Application of unmanned aerial systems for high throughput phenotyping of large wheat breeding nurseries

Background

Low cost unmanned aerial systems (UAS) have great potential for rapid proximal measurements of plants in agriculture. In the context of plant breeding and genetics, current approaches for phenotyping a large number of breeding lines under field conditions require substantial investments in time, cost, and labor. For field-based high-throughput phenotyping (HTP), UAS platforms can provide high-resolution measurements for small plot research, while enabling the rapid assessment of tens-of-thousands of field plots. The objective of this study was to complete a baseline assessment of the utility of UAS in assessment field trials as commonly implemented in wheat breeding programs. We developed a semi-automated image-processing pipeline to extract plot level data from UAS imagery. The image dataset was processed using a photogrammetric pipeline based on image orientation and radiometric calibration to produce orthomosaic images. We also examined the relationships between vegetation indices (VIs) extracted from high spatial resolution multispectral imagery collected with two different UAS systems (eBee Ag carrying MultiSpec 4C camera, and IRIS+ quadcopter carrying modified NIR Canon S100) and ground truth spectral data from hand-held spectroradiometer.

Results

We found good correlation between the VIs obtained from UAS platforms and ground-truth measurements and observed high broad-sense heritability for VIs. We determined radiometric calibration methods developed for satellite imagery significantly improved the precision of VIs from the UAS. We observed VIs extracted from calibrated images of Canon S100 had a significantly higher correlation to the spectroradiometer (r = 0.76) than VIs from the MultiSpec 4C camera (r = 0.64). Their correlation to spectroradiometer readings was as high as or higher than repeated measurements with the spectroradiometer per se.

Conclusion

The approaches described here for UAS imaging and extraction of proximal sensing data enable collection of HTP measurements on the scale and with the precision needed for powerful selection tools in plant breeding. Low-cost UAS platforms have great potential for use as a selection tool in plant breeding programs. In the scope of tools development, the pipeline developed in this study can be effectively employed for other UAS and also other crops planted in breeding nurseries.

     

CNS mastitis: nothing to worry about?

In this paper, we analyzed a very large field data set on intramammary infections (IMI) and the associated somatic cell count (SCC) in dairy cows. The objective of the study was to analyze the impact of coagulase-negative staphylococci (CNS) IMI on cow SCC, both mean and variability, and on the potential of these infections to have a major impact on the bulk milk SCC (BMSCC). Data and milk samples for bacterial culture were collected by Quality Milk Production Services (QMPS) between 1992 and March of 2007. The QMPS program services dairy farms in New York State and other states in the Northeastern USA and operates in conjunction with Cornell University. Only records from cows where SCC and milk production data were available, and where only one organism was isolated from bacterial cultures of milk samples (or where culture was negative) were used for this analysis. A total of 352,614 records from 4200 whole herd mastitis screening sampling qualified for this study. Within herds an average of 15% (S.D. 12%) of cows sampled were infected with CNS, ranging between 0 and 100%. Average within herd prevalence of cows with a CNS IMI and an SCC over 200,000 cells/ml was 2% (S.D. 4%) with a minimum of 0% and a maximum of 50%. Results of linear mixed models showed three distinct populations of IMI statuses: negative cultures with the lowest SCC; CNS and Corynebacterium bovis with a moderate increase in SCC, and Streptococcus agalactiae, Streptococcus spp. and Staphylococcus aureus showing an important increase in SCC. Surprisingly, milk production was slightly but significantly higher in CNS infected cows compared to culture-negative cows, whereas it was strongly reduced in cows with a major pathogen IMI. The percentage contribution of CNS infections to the BMSCC was 17.9% in herds with a BMSCC less than 200,000 cells/ml. This value decreased to 11.9 and 7.9% in herds with bulk milk SCC between 200,000 and 400,000 and over 400,000 cells/ml, respectively. We concluded that very few herds with milk quality problems would have an important increase in BMSCC that could be mostly attributed to CNS infections. On the other hand, in herds with low BMSCC, CNS infections may be an important contributor to the total number of somatic cells in the bulk milk.     

Hip dysplasia in a 6-year-old Salz ram

A 6-year old Salz ram was presented with a history of poor body condition, progressive gait abnormalities, pelvic limb lameness, and difficulty with copulation. Based on the history, clinical signs, hip palpation, and radiography, a diagnosis of hip dysplasia, previously unreported in sheep, was made.     

