AirMeasurer: open-source software to quantify static and dynamic traits derived from multiseason aerial phenotyping to empower genetic mapping studies in rice.

Low-altitude aerial imaging, an approach that can collect large-scale plant imagery, has grown in popularity recently. Amongst many phenotyping approaches, unmanned aerial vehicles (UAVs) possess unique advantages as a consequence of their mobility, flexibility and affordability. Nevertheless, how to extract biologically relevant information effectively has remained challenging. Here, we present AirMeasurer, an open-source and expandable platform that combines automated image analysis, machine learning and original algorithms to perform trait analysis using 2D/3D aerial imagery acquired by low-cost UAVs in rice (Oryza sativa) trials. We applied the platform to study hundreds of rice landraces and recombinant inbred lines at two sites, from 2019 to 2021. A range of static and dynamic traits were quantified, including crop height, canopy coverage, vegetative indices and their growth rates. After verifying the reliability of AirMeasurer-derived traits, we identified genetic variants associated with selected growth-related traits using genome-wide association study and quantitative trait loci mapping. We found that the AirMeasurer-derived traits had led to reliable loci, some matched with published work, and others helped us to explore new candidate genes. Hence, we believe that our work demonstrates valuable advances in aerial phenotyping and automated 2D/3D trait analysis, providing high-quality phenotypic information to empower genetic mapping for crop improvement.

Timing for antioxidant-priming against rice seed ageing: optimal only in non-resistant stage.

Seed deterioration due to ageing strongly affects both germplasm preservation and agricultural production. Decelerating seed deterioration and boosting seed viability become increasingly urgent. The loss of seed viability is inevitable even under cold storage. For species with short-lived seed or for regions with poor preservation infrastructure where cold storage is not readily available, seed enhancement is more reliable to increase seed viability and longevity. Antioxidant priming as a way of seed enhancement usually improves seed germination. As for post-priming survival, however, significant uncertainty exists. The controversy lies particularly on seeds of high germination percentage (GP > 95%) whose viability is hardly improvable and the benefits of priming depend on prolonging seed longevity. Therefore, this study timed antioxidant priming to prolong the longevity of high-viability seeds under artificially accelerated ageing (AAA). Rice (Nipponbare) seeds (GP > 97%) under room-temperature-storage (RTS) for 6 months. were resistant to AAA first with little viability loss for a certain period, the resistant stage. This resistance gradually vanished without GP change, during a prolonged RTS period which was named the vulnerable stage. According to the results, although antioxidant priming severely curtailed the resistant stage for seeds with a long plateau in the survival curve, it decelerated viability loss for seeds in the vulnerable stage. In complement to seed storage, priming potentially retains high seed GP which would decrease without seed enhancement. To maximize the benefits of priming for high-GP seeds, two time points are advised as the start of a time window for priming: (1) just at the end of the resistant stage without notable viability loss, which is hard to grasp by GP monitoring; (2) slight but identifiable GP decline.

Dehiscence method: a seed-saving, quick and simple viability assessment in rice.

BACKGROUND: Seed viability monitoring is very important in ex situ germplasm preservation to detect germplasm deterioration. This requires seed-, time- and labor- saving methods with high precision to assess seed germination as viability. Although the current non-invasive, rapid, sensing methods (NRSs) are time- and labor-saving, they lack the precision and simplicity which are the virtues of traditional germination. Moreover, they consume a considerable amount of seeds to adjust sensed signals to germination percentage, which disregards the seed-saving objective. This becomes particularly severe for rare or endangered species whose seeds are already scarce. Here we propose a new method that is precise, low-invasive, simple, and quick, which involves analyzing the pattern of dehiscence (seed coat rupture), followed by embryonic protrusion. RESULTS: Dehiscence proved simple to identify. After the trial of 20 treatments from 3 rice varieties, we recognized that dehiscence percentage at the 48th hour of germination (D(48)) correlates significantly with germination rate for tested seed lots. In addition, we found that the final germination percentage corresponded to D(48) plus 5. More than 70% of the seeds survived post-dehiscence desiccation for storage. Hydrogen peroxide (1 mM) as the solution for imbibition could further improve the survival. The method also worked quicker than tetrazolium which is honored as a fast, traditional method, in detecting less vigorous but viable seeds. CONCLUSION: We demonstrated the comprehensive virtues of dehiscence method in assessing rice seed: it is more precise and easier to use than NRSs and is faster and more seed-saving than traditional methods. We anticipate modifications including artificial intelligence to extend our method to increasingly diverse circumstances and species.