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Lead (Pb) in the soil affects the growth and development of plants and causes damages to the human body through the food chain. Here, we identified and cloned a Pb-tolerance gene ZmPIP2;5 based on a weighted gene co-expression network analysis and gene-based association studies. We showed that ZmPIP2;5 encodes a plasma membrane aquaporin and positively regulated Pb tolerance and accumulation in Arabidopsis and yeast. Overexpression of Z mPIP2;5 increased root length and fresh weight of Arabidopsis seedlings under Pb stress. Heterologous expression of ZmPIP2;5 in yeast caused the enhanced growth speed under Pb treatment and Pb accumulation in yeast cells. A (T/A) SNP in the ZmPIP2;5 promoter affected the expression abundance of ZmPIP2;5 and thereby led to the difference in Pb tolerance among different maize lines. Our study helps to understand the mechanism underlying plant tolerance to Pb stress and provides new ideas for breeding Pb-tolerance maize varieties via molecular marker-assisted selection. • ZmPIP2;5 was identified using a gene-based association analysis. • ZmPIP2;5 was verified to positively regulate the Pb tolerance. • T/A variation in the promoter of ZmPIP2;5 led to the difference of Pb tolerance. • Increased ZmPIP2;5 promoted maize adaption to Pb stress. • ZmPIP2;5 improved plant tolerance to Pb probably by maintaining water balance. [ABSTRACT FROM AUTHOR]

Ear shank length (ESL) has significant effects on grain yield and kernel dehydration rate in maize. Herein, linkage mapping and genome-wide association study were combined to reveal the genetic architecture of maize ESL. Sixteen quantitative trait loci (QTL) were identified in the segregation population, among which five were repeatedly detected across multiple environments. Meanwhile, 23 single nucleotide polymorphisms were associated with the ESL in the association panel, of which four were located in the QTL identified by linkage mapping and were designated as the population-common loci. A total of 42 genes residing in the linkage disequilibrium regions of these common variants and 12 of them were responsive to ear shank elongation. Of the 12 genes, five encode leucine-rich repeat receptor-like protein kinases, proline-rich proteins, and cyclin11, respectively, which were previously shown to regulate cell division, expansion, and elongation. Gene-based association analyses revealed that the variant located in Cyclin11 promoter affected the ESL among different lines. Cyclin11 showed the highest expression in the ear shank 15 days after silking among diverse tissues of maize, suggesting its role in modulating ESL. Our study contributes to the understanding of the genetic mechanism underlying maize ESL and genetic modification of maize dehydration rate and kernel yield. [ABSTRACT FROM AUTHOR]

Salinization seriously threatens the normal growth of maize, especially at the seedling stage. Recent studies have demonstrated that circular RNAs (circRNAs) play vital roles in the regulation of plant stress resistance. Here, we performed a genome-wide association study (GWAS) on the survival rate of 300 maize accessions under a salt stress treatment. A total of 5 trait-associated SNPs and 86 candidate genes were obtained by the GWAS. We performed RNA sequencing for 28 transcriptome libraries derived from 2 maize lines with contrasting salt tolerance under normal and salt treatment conditions. A total of 1217 highly expressed circRNAs were identified, of which 371 were responsive to a salt treatment. Using PCR and Sanger sequencing, we verified the reliability of these differentially expressed circRNAs. An integration of the GWAS and RNA-Seq analyses uncovered two differentially expressed hub genes (Zm00001eb013650 and Zm00001eb198930), which were regulated by four circRNAs. Based on these results, we constructed a regulation model of circRNA/miRNA/mRNA that mediated salt stress tolerance in maize. By conducting hub gene-based association analyses, we detected a favorable haplotype in Zm00001eb198930, which was responsible for high salt tolerance. These results help to clarify the regulatory relationship between circRNAs and their target genes as well as to develop salt-tolerant lines for maize breeding. [ABSTRACT FROM AUTHOR]

