Genome-wide identification of <i>ZmHMAs</i> and association of natural variation in <i>ZmHMA2</i> and <i>ZmHMA3</i> with leaf cadmium accumulation in maize

Abstract

P_1B-type ATPases, known as heavy metal ATPases (HMAs), play an important role in the control of cadmium (Cd) accumulation in plants. In this study, a total of 12 <i>ZmHMA</i> genes were identified in the maize genome and particularly classified into six clusters based on their phylogenetic relationship and motif compositions. Furthermore, the expression patterns of different <i>ZmHMA</i> genes varied with developmental stages, and were tissue specific under normal conditions. <i>ZmHMA2</i> and <i>ZmHMA3</i> genes exhibited significant up-regulation under Cd treatment. Eventually, the association analysis between 103 inbred lines and alleles in <i>ZmHMA2</i> and <i>ZmHMA3</i> revealed that one insertion-deletion (InDel) in the intron from <i>ZmHMA2</i> was associated with leaf Cd concentration under low Cd condition at the seedling stage. Twenty polymorphisms in <i>ZmHMA3</i> were significantly associated with leaf Cd concentration under various Cd levels at seedling and maturing stages. Five single nucleotide polymorphisms (SNPs) and two InDels of these significantly associated polymorphic loci from <i>ZmHMA3</i> caused the amino acid substitutions and insertion or deletion events. Importantly, the proteins encoded by <i>ZmHMA2</i> and <i>ZmHMA3</i> genes were located in the plasma membrane. This comprehensive analysis will provide an important theoretical basis for future functional verification of <i>ZmHMA</i> genes to unravel the mechanisms of Cd accumulation in leaves of maize. Additionally, the favorable alleles in <i>ZmHMA3</i> will lay a foundation for the marker-assisted selection of low Cd accumulation in maize.