Epistasis between genetic variations on MdMYB109 and MdHXK1 exerts a large effect on sugar content in apple fruit.

Many quantitative traits are controlled by multiple genetic variations with minor effects, making it challenging to resolve the underlying genetic network and to apply functional markers in breeding. Affected by up to a hundred quantitative trait loci (QTLs), fruit-soluble sugar content is one of the most complex quantitative traits in apple (Malus sp.).

Allele-specific expression of AP2-like ABA repressor 1 regulates iron uptake by modulating rhizosphere pH in apple.

Genetic variation within a species can result in allelic expression for natural selection or breeding efforts. Here, we identified an iron (Fe) deficiency-inducible gene, AP2-like ABA repressor 1 (MdABR1), in apple (Malus domestica). MdABR1 exhibited differential expression at the allelic level (MdABR131A and MdABR131G) in response to Fe deficiency.

Natural variations in MdNAC18 exert major genetic effect on apple fruit harvest date by regulating ethylene biosynthesis genes.

Dissecting the genetic control of apple fruit harvest date (AFHD) into multiple Mendelian factors poses a significant challenge in modern genetics. Here, a quantitative trait locus (QTL) for AFHD was fine-mapped to the NAC transcription factor (TF) MdNAC18 within the interval defined by the overlap of QTLs Z03.5/Z03.

Bacillus B2 promotes root growth and enhances phosphorus absorption in apple rootstocks by affecting MhMYB15.

Due to the chelation of phosphorus in the soil, it becomes unavailable for plant growth and development. The mechanisms by which phosphorus-solubilizing bacteria activate immobilized phosphorus to promote the growth and development of woody plants, as well as the intrinsic molecular mechanisms, are not clear. Through the analysis of microbial communities in the rhizosphere 16S V3-V4 and a homologous gene encoding microbial alkaline phosphomonoesterase (phoD) in phosphate-efficient (PE) and phosphate-inefficient apple rootstocks, it was found that PE significantly enriched beneficial rhizobacteria.

Movement of ACC oxidase 3 mRNA from seeds to flesh promotes fruit ripening in apple.

Xenia, the phenomenon in which the pollen genotype directly affects the phenotypic characteristics of maternal tissues (i.e., fruit ripening), has applications in crop production and breeding.

switches the lateral root elongation to regulate dwarfing in apple plants.

Apple rootstock dwarfing and dense planting are common practices in apple farming. However, the dwarfing mechanisms are not understood. In our study, the expression of in the root system of dwarfing rootstock 'M9' was lower than in the vigorous rootstock from due to the deletion of the WUSATAg element in the promoter of the 'M9' genotype.

Mitogen-activated protein kinase MxMPK3-2 mediated phosphorylation of MxZR3.1 participates in regulating iron homoeostasis in apple rootstocks.

The micronutrient iron plays a crucial role in the growth and development of plants, necessitating meticulous regulation for its absorption by plants. Prior research has demonstrated that the transcription factor MxZR3.1 restricts iron absorption in apple rootstocks; however, the precise mechanism by which MxZR3.

miR164-MhNAC1 regulates apple root nitrogen uptake under low nitrogen stress.

Nitrogen is an essential nutrient for plant growth and serves as a signaling molecule to regulate gene expression inducing physiological, growth and developmental responses. An excess or deficiency of nitrogen may have adverse effects on plants. Studying nitrogen uptake will help us understand the molecular mechanisms of utilization for targeted molecular breeding.

Near-gapless and haplotype-resolved apple genomes provide insights into the genetic basis of rootstock-induced dwarfing.

Dwarfing rootstocks have transformed the production of cultivated apples; however, the genetic basis of rootstock-induced dwarfing remains largely unclear. We have assembled chromosome-level, near-gapless and haplotype-resolved genomes for the popular dwarfing rootstock 'M9', the semi-vigorous rootstock 'MM106' and 'Fuji', one of the most commonly grown apple cultivars. The apple orthologue of auxin response factor 3 (MdARF3) is in the Dw1 region of 'M9', the major locus for rootstock-induced dwarfing.

Genetic variations in participate in the negative regulation of mesocarp cell division and fruit size in species.

Unlabelled: Final fruit size of apple () cultivars is related to both mesocarp cell division and cell expansion during fruit growth, but it is unclear whether the cell division and/or cell enlargement determine most of the differences in fruit size between species. In this study, by using an interspecific hybrid population between "Zisai Pearl" and cultivar "Red Fuji," we found that the mesocarp cell number was the main causal factor of diversity in fruit size between species. Rapid increase in mesocarp cell number occurred prior to 28 days after anthesis (DAA), while cell size increased gradually after 28 DAA until fruit ripening.

Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits.

Structural variations (SVs) and copy number variations (CNVs) contribute to trait variations in fleshy-fruited species. Here, we assemble 10 genomes of genetically diverse Malus accessions, including the ever-green cultivar 'Granny Smith' and the widely cultivated cultivar 'Red Fuji'. Combining with three previously reported genomes, we assemble the pan-genome of Malus species and identify 20,220 CNVs and 317,393 SVs.

MdGRF11-MdARF19-2 module acts as a positive regulator of drought resistance in apple rootstock.

14-3-3 proteins play an important role in the response of plants to drought resistance. In this study, 14-3-3 protein MdGRF11 was cloned from Malus xiaojinensis, and its positive regulation of drought resistance was verified using Orin calli and M. xiaojinensis plants.

