MODEM: multi-omics data envelopment and mining in maize

Abstract

MODEM is a comprehensive database of maize multidimensional omics data, including genomic, transcriptomic, metabolic and phenotypic information from the cellular to individual plant level. This initial release contains approximately 1.06 M high quality SNPs for 508 diverse inbred lines obtained by combining variations from RNA sequencing on whole kernels (15 days after pollination) of 368 lines and a 50 K array for all 508 individuals. As all of these data were derived from the same diverse panel of lines, the database also allows various types of genetic mapping (including characterization of phenotypic QTLs, pQTLs; expression QTLs, eQTLs and metabolic QTLs, mQTLs). MODEM is thus designed to promote a better understanding of maize genetic architecture and deep functional annotation of the complex maize genome (and potentially those of other crop plants) and to explore the genotype–phenotype relationships and regulation of maize kernel development at multiple scales, which is also comprehensive for developing novel methods. MODEM is additionally designed to link with other databases to make full use of current resources, and it provides visualization tools for easy browsing. All of the original data and the related mapping results are freely available for easy query and download. This platform also provides helpful tools for general analyses and will be continually updated with additional materials, features and public data related to maize genetics or regulation as they become available.Database URL: (http://modem.hzau.edu.cn)

An allele of ZmPORB2 encoding a protochlorophyllide oxidoreductase promotes tocopherol accumulation in both leaves and kernels of maize

“…In the KC population, qVE5 explained the largest proportion of the phenotypic variation (Table S1) and was narrowed down to a 3.46-Mb interval (Figure 2a). To identify qVE5, a heterogeneous inbred family (HIF-1171) in the 3.46-Mb region was selected from the F 6 generation of the cross K22/CI7 (Liu et al, 2016). HIF-1171 was heterozygous in a region flanked by markers PZA03161.1 (13.58 Mb) and PZA02058.1 (29.27 Mb), covering a 15.69 Mb genomic region harbouring qVE5 (Figure 2b).…”

Kernel size‐related genes revealed by an integrated eQTL analysis during early maize kernel development

“…(d) Comparison of kernel length between the two haplotypes based on the most significantly associated SNP of GRMZM 2G099074. The kernel length data were used from previous studies (Liu et al ., ).…”

“…We next conducted QTT analysis to explore genes related to kernel length that are expressed in the 5‐DAP kernels. This analysis employed a linear regression model to characterize relationships between published kernel length data for each inbred line in the association panel (Liu et al ., ) and the expression data for each of the 18 377 genes that were associated with eQTLs in each inbred line of the population. Using a cut‐off value of P < 0.05 and expression level of population median > 1, 905 of the genes associated with eQTLs were deemed as significant QTTs.…”

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“…These techniques can be transversally used as happened in rice 18,19 or wheat, 20 although the greater experience with newer applications and results come from maize. 21,22 The progress in this important field that improves food quality can be appreciated by the various databases 23 that are similar to those of human data on genome, exome, gene alterations, SNIPS and epigenetic changes. For more detailed information on these aspects see the specific publications elsewhere.…”