SUMMARY: The ability of immature maize (Zea mays) embryos to form embryonic calluses (ECs) is highly genotype dependent, which limits transgenic breeding development in maize. Here, we report the association map‐based cloning of ZmSAUR15 using an association panel (AP) consisting of 309 inbred lines with diverse formation abilities for ECs. We demonstrated that ZmSAUR15, which encodes a small auxin‐upregulated RNA, acts as a negative effector in maize EC induction. Polymorphisms in the ZmSAUR15 promoter that influence the expression of ZmSAUR15 transcripts modulate the EC induction capacity in maize. ZmSAUR15 is involved in indole‐3‐acetic acid biosynthesis and cell division in immature embryo‐derived callus. The ability of immature embryos to induce EC formation can be improved by the knockout of ZmSAUR15, which consequently increases the callus regeneration efficiency. Our study provides new insights into overcoming the genotypic limitations associated with EC formation and improving genetic transformation in maize. Significance Statement: Embryonic callus formation is highly genotype dependent in maize, which largely limits maize transgenic breeding development. This study found that ZmSAUR15 negatively effects embryonic callus formation in maize. The polymorphisms in the ZmSAUR15 promoter influence its expression. Furthermore, ZmSAUR15 modulates indole‐3‐acetic acid biosynthesis and cell division in callus. [ABSTRACT FROM AUTHOR]

The discovery and characterization of the opaque endosperm gene provide ideas and resources for the production and application of maize. We found an o213 mutant whose phenotype was opaque and shrunken endosperm with semi-dwarf plant height. The protein, lipid, and starch contents in the o213 endosperm were significantly decreased, while the free amino acid content in the o213 endosperm significantly increased. The aspartic acid, asparagine, and lysine contents were raised in the o213 endosperm by 6.5-, 8.5-, and 1.7-fold, respectively. Genetic analysis showed that this o213 mutant is a recessive single-gene mutation. The position mapping indicated that o213 is located in a 468-kb region that contains 11 protein-encoding genes on the long arm of chromosome 5. The coding sequence analysis of candidate genes between the WT and o213 showed that ZmYSL2 had only a single-base substitution (A–G) in the fifth exon, which caused methionine substitution to valine. Sequence analysis and the allelic test showed that o213 is a new mutant allele of ZmYSL2. The qRT-PCR results indicated that o213 is highly expressed in the stalks and anthers. Subcellular localization studies showed that o213 is a membrane transporter. In the variation analysis of o213, the amplification of 65 inbred lines in GWAS showed that this 3-bp deletion of the first exon of o213 was found only in temperate inbred lines, implying that the gene was artificially affected in the selection process. Our results suggest that o213 is an important endosperm development gene and may serve as a genetic resource. [ABSTRACT FROM AUTHOR]

Key message: Two read depth methods were jointly used in next-generation sequencing data to identify deletions in maize population. GWAS by deletions were analyzed for gene expression pattern and classical traits, respectively. Many studies have confirmed that structural variation (SV) is pervasive throughout the maize genome. Deletion is one type of SV that may impact gene expression and cause phenotypic changes in quantitative traits. In this study, two read count approaches were used to analyze the deletions in the whole-genome sequencing data of 270 maize inbred lines. A total of 19,754 deletion windows overlapped 12,751 genes, which were unevenly distributed across the genome. The deletions explained population structure well and correlated with genomic features. The deletion proportion of genes was determined to be negatively correlated with its expression. The detection of gene expression quantitative trait loci (eQTL) indicated that local eQTL were fewer but had larger effects than distant ones. The common associated genes were related to basic metabolic processes, whereas unique associated genes with eQTL played a role in the stress or stimulus responses in multiple tissues. Compared with the eQTL detected by SNPs derived from the same sequencing data, 89.4% of the associated genes could be detected by both markers. The effect of top eQTL detected by SNPs was usually larger than that detected by deletions for the same gene. A genome-wide association study (GWAS) on flowering time and plant height illustrated that only a few loci could be consistently captured by SNPs, suggesting that combining deletion and SNP for GWAS was an excellent strategy to dissect trait architecture. Our findings will provide insights into characteristic and biological function of genome-wide deletions in maize. [ABSTRACT FROM AUTHOR]

