Genome re-sequencing reveals the evolutionary history of peach fruit edibility

Identification, characterization and expression analysis of lineage-specific genes within 'Zhongyoutao 14' peach (Prunus persica)

BACKGROUND

With the development of sequencing technology and the rapid increasing in the number of sequenced genomes, lineage-specific genes (LSGs) have been identified and characterized across various species. Similar to other conserved functional genes, LSGs play a crucial role in biological evolution and development. However, the understanding of LSGs remains limited. This study aims to identify significant gene expression profiles of LSGs in peach, which may contribute to the development of specific tissues and important traits.

METHODS

Seven peach and 341 exogenous species genomes were used in this study. Firstly, the coding sequences of CN14 peach were compared with other genomes to discover LSGs. Next, the LSGs of CN14 peach were compared with other peach genomes to identify the peach specific genes and orphan genes. Furthermore, the tissue specificity expressed PSGs and orphan genes were identified using transcriptome data. In addition, the genes specific expressed in stem might response to GA3 treatment were identified using RT-qPCR.

RESULT

A total of 74 peach specific genes (PSGs) and 91 Orphan genes were identified. The PSGs and orphan genes had fewer exon numbers, shorter gene lengths and lower molecular weight compared with evolutionarily conserved genes (ECGs). Part of these PSGs and Orphan genes were shown an obvious tissue specificity expression pattern at stem, fruit and flower. Three PSGs and three Orphan genes were identified within the QTLs associated with temperature-sensitive semi-dwarf (TSSD), maturity date (Md), and red flesh around stone (Rfas). Three PSGs and seven Orphan genes were identified in response to GA3, these genes might play important role in stem development of peach.

CONCLUSION

The identification and characterization of PSGs and Orphan genes not only provide valuable peach-specific genetic resources, but also might contribute to peach specific biological process.

Graph pangenome reveals the regulation of malate content in blood-fleshed peach by NAC transcription factors

BACKGROUND

Fruit acidity and color are important quality attributes in peaches. Although there are some exceptions, blood-fleshed peaches typically have a sour taste. However, little is known about the genetic variations linking organic acid and color regulation in peaches.

RESULTS

Here, we report a peach graph-based pangenome constructed from sixteen individual genome assemblies, capturing abundant structural variations and 82.3 Mb of sequences absent in the reference genome. Pangenome analysis reveals a long terminal repeat retrotransposon insertion in the promoter of the NAC transcription factor (TF) PpBL in blood-fleshed peaches, which enhances PpBL expression. Genome-wide association study identifies a significant association between PpBL and malate content. Silencing PpBL in peach fruit and ectopic overexpression of PpBL in tomatoes confirm that PpBL is a positive regulator of malate accumulation. Furthermore, we demonstrate that PpBL works synergistically with another NAC TF, PpNAC1, to activate the transcription of the aluminum-activated malate transporter PpALMT4, leading to increased malate content.

CONCLUSIONS

These findings, along with previous research showing that PpBL and PpNAC1 also regulate anthocyanin accumulation, explain the red coloration and sour taste in blood-fleshed peach fruits.

Whole-Genome Sequencing Reveals the Progress of Genetic Breeding in Eriocheir sinensis

Eriocheir sinensis is an important and popular crustacean species in China, producing huge economic benefits. Large individuals of E. sinensis are preferred due to market demand. The long-term goal of our research group is to produce a new variety of E. sinensis with better growth performance and stronger abilities to resist environmental changes through mass selection. The present study aimed to evaluate the progress of the genetic breeding of E. sinensis by analyzing the genetic diversity and genetic distance between the basic breeding population (pooled population of Suqian and Yixing, G0) and generation 1 (G1) using whole-genome sequencing (WGS). The growth traits, including body weight, shell length, shell width, and third appendage length, in the G1 generation increased by 8.3%, 7.9%, 9.6%, and 9.3%, respectively, compared with those of the G0 generation, indicating that the G1 generation showed better growth performance. A total of 372,448,393 high-quality single nucleotide polymorphisms (SNPs) were detected in 40 E. sinensis individuals, with an average of 9,331,209.83 SNPs. The fixation index values were 0.007 between the Yixing and Suqian populations and 0.015 between the G0 generation and G1 generation, indicating a close genetic background between these groups, especially when considered in combination with the phylogenetic tree and principal component analysis. All of these data suggest that genetic information was stably inherited by the G1 generation, with no introduction of foreign genetic information during the genetic breeding process. In addition, the genetic diversity analysis revealed that the G0 and G1 generations showed a high level of genetic diversity and a relatively stable genetic structure. The present study evaluated the recent progress of the genetic improvement of E. sinensis by our research group, providing valuable evidence for further genetic improvement in this species. Future studies will be performed to select growth-related SNPs and genes through genome-wide association studies.

Genomes of autotetraploid wild and cultivated Ziziphus mauritiana reveal polyploid evolution and crop domestication

Indian jujube (Ziziphus mauritiana) holds a prominent position in the global fruit and pharmaceutical markets. Here, we report the assemblies of haplotype-resolved, telomere-to-telomere genomes of autotetraploid wild and cultivated Indian jujube plants using a 2-stage assembly strategy. The generation of these genomes permitted in-depth investigations into the divergence and evolutionary history of this important fruit crop. Using a graph-based pan-genome constructed from 8 monoploid genomes, we identified structural variation (SV)-FST hotspots and SV hotspots. Gap-free genomes provide a means to obtain a global view of centromere structures. We identified presence-absence variation-related genes in 4 monoploid genomes (cI, cIII, wI, and wIII) and resequencing populations. We also present the population structure and domestication trajectory of the Indian jujube based on the resequencing of 73 wild and cultivated accessions. Metabolomic and transcriptomic analyses of mature fruits of wild and cultivated accessions unveiled the genetic basis underlying loss of fruit astringency during domestication of Indian jujube. This study reveals mechanisms underlying the divergence, evolution, and domestication of the autotetraploid Indian jujube and provides rich and reliable genetic resources for future research.

