Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes

Abstract

Background: Plant gametophytes play central roles in sexual reproduction. A hallmark of the plant life cycle is that gene expression is required in the haploid gametophytes. Consequently, many mutant phenotypes are expressed in this phase. Results:We perform a quantitative RNA-seq analysis of embryo sacs, comparator ovules with the embryo sacs removed, mature pollen, and seedlings to assist the identification of gametophyte functions in maize. Expression levels were determined for annotated genes in both gametophytes, and novel transcripts were identified from de novo assembly of RNA-seq reads. Transposon-related transcripts are present in high levels in both gametophytes, suggesting a connection between gamete production and transposon expression in maize not previously identified in any female gametophytes. Two classes of small signaling proteins and several transcription factor gene families are enriched in gametophyte transcriptomes. Expression patterns of maize genes with duplicates in subgenome 1 and subgenome 2 indicate that pollen-expressed genes in subgenome 2 are retained at a higher rate than subgenome 2 genes with other expression patterns. Analysis of available insertion mutant collections shows a statistically significant deficit in insertions in gametophyte-expressed genes.

Genome sequence of Jatropha curcas L., a non‐edible biodiesel plant, provides a resource to improve seed‐related traits

“…Female flowers had many more up‐regulated DETFs (76 DETFs) than male flowers (23 DETFs). Most AP2‐EREBP DETFs were up‐regulated in female flowers, which is reminiscent of the enrichment of AP2‐EREBP in embryo sac‐enriched tissue samples in maize (Chettoor et al ., ). The most highly enriched DETF in male flowers was MADS, with 7 of 15 MADS DETF.…”

“…The most highly enriched DETF in male flowers was MADS, with 7 of 15 MADS DETF. This is consistent with the finding that, in Arabidopsis and maize, MADS transcripts are over‐represented in male pollen, which supports an ancient role for these genes in the male gametophyte (Chettoor et al ., ; Kwantes et al ., ; Verelst et al ., ). The second most enriched DETF in male flowers, WRKY, has been reported to be required for male gametogenesis in Arabidopsis (Guan et al ., ).…”

Zygotic Genome Activation Occurs Shortly after Fertilization in Maize

“…We therefore investigated the presence of transcripts derived from genes expressed in maternal nucellus tissue surrounding embryo sacs (Chettoor et al, 2014) to evaluate the possibility of contamination. None of the nucellusexpressed genes, including GRMZM2G570791 (a-subunit of DNAdirected RNA polymerase), GRMZM2G125823 (heparanase-like protein), GRMZM2G099420 (cinnamoyl CoA reductase), and GRMZM5G803276 and GRMZM2G336859 (encoding unknown proteins), were detected in any of our data sets.…”

Plant germline formation: common concepts and developmental flexibility in sexual and asexual reproduction

“…Nevertheless, recent methodological advances have allowed the transcriptional profiling of such rare cell types by combining laserassisted microdissection or micromanipulation with microarray and/ or RNA-Seq analyses. These studies have provided novel insights into the transcriptional basis of germline specification and development (Wüest et al, 2010;Schmidt et al, 2011Schmidt et al, , 2012Schmidt et al, , 2014Okada et al, 2013;Wüest et al, 2013;Abiko et al, 2013;Anderson et al, 2013;Chettoor et al, 2014).…”