Differences in meristem size and expression of branching genes are associated with variation in panicle phenotype in wild and domesticated African rice

Spatial expression patterns of panicle-related genes are conserved between the two African rice species

This study was based on the assumption that orthologous genes have a conserved function in African rice species compared to O. sativa. This assumption was supported by the fact that there are no non-synonymous changes in orthologous genes between the two species. Moreover, we observed that the spatial expression patterns of the panicle-related genes tested in this study were similar in O. glaberrima and O. barthii.

The O. sativa SPL14 and LAX1 genes and their orthologs in the two African rice species (our study) and in maize (TASSELSHEATH4 and BARREN STALK1, respectively) are expressed at the adaxial boundary adjacent to all branch meristems [25, 37, 39–42]. The O. sativa miR156/miR529/SPL14 regulatory pathway was shown to be involved in the control of panicle branching, notably through the regulation of LAX1 gene expression, which is also reported to be involved in axillary meristem initiation [19, 24, 25, 39–41]. In situ hybridization analysis of SPL14 gene and miRNA expression patterns in the two African rice species revealed that their expression patterns either did not overlap or only overlapped partially: miR529 and miR156 were detected in the center but not in the flank of branch meristems where SPL14 mRNAs were accumulated (Fig. 5). These spatially separated expression domains suggest a regulatory mechanism based on spatial restriction or mutual exclusion rather than on dampening regulation [43]. In other species, separated patterns were observed for miR156 and SPL14-like genes in Arabidopsis thaliana (SPL9 gene) and in O. sativa during the vegetative phase albeit with slight differences, with SPL14-like gene transcripts observed along with miR156 accumulation in both the shoot apical meristem and in leaf primordia [44–46]. This suggests a similar microRNA-dependent regulatory mechanism of SPL gene expression, irrespective of the type of microRNA and of the developmental context. However, the spatial expression of SPL9 was not affected in A. thaliana se1 and ago1–27 mutants, which have reduced miR156 accumulation, suggesting that miR156 is not the main regulator of SPL9 spatial accumulation in leaf primordia [44].

The O. sativa APO2/RFL gene, orthologous to the eudicot floral promoting gene LEAFY (LFY) [14], and the TAW1 gene belonging to the small ALOG (Arabidopsis LSH1 and Oryza G1) gene family have been described as negative regulators of the transition to spikelet meristem fate [32, 34, 35]. However, based on their expression patterns and mutant phenotypes, it would be more accurate to consider these two genes as promoting factors of indeterminate meristematic activity in grass inflorescences. The delay of spikelet meristem specification in the loss of function mutant background may be considered as a consequence of an alteration of branch meristem functioning. In the present study, transcripts of the African rice species orthologs of O. sativa APO2/RFL and TAW1 were detected in both branch and spikelet meristems. The APO2 ortholog expression pattern observed in our study is similar to the one described by [32] in O. sativa. Similarly, a recent analysis of gene expression profiling of reproductive meristem types in early rice inflorescences by laser microdissection has shown that the APO2/RFL gene is expressed in spikelet meristems [47]. The TAW1 ortholog expression pattern observed in the two African rice species differed from the pattern reported in O. sativa [35, 47], in which transcripts were detected only in branch meristems and not in spikelet meristems. However, the expression level of the O. barthii and O. glaberrima TAW1 orthologs is still lower in spikelet than in branch meristems (Additional file 6). This suggests that partial divergence of function might have occurred between TAW1 orthologs genes in Asian and African rice species.

In contrast to the aforementioned genes, the O. sativa spikelet-promoting LHS1/OsMADS1 gene, along with its African rice orthologs, is only expressed in the spikelet meristems ([20, 38]; this study). The maize LHS1 orthologs ZMM8 and ZMM14 are expressed only in the upper floret, and within floral organs of certain sampled taxa, indicating that these genes are involved in the determinacy of the spikelet meristem and in the distinction of upper florets and lower florets in maize inflorescences [48]. In addition, the wheat LHS1 ortholog (WLHS1) is also expressed slightly differently from rice LHS1, the transcript of WLHS1 accumulating at high levels in floret organs (i.e., lemma, palea, pistil, glume) [49]. The LHS1-like SEPALLATA (SEP) genes have been linked with the origin and diversification of the grass spikelet [50].

Overall, we observed a strict conservation of the spatial expression domains of these genes between O. glaberrima and O. barthii, indicating that the spatial regulation of these genes was not affected during African rice domestication. In addition, an extension of the expression domain of TAW1 orthologs to spikelets and floret meristems was observed compared to O. sativa, suggesting an extension of the functional domain of TAW1 orthologs in African rice.