Seed germination directly affect maize yield and grain quality. Low-temperature reduces maize yield by affecting seed germination and seedling growth. However, the molecular mechanism of maize seed germination under low-temperature remains unclear. In this study, the transcriptome data of two maize inbred lines SCL127 (chilling-sensitive) and SCL326 (chilling-tolerant) were analyzed at five time points (0 H, 4 H, 12 H, 24 H, and 48 H) under low-temperature conditions. Through the comparison of SCL127-0 H-vs-SCL326-0 H (Group I), SCL127-4 H-vs-SCL326-4 H (Group Ⅱ), SCL127-12 H-vs-SCL326-12 H (Group Ⅲ), SCL127-24 H-vs-SCL326-24 H (Group Ⅳ), and SCL127-48 H-vs SCL326-48 H (Group Ⅴ), a total of 8,526 differentially expressed genes (DEGs) were obtained. Weighted correlation network analysis revealed that Zm00001d010445 was the hub gene involved in seed germination under low-temperature conditions. Zm00001d010445 -based association analysis showed that Hap Ⅱ (G) was the excellent haplotype for seed germination under low-temperature conditions. These findings provide a new perspective for the study of the genetic architecture of maize tolerance to low-temperature and contribute to the cultivation of maize varieties with low-temperature tolerance. • RNA-seq was performed on two maize lines under low-temperature. • Zm00001d010445 was identified to affect maize germination. [ABSTRACT FROM AUTHOR]

Aluminum (Al) toxicity is one of the primary factors limiting crop production in acid soils worldwide. The cell wall is the major target of Al toxicity owing to the presence of many Al binding sites. Previous studies have found that XTH , encoding xyloglucan endohydrolase (XEH) and xyloglucan endotransglucosylase (XET), could participate in cell wall extension and affect the binding ability of the cell wall to Al by impeding the activities of these two enzymes. In this study, we found that ZmXTH , an XTH gene in maize, was involved in Al detoxification. The Al-induced up-regulation of ZmXTH occurred in the roots, prominently in the root tips. Additionally, the expression of ZmXTH was specifically induced by Al3+ but no other divalent or trivalent cations. Compared with the wild-type Arabidopsis , ZmXTH overexpressing plants grew more healthy and had decreased Al content in their root and root cell wall after Al stress. Overall, the results suggest that ZmXTH could confer the Al tolerance of transgenic Arabidopsis plants by reducing the Al accumulation in their roots and cell walls. [ABSTRACT FROM AUTHOR]

• ZmMATE6 gene from maize was cloned and transformed into Arabidopsis thaliana. • Overexpression of ZmMATE6 in Arabidopsis resulted in enhancing the resistance to Al. • Transgenic Arabidopsis exhibited increased citrate exudation and decreased Al accumulation in roots. • The loss of function caused by the substitution of the fifth residue of CEM domain may also be related to other factors. The yields of cereal crops grown on acidic soils are often reduced by aluminum (Al) toxicity because the prevalence of toxic Al3+ cations increases as pH falls below 5.0. The Al-dependent release of citrate from resistant lines of maize is controlled by ZmMATE1 which encodes a multidrug and toxic compound extrusion (MATE) transporter protein. ZmMATE6 is another member of this family in maize whose expression is also increased by Al treatment. We investigated the function of this gene in more detail to determine whether it also contributes to Al resistance. Quantitative RT-PCR measurements found that ZmMATE6 was expressed in the roots and leaves of Al-resistant and sensitive inbred lines. Treatment with Al induced ZmMATE6 expression in all tissues but several other divalent or trivalent cations tested had no effect on expression. This expression pattern and the induction by Al treatment was confirmed in ZmMATE6 promoter–β-glucuronidase fusion lines. Heterogeneous expression of ZmMATE6 displayed a greater Al-activated release of citrate from the roots and was significantly resistant to Al toxicity than controls. This was associated with reduced accumulation of Al in the root tissues. Our results demonstrated that ZmMATE6 expression is induced by Al and functions as a citrate transporter. [ABSTRACT FROM AUTHOR]