key: cord-0830992-zkajl0m8
authors: Ma, Xingliang; Ernest, Joanne
title: Tracing the Origins of Agricultural Products with Barcoded Microbial Spores
date: 2020-07-22
journal: Mol Plant
DOI: 10.1016/j.molp.2020.07.014
sha: d7515b45da8cd66ffffbbfad8d26a4d65ff81dbb
doc_id: 830992
cord_uid: zkajl0m8

nan

Editor's Highlights 1

The globalization of agricultural trade has greatly improved our access to cereals, vegetables, 3 and fruits. However, complicated trade routes and supply chains make it impossible to trace the 4 origin of agricultural products. This is particularly problematic when the source of food 5 contamination cannot be determined with the currently available methods. For example, a recent 6 recall of contaminated romaine lettuce from North American shelves had caused significant 7 economic losses and raised public concerns on food safety before a lengthy investigation 8 pinpointed the origin of the outbreak. A recent study by Springer's team from the Harvard 9 Medical School has described the so-called Barcoded Microbial Spores (BMS) method, which 10 enables safe, rapid, and high-resolution tracing of the origins of agricultural products (Qian et al., were transformed into the genomes of a common spore-forming bacterium (Bacillus subtilis) and 17 fungus (Saccharomyces cerevisiae). To minimize risk to the environment, the engineered BMS 18 organisms were impaired in their germination and growth under natural conditions either by 19 removing genes essential for germination (B. subtilis) or by boiling (S. cerevisiae). 20 After these barcoded spores were inoculated onto various surfaces of interest, origin and contact 21 tracing was conducted using a Cas13a-based RNA detection technique known as SHERLOCK

(Gootenberg et al., 2017) ( Figure 1) . Notably, the SHERLOCK assay has been used for testing 23 Zika and SARS-CoV-2 (causing COVID-19) viruses. Combining with a high-efficient spore 24 lysis procedure, the authors could detect BMS with single-molecule sensitivity, and when paired 25 with SANGER sequencing, could correctly pinpoint the origins of inoculated leafy plant samples 26 from a mixture without cross contamination (Figure 1 ).

BMS technology holds great potential in the precise tracing of agricultural products and thus the 28 sources of foodborne illnesses. Firstly, the use of the custom-designed 28-bp Cas13a target as the 29 barcode indicates that the specificity of BMS sequence has a near-unlimited ability for variation.

Secondly, BMS can persist on sand, soil, carpet, and wood for months, independent of weather 31 conditions, and is detectable on food products, even after washing, boiling, microwaving, or 32 frying. Thirdly, the isothermal nature of SHERLOCK assay enables paper spot in-field testing, 33 and primary presence/absence screening can be conducted using a mobile phone, thereby 34 enabling high-throughput field screening followed by the laboratory identification of the specific 

Insect pests are one of the major causes of crop loss worldwide. Currently, synthetic pesticides 55 are widely used to control pests in agricultural fields, but their overuse often causes serious 56 environmental problems and threatens human health. Different from pesticides, some 57 environmental-friendly chemical elicitors (also known as plant strengtheners), such as 58 benzothiadiazole and jasmonates, although unable to directly kill insects, can induce or enhance 59 plant resistance to pests, emerging as promising substitutes for pesticides. However, most of the 60 reported chemical elicitors can reduce plant growth through hormonal crosstalk, which is 61 undesirable for achieving high yield in crops, thereby limiting their use in agricultural practices. proposed that they may prevent WBPH stylets from reaching the phloem through physical 77 blocking, thereby decreasing food intake ( Figure 1) . Interestingly, the spraying of 4-FPA not 78 only decreased WBPH populations but also increased rice grain yield in the field. Furthermore, 79 4-FPA was found to confer broad-spectrum resistance to other piercing-sucking insects tested, 80 with no harmful effects on spiders, which are the main predatory natural enemies of insect pests 81 on rice plants. 

The CRISPR/Cas-mediated genome editing technology has been widely applied to create knock- Lu, Y., Tian, Y., Shen, R., Yao, Q., Wang, M., Chen, M., Dong, J., Zhang, T., Li, F., Lei, M., et 149 al. (2020) . Targeted, efficient sequence insertion and replacement in rice. Nat Biotechnol. 150 Tsai, S.Q., Zheng, Z., Nguyen, N.T., Liebers, M., Topkar, V.V., Thapar, V., Wyvekens, N., 151 Khayter, C., Iafrate, A.J., Le, L.P., et al. (2015) . GUIDE-seq enables genome-wide profiling of To overcome these setbacks, a team from Wu's and Yan's labs recently developed a strategy 185 known as the integrated peptidogenomic pipeline (Wang et al. 2020) . Using this pipeline, they 186 discovered 1,993 NCPs and 844 CPs in maize. Although non-AUG translation start sites are 187 commonly used in CPs and NCPs, they found that NCPs have some distinct characteristics; e.g., 188 they are shorter and homogeneously distributed in the genome compared with CPs. To validate 189 these identified NCPs, the authors analyzed the available RNA-seq and ribosome profiling data 190 from maize and verified 90.62% and 36.73% of NCPs, respectively. Consistent with previous 191 studies showing that quantitative trait locus (QTLs) are highly associated with noncoding regions 192 in maize, they found that NCPs are significantly associated with several QTL-related traits such 193 as disease resistance, kernel length, and oil content, implying that NCPs are likely involved in 194 regulating these processes. Interestingly, NCPs were also found to be enriched within regions 195 associated with maize domestication and selection. Furthermore, the authors carried out a similar 196 study in Arabidopsis, a dicot model plant, and identified 1,860 NCPs and 2,363 CPs, suggesting 197

In conclusion, this study developed a new peptidogenomic approach and provided strong 201 evidence for the existence of thousands of NCPs in plants. Further studies are needed to study 202 the functions of these NCPs in plants and biological processes they are involved

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