The apricot (Prunus armeniaca L.) genome elucidates Rosaceae evolution and beta-carotenoid synthesis

Multi-environment GWAS uncovers markers associated to biotic stress response and genotype-by-environment interactions in stone fruit trees

While breeding for improved immunity is essential to achieve sustainable fruit production, it also requires to account for genotype-by-environment interactions (G × E), which still represent a major challenge. To tackle this issue, we conducted a comprehensive study to identify genetic markers with main and environment-specific effects on pest and disease response in peach (Prunus persica) and apricot (Prunus armeniaca). Leveraging multienvironment trials (MET), we assessed the genetic architecture of resistance and tolerance to seven major pests and diseases through visual scoring of symptoms in naturally infected core collections, repeated within and between years and sites. We applied a series of genome-wide association models (GWAS) to both maximum of symptom severity and kinetic disease progression. These analyses lead to the identification of environment-shared quantitative trait loci (QTLs), environment-specific QTLs, and interactive QTLs with antagonist or differential effects across environments. We mapped 60 high-confidence QTLs encompassing a total of 87 candidate genes involved in both basal and host-specific responses, mostly consisting of the Leucine-Rich Repeat Containing Receptors (LRR-CRs) gene family. The most promising disease resistance candidate genes were found for peach leaf curl on LG4 and for apricot and peach rust on LG2 and LG4. These findings underscore the critical role of G × E in shaping the phenotypic response to biotic pressure, especially for blossom blight. Last, models including dominance effects revealed 123 specific QTLs, emphasizing the significance of non-additive genetic effects, therefore warranting further investigation. These insights will support the development of marker-assisted selection to improve the immunity of Prunus varieties in diverse environmental conditions.

Haplotype-resolved genome assembly provides new insights into the genomic origin of purple colour in Prunus mume

Prunus mume, an important ornamental woody plant in the Rosaceae family, contains many interspecific hybridizations. Purple colour is a breeding trait of aesthetic value for P. mume, but little is known about the origin and genetic architecture of this trait. Here we address these issues by producing a haplotype-resolved genome from an interspecific hybrid cultivar of P. mume (M) and P. cerasifera 'Pissardii' (C), named P. mume 'Meiren', followed by a detailed molecular characterization. The final length of the diploid genome is 499.47 Mb, with 250.66 Mb of haplotype M (HM) and 248.79 Mb of haplotype C (HC). Approximately 95.42% (476.61 Mb) of the phased assembly is further anchored to 16 homologous chromosomes. Based on the genomic variation, we identify a 1.8 Mb large-fragmented inversion (INV) on chromosome 1b of HC, which co-segregates with purple colour traits of 'Meiren' inherited from its purple C parent 'Pissardii'. We find that a MYB transcription factor, PmmMYB10.5b, resides at the distal breakpoint of the INV, which displays consistent allele-specific expression (ASE). By directly binding to the promoter of anthocyanin synthetic alleles, PmmMYB10.5b serves as a co-activator to promote anthocyanin accumulation in 'Meiren' organs. Notably, the INV identified in 'Meiren' is generated from 'Pissardii' rather than P. cerasifera, which alters the promoter sequence of PmmMYB10.5b, activates its expression and results in the purple colour trait. Results from this study shed light on the evolutionary origin of purple colour in 'Meiren' and could potentially provide guidance on the genetic improvement of colour traits in ornamental woody plants.

Integrated genomic and transcriptomic analyses reveal the genetic and molecular mechanisms underlying hawthorn peel color and seed hardness diversity

Hawthorn (Crataegus pinnatifida) fruit peel color and seed hardness are key traits that significantly impact economic value. We present here the high-quality chromosome-scale genomes of two cultivars, including the hard-seed, yellow-peel C. pinnatifida "Jinruyi" (JRY) and the soft-seed, red-peel C. pinnatifida "Ruanzi" (RZ). The assembled genomes comprising 17 chromosomes are 809.1 Mb and 760.5 Mb in size, achieving scaffold N50 values of 48.5 Mb and 46.8 Mb for JRY and RZ, respectively. Comparative genomic analysis identifies 3.6-3.8 million single nucleotide polymorphisms, 8.5-9.3 million insertions/deletions, and approximately 30 Mb of presence/absence variations across different hawthorn genomes. Through integrating differentially expressed genes and accumulated metabolites, we filter candidate genes CpMYB114 and CpMYB44 associated with differences in hawthorn fruit peel color and seed hardness, respectively. Functional validation confirms that the CpMYB114-CpANS regulates anthocyanin biosynthesis in hawthorn peels, contributing to the observed variation in peel color. CpMYB44-CpCOMT is significantly upregulated in JRY and is verified to promote lignin biosynthesis, resulting in the distinction in seed hardness. Overall, this study reveals the new insights into understanding of distinct peel pigmentation and seed hardness in hawthorn and provides an abundant resource for molecular breeding.

Chromosome-level assembly of Prunus serrula Franch genome

P. serrula is widely distributed in Yunnan, Xizang, and Sichuan, and usually grows at high altitudes between 2,600 and 3,900 meters above sea level. In this study, we obtained a high-quality chromosome-level assembly genome of P. serrula using Illumina sequencing, Oxford Nanopore ultra-long sequencing, and Hi-C technology. The genome was 284.5 Mb in length, with a scaffold N50 of 32.4 Mb and 91.9% of the assembly anchored onto 8 pseudochromosomes. BUSCO completeness value of 98.5% demonstrated a high completed genome, and a total of 35,151 protein-coding genes and 47,340 transcripts were annotated. Overall, this genome delivers valuable genetic resources for further phylogenomic studies and provides insights into the genetic architectures underlying high-altitude adaptation.

Unravelling the Chloroplast Genome of the Kazakh Apricot (Prunus armeniaca L.) Through MinION Long-Read Sequencing

The study of the genetic diversity and adaptation mechanisms of the Kazakh apricot (Prunus armeniaca L.) is essential for breeding programs and the conservation of plant genetic resources in arid environments. Despite this species' ecological and agricultural significance, its chloroplast genome remains poorly studied due to its complex repetitive structure and secondary metabolites that hinder high-molecular-weight DNA (HMW-DNA) extraction and long-read sequencing. To address this gap, our study aims to develop and optimise sequencing protocols for P. armeniaca under arid conditions using Oxford Nanopore's MinION technology. We successfully extracted HMW-DNA with 50-100 ng/μL concentrations and purity (A260/A280) between 1.8 and 2.0, ensuring high sequencing quality. A total of 10 GB of sequencing data was generated, comprising 155,046 reads, of which 74,733 (48.2%) had a Q-score ≥ 8. The average read length was 1679 bp, with a maximum of 31,144 bp. Chloroplast genome assembly resulted in 33,000 contigs with a total length of 1.1 Gb and a BUSCO completeness score of 97.3%. Functional annotation revealed key genes (nalC, AcrE, and mecC-type BlaZ) associated with stress tolerance and a substantial proportion (≈40%) of hypothetical proteins requiring further investigation. GC content analysis (40.25%) and GC skew data suggest the presence of specific regulatory elements linked to environmental adaptation. This study demonstrates the feasibility of using third-generation sequencing technologies to analyse complex plant genomes and highlights the genetic resilience of P. armeniaca to extreme conditions. The findings provide a foundation for breeding programs to improve drought tolerance and conservation strategies to protect Kazakhstan's unique arid ecosystems.

Novel insight of the SVP gene involved in pedicel length based on genomics analysis in cherry

KEY MESSAGE

PcSVP was identified based on Prunus conradinae genome and was further overexpressed in A. thaliana to comfirm it was a key factor in flower development, causing the pedicels elongation. Prunus conradinae is an endemic plant resource in China with high ornamental and economic values. To generate useful genomic resources for expanding insights into the evolutionary history of this important plant, the chromosome-level genome and organelle genomes of P. conradinae are de novo assembled and functionally annotated. The chromosome-level haploid genome of autotetraploid P. conradinae was assembled with 262.79 Mb with 27,802 protein-coding genes annotated. The complete chloroplast and mitochondrial genome of P. conradinae are found to be 157,715 bp and 434,334 bp, respectively. According to evolutionary analysis, P. conradinae was closely related to P. serrulata and P. yedoensis, and they diverged from their common ancestor approximately 6.0 million years ago. There were 108 gene families that significantly expanded during P. conradinae evolution and 56 shared positively selected genes. Selective sweep analysis based on the whole-genome resequencing of wild cherries from Fujian and Zhejiang indicated that genes involved in flower development and stress responses were potentially under selection. Pedicel length varied greatly among Prunus species and was a significant identifying characteristic. Ectopic overexpression of PcSVP in Arabidopsis thaliana suggested that it was a key factor in flower development, causing the sepals curling and pedicels elongation. These findings will contribute to the discovery of key functional genes involved in the agronomic or biological traits of P. conradinae, as well as the future development, utilisation and germplasm conservation of wild cherries.

