 matched normal samples via an unsupervised hierarchical algorithm with a view to evaluating the association between the resulting subtypes (clusters) (n = 4) and clinical and molecular characteristics. Finally, a molecular classifier was developed, and it detected 1 high-risk molecular subtype in the training dataset (GSE119810) and 2 independent validation datasets (GSE20718 and GSE22516). Our results revealed four molecular subtypes (C2–C5) in malignant CMTs. Furthermore, the normal samples constituted a distinct group in the clustering analysis. Marked significant associations were observed between the molecular subtypes (especially C5) and clinical/molecular features, including positive lymphatic invasion, high tumour grades, histopathology diagnoses, short survival and high TP53 mutation rates (ps <.05). The high-risk subtype (C5) was further characterized through the development of a cell cycle-based gene signature, which comprised 37 proliferation-related genes according to the support vector machine algorithm. This signature identified the high-risk group in both training and validation datasets (ps <.001). In the validation analysis, our potential classifier robustly predicted patients with positive lymphatic invasion, metastases and short survival.     

Rate-distortion tradeoff to optimize high-throughput phenotyping systems. Application to X-ray images of seeds

In the context of high-throughput plant phenotyping, measurements are carried out on large populations of plants and produce large amounts of data to be analyzed and stored. The need for automated phenotyping in plant biology opens new fields of application for image acquisition and compression algorithms. In this report, we focus on X-ray imaging for high-throughput analysis of seeds. A practical tradeoff between the tolerated distortion on images and image acquisition rates is demonstrated for measurement, visual inspection or pattern recognition. In these contexts, using the same methodology, we quantify the highest acquisition and compression rates achievable while preserving all the useful biological information with standard lossy compression formats. Using a study case, we quantitatively demonstrate the interest of considering the final biological task as a priori knowledge to optimize the design of phenotyping systems.     

基于三维点云的叶面积估算方法

为实现低成本无损精确测定叶片面积,基于运动恢复结构算法获取点云,提出了一种融合叶片点云分割、表面重建及叶片面积无损估测等过程的植物叶片面积提取方法。首先,基于运动结构恢复算法,以智能手机获取的可见光图像重建植物的三维点云;其次,为了还原叶片表面形状,基于HSV颜色空间,使用阈值分割法去除叶片点云的噪点;使用K-means聚类算法对点云的三维坐标矩阵进行分类,实现单片叶片点云的分割;基于滚球算法重建叶片的表面网格模型;最后,通过计算网格面积求得叶片面积。与常规叶面积测定方法进行了对比,本文方法的计算结果与扫描叶片法测定值相比平均误差为1.21cm2,误差占叶片面积的平均百分比为4.67%;与叶形纸称量法测定值相比平均误差为1.41cm2,误差占叶片面积的平均百分比为6.05%。结果表明,本文方法成本低、精确度高,可满足植物叶片面积无损精确测定的需求。