Genomic and physiological dissection of traits associated with temperate aerobic rice adaptation

Due to the looming water crisis and labour scarcity, aerobic rice production (AP) may provide an alternative to traditional flooded culture by growing rice under non-flooded yet well-watered conditions. However, without permanent water, genotypes are more vulnerable to low temperature (LT) events in temperate regions, particularly at the young microspore stage (YMS). Hence, development of genotypes with narrow root cone angle (RCA) leading to deeper roots combined with LT tolerance at YMS are proposed as key AP adaptation traits. Using recombinant inbred lines derived from an LT tolerant Australian variety Sherpa and a tropical japonica variety IRAT109, seventeen experiments were conducted in both field and glasshouse in different water availability conditions. These experiments were coupled with genotyping-by-sequencing and whole genome resequencing (WGRS) to identify and dissect key AP adaptation traits, map and validate associated genomic regions, and develop molecular markers. Average grain yield in well-watered conditions was 9.4 t/ha, with promising genotypes yielding 12.0-13.4 t/ha. Genotypes with narrow RCA increased the proportion of deep roots (7.4–17.7%) and total root length (69.7%). The advantage was further reflected in cooler canopy temperatures (0.3–1.0°C), higher stomatal conductance, and ultimately, higher grain yield than wide RCA genotypes (14-62%). LT tolerant genotypes produced higher total pollen per spikelet, higher number of dehisced anthers, and pollen on stigma and subsequently, lower spikelet sterility (SS) than susceptible genotypes. Eight genomic regions were found to control RCA with qRCA4 being the major quantitative trait locus (QTL) explaining 24.3% of the genotypic variation. Four candidate genes associated with root development and plant response to abiotic stress stimulus have been identified in the region. The effect of qRCA4 was validated across several genetic backgrounds and subsequently, high throughput KASP molecular markers were developed. Three QTL were associated with LT tolerance and qYMCT3/qDTHW3.1 was associated with SS and heading in the population. WGRS and bioinformatic analyses identified OsMADS50 as the best candidate gene for qYMCT3/qDTHW3.1 and was shown to link LT-sensing and flowering in rice. This study provided physiological and genomic understanding of AP-related traits and with genomics-based breeding, could hasten development of AP-adapted, climate-resilient varieties.