Confirmation of a Gametophytic Self-Incompatibility in Oryza longistaminata

Natural variation in salt-induced changes in root:shoot ratio reveals SR3G as a negative regulator of root suberization and salt resilience in Arabidopsis

Soil salinity is one of the major threats to agricultural productivity worldwide. Salt stress exposure alters root and shoots growth rates, thereby affecting overall plant performance. While past studies have extensively documented the effect of salt stress on root elongation and shoot development separately, here we take an innovative approach by examining the coordination of root and shoot growth under salt stress conditions. Utilizing a newly developed tool for quantifying the root:shoot ratio in agar-grown Arabidopsis seedlings, we found that salt stress results in a loss of coordination between root and shoot growth rates. We identify a specific gene cluster encoding domain-of-unknown-function 247 (DUF247), and characterize one of these genes as Salt Root:shoot Ratio Regulator Gene (SR3G). Further analysis elucidates the role of SR3G as a negative regulator of salt stress tolerance, revealing its function in regulating shoot growth, root suberization, and sodium accumulation. We further characterize that SR3G expression is modulated by WRKY75 transcription factor, known as a positive regulator of salt stress tolerance. Finally, we show that the salt stress sensitivity of wrky75 mutant is completely diminished when it is combined with sr3g mutation. Together, our results demonstrate that utilizing root:shoot ratio as an architectural feature leads to the discovery of a new stress resilience gene. The study's innovative approach and findings not only contribute to our understanding of plant stress tolerance mechanisms but also open new avenues for genetic and agronomic strategies to enhance crop environmental resilience.

Insight into the Characterization of Two Female Suppressor Gene Families: SOFF and SyGI in Plants

BACKGROUND/OBJECTIVES

The Suppressor of Female Function (SOFF) and Shy Girl (SyGI) gene families play vital roles in sex determination in dioecious plants. However, their evolutionary dynamics and functional characteristics remain largely unexplored.

METHODS

Through this study, a systematic bioinformatics analysis of SOFF and SyGI families was performed in plants to explore their evolutionary relationships, gene structures, motif synteny and functional predictions.

RESULTS

Phylogenetic analysis showed that the SOFF family expanded over time and was divided into two subfamilies and seven groups, while SyGI was a smaller family made of compact molecules with three groups. Synteny analysis revealed that 125 duplicated gene pairs were identified in Kiwifruit where WGD/segmental duplication played a major role in duplicating these events. Structural analysis predicted that SOFF genes have a DUF 247 domain with a transmembrane region, while SyGI sequences have an REC-like conserved domain, with a "barrel-shaped" structure consisting of five α-helices and five β-strands. Promoter region analysis highlighted their probable regulatory roles in plant development, hormone signaling and stress responses. Protein interaction analysis exhibited only four SOFF genes with a close interaction with other genes, while SyGI genes had extensive interactions, particularly with cytokinin signal transduction pathways.

CONCLUSIONS

The current study offers a crucial understanding of the molecular evolution and functional characteristics of SOFF and SyGI gene families, providing a foundation for future functional validation and genetic studies on developmental regulation and sex determination in dioecious plants. Also, this research enhances our insight into plant reproductive biology and offers possible targets for breeding and genetic engineering approaches.

BnaPLDα1-BnaMPK6 Involved in NaCl-Mediated Overcoming of Self-Incompatibility in Brassica napus L

