Transposable elements in Rosaceae: insights into genome evolution, expression dynamics, and syntenic gene regulation.

Transposable elements (TEs) exert significant influence on plant genomic structure and gene expression. Here, we explored TE-related aspects across 14 Rosaceae genomes, investigating genomic distribution, transposition activity, expression patterns, and nearby differentially expressed genes (DEGs). Analyses unveiled distinct long terminal repeat retrotransposon (LTR-RT) evolutionary patterns, reflecting varied genome size changes among nine species over the past million years. In the past 2.5 million years, Rubus idaeus showed a transposition rate twice as fast as Fragaria vesca, while Pyrus bretschneideri displayed significantly faster transposition compared with Crataegus pinnatifida. Genes adjacent to recent TE insertions were linked to adversity resistance, while those near previous insertions were functionally enriched in morphogenesis, enzyme activity, and metabolic processes. Expression analysis revealed diverse responses of LTR-RTs to internal or external conditions. Furthermore, we identified 3695 pairs of syntenic DEGs proximal to TEs in Malus domestica cv. 'Gala' and M. domestica (GDDH13), suggesting TE insertions may contribute to varietal trait differences in these apple varieties. Our study across representative Rosaceae species underscores the pivotal role of TEs in plant genome evolution within this diverse family. It elucidates how these elements regulate syntenic DEGs on a genome-wide scale, offering insights into Rosaceae-specific genomic evolution.

MbHY5-MbYSL7 mediates chlorophyll synthesis and iron transport under iron deficiency in Malus baccata.

Iron (Fe) plays an important role in cellular respiration and catalytic reactions of metalloproteins in plants and animals. Plants maintain iron homeostasis through absorption, translocation, storage, and compartmentalization of iron via a cooperative regulative network. Here, we showed different physiological characteristics in the leaves and roots of Malus baccata under Fe sufficiency and Fe deficiency conditions and propose that MbHY5 (elongated hypocotyl 5), an important transcription factor for its function in photomorphogenesis, participated in Fe deficiency response in both the leaves and roots of M. baccata. The gene co-expression network showed that MbHY5 was involved in the regulation of chlorophyll synthesis and Fe transport pathway under Fe-limiting conditions. Specifically, we found that Fe deficiency induced the expression of MbYSL7 in root, which was positively regulated by MbHY5. Overexpressing or silencing MbYSL7 influenced the expression of MbHY5 in M. baccata.

Genome-Wide Analysis of the WRKY Gene Family in Malus domestica and the Role of MdWRKY70L in Response to Drought and Salt Stresses.

The WRKY transcription factors are unique regulatory proteins in plants, which are important in the stress responses of plants. In this study, 113 WRKY genes were identified from the apple genome GDDH13 and a comprehensive analysis was performed, including chromosome mapping, and phylogenetic, motif and collinearity analysis. MdWRKYs are expressed in different tissues, such as seeds, flowers, stems and leaves. We analyzed seven WRKY proteins in different groups and found that all of them were localized in the nucleus. Among the 113 MdWRKYs, MdWRKY70L was induced by both drought and salt stresses. Overexpression of it in transgenic tobacco plants conferred enhanced stress tolerance to drought and salt. The malondialdehyde content and relative electrolyte leakage values were lower, while the chlorophyll content was higher in transgenic plants than in the wild-type under stressed conditions. In conclusion, this study identified the WRKY members in the apple genome GDDH13, and revealed the function of MdWRKY70L in the response to drought and salt stresses.

In Situ Construction of TiC-Ti3SiC2 Gradient Hybrid Interphase Coated SiC Fibers for Suppression of Specular Reflection and Non-Specular Scattering.

TiC-Ti3SiC2 gradient hybrid interphase on the surface of SiC fibers was successfully obtained through the molten salt method. The electromagnetic parameters of the prepared samples can be accurately controlled by adjusting the reaction temperature. A significant bimodal effect is observed in electromagnetic parameters patterns, corresponding to the double interface layer. TiC-Ti3SiC2 gradient hybrid interphase plays a dominant role in impedance matching, as well as in the attenuation layer through multi-interfacial polarization and conduction loss. Through the co-evaluation of the suppression of specular reflection and non-specular scattering properties of the samples, the SiC fiber with the TiC-Ti3SiC2 gradient hybrid interphase is expected to be a high temperature resistant radar absorbing material for future stealth aircraft.

Overexpression of MdATG8i Enhances Drought Tolerance by Alleviating Oxidative Damage and Promoting Water Uptake in Transgenic Apple.

