Genome-wide association study for seedling heat tolerance under two temperature conditions in bread wheat (Triticum aestivum L.).

BACKGROUND: As the greenhouse effect intensifies, global temperatures are steadily increasing, posing a challenge to bread wheat (Triticum aestivum L.) production. It is imperative to comprehend the mechanism of high temperature tolerance in wheat and implement breeding programs to identify and develop heat-tolerant wheat germplasm and cultivars. RESULTS: To identify quantitative trait loci (QTL) related to heat stress tolerance (HST) at seedling stage in wheat, a panel of 253 wheat accessions which were re-sequenced used to conduct genome-wide association studies (GWAS) using the factored spectrally transformed linear mixed models (FaST-LMM). For most accessions, the growth of seedlings was found to be inhibited under heat stress. Analysis of the phenotypic data revealed that under heat stress conditions, the main root length, total root length, and shoot length of seedlings decreased by 47.46%, 49.29%, and 15.19%, respectively, compared to those in normal conditions. However, 17 varieties were identified as heat stress tolerant germplasm. Through GWAS analysis, a total of 115 QTLs were detected under both heat stress and normal conditions. Furthermore, 15 stable QTL-clusters associated with heat response were identified. By combining gene expression, haplotype analysis, and gene annotation information within the physical intervals of the 15 QTL-clusters, two novel candidate genes, TraesCS4B03G0152700/TaWRKY74-B and TraesCS4B03G0501400/TaSnRK3.15-B, were responsive to temperature and identified as potential regulators of HST in wheat at the seedling stage. CONCLUSIONS: This study conducted a detailed genetic analysis and successfully identified two genes potentially associated with HST in wheat at the seedling stage, laying a foundation to further dissect the regulatory mechanism underlying HST in wheat under high temperature conditions. Our finding could serve as genomic landmarks for wheat breeding aimed at improving adaptation to heat stress in the face of climate change.

Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat.

Spike architecture influences both grain weight and grain number per spike, which are the two major components of grain yield in bread wheat (Triticum aestivum L.). However, the complex wheat genome and the influence of various environmental factors pose challenges in mapping the causal genes that affect spike traits. Here, we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in wheat. We identified 170 loci that are responsible for variations in spike length, spikelet number per spike, and grain number per spike through genome-wide association study and meta-QTL analyses. We constructed gene regulatory networks for young inflorescences at the double ridge stage and the floret primordium stage, in which the spikelet meristem and the floret meristem are predominant, respectively, by integrating transcriptome, histone modification, chromatin accessibility, eQTL, and protein-protein interactome data. From these networks, we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike traits. The functions of TaZF-B1, VRT-B2, and TaSPL15-A/D in establishment of wheat spike architecture were verified. This study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.

Wheat ESCRT-III protein TaSAL1 regulates male gametophyte transmission and controls tillering and heading date.

Charged multivesicular protein 1 (CHMP1) is a member of the endosomal sorting complex required for transport-III (ESCRT-III) complex that targets membrane localized signaling receptors to intralumenal vesicles in the multivesicular body of the endosome and eventually to the lysosome for degradation. Although CHMP1 plays roles in various plant growth and development processes, little is known about its function in wheat. In this study, we systematically analysed the members of the ESCRT-III complex in wheat (Triticum aestivum) and found that their orthologs were highly conserved in eukaryotic evolution. We identified CHMP1 homologous genes, TaSAL1s, and found that they were constitutively expressed in wheat tissues and essential for plant reproduction. Subcellular localization assays showed these proteins aggregated with and closely associated with the endoplasmic reticulum when ectopically expressed in tobacco leaves. We also found these proteins were toxic and caused leaf death. A genetic and reciprocal cross analysis revealed that TaSAL1 leads to defects in male gametophyte biogenesis. Moreover, phenotypic and metabolomic analysis showed that TaSAL1 may regulate tillering and heading date through phytohormone pathways. Overall, our results highlight the role of CHMP1 in wheat, particularly in male gametophyte biogenesis, with implications for improving plant growth and developing new strategies for plant breeding and genetic engineering.

Chemical-tag-based semi-annotated metabolomics facilitates gene identification and specialized metabolic pathway elucidation in wheat.