Self-incompatibility (SI) is an important genetic mechanism exploited by numerous angiosperm species to prevent inbreeding. This mechanism has been widely used in the breeding of SI trilinear hybrids of Brassica napus. The SI responses in these hybrids can be overcome by using a salt (NaCl) solution, which is used for seed propagation in SI lines. However, the mechanism underlying the NaCl-induced breakdown of the SI response in B. napus remains unclear. Here, we investigated the role of two key proteins, BnaPLDα1 and BnaMPK6, in the breakdown of SI induced by NaCl. Pollen grain germination and seed set were reduced in BnaPLDα1 triple mutants following incompatible pollination with NaCl treatment. Conversely, SI responses were partially abolished by overexpression of BnaC05.PLDα1 without salt treatment. Furthermore, we observed that phosphatidic acid (PA) produced by BnaPLDα1 bound to B. napus BnaMPK6. The suppression and enhancement of the NaCl-induced breakdown of the SI response in B. napus were observed in BnaMPK6 quadruple mutants and BnaA05.MPK6 overexpression lines, respectively. Moreover, salt-induced stigmatic reactive oxygen species (ROS) accumulation had a minimal effect on the NaCl-induced breakdown of the SI response. In conclusion, our results demonstrate the essential role of the BnaPLDα1-PA-BnaMPK6 pathway in overcoming the SI response to salt treatment in SI B. napus. Additionally, our study provides new insights into the relationship between SI signaling and salt stress response. SIGNIFICANCE STATEMENT: A new molecular mechanism underlying the breakdown of the NaCl-induced self-incompatibility (SI) response in B. napus has been discovered. It involves the induction of BnaPLDα1 expression by NaCl, followed by the activation of BnaMPK6 through the production of phosphatidic acid (PA) by BnaPLDα1. Ultimately, this pathway leads to the breakdown of SI. The involvement of the BnaPLDα1-PA-BnaMPK6 pathway in overcoming the SI response following NaCl treatment provides new insights into the relationship between SI signalling and the response to salt stress.

Spatiotemporal transcriptomic atlas of rhizome formation in Oryza longistaminata

Rhizomes are modified stems that grow underground and produce new individuals genetically identical to the mother plant. Recently, a breakthrough has been made in efforts to convert annual grains into perennial ones by utilizing wild rhizomatous species as donors, yet the developmental biology of this organ is rarely studied. Oryza longistaminata, a wild rice species featuring strong rhizomes, provides a valuable model for exploration of rhizome development. Here, we first assembled a double-haplotype genome of O. longistaminata, which displays a 48-fold improvement in contiguity compared to the previously published assembly. Furthermore, spatiotemporal transcriptomics was performed to obtain the expression profiles of different tissues in O. longistaminata rhizomes and tillers. Two spatially reciprocal cell clusters, the vascular bundle 2 cluster and the parenchyma 2 cluster, were determined to be the primary distinctions between the rhizomes and tillers. We also captured meristem initiation cells in the sunken area of parenchyma located at the base of internodes, which is the starting point for rhizome initiation. Trajectory analysis further indicated that the rhizome is regenerated through de novo generation. Collectively, these analyses revealed a spatiotemporal transcriptional transition underlying the rhizome initiation, providing a valuable resource for future perennial crop breeding.

Comparative stigmatic transcriptomics reveals self and cross pollination responses to heteromorphic incompatibility in Plumbago auriculata Lam

"Heteromorphic self-incompatibility" (HetSI) in plants is a mechanism of defense to avoid self-pollination and promote outcrossing. However, the molecular mechanism underlying HetSI remains largely unknown. In this study, RNA-seq was conducted to explore the molecular mechanisms underlying self-compatible (SC, "T × P" and "P × T") and self-incompatible (SI, "T × T" and "P × P") pollination in the two types of flowers of Plumbago auriculata Lam. which is a representative HetSI plant. By comparing "T × P" vs. "T × T", 3773 (1407 upregulated and 2366 downregulated) differentially expressed genes (DEGs) were identified, 1261 DEGs between "P × T" and "P × P" (502 upregulated and 759 downregulated). The processes in which these DEGs were significantly enriched were "MAPK (Mitogen-Activated Protein Kinases-plant) signaling pathway", "plant-pathogen interaction","plant hormone signal transduction", and "pentose and glucuronate interconversion" pathways. Surprisingly, we discovered that under various pollination conditions, multiple notable genes that may be involved in HetSI exhibited distinct regulation. We can infer that the HetSI strategy might be unique in P. auriculata. It was similar to "sporophytic self-incompatibility" (SSI) but the HetSI mechanisms in pin and thrum flowers are diverse. In this study, new hypotheses and inferences were proposed, which can provide a reference for crop production and breeding.