Haplotype-resolved genome of a heterozygous wild peach reveals the PdaWRKY4-PdaCYP716A1 module mediates resistance to aphids by regulating betulin biosynthesis

Wild species of domesticated crops provide valuable genetic resources for resistance breeding. Prunus davidiana, a wild relative of peach with high heterozygosity and diverse stress tolerance, exhibits high resistance against aphids. However, the highly heterozygous genome of P. davidiana makes determining the underlying factors influencing resistance traits challenging. Here, we present the 501.7 Mb haplotype-resolved genome assembly of P. davidiana. Genomic comparisons of the two haplotypes revealed 18,152 structural variations, 2,699 Pda_hap1-specific and 2,702 Pda_hap2-specific genes, and 1,118 allele-specific expressed genes. Genome composition indicated 4.1% of the P. davidiana genome was non-peach origin, out of which 94.5% was derived from almond. Based on the haplotype genome, the aphid resistance quantitative trait locus (QTL) was mapped at the end of Pda03. From the aphid resistance QTL, PdaWRKY4 was identified as the major dominant gene, with a 9-bp deletion in its promoter of the resistant phenotype. Specifically, PdaWRKY4 regulates aphid resistance by promoting PdaCYP716A1-mediated anti-aphid metabolite betulin biosynthesis. Moreover, we employed a genome design to develop a breeding workflow for rapidly and precisely producing aphid-resistant peaches. In conclusion, this study identifies a novel aphid resistance gene and provides insights into genome design for the development of resistant fruit cultivars.

Multi-omics analysis unravels chemical roadmap and genetic basis for peach fruit aroma improvement

Selection of fruits with enhanced health benefits and superior flavor is an important aspect of peach breeding. Understanding the genetic interplay between appearance and flavor chemicals remains a major challenge. We identify the most important volatiles contributing to consumer preferences for peach, thus establishing priorities for improving flavor quality. We quantify volatiles of a peach population consisting of 184 accessions and demonstrate major reductions in the important flavor volatiles linalool and Z-3-hexenyl acetate in red-fleshed accessions. We identify 474 functional gene regulatory networks (GRNs), among which GRN05 plays a crucial role in controlling both red flesh and volatile content through the NAM/ATAF1/2/CUC (NAC) transcription factor PpBL. Overexpressing PpBL results in reduced expression of PpNAC1, a positive regulator for Z-3-hexenyl acetate and linalool synthesis. Additionally, we identify haplotypes for three tandem PpAATs that are significantly correlated with reduced gene expression and ester content. We develop genetic resources for improvement of fruit quality.

Origins and Genetic Characteristics of Egyptian Peach

Peach (Prunus persica), a significant economic fruit tree in the Rosaceae family, is extensively cultivated in temperate and subtropical regions due to its abundant genetic diversity, robust adaptability, and high nutritional value. Originating from China over 4000 years ago, peaches were introduced to Persia through the Silk Road during the Han Dynasty and gradually spread to India, Greece, Rome, Egypt, Europe, and America. Currently grown in more than 80 countries worldwide, the expansion of peach cultivation in Egypt is mainly due to the development and utilization of peach varieties with low chilling requirements. These varieties exhibit unique phenotypic characteristics such as early maturity, reduced need for winter cold temperatures, low water requirements, and high economic value. In this study, a systematic analysis was conducted on the genetic characteristics and kinship relationships of peaches with low chilling requirements in Egypt. We conducted a comprehensive evolutionary and Identity-by-Descent (IBD) analysis on over 300 peach core germplasm resources, including Egyptian cultivars with low chilling requirements, to investigate their origin and genetic characteristics. The evolutionary analysis revealed that 'Bitter almond' is closely related to China's wild relative species Prunus tangutica Batal, while 'Early grand' shares one branch with Chinese ornamental peach cultivars, and 'Nemaguard' clusters with some ancient local varieties from China. The IBD analysis also indicated similar genetic backgrounds, suggesting a plausible origin from China. Similarly, the analysis suggested that 'Swelling' may have originated from the Czech Republic while 'Met ghamr' has connections to South Africa. 'Desert red', 'Early swelling', and 'Florida prince' are likely derived from Brazil. These findings provide valuable insights into the genetic characteristics of Egyptian peach cultivars. They offer a significant foundation for investigating the origin and spread of cultivated peaches worldwide and serve as a valuable genetic resource for breeding low chilling requirement cultivars, which is of considerable significance for the advancement of peach cultivation in Egypt.

Whole-genome resequencing of Hu sheep identifies candidate genes associated with agronomic traits

The phenotypic diversity resulting from artificial or natural selection of sheep has made a significant contribution to human civilization. Hu sheep are a local sheep breed unique to China with high reproductive rates and rapid growth. Genomic selection signatures have been widely used to investigate the genetic mechanisms underlying phenotypic variation in livestock. Here, we conduct whole-genome sequencing of 207 Hu sheep and compare them with the wild ancestors of domestic sheep (Asiatic mouflon) to investigate the genetic characteristics and selection signatures of Hu sheep. Based on six signatures of selection approaches, we detect genomic regions containing genes related to reproduction (BMPR1B, BMP2, PGFS, CYP19, CAMK4, GGT5, and GNAQ), vision (ALDH1A2, SAG, and PDE6B), nervous system (NAV1), and immune response (GPR35, SH2B2, PIK3R3, and HRAS). Association analysis with a population of 1299 Hu sheep reveals that those missense mutations in the GPR35 (GPR35 g.952651 A>G; GPR35 g.952496 C>T) and NAV1 (NAV1 g.84216190 C>T; NAV1 g.84227412 G>A) genes are significantly associated (P < 0.05) with immune and growth traits in Hu sheep, respectively. This research offers unique insights into the selection characteristics of Hu sheep and facilitates further genetic improvement and molecular investigations.

