Hay, F. | bioRxiv Science

bioRxiv2022

Identification of the rice Rc gene as a main regulator of seed survival under dry storage conditions

Seed deterioration during storage results in poor germination, reduced seed vigor, and non-uniform seedling emergence. The rate of aging depends on storage conditions (RH, temperature, and oxygen) and genetic factors. This study aims to identify these genetic factors determining the longevity of rice seeds stored under experimental aging conditions mimicking long-term dry storage. Genetic variation for tolerance to aging was studied in 300 Indica rice accessions and storing dry seeds under elevated partial pressure of oxygen (EPPO) condition, using a genome-wide association study. The association analysis yielded eleven unique regions across the genome for all measured germination parameters after aging. These genomic regions differed from regions previously identified in rice under humid experimental aging conditions. The significant single nucleotide polymorphism in the most prominent region was located within the Rc gene, encoding a bHLH transcription factor. Storage experiments using isogenic rice lines (SD7-1D (Rc) and SD7-1d (rc)) with the same allelic variation confirmed the functional role of the Rc gene, conferring a stronger tolerance to dry EPPO aging. A functional Rc gene results in the accumulation of pro-anthocyanidins in the pericarp of rice seeds, an important sub-class of flavonoids having strong antioxidant activity, which may explain why genotypes with an allelic variation for this gene show variation in seed tolerance to dry EPPO aging.

plant biology↗

bioRxiv2021

Spatiotemporal Dynamics of Stemphylium Leaf Blight and Potential Inoculum Sources in New York Onion Fields

Stemphylium leaf blight (SLB) caused by Stemphylium vesicarium is the dominant foliar disease affecting large-scale onion production in New York. The disease is managed by fungicides, but control failures are prevalent and recently attributed to fungicide resistance. Little is known of the relative role of inoculum sources in initiation and spread of SLB epidemics. The spatial and spatiotemporal dynamics of SLB epidemics in six onion fields were evaluated along linear transects in 2017 and 2018. Average SLB incidence increased from 0 to 100% throughout the cropping seasons with an average final lesion length of 28.3 cm. Disease progress was typical of a polycyclic epidemic and the logistic model provided the best fit to 83.3% of the datasets. Spatial patterns were better described by the beta-binomial than binomial distribution in half of the datasets and random patterns were more frequently observed by the index of dispersion. Geostatistical analyses of spatial pattern also found a low frequency of datasets with aggregation. Spatiotemporal analysis of epidemics detected that the aggregation was influenced by disease incidence. However, diseased units were not associated with the previous time period according to the spatiotemporal association function of SADIE. Variable spatial patterns suggested mixed inoculum sources dependent upon location, and likely an external inoculum source at the sampling scale used in this study. Plate testing of 28 commercially available organic onion seedlots from 2017 and 2018 did not detect S. vesicarium. This finding suggests that although S. vesicarium has been reported as seed transmitted, this is unlikely to be a significant inoculum source in commercially available organic seed lots and even less so in fungicide-treated seed used to establish conventional fields. A small-plot replicated trial was also conducted in each of two years to quantify the effect of S. vesicarium-infested onion residue on SLB epidemics in a field isolated from other onion fields. SLB incidence was significantly reduced in plots without residue compared to those in which residue remained on the soil surface. Burial of infested residue also significantly reduced epidemic progress in one year. The effect of infested onion residue on SLB epidemics in the subsequent onion crop suggests rotation or residue management may have a substantial effect on epidemics. However, the presence of an inoculum source external to fields in onion production regions as indicated by a lack of spatial aggregation may reduce the efficacy of in-field management techniques.

plant biology↗