Molecular insights into self-incompatibility systems: From evolution to breeding

Plants have evolved diverse self-incompatibility (SI) systems for outcrossing. Since Darwin's time, considerable progress has been made toward elucidating this unrivaled reproductive innovation. Recent advances in interdisciplinary studies and applications of biotechnology have given rise to major breakthroughs in understanding the molecular pathways that lead to SI, particularly the strikingly different SI mechanisms that operate in Solanaceae, Papaveraceae, Brassicaceae, and Primulaceae. These best-understood SI systems, together with discoveries in other "nonmodel" SI taxa such as Poaceae, suggest a complex evolutionary trajectory of SI, with multiple independent origins and frequent and irreversible losses. Extensive exploration of self-/nonself-discrimination signaling cascades has revealed a comprehensive catalog of male and female identity genes and modifier factors that control SI. These findings also enable the characterization, validation, and manipulation of SI-related factors for crop improvement, helping to address the challenges associated with development of inbred lines. Here, we review current knowledge about the evolution of SI systems, summarize key achievements in the molecular basis of pollen‒pistil interactions, discuss potential prospects for breeding of SI crops, and raise several unresolved questions that require further investigation.

The triticale mature pollen and stigma proteomes - assembling the proteins for a productive encounter

Triticeae crops are major contributors to global food production and ensuring their capacity to reproduce and generate seeds is critical. However, despite their importance our knowledge of the proteins underlying Triticeae reproduction is severely lacking and this is not only true of pollen and stigma development, but also of their pivotal interaction. When the pollen grain and stigma are brought together they have each accumulated the proteins required for their intended meeting and accordingly studying their mature proteomes is bound to reveal proteins involved in their diverse and complex interactions. Using triticale as a Triticeae representative, gel-free shotgun proteomics was used to identify 11,533 and 2977 mature stigma and pollen proteins respectively. These datasets, by far the largest to date, provide unprecedented insights into the proteins participating in Triticeae pollen and stigma development and interactions. The study of the Triticeae stigma has been particularly neglected. To begin filling this knowledge gap, a developmental iTRAQ analysis was performed revealing 647 proteins displaying differential abundance as the stigma matures in preparation for pollination. An in-depth comparison to an equivalent Brassicaceae analysis divulged both conservation and diversification in the makeup and function of proteins involved in the pollen and stigma encounter. SIGNIFICANCE: Successful pollination brings together the mature pollen and stigma thus initiating an intricate series of molecular processes vital to crop reproduction. In the Triticeae crops (e.g. wheat, barley, rye, triticale) there persists a vast deficit in our knowledge of the proteins involved which needs to be addressed if we are to face the many upcoming challenges to crop production such as those associated with climate change. At maturity, both the pollen and stigma have acquired the protein complement necessary for their forthcoming encounter and investigating their proteomes will inevitably provide unprecedented insights into the proteins enabling their interactions. By combining the analysis of the most comprehensive Triticeae pollen and stigma global proteome datasets to date with developmental iTRAQ investigations, proteins implicated in the different phases of pollen-stigma interaction enabling pollen adhesion, recognition, hydration, germination and tube growth, as well as those underlying stigma development were revealed. Extensive comparisons between equivalent Triticeae and Brassiceae datasets highlighted both the conservation of biological processes in line with the shared goal of activating the pollen grain and promoting pollen tube invasion of the pistil to effect fertilization, as well as the significant distinctions in their proteomes consistent with the considerable differences in their biochemistry, physiology and morphology.

