ZEAMAP, a comprehensive database adapted to the maize multi-omics era

Abstract

As one of the most extensively cultivated crops, maize (Zea mays L.) has been extensively studied by researchers and breeders for over a century. With advances in high-throughput detection of various omics data, a wealth of multi-dimensional and multi-omics information has been accumulated for maize and its wild relative, teosinte. Integration of this information has the potential to accelerate genetic research and generate improvements in maize agronomic traits. To this end, we constructed ZEAMAP (http://www.zeamap.com), a comprehensive database incorporating multiple reference genomes, annotations, comparative genomics, transcriptomes, open chromatin regions, chromatin interactions, high-quality genetic variants, phenotypes, metabolomics, genetic maps, genetic mapping loci, population structures and domestication selection signals between teosinte and maize. ZEAMAP is user-friendly, with the ability to interactively integrate, visualize and cross-reference multiple different omics datasets. and linkage analysis, the population structure and pedigrees of each germplasm and the selective signals between different teosinte subspecies and maize. ZEAMAP generated comprehensive functional annotations for the annotated gene models in each assembly, and provided useful tools for users to search, analyze and visualize all these different omics data.

The genetic architecture of the dynamic changes in grain moisture in maize

“…The mixed linear model allows the significance of a correlation between genome‐wide SNPs and target trait variation to be tested by controlling population structure and related kinship. The 1.25 million high‐quality SNPs (MAF > 5%) and the estimated population structure and kinship in the 513 diverse inbred lines were used in a previous study of agronomic traits (Gui et al ., 2020; Liu et al ., 2017a). To reduce the redundancy of the SNP information, we estimated the effective number of independent tests (Ne) of the 1.25 million SNPs to be 490,547 based on linkage disequilibrium using GEC software (Li et al ., 2012).…”

Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA

“…Some newly predicted miRNAs are statistically associated with maize traits. As shown in Figure 4E, in the tail region of zma-miR_N221a-5p, there is a single nucleotide polymorphism (SNP; rs#chr6: 22134053) that has been reported to be significantly associated with the metabolic trait “Np.Npp_Feruloyl.caffeoyl_spermidine_derivative_E1” ( P -value = 4.7E-6) [45]. This genetic variant (AA/GG) may influence target gene selection (56 vs .…”

Genome-wide association study reveals the genetic architecture of root hair length in maize

“…Detailed information about the origins of these lines was described in previous studies [42,43]. The 1.25 million high-quality SNPs (MAF > 5%) and the estimated population structure and kinship were assessed using the method previously described [97,98].…”