Chromosome-level genome assembly of tetraploid Chinese cherry (Prunus pseudocerasus)

Chinese cherry belongs to the family Rosaceae, genus Prunus, and has high nutritional and economic value. 'Duiying' is a Chinese cherry variety local to Beijing, and has better performance than sweet cherry in terms of disease resistance. However, disease resistance resources of 'Duiying' have not been fully exploited partially due to the lack of a high-quality genome. In this study, we report a high-quality chromosome-scale genome assembly for Chinese cherry 'Duiying', by combining PacBio HiFi, Bionano and Hi-C sequencing data. The assembled genome has a size of 1035.19 Mb, with a scaffold N50 of 28.99 Mb, and 978.61 Mb (94.54%) assembled into 32 pseudochromosomes. A total of 547.16 Mb (52.86%) sequences were identified as repetitive sequences, and 114,451 protein-coding genes were annotated. Moreover, a total of 1635 microRNA (miRNA), 6637 transfer RNA (tRNA), 38,258 ribosomal RNA (rRNA), and 169 small nuclear RNAs (snRNA) genes were identified. The genome assembly presented here provides valuable genomic resources to enhance our understanding of genetic and molecular basis of Chinese cherry.

Dried Apricot Polyphenols Suppress the Growth of A549 Human Lung Adenocarcinoma Cells by Inducing Apoptosis via a Mitochondrial-Dependent Pathway

Dried apricots are rich in a variety of polyphenols, which have anti-cancer activity. In this study, 949 phenolic substances were found by means of UPLC-MS/MS, mainly including 2',7-dihydroxy-3',4'-dimethoxyisoflavan, scopoletin, rutin, quercetin-3-O-robinobioside, and elaidolinolenic acid. The results indicated that dried apricot polyphenols (DAPs) could cause cell cycle arrest in the G0/G1 and G2/M phases by decreasing the cyclin D1, CDK4, cyclin B1, CDK1, and CDK6 levels in A549 human lung adenocarcinoma cells. Moreover, the ROS and Bax levels were increased, and the Bcl-2 and mitochondrial membrane potential were decreased in A549 cells treated with DAP, increasing caspase-9, caspase-3, and cleaved-PARP1 activities and leading to apoptosis of the A549 cells. Meanwhile, tumor growth was also inhibited by DAPs in an A549 tumor-bearing mouse model, Bax and caspase-3 were upregulated, and Bcl-2 was downregulated, inducing apoptosis of lung cancer cells. In conclusion, DAPs could inhibit lung cancer cell growth by inducing apoptosis due to cell cycle arrest and mitochondria-dependent pathways.

Analysis of Kinship and Population Genetic Structure of 53 Apricot Resources Based on Whole Genome Resequencing

Based on the single nucleotide polymorphism (SNP) markers developed by whole genome resequencing (WGRS), the relationship and population genetic structure of 53 common apricot (P. armeniaca) varieties were analyzed to provide a theoretical basis for revealing the phylogenetic relationship and classification of the common apricot. WGRS was performed on 53 common apricot varieties, and high-quality SNP sites were obtained after alignment with the "Yinxiangbai" apricot genome as a reference. Phylogenetic analysis, G matrix analysis, principal component analysis, and population structure analysis were performed using Genome-wide Complex Trait Analysis (GCTA), FastTree, Admixture, and other software. The average comparison ratio between the sequencing results and the reference genome was 97.66%. After strict screening, 88,332,238 high-quality SNP sites were finally obtained. Based on the statistical SNP variation type, it was found that LNLJX had the largest number of variations (3,951,322) and the lowest base transition/base transversion ratio (ts/tv = 1.77), indicating that its gene exchange events occurred less frequently. Based on the SNP point estimation of the relationship and genetic distance between samples, the relationship between species was 1.41-0.01, among which PLDJX and BK1 had the closest relationship of 1.41, and YZH and LGWSX had the farthest relationship of 0.01. The genetic distance between species was 0.00367-0.264344, the genetic distance between HMX and JM was the closest, and the genetic distance between WYX and YX was the farthest, which was the largest. Phylogenetic tree, PCA, and genetic structure analysis results all divided 53 common apricot varieties into four groups, and the classification results were consistent. The SNP markers mined using WGRS technology are useful not only to analyze the variation of common apricots, but also to effectively identify their kinship and genetic structure, which plays a critical role in the classification and utilization of common apricot germplasm resources.

Study on the Mechanisms of Flavor Compound Changes During the Lactic Fermentation Process of Peach and Apricot Mixed Juice

This study employed headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) and liquid chromatography-mass spectrometry (LC-MS) for non-targeted metabolomics analyses to examine the impact of mixed fermentation with various lactic acid bacteria (LAB) on the flavor compounds and metabolites of peach and apricot mixed juice (PAMJ), specifically focusing on the alterations of volatile compounds and non-volatile metabolites, as well as their metabolic pathways during the fermentation process. A total of 185 volatiles were identified using HS-SPME-GC-MS analysis, revealing significant differential metabolites, including eugenol, benzaldehyde, and γ-decalactone etc. The results indicated that lactic fermentation significantly enhanced the overall flavor of the juice toward the end of the fermentation process. In the interim, untargeted metabolomics utilizing LC-MS identified 1846 divergent metabolites, with 564 exhibiting up-regulation and 1282 demonstrating down-regulation. The metabolic pathway study performed by the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed significant changes in the metabolic levels of amino acids and saccharides after the lactic fermentation of PAMJ. Primarily associated with amino acid metabolism and starch and sucrose metabolism pathways. This work establishes a theoretical foundation for advancing fermented fruit juices with superior quality.

Genome-wide identification of the Dof gene family: How it plays a part in mediating cold stress response in Prunus mume

DNA binding with a finger transcription factor (Dof) takes part in several plant physiological activities such as seed germination, flowering time, cold and drought resistance. Although the function, molecular phylogeny and expression pattern of Dof genes in Prunus mume was not clear yet. Here, the gene structure, motif, chromosome location and phylogenetic relationship of the Dof gene family in Prunus species was explored. We identified 24 members of the Dof gene family from P. mume, which were divided into 3 different subgroups. All these PmDof genes can be mapped to the pseudochromosome. Only one pair of tandem duplication genes are located in Chr3, whereas 8 pairs of segmentally duplicated PmDof genes located in Chr1, Chr2, Chr4, Chr5, and Chr7. Motif and gene structure analysis showed that each group had a similar conservative motif and similar exon/intron composition. Cis-acting elements analysis indicate that PmDofs may be involved in regulating abiotic stress response. Gene expression patterns showed that most PmDofs genes were specifically expressed in different tissues and at different stages. We next found that PmDofs genes display an obvious expression preference or specificity in cold stress response according to qRT-PCR analysis. We further observe a great cold resistance in PmDof10/11/20 OE lines, they showed lower electrolyte leakage rate, MDA content and higher soluble sugar/protein, POD/SOD/proline content than WT after -5 °C 6h freezing treatment. This research offers fresh perspectives on the development of PmDofs, enhancing our comprehension of the structure and role of plant Dof gene families.

Chromosome-scale genome assembly of Docynia delavayi provides new insights into the α-farnesene biosynthesis

Docynia delavayi is an economically significant fruit species with a high market potential due to the special aroma of its fruit. Here, a 653.34 Mb high-quality genome of D. delavayi was first reported, of which 93.8 % of the sequences (612.98 Mb) could be anchored to 17 chromosomes, containing 48,325 protein-coding genes. Ks analysis proved that two whole genome duplication (WGD) events occurred in D. delavayi, resulting in the expansion of genes associated with terpene biosynthesis, which promoted its fruit-specific aroma production. Combined multi-omics analysis, α-farnesene was detected as the most abundant aroma substance emitted by D. delavayi fruit during storage, meanwhile one α-farnesene synthase gene (AFS) and 15 transcription factors (TFs) were identified as the candidate genes potentially involved in α-farnesene biosynthesis. Further studies for the regulation network of α-farnesene biosynthesis revealed that DdebHLH, DdeERF1 and DdeMYB could activate the transcription of DdeAFS. To our knowledge, it is the first report that MYB TF plays a regulatory role in α-farnesene biosynthesis, which will greatly facilitate future breeding programs for D. delavayi.

The pan-plastome of Prunus mume: insights into Prunus diversity, phylogeny, and domestication history

Backgrounds

Prunus mume in the Rosaceae and commonly referred to as mei or Chinese plum is widely used as a traditional ornamental flowering plant and fruit tree in China. Although some population and genetic analyses have been conducted for this species, no extensive comparisons of genetic variation from plastomes have yet been investigated.

Methods

We de novo assembled a total of 322 complete P. mume plastomes in this study and did a series of comparative analyses to better resolve pan-plastomic patterns of P. mume. To determine the phylogeny and domestication history of this species, we reconstructed the phylogenetic tree of Prunus genus, and resolved the population structure of P. mume. We also examined the nucleotide variation of P. mume to find potential DNA barcodes.