Water deficit adversely affects apple (Malus domestica) productivity on the Loess Plateau. Autophagy plays a key role in plant responses to unfavorable environmental conditions. Previously, we demonstrated that a core apple autophagy-related protein, MdATG8i, was responsive to various stresses at the transcript level. Here, we investigated the function of this gene in the response of apple to severe drought and found that its overexpression (OE) significantly enhanced drought tolerance. Under drought conditions, MdATG8iOE apple plants exhibited less drought-related damage and maintained higher photosynthetic capacities compared with the wild type (WT). The accumulation of ROS (reactive oxygen species) was lower in OE plants under drought stress and was accompanied by higher activities of antioxidant enzymes. Besides, OE plants accumulated lower amounts of insoluble or oxidized proteins but greater amounts of amino acids and flavonoid under severe drought stress, probably due to their enhanced autophagic activities. Particularly, MdATG8iOE plants showed higher root hydraulic conductivity than WT plants did under drought conditions, indicating the enhanced ability of water uptake. In summary, the overexpression of MdATG8i alleviated oxidative damage, modulated amino acid metabolism and flavonoid synthesis, and improved root water uptake, ultimately contributing to enhanced drought tolerance in apple.

Insights into the effect of human civilization on Malus evolution and domestication.

The evolutionary history of the Malus genus has not been well studied. In the current study, we presented genetic evidence on the origin of the Malus genus based on genome sequencing of 297 Malus accessions, revealing the genetic relationship between wild species and cultivated apples. Our results demonstrated that North American and East Asian wild species are closer to the outgroup (pear) than Central Asian species, and hybrid species including natural (separated before the Pleistocene, about 2.5 Mya) and artificial hybrids (including ornamental trees and rootstocks) are between East and Central Asian wild species. Introgressions from M. sylvestris in cultivated apples appeared to be more extensive than those from M. sieversii, whose genetic background flowed westward across Eurasia and eastward to wild species including M. prunifolia, M. × asiatica, M. × micromalus, and M. × robust. Our results suggested that the loss of ancestral gene flow from M. sieversii in cultivated apples accompanied the movement of European traders around the world since the Age of Discovery. Natural SNP variations showed that cultivated apples had higher nucleotide diversity than wild species and more unique SNPs than other apple groups. An apple ERECTA-like gene that underwent selection during domestication on 15th chromosome was identified as a likely major determinant of fruit length and diameter, and an NB-ARC domain-containing gene was found to strongly affect anthocyanin accumulation using a genome-wide association approach. Our results provide new insights into the origin and domestication of apples and will be useful in new breeding programmes and efforts to increase fruit crop productivity.

Silencing MdGH3-2/12 in apple reduces cadmium resistance via the regulation of AM colonization.

Arbuscular mycorrhizal fungi (AMF) can form a symbiotic relationship with most terrestrial plant roots, promote plant growth, and heavy metal (HM) tolerance and thus plays a crucial role in phytoremediation. However, research on the relationship between colonization level and HM tolerance is limited. In this study, apple (Malus domestica) Gretchen Hagen3 genes MdGH3-2/12 silencing plants were treated with four AMF and Cd combination treatments to determine AMF colonization levels, biomass, Cd accumulation, photosynthesis, fluorescence, reactive oxygen species (ROS) and antioxidant substance accumulation, and Cd uptake, transport and detoxification gene expression levels. Results indicate the greater sensitivity of transgenic plants under AMF inoculation and Cd treatment compared with wild type (WT) via lower AMF colonization levels, biomass accumulation, photosynthetic parameters, and the accumulation and clearance homeostasis of ROS, as well as lower detoxification expression levels and higher Cd uptake and transport expression levels. Our study essentially demonstrates that MdGH3-2/12 plays an important role in Cd stress tolerance by regulating AM colonization in apple.

Melatonin increases the performance of Malus hupehensis after UV-B exposure.

Melatonin, an evolutionarily conserved molecule, is implicated in numerous physiological processes in plants. To explore the potential roles of melatonin in response to UV-B radiation, we examined the influence of exogenous melatonin on Malus hupehensis Rehd. seedlings under two levels of UV-B radiation. Under UV-B stress, seedlings showed significant reduction in plant growth, biomass production, and root system development. However, 1 µM melatonin solution markedly alleviated these effects, especially at the higher dosage of UV-B radiation. The inhibitory effects of UV-B radiation on photosynthetic parameters, chlorophyll fluorescence parameters, stomatal apertures, chlorophyll levels and leaf membrane damages were also markedly alleviated with melatonin application. Melatonin treatment was also associated with higher activity and expression of genes encoding antioxidant enzymes (ascorbate peroxidase, catalase and peroxidase) and greater decline of H2O2 content in leaves exposed to UV-B. Moreover, exogenous melatonin treatment and UV-B stress increased the concentration of endogenous melatonin. The content of several phenolic compounds, including chlorogenic acid, phloridzin and quercetin-3-galactoside, also increased under UV-B stress, and these were further elevated significantly with melatonin addition. This study provides insight into the role(s) of endogenous melatonin in response to UV-B stress, and will facilitate application of exogenous melatonin in agriculture.

Genome-wide identification of genes involved in polyamine biosynthesis and the role of exogenous polyamines in Malus hupehensis Rehd. under alkaline stress.