PPGV: a comprehensive database of peach population genome variation

Peach tree is one of the most important fruit trees in the world, and it has been cultivated for more than 7,500 years. In recent years, the genome and population resequencing of peach trees have been published continuously, which has effectively promoted the research of peach tree genetics and breeding. In order to promote the further mining and utilization of these data, we integrated and constructed a comprehensive peach genome and variation database (PPGV, http://peachtree.work/home ). The PPGV contains 10 sets of published peach tree genome data, as well as genomic variation information for 1,378 peach tree samples (the resequencing data of 1,378 samples were aligned with the high-quality genomes of Lovell, CN14 and Chinesecling, respectively, for mutation detection). A variety of useful and flexible tools, such as BLAST, Gene ID Convert, KEGG/GO Enrichment, Primer Design and Gene function, were also specially designed for searching data and assisting in breeding.

Genome variation and LTR-RT analyses of an ancient peach landrace reveal mechanism of blood-flesh fruit color formation and fruit maturity date advancement

Peach (Prunus persica) landrace has typical regional characteristics, strong environmental adaptability, and contains many valuable genes that provide the foundation for breeding excellent varieties. Therefore, it is necessary to assemble the genomes of specific landraces to facilitate the localization and utilization of these genes. Here, we de novo assembled a high-quality genome from an ancient blood-fleshed Chinese landrace Tianjin ShuiMi (TJSM) that originated from the China North Plain. The assembled genome size was 243.5 Mb with a contig N50 of 23.7 Mb and a scaffold N50 of 28.6 Mb. Compared with the reported peach genomes, our assembled TJSM genome had the largest number of specific structural variants (SVs) and long terminal repeat-retrotransposons (LTR-RTs). Among the LTR-RTs with the potential to regulate their host genes, we identified a 6688 bp LTR-RT (named it blood TE) in the promoter of NAC transcription factor-encoding PpBL, a gene regulating peach blood-flesh formation. The blood TE was not only co-separated with the blood-flesh phenotype but also associated with fruit maturity date advancement and different intensities of blood-flesh color formation. Our findings provide new insights into the mechanism underlying the development of the blood-flesh color and determination of fruit maturity date and highlight the potential of the TJSM genome to mine more variations related to agronomic traits in peach fruit.

Genome sequencing revealed the red-flower trait candidate gene of a peach landrace

Peach (Prunus persica) is an economically important fruit crop globally and an excellent material for genomic studies. While considerable progress has been made in unveiling trait-associated genes within cultivars and wild relatives, certain novel genes controlling valuable traits in peach landraces, such as the red-flowering gene, remained unclear. In this study, we sequenced and assembled the diploid genome of the red-flower landrace 'Yingzui' (abbreviated as 'RedY'). Multi-omics profiling of red petals of 'RedY' revealed the intensified red coloration associated with anthocyanins accumulation and concurrent decline in flavonols. This phenomenon is likely attributed to a natural variant of Flavonol Synthase (FLS) harboring a 9-bp exonic insertion. Intriguingly, the homozygous allelic configurations of this FLS variant were only observed in red-flowered peaches. Furthermore, the 9-bp sequence variation tightly associated with pink/red petal color in genome-wide association studies (GWAS) of collected peach germplasm resources. Functional analyses of the FLS variant, purified from procaryotic expression system, demonstrated its diminished enzymatic activity in flavonols biosynthesis, impeccably aligning with the cardinal trait of red flowers. Therefore, the natural FLS variant was proposed as the best candidate gene for red-flowering trait in peach. The pioneering unveiling of the red-flowered peach genome, coupled with the identification of the candidate gene, expanded the knowledge boundaries of the genetic basis of peach traits and provided valuable insights for future peach breeding efforts.

Genome-wide presence/absence variation discovery and its application in Peach (Prunus persica)

Gene presence/absence variation (PAV) is an important contributor to the studies of genetic diversity, gene identification, and molecular marker development in plants. In the present study, 100 peach (Prunus persica) accessions were used for genome resequencing to identify PAVs. Alignmentwith a reference genome yielded a total of 2.52 Mb non-reference sequences and 923 novel genes were identified. The dispensable PAVs were enriched in resistance, perhaps reflecting their roles in plant adaptation to various environments. Furthermore, selection sweeps associated with peach domestication and improvement were identified based on PAV data. Only 4.3% and 13.4% of domestication and improvement sweeps, respectively, were identified simultaneously using single nucleotide polymorphism (SNP) data, suggesting flexible identification between the different methods. To further verify the applicability of PAV identification, a genome-wide association study was conducted using 21 agronomic traits. Some of the identified loci were consistent with those reported in previous studies, while some were mapped for the first time; the latter included petiole length, petiole gland shape, and petiole gland number. Through tissue-specific expression analysis and gene transformation experiments, a novel gene, evm.model.Contig322_A94.1, was identified and found to be involved in chilling requirements. We speculated that this novel gene might regulate the trait by participating in the ABA signaling pathway. The PAVs identified in P. persica provide valuable resources for mapping the entire gene set and identifying optional markers for molecular selection in future studies.

Mycotoxin Determination in Peaches and Peach Products with a Modified QuEChERS Extraction Procedure Coupled with UPLC-MS/MS Analysis

Peaches are the most significant temperate fruit crop worldwide. However, peach fruits are susceptible to fungal and mycotoxin contamination. Consequently, monitoring the residual levels of multiple mycotoxins in peaches and related products is essential. In this study, a novel method based on QuEChERS extraction, followed by ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) detection, was developed for analyzing 14 mycotoxins in peaches and peach products from China. Matrix-matched calibrations were employed to accurately quantify the mycotoxins and compensate for matrix effects. Recoveries for the target analytes ranged from 84.6% to 117.6%, with intra-day and inter-day precision below 20%. The limits of quantification were 2 or 5 μg/L for the 14 mycotoxins. This method was utilized to detect the presence of target mycotoxins in 109 fresh peaches, 100 diseased peaches, and 89 peach products from China. Six mycotoxins were identified in the rotten parts of the diseased peaches, with concentrations ranging from 5.2 to 1664.3 µg/kg. In the remaining parts of the diseased peach samples, only two toxins, alternariol (AOH) and alternariol monomethyl ether (AME), were quantified at levels of 15.3 µg/kg and 15.5 µg/kg, respectively. No mycotoxins were detected in fresh peaches. For peach products, all contamination levels were below the quantitative limits and significantly lower than the maximum legal limits established for the products.

