ORIGINAL ARTICLE Application of Fluorescence Spectroscopy in Wheat Crop: Early Disease Detection and Associated Molecular Changes Babar Manzoor Atta 1 & Muhammad Saleem 1 & Hina Ali 1 & Muhammad Bilal 1 & Muhammad Fayyaz 2 Received: 23 March 2020 /Accepted: 14 May 2020 # Springer Science+Business Media, LLC, part of Springer Nature 2020 Abstract The application of fluorescence spectroscopy combined with chemometrics was explored in the current study for the detection of stripe rust in wheat. The healthy and stripe rust leaves were collected from the disease screening nursery. The variations in the blue-green region and chlorophyll fluorescence intensity in leaves provides the basis for the detection of stripe rust infection. With the progress of disease, the variations in the synchronous fluorescence spectroscopy (SFS) spectrum was witnessed. SFS is an excellent tool for the simultaneous measurement of multiple compound samples, in case of plants it generates evidence regarding the occurrence of leaf fluorophore bands thus revealing the biochemical variations going on at different infection stages. Based on the results of the current study, it is inferred that p-coumaric acid has the highest intensity in healthy samples followed by the asymptomatic leaf samples, whereas the band intensity of α-tocopherol, sinapic acid, chlorogenic acid, ferulic acid, tannins, flavonoid, carotenoids and anthocyanins increases in the diseased and the asymptomatic samples accordingly to the rust infection. Principal component analysis (PCA) beautifully differentiated the healthy and the infected leaf samples. It is evident that the asymptomatic samples are grouped with the diseased samples or independently; indicating the start of disease infection, the decision that is hard to make with the visual assessments. The results of the current study suggest that the fluorescence emission and the SFS spectral signatures acquired for stripe rust could be utilized as fingerprints for early disease detection. Keywords Chlorophyll . Early detection . Leaf fluorophores . Polyphenols . Principal component analysis . Stripe rust . Synchronous fluorescence spectroscopy . Wheat Introduction Wheat is the most important staple food crop [1] and is most extensively grown crop that provides 20 percent of daily protein/calories intake for 4.5 billion people around the globe [2]. The predicted global population in 2050 is 9 billion, to meet the expected increased demand of 60 percent, the annual wheat yield must increase from the current level of 1% to at least 1.6% [2]. The major constraint to the global wheat production is biotic stresses which mainly includes the wheat rusts. The three rusts of wheat namely; stripe (yellow) rust, leaf (brown) rust and stem (black) rust are most feared ones due to the rapidity with which they spread and devastate the crop. According to Ali et al. [3] all the three rusts are distrib- uted globally and cause massive losses in different environ- ments favoring disease epidemics. Although, stripe rust is the most destructive cereal rust compared to the leaf and stem rusts [4] and it has been witnessed as a rising problem with worldwide recurrent invasions due to combination of various factors including high migration and mutation capacity, adapt- ability, presence of recombinant & diverse nature of popula- tions and development of new variants via sexual cycle [3]. The stripe rust of wheat is caused by Puccinia striiformis f.sp. tritici, which is an airborne biotrophic fungal pathogen [5]. This disease has the capability of fast spreading to the new regions and crop cultivars [6]. The stripe rust fungus grows on the plant leaves and produce elongated lesions (stripes) of yellow-orange spores, thus reducing the photosynthetic area * Babar Manzoor Atta babar_niab@hotmail.com 1 Agri. & Biophotonics Division, National Institute of Lasers and Optronics College, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad 45650, Pakistan 2 Crop Diseases Research Institute (CDRI), National Agricultural Research Centre (NARC), Park Road, Islamabad 44000, Pakistan Journal of Fluorescence https://doi.org/10.1007/s10895-020-02561-8