A transposable element in a NAC gene is associated with drought tolerance in maize seedlings.

Hude Mao,Zhigang Li,Lam-Son Phan Tran,Shengxue Liu,Xiaohong Yang,Hongwei Wang,Feng Qin,Jianbing Yan,Jiansheng Li

doi:10.1038/ncomms9326

Abstract

Drought represents a major constraint on maize production worldwide. Understanding the genetic basis for natural variation in drought tolerance of maize may facilitate efforts to improve this trait in cultivated germplasm. Here, using a genome-wide association study, we show that a miniature inverted-repeat transposable element (MITE) inserted in the promoter of a NAC gene (ZmNAC111) is significantly associated with natural variation in maize drought tolerance. The 82-bp MITE represses ZmNAC111 expression via RNA-directed DNA methylation and H3K9 dimethylation when heterologously expressed in Arabidopsis. Increasing ZmNAC111 expression in transgenic maize enhances drought tolerance at the seedling stage, improves water-use efficiency and induces upregulation of drought-responsive genes under water stress. The MITE insertion in the ZmNAC111 promoter appears to have occurred after maize domestication and spread among temperate germplasm. The identification of this MITE insertion provides insight into the genetic basis for natural variation in maize drought tolerance.

Highlights

Drought represents a major constraint on maize production worldwide
On the basis of our combined genome-wide association study (GWAS) and transgenic approach, we propose that the causative variation at the ZmNAC111 locus is likely an 82-bp miniature inverted-repeat transposable element (MITE) insertion in the gene promoter, which may repress the gene expression through DNA and histone hypermethylation via the RNA-directed DNA methylation (RdDM) pathway
We identified the 82-bp MITE insertion in a location that was 572-bp upstream of the ZmNAC111 coding region, which was correlated with lower ZmNAC111 expression and drought susceptibility (Fig. 2b)

Summary

Introduction

Drought represents a major constraint on maize production worldwide. Understanding the genetic basis for natural variation in drought tolerance of maize may facilitate efforts to improve this trait in cultivated germplasm. Using a genome-wide association study, we show that a miniature inverted-repeat transposable element (MITE) inserted in the promoter of a NAC gene (ZmNAC111) is significantly associated with natural variation in maize drought tolerance. Traditional QTL mapping, based on the genetic linkage of a certain trait with the molecular marker within a bi-parental segregation population, usually recombinant inbred lines (RILs), has been successfully used to identify the genes underlying QTLs for glume architecture[8], branched architecture[9], flowering time[10], photoperiod sensitivity[11], resistance to head smut[12] and so on. Genome-wide association study (GWAS), which is based on genetic linkage disequilibrium (LD) and makes use of natural variation and recombinants, has been used as a novel strategy for dissecting complex trait loci in plants[14,15,16,17]. Enrichment of chromatin histone[3] lysine 9 dimethylation (H3K9me2), which is mainly catalysed by a histone methyltransferase, SUVH4 ( named KYP), couples the DNA methylation in the adjacent regions[30,34]

Methods

Results

Conclusion