The qLTG1.1 candidate gene CsGAI regulates low temperature seed germination in cucumber

Candidate genes associated with low temperature tolerance in cucumber adult plants identified by combining GWAS & QTL mapping

Fruit quality and yield are reduced when cucumber (Cucumis sativus L.) plants are exposed to low temperature (LT) stress, yet, the inheritance and genes linked to cold tolerance in adult plants have not been reported yet. Here, the LT-tolerance of 120 cucumber accessions representing four ecotypes were evaluated by GWAS, and also, in 140 recombinant inbred lines (RILs) derived from a biparental cross. Plants were exposed to naturally occurring LT environments in a plastic greenhouse, in winter 2022, and 2023, and a low temperature injury index (LTII) was employed to evaluate plant performance. Genetic analysis revealed that the LT-tolerance evaluated in the adult cucumber plants was a multigenic quantitative trait, and that 18 of the 120 accessions were highly LT tolerant by our LTII assessment. Two loci (gLTT1.1 and gLTT3.1) exhibited strong signals that were consistent and stable in two environments. In addition, two QTLs-qLTT1.2 on chromosome (Chr.) 1, and qLTT3.1 on Chr. 3, were discovered in all tests using RIL population derived from a cross between LT-sensitive 'CsIVF0106', and LT-tolerant 'CsIVF0168'. qLTT1.2 was delimited to a 1.24-Mb region and qLTT3.1 was narrowed to a 1.43-Mb region. Interestingly, a peak single nucleotide polymorphism (SNP) at gLTT1.1 and gLTT3.1 was also found in qLTT1.2 and qLTT3.1, respectively. These loci were thus renamed as gLTT1.1 and gLTT3.1. In these regions, 25 genes were associated with the LT response. By identifying differences in haplotypes and transcript profiles among these genes, we identified four candidates: CsaV3_1G012520 (an ethylene-responsive transcription factor) and CsaV3_1G013060 (a RING/U-box superfamily protein) in gLTT1.1, and two RING-type E3 ubiquitin transferases at CsaV3_3G018440 and CsaV3_3G017700 in gLTT3.1 that may regulate LT-tolerance in adult cucumber. Interestingly, the accessions in which the LT-tolerant haplotypes for two loci were pyramided, displayed maximally high tolerance for LT. These findings therefore provide a solid foundation for the identification of LT-tolerant genes and the molecular breeding of cucumber with LT-tolerance.

OsNAL11 and OsGASR9 Regulate the Low-Temperature Germination of Rice Seeds by Affecting GA Content

Low temperatures cause serious threat to rice seed emergence, which has become one of the main limiting factors in the production of direct seeding rice. It is of great importance to study the genes controlling low-temperature tolerance during seed germination and to mine the possible regulatory mechanism for developing new rice varieties with immense low-temperature germination ability. In the current research study, two types of mutants of nal11 and gasr9, derived from the WT (wild type) ZH11, were used for the analysis of low-temperature germinability. The results showed that the nal11 and gasr9 mutants displayed no significant difference in germination rate with ZH11 at room temperature, but the mutants showed significantly lower germination rates, germination potential and germination index, and slowed seedling growth in the simulated direct seeding experiments at low temperatures compared to ZH11. Additionally, the activity of POD, SOD, CAT, and anti-superoxide anion radial activity were significantly reduced, but the levels of MDA and H2O2 were significantly higher in the nal11 and gasr9 mutant seeds that were germinated at low temperatures compared to ZH11. Further analysis revealed that the levels of total active GA, especially GA4 and GA7, were significantly lower in the nal11 and gasr9 mutants than that in ZH11 during low-temperature germination. Based on qRT-PCR analysis, the expression levels of some GA synthesis-related genes were higher, whereas some were lower in the nal11 and gasr9 mutants than those in ZH11, however, the GA metabolism-related genes OsGA2ox8 and OsGA2ox10 and the GA signaling negative regulator gene SLR1 were significantly up-regulated in both nal11 and gasr9 mutants at several time points during low-temperature germination. This may explain the lower GA levels in the nal11 and gasr9 mutants. Furthermore, the interaction between the OsNAL11 and OsGASR9 proteins was confirmed by Y2H, LUC, and Co-IP assays. This study provides preliminary insights into the regulatory mechanism of the OsNAL11 and OsGASR9 genes, which control the low-temperature germination of rice seeds by affecting the GA pathway. Our study will provide the basis for further mining the molecular mechanisms of low-temperature germination in rice and valuable theoretical reference for breeding varieties with strong low-temperature germinability.

Transcriptome analysis unveiled the genetic basis of rapid seed germination strategies in alpine plant Rheum pumilum

Rheum pumilum stands as both a quintessential alpine plant and a significant traditional Chinese and Tibetan medicinal herb. Unraveling the molecular intricacies of seed germination in Rh. pumilum not only unveils the genetic foundations of plant seed germination strategies in high-altitude environments but also offers insights for cultivating Rh. pumilum medicinal materials. Employing transcriptome sequencing and the Weighted Gene Co-expression Network Analysis, this study delved into the shifts in gene expression levels across various stages of seed germination in Rh. pumilum. The process of seed germination in Rh. pumilum entails a cascade of complex physiological events. Six hormones (ABA, IAA, ETH, GA, BR, CK) emerged as pivotal players in seeds breaking in shells and the facilitation of rapid seed germination in Rh. pumilum. Fourteen transcription factor families (LOB, GRAS, B3, bHLH, bZIP, EIL, MYB, MYB related, NAC, TCP, WRKY, HSF, PLATZ, and SBP) along with four key genes (E2.4.1.13, EIN3, BZR, and BIN2) were identified that may be associated with both biotic and abiotic environmental stress. The ETR, ACACA and ATPeV0C genes were linked with energy accumulation during the initial stages of seed germination, CYP707A may play an important role in breaking seed dormancy, while the BRI1 gene may be correlated with swift seed germination. Additionally, several unidentified genes were recognized to play key roles in seed germination of Rh. pumilum, warranting further investigation. Moreover, Rh. pumilum demonstrates full activation of crucial physiological functions such as energy metabolism, signal transduction, and responses to biological and abiotic stresses during the seed breaking in shells. This study provides molecular evidence elucidating the swift seed germination strategies adopted by alpine plants to thrive in high-altitude environments. Furthermore, it serves as a foundational reference for enhancing seed germination rates and breeding practices to promote the sustainable development of Rh. pumilum medicinal materials.