Results

The assembled plastomes exhibited a typical quadripartite structure and ranged from 157,871 bp to 158,213 bp in total size with a GC content ranging from 36.73 to 36.75%. A total of 112 unique genes were identified. Single nucleotide variants (SNVs) were the most common variants found among the plastomes, followed by nucleotide insertions/deletions (InDels), and block substitutions with the intergenic spacer (IGS) regions containing the greatest number of variants. From the pan-plastome data six well-supported genetic clusters were resolved using multiple different population structure analyses. The different cultivars were unevenly distributed among multiple clades. We also reconstructed a phylogeny for multiple species of Prunus to better understand genus level diversity and history from which a complex introgressive relationship between mei and other apricots/plums was resolved.

Conclusion

This study constructed the pan-plastome of P. mume, which indicated the domestication of P. mume involved multiple genetic origins and possible matrilineal introgression from other species. The phylogenetic analysis in Prunus and the population structure of P. mume provide an important maternal history for Prunus and the groundwork for future studies on intergenomic sequence transfers, cytonuclear incompatibility, and conservation genetics.

A phased genome of the highly heterozygous 'Texas' almond uncovers patterns of allele-specific expression linked to heterozygous structural variants

The vast majority of traditional almond varieties are self-incompatible, and the level of variability of the species is very high, resulting in a high-heterozygosity genome. Therefore, information on the different haplotypes is particularly relevant to understand the genetic basis of trait variability in this species. However, although reference genomes for several almond varieties exist, none of them is phased and has genome information at the haplotype level. Here, we present a phased assembly of genome of the almond cv. Texas. This new assembly has 13% more assembled sequence than the previous version of the Texas genome and has an increased contiguity, in particular in repetitive regions such as the centromeres. Our analysis shows that the 'Texas' genome has a high degree of heterozygosity, both at SNPs, short indels, and structural variants level. Many of the SVs are the result of heterozygous transposable element insertions, and in many cases, they also contain genic sequences. In addition to the direct consequences of this genic variability on the presence/absence of genes, our results show that variants located close to genes are often associated with allele-specific gene expression, which highlights the importance of heterozygous SVs in almond.

Haplotype-resolved genome of Prunus zhengheensis provides insight into its evolution and low temperature adaptation in apricot

Prunus zhengheensis, an extremely rare population of apricots, originated in warm South-East China and is an excellent material for genetic breeding. However, most apricots and two related species (P. sibirica, P. mandshurica) are found in the cold northern regions in China and the mechanism of their distribution is still unclear. In addition, the classification status of P. zhengheensis is controversial. Thus, we generated a high-quality haplotype-resolved genome for P. zhengheensis, exploring key genetic variations in its adaptation and the causes of phylogenetic incongruence. We found extensive phylogenetic discordances between the nuclear and organelle phylogenies of P. zhengheensis, which could be explained by incomplete lineage sorting. A 242.22-Mb pan-genome of the Armeniaca section was developed with 13 chromosomal genomes. Importantly, we identified a 566-bp insertion in the promoter of the HSFA1d gene in apricot and showed that the activity of the HSFA1d promoter increased under low temperatures. In addition, HSFA1d overexpression in Arabidopsis thaliana indicated that HSFA1d positively regulated plant growth under chilling. Therefore, we hypothesized that the insertion in the promoter of HSFA1d in apricot improved its low-temperature adaptation, allowing it to thrive in relatively cold locations. The findings help explain the weather adaptability of Armeniaca plants.

Genomic evidence for evolutionary history and local adaptation of two endemic apricots: Prunus hongpingensis and P. zhengheensis

Apricot, belonging to the Armeniaca section of Rosaceae, is one of the economically important crop fruits that has been extensively cultivated. The natural wild apricots offer valuable genetic resources for crop improvement. However, some of them are endemic, with small populations, and are even at risk of extinction. In this study we unveil chromosome-level genome assemblies for two southern China endemic apricots, Prunus hongpingensis (PHP) and P. zhengheensis (PZH). We also characterize their evolutionary history and the genomic basis of their local adaptation using whole-genome resequencing data. Our findings reveal that PHP and PZH are closely related to Prunus armeniaca and form a distinct lineage. Both species experienced a decline in effective population size following the Last Glacial Maximum (LGM), which likely contributed to their current small population sizes. Despite the observed decrease in genetic diversity and heterozygosity, we do not observe an increased accumulation of deleterious mutations in these two endemic apricots. This is likely due to the combined effects of a low inbreeding coefficient and strong purifying selection. Furthermore, we identify a set of genes that have undergone positive selection and are associated with local environmental adaptation in PHP and PZH, respectively. These candidate genes can serve as valuable genetic resources for targeted breeding and improvement of cultivated apricots. Overall, our study not only enriches our comprehension of the evolutionary history of apricot species but also offers crucial insights for the conservation and future breeding of other endemic species amidst rapid climate changes.

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. Comparing 'M9' and 'MM106' genomes revealed a 9,723-bp allele-specific long terminal repeat retrotransposon/gypsy insertion, DwTE, located upstream of MdARF3. DwTE is cosegregated with the dwarfing trait in two segregating populations, suggesting its prospective utility in future dwarfing rootstock breeding. In addition, our pipeline discovered mobile mRNAs that may contribute to the development of dwarfed scion architecture. Our research provides valuable genomic resources and applicable methodology, which have the potential to accelerate breeding dwarfing rootstocks for apple and other perennial woody fruit trees.

15-cis-Phytoene Desaturase and 15-cis-Phytoene Synthase Can Catalyze the Synthesis of β-Carotene and Influence the Color of Apricot Pulp

Fruit color affects its commercial value. β-carotene is the pigment that provides color for many fruits and vegetables. However, the molecular mechanism of β-carotene metabolism during apricot ripening is largely unknown. Here, we investigated whether β-carotene content affects apricot fruit color. First, the differences in β-carotene content between orange apricot 'JTY' and white apricot 'X15' during nine developmental stages (S1-S9) were compared. β-carotene contents highly significantly differed between 'JTY' and 'X15' from S5 (color transition stage) onwards. Whole-transcriptome analysis showed that the β-carotene synthesis genes 15-cis-phytoene desaturase (PaPDS) and 15-cis-phytoene synthase (PaPSY) significantly differed between the two cultivars during the color transition stage. There was a 5 bp deletion in exon 11 of PaPDS in 'X15', which led to early termination of amino acid translation. Gene overexpression and virus-induced silencing analysis showed that truncated PaPDS disrupted the β-carotene biosynthesis pathway in apricot pulp, resulting in decreased β-carotene content and a white phenotype. Furthermore, virus-induced silencing analysis showed that PaPSY was also a key gene in β-carotene biosynthesis. These findings provide new insights into the molecular regulation of apricot carotenoids and provide a theoretical reference for breeding new cultivars of apricot.

A High-Quality Reference Genome Assembly of Prinsepia uniflora (Rosaceae)

This study introduces a meticulously constructed genome assembly at the chromosome level for the Rosaceae family species Prinsepia uniflora, a traditional Chinese medicinal herb. The final assembly encompasses 1272.71 megabases (Mb) distributed across 16 pseudochromosomes, boasting contig and super-scaffold N50 values of 2.77 and 79.32 Mb, respectively. Annotated within this genome is a substantial 875.99 Mb of repetitive sequences, with transposable elements occupying 777.28 Mb, constituting 61.07% of the entire genome. Our predictive efforts identified 49,261 protein-coding genes within the repeat-masked assembly, with 45,256 (91.87%) having functional annotations, 5127 (10.41%) demonstrating tandem duplication, and 2373 (4.82%) classified as transcription factor genes. Additionally, our investigation unveiled 3080 non-coding RNAs spanning 0.51 Mb of the genome sequences. According to our evolutionary study, P. uniflora underwent recent whole-genome duplication following its separation from Prunus salicina. The presented reference-level genome assembly and annotation for P. uniflora will significantly facilitate the in-depth exploration of genomic information pertaining to this species, offering substantial utility in comparative genomics and evolutionary analyses involving Rosaceae species.

Genome assembly and resequencing analyses provide new insights into the evolution, domestication and ornamental traits of crape myrtle

Crape myrtle (Lagerstroemia indica) is a globally used ornamental woody plant and is the representative species of Lagerstroemia. However, studies on the evolution and genomic breeding of L. indica have been hindered by the lack of a reference genome. Here we assembled the first high-quality genome of L. indica using PacBio combined with Hi-C scaffolding to anchor the 329.14-Mb genome assembly into 24 pseudochromosomes. We detected a previously undescribed independent whole-genome triplication event occurring 35.5 million years ago in L. indica following its divergence from Punica granatum. After resequencing 73 accessions of Lagerstroemia, the main parents of modern crape myrtle cultivars were found to be L. indica and L. fauriei. During the process of domestication, genetic diversity tended to decrease in many plants, but this was not observed in L. indica. We constructed a high-density genetic linkage map with an average map distance of 0.33 cM. Furthermore, we integrated the results of quantitative trait locus (QTL) using genetic mapping and bulk segregant analysis (BSA), revealing that the major-effect interval controlling internode length (IL) is located on chr1, which contains CDL15, CRG98, and GID1b1 associated with the phytohormone pathways. Analysis of gene expression of the red, purple, and white flower-colour flavonoid pathways revealed that differential expression of multiple genes determined the flower colour of L. indica, with white flowers having the lowest gene expression. In addition, BSA of purple- and green-leaved individuals of populations of L. indica was performed, and the leaf colour loci were mapped to chr12 and chr17. Within these intervals, we identified MYB35, NCED, and KAS1. Our genome assembly provided a foundation for investigating the evolution, population structure, and differentiation of Myrtaceae species and accelerating the molecular breeding of L. indica.

l-Glutamate maintains the quality of apple fruit by mediating carotenoid, sorbitol and sucrose metabolisms

BACKGROUND

l-Glutamate is involved in many important chemical reactions in horticultural products and improves postharvest disease resistance. Quality decline of apple fruit caused by senescence and fungus invasion often leads to tremendous losses during logistics. This study was performed to evaluate the variations of quality attributes, carotenoid, sorbitol and sucrose metabolisms in apples (cv. Qiujin) after l-glutamate dipping treatment.

