玉米遗传育种Maize Genetics · Breeding · Germplasm Resources
The B-box (BBX) family of proteins consists of zinc-finger transcription factors with one or two highly conserved B-box motifs at their N-termini. BBX proteins play crucial roles in various aspects of plant growth and development, including seedling photomorphogenesis, shade avoidance, flowering time, and biotic and abiotic stress responses. Previous studies have identified many different BBXs from several plant species, although the BBX family members in maize are largely unknown. Genome-wide identification and comprehensive analysis of maize BBX (ZmBBX) expression and interaction networks would therefore provide valuable information for understanding their functions. In this study, 36 maize BBXs in three major clades were identified. The ZmBBXs within a given clade were found to share similar domains, motifs, and genomic structures. Gene duplication analyses revealed that the expansion of BBX proteins in maize has mainly occurred by segmental duplication. The expression levels of ZmBBXs were analyzed in various organs and tissues, and under different abiotic stress conditions. Protein–protein interaction networks of ZmBBXs were established using bioinformatic tools and verified by bimolecular fluorescence complementation (BiFC) assays. Our findings can facilitate a greater understanding of the complexity of the ZmBBX family and provide novel clues for unravelling ZmBBX protein functions
Chromatin accessibility plays a vital role in gene transcriptional regulation. However, the regulatory mechanism of chromatin accessibility, as well as its role in regulating crucial gene expression and kernel development in maize (Zea mays) are poorly understood. In this study, we isolated a maize kernel mutant designated as defective kernel219 (dek219), which displays opaque endosperm and embryo abortion. Dek219 encodes the DICER-LIKE1 (DCL1) protein, an essential enzyme in miRNA biogenesis. Loss of function of Dek219 results in significant reductions in the expression levels of most miRNAs and histone genes. Further research showed that the Heat shock transcription factor17 (Hsf17)-Zm00001d016571 module may be one of the factors affecting the expression of histone genes. Assay results for transposase-accessible chromatin sequencing (ATAC-seq) indicated that the chromatin accessibility of dek219 is altered compared with that of wild type (WT), which may regulate the expression of crucial genes in kernel development. By analyzing differentially expressed genes (DEGs) and differentially accessible chromatin regions (ACRs) between WT and dek219, we identified 119 candidate genes that are regulated by chromatin accessibility, including some reported to be crucial genes for kernel development. Taken together, these results suggest that Dek219 affects chromatin accessibility and the expression of crucial genes that are required for maize kernel development
Genetic dissection of ear-related traits using immortalized F2 population in maize
Ear-related traits are often selection targets for maize improvement. This study used an immortalized F2 (IF2) population to elucidate the genetic basis of ear-related traits. Twelve ear-related traits (namely, row number (RN), kernel number per row (KNPR), ear length (EL), ear diameter (ED), ten-kernel thickness (TKT), ear weight (EW), cob diameter (CD), kernel length (KL), kernel width (KW), grain weight per ear (GW), 100-kernel weight (HKW), and grain yield per plot (GY)), were collected from the IF2 population. The ear-related traits were comprised of 265 crosses derived from 516 individuals of the recombinant inbred lines (RILs) under two separated environments in 2017 and 2018, respectively. Quantitative trait loci (QTLs) analyses identified 165 ear traits related QTLs, which explained phenotypic variation ranging from 0.1 to 12.66%. Among the 165 QTLs, 19 underlying nine ear-related traits (CD, ED, GY, RN, TKT, HKW, KL, GW, and KNPR) were identified across multiple environments and recognized as reliable QTLs. Furthermore, 44.85% of the total QTLs showed an overdominance effect, and 12.72% showed a dominance effect. Additionally, we found 35 genomic regions exhibiting pleiotropic effects across the whole maize genome, and 17 heterotic loci (HLs) for RN, EL, ED and EW were identified. The results provide insights into genetic components of ear-related traits and enhance the understanding of the genetic basis of heterosis in maize.
Quality protein maize (QPM) (Zea mays L.) varieties contain enhanced levels of tryptophan and lysine, exhibiting improved nutritive value for humans and livestock. However, breeding QPM varieties remains challenging due to the complex process of rebalancing storage protein. This study conducted transcriptome and proteome analyses to investigate the process of storage proteins rebalancing in opaque2 (o2) and QPM. We found a weak correlation between the transcriptome and proteome, suggesting a significant modulating effect of post-transcriptional events on non-zein protein abundances in Mo17o2 and QPM. These results highlight the advantages of proteomics. Compared with Mo17, 672 differentially expressed proteins (DEPs) were identified both in Mo17o2 and QPM, and several of them were associated with storage protein, starch, and amino acid synthesis. We identified 178 non-zeins as DEPs in Mo17o2 and QPM kernels. The up-regulated non-zein DEPs were enriched in lysine, tryptophan, and methionine, which affected the protein quality. Co-expression network analysis identified regulators of storage protein synthesis in QPM, including O2, PBF1, and several transcription factors. Our results revealed how storage protein rebalancing occurs and identified non-zein DEPs that may facilitate superior-quality QPM breeding.
Genetic transformation has been an effective technology for improving the agronomic traits of maize. However, it is highly reliant on the use of embryonic callus (EC) and shows a serious genotype dependence. In this study, we performed genomic sequencing for 80 core maize germplasms and constructed a high-density genomic variation map using our newly developed pipeline (MQ2Gpipe). Based on the induction rate of EC (REC), these inbred lines were categorized into three subpopulations. The low-REC germplasms displayed more abundant genetic diversity than the high-REC germplasms. By integrating a genome-wide selective signature screen and region-based association analysis, we revealed 95.23 Mb of selective regions and 43 REC-associated variants. These variants had phenotypic variance explained values ranging between 21.46 and 49.46%. In total, 103 candidate genes were identified within the linkage disequilibrium regions of these REC-associated loci. These genes mainly participate in regulation of the cell cycle, regulation of cytokinesis, and other functions, among which MYB15 and EMB2745 were located within the previously reported QTL for EC induction. Numerous leaf area-associated variants with large effects were closely linked to several REC-related loci, implying a potential synergistic selection of REC and leaf size during modern maize breeding.