Zinc (Zn) deficiency is one of the most common micronutrient disorders in cereal plants, greatly impairing crop productivity and nutritional quality. Identifying the genes associated with Zn deficiency tolerance is the basis for understanding the genetic mechanism conferring tolerance. In this study, the K22×BY815 and DAN340×K22 recombination inbred line (RIL) populations, which were derived from Zn-inefficient and Zn-efficient inbred lines, were utilized to detect the quantitative trait loci (QTLs) associated with Zn deficiency tolerance and to further identify candidate genes within these loci. The BLUP (Best Linear Unbiased Prediction) values under Zn-deficient condition (-Zn) and the ratios of the BLUP values under Zn deficient condition to the BLUP values under Zn-sufficient condition (-Zn/CK) were used to perform linkage mapping. In QTL analysis, 21 QTLs and 33 QTLs controlling the Zn score, plant height, shoot and root dry weight, and root-to-shoot ratio were detected in the K22×BY815 population and the DAN340×K22 population, explaining 5.5–16.6% and 4.2–23.3% of phenotypic variation, respectively. In addition, seventeen candidate genes associated with the mechanisms underlying Zn deficiency tolerance were identified in QTL colocalizations or the single loci, including the genes involved in the uptake, transport, and redistribution of Zn (ZmIRT1, ZmHMAs, ZmNRAMP6, ZmVIT, ZmNAS3, ZmDMAS1, ZmTOM3), and the genes participating in the auxin and ethylene signal pathways (ZmAFBs, ZmIAA17, ZmETR, ZmEIN2, ZmEIN3, ZmCTR3, ZmEBF1). Our findings will broaden the understanding of the genetic structure of the tolerance to Zn deficiency in maize.

Iron (Fe) is a mineral micronutrient for plants, and Fe deficiency is a major abiotic stress in crop production because of its low solubility under aerobic and alkaline conditions. In this study, 18 maize inbred lines were used to preliminarily illustrate the physiological mechanism underlying Fe deficiency tolerance. Then biparental linkage analysis was performed to identify the quantitative trait loci (QTLs) and candidate genes associated with Fe deficiency tolerance using the recombinant inbred line (RIL) population derived from the most Fe-efficient (Ye478) and Fe-inefficient (Wu312) inbred lines. A total of 24 QTLs was identified under different Fe nutritional status in the Ye478 × Wu312 RIL population, explaining 6.1–26.6% of phenotypic variation, and ten candidate genes were identified. Plants have evolved two distinct mechanisms to solubilize and transport Fe to acclimate to Fe deficiency, including reduction-based strategy (strategy I) and chelation-based strategy (strategy II), and maize uses strategy II. However, not only genes involved in Fe homeostasis verified in strategy II plants (strategy II genes), which included ZmYS1, ZmYS3, and ZmTOM2, but also several genes associated with Fe homeostasis in strategy I plants (strategy I genes) were identified, including ZmFIT, ZmPYE, ZmILR3, ZmBTS, and ZmEIN2. Furthermore, strategy II gene ZmYS1 and strategy I gene ZmBTS were significantly upregulated in the Fe-deficient roots and shoots of maize inbred lines, and responded to Fe deficiency more in shoots than in roots. Under Fe deficiency, greater upregulations of ZmYS1 and ZmBTS were observed in Fe-efficient parent Ye478, not in Fe-inefficient parent Wu312. Beyond that, ZmEIN2 and ZmILR3, were found to be Fe deficiency-inducible in the shoots. These findings indicate that these candidate genes may be associated with Fe deficiency tolerance in maize. This study demonstrates the use of natural variation to identify important Fe deficiency-regulated genes and provides further insights for understanding the response to Fe deficiency stress in maize.