Transcriptomic Analysis Reveals a Comprehensive Calcium- and Phytohormone-Dominated Signaling Response in Leymus chinensis Self-Incompatibility

Carboxylic acid accumulation and secretion contribute to the alkali-stress tolerance of halophyte Leymus chinensis

Leymus chinensis is a dominant halophytic grass in alkalized grasslands of Northeast China. To explore the alkali-tolerance mechanism of L. chinensis, we applied a widely targeted metabolomic approach to analyze metabolic responses of its root exudates, root tissues and leaves under alkali-stress conditions. L. chinensis extensively secreted organic acids, phenolic acids, free fatty acids and other substances having -COOH or phosphate groups when grown under alkali-stress conditions. The buffering capacity of these secreted substances promoted pH regulation in the rhizosphere during responses to alkali stress. L. chinensis leaves exhibited enhanced accumulations of free fatty acids, lipids, amino acids, organic acids, phenolic acids and alkaloids, which play important roles in maintaining cell membrane stability, regulating osmotic pressure and providing substrates for the alkali-stress responses of roots. The accumulations of numerous flavonoids, saccharides and alcohols were extensively enhanced in the roots of L. chinensis, but rarely enhanced in the leaves, under alkali-stress conditions. Enhanced accumulations of flavonoids, saccharides and alcohols increased the removal of reactive oxygen species and alleviated oxygen damage caused by alkali stress. In this study, we revealed the metabolic response mechanisms of L. chinensis under alkali-stress conditions, emphasizing important roles for the accumulation and secretion of organic acids, amino acids, fatty acids and other substances in alkali tolerance.

The effect of modifier and a water-soluble fertilizer on two forages grown in saline-alkaline soil

Saline-alkali soil significantly impairs crop growth. This research employs the impacts of the modifier and water-soluble fertilizer, as well as their interaction, on the root systems of alfalfa and leymus chinensis in saline-alkali soil. The results exhibit that the hydrochar source modifier effectively enhances the root growth of both forage species. There are certain improvements in the root growth indicators of both crops at a dosage of 20 g/kg. Root enzyme activity and rhizosphere soil enzyme activity are enhanced in alfalfa, showing significant improvements in the first planting compared to the second planting. The application of water-soluble fertilizers also promotes root growth and root dehydrogenase activity. The root dehydrogenase activity of alfalfa and leymus chinensis are enhanced 62.18% and 10.15% in first planting than that of blank, respectively. Additionally, the two-factor variance analysis revealed a correlation between rhizosphere soil enzyme activity and changes in root traits. Higher rhizosphere soil enzyme activity is observed in conjunction with better root growth. The combined application of a modifier and water-soluble fertilizer has demonstrated a significant interaction effect on various aspects of the first planting of alfalfa and leymus chinensis. Moreover, the combined application of the modifier and water-soluble fertilizer has yielded superior results when compared to the individual application of either the modifier or the water-soluble fertilizer alone. This combined approach has proven effective in improving saline-alkali soil conditions and promoting crop growth in such challenging environments.

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.

Comparative physiochemical and transcriptomic analysis reveals the influences of cross-pollination on ovary and fruit development in pummelo (Citrus maxima)

'Shuijingmiyou' pummelo (SJ), one of the most popular fruits in Yunnan province of China, is of relatively low fruit shape (FS) quality. In this study, we compared the FS promoting effects of cross pollinations using pollens from seven pummelo varieties, and found that 'Guanximiyou' pummelo (GX) cross-pollination showed the best FS promoting effects on SJ fruits by shortening its fruit neck. To explore the underlying mechanism, physiochemical and transcriptomic differences between self- and cross-pollinated SJ ovaries (SJO and GXO) were investigated. Higher salicylic acid, gibberellin and indole acetic acid contents and superoxide dismutase, peroxidase and catalase activities, and lower polyphenol oxidase activity were determined in GXO compared with SJO. Enrichment analysis of the identified 578 differentially expressed genes (123 up-regulated and 455 down-regulated) in GXO showed that genes involved in solute transport, RNA biosynthesis, phytohormone action and cell wall organization were significantly enriched. The results obtained in this study will be helpful in understanding the influences of cross-pollination on pummelo ovary and fruit development, and can provide the basis for clarifying the underlying mechanism of cross-pollination improved fruit quality.

