Maize (Zea mays L.), a globally significant cereal crop, is produced in vast quantities worldwide. However, its growth is severely constrained by low temperatures, particularly during seed germination, which significantly impairs seedling emergence. In this study, genetic diversity across six germination-associated phenotypic traits (RGR, RSL, RTL, RRSA, RRV, and RSVI) of 304 inbred lines was analyzed, to evaluate the capacity of these lines for low-temperature tolerance. Genome-wide association study (GWAS) was carried out by combining six germination-associated phenotypic traits and genotypic data from 30-fold resequencing. The gene ZmBARK1 was identified through integrated GWAS and RNA-seq analyses, and its association with low-temperature tolerance during maize germination was validated by quantitative real-time PCR (qRT-PCR). ZmBARK1, encoding BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1, was located on the bin 4.09 region of maize chromosome 4. Amino acid comparison and subcellular localization analyses revealed that ZmBARK1 is highly homologous to AtBAK1 and is localized to the plasma membrane of the cell, which may be involved in regulating brassinosteroid (BR) signaling. In addition, we revealed the role of ZmBARK1 in low-temperature tolerance during maize germination. Compared with wild-type (WT), the ethyl methanesulfonate (EMS) mutant zmbark1 was characterized by substantially enhanced low-temperature tolerance. Overall, these findings provide promising candidate genes, improve low-temperature tolerance in maize, and advance the understanding of regulatory mechanisms underlying maize’s response to low-temperature stress.

Southern corn rust (SCR) is an airborne fungal disease caused by Puccinia polysora Underw. (P. polysora) that adversely impacts maize quality and yields worldwide. Screening for new elite SCR-resistant maize loci or genes has the potential to enhance overall resistance to this pathogen. Using phenotypic SCR resistance-related data collected over two years and three geographical environments, a genome-wide association study was carried out in this work, which eventually identified 91 loci that were substantially correlated with SCR susceptibility. These included 13 loci that were significant in at least three environments and overlapped with 74 candidate genes (B73_RefGen_v4). Comparative transcriptomic analyses were then performed to identify the genes related to SCR infection, with 2,586 and 797 differentially expressed genes (DEGs) ultimately being identified in the resistant Qi319 and susceptible 8112 inbred lines following P. polysora infection, respectively, including 306 genes common to both lines. Subsequent integrative multi-omics investigations identified four potential candidate SCR response-related genes. One of these genes is ZmHCT9, which encodes the protein hydroxycinnamoyl transferase 9. This gene was up-regulated in susceptible inbred lines and linked to greater P. polysora resistance as confirmed through cucumber mosaic virus (CMV)-based virus induced-gene silencing (VIGS) system-mediated gene silencing. These data provide important insights into the genetic basis of the maize SCR response. They will be useful for for future research on potential genes related to SCR resistance in maize.

Flowering time (FT) is a key maize domestication trait, variation in which allows maize to grow in a wide range of latitudes. Although previous studies have investigated the genetic control of FT-related traits per se, few studies of FT hybrid performance have been published. We characterized the genomic architecture associated with hybrid performance for FT in a hybrid panel by testcrossing Chang 7–2 with 328 Ye478×Qi319 recombinant inbred lines (RILs). We identified 11 quantitative trait loci (QTL) for hybrid performance in FT-related traits, including a major QTL qFH10 that controls hybrid performance and heterosis in a summer maize-growing region. However, this locus acts in regulating FT traits per se only in a spring maize-growing region. We validated ZmCCT10 as a candidate gene for qFH10 and found that differences between hybrids and their parental lines in DNA methylation in the differentially methylated region (DMR, –700 to –1520) of the ZmCCT10 promoter affected gene expression pattern and thereby FT in the summer maize-growing region.