A Novel Mutation of the NARROW LEAF 1 Gene Adversely Affects Plant Architecture in Rice (Oryza sativa L.)

Abstract

Plant architecture is critical for enhancing the adaptability and productivity of crop plants. Mutants with an altered plant architecture allow researchers to elucidate the genetic network and the underlying mechanisms. In this study, we characterized a novel nal1 rice mutant with short height, small panicle, and narrow and thick deep green leaves that was identified from a cross between a rice cultivar and a weedy rice accession. Bulked segregant analysis coupled with genome re-sequencing and cosegregation analysis revealed that the overall mutant phenotype was caused by a 1395-bp deletion spanning over the last two exons including the transcriptional end site of the nal1 gene. This deletion resulted in chimeric transcripts involving nal1 and the adjacent gene, which were validated by a reference-guided assembly of transcripts followed by PCR amplification. A comparative transcriptome analysis of the mutant and the wild-type rice revealed 263 differentially expressed genes involved in cell division, cell expansion, photosynthesis, reproduction, and gibberellin (GA) and brassinosteroids (BR) signaling pathways, suggesting the important regulatory role of nal1. Our study indicated that nal1 controls plant architecture through the regulation of genes involved in the photosynthetic apparatus, cell cycle, and GA and BR signaling pathways.

Combined genome‐wide association study and epistasis analysis reveal multifaceted genetic architectures of plant height in Asian cultivated rice

“…Known and putative PH regulatory genes identified in the 619 accessions (Supporting Information: et al, 2022), strigolactone (SL) signalling (D53L, L. Jiang et al, 2013), and crosstalk between GA and BR (NAL1, Subudhi et al, 2020). This result agreed with existing knowledge that rice PH is regulated mainly by GA, BR and SL (F. Liu, Wang, et al, 2018), and reflected a general global architecture likely associated with rice domestication.…”

“…Therefore, it may be worthwhile to re-analyse published plant GWAS datasets using this strategy to identify novel causal genes, particularly in those experiments where GWAS on a large population exhibits a single sharp and significant peak in the Manhattan plot, to explore and unravel local adaptation and evolution of key traits. Known and putative PH regulatory genes identified in the 619 accessions (Supporting Information: Table S4) were associated with hormone pathways, such as GA homoeostasis (SD1, Sasaki et al, 2002), brassinosteroid (BR) signalling (WAK10d, WAK11 homologue, Yue et al, 2022;OsVQ4, OsVQ25 homologue, Hao et al, 2022), strigolactone (SL) signalling (D53L, L. Jiang et al, 2013), and crosstalk between GA and BR (NAL1, Subudhi et al, 2020). This result agreed with existing knowledge that rice PH is regulated mainly by GA, BR and SL (F. Liu, Wang, et al, 2018), and reflected a general global architecture likely associated with rice domestication.…”

“…For in situ hybridisation, fresh elongation stem samples were collected and fixed in FAA solution (50% ethanol, 10% formaldehyde and 5% acetic acid), dehydrated with a graded ethanol solution, infiltrated, embedded in paraffin, and then sectioned into 8 μm sections using a Leica microtome (RM2235). Digoxygenin‐labelled in situ hybridisation and probe detection were performed as previously described (Su et al, 2021). All primers are listed in Supporting Information: Table .…”

Multi-model genome-wide association studies of leaf anatomical traits and vein architecture in rice

“…From the numerous numbers of significant loci and candidate genes associated with eight leaf anatomical and vein traits, the three non-synonymous SNPs near NAL1 detected in ML traits are most intriguing, since the phenotype of NAL1 deletion mutant is narrow, thicker leaves with increased mesophyll cells layer number ( Subudhi et al., 2020 ). The other remarkable phenotype of the NAL1 mutant is the reduction in the number of minor veins and the interveinal distance which is consistent with our GWAS results identifying a significant SNP located near NAL1 associated with the IVD trait.…”

“…Additionally, a single nucleotide mutation of NAL1 accounted for variation in the distance between small vascular bundle, flag leaf width, and thickness in rice ( Taguchi et al., 2015 ). Moreover, BZR4 , the candidate gene for MNVW identified by both BLINK and FarmCPU is upregulated in the NAL1 deletion mutant which might be responsible for the reduction in the number of minor veins and triggering alteration in leaf width ( Subudhi et al., 2020 ). NAL1 plays a crucial role in the cell cycle and cell division affecting vein patterning and leaf width since the early stage of leaf primordium initiation and involves in rice yield traits including chlorophyll content, photosynthetic rate, panicle length, and the number of spikelets per panicle ( Takai et al., 2010 ; Fujita et al., 2013 ; Zhang et al., 2014 ; Jiang et al., 2015 ; Lin et al., 2019 ).…”