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

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.

Lost in Translation: Physiological Roles of Stored mRNAs in Seed Germination

“…As the evaluation of seed longevity during natural aging takes a long time, 'controlled deterioration treatment (CDT)' or 'accelerated aging', in which seeds are placed under high relative humidity and high temperature, have been used to accelerate seed deterioration as well as to compare transcriptomes Plants 2020, 9, 347 8 of 14 in deteriorating seeds [83,88,89]. Many of the differentially expressed genes reported were from the up-accumulation of transcripts during CDT, perhaps because the cells within the seed are no longer in a glassy state due to the high humidity and temperature, which would facilitate the occurrence of cellular processes such as de novo transcription [83].…”

“…Many of the differentially expressed genes reported were from the up-accumulation of transcripts during CDT, perhaps because the cells within the seed are no longer in a glassy state due to the high humidity and temperature, which would facilitate the occurrence of cellular processes such as de novo transcription [83]. Nevertheless, transcripts whose abundance was reduced during CDT were related to programmed cell death, antioxidants, seed storage proteins, heat shock transcription factors, and the glycolytic pathway [83,88,89], implying the importance of these stored mRNAs for longevity. In both natural and artificial conditions, special attention must be given to the normalization of transcriptomes between samples as well as the selection of appropriate reference genes for qPCR analyses, as RNA integrity in aged seeds will be more or less impaired.…”

Transcriptome analysis of leafy near‐isogenic lines provides molecular insights into floral transition in maize (Zea mays)

“…All sequenced reads from each sample were aligned to the maize B73 reference genome (AGPv4) using HISAT2 with the parameters “—rna‐strandness RF” (Li et al., 2019; Trapnell, Pachter, & Salzberg, 2009). The number of mapped reads for each gene was counted from unique mapping reads with HTSeq‐count version 0.9.1 with the parameters “‐s reverse” (Anders, Pyl, & Huber, 2015).…”

Genetic Aspects and Molecular Causes of Seed Longevity in Plants—A Review

“…In each region, three to eight previously identified aging-related QTLs were located, confirming the importance of these regions in controlling seed longevity in different maize populations. The parents (I178 and X178) of the same population used in this study [ 136 ] were also subjected to transcriptome sequencing before and after five days of AA treatment [ 137 ], which resulted in the detection of 286 and 220 differentially expressed genes (DEGs) 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, organelles, and membrane.…”