Integrated linkage mapping and genome-wide association study to dissect the genetic basis of zinc deficiency tolerance in maize at seedling stage

Abstract

Zinc (Zn) deficiency is the most widespread micronutrient deficiency, affecting yield and quality of crops worldwide. Identifying genes associated with Zn-deficiency tolerance in maize is a basis for elucidating its genetic mechanism. A K22 × CI7 recombinant inbred population consisting of 210 lines and an association panel of 508 lines were used to identify genetic loci influencing Zn-deficiency tolerance. Under –Zn and –Zn/CK conditions, 15 quantitative trait loci (QTL) were detected, each explaining 5.7%–12.6% of phenotypic variation. Sixty-one significant single-nucleotide polymorphisms (SNPs) were identified at P < 10−5 by genome-wide association study (GWAS), accounting for 5%–14% of phenotypic variation. Among respectively 198 and 183 candidate genes identified within the QTL regions and the 100-kb regions flanking these significant SNPs, 12 were associated with Zn-deficiency tolerance. Among these candidate genes, four genes associated with hormone signaling in response to Zn-deficiency stress were co-localized with QTL or SNPs, including the genes involved in the auxin (ZmARF7), and ethylene (ZmETR5, ZmESR14, and ZmEIN2) signaling pathways. Three candidate genes were identified as being responsible for Zn transport, including ZmNAS3 detected by GWAS, ZmVIT and ZmYSL11 detected by QTL mapping. Expression of ZmYSL11 was up-regulated in Zn-deficient shoots. Four candidate genes that displayed different expression patterns in response to Zn deficiency were detected in the regions overlapping peak GWAS signals, and the haplotypes for each candidate gene were further analyzed.