Towards increased shading potential: a combined phenotypic and genetic analysis of rice shoot architecture

Abstract

Rice feeds more than half of the world's human population. In modern rice farming, a major constraint for productivity is weed proliferation and the ecological impact of herbicide application. Increased weed competitiveness of commercial rice varieties requires enhanced shade casting to limit growth of shade-sensitive weeds and the need for herbicide. We aimed to identify traits that enhance rice shading capacity based on the canopy architecture and the underlying genetic components. We performed a phenotypic screen of a rice diversity panel comprised of 344 varieties, examining 13 canopy architecture traits linked with shading capacity in 4-week-old plants. The analysis revealed a vast range of phenotypic variation across the diversity panel. We used trait correlation and clustering to identify core traits that define shading capacity to be shoot area, number of leaves, culm and solidity (the compactness of the shoot). To simplify the complex canopy architecture, these traits were combined into a Shading Rank metric that is indicative of a plant's ability to cast shade. Genome wide association study (GWAS) revealed genetic loci underlying canopy architecture traits, out of which five loci were substantially contributing to shading potential. Subsequent haplotype analysis further explored allelic variation and identified seven haplotypes associated with increased shading. Identification of traits contributing to shading capacity and underlying allelic variation presented in this study will serve future genomic assisted breeding programmes. The investigated diversity panel, including widely grown varieties, shows that there is big potential and genetic resources for improvement of elite breeding lines. Implementing increased shading in rice breeding will make its farming less dependent on herbicides and contribute towards more environmentally sustainable agriculture.

Flooding tolerance in the major rice weed Echinochloa crus-galli

“…Four different rice (O. sativa) varieties were selected for their high (Shim Balte and Mudgo) or low (Della and Luk Takhar) shade-casting potential based on Huber et al (2021). Seeds were provided from International Rice Genebank Center (IRGC), International Rice Research Institute (IRRI).…”

“…We selected two high shadecasting varieties (Mudgo and Shim Balte) and two low shade-casting varieties (Della and Luk Thakar). This classification is based on the predicted shading capacity of these rice varieties achieved through a combination of different shoot architectural traits as described in Huber et al (2021). Rice seeds were sown two weeks prior to the weed to mimic a typical field situation where rice gets a competitive advantage over the weed and time to shade it.…”

“…The weed was again grown together with rice, but the selection of rice varieties was expanded. A panel of 11 rice genotypes was used, ranging from high to low shading ability (Table 5.1) (Huber et al, 2021). The shading capacity of these rice varieties was estimated using different shoot architectural traits as described in Huber et al (2021).…”

“…A first selection of two high and two low shade-casting rice (O. sativa) varieties was used in a pot experiment in the greenhouse to monitor the effects on weed growth. The shading capacity of these rice varieties is achieved through different shoot architectural traits (Huber et al, 2021). The aim was to identify how long we need to manage weeds at an early stage by other methods (e.g.…”

“…flooding) before crop-induced shading can effectively suppress weeds. Subsequently, a larger selection of 11 different rice varieties with variable shade-casting capacity, also selected from Huber et al (2021), were evaluated in the field. Different weed traits were followed during the vegetative stage development of the weed and the ground cover for each plot was recorded over time through two distinct methods to monitor the association of canopy shade and weed development.…”