Seroprevalence and risk factors for Neospora caninum in sheep in the state Minas Gerais, southeastern Brazil

The aim of this study was to determine the prevalence and risk factors associated with infection due to Neospora caninum in serum samples from 488 sheep originating from 63 farms in 63 municipalities distributed across eight of the twelve mesoregions of the state Minas Gerais, southeastern Brazil. For detection of N. caninum the sheep serum samples were subjected to the indirect fluorescence antibody test (IFAT ≥ 50). To identify the risk factors associated with infection due to N. caninum a questionnaire was filled out for each herd by interviewing, the individual responsible for the herd, demanding information on the general characteristics of the property. Sixty-four sheep sera (13.1%; 95% CI=10.3-16.4) presented IgG-specific anti-N. caninum antibodies with the following titers: 50 (49; 76.6%), 100 (7; 10.9%), 200 (4; 6.2%), 400 (3; 4.7%) and 800 (1; 1.6%). The prevalence of infected sheep per mesoregion ranged from 0 to 28.1%. Out of the 63 farms sampled, 31 (49.2%; 95% CI=36.4-62.1) presented at least one seropositive sheep. No significant association was found between the presence of anti-N. caninum antibodies and the risk factors evaluated on the farms, except for the mesoregion variable (p=0.004; OR=0.429; CI95%=0.182-1.008). These results indicate that there is a need for additional research to define the epidemiological importance of this parasite as a cause of reproductive problems in sheep herds in Minas Gerais.     

2013年沈阳地区汛期水情趋势分析

针对沈阳地区旱涝发生的基本规律,根据多年来开展水文中长期预报所应用的理论和方法,总结水情趋势预测工作的经验,对2013年水情趋势进行分析预测。     

银耳α–微管蛋白基因的克隆及序列分析

 根据GenBank上已发表的其他真菌α–微管蛋白基因序列中的保守区域设计简并引物,扩增出银耳α–微管蛋白基因的cDNA部分序列。分别利用SEFA-PCR方法和RACE技术,克隆了银耳α–微管蛋白基因的DNA和cDNA全长序列。银耳α–微管蛋白基因DNA全长1 962 bp,含有9个内含子,cDNA全长1 347 bp,编码448个氨基酸。生物信息学分析结果表明：银耳α–微管蛋白基因的cDNA序列与新型隐球酵母有80%相似性,编码的蛋白质属于Tubulin_FtsZ超家族中的α–微管蛋白亚家族,氨基酸序列中存在保守的GTP结合区域GGGTGSG,系统发育树显示银耳与新型隐球酵母距离最近。     

2018年山东省猪伪狂犬病野毒抗体流行病学调查

为了解2018年山东省猪伪狂犬病病毒(PRV)感染情况,对山东省99家猪场共2 240份血清样品进行了PRV gE-ELISA抗体检测。结果:猪场PRV gE抗体阳性率为82.83%(82/99),样本血清gE抗体阳性率为61.74%(1383/2240),而且春季样品阳性率最高,冬季较低。哺乳母猪血清阳性率最高,可达96.00%,其次是种公猪和后备母猪,表明该地区PRV野毒感染率依然较高,制定科学合理免疫程序并加强该病综合防控十分必要。     

Tissue reaction to Cysticercus bovis in the lung of artificially infected cattle

The tissue reaction to Cysticercus bovis in the lung of cattle with an experimental infection was an inflammatory rim originating in the immediate vicinity of the cysts. The cysts recovered at days 83 and 102 p.i. contained living cysticerci. The rim was composed either of a layer of high histiocytes organized in palisades (at day 83 p.i.), or a lyer of flat histiocytes (at day 102 p.i.). The outer layer of the rim consisted of fibroblasts, reticular cells and a different number of eosinophil- and neutrophil luekocytes. On the periphery, the rim was formed by granulation tissue infiltrated with lymphoplasmocytes. At the border between the layers of the inflammatory rim there were conspicuous foci of a necrotic appearance typical of a tissue reaction to C. bovis.     

广西片形吸虫中间宿主—小土窝螺线粒体rrnL基因遗传多态性研究

为研究广西小土窝螺不同地理株线粒体大亚基（large subunit ribosomal rRNA,rrnL）基因的遗传多态性,对广西大片吸虫6个流行地区96个小土窝螺样品的rrnL基因进行PCR扩增,通过单链构象多态性（single strand conformation polymorphism,SSCP）技术筛选出具有代表性的样品进行克隆、测序,并用DNAStar 5.0及MEGA 4.0软件加以比对分析。结果显示,6个地区小土窝螺rrnL基因PCR扩增长度约500 bp,在长度为273 bp的序列中检测到15个变异位点,占核苷酸总数的5.49%。百色、南宁和桂林3个地区相同地理株间存在较大的遗传差异。种系发育分析表明,线粒体rrnL基因在一定程度上不是研究小土窝螺种群遗传变异的良好分子标记。本研究为阐明片形吸虫中间宿主—小土窝螺的种群遗传关系提供了基础数据。