RESUITS

l-Glutamate immersion maintained high values of L*, a* and b*, flesh firmness, titratable acidity, as well as the total soluble solids, soluble sugar, reducing sugar and ascorbic acid contents in apples. l-Glutamate also decreased mass loss, respiratory rate and ethylene release, enhanced sucrose synthase-cleavage, acid invertase and neutral invertase activities, whereas reduced sorbitol dehydrogenase, sucrose phosphate synthase, sucrose synthase synthesis and sorbitol oxidase activities in apples. Moreover, l-glutamate inhibited lutein, β-carotene and lycopene accumulation, and down-regulated phytoene synthase, lycopene β-cyclase, ζ-carotene desaturase, phytoene desaturase, carotenoid isomerase, ζ-carotene isomerase and carotenoids cleavage dioxygenase gene expressions, but up-regulated 9-cis-epoxycarotenoid dioxygenase gene expression in apples.

CONCLUSION

Postharvest l-glutamate dipping treatment can keep apple quality by modulating key enzyme activity and gene expression in sorbitol, sucrose and carotenoid metabolisms. © 2023 Society of Chemical Industry.

A Chromosome-Level Genome of 'Xiaobaixing' (Prunus armeniaca L.) Provides Clues to Its Domestication and Identification of Key bHLH Genes in Amygdalin Biosynthesis

Apricot is a widely cultivated fruit tree of the drupe family, and its sweet/bitter kernel traits are important indicators of the quality and merchantability of apricots. The sweetness/bitterness traits were mainly determined by amygdalin content. However, the lack of high-quality genomes has limited insight into the traits. In this study, a high-quality genome of 'Xiaobaixing' was obtained by using single-molecule sequencing and chromosome-conformation capture techniques, with eight chromosomes of 0.21 Gb in length and 52.80% repetitive sequences. A total of 29,157 protein-coding genes were predicted with contigs N50 = 3.56 Mb and scaffold N50 = 26.73 Mb. Construction of phylogenetic trees of 15 species of Rosaceae fruit trees, with 'Xiaobaixing' differentiated by 5.3 Ma as the closest relative to 'Yinxiangbai'. GO functional annotation and KEGG enrichment analysis identified 227 specific gene families to 'Xiaobaixing', with 569 expansion-gene families and 1316 contraction-gene families, including the significant expansion of phenylalanine N-monooxygenase and β-glucosidase genes associated with amygdalin synthesis, significant contraction of wild black cherry glucoside β-glucosidase genes, amygdalin β-glucosidase genes, and β-glucosidase genes, and significant enrichment of positively selected genes in the cyanogenic amino acid metabolic pathway. The 88 bHLH genes were identified in the genome of 'Xiaobaixing', and ParbHLH66 (rna-Par24659.1) was found to be a key gene for the identification of sweet/bitter kernels of apricots. The amino acid sequence encoded by its gene is highly conserved in the species of Prunus mume, Prunus dulcis, Prunus persica, and Prunus avium and may be participating in the regulation of amygdalin biosynthesis, which provides a theoretical foundation for the molecular identification of sweet/bitter kernels of apricots.

Phylogeography of 912 Cherry Accessions Insight into Independent Origins of Fruiting Cherries and Domestication Footprints of Cultivated Chinese Cherry (Prunus pseudocerasus Lindl.)

The subgenus Cerasus (Rosaceae) contain numerous fruit trees and ornamentals with high economic values. The origin and genetic divergence among various types of fruiting cherries always remain a perplexing issue. We employed three plastom fragments and ITS sequence matrices derived from 912 cherry accessions to elucidate the phylogeographic structure and genetic relationship among fruiting cherries, as well as the origin and domestication of cultivated Chinese cherry. The integration of haplotype genealogies, Approximate Bayesian computation (ABC) approach and estimation of genetic differentiation within and between different groups and lineages has facilitated the resolution of several previously unresolved questions. Firstly, distant phylogenetic relationships between Cerasus and Microcerasus accessions, as indicated by both nuclear and chloroplast data, suggested independent origins and evolution for these two taxa. Moreover, two distinct geographic origin centers (Europe and China) have been confirmed, with significant phylogeographic signals and high genetic differentiation observed between cherries from these regions. This may be attributed to long-term geographic isolation caused by Himalaya-Hengduan Mountains. Our phylogeographic analyses and ABC analysis suggested that cherries inhabiting in China may have undergone multiple hybridization events during the glacial refugia of the eastern edge and southern Himalaya-Hengduan Mountains, followed by rapid radiation throughout their current habitats during interglacial period. The discrepancy between nuclear and chloroplast data may be attributed to hybridization events and incomplete lineage sorting. Furthermore, we speculated that the domesticated Chinese cherries were derived from wild accessions in Longmenshan Fault Zones approximately 2600 years ago. We have also traced the domestication processes and dispersal routes of cultivated Chinese cherries.

Genome-Wide Identification of the MAPK and MAPKK Gene Families in Response to Cold Stress in Prunus mume

Protein kinases of the MAPK cascade family (MAPKKK-MAPKK-MAPK) play an essential role in plant stress response and hormone signal transduction. However, their role in the cold hardiness of Prunus mume (Mei), a class of ornamental woody plant, remains unclear. In this study, we use bioinformatic approaches to assess and analyze two related protein kinase families, namely, MAP kinases (MPKs) and MAPK kinases (MKKs), in wild P. mume and its variety P. mume var. tortuosa. We identify 11 PmMPK and 7 PmMKK genes in the former species and 12 PmvMPK and 7 PmvMKK genes in the latter species, and we investigate whether and how these gene families contribute to cold stress responses. Members of the MPK and MKK gene families located on seven and four chromosomes of both species are free of tandem duplication. Four, three, and one segment duplication events are exhibited in PmMPK, PmvMPK, and PmMKK, respectively, suggesting that segment duplications play an essential role in the expansion and evolution of P. mume and its gene variety. Moreover, synteny analysis suggests that most MPK and MKK genes have similar origins and involved similar evolutionary processes in P. mume and its variety. A cis-acting regulatory element analysis shows that MPK and MKK genes may function in P. mume and its variety's development, modulating processes such as light response, anaerobic induction, and abscisic acid response as well as responses to a variety of stresses, such as low temperature and drought. Most PmMPKs and PmMKKs exhibited tissue-specifific expression patterns, as well as time-specific expression patterns that protect them through cold. In a low-temperature treatment experiment with the cold-tolerant cultivar P. mume 'Songchun' and the cold-sensitive cultivar 'Lve', we find that almost all PmMPK and PmMKK genes, especially PmMPK3/5/6/20 and PmMKK2/3/6, dramatically respond to cold stress as treatment duration increases. This study introduces the possibility that these family members contribute to P. mume's cold stress response. Further investigation is warranted to understand the mechanistic functions of MAPK and MAPKK proteins in P. mume development and response to cold stress.

Comparative Anatomical and Transcriptomics Reveal the Larger Cell Size as a Major Contributor to Larger Fruit Size in Apricot

Fruit size is one of the essential quality traits and influences the economic value of apricots. To explore the underlying mechanisms of the formation of differences in fruit size in apricots, we performed a comparative analysis of anatomical and transcriptomics dynamics during fruit growth and development in two apricot cultivars with contrasting fruit sizes (large-fruit Prunus armeniaca 'Sungold' and small-fruit P. sibirica 'F43'). Our analysis identified that the difference in fruit size was mainly caused by the difference in cell size between the two apricot cultivars. Compared with 'F43', the transcriptional programs exhibited significant differences in 'Sungold', mainly in the cell expansion period. After analysis, key differentially expressed genes (DEGs) most likely to influence cell size were screened out, including genes involved in auxin signal transduction and cell wall loosening mechanisms. Furthermore, weighted gene co-expression network analysis (WGCNA) revealed that PRE6/bHLH was identified as a hub gene, which interacted with 1 TIR1, 3 AUX/IAAs, 4 SAURs, 3 EXPs, and 1 CEL. Hence, a total of 13 key candidate genes were identified as positive regulators of fruit size in apricots. The results provide new insights into the molecular basis of fruit size control and lay a foundation for future breeding and cultivation of larger fruits in apricot.

