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Background  Natural variations derived from both evolutionary selection and genetic recombination, presume to have important functions to respond to various abiotic stresses, which could be used to improve drought tolerance via genomic selection.    Results  In the present study, the NAC-encoding gene of  ZmNAC080308  was cloned and sequenced in 199 inbred lines in maize. Phylogenetic analysis showed that  ZmNAC080308  is closely clusteredinto the same group with other well-known NAC genes responding to improve drought tolerance. In total, 86 SNPs and 47 InDels were identified in the generic region of  ZmNAC080308 , 19 of these variations were associated with GY (grain yield) in different environments. Nine variations in the 5’-UTR region of  ZmNAC080308  are closely linked, they might regulate the gene expression and respond to improve GY under drought condition via  Sp1 -mediated transactivation. Two haplotypes (Hap1 and Hap2) identified in the, 5’-UTR region using the nine variations, and Hap2 containing insertion variants, exhibited 15.47 % higher GY under drought stress condition. Further, a functional marker was developed to predict the drought stress tolerance in a US maize inbred line panel. Lines carrying Hap2 exhibited > 10 % higher GY than those carrying Hap1 under drought stress condition. In  Arabidopsis , overexpression  ZmNAC080308  enhanced drought tolerance.    Conclusions   ZmNAC080308  is an important gene responding to drought tolerance, a functional marker is developed for improving maize drought tolerance by selecting this gene.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03072-9.

Natural variations in the non-coding region of ZmNAC080308 contributes maintaining grain yield under drought stress in maize