The importance of metabolite modification and species-specific metabolic pathways has long been recognized. However, linking the chemical structure of metabolites to gene function in order to explore the genetic and biochemical basis of metabolism has not yet been reported in wheat (Triticum aestivum). Here, we profiled metabolic fragment enrichment in wheat leaves and consequently applied chemical-tag-based semi-annotated metabolomics in a genome-wide association study in accessions of wheat. The studies revealed that all 1,483 quantified metabolites have at least one known functional group whose modification is tailored in an enzyme-catalyzed manner and eventually allows efficient candidate gene mining. A Triticeae crop-specific flavonoid pathway and its underlying metabolic gene cluster were elucidated in further functional studies. Additionally, upon overexpressing the major effect gene of the cluster TraesCS2B01G460000 (TaOMT24), the pathway was reconstructed in rice (Oryza sativa), which lacks this pathway. The reported workflow represents an efficient and unbiased approach for gene mining using forward genetics in hexaploid wheat. The resultant candidate gene list contains vast molecular resources for decoding the genetic architecture of complex traits and identifying valuable breeding targets and will ultimately aid in achieving wheat crop improvement.

TaSPL17s act redundantly with TaSPL14s to control spike development and their elite haplotypes may improve wheat grain yield.

Wheat is a staple crop for the world's population, and there is constant pressure to improve grain yield, which is largely determined by plant architecture. SQUAMOSA promotor-binding protein-like (SPL) genes have been widely studied in rice, including their effects on plant architecture, grain development, and grain yield. However, the function of SPL homologous genes in wheat has not been well investigated. In this study, TaSPL14s and TaSPL17s, wheat's closest orthologous of OsSPL14, were functionally investigated using gene-editing assays, revealing that these genes redundantly influence plant height, tiller number, spike length, and thousand-grain weight (TGW). Bract outgrowth was frequently observed in the hexa-mutant, occasionally in the quintuple mutant but never in the wild type. Transcriptome analysis revealed that the expression of many spike development-associated genes was altered in taspl14taspl17 hexa-mutants compared to that in the wild type. In addition, we analyzed the sequence polymorphisms of TaSPL14s and TaSPL17s among wheat germplasm and found superior haplotypes of TaSPL17-A and TaSPL17-D with significantly higher TGW, which had been positively selected during wheat breeding. Accordingly, dCAPS and KASP markers were developed for TaSPL17-A and TaSPL17-D, respectively, providing a novel insight for molecular marker-assisted breeding in wheat. Overall, our results highlight the role of TaSPLs in regulating plant architecture and their potential application for wheat grain yield improvement through molecular breeding.

Cloning of the wheat leaf rust resistance gene Lr47 introgressed from Aegilops speltoides.

Leaf rust, caused by Puccinia triticina Eriksson (Pt), is one of the most severe foliar diseases of wheat. Breeding for leaf rust resistance is a practical and sustainable method to control this devastating disease. Here, we report the identification of Lr47, a broadly effective leaf rust resistance gene introgressed into wheat from Aegilops speltoides. Lr47 encodes a coiled-coil nucleotide-binding leucine-rich repeat protein that is both necessary and sufficient to confer Pt resistance, as demonstrated by loss-of-function mutations and transgenic complementation. Lr47 introgression lines with no or reduced linkage drag are generated using the Pairing homoeologous1 mutation, and a diagnostic molecular marker for Lr47 is developed. The coiled-coil domain of the Lr47 protein is unable to induce cell death, nor does it have self-protein interaction. The cloning of Lr47 expands the number of leaf rust resistance genes that can be incorporated into multigene transgenic cassettes to control this devastating disease.

Centromere Plasticity With Evolutionary Conservation and Divergence Uncovered by Wheat 10+ Genomes.

