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

Abstract

Background Leaf angle 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 plant layers and more horizontal leaves in the lower canopy, maximizing 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 gene, colocalizing with a major-effect QTL on chromosome 7, has been validated. Additionally, the genetic architecture of leaf angle across canopy layers remains to be elucidated. Results This study characterized the canopy-layer specific transcriptome of five sorghum genotypes using RNA sequencing. A set of 284 differentially expressed genes for at least one layer comparison (FDR < 0.05) co-localized with 69 leaf angle QTL and were consistently identified across genotypes. These genes are involved in transmembrane transport, hormone regulation, oxidation-reduction process, response to stimuli, lipid metabolism, and photosynthesis. The most relevant eleven candidate genes for layer-specific angle modification include those homologous to genes controlling leaf angle in rice and maize or genes associated with cell size/expansion, shape, and cell number. Conclusions Considering the predicted functions of candidate genes, their potential undesirable pleiotropic effects should be further investigated across tissues and developmental stages. Future validation of proposed candidates and exploitation through genetic engineering or gene editing strategies targeted to collar cells will bring researchers closer to the realization of a “smart canopy” sorghum.

The transcriptional regulatory network of hormones and genes under salt stress in tomato plants (Solanum lycopersicum L.)

“…High-throughput RNA sequencing (RNA-seq) had become one of widespread methods for measuring transcriptional expression profiles of genes ( Natukunda et al., 2022 ). Based on the temporal gene expression analysis, Kuang et al.…”

Towards increased shading capacity: A combined phenotypic and genetic analysis of rice shoot architecture

“…Since we have performed our experiments under stable conditions in a controlled environment, it will be relevant to perform field trials when testing improved varieties since rice varieties may differentially adapt some of the observed architecture variables under different planting densities and the associated changes in light composition and availability. Furthermore, plant architecture is also plastic throughout development, and although relatively horizontal angles would improve weed‐shading early on, more erect leaves would prevent crop shading in later stages (Mantilla‐Perez et al, 2020; Murchie & Burgess, 2022; Natukunda et al, 2022). Another aspect of weed competitiveness that was not covered in our study would be the root systems, for which the rapidly evolving high‐throughput phenotyping methods are a major opportunity to resolve comparable questions as done here for shoot architecture.…”

Genetic control of morphological traits useful for improving sorghum

“…Dw3, a well-known auxin transporter gene that has a major effect on sorghum plant height, also has pleiotropic effects on leaf angle (Truong et al 2015). Some studies have detected similar loci associated with Dw3 involved in the regulation of leaf angle (Mantilla- Perez et al 2020, Natukunda et al 2022, Zhi et al 2022; however, QTL analysis using a RIL population in which both parents carried the same Dw3 allele also detected a QTL for leaf angle in this region (Truong et al 2015), suggesting that another gene close to Dw3 may also be involved in leaf angle regulation in sorghum. RNA-seq data suggested that Sobic.007G165800 (BAHD acyltransferase DCR, a homolog of rice Slender Grain), Sobic.007G166900 (WALLS ARE THIN 1), Sobic.007G175600 (small auxin up-regulated RNA 36), Sobic.007G153001 (potassium ion transporter), and Sobic.007G160400 (zinc-finger homeodomain protein 2) are novel candidate genes co-localized with QTL in the Dw3 region (Natukunda et al 2022).…”

“…RNA-seq data suggested that Sobic.007G165800 (BAHD acyltransferase DCR, a homolog of rice Slender Grain ), Sobic.007G166900 ( WALLS ARE THIN 1 ), Sobic.007G175600 (small auxin up‑regulated RNA 36), Sobic.007G153001 (potassium ion transporter), and Sobic.007G160400 (zinc‑finger homeodomain protein 2) are novel candidate genes co-localized with QTL in the Dw3 region ( Natukunda et al 2022 ). Combining the results of GWAS and QTL analysis with RNA-seq data, the following eleven candidate genes responsible for leaf angle regulation were identified: Sobic.001G161500 (Aux/IAA transcription factor IAA12), Sobic.001G166401 (homolog of rice GA20 oxidase 4, which catalyzes oxidation steps during GA biosynthesis), Sobic.001G170301 (homologous to the GA-stimulated transcript OsGASR2 ), Sobic.001G172400 (cytochrome P450 85A1 homologous to the rice brassinosteroid-deficient dwarf1 that catalyzes the C6 oxidation step during BR biosynthesis), Sobic.002G353200 (BZR1/BES1 transcription factor), Sobic.003G036700 (homolog of OsCKX1 , which encodes a cytokinin dehydrogenase 1), Sobic.003G096100 ( WALLS ARE THIN 1 ), Sobic.003G133800 (leucine-rich repeat protein associated with BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED RECEPTOR KINASE 1), Sobic.004G178000 (homologous to OsRR2 , the predicted negative regulator of cytokinin signaling), Sobic.005G030400 (cytochrome P450 90A1, homologous to OsCPD1 / 2 ), and Sobic.006G091700 (putative 12-oxophytodienoate reductase involved in JA biosynthesis) ( Mantilla-Perez et al 2020 , Natukunda et al 2022 ). The sorghum leaf arrangement is currently far from that proposed in the “smart canopy” model ( Mantilla-Perez et al 2020 ).…”