Dissecting the genetic architecture of waterlogging stress-related traits uncovers a key waterlogging tolerance gene in maize

The Early Growth of Maize Under Waterlogging Stress, as Measured by Growth, Biochemical, and Molecular Characteristics

An effective strategy to address the impacts of climate change on maize involves early planting, which mitigates drought stress during critical growth phases, preventing yield reductions. The research assessed two maize inbred lines (sensitive and tolerant to low temperature) under conditions of waterlogging stress. This is crucial since early sowing often faces both low temperatures and heavy rain. Morphological, biochemical, and molecular responses were recorded after 24 h, 72 h, and 7 days of stress during the growth stage of 5-day-old seedlings. The findings indicated a more pronounced decline in all morphological characteristics in the sensitive line. Both genotypes displayed an increased root-to-shoot ratio, suggesting that the shoots deteriorate more rapidly than the roots. Physiological evaluations demonstrated that the tolerant line was more effective in managing ROS levels compared to the sensitive line. The involvement of H2O2 in aerenchyma formation implies that the decreased POD activity and elevated MDA levels observed after seven days may be associated with aerenchyma development in the tolerant line. Genes essential for PSII function revealed that waterlogging adversely affected photosynthesis in the sensitive genotype. In summary, the low-temperature tolerant genotype exhibited significant resilience to waterlogging, indicating potential interaction between the pathways governing these two abiotic stressors.

Transcriptome analysis reveals ZmERF055 contributes to waterlogging tolerance in sweetcorn

Waterlogging is a major disaster damaging crop production. However, most sweetcorn cultivars are not tolerant to waterlogging, which severely threatens their production. In order to understand the genetic mechanisms underlying waterlogging tolerance in sweetcorn, this study conducted a comprehensive investigation of sweetcorn waterlogging tolerance at the levels of physiology, biochemistry, and transcriptome in two sweetcorn CSSLs (chromosome segment substitution lines), D120 and D81. We found that D120 showed increased plant height, root length, root area, adventitious root numbers, antioxidant enzyme activities, and aerenchyma area ratio compared to D81. The transcriptome results showed that 2492 and 2351 differentially expressed genes (DEGs) were obtained at 4 h and 8 h of waterlogging treatment, respectively. Genes involved in reactive oxygen species (ROS) homeostasis, photosynthesis, and alcohol fermentation are sensitive in the waterlogging tolerant genotype D120, resulting in enhanced ROS scavenging ability, adventitious roots, and aerenchyma formation. Additionally, ethylene-, auxin-, and ABA-related genes exhibited different responses to waterlogging stress in sweetcorn. We integrated transcriptome and differential chromosomal fragments data and identified that ZmERF055 on chromosome 9 was directly involved in waterlogging stress. ZmERF055-overexpressing plants consistently exhibited significantly increased waterlogging tolerance and ROS homeostasis in Arabidopsis. These results offer a network of plant hormone signaling, ROS homeostasis, and energy metabolism co-modulating waterlogging tolerance in sweetcorn. Additionally, the findings support ZmERF055 as a potential ideal target gene in crop breeding to improve plant waterlogging tolerance.

Genome sequencing reveals evidence of adaptive variation in the genus Zea

Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in wild relatives of maize. Here, we characterize a high-density genomic variation map from 744 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 70 million single-nucleotide polymorphisms. The variation map reveals evidence of selection within taxa displaying novel adaptations. We focus on adaptive alleles in highland teosinte and temperate maize, highlighting the key role of flowering-time-related pathways in their adaptation. To show the utility of variants in these data, we generate mutant alleles for two flowering-time candidate genes. This work provides an extensive sampling of the genetic diversity of Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.

