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Identification of the potential genes regulating seed germination speed in maize

ABSTRACT: Purpose: To identify the potential genes that regulate seed germination speed in maize, we performed a time-series transcriptome analysis with two inbred maize lines (72-3 fast germination, F9721 slow germination) during the seed germination and compared the differentially expressed genes (DEGs) in transcriptome with genes identified by GWAS Methods: Methods: mRNA profiles of two maize inbred lines 72-3 and F9721 showing divergent seed germination at six stages during germination were generated by deep sequencing, in triplicate, using Illumina Hiseq2500. The sequence reads that passed quality filters were analyzed at the gene level. Hisat2 was used to align clean reads to maize B73 reference genome, and HTSeq was used to count transcript abundance. DESeq2 models were used to compare DEGs at each germination stage within or between samples Results: Comparative transcriptome study identified 12 hours after imbibition (HAI) as the critical stage responsible for the variation of germination speed. The DEGs between 72-3 and F9721 were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, oxidoreductase activity pathways, hormone signal transduction, and amino acid transporter activity pathways Conclusions: Combined with evidence from gene expression data, GWAS, and gene synteny with other model species, we finally anchored three genes as the likely candidate genes regulating germination speed in maize

ORGANISM(S): Zea mays

PROVIDER: GSE193292 | GEO | 2022/03/02

REPOSITORIES: GEO

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Project description:Seed germination is a complex trait determined by the interaction of hormonal, metabolic, genetic, and environmental components. Variability of this trait in crops has a big impact on seedling establishment and yield in the field. Classical studies of this trait in crops have focused mainly on the analyses of one level of regulation in the cascade of events leading to seed germination. We have carried out an integrative and extensive approach to deepen our understanding of seed germination in Brassica napus by generating transcriptomic, metabolic and hormonal data at different stages upon seed imbibition. Deep phenotyping of different seed germination associated traits in six winter-type B. napus accessions has revealed that seed germination kinetics, in particular seed germination speed, are major contributors to the variability of this trait. Metabolic profiling of these accessions has allowed us to describe a common pattern of metabolic change and to identify the levels of malate and aspartate metabolites as putative metabolic markers to estimate germination performance. Additionally, analysis of seed content of different hormones suggests that hormonal balance between ABA, GA and IAA at crucial time points during this process might underlie seed germination differences in these accessions. In this study, we have also defined the major transcriptome changes accompanying the germination process in B. napus. Furthermore, we have observed that earlier activation of key germination regulatory genes seems to generate the differences in germination speed observed between accessions in B. napus. Finally, we have found that protein-protein interactions between some of these key regulators are conserved in B. napus suggesting a shared regulatory network with other plants species. Altogether, our results provide a comprehensive and detailed picture of seed germination dynamics in oilseed rape. This new framework will be extremely valuable, not only to evaluate germination performance of B. napus accessions, but also to identify key targets for crop improvement in this important process.

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Identification of the potential genes regulating seed germination speed in maize

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