Centromeres (CEN) are the chromosomal regions that play a crucial role in maintaining genomic stability. The underlying highly repetitive DNA sequences can evolve quickly in most eukaryotes, and promote karyotype evolution. Despite their variability, it is not fully understood how these widely variable sequences ensure the homeostasis of centromere function. In this study, we investigated the genetics and epigenetics of CEN in a population of wheat lines from global breeding programs. We captured a high degree of sequences, positioning, and epigenetic variations in the large and complex wheat CEN. We found that most CENH3-associated repeats are Cereba element of retrotransposons and exhibit phylogenetic homogenization across different wheat lines, but the less-associated repeat sequences diverge on their own way in each wheat line, implying specific mechanisms for selecting certain repeat types as functional core CEN. Furthermore, we observed that CENH3 nucleosome structures display looser wrapping of DNA termini on complex centromeric repeats, including the repositioned CEN. We also found that strict CENH3 nucleosome positioning and intrinsic DNA features play a role in determining centromere identity among different lines. Specific non-B form DNAs were substantially associated with CENH3 nucleosomes for the repositioned centromeres. These findings suggest that multiple mechanisms were involved in the adaptation of CENH3 nucleosomes that can stabilize CEN. Ultimately, we proposed a remarkable epigenetic plasticity of centromere chromatin within the diverse genomic context, and the high robustness is crucial for maintaining centromere function and genome stability in wheat 10+ lines as a result of past breeding selections.

Deciphering genetic basis of developmental and agronomic traits by integrating high-throughput optical phenotyping and genome-wide association studies in wheat.

Dissecting the genetic basis of complex traits such as dynamic growth and yield potential is a major challenge in crops. Monitoring the growth throughout growing season in a large wheat population to uncover the temporal genetic controls for plant growth and yield-related traits has so far not been explored. In this study, a diverse wheat panel composed of 288 lines was monitored by a non-invasive and high-throughput phenotyping platform to collect growth traits from seedling to grain filling stage and their relationship with yield-related traits was further explored. Whole genome re-sequencing of the panel provided 12.64 million markers for a high-resolution genome-wide association analysis using 190 image-based traits and 17 agronomic traits. A total of 8327 marker-trait associations were detected and clustered into 1605 quantitative trait loci (QTLs) including a number of known genes or QTLs. We identified 277 pleiotropic QTLs controlling multiple traits at different growth stages which revealed temporal dynamics of QTLs action on plant development and yield production in wheat. A candidate gene related to plant growth that was detected by image traits was further validated. Particularly, our study demonstrated that the yield-related traits are largely predictable using models developed based on i-traits and provide possibility for high-throughput early selection, thus to accelerate breeding process. Our study explored the genetic architecture of growth and yield-related traits by combining high-throughput phenotyping and genotyping, which further unravelled the complex and stage-specific contributions of genetic loci to optimize growth and yield in wheat.

Genome wide association and haplotype analyses for the crease depth trait in bread wheat (Triticum aestivum L.).

Wheat grain has a complex structure that includes a crease on one side, and tissues within the crease region play an important role in nutrient transportation during wheat grain development. However, the genetic architecture of the crease region is still unclear. In this study, 413 global wheat accessions were resequenced and a method was developed for evaluating the phenotypic data of crease depth (CD). The CD values exhibited continuous and considerable large variation in the population, and the broad-sense heritability was 84.09%. CD was found to be positively correlated with grain-related traits and negatively with quality-related traits. Analysis of differentiation of traits between landraces and cultivars revealed that grain-related traits and CD were simultaneously improved during breeding improvement. Moreover, 2,150.8-Mb genetic segments were identified to fall within the selective sweeps between the landraces and cultivars; they contained some known functional genes for quality- and grain-related traits. Genome-wide association study (GWAS) was performed using around 10 million SNPs generated by genome resequencing and 551 significant SNPs and 18 QTLs were detected significantly associated with CD. Combined with cluster analysis of gene expression, haplotype analysis, and annotated information of candidate genes, two promising genes TraesCS3D02G197700 and TraesCS5A02G292900 were identified to potentially regulate CD. To the best of our knowledge, this is the first study to provide the genetic basis of CD, and the genetic loci identified in this study may ultimately assist in wheat breeding programs.

Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis.

