Search

Root system architecture is pivotal for the acquisition of water and nutrients in maize, serving as an essential foundation for achieving high and stable yields. Identification of the genetic components and natural variations determining root traits may facilitate molecular breeding of maize varieties with better root traits. Melatonin plays an important role in plant physiology and development. In this study, nine melatonin biosynthesis genes were re-sequenced in 348 inbred lines, 68 landraces, and 32 teosintes to investigate variations related to maize root traits. The analysis of nucleotide diversity suggested that these genes may have undergone selection, particularly within their promoter regions. Marker–trait association analysis identified 26 variants significantly associated with six root traits. Five variations within the ZmTDC4 promoter were significantly correlated with both total root length (TRL) and lateral root length (LRL). Among these, SNP-1784 explained the most phenotypic variation of root traits, including TRL and LRL, that has undergone selection throughout maize domestication and improvement. Furthermore, knockout of ZmTDC4 in maize resulted in a pronounced reduction in root length, underscoring its critical role in root development. Collectively, these findings elucidate the role of melatonin synthesis genes in root development and identified favorable alleles, thus providing key loci for breeding maize varieties with superior root systems. [ABSTRACT FROM AUTHOR]

Nitrogen (N) availability determines higher plant productivity and yield. However, the molecular mechanisms governing N acquisition and utilization remain largely unknown in maize. In this study, ATAC-seq, RNA-seq, and Ribo-seq analyses were conducted in maize roots under different N supply conditions. A set of differentially expressed genes enriched in N and phenylpropanoid metabolisms at both the transcription and translation levels were highlighted. Interestingly, less than half of low-N responsive genes were shared between transcription and translation. The alteration of translational efficiency (TE) is also an important mechanism by which maize responds to LN. In addition, we identified low-N-induced open chromatin regions (OCRs) and observed an enrichment of transcription factor (TF) binding motifs. Furthermore, we constructed a transcriptional regulatory network for maize roots subjected to low-N. These findings extend our understanding of N availability response and provide new insights for improving N use efficiency (NUE). [ABSTRACT FROM AUTHOR]

The nutritional composition and overall quality of maize kernels are largely determined by the key chemical components: protein, oil, and starch. Nevertheless, the genetic basis underlying these nutritional quality traits during grain filling remains poorly understood. In this study, the concentrations of protein, oil, and starch were studied in 204 recombinant inbred lines resulting from a cross between DH1M and T877 at four different stages post-pollination. All the traits exhibited considerable phenotypic variation. During the grain-filling stage, the levels of protein and starch content generally increased, whereas oil content decreased, with significant changes observed between 30 and 40 days after pollination. Quantitative trait locus (QTL) mapping was conducted and a total of 32 QTLs, comprising 14, 12, and 6 QTLs for grain protein, oil, and starch content were detected, respectively. Few QTLs were consistently detectable across different time points. By integrating QTL analysis, global gene expression profiling, and comparative genomics, we identified 157, 86, and 54 differentially expressed genes harboring nonsynonymous substitutions between the parental lines for grain protein, oil, and starch content, respectively. Subsequent gene function annotation prioritized 15 candidate genes potentially involved in regulating grain quality traits, including those encoding transcription factors (NAC, MADS-box, bZIP, and MYB), cell wall invertase, cellulose-synthase-like protein, cell division cycle protein, trehalase, auxin-responsive factor, and phloem protein 2-A13. Our study offers significant insights into the genetic architecture of maize kernel nutritional quality and identifies promising QTLs and candidate genes, which are crucial for the genetic enhancement of these traits in maize breeding programs. Supplementary Material Supplementary Material File [ABSTRACT FROM AUTHOR]

Elucidating the genetic basis of starch pasting and gelatinization properties is crucial for enhancing the quality of maize and its utility as feed and industrial raw material. In maize, ZmSBE genes encode important starch branching enzymes in the starch biosynthesis pathway. In this study, we re-sequenced the genomic sequences of ZmSBEI, ZmSBEIIa, ZmSBEIIb, and ZmSBEIII in three lines called 335 inbred lines, 68 landrace lines, and 32 teosinte lines. Analyses of nucleotide polymorphisms and haplotype diversity revealed differences in the selection patterns of ZmSBEI, ZmSBEIIa, ZmSBEIIb, and ZmSBEIII during maize domestication and improvement. A marker–trait association analysis of inbred lines detected 22 significant loci, including 18 SNPs and 4 indels significantly associated with three maize starch physicochemical properties. The allele frequencies of two variants (SNP17249C and SNP5055G) were examined in three lines. The frequency of SNP17249C in ZmSBEIIb was highest in teosinte lines, followed by landrace lines, and inbred lines, whereas there were no significant differences in the frequency of SNP5055G in ZmSBEIII among the three lines. These results suggest that ZmSBE genes play an important role in the phenotypic variations in the starch physicochemical properties in maize. The genetic variants detected in this study may be used to develop functional markers for improving maize starch quality. [ABSTRACT FROM AUTHOR]