Genome evolution and initial breeding of the Triticeae grass Leymus chinensis dominating the Eurasian Steppe

Leymus chinensis, a dominant perennial grass in the Eurasian Steppe, is well known for its remarkable adaptability and forage quality. Hardly any breeding has been done on the grass, limiting its potential in ecological restoration and forage productivity. To enable genetic improvement of the untapped, important species, we obtained a 7.85-Gb high-quality genome of L. chinensis with a particularly long contig N50 (318.49 Mb). Its allotetraploid genome is estimated to originate 5.29 million years ago (MYA) from a cross between the Ns-subgenome relating to Psathyrostachys and the unknown Xm-subgenome. Multiple bursts of transposons during 0.433-1.842 MYA after genome allopolyploidization, which involved predominantly the Tekay and Angela of LTR retrotransposons, contributed to its genome expansion and complexity. With the genome resource available, we successfully developed a genetic transformation system as well as the gene-editing pipeline in L. chinensis. We knocked out the monocot-specific miR528 using CRISPR/Cas9, resulting in the improvement of yield-related traits with increases in the tiller number and growth rate. Our research provides valuable genomic resources for Triticeae evolutionary studies and presents a conceptual framework illustrating the utilization of genomic information and genome editing to accelerate the improvement of wild L. chinensis with features such as polyploidization and self-incompatibility.

Comparison of two contrasting Leymus chinensis accessions reveals the roles of the cell wall and auxin in rhizome development

Leymus chinensis, a perennial native forage grass, is widely distributed in the steppes of Inner Mongolia as the dominant species. The main reproductive strategy of this grass is clonal propagation, which occurs via the proliferation of subterranean horizontal stems known as rhizomes. To elucidate the mechanism underlying rhizome development in this grass, we collected 60 accessions of L. chinensis and evaluated their rhizome development. One accession, which we named SR-74 (Strong Rhizomes), had significantly better rhizome development capacity than the accession WR-16 (Weak Rhizomes) in terms of rhizome number, total and primary rhizome length, and number of rhizome seedlings. Rhizome elongation was positively correlated with the number of internodes in the rhizome, which affected plant biomass. Compared to WR-16, SR-74 had higher rhizome tip hardness, higher abundance of transcripts participating in the biosynthesis of cell wall components, and higher levels of the metabolites L-phenylalanine, trans-cinnamic acid, 3-coumaric acid, ferulic acid, and coniferin. These metabolites in the phenylpropanoid biosynthesis pathway are precursors of lignin. In addition, SR-74 rhizomes contained higher amounts of auxin and auxin metabolites, including L-Trp, IPA, IBA, IAA and IAA-Asp, as well as upregulated expression of the auxin biosynthesis and signaling genes YUCCA6, YUCCA8, YUCCA10, YUCCA11, PIN1, PIN2, UGT1, UGT2, UGT4, UGT10, GH3, IAA7, IAA23, and IAA30. We propose a network between auxin signaling and the cell wall underlying rhizome development in L. chinensis.

Hormonal Signaling during dPCD: Cytokinin as the Determinant of RNase-Based Self-Incompatibility in Solanaceae

Research into molecular mechanisms of self-incompatibility (SI) in plants can be observed in representatives of various families, including Solanaceae. Earlier studies of the mechanisms of S-RNase-based SI in petunia (Petunia hybrida E. Vilm.) demonstrate that programmed cell death (PCD) is an SI factor. These studies suggest that the phytohormon cytokinin (CK) is putative activator of caspase-like proteases (CLPs). In this work, data confirming this hypothesis were obtained in two model objects-petunia and tomato (six Solanaceae representatives). The exogenous zeatin treatment of tomato and petunia stigmas before a compatible pollination activates CLPs in the pollen tubes in vivo, as shown via the intravital imaging of CLP activities. CK at any concentration slows down the germination and growth of petunia and tomato male gametophytes both in vitro and in vivo; shifts the pH of the cytoplasm (PHc) to the acid region, thereby creating the optimal conditions for CLP to function and inhibiting the F-actin formation and/or destructing the cytoskeleton in pollen tubes to point foci during SI-induced PCD; and accumulates in style tissues during SI response. The activity of the ISOPENTENYLTRANSFERASE 5 (IPT5) gene at this moment exceeds its activity in a cross-compatible pollination, and the levels of expression of the CKX1 and CKX2 genes (CK OXIDASE/DEHYDROGENASE) are significantly lower in self-incompatible pollination. All this suggests that CK plays a decisive role in the mechanism underlying SI-induced PCD.

