Genome-wide identification of the longan R2R3-MYB gene family and its role in primary and lateral root.

R2R3-MYB is an important transcription factor family that regulates plant growth and development. Root development directly affects the absorption of water and nutrients by plants. Therefore, to understand the regulatory role of R2R3-MYB transcription factor family in root development of longan, this study identified the R2R3-MYB gene family members at the genome-wide level, and analyzed their phylogenetic characteristics, physical and chemical properties, gene structure, chromosome location and tissue expression. The analysis identified 124 R2R3-MYB family members in the longan genome. Phylogenetic analysis divided these members into 22 subfamilies, and the members of the unified subfamily had similar motifs and gene structures. The result of qRT-PCR showed that expression levels of DlMYB33, DlMYB34, DlMYB59, and DlMYB77 were significantly higher in main roots than in lateral as opposed to those of DlMYB35, DlMYB69, DlMYB70, and DlMYB83, which were significantly lower. SapBase database prediction and miRNAs sequencing results showed that 34 longan miRNAs could cleave R2R3-MYB, including 17 novel miRNAs unique to longan. The qRT-PCR and subcellular localization experiments of DlMYB92 and DlMYB98 showed that DlMYB92 is a key factor that regulates transcription in the nucleus and participates in the regulation of longan lateral root development. Longan also has a conserved miRNA-MYB-lateral root development regulation mechanism. This study provides a reference for further research on the transcriptional regulation of the miRNA-R2R3-MYB module in the root development of longan.

Current knowledge of bermudagrass responses to abiotic stresses.

Bermudagrass (Cynodon spp.) is a common turfgrass found in parks, landscapes, sports fields, and golf courses. It is also grown as a forage crop for animal production in many countries. Consequently, bermudagrass has significant ecological, environmental, and economic importance. Like many other food crops, bermudagrass production also faces challenges from various abiotic and biotic stresses. In this review we will focus on abiotic stresses and their impacts on turfgrass quality and yield. Among the abiotic stresses, drought, salinity and cold stress are known to be the most damaging stresses that can directly affect the production of turfgrass worldwide. In this review, we also discuss the impacts of nutrient supply, cadmium, waterlogging, shade and wear stresses on bermudagrass growth and development. Detailed discussions on abiotic stress effects on bermudagrass morphology, physiology, and gene expressions should benefit our current understanding on molecular mechanisms controlling bermudagrass tolerance against various abiotic stresses. We believe that the rapid development of transcriptomics and proteomics, as well as bermudagrass stable transformation technologies will promote the production of new bermudagrass cultivars with desirable tolerance against abiotic stresses.

Overexpression of CdtCIPK21 from triploid bermudagrass reduces salt and drought tolerance but increases chilling tolerance in transgenic rice.

Calcineurin B-like-interacting protein kinase (CIPK) is a serine/threonine kinase, which transmits the Ca2+ signal sensed by CBL proteins. A CdtCIPK21 showing highly identical to OsCIPK21 in rice was isolated from triploid bermudagrass (Cynodon dactylon × Cynodon transvaalensis). CdtCIPK21 transcript could be detected in roots, rhizomes, stems, stolons, and leaves, with highest level in roots. It was induced by salinity, dehydration and chilling, but reduced by ABA treatment. Transgenic rice plants overexpressing CdtCIPK21 had decreased salt and drought tolerance as well as ABA sensitivity but increased chilling tolerance. Lower SOD and CAT activities was observed in transgenic lines under salinity and drought stress conditions, but higher levels under chilling stress. Similarly, lower levels of proline concentration and P5CS1 and P5CS2 transcripts were maintained in transgenic lines under salinity and drought stresses, and higher levels were maintained under chilling. In addition, transgenic lines had lower transcript levels of ABA-independent genes (OsDREB1A, OsDREB1B, and OsDREB2A) and ABA responsive genes (OsLEA3, OsLIP9, and OsRAB16A) under salinity and drought but higher levels under chilling compared with WT. The results suggest that CdtCIPK21 regulates salt and drought tolerance negatively and chilling tolerance positively, which are associated with the altered ABA sensitivity, antioxidants, proline accumulation and expression of ABA-dependent and ABA-independent stress responsive genes.

Genome-wide identification of Mg2+ transporters and functional characteristics of DlMGT1 in Dimocarpus longan.