Genome assembly, resequencing and genome-wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry

Flowering cherry is a very popular species around the world. High-quality genome resources for different elite cultivars are needed, and the understanding of their origins and the regulation of key ornamental traits are limited for this tree. Here, a high-quality chromosome-scale genome of Prunus campanulata 'Plena' (PCP), which is a native and elite flowering cherry cultivar in China, was generated. The contig N50 of the genome was 18.31 Mb, and 99.98% of its contigs were anchored to eight chromosomes. Furthermore, a total of 306 accessions of flowering cherry germplasm and six lines of outgroups were collected. Resequencing of these 312 lines was performed, and 761 267 high-quality genomic variants were obtained. The origins of flowering cherry were predicted, and these 306 accessions could be classified into three clades, A, B and C. According to phylogenetic analysis, we predicted two origins of flowering cherry. Flowering cherry in clade A originated in southern China, such as in the Himalayan Mountains, while clades B and C originated in northeastern China. Finally, a genome-wide association study of flower colour was performed for all 312 accessions of flowering cherry germplasm. A total of seven quantitative trait loci (QTLs) were identified. One gene encoding glycosylate transferase was predicted as the candidate gene for one QTL. Taken together, our results provide a valuable genomic resource and novel insights into the origin, evolution and flower colour variations of flowering cherry.

BCH1 expression pattern contributes to the fruit carotenoid diversity between peach and apricot

Peach (Prunus persica L. Batsch) and apricot (Prunus armeniaca L.) are two species of economic importance for fruit production in the genus Prunus. Peach and apricot fruits exhibit significant differences in carotenoid levels and profiles. HPLC-PAD analysis showed that a greater content of β-carotene in mature apricot fruits is primarily responsible for orange color, while peach fruits showed a prominent accumulation of xanthophylls (violaxanthin and cryptoxanthin) with yellow color. There are two β-carotene hydroxylase genes in both peach and apricot genomes. Transcriptional analysis revealed that BCH1 expresses highly in peach but lowly in apricot fruit, showing a correlation with peach and apricot fruit carotenoid profiles. By using a carotenoid engineered bacterial system, it was demonstrated that there was no difference in the BCH1 enzymatic activity between peach and apricot. Comparative analysis about the putative cis-acting regulatory elements between peach and apricot BCH1 promoters provided important information for our understanding of the differences in promoter activity of the BCH1 genes in peach and apricot. Therefore, we investigated the promoter activity of BCH1 gene through a GUS detection system, and confirmed that the difference in the transcription level of the BCH1 gene resulted from the difference of the promoter function. This study provides important perspective to understanding the diversity of carotenoid accumulation in Prunus fruits such as peach and apricot. In particular, BCH1 gene is proposed as a main predictor for β-carotene content in peach and apricot fruits during the ripening process.

Advances in genomics for diversity studies and trait improvement in temperate fruit and nut crops under changing climatic scenarios

Genetic improvement of temperate fruit and nut crops through conventional breeding methods is not sufficient alone due to its extreme time-consuming, cost-intensive, and hard-to-handle approach. Again, few other constraints that are associated with these species, viz., their long juvenile period, high heterozygosity, sterility, presence of sexual incompatibility, polyploidy, etc., make their selection and improvement process more complicated. Therefore, to promote precise and accurate selection of plants based on their genotypes, supplement of advanced biotechnological tools, viz., molecular marker approaches along with traditional breeding methods, is highly required in these species. Different markers, especially the molecular ones, enable direct selection of genomic regions governing the trait of interest such as high quality, yield, and resistance to abiotic and biotic stresses instead of the trait itself, thus saving the overall time and space and helping screen fruit quality and other related desired traits at early stages. The availability of molecular markers like SNP (single-nucleotide polymorphism), DArT (Diversity Arrays Technology) markers, and dense molecular genetic maps in crop plants, including fruit and nut crops, led to a revelation of facts from genetic markers, thus assisting in precise line selection. This review highlighted several aspects of the molecular marker approach that opens up tremendous possibilities to reveal valuable information about genetic diversity and phylogeny to boost the efficacy of selection in temperate fruit crops through genome sequencing and thus cultivar improvement with respect to adaptability and biotic and abiotic stress resistance in temperate fruit and nut species.

The Role of Italy in the Use of Advanced Plant Genomic Techniques on Fruit Trees: State of the Art and Future Perspectives

Climate change is deeply impacting the food chain production, lowering quality and yield. In this context, the international scientific community has dedicated many efforts to enhancing resilience and sustainability in agriculture. Italy is among the main European producers of several fruit trees; therefore, national research centers and universities undertook several initiatives to maintain the specificity of the 'Made in Italy' label. Despite their importance, fruit crops are suffering from difficulties associated with the conventional breeding approaches, especially in terms of financial commitment, land resources availability, and long generation times. The 'new genomic techniques' (NGTs), renamed in Italy as 'technologies for assisted evolution' (TEAs), reduce the time required to obtain genetically improved cultivars while precisely targeting specific DNA sequences. This review aims to illustrate the role of the Italian scientific community in the use of NGTs, with a specific focus on Citrus, grapevine, apple, pear, chestnut, strawberry, peach, and kiwifruit. For each crop, the key genes and traits on which the scientific community is working, as well as the technological improvements and advancements on the regeneration of local varieties, are presented. Lastly, a focus is placed on the legal aspects in the European and in Italian contexts.

Identification of key gene networks related to the freezing resistance of apricot kernel pistils by integrating hormone phenotypes and transcriptome profiles

BACKGROUND

Apricot kernel, a woody oil tree species, is known for the high oil content of its almond that can be used as an ideal feedstock for biodiesel production. However, apricot kernel is vulnerable to spring frost, resulting in reduced or even no yield. There are no effective countermeasures in production, and the molecular mechanisms underlying freezing resistance are not well understood.

RESULTS

We used transcriptome and hormone profiles to investigate differentially responsive hormones and their associated co-expression patterns of gene networks in the pistils of two apricot kernel cultivars with different cold resistances under freezing stress. The levels of auxin (IAA and ICA), cytokinin (IP and tZ), salicylic acid (SA) and jasmonic acid (JA and ILE-JA) were regulated differently, especially IAA between two cultivars, and external application of an IAA inhibitor and SA increased the spring frost resistance of the pistils of apricot kernels. We identified one gene network containing 65 hub genes highly correlated with IAA. Among these genes, three genes in auxin signaling pathway and three genes in brassinosteroid biosynthesis were identified. Moreover, some hub genes in this network showed a strong correlation such as protein kinases (PKs)-hormone related genes (HRGs), HRGs-HRGs and PKs-Ca²⁺ related genes.

CONCLUSIONS

Ca²⁺, brassinosteroid and some regulators (such as PKs) may be involved in an auxin-mediated freezing response of apricot kernels. These findings add to our knowledge of the freezing response of apricot kernels and may provide new ideas for frost prevention measures and high cold-resistant apricot breeding.

Down-regulation of NCED leads to the accumulation of carotenoids in the flesh of F1 generation of peach hybrid

Flesh color is an important target trait in peach [Prunus persica (L.) Batsch] breeding. In this study, two white-fleshed peach cultivars were crossed [Changsong Whitepeach (WP-1) × 'Xiacui'], and their hybrid F₁ generation showed color segregation of white flesh (BF1) and yellow flesh (HF1). Metabolome analysis revealed that the flesh color segregation in the hybrid F₁ generation was related to the carotenoid content. The decrease in β-carotene and β-cryptoxanthin in BF1 flesh and increase in β-cryptoxanthin oleate, rubixanthin caprate, rubixanthin laurate and zeaxanthin dipalmitate in HF1 flesh contributed to their difference in carotenoid accumulation. Transcriptome analysis demonstrated that compared with BF1, HF1 showed significant up-regulation and down-regulation of ZEP and CCD8 at the core-hardening stage, respectively, while significant down-regulation of NCED in the whole fruit development stage. The down-regulation of NCED might inhibit the breakdown of the violaxanthin and its upstream substances and further promote the accumulation of carotenoids, resulting in yellow flesh. Therefore, NCED may be a key gene controlling the fruit color traits of peach. In this study, targeted metabolomics and transcriptomics were used to jointly explore the mechanism controlling the fruit color of peach, which may help to identify the key genes for the differences in carotenoid accumulation and provide a reference for the breeding of yellow-fleshed peach.