Genomic Resequencing Unravels the Genetic Basis of Domestication, Expansion, and Trait Improvement in Morus Atropurpurea

Mulberry is an economically important plant in the sericulture industry and traditional medicine. However, the genetic and evolutionary history of mulberry remains largely unknown. Here, this work presents the chromosome-level genome assembly of Morus atropurpurea (M. atropurpurea), originating from south China. Population genomic analysis using 425 mulberry accessions reveal that cultivated mulberry is classified into two species, M. atropurpurea and M. alba, which may have originated from two different mulberry progenitors and have independent and parallel domestication in north and south China, respectively. Extensive gene flow is revealed between different mulberry populations, contributing to genetic diversity in modern hybrid cultivars. This work also identifies the genetic architecture of the flowering time and leaf size. In addition, the genomic structure and evolution of sex-determining regions are identified. This study significantly advances the understanding of the genetic basis and domestication history of mulberry in the north and south, and provides valuable molecular markers of desirable traits for mulberry breeding.

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.

Resequencing of Rosa rugosa accessions revealed the history of population dynamics, breed origin, and domestication pathways

BACKGROUND

Rosa rugosa is a shrub that originated in China and has economic and ecological value. However, during the development of R. rugosa, the genetic background was chaotic, and the genetic structure among different wild populations was unclear, as well as wild and cultivated accessions. Here, we report whole-genome resequencing of wild and cultivated R. rugosa accessions.

RESULTS

A total of 19,041,284 SNPs were identified in 188 R. rugosa accessions and 3 R. chinensis accessions by resequencing. Population genetic analysis revealed that cultivated and wild groups were separated very early. All R. rugosa accessions were divided into 8 categories based on genetic structure: (1) Weihai, Yantai, and Liaoning category, (2) Jilin category, and (3) Hammonasset category (above three are wild); (4) traditional varieties, (5) hybrids between R. rugosa and R. chinensis, (6) Zizhi Rose, (7) Kushui Rose, (8) hybrids between R. rugosa and R. multiflora. We found that the heterozygosity and genetic diversity of wild accessions were generally lower than those of cultivated individuals. The genes that were selected during cultivation were identified, and it was found that these genes were mainly related to environmental adaptation and growth.

CONCLUSIONS

The Jilin population was the oldest population and later migrated to Liaoning and then migrated to Yantai and Weihai by sea regression in the Bohai Basin. The Hammonasset naturalized population probably originated from the Jilin population and then experienced separate differentiation. The long-term asexual reproduction pattern of R. rugosa decreased genetic diversity in the wild population. During R. rugosa cultivation, the ancestors of the Jilin population were involved in breeding traditional varieties, after which almost no wild individuals were engaged in breeding. However, in recent decades, cross breeding of R. rugosa started the utilization of wild germplasms. In comparison, some other species play important roles in variety formation. Few genes related to economic traits were selected, suggesting no directional domestication in the R. rugosa cultivation process.

A high-quality assembled genome of a representative peach landrace, 'Feichenghongli', and analysis of distinct late florescence and narrow leaf traits

BACKGROUND

Peach (Prunus persica L. Batsch) is one of the most popular fruits worldwide. Although the reference genome of 'Lovell' peach has been released, the diversity of genome-level variations cannot be explored with one genome. To detect these variations, it is necessary to assemble more genomes.

RESULTS

We sequenced and de novo assembled the genome of 'Feichenghongli' (FCHL), a representative landrace with strict self-pollination, which maintained the homozygosity of the genome as much as possible. The chromosome-level genome of FCHL was 239.06 Mb in size with a contig N50 of 26.93 Mb and only 4 gaps at the scaffold level. The alignment of the FCHL genome with the reference 'Lovell' genome enabled the identification of 432535 SNPs, 101244 insertions and deletions, and 7299 structural variants. Gene family analysis showed that the expanded genes in FCHL were enriched in sesquiterpenoids and triterpenoid biosynthesis. RNA-seq analyses were carried out to investigate the two distinct traits of late florescence and narrow leaves. Two key genes, PpDAM4 and PpAGL31, were identified candidates for the control of flower bud dormancy, and an F-box gene, PpFBX92, was identified as a good candidate gene in the regulation of leaf size.

CONCLUSIONS

The assembled high-quality genome could deepen our understanding of variations among diverse genomes and provide valuable information for identifying functional genes and improving the molecular breeding process.

Evolution-guided multiomics provide insights into the strengthening of bioactive flavone biosynthesis in medicinal pummelo

Pummelo (Citrus maxima or Citrus grandis) is a basic species and an important type for breeding in Citrus. Pummelo is used not only for fresh consumption but also for medicinal purposes. However, the molecular basis of medicinal traits is unclear. Here, compared with wild citrus species/Citrus-related genera, the content of 43 bioactive metabolites and their derivatives increased in the pummelo. Furthermore, we assembled the genome sequence of a variety for medicinal purposes with a long history, Citrus maxima 'Huazhouyou-tomentosa' (HZY-T), at the chromosome level with a genome size of 349.07 Mb. Comparative genomics showed that the expanded gene family in the pummelo genome was enriched in flavonoids-, terpenoid-, and phenylpropanoid biosynthesis. Using the metabolome and transcriptome of six developmental stages of HZY-T and Citrus maxima 'Huazhouyou-smooth' (HZY-S) fruit peel, we generated the regulatory networks of bioactive metabolites and their derivatives. We identified a novel MYB transcription factor, CmtMYB108, as an important regulator of flavone pathways. Both mutations and expression of CmtMYB108, which targets the genes PAL (phenylalanine ammonia-lyase) and FNS (flavone synthase), displayed differential expression between Citrus-related genera, wild citrus species and pummelo species. This study provides insights into the evolution-associated changes in bioactive metabolism during the origin process of pummelo.