BACKGROUND: Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs to the transcriptome, is critical for determining the traits that influence wheat growth and development. Asymmetric transcription of homoeologs has been so far investigated in a tissue or organ-specific manner, which could be misleading due to a mixture of cell types. RESULTS: Here, we perform single nuclei RNA sequencing and ATAC sequencing of wheat root to study the asymmetric gene transcription, reconstruct cell differentiation trajectories and cell-type-specific gene regulatory networks. We identify 22 cell types. We then reconstruct cell differentiation trajectories that suggest different origins between epidermis/cortex and endodermis, distinguishing bread wheat from Arabidopsis. We show that the ratio of asymmetrically transcribed triads varies greatly when analyzing at the single-cell level. Hub transcription factors determining cell type identity are also identified. In particular, we demonstrate that TaSPL14 participates in vasculature development by regulating the expression of BAM1. Combining single-cell transcription and chromatin accessibility data, we construct the pseudo-time regulatory network driving root hair differentiation. We find MYB3R4, REF6, HDG1, and GATAs as key regulators in this process. CONCLUSIONS: Our findings reveal the transcriptional landscape of root organization and asymmetric gene transcription at single-cell resolution in polyploid wheat.

QTL Mapping for Wheat Seed Dormancy in a Yangmai16/Zhongmai895 Double Haploid Population.

Pre-harvest sprouting (PHS) of wheat reduces grain yield and quality, and it is strongly affected by seed dormancy. Therefore, identification of quantitative trait loci (QTL) for seed dormancy is essential for PHS resistance breeding. A doubled haploid (DH) population, consisting of 174 lines from the cross between Yangmai16 (YM16) and Zhongmai895 (ZM895) was used to detect QTLs for seed dormancy and grain color. For seed dormancy, a total of seven QTLs were detected on chromosomes 2A, 3A, 3D, 4D, 5B and 5D over four environments, among which Qdor.hzau-3A, Qdor.hzau-3D.1 and Qdor.hzau-3D.2 were stably detected in more than two environments. For grain color, only two QTLs, Qgc.hzau-3A and Qgc.hzau-3D were detected on chromosomes 3A and 3D, which physically overlapped with Qdor.hzau-3A and Qdor.hzau-3D.1, respectively. Qdor.hzau-3D.2 has never been reported elsewhere and is probably a novel locus with allelic effect of seed dormancy contributed by weakly dormant parent ZM895, and a KASP marker was developed and validated in a wheat natural population. This study provides new information on the genetic dissection of seed dormancy, which may aid in further improvement for marker-assisted wheat breeding for PHS resistance.

Tuning the Thermoresponsivity of Amphiphilic Copolymers via Stereocomplex Crystallization of Hydrophobic Blocks.

Thermoresponsive polymers that exhibit a cloud point temperature (Tcp) are an important class of stimuli-responsive polymers that have great potential for biomedical applications. Precise tuning of the Tcp is of fundamental importance for designing thermoresponsive polymers. However, tuning the Tcp generally requires sophisticated control over the chemical and assembled structures of thermoresponsive polymers. Here, we report a simple yet effective method to tune the Tcp of thermoresponsive polymers only by mixing and varying the mixing ratios of amphiphilic copolymer pair that contains l- and d-configured hydrophobic blocks in a dilute solution. Stereocomplex (SC) crystallization of the l- and d-configured blocks led to form core-shell micelles with a larger size, a bigger core, and a higher aggregation number, which facilitated the intermicellar aggregation upon heating due to improved intermicellar attractions. SC crystallization of the hydrophobic blocks improved the separation efficacy of the thermoresponsive copolymers for removal of hydrophobic pollutants from water.

A G-protein pathway determines grain size in rice.

Manipulating grain size is an effective strategy for increasing cereal yields. Here we identify a pathway composed of five subunits of the heterotrimeric G proteins that regulate grain length in rice. The Gß protein is essential for plant survival and growth. Gα provides a foundation for grain size expansion. Three Gγ proteins, DEP1, GGC2 and GS3, antagonistically regulate grain size. DEP1 and GGC2, individually or in combination, increase grain length when in complex with Gß. GS3, having no effect on grain size by itself, reduces grain length by competitively interacting with Gß. By combining different G-protein variants, we can decrease grain length by up to 35% or increase it by up to 19%, which leads to over 40% decreasing to 28% increasing of grain weight. The wide existence of such a conserved system among angiosperms suggests a possible general predictable approach to manipulating grain/organ sizes.

Stereocomplexed physical hydrogels with high strength and tunable crystallizability.