Nitrogen (N) is one of the most important factors affecting crop production. Root morphology exhibits a high degree of plasticity to nitrogen deficiency. However, the mechanisms underlying the root foraging response under low-N conditions remain poorly understood. In this study, we analyzed 213 maize inbred lines using hydroponic systems and regarding their natural variations in 22 root traits and 6 shoot traits under normal (2 mM nitrate) and low-N (0 mM nitrate) conditions. Substantial phenotypic variations were detected for all traits. N deficiency increased the root length and decreased the root diameter and shoot related traits. A total of 297 significant marker-trait associations were identified by a genome-wide association study involving different N levels and the N response value. A total of 51 candidate genes with amino acid variations in coding regions or differentially expressed under low nitrogen conditions were identified. Furthermore, a candidate gene ZmNAC36 was resequenced in all tested lines. A total of 38 single nucleotide polymorphisms and 12 insertions and deletions were significantly associated with lateral root length of primary root, primary root length between 0 and 0.5 mm in diameter, primary root surface area, and total length of primary root under a low-N condition. These findings help us to improve our understanding of the genetic mechanism of root plasticity to N deficiency, and the identified loci and candidate genes will be useful for the genetic improvement of maize tolerance cultivars to N deficiency. [ABSTRACT FROM AUTHOR]

The primary root is critical for early seedling growth and survival. To understand the molecular mechanisms governing primary root development, we performed a dynamic transcriptome analysis of two maize (Zea mays) inbred lines with contrasting primary root length at nine time points over a 12-day period. A total of 18 702 genes were differentially expressed between two lines or different time points. Gene enrichment, phytohormone content determination, and metabolomics analysis showed that auxin biosynthesis and signal transduction, as well as the phenylpropanoid and flavonoid biosynthesis pathways, were associated with root development. Co-expression network analysis revealed that eight modules were associated with lines/stages, as well as primary or lateral root length. In root-related modules, flavonoid metabolism accompanied by auxin biosynthesis and signal transduction constituted a complex gene regulatory network during primary root development. Two candidate genes (rootless concerning crown and seminal roots , rtcs and Zm00001d012781) involved in auxin signaling and flavonoid biosynthesis were identified by co-expression network analysis, QTL-seq and functional annotation. These results increase our understanding of the regulatory network controlling the development of primary and lateral root length, and provide a valuable genetic resource for improvement of root performance in maize. [ABSTRACT FROM AUTHOR]

Root length is a determining factor of the root system architecture, which is essential for the uptake of water, nutrients and plant anchorage. In this study, ZmMADS60 was resequenced in 285 inbred lines, 68 landraces and 32 teosintes to detect the nucleotide diversity and natural variations associated with root length. Nucleotide diversity and neutral tests revealed that ZmMADS60 might be selected in domestication and improvement processes. ZmMADS60 in maize retained only 40.1% and 66.9% of the nucleotide diversity found in teosinte and landrace, respectively. Gene-based association analysis of inbred lines identified nine variants that were significantly associated with primary root length (PRL), lateral root length (LRL), root length between 0 mm and 0.5 mm in diameter (RL005) and total root length (TRL). One single-nucleotide polymorphism SNP1357 with pleiotropic effects was significantly associated with LRL, RL005 and TRL. The frequency of the increased allele T decreased from 68.8% in teosintes to 52.9% and 38.9% in the landrace and inbred lines, respectively. The frequency of the increased allele of another significant SNP723 associated with PRL also decreased during the maize domestication and improvement processes. The results of this study reveal that ZmMADS60 may be involved in the elongation of primary and lateral roots in the seedling stage and that significant variants can be used to develop functional markers to improve root length in maize. [ABSTRACT FROM AUTHOR]

Root system plays an essential role in water and nutrient acquisition in plants. Understanding the genetic basis of root development will be beneficial for breeding new cultivars with efficient root system to enhance resource use efficiency in maize. Here, the natural variation of 13 root and 3 shoot traits was evaluated in 297 maize inbred lines and genome-wide association mapping was conducted to identify SNPs associated with target traits. All measured traits exhibited 2.02- to 21.36-fold variations. A total of 34 quantitative trait loci (QTLs) were detected for 13 traits, and each individual QTL explained 5.7% to 15.9% of the phenotypic variance. Three pleiotropic QTLs involving five root traits were identified; SNP_2_104416607 was associated with lateral root length (LRL), root surface area (RA), root length between 0 and 0.5mm in diameter (RL005), and total root length (TRL); SNP_2_184016997 was associated with RV and RA, and SNP_4_168917747 was associated with LRL, RA and TRL. The expression levels of candidate genes in root QTLs were evaluated by RNA-seq among three long-root lines and three short-root lines. A total of five genes that showed differential expression between the long- and short-root lines were identified as promising candidate genes for the target traits. These QTLs and the potential candidate genes are important source data to understand root development and genetic improvement of root traits in maize. [ABSTRACT FROM AUTHOR]