Target and suspect screening of pesticide residues in soil samples from peach orchards using liquid chromatography quadrupole time-of-flight mass spectrometry

Agricultural soil contamination by pesticide residues has become a serious issue of increasing concern due to their high persistence and toxicity to non-target species. However, as the world's largest peach producer, national scale surveys on pesticide residues in peach orchard soils are scarce in China. In this study, a target and suspect screening method covering over 200 pesticides commonly used in peach orchards was developed using ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry in MS^E. An identification strategy using different data processing parameters was developed to identify the pesticide occurrence in soil. The method was applied to soil samples from typical peach orchards in 12 regions across China. The present work also discusses in detail the frequency of occurrence, concentration of pesticides, spatial distribution of multiresidues, and relationship between pesticide occurrence and soil properties. In the tested soil samples, 21 herbicides (level 1), 31 fungicides (level 2a), 24 insecticides (level 2a), and 3 growth regulators (level 2a) were identified. The total concentrations of quantifiable herbicides in the soil samples ranged from 1.05 to 327 ng/g. Only in 5.4% of the soil samples, no pesticide residues were present. By contrast, more than 86% of the total contained multiple residues. This study represents the first large-scale survey of pesticides in soil from peach orchards and provides comprehensive and accurate information on the pesticide residue status for risk assessment.

Biodiversity Evaluation and Preservation of Italian Stone Fruit Germplasm (Peach and Apricot) in Southern Italy

The Prunus genus encompasses a group of economically important and closely related crops, sharing an essentially common genome and, thereby, a high level of conserved and transferable microsatellite (SSR) loci. In Southern Italy, many of the local and/or neglected varieties are abandoned and at risk of extinction due to the high degree of urbanization and agricultural intensification, despite their value as genetic resources for crop improvement. This research aimed to genetically and morphologically characterize the traditional apricot (P. armenica) and peach (P. persica) germplasms collected in old family orchards. Most of the official descriptor categories were scored, thus revealing a rather high level of phenotypic variation in both collections. Genetic data allowed the discovery of diversity masked by morphological traits. Genotyping in 15 and 18 SSRs, eight of which were transferable across both species, showed an average polymorphic informativeness (PIC) of 0.44 and 0.59 for apricot and peach, respectively, and a total of 70 and 144 alleles. A reliable identification of each genotype was achieved, and the presence of possible mislabeling and/or erroneous denominations was solved. These results are encouraging for the valorization of the still poorly explored Italian Prunus germplasm, with significant economic consequences for bioresource conservation and management.

Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis)

A high-density single nucleotide polymorphism (SNP) array is essential to enable faster progress in plant breeding for new cultivar development. In this regard, we have developed an Axiom 60K almond SNP array by resequencing 81 almond accessions. For the validation of the array, a set of 210 accessions were genotyped and 82.8% of the SNPs were classified in the best recommended SNPs. The rate of missing data was between 0.4% and 2.7% for the almond accessions and less than 15.5% for the few peach and wild accessions, suggesting that this array can be used for peach and interspecific peach × almond genetic studies. The values of the two SNPs linked to the RMja (nematode resistance) and SK (bitterness) genes were consistent. We also genotyped 49 hybrids from an almond F2 progeny and could build a genetic map with a set of 1159 SNPs. Error rates, less than 1%, were evaluated by comparing replicates and by detection of departures from Mendelian inheritance in the F2 progeny. This almond array is commercially available and should be a cost-effective genotyping tool useful in the search for new genes and quantitative traits loci (QTL) involved in the control of agronomic traits.

Bearing Fruit: Miocene Apes and Rosaceous Fruit Evolution

Extinct megafaunal mammals in the Americas are often linked to seed-dispersal mutualisms with large-fruiting tree species, but large-fruiting species in Europe and Asia have received far less attention. Several species of arboreal Maloideae (apples and pears) and Prunoideae (plums and peaches) evolved large fruits starting around nine million years ago, primarily in Eurasia. As evolutionary adaptations for seed dispersal by animals, the size, high sugar content, and bright colorful visual displays of ripeness suggest that mutualism with megafaunal mammals facilitated the evolutionary change. There has been little discussion as to which animals were likely candidate(s) on the late Miocene landscape of Eurasia. We argue that several possible dispersers could have consumed the large fruits, with endozoochoric dispersal usually relying on guilds of species. During the Pleistocene and Holocene, the dispersal guild likely included ursids, equids, and elephantids. During the late Miocene, large primates were likely also among the members of this guild, and the potential of a long-held mutualism between the ape and apple clades merits further discussion. If primates were a driving factor in the evolution of this large-fruit seed-dispersal system, it would represent an example of seed-dispersal-based mutualism with hominids millions of years prior to crop domestication or the development of cultural practices, such as farming.

Potential of traditional Chilean blood-fleshed peach to support livelihood opportunities in local agriculture

The blood-flesh peach or vineyard peach is an older heritage cultivar with juicy red-flesh and tart-sweet flavor. They are popular in France, where more than 200 years ago wine growers used to plant them on the vineyards as biological markers to detect the presence of powdery mildew. It is present in countries such as China, Italy, New Zealand, Australia and USA however, it remains a very rare variety worldwide. In Chile, the blood-flesh peach has a centenary presence in rural orchards where is called “Durazno Betarraga.” Reproduced by seeds, it has pass through generations of family farmers and has been adapted to local environmental conditions. This red-flesh peach is a local variety considered part of their traditional diets, however, cultural changes in food consumption, short postharvest life and water scarcity due to climate change are threatening its conservation. One of the objectives of the International Year of Fruits and Vegetables, as defined by the FAO, is to integrate small holders and family farmers into value chains for sustainable production and consumption of fruits and vegetables recognizing the contributions of farmer's landraces to their food security, nutrition, livelihoods and income. To promote this objective, we present the work we have been carry out for several years with a farming community. We have conducted ethnographic research to provide a qualitative description of the agricultural value of the blood peach in a limited territory of the Maule Region defined as the study area. For the quantitative section of our research we analyzed the antioxidant capacity (ORAC) and total polyphenol content and compared them with those of other fruits. To gather information on the presence of the blood-fleshed peach in other regions of Chile, we used a citizen science approach through social networks. We propose that this local variety is an innovative raw material to develop healthy fruit-based food, thus encouraging its conservation and consumption with a positive social and economic impact for the community and the local food system.