Longan (Dimocarpus Longan) is one of the most important fruit crops in Southern China. Lack of available Mg in acidic soil conditions is a limitation to further increasing longan yield. Magnesium transporter (MGT/MRS2) mediates the uptake, transport, and redistribution of Mg2+ in higher plants. To understand the role of MGTs family members in longan Mg deficiency. We identified and analyzed the protein characteristics, phylogeny, expression changes, subcellular localization, and transcriptional regulation of DlMGTs members. The results showed that, twelve DlMGTs are localized in the cell membrane, chloroplast, and nucleus. The evolutionary differences in MGTs between herbaceous and woody species in different plants. The DlMGTs promoters contained many cis-acting elements and transcription factor binding sites related to the hormone, environmental, and stress response. Subcellular localization assays showed that DlMGT1 localizes in the cell membrane of Arabidopsis protoplasts. The candidate transcription factor DlGATA16, which may regulate the expression of DlMGT1, was localized in the nucleus of tobacco leaves. Dual luciferase analysis demonstrated that DlGATA16 is a potential factor regulating the transcriptional activity of DlMGT1. In this study, we identified and analyzed DlMGTs on a genome-wide scale and the subcellular localization and interaction of DlMGT1 and DlGATA16, which has important implications for further functional analysis studies of MGTs and the use of MGT for longan genetic improvement.

Transcriptome sequencing and DEG analysis in different developmental stages of floral buds induced by potassium chlorate in Dimocarpus longan.

Potassium chlorate can promote off-season flowering in longan, but the molecular mechanisms are poorly understood. In this study, four-year-old 'Shixia' longan trees were injected in the trunk with potassium chlorate, and terminal buds were sampled and analyzed using transcriptomics and bioinformatics tools. To generate a reference longan transcriptome, we obtained 207,734 paired-end reads covering a total of 58,514,149 bp, which we assembled into 114,445 unigenes. Using this resource, we identified 3,265 differentially expressed genes (DEGs) that were regulated in longan terminal buds in response to potassium chlorate treatment for 2, 6 or 30 days, including 179 transcription factor genes. By reference to the Arabidopsis literature, we then defined 38 longan genes involved in flowering, from which we constructed the longan flowering pathway. According to RNA-seq data, at least 24 of these genes, which participate in multiple signaling pathways, are involved in potassium chlorate-stimulated floral induction, and the differential regulation in terminal buds of ten floral pathway genes (GI, CO, GID1, GA4, GA5, FLC, AP1, LFY, FT and SOC1) was confirmed by qRT-PCR. These data will contribute to an improved understanding of the functions of key genes involved in longan floral induction by potassium chlorate.

Biological control agents colonize litchi fruit during storage and stimulate physiological responses to delay pericarp browning.

Introduction: Litchi is an economically important fruit in subtropical countries, but pericarp browning can limit its shelf life outside of controlled storage conditions. Effective and sustainable biological control strategies are needed to protect fruit against postharvest browning. Results and Discussion: In this study, we show that the four bacterial strains Bacillus licheniformis HS10, B. amyloliquefaciens LI24 and PP19, and Exiguobacterium acetylicum SI17 can delay fruit browning in both laboratory trials (LTs) and field plus laboratory trials (FLTs). Strains HS10, LI24, PP19 and SI17 showed 47.74%, 35.39%, 33.58% and 32.53% browning-inhibitory efficacy respectively at 180 h in LT. Litchi sarcocarp interior sourced isolate SI17 showed 74.05% inhibit-brown efficacy at 216 h in FLTs, performing better in FLT than in LT. Furthermore, strains PP19 and SI17 colonized the fruit pericarp and increased total phenolic and anthocyanin contents but decreased peroxidase and polyphenol oxidase activity. This is the first report of E. acetylicum (SI17) and B. licheniformis (HS10) strains acting as biological control agents (BCAs) to delay postharvest browning in litchi fruit. We conclude that PP19 and SI17 are promising BCAs against fruit browning, and their application could be effective for prolonging the shelf life of harvested litchi fruit.

Genomic insights into longan evolution from a chromosome-level genome assembly and population genomics of longan accessions.

Longan (Dimocarpus longan) is a subtropical fruit best known for its nutritious fruit and regarded as a precious tonic and traditional medicine since ancient times. High-quality chromosome-scale genome assembly is valuable for functional genomic study and genetic improvement of longan. Here, we report a chromosome-level reference genome sequence for longan cultivar JDB with an assembled genome of 455.5 Mb in size anchored to fifteen chromosomes, representing a significant improvement of contiguity (contig N50 = 12.1 Mb, scaffold N50 = 29.5 Mb) over a previous draft assembly. A total of 40 420 protein-coding genes were predicted in D. longan genome. Synteny analysis suggests longan shares the widespread gamma event with core eudicots, but has no other whole genome duplications. Comparative genomics showed that D. longan genome experienced significant expansions of gene families related to phenylpropanoid biosynthesis and UDP-glucosyltransferase. Deep genome sequencing analysis of longan cultivars identified longan biogeography as a major contributing factor for genetic diversity, and revealed a clear population admixture and introgression among cultivars of different geographic origins, postulating a likely migration trajectory of longan overall confirmed by existing historical records. Finally, genome-wide association studies (GWAS) of longan cultivars identified quantitative trait loci (QTL) for six different fruit quality traits and revealed a shared QTL containing three genes for total soluble solid and seed weight. The chromosome-level reference genome assembly, annotation and population genetic resource for D. longan will facilitate the molecular studies and breeding of desirable longan cultivars in the future.