Physical hydrogels crosslinked by non-covalent interactions have attained increasing attention due to their good mechanical properties and processability. However, the use of feasible and controllable non-covalent interactions is highly essential for preparing such hydrogels. In this article, we report on stereocomplexed physical hydrogels prepared by simple casting and swelling of amphiphilic graft copolymers bearing a poly(acrylic acid) (PAA) backbone and poly(l-lactic acid) (PLLA) or poly(d-lactic acid) (PDLA) stereocomplexable side chains. The microstructure, swelling behavior, and mechanical and shape memory properties of the obtained hydrogels can be tuned by varying the copolymer composition and stereocomplex (SC) crystallization of PLLA/PDLA enantiomeric chains. The long PLLA or PDLA chains segregate to form hydrophobic, crystallized domains in water, serving as physical crosslinking junctions for hydrogels. SC crystallization between PLLA and PDLA further enhances the number density of physical crosslinkers of enantiomerically mixed hydrogels. The SC content increases as the PLLA/PDLA ratio approaches 1/1 in enantiomerically mixed hydrogels. The average distance between crosslinking junctions declines for the hydrogels with a high PLLA (or PDLA) mass fraction (MPLA) and SC content, due to the increased number density of physical crosslinkers. Accordingly, the tensile strength and the Young's modulus increase but the swelling ratio and the elongation-at-break of the hydrogels decrease with an increase in MPLA and SC content. The hydrogels exhibit shape memory behavior; the shape fixing ability is enhanced by the SC crystallization of PLLA/PDLA side chains in the hydrogels.

Arabidopsis BTB/POZ protein-dependent PENETRATION3 trafficking and disease susceptibility.

The outermost cell layer of plant roots (epidermis) constantly encounters environmental challenges. The epidermal outer plasma membrane domain harbours the PENETRATION3 (PEN3)/ABCG36/PDR8 ATP-binding cassette transporter that confers non-host resistance to several pathogens. Here, we show that the Arabidopsis ENDOPLASMIC RETICULUM-ARRESTED PEN3 (EAP3) BTB/POZ-domain protein specifically mediates PEN3 exit from the endoplasmic reticulum and confers resistance to a root-penetrating fungus, providing prime evidence for BTB/POZ-domain protein-dependent membrane trafficking underlying disease resistance.

A Framework for Lateral Membrane Trafficking and Polar Tethering of the PEN3 ATP-Binding Cassette Transporter.

The outermost cell layer of plants, the epidermis, and its outer (lateral) membrane domain facing the environment are continuously challenged by biotic and abiotic stresses. Therefore, the epidermis and the outer membrane domain provide important selective and protective barriers. However, only a small number of specifically outer membrane-localized proteins are known. Similarly, molecular mechanisms underlying the trafficking and the polar placement of outer membrane domain proteins require further exploration. Here, we demonstrate that ACTIN7 (ACT7) mediates trafficking of the PENETRATION3 (PEN3) outer membrane protein from the trans-Golgi network (TGN) to the plasma membrane in the root epidermis of Arabidopsis (Arabidopsis thaliana) and that actin function contributes to PEN3 endocytic recycling. In contrast to such generic ACT7-dependent trafficking from the TGN, the EXOCYST84b (EXO84b) tethering factor mediates PEN3 outer-membrane polarity. Moreover, precise EXO84b placement at the outer membrane domain itself requires ACT7 function. Hence, our results uncover spatially and mechanistically distinct requirements for ACT7 function during outer lateral membrane cargo trafficking and polarity establishment. They further identify an exocyst tethering complex mediator of outer lateral membrane cargo polarity.

Thermoresponsive physical hydrogels of poly(lactic acid)/poly(ethylene glycol) stereoblock copolymers tuned by stereostructure and hydrophobic block sequence.