Multi-environment genomic prediction for soluble solids content in peach (Prunus persica)

Genotype-by-environment interaction (G × E) is a common phenomenon influencing genetic improvement in plants, and a good understanding of this phenomenon is important for breeding and cultivar deployment strategies. However, there is little information on G × E in horticultural tree crops, mostly due to evaluation costs, leading to a focus on the development and deployment of locally adapted germplasm. Using sweetness (measured as soluble solids content, SSC) in peach/nectarine assessed at four trials from three US peach-breeding programs as a case study, we evaluated the hypotheses that (i) complex data from multiple breeding programs can be connected using GBLUP models to improve the knowledge of G × E for breeding and deployment and (ii) accounting for a known large-effect quantitative trait locus (QTL) improves the prediction accuracy. Following a structured strategy using univariate and multivariate models containing additive and dominance genomic effects on SSC, a model that included a previously detected QTL and background genomic effects was a significantly better fit than a genome-wide model with completely anonymous markers. Estimates of an individual's narrow-sense and broad-sense heritability for SSC were high (0.57-0.73 and 0.66-0.80, respectively), with 19-32% of total genomic variance explained by the QTL. Genome-wide dominance effects and QTL effects were stable across environments. Significant G × E was detected for background genome effects, mostly due to the low correlation of these effects across seasons within a particular trial. The expected prediction accuracy, estimated from the linear model, was higher than the realised prediction accuracy estimated by cross-validation, suggesting that these two parameters measure different qualities of the prediction models. While prediction accuracy was improved in some cases by combining data across trials, particularly when phenotypic data for untested individuals were available from other trials, this improvement was not consistent. This study confirms that complex data can be combined into a single analysis using GBLUP methods to improve understanding of G × E and also incorporate known QTL effects. In addition, the study generated baseline information to account for population structure in genomic prediction models in horticultural crop improvement.

Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance

Background

Peach (Prunus persica) is an economically important stone fruit crop in Rosaceae and widely cultivated in temperate and subtropical regions, emerging as an excellent material to study the interaction between plant and environment. During its genus, there are four wild species of peach, all living in harsh environments. For example, one of the wild species, P. mira, originates from the Qinghai-Tibet Plateau (QTP) and exhibits strong cold/ultraviolet ray environmental adaptations. Although remarkable progresses in the gene discovery of fruit quality-related traits in peach using previous assembled genome were obtained, genomic basis of the response of these wild species to different geographical environments remains unclear.

Results

To uncover key genes regulating adaptability in different species and analyze the role of genetic variations in resistance formation, we performed de novo genome assembling of four wild relatives of peach (P. persica), P. mira, P. davidiana, P. kansuensis, and P. ferganensis and resequenced 175 peach varieties. The phylogenetic tree showed that the divergence time of P. mira and other wild relatives of peach was 11.5 million years ago, which was consistent with the drastic crustal movement of QTP. Abundant genetic variations were identified in four wild species when compared to P. persica, and the results showed that plant-pathogen interaction pathways were enriched in genes containing small insertions and deletions and copy number variations in all four wild relatives of peach. Then, the data were used to identify new genes and variations regulating resistance. For example, presence/absence variations which result from a hybridization event that occurred between P. mira and P. dulcis enhanced the resistance of their putative hybrid, P. davidiana. Using bulked segregant analysis, we located the nematode resistance locus of P. kansuensis in chromosome 2. Within the mapping region, a deletion in the promoter of one NBS-LRR gene was found to involve the resistance by regulating gene expression. Furthermore, combined with RNA-seq and selective sweeps analysis, we proposed that a deletion in the promoter of one CBF gene was essential for high-altitude adaptation of P. mira through increasing its resistance to low temperature.

Conclusions

In general, the reference genomes assembled in the study facilitate our understanding of resistance mechanism of perennial fruit crops, and provide valuable resources for future breeding and improvement.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01342-y.

Impacts of Chronic Habitat Fragmentation on Genetic Diversity of Natural Populations of Prunus persica in China

Wild peach is an important resource for improving existing peach varieties. However, the extant populations of wild peach show fragmented distribution due to human disturbance and geographic isolation. In this study, we used natural populations (or wild populations) of Prunus persica (Rosaceae) to assess the genetic effects of habitat fragmentation. A total of 368 individuals sampled from 16 natural populations were analyzed using 23 polymorphic simple sequence repeat (SSR) markers. Prunus persica maintained low within-population genetic variation and high level of genetic differentiation. Two genetic clusters were revealed based on three different methods (UPGMA, PCoA, and STRUCTURE). All populations showed a significant heterozygosity deficiency and most extant populations experienced recent reduction in population size. A significant isolation by distance (IBD) was observed with Mantel's test. Compared to historical gene flow, contemporary gene flow was restricted among the studied populations, suggesting a decrease in gene flow due to habitat fragmentation. Habitat fragmentation has impacted population genetic variation and genetic structure of P. persica. For breeding and conservation purpose, collecting as many individuals as possible from multiple populations to maximize genetic diversity was recommended during the process of germplasm collection. In addition, populations from central China had higher genetic diversity, suggesting these populations should be given priority for conservation and germplasm collection.

