Natural variation and domestication selection of ZmSULTR3;4 is associated with maize lateral root length in response to salt stress

Abstract

Soil salinity is a major constraint that restricts crop productivity worldwide. Lateral roots (LRs) are important for water and nutrient acquisition, therefore understanding the genetic basis of natural variation in lateral root length (LRL) is of great agronomic relevance to improve salt tolerance in cultivated germplasms. Here, using a genome-wide association study, we showed that the genetic variation in ZmSULTR3;4, which encodes a plasma membrane-localized sulfate transporter, is associated with natural variation in maize LRL under salt stress. The transcript of ZmSULTR3;4 was found preferentially in the epidermal and vascular tissues of root and increased by salt stress, supporting its essential role in the LR formation under salt stress. Further candidate gene association analysis showed that DNA polymorphisms in the promoter region differentiate the expression of ZmSULTR3;4 among maize inbred lines that may contribute to the natural variation of LRL under salt stress. Nucleotide diversity and neutrality tests revealed that ZmSULTR3;4 has undergone selection during maize domestication and improvement. Overall, our results revealed a regulatory role of ZmSULTR3;4 in salt regulated LR growth and uncovered favorable alleles of ZmSULTR3;4, providing an important selection target for breeding salt-tolerant maize cultivar.

Natural variation in ZmNAC087 contributes to total root length regulation in maize seedlings under salt stress

“…These findings are in line with our GWAS results and demonstrate the effectiveness of using GWAS to identify natural variations associated with salt tolerance in maize. Importantly, our study provides additional evidence for the influence of natural variations in the promoter region on gene function, which is in agreement with previous findings on the impact of natural variations in ZmSULTR3;4 and ZmCBL8 promoters on maize salt tolerance [ 13 , 65 ]. However, the high degree of LD among the identified polymorphisms hampers the identification of the causal site in Hap2 responsible for increased ZmNAC087 expression in maize varieties with this haplotype.…”

“…Despite the cloning of many transcription factors (TFs) necessary for root survival in saline environments [ 62 – 64 ], the contribution of allelic sequence variations to salt stress-induced root phenotypic differences remains largely unknown. To date, only a few salt-tolerant QTLs have been identified through association mapping [ 18 , 50 , 59 , 65 ]. In this study, we used association mapping to pinpoint the genetic variations linked to maize salt tolerance and identified significant SNPs/Indels in ZmNAC087 promoter that significantly correlated with the root length (TRL) in salt-stressed maize seedlings.…”

“…Genetic diversity provides valuable resources for improving crop yield and stress resistance [ 55 , 67 , 68 ]. Several stress-related genes, such as ZmSULTR3:4 , bZIP68 , and KRN4 , have experienced strong selection during the genetic improvement of maize [ 65 , 69 , 70 ]. Here, we observed a consistent decline in genetic diversity of ZmNAC087 in maize inbred lines compared with landraces and teosintes.…”

“…The dual luciferase promoter activity assays were conducted following a previously described method [ 65 ]. Briefly, ~ 1.4-kb fragments of the ZmNAC087 promoter were cloned into the pGreen II-0800-LUC vector.…”