Spontaneous, Artificial, and Genome Editing-Mediated Mutations in Prunus

Mutation is a source of genetic diversity widely used in breeding programs for the acquisition of agronomically interesting characters in commercial varieties of the Prunus species, as well as in the rest of crop species. Mutation can occur in nature at a very low frequency or can be induced artificially. Spontaneous or bud sport mutations in somatic cells can be vegetatively propagated to get an individual with the mutant phenotype. Unlike animals, plants have unlimited growth and totipotent cells that let somatic mutations to be transmitted to the progeny. On the other hand, in vitro tissue culture makes it possible to induce mutation in plant material and perform large screenings for mutant’s selection and cleaning of chimeras. Finally, targeted mutagenesis has been boosted by the application of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 and Transcription activator-like effector nuclease (TALEN) editing technologies. Over the last few decades, environmental stressors such as global warming have been threatening the supply of global demand for food based on population growth in the near future. For this purpose, the release of new varieties adapted to such changes is a requisite, and selected or generated Prunus mutants by properly regulated mechanisms could be helpful to this task. In this work, we reviewed the most relevant mutations for breeding traits in Prunus species such as flowering time, self-compatibility, fruit quality, and disease tolerance, including new molecular perspectives in the present postgenomic era including CRISPR/Cas9 and TALEN editing technologies.

Accurate Chromosome Identification in the Prunus Subgenus Cerasus (Prunus pseudocerasus) and its Relatives by Oligo-FISH

A precise, rapid and straightforward approach to chromosome identification is fundamental for cytogenetics studies. However, the identification of individual chromosomes was not previously possible for Chinese cherry or other Prunus species due to the small size and similar morphology of their chromosomes. To address this issue, we designed a pool of oligonucleotides distributed across specific pseudochromosome regions of Chinese cherry. This oligonucleotide pool was amplified through multiplex PCR with specific internal primers to produce probes that could recognize specific chromosomes. External primers modified with red and green fluorescence tags could produce unique signal barcoding patterns to identify each chromosome concomitantly. The same oligonucleotide pool could also discriminate all chromosomes in other Prunus species. Additionally, the 5S/45S rDNA probes and the oligo pool were applied in two sequential rounds of fluorescence in situ hybridization (FISH) localized to chromosomes and showed different distribution patterns among Prunus species. At the same time, comparative karyotype analysis revealed high conservation among P. pseudocerasus, P. avium, and P. persica. Together, these findings establish this oligonucleotide pool as the most effective tool for chromosome identification and the analysis of genome organization and evolution in the genus Prunus.

Integrated Metabolomic and Transcriptomic Analyses Reveal the Basis for Carotenoid Biosynthesis in Sweet Potato (Ipomoea batatas (L.) Lam.) Storage Roots

Carotenoids are important compounds of quality and coloration within sweet potato storage roots, but the mechanisms that govern the accumulation of these carotenoids remain poorly understood. In this study, metabolomic and transcriptomic analyses of carotenoids were performed using young storage roots (S2) and old storage roots (S4) from white-fleshed (variety S19) and yellow-fleshed (variety BS) sweet potato types. S19 storage roots exhibited significantly lower total carotenoid levels relative to BS storage roots, and different numbers of carotenoid types were detected in the BS-S2, BS-S4, S19-S2, and S19-S4 samples. β-cryptoxanthin was identified as a potential key driver of differences in root coloration between the S19 and BS types. Combined transcriptomic and metabolomic analyses revealed significant co-annotation of the carotenoid and abscisic acid (ABA) metabolic pathways, PSY (phytoene synthase), CHYB (β-carotene 3-hydroxylase), ZEP (zeaxanthin epoxidase), NCED3 (9-cis-epoxycarotenoid dioxygenase 3), ABA2 (xanthoxin dehydrogenase), and CYP707A (abscisic acid 8'-hydroxylase) genes were found to be closely associated with carotenoid and ABA content in these sweet potato storage roots. The expression patterns of the transcription factors OFP and FAR1 were associated with the ABA content in these two sweet potato types. Together, these results provide a valuable foundation for understanding the mechanisms governing carotenoid biosynthesis in storage roots, and offer a theoretical basis for sweet potato breeding and management.

Genetic dissection of fruit maturity date in apricot (P. armeniaca L.) through a Single Primer Enrichment Technology (SPET) approach

Background

Single primer enrichment technology (SPET) is an emerging and increasingly popular solution for high-throughput targeted genotyping in plants. Although SPET requires a priori identification of polymorphisms for probe design, this technology has potentially higher reproducibility and transferability compared to other reduced representation sequencing (RRS) approaches, also enabling the discovery of closely linked polymorphisms surrounding the target one.

Results

The potential for SPET application in fruit trees was evaluated by developing a 25K target SNPs assay to genotype a panel of apricot accessions and progenies. A total of 32,492 polymorphic sites were genotyped in 128 accessions (including 8,188 accessory non-target SNPs) with extremely low levels of missing data and a significant correlation of allelic frequencies compared to whole-genome sequencing data used for array design. Assay performance was further validated by estimating genotyping errors in two biparental progenies, resulting in an overall 1.8% rate. SPET genotyping data were used to infer population structure and to dissect the architecture of fruit maturity date (MD), a quantitative reproductive phenological trait of great agronomical interest in apricot species. Depending on the year, GWAS revealed loci associated to MD on several chromosomes. The QTLs on chromosomes 1 and 4 (the latter explaining most of the phenotypic variability in the panel) were the most consistent over years and were further confirmed by linkage mapping in two segregating progenies.

Conclusions

Besides the utility for marker assisted selection and for paving the way to in-depth studies to clarify the molecular bases of MD trait variation in apricot, the results provide an overview of the performance and reliability of SPET for fruit tree genetics.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08901-1.

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. Three PPI candidate genes were found, and they contained 318-1349 amino acids and 3-7 introns. Under Fe deficiency stress, we analyzed the expression of all the PPI genes in roots of apple rootstock Malus xiaojinensis. Expression of the gene MD11G1247800, designated PPI1, is obviously induced by Fe deficiency treatment in M. xiaojinensis. We first cloned MxPPI1 from M. xiaojinensis and determined its subcellular localization, which indicated that it is localized in the cell membrane and nucleus in tobacco. We found that the level of expression of the MxPPI1 protein increased significantly under Fe deficiency stress in apple calli. Moreover, overexpressing MxPPI1 in apple calli enhanced the activities of ferric chelate reductase and H⁺-ATPase, H⁺ secretion, MxHA2 gene expression and total Fe content when compared with the wild type calli. We further found that MxPPI1 interacted with MxHA2 using bimolecular fluorescence complementation and luciferase complementation assays. Overall, we demonstrated that MxPPI1 interacts with MxHA2 to enhance the activity of H⁺-ATPase to regulate Fe absorption in M. xiaojinensis.

Integration of genome and transcriptome reveal molecular regulation mechanism of early flowering trait in Prunus genus (Prunus mume and Prunus persica)

Flowering time is crucial for the survival and reproduction. Prunus genus belongs to the Rosaceae family and includes several hundred species of flowering trees and shrubs with important ornamental and economic values. However, the molecular mechanism underlying early flowering in Prunus genus is unclear. Here, we utilized the genome and transcriptome of P. mume and P. persica to explore the transcriptional regulation mechanism of early flowering. Comparative genomics found that genes accounting for 92.4% of the total P. mume genome and 91.2% of the total P. persica genome belonged to orthogroups. A total of 19,169 orthogroups were found between P. mume and P. persica, including 20,431 corresponding orthologues and 20,080 collinearity gene pairs. A total of 305 differentially expressed genes (DEGs) associated with early flowering were found, among which FT, TLI65, and NAP57 were identified as hub genes in the early flowering regulation pathway. Moreover, we identified twenty-five transcription factors (TFs) from nine protein families, including MADS-box, AP2/ERF, and MYB. Our results provide insights into the underlying molecular model of flowering time regulation in Prunus genus and highlight the utility of multi-omics in deciphering the properties of the inter-genus plants.

Whole Transcriptome Analyses of Apricots and Japanese Plum Fruits after 1-MCP (Ethylene-Inhibitor) and Ethrel (Ethylene-Precursor) Treatments Reveal New Insights into the Physiology of the Ripening Process

The physiology of Prunus fruit ripening is a complex and not completely understood process. To improve this knowledge, postharvest behavior during the shelf-life period at the transcriptomic level has been studied using high-throughput sequencing analysis (RNA-Seq). Monitoring of fruits has been analyzed after different ethylene regulator treatments, including 1-MCP (ethylene-inhibitor) and Ethrel (ethylene-precursor) in two contrasting selected apricot (Prunus armeniaca L.) and Japanese plum (P. salicina L.) cultivars, ‘Goldrich’ and ‘Santa Rosa’. KEEG and protein–protein interaction network analysis unveiled that the most significant metabolic pathways involved in the ripening process were photosynthesis and plant hormone signal transduction. In addition, previously discovered genes linked to fruit ripening, such as pectinesterase or auxin-responsive protein, have been confirmed as the main genes involved in this process. Genes encoding pectinesterase in the pentose and glucuronate interconversions pathway were the most overexpressed in both species, being upregulated by Ethrel. On the other hand, auxin-responsive protein IAA and aquaporin PIP were both upregulated by 1-MCP in ‘Goldrich’ and ‘Santa Rosa’, respectively. Results also showed the upregulation of chitinase and glutaredoxin 3 after Ethrel treatment in ‘Goldrich’ and ‘Santa Rosa’, respectively, while photosystem I subunit V psaG (photosynthesis) was upregulated after 1-MCP in both species. Furthermore, the overexpression of genes encoding GDP-L-galactose and ferredoxin in the ascorbate and aldarate metabolism and photosynthesis pathways caused by 1-MCP favored antioxidant activity and therefore slowed down the fruit senescence process.