Stigmatic Transcriptome Analysis of Self-Incompatible and Compatible Pollination in Corylus heterophylla Fisch. × Corylus avellana L

Self-incompatibility (SI) protects plants from inbreeding depression due to self-pollination and promotes the outcrossing process to maintain a high degree of heterozygosity during evolution. Corylus is an important woody oil and nut species that shows sporophytic SI (SSI). Yet the molecular mechanism of SI in Corylus remains largely unknown. Here we conducted self- ("Dawei" × "Dawei") and cross-pollination ("Dawei" × "Liaozhen No. 7") experiments and then performed an RNA-Seq analysis to investigate the mechanism of pollen-stigma interactions and identify those genes that may be responsible for SSI in Corylus. We uncovered 19,163 up- and 13,314 downregulated genes from the comparison of different pollination treatments. These differentially expressed genes (DEGs) were significantly enriched in plant-pathogen interaction, plant hormone signal transduction, and MAPK signaling pathway-plant. We found many notable genes potentially involved in pollen-stigma interactions and SSI mechanisms, including genes encoding receptor-like protein kinases (RLK), calcium-related genes, disease-resistance genes, and WRKY transcription factors. Four upregulated and five downregulated DEGs were consistently identified in those comparison groups involving self-incompatible pollination, suggesting they had important roles in pollen-pistil interactions. We further identified the S-locus region of the Corylus heterophylla genome based on molecular marker location. This predicted S-locus contains 38 genes, of which 8 share the same functional annotation as the S-locus genes of Corylus avellana: two PIX7 homologous genes (EVM0002129 and EVM0025536), three MIK2 homologous genes (EVM0002422, EVM0005666, and EVM0009820), one aldose 1-epimerase (EVM0002095), one 3-dehydroquinate synthase II (EVM0021283), and one At3g28850 homologous gene (EVM0016149). By characterizing the pistil process during the early postpollination phase via transcriptomic analysis, this study provides new knowledge and lays the foundation for subsequent analyses of pollen-pistil interactions.

Genetic structure in patchy populations of a candidate foundation plant: a case study of Leymus chinensis using genetic and clonal diversity

PREMISE

The distribution of genetic diversity on the landscape has critical ecological and evolutionary implications. This may be especially the case on a local scale for foundation plant species because they create and define ecological communities, contributing disproportionately to ecosystem function.

METHODS

We examined the distribution of genetic diversity and clones, which we defined first as unique multilocus genotypes (MLG), and then by grouping similar MLGs into multilocus lineages. We used 186 markers from inter-simple sequence repeats (ISSR) across 358 ramets from 13 patches of the foundation grass Leymus chinensis. We examined the relationship between genetic and clonal diversities, their variation with patch size, and the effect of the number of markers used to evaluate genetic diversity and structure in this species.

RESULTS

Every ramet had a unique MLG. Almost all patches consisted of individuals belonging to a single multilocus lineages. We confirmed this with a clustering algorithm to group related genotypes. The predominance of a single lineage within each patch could be the result of the accumulation of somatic mutations, limited dispersal, some sexual reproduction with partners mainly restricted to the same patch, or a combination of all three.

CONCLUSIONS

We found strong genetic structure among patches of L. chinensis. Consistent with previous work on the species, the clustering of similar genotypes within patches suggests that clonal reproduction combined with somatic mutation, limited dispersal, and some degree of sexual reproduction among neighbors causes individuals within a patch to be more closely related than among patches.

Identification of Candidate Genes for Self-Compatibility in Perennial Ryegrass (Lolium perenne L.)

Self-incompatibility (SI) is a genetic mechanism preventing self-pollination in ~40% of plant species. Two multiallelic loci, called S and Z, control the gametophytic SI system of the grass family (Poaceae), which contains all major forage grasses. Loci independent from S and Z have been reported to disrupt SI and lead to self-compatibility (SC). A locus causing SC in perennial ryegrass (Lolium perenne L.) was previously mapped on linkage group (LG) 5 in an F2 population segregating for SC. Using a subset of the same population (n = 68), we first performed low-resolution quantitative trait locus (QTL) mapping to exclude the presence of additional, previously undetected contributors to SC. The previously reported QTL on LG 5 explained 38.4% of the phenotypic variation, and no significant contribution from other genomic regions was found. This was verified by the presence of significantly distorted markers in the region overlapping with the QTL. Second, we fine mapped the QTL to 0.26 centimorgan (cM) using additional 2,056 plants and 23 novel sequence-based markers. Using Italian ryegrass (Lolium multiflorum Lam.) genome assembly as a reference, the markers flanking SC were estimated to span a ~3 Mb region encoding for 57 predicted genes. Among these, seven genes were proposed as relevant candidate genes based on their annotation and function described in previous studies. Our study is a step forward to identify SC genes in forage grasses and provides diagnostic markers for marker-assisted introgression of SC into elite germplasm.

