A natural single‐nucleotide polymorphism variant in sulfite reductase influences sulfur assimilation in maize

Abstract

Summary Plants absorb sulfur from the environment and assimilate it into suitable forms for the biosynthesis of a broad range of molecules. Although the biochemical pathway of sulfur assimilation is known, how genetic differences contribute to natural variation in sulfur assimilation remains poorly understood. Here, using a genome‐wide association study, we uncovered a single‐nucleotide polymorphism (SNP) variant in the sulfite reductase (SiR) gene that was significantly associated with SiR protein abundance in a maize natural association population. We also demonstrated that the synonymous C to G base change at SNP69 may repress translational activity by altering messenger RNA secondary structure, which leads to reduction in ZmSiR protein abundance and sulfur assimilation activity. Population genetic analyses showed that the SNP69C allele was likely a variant occurring after the initial maize domestication and accumulated with the spread of maize cultivation from tropical to temperate regions. This study provides the first evidence that genetic polymorphisms in the exon of ZmSiR could influence the protein abundance through a posttranscriptional mechanism and in part contribute to natural variation in sulfur assimilation. These findings provide a prospective target to improve maize varieties with proper sulfur nutrient levels assisted by molecular breeding and engineering.

Natural polymorphisms in ZmIRX15A affect water‐use efficiency by modulating stomatal density in maize

“…In addition, free energy prediction of mRNA secondary structure revealed that the Hap2 ZmIRX15A mRNA was more stable than the Hap1 ZmIRX15A mRNA (Figure 3a). It has been well known that less RNA secondary structure of minimum free energy (MFE) correlates with higher mRNA stability and translation efficiency (Akdeli et al ., 2014; Jiang et al ., 2021; Mauger et al ., 2019; Wang et al ., 2006). As a result, ZmIRX15A Hap2 mRNA tended to have a higher probability of forming a relatively more stable secondary structure, presumably affecting the translation of ZmIRX15A mRNA.…”

“…To assess any changes in mRNA structure caused by the variant InDel1089, qRT‐PCR experiments were performed using primers DMS‐F1 (nucleotides 188–205 of the ZmIRX15A exon2), DMS‐F2 (nucleotides 68–88 of the ZmIRX15A 3′UTR), and DMS‐R (complementary to nucleotides 106–125 of the ZmIRX15A ‐UTR). The truncation rate for InDel1089 mRNA was calculated as follows (Jiang et al ., 2021): (Cq (DMS‐F2/R), PCR cycle number using DMS‐F2/DMS‐R primer; Cq (DMS‐F1/R), PCR cycle number using DMS‐F1/DMS‐R primer).…”

“…To assess any changes in mRNA structure caused by the variant InDel1089, qRT-PCR experiments were performed using primers DMS-F1 (nucleotides 188-205 of the ZmIRX15A exon2), DMS-F2 (nucleotides 68-88 of the ZmIRX15A 3 0 UTR), and DMS-R (complementary to nucleotides 106-125 of the ZmIRX15A-UTR). The truncation rate for InDel1089 mRNA was calculated as follows (Jiang et al, 2021)…”

Association mapping uncovers maize ZmbZIP107 regulating root system architecture and lead absorption under lead stress

“…Combining GWAS and gene-based association analysis to identify causal gene of maize tolerance to Pb stress GWAS is an effective method to dissect the genetic basis of quantitative traits. It has been widely applied to identify a variety of complex traits in plant species, including Pb accumulation (Zhao et al, 2018), protein abundance (Jiang et al, 2021), root configuration-related traits (Wang et al, 2019), yield-related traits (Sharma et al, 2018), salt tolerance (Ma et al, 2021b), and so on. Gene-based association analysis is the most widespread method for associating the functional variation loci of candidate genes with the phenotypes they produce (Li et al, 2019).…”