An LTR retrotransposon in the promoter of a PsMYB10.2 gene associated with the regulation of fruit flesh color in Japanese plum

Japanese plums exhibit wide diversity of fruit coloration. The red to black hues are caused by the accumulation of anthocyanins, while their absence results in yellow, orange or green fruits. In Prunus, MYB10 genes are determinants for anthocyanin accumulation. In peach, QTLs for red plant organ traits map in an LG3 region with three MYB10 copies (PpMYB10.1, PpMYB10.2 and PpMYB10.3). In Japanese plum the gene copy number in this region differs with respect to peach: there are at least three copies of PsMYB10.1, with the expression of one of them (PsMYB10.1a) correlating with fruit skin color. The objective of this study was to determine a possible role of LG3-PsMYB10 genes in the natural variability of the flesh color trait and to develop a molecular marker for marker-assisted selection (MAS). We explored the variability within the LG3-PsMYB10 region using long-range sequences obtained in previous studies through CRISPR-Cas9 enrichment sequencing. We found that the PsMYB10.2 gene was only expressed in red flesh fruits. Its role in promoting anthocyanin biosynthesis was validated by transient overexpression in Japanese plum fruits. The analysis of long-range sequences identified an LTR retrotransposon in the promoter of the expressed PsMYB10.2 gene that explained the trait in 93.1% of the 145 individuals analyzed. We hypothesize that the LTR retrotransposon may promote the PsMYB10.2 expression and activate the anthocyanin biosynthesis pathway. We propose for the first time the PsMYB10.2 gene as candidate for the flesh color natural variation in Japanese plum and provide a molecular marker for MAS.

Transcriptome analysis of flower bud identified genes associated with pistil abortions between long branches and spur twigs in apricots (Prunus armeniaca L.)

Pistil abortions of flower buds occur frequently in many apricot cultivars, especially in long branches. However, the molecular mechanism underlying pistil abortion in apricots remains unclear. To better understand the molecular mechanism of pistil abortions between long branches and spur twigs, paraffin sections and high-throughput sequencing technology were employed to analyze the expression patterns of genes associated with pistil abortions during later flower bud development stage in ‘Shajinhong’ apricot. The result of stage III (separation of bud scales) was the critical stage of pistil abortion in apricots. A total of 163 differentially expressed genes were identified as candidate genes related to pistil abortion in long branches. These genes are implicated in programmed cell death, hormone signaling, cell wall degeneration, and the carbohydrate metabolism pathway. The results showed that the up-regulation of gene expression of Xyloglucan endotransglucosylase/hydrolase and β-glucosidase in flower buds might be the direct cause of cell wall breakdown and pistil necrosis in long branches. We hypothesize that there is a molecular relationship between pistil abortion before blooming and cellulose degradation, and then carbohydrate transport in the case of carbon deficiency in long branches. Our work provides new insights into cellulose degradation in abortion pistils and valuable information on flower development in apricots, and also provides a useful reference for cultivation regulation in apricot or other fruit crops.

Integrative Analysis of the DICER-like (DCL) Genes From Peach (Prunus persica): A Critical Role in Response to Drought Stress

DICER-likes (DCLs) proteins are the core component for non-coding RNA (ncRNA) biogenesis, playing essential roles in some biological processes. The DCL family has been characterized in model plants, such as Arabidopsis, rice, and poplar. However, the evolutionary aspect and the expression mechanism under drought stress were scarce and have never been reported and characterized in one of the most important worldwide cultivated fruit trees, peach (Prunus persica). Eight DCLs genes in the Prunus persica genome were detected, in addition to 51 DCLs in the other seven Rosaceae genomes. The phylogenetic analysis with Arabidopsis thaliana and RTL1 gene as outgroups suggested that DCL members are divided into four clades: DCL1, DCL2, DCL3, and DCL4 with several gene gain/loss events of DCL gene copies through the evolutionary tract of the Rosacea family. The number of homologous DCL copies within each clade, along with the chromosomal location indicated gene duplication event of the DCL2 gene occurred once for the subfamily Amygdaloideae and twice for Pyrus communis and Prunus dulics and trice for the P. persica on Chromosome number 7 genes. Another duplication event was found for the DCL3 gene that occurred once for all the eight Rosaceae species with no match in A. thaliana. The DCL genetic similarity and activity was evaluated using BLASTp and previously published RNA-seq data among different tissues and over different time points of peach trees exposed to drought conditions. Finally, the expression pattern of PrupeDCLs in response to drought stress was identified, and two of these members, Prupe.7G047900 and Prupe.6G363600, were found as main candidate genes for response to drought stress. Our data presented here provide useful information for a better understanding of the molecular evolution of DCL genes in Rosaceae genomes, and the function of DCLs in P. persica.

The chromosome-level genome provides insight into the molecular mechanism underlying the tortuous-branch phenotype of Prunus mume

Plant with naturally twisted branches is referred to as a tortuous-branch plant, which have extremely high ornamental value due to their zigzag shape and the natural twisting of their branches. Prunus mume is an important woody ornamental plant. However, the molecular mechanism underlying this unique trait in Prunus genus is unknown. Here, we present a chromosome-level genome assembly of the cultivated P. mume var. tortuosa created using Oxford Nanopore combined with Hi-C scaffolding, which resulted in a 237.8 Mb genome assembly being anchored onto eight pseudochromosomes. Molecular dating indicated that P. mume is the most recently differentiated species in Prunus. Genes associated with cell division, development and plant hormones play essential roles in the formation of tortuous branch trait. A putative regulatory pathway for the tortuous branch trait was constructed based on gene expression levels. Furthermore, after transferring candidate PmCYCD genes into Arabidopsis thaliana, we found that seedlings overexpressing these genes exhibited curled rosette leaves. Our results provide insights into the evolutionary history of recently differentiated species in Prunus genus, the molecular basis of stem morphology, and the molecular mechanism underlying the tortuous branch trait and highlight the utility of multi-omics in deciphering the properties of P. mume plant architecture.

An Identification and Expression Analysis of the ABCG Genes Related to Benzaldehyde Transportation among Three Prunus Species

The plants of Prunus mostly bloom in early spring, and the flowers of various species possess their individual floral scent characteristics; Prunus mume, especially, can volatilize a large amount of benzenoid compounds into the air during the flowering phase. In order to elucidate the molecular basis of the differences in the volatile capacity of aromatic substances among Prunus flowers, the endogenous and the headspace volatile components and the expression of ABCG genes were studied among P. mume, P. armeniaca, and P. persica. We detected the floral components in the three species by gas chromatography-mass spectrometry (GC-MS), and we found that benzaldehyde was the key component. Meanwhile, the volatilization efficiency of benzaldehyde in P. mume and P. armeniaca were much higher than that in P. persica. Furthermore, 130, 135, and 133 ABC family members from P. mume, P. armeniaca, and P. persica were identified, respectively. WGCNA analysis demonstrated that candidate ABCG genes were positively correlated with benzaldehyde volatilization efficiency. Moreover, quantitative Real-time PCR indicated that ABCG17 was more likely to be involved in the transmembrane transport of benzaldehyde. This study aimed to provide a theoretical basis for elucidating the transmembrane transport of benzaldehyde and to further the valuable information for fragrant flower breeding in Prunus.

Profiling of Primary Metabolites and Volatiles in Apricot (Prunus armeniaca L.) Seed Kernels and Fruits in the Context of Its Different Cultivars and Soil Type as Analyzed Using Chemometric Tools

The goal of this study was to assess nutrient primary metabolites and aroma determinants in Prunus armeniaca L. fruits and seed kernels grown in Egypt represented by its different cultivars and agricultural conditions i.e., two different soil types (muddy versus sandy). Two techniques were employed to assess non-volatile and volatile metabolites using gas chromatography mass-spectrometry (GC-MS) post silylation, and headspace solid-phase micro-extraction (HS-SPME) coupled GC-MS, respectively. A total of 36 peaks belonging to sugars, fatty acids/esters and organic acids were identified by GC–MS in various apricot fruits and seed kernels cultivars. Glucose and sucrose were enriched in apricot fruits compared to the seed kernels. A total of 70 volatiles were identified, with lactones, alcohols and esters representing the main classes of apricot volatiles accounting for its discrete aroma. (E)-Anethole, β-ionone, γ-decanolactone and methyl palmitate were the major peaks contributing to the discrimination between various fruit cultivars and providing novel insight on apricot metabolome.

