Dissection of canopy layer-specific genetic control of leaf angle in Sorghum bicolor by RNA sequencing

Authors: NATUKUNDA, MARTHA - Iowa State University; MANTILLA-PEREZ, MARIA - Iowa State University; Graham, Michelle; LIU, PENG - Iowa State University; SALAS-FERNANDEZ, MARIA - Iowa State University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/10/2021
Publication Date: 2/3/2022
Citation: Natukunda, M.I., Mantilla-Perez, M.B., Graham, M.A., Liu, P., Salas-Fernandez, M.G. 2022. Dissection of canopy layer-specific genetic control of leaf angle in Sorghum bicolor by RNA sequencing. BMC Genomics. 23. Article 95. https://doi.org/10.1186/s12864-021-08251-4.
DOI: https://doi.org/10.1186/s12864-021-08251-4

Interpretive Summary: Leaf angle is an important plant architecture trait, affecting plant density, light interception efficiency, photosynthetic rate, and yield. The “smart canopy” model proposes that having more vertical leaves in the top layers, and more horizontal leaves in the lower canopy, will maximize overall light conversion efficiency and photosynthesis. However, sorghum leaf arrangement is the opposite and could be improved. While a number of genomic regions in sorghum contribute to leaf angle, only a single gene in these regions, the Dwarf3 (Dw3) auxin transporter, has a validated role in controlling leaf angle. In this study, we used gene expression analyses to monitor gene activity across the plant canopy in five sorghum genotypes, each having different versions of the Dw3 gene and with significant leaf angle differences. From this study we identified 284 genes whose activity differed across the canopy in all five genotypes and which corresponded to previously identified regions of the sorghum genome associated with leaf angle. The majority of these genes are involved in transmembrane transport, hormone regulation, response to stimuli, lipid metabolism, and photosynthesis. In addition, we identified nine candidate genes that were similar to known leaf angle genes in other species. Further characterization of these genes will allow sorghum researchers to develop a “smart canopy” for sorghum and improve yield.

Technical Abstract: Leaf angle, the inclination between the leaf blade midrib and main stem, is an important plant architecture trait, affecting plant density, light interception efficiency, photosynthetic rate, and yield. The “smart canopy” model proposes more vertical leaves in the top layers, and more horizontal leaves in the lower canopy, maximizing overall conversion efficiency and photosynthesis. Sorghum leaf arrangement is opposite to that proposed in the “smart canopy” model, indicating the need for improvement. Although leaf angle quantitative trait loci (QTL) have been previously reported, only the Dwarf3 (Dw3) auxin transporter, colocalizing with a major-effect QTL on chromosome 7, has been validated, leaving a significant knowledge gap regarding the genetic control of this trait. This study characterized the canopy-layer specific transcriptome for five sorghum genotypes contrasting in the Dw3 haplotype using RNA sequencing. A set of 284 DE genes (for at least one layer comparison) colocalized with 71 leaf angle QTL and were consistently identified across genotypes, irrespective of the Dw3 haplotype. These genes are involved in transmembrane transport, hormone regulation, oxidation-reduction process, response to stimuli, lipid metabolism, and photosynthesis (FDR<0.05). The most relevant novel nine candidates for layer-specific leaf angle modification include those homologous to genes controlling leaf angle in other species or associated with collar cell growth. Future validation of proposed candidates and utilization in breeding programs will bring sorghum researchers closer to the realization of a “smart canopy” crop.