Natural Variation in Epigenetic Pathways Affects the Specification of Female Gamete Precursors in Arabidopsis

Abstract

In angiosperms, the transition to the female gametophytic phase relies on the specification of premeiotic gamete precursors from sporophytic cells in the ovule. In Arabidopsis thaliana, a single diploid cell is specified as the premeiotic female gamete precursor. Here, we show that ecotypes of Arabidopsis exhibit differences in megasporogenesis leading to phenotypes reminiscent of defects in dominant mutations that epigenetically affect the specification of female gamete precursors. Intraspecific hybridization and polyploidy exacerbate these defects, which segregate quantitatively in F2 populations derived from ecotypic hybrids, suggesting that multiple loci control cell specification at the onset of female meiosis. This variation in cell differentiation is influenced by the activity of ARGONAUTE9 (AGO9) and RNA-DEPENDENT RNA POLYMERASE6 (RDR6), two genes involved in epigenetic silencing that control the specification of female gamete precursors. The pattern of transcriptional regulation and localization of AGO9 varies among ecotypes, and abnormal gamete precursors in ovules defective for RDR6 share identity with ectopic gamete precursors found in selected ecotypes. Our results indicate that differences in the epigenetic control of cell specification lead to natural phenotypic variation during megasporogenesis. We propose that this mechanism could be implicated in the emergence and evolution of the reproductive alternatives that prevail in flowering plants.

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

“…Among the latter, our analysis confirmed the previously reported strong effect of CMT2 itself on CMT2-dependent mCHH (Dubin et al, 2015), but the top SNP here is considerably closer to the gene (chr4:10,422,486, 1.2 kb downstream of CMT2 , −log10 p = 7.88). Another striking candidate was ARGONAUTE 9 ( AGO9 ), which is involved in siRNA silencing, and for which natural variants have been connected to differences in epigenetic control of cell specification (Rodriguez-Leal et al, 2015). Interestingly, AGO9 appears to be associated both with RdDM- and CMT2-dependent mCHH, although the SNPs associated differ, suggesting that different alleles are involved.…”

A Multigenic Network of ARGONAUTE4 Clade Members Controls Early Megaspore Formation in Arabidopsis

“…For this type of ovule, we defined three phenotypic classes based on the number of enlarged subepidermal cells reminiscent of gametophytic precursors corresponding to the MMC: class I includes ovules with a single gametophytic precursor, which by its subepidermal position corresponds to the MMC (Figure 1, A and B); class II corresponds to premeiotic ovules with two gametophytic precursors resembling twin MMCs (Figure 1C); and class III corresponds to premeiotic ovules containing more than two cells resembling the MMC (Figure 1, D and E). Under greenhouse conditions, 9.8% ( n = 934) and 17.2% ( n = 429) of Col and L er ovules showed two MMCs, respectively (Table 1), confirming that Arabidopsis ecotypes exhibit naturally occurring variation in the number of ovules with ectopic gametophytic precursors (Rodríguez-Leal et al 2015). In contrast to wild type, ago9-3 behaved as a dominant mutation showing 20.68% ± 2.18 ( n = 385) and 28.93% ± 3.36 ( n = 508) class II and class III ovules in heterozygous and homozygous mutant individuals, respectively.…”

“…To elucidate if close relatives of AGO9 could have a role in the somatic-to-reproductive transition, we cytologically characterized early ovule development in mutant plants defective in AGO4 , AGO6 , and AGO8 . We started by conducting a quantitative characterization of stage 1 ovules following the classification reported by Rodríguez-Leal et al (Rodríguez-Leal et al 2015). Stage 1 corresponds to premeiotic ovule primordia having a well-defined proximal-distal axis and absence of integument initiation.…”

“…Interestingly, the complete loss of function of these genes can result in the absence of a mutant phenotype, as compared to wild-type plants; however, our results also suggest that suppression of this mutant phenotype is dependent on the ago4 allelic variants tested and their genetic backgrounds, likely contributing to the compensatory phenomenon revealed by genetic interactions among members of the AGO4 clade. Recent reports showed that different ecotypes of Arabidopsis exhibit equivalent phenotypes at variable frequencies, and that interecotypic hybridization exacerbates the frequency of supernumerary gametophytic precursors, suggesting that multiple loci control cell specification at the onset of female meiosis (Rodríguez-Leal et al 2015). …”

Genome-wide transcriptome analysis of female-sterile rice ovule shed light on its abortive mechanism

“…Argonaute (AGO) proteins are vital components of the RNA-induced silencing complex (RISC). They are associated with epigenetic silencing (Zilberman et al 2004) and could control female gamete formation (Olmedo-Monfil et al 2010;Rodriguez-Leal et al 2015). In Arabidopsis, AGO5 is expressed in somatic cells.…”