The synthesis of triacylglycerol by diacylglycerol acyltransferases (CsDGAT1A and CsDGAT2D) is essential for tolerance of cucumber's resistance to low-temperature stress

KEY MESSAGE

CsDGAT1A and CsDGAT2D play a positive regulatory role in cucumber's response to low-temperature stress and positively regulate the synthesis of triacylglycerol (TAG). Triacylglycerol (TAG), a highly abundant and significant organic compound in plants, plays crucial roles in plant growth, development, and stress responses. The final acetylation step of TAG synthesis is catalyzed by diacylglycerol acyltransferases (DGATs). However, the involvement of DGATs in cucumber's low-temperature stress response remains unexplored. This study focused on two DGAT genes, CsDGAT1A and CsDGAT2D, investigating their function in enhancing cucumber's low-temperature stress tolerance. Our results revealed that both proteins were the members of the diacylglycerol acyltransferase family and were predominantly localized in the endoplasmic reticulum. Functional analysis demonstrated that transient silencing of CsDGAT1A and CsDGAT2D significantly compromised cucumber's low-temperature stress tolerance, whereas transient overexpression enhanced it. Furthermore, the TAG content quantification indicated that CsDGAT1A and CsDGAT2D promoted TAG accumulation. In conclusion, this study elucidates the lipid metabolism mechanism in cucumber's low-temperature stress response and offers valuable insights for the cultivation of cold-tolerant cucumber plants.

GWAS reveals novel loci and identifies a pentatricopeptide repeat-containing protein (CsPPR) that improves low temperature germination in cucumber

Low temperatures (LTs) negatively affect the percentage and rate of cucumber (Cucumis sativus L.) seed germination, which has deleterious effects on yield. Here, a genome-wide association study (GWAS) was used to identify the genetic loci underlying low temperature germination (LTG) in 151 cucumber accessions that represented seven diverse ecotypes. Over two years, phenotypic data for LTG i.e., relative germination rate (RGR), relative germination energy (RGE), relative germination index (RGI) and relative radical length (RRL), were collected in two environments, and 17 of the 151 accessions were found to be highly cold tolerant using cluster analysis. A total of 1,522,847 significantly associated single-nucleotide polymorphism (SNP) were identified, and seven loci associated with LTG, on four chromosomes, were detected: gLTG1.1, gLTG1.2, gLTG1.3, gLTG4.1, gLTG5.1, gLTG5.2, and gLTG6.1 after resequencing of the accessions. Of the seven loci, three, i.e., gLTG1.2, gLTG4.1, and gLTG5.2, showed strong signals that were consistent over two years using the four germination indices, and are thus strong and stable for LTG. Eight candidate genes associated with abiotic stress were identified, and three of them were potentially causal to LTG: CsaV3_1G044080 (a pentatricopeptide repeat-containing protein) for gLTG1.2, CsaV3_4G013480 (a RING-type E3 ubiquitin transferase) for gLTG4.1, and CsaV3_5G029350 (a serine/threonine-protein kinase) for gLTG5.2. The function for CsPPR (CsaV3_1G044080) in regulating LTG was confirmed, as Arabidopsis lines ectopically expressing CsPPR showed higher germination and survival rates at 4°C compared to the wild-type, which preliminarily illustrates that CsPPR positively regulates cucumber cold tolerance at the germination stage. This study will provide insights into cucumber LT-tolerance mechanisms and further promote cucumber breeding development.

Transcriptomic and QTL Analysis of Seed Germination Vigor under Low Temperature in Weedy Rice WR04-6

Low temperature is one of the major factors affecting rice germination, and low temperature germination (LTG) is an important agronomic trait. Although significant progress has been made in the study of rice LTG, the molecular mechanism of LTG remains poorly understood. To explore more rice LTG gene resources, we first demonstrated that weedy rice WR04-6 (Oryza sativa f. spontanea) had significantly higher LTG ability at 10 °C than the cultivated rice Qishanzhan (QSZ Oryza sativa L. ssp. indica). RNA-seq was used to investigate the gene expression of WR04-6 and QSZ at 10 °C for 10, 12 and 14 days after imbibition (DAI) of seed germination. The results of Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment revealed that the differentially expressed genes (DEGs) between WR04-6 and QSZ were mainly concentrated on the response to starch catabolic processes and the response to abscisic acid (ABA). This is consistent with the results of α-amylase activity, ABA and gibberellins (GA) treatment. A recombinant inbred line (RIL) population derived from a cross between WR04-6 and QSZ and its high-density SNP genetic map were used to detect quantitative trait loci (QTL) for LTG rates. The results showed that two new QTLs were located on chromosome 3 and chromosome 12. Combined with the mapped QTLs and RNA-seq DEGs, sixteen candidate genes potentially associated with LTG were identified. Validation of the expression of the candidates by qRT-PCR were consistent with the RNA-seq data. These results will enable us to understand the genetic basis of LTG in weedy rice and provide new genetic resources for the generation of rice germplasm with improved LTG.