Genome-wide identification of the SWEET gene family mediating the cold stress response in Prunus mume

The Sugars Will Eventually be Exported Transporter (SWEET) gene family encodes a family of sugar transporters that play essential roles in plant growth, reproduction, and biotic and abiotic stresses. Prunus mume is a considerable ornamental wood plant with high edible and medicinal values; however, its lack of tolerance to low temperature has severely limited its geographical distribution. To investigate whether this gene family mediates the response of P. mume to cold stress, we identified that the P. mume gene family consists of 17 members and divided the family members into four groups. Sixteen of these genes were anchored on six chromosomes, and one gene was anchored on the scaffold with four pairs of segmental gene duplications and two pairs of tandem gene duplications. Cis-acting regulatory element analysis indicated that the PmSWEET genes are potentially involved in P. mume development, including potentially regulating roles in procedure, such as circadian control, abscisic acid-response and light-response, and responses to numerous stresses, such as low-temperature and drought. We performed low-temperature treatment in the cold-tolerant cultivar 'Songchun' and cold-sensitive cultivar 'Zaolve' and found that the expression of four of 17 PmSWEETs was either upregulated or downregulated with prolonged treatment times. This finding indicates that these family members may potentially play a role in cold stress responses in P. mume. Our study provides a basis for further investigation of the role of SWEET proteins in the development of P. mume and its responses to cold stress.

Comparative Analysis of Transposable Elements and the Identification of Candidate Centromeric Elements in the Prunus Subgenus Cerasus and Its Relatives

The subgenus Cerasus and its relatives include many crucial economic drupe fruits and ornamental plants. Repetitive elements make up a large part of complex genomes, and some of them play an important role in gene regulation that can affect phenotypic variation. However, the variation in their genomes remains poorly understood. This work conducted a comprehensive repetitive sequence identification across the draft genomes of eight taxa of the genus Prunus, including four of the Prunus subgenus Cerasus (Prunus pseudocerasus, P. avium, P. yedoensis and P. × yedoensis) as well as congeneric species (Prunus salicina, P. armeniaca, P. dulcis and P. persica). Annotation results showed high proportions of transposable elements in their genomes, ranging from 52.28% (P. armeniaca) to 61.86% (P. pseudocerasus). The most notable differences in the contents of long terminal repeat retrotransposons (LTR-RTs) and tandem repeats (TRs) were confirmed with de novo identification based on the structure of each genome, which significantly contributed to their genome size variation, especially in P. avium and P.salicina. Sequence comparisons showed many similar LTR-RTs closely related to their phylogenetic relationships, and a highly similar monomer unit of the TR sequence was conserved among species. Additionally, the predicted centromere-associated sequence was located in centromeric regions with FISH in the 12 taxa of Prunus. It presented significantly different signal intensities, even within the diverse interindividual phenotypes for Prunus tomentosa. This study provides insight into the LTR-RT and TR variation within Prunus and increases our knowledge about its role in genome evolution.

Biochemical Characterization of Some Varieties of Apricot Present in the Vesuvius Area, Southern Italy

The witnesses of the millenary history of Campania felix in southern Italy highlighted that several fruit and vegetables cultivated in such territory could potentially be a treasure trove of important health elements. Our work evaluated the content of β-carotene, ascorbic acid, and total phenolics and the antioxidant activity of ten typical varieties of apricots cultivated in the Vesuvius area in the Campania region. The total polyphenols varied between 10.24 and 34.04 mg/100 g of a fresh sample. The amount of ascorbic acid also varied greatly, ranging from 2.65 to 10.65 mg/100 g of a fresh product. B-Carotene reached values up to 0.522 mg/100 g of the fresh sample. The correlation analysis performed, accounting for these parameters, showed that the antioxidant activity, calculated by 2,2-diphenyl-1-picrylhydrazyl (DPPH assay) and azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) tests, was influenced mainly by the content of total polyphenols, with ρ = −0.762 and ρ = 0.875 when we considered DPPH and ABTS tests, respectively, slightly less by the content of ascorbic acid, and not by β-carotene. The dendrogram clustered eight varieties into two main groups; on the other hand, two varieties (“Vitillo” and “Preveta bella”) seemed hierarchically distant. The gas chromatography–mass spectrometry (GC–MS) analysis of volatile organic compounds (VOCs), herein performed for the first time, demonstrated the influence of the varieties on the VOC profiles, both from a qualitative and semiquantitative perspective, discriminating the varieties in different clusters, each of which was characterized by specific notes. α-Terpinolene was the only terpene identified by GC–MS that appeared to affect the antioxidant activity.

Pomological Traits and Genome Size of Prunus armeniaca L. Considering to Geographical Origin

Apricot (Prunus armeniaca L.) is an important fruit crop and member of the Prunus genus of the Rosaceae family that is planted in many temperate regions worldwide. The quality of fruit is assessed by many pomological parameters which can serve as a decisive factor in apricot breeding, because the introduction of new cultivars is required. These parameters can differ with climate conditions, geographical location or geographic ecological origin. Similarly, another biological characteristic can be measured depending on these terms. The present study was conducted with the aim of estimating pomological traits together with the nuclear DNA content of 35 apricot cultivars with different geographical origins. Only CV values lower than 5% were considered in flow cytometry analysis. All analyzed cultivars were diploid and the genome size value ranged from 0.587 to 0.644 pg/2C, where Turkish apricots reached the highest value (on average 0.628 pg/2C) followed by the European group (on average 0.625 pg/2C). A Spearman-rank correlation was used and the different correlation was found for specific geographical groups of apricot cultivars. The genome size values of apricots and related botanical species P. mume, P. sibirica and P. ansu showed to be very similar values.

Integrated Metabolome and Transcriptome Analysis of Fruit Flavor and Carotenoids Biosynthesis Differences Between Mature-Green and Tree-Ripe of cv. "Golden Phoenix" Mangoes (Mangifera indica L.)

The commodity value of fruits is directly affected by fruit flavor and color. Secondary metabolites, such as amino acids, organic acids, esters, and β-carotene, are important synthetic products, which are of great significance in the flavor formation of mango fruits. In this study, a total of 309 different metabolites, consisting of organic acids, amino acids, phenolic acids, and saccharides, and a further 84 types of volatile organic compounds (VOCs) were identified in differential levels in TR vs. MG mango fruit stages. The major volatile compounds found were ester [2(3H)-furanone, 5-ethyldihydro; N-(2,5-ditrifluoromethylbenzoyl)-D-alanine, pentyl ester; and Octanoic acid, ethyl ester], aldehyde (benzaldehyde, 3-ethyl, and nonanal), and phenol [2-(1,1-dimethylethyl)-6-(1-methylethyl) phenol]. The analysis of carotenoid contents identified 68 carotenoids and we report for the first-time significant contents of zeaxanthin palmitate and (E/Z)-phytoene in mango fruits. α-carotene was a further major contributor to carotene contents with lesser contributions from 5,6epoxy-lutein-caprate-palmitate, β-carotene, lutein oleate, and β-cryptoxanthin. What is more, lutein content was significantly decreased in TR vs. MG fruit. RT-qPCR analysis revealed that relative to the MG stage, the expression of carotenogenic genes GGPS, PSY, LCYB, and ZEP was downregulated in TR mango fruit, whereas the transcript levels of PSD, CHYB, and NCED were downregulated. Additionally, the transcription level of some transcription factors (MYB, bHLH, and NAC) was highly correlated with pigment content in the pulp and may be responsible for carotenoid accumulation. The results describe major differences in metabolic pathways during the transition from MG to the TR stage of fruit ripening that are likely to contribute alterations in fruit flavor and provide several associated genes to be further studied in mango fruit.

Construction of a High-Density Genetic Map and Identification of Quantitative Trait Loci Linked to Fruit Quality Traits in Apricots Using Specific-Locus Amplified Fragment Sequencing

Improving fruit quality is one of the main tasks in modern commercial apricot breeding. Because of the lack of high-density linkage maps and fine mapping, it is difficult to obtain molecular markers that can assist in breeding for quantitative inheritance of fruit quality traits. In this study, specific-locus amplified fragment sequencing was used to genotype 169 seedlings of F1 apricot (Prunus armeniaca L.) progenies derived from crossing "Chuanzhihong" (H) with "Saimaiti" (S). After aligning to the Prunus armeniaca reference genome and filtering out low-quality variants, 6,012 high-quality single nucleotide polymorphisms were obtained and employed to construct a genetic map for each parent. The genetic linkage maps showed eight linkage groups of apricot, covering a distance of 809.6 cM in "H" and 1076.4 cM in "S". The average distance between markers in "H" and "S" was 0.62 and 0.95 cM, respectively. To map quantitative trait loci (QTLs) for fruit quality, we investigated fruit quality traits, including fruit weight (FW), fruit height (FH), fruit lateral width (FL), fruit ventral width (FV), soluble solids content (SSC), and fruit firmness (FF) for all seedlings genotyped in 2018 and 2019. Eleven and nine QTLs linked to fruit quality traits were anchored on the "H" and "S" maps, respectively, and 1,138 putative candidate genes for 16 most significant regions on the corresponding chromosome were identified based on gene annotation. Among them, fruit size contained 648 genes in 11 intervals on the reference genome, SSC contained 372 genes in 3 intervals, and FF contained 117 genes in 2 intervals. Our findings uncovered the genetic basis of apricot fruit quality, and provided candidate genes for further molecular genetic studies on fruit quality and QTL targets for future marker-assisted selection of apricot quality improvement breeding.