Meta-QTL analysis and candidate genes identification for various abiotic stresses in maize (Zea mays L.) and their implications in breeding programs

Global climate change leads to the concurrence of a number of abiotic stresses including moisture stress (drought, waterlogging), temperature stress (heat, cold), and salinity stress, which are the major factors affecting maize production. To develop abiotic stress tolerance in maize, many quantitative trait loci (QTL) have been identified, but very few of them have been utilized successfully in breeding programs. In this context, the meta-QTL analysis of the reported QTL will enable the identification of stable/real QTL which will pave a reliable way to introgress these QTL into elite cultivars through marker-assisted selection. In this study, a total of 542 QTL were summarized from 33 published studies for tolerance to different abiotic stresses in maize to conduct meta-QTL analysis using BiomercatorV4.2.3. Among those, only 244 major QTL with more than 10% phenotypic variance were preferably utilised to carry out meta-QTL analysis. In total, 32 meta-QTL possessing 1907 candidate genes were detected for different abiotic stresses over diverse genetic and environmental backgrounds. The MQTL2.1, 5.1, 5.2, 5.6, 7.1, 9.1, and 9.2 control different stress-related traits for combined abiotic stress tolerance. The candidate genes for important transcription factor families such as ERF, MYB, bZIP, bHLH, NAC, LRR, ZF, MAPK, HSP, peroxidase, and WRKY have been detected for different stress tolerances. The identified meta-QTL are valuable for future climate-resilient maize breeding programs and functional validation of candidate genes studies, which will help to deepen our understanding of the complexity of these abiotic stresses.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01294-9.

Identification of major QTL for waterlogging tolerance in maize using genome-wide association study and bulked sample analysis

Waterlogging has increasingly become one of the major constraints to maize (Zea mays L.) production in some maize growing areas as it seriously decreases the yield. Waterlogging tolerance in maize germplasm provides a basis for maize waterlogging improvement. In this study, nine seedling traits, plant height (PH), root length (RL), shoot dry weight (SDW), root dry weight (RDW), adventitious root number (ARN), node number of brace root (BRNN), brace root number (BRN), brace root dry weigh (BRDW), survival rate (SR), and the secondary traits that were defined as relative phenotypic value of seedling traits under waterlogging and control treatments were used in a natural population that contain 365 inbred lines to evaluate the waterlogging tolerance of tropical maize. The result showed that maize waterlogging tolerance was genetically controlled and seedling traits were significantly different between the control and waterlogging treatments. PH, RL, SDW, and RDW are important seedling traits for waterlogging tolerance identification. Some tropical maize inbred lines were identified with extreme waterlogging tolerance that can provide an important germplasm resource for breeding. Population structure analysis showed that two major phylogenetic subgroups in tropical maize could be identified. Genome-wide association study (GWAS) using 39,266 single nucleotide polymorphisms (SNPs) across the whole genome identified 49 trait-SNPs distributed on over all 10 chromosomes excluding chromosome 10. Seventy-one significant SNPs, distributed on all 10 chromosomes excluding chromosome 5, were identified by extend bulked sample analysis (Ext-BSA) based on the inbred lines with extreme phenotypes. GWAS and Ext-BSA identified the same loci on bin1.07, bin6.01, bin2.09, bin6.04, bin7.02, and bin7.03. Nine genes were proposed as potential candidate genes. Cloning and functional validation of these genes would be helpful for understanding the molecular mechanism of waterlogging tolerance in maize.

A group VII ethylene response factor gene, ZmEREB180, coordinates waterlogging tolerance in maize seedlings

Group VII ethylene response factors (ERFVIIs) play important roles in ethylene signalling and plant responses to flooding. However, natural ERFVII variations in maize (ZmERFVIIs) that are directly associated with waterlogging tolerance have not been reported. Here, a candidate gene association analysis of the ZmERFVII gene family showed that a waterlogging-responsive gene, ZmEREB180, was tightly associated with waterlogging tolerance. ZmEREB180 expression specifically responded to waterlogging and was up-regulated by ethylene; in addition, its gene product localized to the nucleus. Variations in the 5'-untranslated region (5'-UTR) and mRNA abundance of this gene under waterlogging conditions were significantly associated with survival rate (SR). Ectopic expression of ZmEREB180 in Arabidopsis increased the SR after submergence stress, and overexpression of ZmEREB180 in maize also enhanced the SR after long-term waterlogging stress, apparently through enhanced formation of adventitious roots (ARs) and regulation of antioxidant levels. Transcriptomic assays of the transgenic maize line under normal and waterlogged conditions further provided evidence that ZmEREB180 regulated AR development and reactive oxygen species homeostasis. Our study provides direct evidence that a ZmERFVII gene is involved in waterlogging tolerance. These findings could be applied directly to breed waterlogging-tolerant maize cultivars and improve our understanding of waterlogging stress.