Comparative analysis of the accelerated aged seed transcriptome profiles of two maize chromosome segment substitution lines

PLoS One. 2019 Nov 11;14(11):e0216977. doi: 10.1371/journal.pone.0216977. eCollection 2019.

Abstract

Seed longevity is one of the most essential characteristics of seed quality. Two chromosome segment substitution lines, I178 and X178, which show significant differences in seed longevity, were subjected to transcriptome sequencing before and after five days of accelerated aging (AA) treatments. Compared to the non-aging treatment, 286 and 220 differentially expressed genes (DEGs) were identified after 5 days of aging treatment in I178 and X178, respectively. Of these DEGs, 98 were detected in both I178 and X178, which were enriched in Gene Ontology (GO) terms of the cellular component of the nuclear part, intracellular part, organelle and membrane. Only 86 commonly downregulated genes were enriched in GO terms of the carbohydrate derivative catabolic process. Additionally, transcriptome analysis of alternative splicing (AS) events in I178 and X178 showed that 63.6% of transcript isoforms occurred AS in all samples, and only 1.6% of transcript isoforms contained 169 genes that exhibited aging-specific AS arising after aging treatment. Combined with the reported QTL mapping result, 7 DEGs exhibited AS after aging treatment, and 13 DEGs in mapping interval were potential candidates that were directly or indirectly related to seed longevity.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing
  • Chromosomes, Plant / genetics
  • Computer Simulation
  • Food Storage
  • Gene Expression Profiling
  • Gene Ontology
  • Plant Breeding
  • RNA, Plant / genetics
  • RNA-Seq
  • Seeds / genetics
  • Time Factors
  • Transcriptome
  • Zea mays / classification
  • Zea mays / genetics*

Substances

  • RNA, Plant

Grants and funding

This work was support by National Key R&D Program of China (2017YFD0102001-3 & 2018YFD0100900-3), National Natural Science Foundation of China (31701437 & 31771891) and the China Agriculture Research System (CARS-02-10) and Ministry of Agriculture of China (2016ZX08003-002). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.