Floral Induction of Longan (Dimocarpus longan) by Potassium Chlorate: Application, Mechanism, and Future Perspectives.

Longan (Dimocarpus longan L.) is one of the most important tropical and subtropical fruits in the world. Longan fruit has high nutritional and medical value, and is regarded as a treasure among fruits. Since it was first reported that potassium chlorate (KClO3) could be successfully applied to promote flowering in longan, this compound has been widely used in the production of on-season and off-season longan fruits. KClO3 has thus played a great role in promoting the development of the longan industry. In this review, we summarize the application methods, influencing factors, and physiological and molecular mechanisms associated with KClO3-mediated induction of longan flowering. It can be deduced that leaves may play a crucial role in the transport of and response to KClO3. Leaves supply carbon and nitrogen nutrition, and hormone and signaling molecules needed for the differentiation of apical buds. Moreover, cytokinins may be crucial for KClO3-mediated induction of longan flowering. More effort should be focused on studying the molecular mechanisms underlying this process. This will not only help us to better understand floral induction by KClO3 in longan but also enrich our understanding of flowering regulation mechanisms in woody plants.

Investigating the Mechanism of Unilateral Cross Incompatibility in Longan (Dimocarpus longan Lour.) Cultivars (Yiduo × Shixia).

Longan (Dimocarpus longan Lour.) is an important subtropical fruit tree in China. Nearly 90% of longan fruit imports from Thailand are from the cultivar Yiduo. However, we have observed that there exists a unilateral cross incompatibility (UCI) when Yiduo is used as a female parent and Shixia (a famous Chinese cultivar) as a male parent. Here, we performed a comparative transcriptome analysis coupled with microscopy of pistils from two reciprocal pollination combinations [Shixia♂ × Yiduo♀(SY) and Yiduo♀ × Shixia♂(YS)] 4, 8, 12, and 24 h after pollination. We also explored endogenous jasmonic acid (JA) and jasmonyl isoleucine (JA-Ile) levels in pistils of the crosses. The microscopic observations showed that the UCI was sporophytic. The endogenous JA and JA-Ile levels were higher in YS than in SY at the studied time points. We found 7,251 differentially expressed genes from the transcriptome analysis. Our results highlighted that genes associated with JA biosynthesis and signaling, pollen tube growth, cell wall modification, starch and sucrose biosynthesis, and protein processing in endoplasmic reticulum pathways were differentially regulated between SY and YS. We discussed transcriptomic changes in the above-mentioned pathways regarding the observed microscopic and/or endogenous hormone levels. This is the first report on the elaboration of transcriptomic changes in longan reciprocal pollination combination showing UCI. The results presented here will enable the longan breeding community to better understand the mechanisms of UCI.

Biocontrol Using Bacillus amyloliquefaciens PP19 Against Litchi Downy Blight Caused by Peronophythora litchii.

Bacillus amyloliquefaciens has been widely used in the agriculture, food, and medicine industries. Isolate PP19 was obtained from the litchi fruit carposphere and showed biocontrol efficacy against litchi downy blight (LDB) whether applied preharvest or postharvest. To further understand the underlying regulatory mechanisms, the genome of PP19 was sequenced and analyzed. The genome comprised a 3,847,565 bp circular chromosome containing 3990 protein-coding genes and 121 RNA genes. It has the smallest genome among 36 sequenced strains of B. amyloliquefaciens except for RD7-7. In whole genome phylogenetic analysis, PP19 was clustered into a group with known industrial applications, indicating that it may also produce high-yield metabolites that have yet to be identified. A large chromosome structural variation and large numbers of single nucleotide polymorphisms (SNPs) between PP19 (industrial strain) and UMAF6639 (plant-associated strain) were detected through comparative analysis, which may shed light on their functional differences. Preharvest treatment with PP19 enhanced resistance to LDB, by decreasing the plant H2O2 content and increasing the SOD activity. This is the first report of an industrial strain of B. amyloliquefaciens showing a plant-associated function and with major potential for the biocontrol of LDB.