De novo chromosome-level genome of a semi-dwarf cultivar of Prunus persica identifies the aquaporin PpTIP2 as responsible for temperature-sensitive semi-dwarf trait and PpB3-1 for flower type and size

Peach (Prunus persica) is one of the most important fruit crops globally, but its cultivation can be hindered by large tree size. 'Zhongyoutao 14' (CN14) is a temperature-sensitive semi-dwarf (TSSD) cultivar which might be useful as breeding stock. The genome of CN14 was sequenced and assembled de novo using single-molecule real-time sequencing and chromosome conformation capture assembly. A high-quality genome was assembled and annotated, with 228.82 Mb mapped to eight chromosomes. Eighty-six re-sequenced F₁ individuals and 334 previously re-sequenced accessions were used to identify candidate genes controlling TSSD and flower type and size. An aquaporin tonoplast intrinsic protein (PpTIP2) was a strong candidate gene for control of TSSD. Sequence variations in the upstream regulatory region of PpTIP2 correlated with different transcriptional activity at different temperatures. PpB3-1, a candidate gene for flower type (SH) and flower size, contributed to petal development and promoted petal enlargement. The locus of another 12 agronomic traits was identified through genome-wide association study. Most of these loci exhibited consistent and precise association signals, except for flesh texture and flesh adhesion. A 6015-bp insertion in exon 3 and a 26-bp insertion upstream of PpMYB25 were associated with fruit hairless. Along with a 70.5-Kb gap at the F-M locus in CN14, another two new alleles were identified in peach accessions. Our findings will not only promote genomic research and agronomic breeding in peach but also provide a foundation for the peach pan-genome.

De novo chromosome-level genome of a semi-dwarf cultivar of Prunus persica identifies the aquaporin PpTIP2 as responsible for temperature-sensitive semi-dwarf trait and PpB3-1 for flower type and size

Peach (Prunus persica) is one of the most important fruit crops globally, but its cultivation can be hindered by large tree size. 'Zhongyoutao 14' (CN14) is a temperature-sensitive semi-dwarf (TSSD) cultivar which might be useful as breeding stock. The genome of CN14 was sequenced and assembled de novo using single-molecule real-time sequencing and chromosome conformation capture assembly. A high-quality genome was assembled and annotated, with 228.82 Mb mapped to eight chromosomes. Eighty-six re-sequenced F₁ individuals and 334 previously re-sequenced accessions were used to identify candidate genes controlling TSSD and flower type and size. An aquaporin tonoplast intrinsic protein (PpTIP2) was a strong candidate gene for control of TSSD. Sequence variations in the upstream regulatory region of PpTIP2 correlated with different transcriptional activity at different temperatures. PpB3-1, a candidate gene for flower type (SH) and flower size, contributed to petal development and promoted petal enlargement. The locus of another 12 agronomic traits was identified through genome-wide association study. Most of these loci exhibited consistent and precise association signals, except for flesh texture and flesh adhesion. A 6015-bp insertion in exon 3 and a 26-bp insertion upstream of PpMYB25 were associated with fruit hairless. Along with a 70.5-Kb gap at the F-M locus in CN14, another two new alleles were identified in peach accessions. Our findings will not only promote genomic research and agronomic breeding in peach but also provide a foundation for the peach pan-genome.

Construction of a collection of introgression lines of "Texas" almond DNA fragments in the "Earlygold" peach genetic background

Peach [Prunus persica L. Batsch] is one of the major temperate fruit tree species, the commercial materials of which have a low level of genetic variability. Almond [P. dulcis (Mill) DA Webb], a close relative of peach cultivated for its kernels, has a much higher level of diversity. The species are inter-compatible and often produce fertile hybrids, almond being a possible source of new genes for peach that could provide biotic and abiotic stress tolerance traits. In this paper we describe the development of a collection of peach-almond introgression lines (ILs) having a single fragment of almond (cv. Texas) in the peach background (cv. Earlygold). Lines with few introgressions were selected with markers from successive generations from a "Texas" × "Earlygold" F1 hybrid, initially using a set of SSRs and later with the 18 k peach SNP chip, allowing for the final extraction of 67 lines, 39 with almond heterozygous introgressions covering 99% of the genome, and 28 with homozygous introgressions covering 83% of the genome. As a proof of concept, four major genes and four quantitative characters were examined in the selected ILs giving results generally consistent with previous information on the genetics of these characters. This collection is the first of its kind produced in a woody perennial species and promises to be a valuable tool for genetic analyses, including dissection of quantitative traits, positional cloning, epistasis and as prebreeding material to introgress almond genes of interest into the peach commercial gene pool.

Multi-omics approaches identify a key gene, PpTST1, for organic acid accumulation in peach

Organic acid content in fruit is an important determinant of peach organoleptic quality, which undergoes considerable variations during development and maturation. However, its molecular mechanism remains largely unclear. In this study, an integrative approach of genome-wide association studies and comparative transcriptome analysis were applied to identify candidate genes involved in organic acid accumulation in peach. A key gene PpTST1, encoding tonoplast sugar transporter, was identified and the genotype of PpTST1 with a single-base transversion (G1584T) in the third exon which leads to a single amino acid substitution (Q528H) was associated with low level of organic acid content in peach. Overexpression of PpTST1His resulted in reduced organic acid content along with increased sugar content both in peach and tomato fruits, suggesting its dual function in sugar accumulation and organic acid content reduction. Two V-type proton ATPases interact with PpTST1 in yeast two-hybridization assay. In addition, the G1584T transversion appeared and gradually accumulated during domestication and improvement, which indicated that PpTST1 was under selection. The identification and characterization of PpTST1 would facilitate the improvement of peach fruit quality.