CBABC-type poly(lactic acid) (PLA)/poly(ethylene glycol) (PEG) pentablock copolymers composed of a central PEG block (A) and enantiomeric poly(l-lactic acid) (PLLA, B), poly(d-lactic acid) (PDLA, C) blocks were synthesized. Such pentablock copolymers form physical hydrogels at high concentrations in an aqueous solution, which stem from the aggregation and physical bridging of copolymer micelles. These gels are thermoresponsive and turn into sols upon heating. Physical gelation, gel-to-sol transition, crystalline state, microstructure, rheological behavior, biodegradation, and drug release behavior of PLA/PEG pentablock copolymers and their gels were investigated; they were also compared with PLA-PEG-PLA triblock copolymers containing the isotactic PLLA or atactic poly(d,l-lactide) (PDLLA) endblocks and PLLA-PEG-PLLA/PDLA-PEG-PDLA enantiomeric mixtures. PLA hydrophobic domains in pentablock copolymer gels changed from a homocrystalline to stereocomplexed structure as the PLLA/PDLA block length ratio approached 1/1. The gel of symmetric pentablock copolymer exhibited a wider gelation region, higher gel-to-sol transition temperature, higher hydrophobic domain crystallinity, larger intermicellar distance, higher storage modulus, and slower degradation and drug release rate compared to those of the asymmetric PLA/PEG pentablock copolymers or triblock copolymers. SAXS results indicated that the PLLA/PDLA blocks stereocomplexation in pentablock copolymers facilitated the intermicellar aggregation and bridging. Cylindrical ordered structures were observed in all the gels formed from the PLA/PEG pentablock and triblock copolymers. The stereocomplexation degree and intermicellar distance of the pentablock copolymer gels increased with heating.

In situ formation and gelation mechanism of thermoresponsive stereocomplexed hydrogels upon mixing diblock and triblock poly(lactic acid)/poly(ethylene glycol) copolymers.

A novel in situ formed gel system with potential biodegradability and biocompatibility is developed by mixing the diblock and triblock poly(lactic acid)/poly(ethylene glycol) (PLA/PEG) copolymers with opposite configurations of PLA blocks. In situ gelation of such system is extremely fast, which happens within 10 s after mixing. In situ gelation, gel-to-sol transition, crystalline structure, microstructures, and mechanical properties of PLA-PEG/PLA-PEG-PLA enantiomerically mixed gels are significantly influenced by the mixing ratio, degree of polymerization for PEG block in triblock (DPPEG,tri) and diblock copolymers (DPPEG,di). It is found that in situ gelation of PLA-PEG/PLA-PEG-PLA enantiomeric mixture just happen at relatively smaller PLA-PEG/PLA-PEG-PLA mass ratio and larger DPPEG,tri. Hydrodynamic diameters of PLA-PEG and PLA-PEG-PLA copolymers in dilute solution increase remarkably upon mixing, indicating the formation of bridging networks. Stereocomplexed crystallites are formed for the PLA hydrophobic domains in PLA-PEG/PLA-PEG-PLA enantiomeric mixtures. As indicated by synchrotron-radiation SAXS analysis, the enantiomeric mixture changes from a compactly to loosely aggregated structure and the intermicellar distance enhances with increasing DPPEG,tri, DPPEG,di, or PLA-PEG-PLA fraction. Gelation mechanism of PLA-PEG/PLA-PEG-PLA enantiomeric mixture is proposed, in which part of PLA-PEG-PLA chains act as the connecting bridges between star and flower-like micelles and the stereocomplexed crystallites in micelle cores act as physically cross-linked points.

RNA-directed DNA methylation is involved in regulating photoperiod-sensitive male sterility in rice.

Photoperiod-sensitive male sterility (PSMS) is a valuable germplasm for hybrid rice breeding. Recently, we cloned pms3, a locus controlling PSMS, which encodes a long non-coding RNA called LDMAR required for normal male fertility of the rice plant under long-day conditions. Increased methylation in the promoter of LDMAR in the PSMS rice (Nongken 58S) relative to the wild-type (Nongken 58) reduced expression of LDMAR leading to male sterility under long-day conditions. In this study, we identified a siRNA named Psi-LDMAR in the LDMAR promoter region that was more abundant in Nongken 58S than in Nongken 58. We showed that Psi-LDMAR was likely derived from AK111270, a transcript obtained from the sense strand of the LDMAR promoter with its 3'-end having a 110-base overlap with the 5'-end of LDMAR. Overexpressing AK111270 in Nongken 58S greatly enriched Psi-LDMAR, which induced RNA-directed DNA methylation in the LDMAR promoter and repressed the expression of LDMAR. Reduction of LDMAR in Nongken 58S changed the critical day length for fertility recovery and delayed the fertility recovery under short-day conditions. This result added to our understanding of the molecular mechanism for PSMS.