MxMPK6-2-mediated phosphorylation enhances the response of apple rootstocks to Fe deficiency by activating PM H -ATPase MxHA2.

Iron (Fe) deficiency significantly affects the growth and development, fruit yield and quality of apples. Apple roots respond to Fe deficiency stress by promoting H secretion, which acidifies the soil. In this study, the plasma membrane (PM) H -ATPase MxHA2 promoted H secretion and root acidification of apple rootstocks under Fe deficiency stress.

Genome-wide analysis of the MdZR gene family revealed MdZR2.2-induced salt and drought stress tolerance in apple rootstock.

The DNL-type zinc finger protein constitutes a zinc ribbon protein (ZR) family, which belongs to a branch of zinc finger protein and plays an essential role in response to abiotic stress. Here, we identified six apple (Malus domestica) MdZR genes. Based on their phylogenetic relationship and gene structure, the MdZR genes were divided into three categories, including MdZR1, MdZR2, and MdZR3.

Strigolactone regulates adventitious root formation via the MdSMXL7-MdWRKY6-MdBRC1 signaling cascade in apple.

Propagation through stem cuttings is a popular method worldwide for species such as fruit tree rootstocks and forest trees. Adventitious root (AR) formation from stem cuttings is crucial for effective and successful clonal propagation of apple rootstocks. Strigolactones (SLs) are newly identified hormones involved in AR formation.

Strigolactones in Plants and Their Interaction with the Ecological Microbiome in Response to Abiotic Stress.

Phytohormones play an essential role in enhancing plant tolerance by responding to abiotic stresses, such as nutrient deficiency, drought, high temperature, and light stress. Strigolactones (SLs) are carotenoid derivatives that occur naturally in plants and are defined as novel phytohormones that regulate plant metabolism, growth, and development. Strigolactone assists plants in the acquisition of defensive characteristics against drought stress by initiating physiological responses and mediating the interaction with soil microorganisms.

Genome-wide identification of WOX family members in nine Rosaceae species and a functional analysis of MdWOX13-1 in drought resistance.

WUSCHEL-related homeobox (WOX) transcription factors (TFs) are important in plant development processes and evolutionary novelties. In this study, a genome-wide comprehensive analysis of WOX genes from nine Rosaceae species was carried out, and their potential roles in Malus were subsequently investigated. 125 WOXs in 9 Rosaceae species were identified and classified into three clades, i.

Kinase MxMPK4-1 and calmodulin-binding protein MxIQM3 enhance apple root acidification during Fe deficiency.

Iron (Fe) deficiency is a long-standing issue in plant mineral nutrition. Ca2+ signals and the mitogen-activated protein kinase (MAPK) cascade are frequently activated in parallel to perceive external cues, but their interplay under Fe deficiency stress remains largely unclear. Here, the kinase MxMPK4-1, which is induced during the response to Fe deficiency stress in apple rootstock Malus xiaojinensis, cooperates with IQ-motif containing protein3 (MxIQM3).

A bulked segregant analysis tool for out-crossing species (BSATOS) and QTL-based genomics-assisted prediction of complex traits in apple.

Introduction: Genomic heterozygosity, self-incompatibility, and rich-in somatic mutations hinder the molecular breeding efficiency of outcrossing plants.

Objectives: We attempted to develop an efficient integrated strategy to identify quantitative trait loci (QTLs) and trait-associated genes, to develop gene markers, and to construct genomics-assisted prediction (GAP) modes.

Methods: A novel protocol, bulked segregant analysis tool for out-crossing species (BSATOS), is presented here, which is characterized by taking full advantage of all segregation patterns (including AB × AB markers) and haplotype information.

Transcription Factor IAA27 Positively Regulates P Uptake through Promoted Adventitious Root Development in Apple Plants.

Phosphate (P) deficiency severely limits the growth and production of plants. Adventitious root development plays an essential role in responding to low phosphorus stress for apple plants. However, the molecular mechanisms regulating adventitious root growth and development in response to low phosphorus stress have remained elusive.

Multi-omics analysis reveals the mechanism of bHLH130 responding to low-nitrogen stress of apple rootstock.

Nitrogen is critical for plant growth and development. With the increase of nitrogen fertilizer application, nitrogen use efficiency decreases, resulting in wasted resources. In apple (Malus domestica) rootstocks, the potential molecular mechanism for improving nitrogen uptake efficiency to alleviate low-nitrogen stress remains unclear.

Genome-wide identification of apple PPI genes and a functional analysis of the response of MxPPI1 to Fe deficiency stress.

Iron (Fe) deficiency affects plant growth and development. The proton pump interactor (PPI) in plants responds to multiple abiotic stresses, although it has not been well characterized under Fe deficiency stress. In this study, we systematically identified and analyzed the PPI gene family in apple.

Changes to bacterial communities and soil metabolites in an apple orchard as a legacy effect of different intercropping plants and soil management practices.

Intercropping is an important soil management practice for increasing orchard productivity and land-use efficiency because it has beneficial effects on soil microbial communities and soil properties. However, there is relatively little information available regarding the effects of different crops/grasses on soil microbial communities and soil metabolic products in apple orchards in arid and semi-arid regions. In this study, we showed the microbial communities of apple, intercropping plants, and sandy waste soil, using the third-generation PacBio SMRT long-read sequencing technology.