Polyamines (PAs) in plants are growth substrates with functions similar to phytohormones. Although they contribute to diverse processes, little is known about their role in stress responses, especially for perennial woody plants. We conducted a genome-wide investigation of 18 sequences involved in PA biosynthesis in the genome of apple (Malus domestica). Further analysis was performed to construct a phylogenetic tree, analyze their protein motifs and gene structures. In addition, we developed their expression profiles in response to stressed conditions. Both MDP0000171041 (MdSAMDC1) and MDP0000198590 (MdSPDS1) were induced by alkaline, salt, ABA, cold, and dehydration stress treatments, suggesting that these genes are the main contributors to activities of S-adenosylmethionine decarboxylase (EC 4.1.1.50) and spermidine synthase (EC 2.5.1.16) in apple. Changes in PA biosynthesis under stress conditions indicated that spermidine and spermine are more essential than putrescine for apple, especially when responding to alkaline or salt stress. When seedlings of M. hupehensis Rehd. were supplied with exogenous PAs, their leaves showed less chlorosis under alkaline stress when compared with untreated plants. This application also inhibited the decline in SPAD levels and reduced relative electrolyte leakage in those stressed seedlings, while increasing their concentration of active iron. These results suggest that the alteration in PA biosynthesis confers enhanced tolerance to alkaline stress in M. hupehensis Rehd.

Genome-wide identification and expression profiling of the SnRK2 gene family in Malus prunifolia.

Sucrose non-fermenting-1-related protein kinase 2 (SnRK2) constitutes a small plant-specific serine/threonine kinase family with essential roles in the abscisic acid (ABA) signal pathway and in responses to osmotic stress. Although a genome-wide analysis of this family has been conducted in some species, little is known about SnRK2 genes in apple (Malus domestica). We identified 14 putative sequences encoding 12 deduced SnRK2 proteins within the apple genome. Gene chromosomal location and synteny analysis of the apple SnRK2 genes indicated that tandem and segmental duplications have likely contributed to the expansion and evolution of these genes. All 12 full-length coding sequences were confirmed by cloning from Malus prunifolia. The gene structure and motif compositions of the apple SnRK2 genes were analyzed. Phylogenetic analysis showed that MpSnRK2s could be classified into four groups. Profiling of these genes presented differential patterns of expression in various tissues. Under stress conditions, transcript levels for some family members were up-regulated in the leaves in response to drought, salinity, or ABA treatments. This suggested their possible roles in plant response to abiotic stress. Our findings provide essential information about SnRK2 genes in apple and will contribute to further functional dissection of this gene family.

Exogenous melatonin improves Malus resistance to Marssonina apple blotch.

We examined whether exogenously applied melatonin could improve resistance to Marssonina apple blotch (Diplocarpon mali) by apple [Malus prunifolia (Willd.) Borkh. cv. Donghongguo]. This serious disease leads to premature defoliation in the main regions of apple production. When plants were pretreated with melatonin, resistance was increased in the leaves. We investigated the potential roles for melatonin in modulating levels of hydrogen peroxide (H2O2), as well the activities of antioxidant enzymes and pathogenesis-related proteins during these plant-pathogen interactions. Pretreatment enabled plants to maintain intracellular H2O2 concentrations at steady-state levels and enhance the activities of plant defence-related enzymes, possibly improving disease resistance. Because melatonin is safe and beneficial to animals and humans, exogenous pretreatment might represent a promising cultivation strategy to protect plants against this pathogen infection.

Influence of rootstock on drought response in young 'Gale Gala' apple (Malus domestica Borkh.) trees.

BACKGROUND: Drought is a major environmental stress limiting plant growth, productivity, and survival worldwide. Rootstocks are widely used to enhance plants resistance to drought stresses. This study determined influence of rootstock on drought responses in 1-year-old 'Gale Gala' apple trees grafted onto Malus sieversii or M. hupehensis. RESULTS: Choice of rootstock resulted in differential response to drought stress. Specifically, M. sieversii caused less drought-induced reduction in relative growth rate, biomass accumulation, leaf area, leaf chlorophyll content, relative water content, photosynthesis rate and maximum chlorophyll fluorescence yield but greater increase in whole-plant water use efficiency compared to M. hupehensis. Secondly, compared with M. hupehensis, M. sieversii caused less drought-induced accumulation of reactive oxygen species but more increase in activities of antioxidant enzymes. In addition, xylem sap abscisic acid concentration was greater in trees grafted onto M. hupehensis than in those grafted onto M. sieversii under drought stress. CONCLUSION: 'Gale Gala' trees' response to drought stress was associated with the rootstock's genotype onto which it was grafted. Trees with M. sieversii as rootstock are more drought resistant than trees with M. hupehensis as rootstock, which suggests that M. sieversii can be widely used as rootstock in arid and semi-arid regions.