Characterization and practical use of self-compatibility in outcrossing grass species

BACKGROUND

Self-incompatibility (SI) systems prevent self-fertilization in several species of Poaceae, many of which are economically important forage, bioenergy and turf grasses. Self-incompatibility ensures cross-pollination and genetic diversity but restricts the ability to fix useful genetic variation. In most inbred crops it is possible to develop high-performing homozygous parental lines by self-pollination, which then enables the creation of F1 hybrid varieties with higher performance, a phenomenon known as heterosis. The inability to fully exploit heterosis in outcrossing grasses is partially responsible for lower levels of improvement in breeding programmes compared with inbred crops. However, SI can be overcome in forage grasses to create self-compatible populations. This is generating interest in understanding the genetical basis of self-compatibility (SC), its significance for reproductive strategies and its exploitation for crop improvement, especially in the context of F1 hybrid breeding.

SCOPE

We review the literature on SI and SC in outcrossing grass species. We review the currently available genomic tools and approaches used to discover and characterize novel SC sources. We discuss opportunities barely explored for outcrossing grasses that SC facilitates. Specifically, we discuss strategies for wide SC introgression in the context of the Lolium-Festuca complex and the use of SC to develop immortalized mapping populations for the dissection of a wide range of agronomically important traits. The germplasm available is a valuable practical resource and will aid understanding the basis of inbreeding depression and hybrid vigour in key temperate forage grass species.

CONCLUSIONS

A better understanding of the genetic control of additional SC loci offers new insight into SI systems, their evolutionary origins and their reproductive significance. Heterozygous outcrossing grass species that can be readily selfed facilitate studies of heterosis. Moreover, SC introduction into a range of grass species will enable heterosis to be exploited in innovative ways in genetic improvement programmes.

Caspase-like proteases and the phytohormone cytokinin as determinants of S-RNAse-based self-incompatibility-induced PCD in Petunia hybrida L

S-RNAse-based self-incompatibility (SI) in petunia (Petunia hybrida L.) is a self-/non-self-recognition system underlying the pistil rejection of self-pollen. Using different methods, including a TUNEL assay, we have recently shown that programmed cell death (PCD) is a factor of the SI in petunia. Here, we show that the growth of self-incompatible pollen tubes in the style tissues during 4 h after pollination is accompanied by five-sixfold increase in a caspase-like protease (CLP) activity. Exogenous cytokinin (CK) inhibits the pollen tube growth and stimulates the CLP activity in compatible pollen tubes. The actin depolymerization with latrunculin B induces a sharp drop in the CLP activity in self-incompatible pollen tubes and its increase in compatible pollen tubes. Altogether, our results suggest that a CLP is involved in the SI-induced PCD and that CK is a putative activator of the CLP. We assume that CK provokes acidification of the cytosol and thus promotes the activation of a CLP. Thus, our results suggest that CK and CLP are involved in the S-RNAse-based SI-induced PCD in petunia. Potential relations between these components in PCD signaling are discussed.

A Leymus chinensis histidine-rich Ca2+-binding protein binds Ca2+/Zn2+ and suppresses abscisic acid signaling in Arabidopsis

Intracellular Ca²⁺ plays an essential role in plant cellular sensing of various environmental stress signals by modulating the activity of Ca²⁺-binding proteins. Leymus chinensis is a dominant forage grass widely distributed in the Eurasian Steppe that is well adapted to drought and salty soils common in the region. Through transcript profiling of L. chinensis roots, we identified a transcript predicted to encode histidine-rich calcium-binding protein (HRC), a protein recently characterized in wheat. L. chinensis HRC (LcH RC) localized in the nucleus, as demonstrated using a transient gene expression method that we developed for this species. Different regions of LcHRC showed affinity for either Ca²⁺ or Zn²⁺, but not Mg²⁺ and Mn²⁺. Arabidopsis thaliana seedlings heterologously overexpressing LcHRC showed greater sensitivity to abscisic acid (ABA), along with decreased expression of some ABA-induced marker genes, but no increase in ABA content. Screening a Arabidopsis cDNA yeast library identified a Tudor/PWWP/MBT-domain-containing protein (AtPWWP3) that interacts with LcHRC. AtPWWP3 also localized in the nucleus and is predicted to mediate gene expression by modifying histone deacetylation. Based on these results, we propose a functional model of LcHRC action.