Fine-Mapping and Comparative Genomic Analysis Reveal the Gene Composition at the S and Z Self-incompatibility Loci in Grasses

Self-incompatibility (SI) is a genetic mechanism of hermaphroditic plants to prevent inbreeding after self-pollination. Allogamous Poaceae species exhibit a unique gametophytic SI system controlled by two multi-allelic and independent loci, S and Z. Despite intense research efforts in the last decades, the genes that determine the initial recognition mechanism are yet to be identified. Here, we report the fine-mapping of the Z-locus in perennial ryegrass (Lolium perenne L.) and provide evidence that the pollen and stigma components are determined by two genes encoding DUF247 domain proteins (ZDUF247-I and ZDUF247-II) and the gene sZ, respectively. The pollen and stigma determinants are located side-by-side and were genetically linked in 10,245 individuals of two independent mapping populations segregating for Z. Moreover, they exhibited high allelic diversity as well as tissue-specific gene expression, matching the expected characteristics of SI determinants known from other systems. Revisiting the S-locus using the latest high-quality whole-genome assemblies revealed a similar gene composition and structure as found for Z, supporting the hypothesis of a duplicated origin of the two-locus SI system of grasses. Ultimately, comparative genomic analyses across a wide range of self-compatible and self-incompatible Poaceae species revealed that the absence of a functional copy of at least one of the six putative SI determinants is accompanied by a self-compatible phenotype. Our study provides new insights into the origin and evolution of the unique gametophytic SI system in one of the largest and economically most important plant families.

Identification of the genes at S and Z reveals the molecular basis and evolution of grass self-incompatibility

Self-incompatibility (SI) is a feature of many flowering plants, whereby self-pollen is recognized and rejected by the stigma. In grasses (Poaceae), the genes controlling this phenomenon have not been fully elucidated. Grasses have a unique two-locus system, in which two independent genetic loci (S and Z) control self-recognition. S and Z are thought to have arisen from an ancient duplication, common to all grasses. With new chromosome-scale genome data, we examined the genes present at S- and Z-loci, firstly in ryegrass (Lolium perenne), and subsequently in ~20 other grass species. We found that two DUF247 genes and a short unstructured protein (SP/ZP) were present at both S- and Z- in all SI species, while in self-compatible species these genes were often lost or mutated. Expression data suggested that DUF247 genes acted as the male components and SP/ZP were the female components. Consistent with their role in distinguishing self- from non-self, all genes were hypervariable, although key secondary structure features were conserved, including the predicted N-terminal cleavage site of SP/ZP. The evolutionary history of these genes was probed, revealing that specificity groups at the Z-locus arose before the advent of various grass subfamilies/species, while specificity groups at the S-locus arose after the split of Panicoideae, Chloridoideae, Oryzoideae and Pooideae. Finally, we propose a model explaining how the proteins encoded at the S and Z loci might function to specify self-incompatibility.

Genetic control of compatibility in crosses between wheat and its wild or cultivated relatives

In the recent years, the agricultural world has been progressing towards integrated crop protection, in the context of sustainable and reasoned agriculture to improve food security and quality, and to preserve the environment through reduced uses of water, pesticides, fungicides or fertilisers. For this purpose, one possible issue is to cross-elite varieties widely used in fields for crop productions with exotic or wild genetic resources in order to introduce new diversity for genes or alleles of agronomical interest to accelerate the development of new improved cultivars. However, crossing ability (or crossability) often depends on genetic background of the recipient varieties or of the donor, which hampers a larger use of wild resources in breeding programmes of many crops. In this review, we tried to provide a comprehensive summary of genetic factors controlling crossing ability between Triticeae species with a special focus on the crossability between wheat (Triticum aestivum L.) and rye (Secale cereale), which lead to the creation of Triticale (x Triticosecale Wittm.). We also discussed potential applications of newly identified genes or markers associated with crossability for accelerating wheat and Triticale improvement by application of modern genomics technologies in breeding programmes.