Rapid Detection of Peach Shoot Blight Caused by Phomopsis amygdali Utilizing a New Target Gene Identified from Genome Sequences Within Loop-Mediated Isothermal Amplification

Peach shoot blight (PSB), caused by Phomopsis amygdali, is a serious threat to the healthy development of the peach industry and leads to 30 to 50% damage to peach production in southern China. In this study, loop-mediated isothermal amplification (LAMP) technology was used to detect the P. amygdali target of a gene of GME6801 that was unique in the whole genome of the pathogen compared with that of Diaporthe (Phomopsis) longicolla TWH P74, Fusarium graminearum PH-1, Colletotrichum gloeosporioides SMCG1 and Magnaporthe oryzae 70-15. Blast comparison of this gene sequence in NCBI database showed that no homologous sequences were found. Therefore, the gene sequence of GME6801 was used to design two pairs of LAMP primers and one pair of PCR primers. The results showed that both primer sets were specific to the 15 strains of P. amygdali, and the other 15 fungal strains presented negative reactions, similar to the control. In addition, 50 pg of genomic DNA of P. amygdali in a 25-μl reaction system could be detected by LAMP assay, which was 100 times more sensitive than PCR. Furthermore, the GME6801 LAMP assay was used to detect artificially inoculated twigs of the pathogen, disease twigs within significantly symptomatic PSB in the fields, and healthy twigs in the same orchard, with detection rates of 100, 75, and 20.8%, respectively. However, detection rates of conventional PCR were separately 100, 62.5, and 16.7%. The results indicated that GME6801-based LAMP could be used for P. amygdali detection as its specificity, sensitivity, and simplicity. This study provides a rapid experimental basis for the identification and prediction of P. amygdali that causes PSB and is beneficial for precise prevention and control of the disease.

Genome sequencing and population resequencing provide insights into the genetic basis of domestication and diversity of vegetable soybean

Vegetable soybean is one of the most important vegetables in China, and the demand for this vegetable has markedly increased worldwide over the past two decades. Here, we present a high-quality de novo genome assembly of the vegetable soybean cultivar Zhenong 6 (ZN6), which is one of the most popular cultivars in China. The 20 pseudochromosomes cover 94.57% of the total 1.01 Gb assembly size, with contig N50 of 3.84 Mb and scaffold N50 of 48.41 Mb. A total of 55 517 protein-coding genes were annotated. Approximately 54.85% of the assembled genome was annotated as repetitive sequences, with the most abundant long terminal repeat transposable elements. Comparative genomic and phylogenetic analyses with grain soybean Williams 82, six other Fabaceae species and Arabidopsis thaliana genomes highlight the difference of ZN6 with other species. Furthermore, we resequenced 60 vegetable soybean accessions. Alongside 103 previously resequenced wild soybean and 155 previously resequenced grain soybean accessions, we performed analyses of population structure and selective sweep of vegetable, grain, and wild soybean. They were clearly divided into three clades. We found 1112 and 1047 genes under selection in the vegetable soybean and grain soybean populations compared with the wild soybean population, respectively. Among them, we identified 134 selected genes shared between vegetable soybean and grain soybean populations. Additionally, we report four sucrose synthase genes, one sucrose-phosphate synthase gene, and four sugar transport genes as candidate genes related to important traits such as seed sweetness and seed size in vegetable soybean. This study provides essential genomic resources to promote evolutionary and functional genomics studies and genomically informed breeding for vegetable soybean.

Elucidation of the Origin of the Monumental Olive Tree of Vouves in Crete, Greece

The olive tree of Vouves in Crete, is considered the oldest producing olive tree in the world with an estimated age exceeding 4000 years. In the present study, we sequenced two samples (from the bottom and the top of the tree) to elucidate the genetic relation of this ancient tree with other olive cvs as well as to gain some insights about its origin. Our results showed that both samples have different genetic origins, proving that this ancient tree has been grafted at least one time. On the basis of whole genome sequences the sample from the top of the Vouves tree showed relation of the same order than half-siblings to one accession corresponding to the present-day Greek cv ‘Mastoidis’. Nevertheless, in the framework of a microsatellite analysis it was found to cluster with the ‘Mastoidis’ samples. The Vouves rootstock (bottom sample) showed a clear grouping with the oleaster samples in a similar way to that of ‘Megaritiki’ Greek cv although it does not show any signal of introgression from them. The genomic analyses did not show a strong relation of this sample with the present-day Greek cvs analyzed in this study so it cannot be proved that it has been used as a source for cultivated olive tree populations represented by available genome sequences. Nevertheless, on the basis of microsatellite analyses, the Vouves rootstock showed affinity with two present-day Greek cvs, one “ancient” rootstock from continental Greece as well as monumental trees from Cyprus. The analysis of the impact of the variants in the gene space revealed an enrichment of genes associated to pathways related with carbohydrate and amino acid metabolism. This is in agreement with what has been found before in the sweep regions related with the process of domestication. The absence of oleaster gene flow, its old age and its variant profile, similar to other cultivated populations, makes it an excellent reference point for domestication studies.

Molecular Insights of Fruit Quality Traits in Peaches, Prunus persica

Fleshy fruits are the most demanded fruits because of their organoleptic qualities and nutritional values. The genus Prunus is a rich source of diversified stone/drupe fruits such as almonds, apricots, plums, sweet cherries, peaches, and nectarines. The fruit-ripening process in Prunus involves coordinated biochemical and physiological changes resulting in changes in fruit texture, aroma gain, color change in the pericarp, sugar/organic acid balance, fruit growth, and weight gain. There are different varieties of peaches with unique palatable qualities and gaining knowledge in the genetics behind these quality traits helps in seedling selection for breeding programs. In addition, peaches have shorter post-harvest life due to excessive softening, resulting in fruit quality reduction and market loss. Many studies have been executed to understand the softening process at the molecular level to find the genetic basis. To summarize, this review focused on the molecular aspects of peach fruit quality attributes and their related genetics to understand the underlying mechanisms.

Frequent germplasm exchanges drive the high genetic diversity of Chinese-cultivated common apricot germplasm

The genetic diversity of germplasm is critical for exploring genetic and phenotypic resources and has important implications for crop-breeding sustainability and improvement. However, little is known about the factors that shape and maintain genetic diversity. Here, we assembled a high-quality chromosome-level reference of the Chinese common apricot 'Yinxiangbai', and we resequenced 180 apricot accessions that cover four major ecogeographical groups in China and other accessions from occidental countries. We concluded that Chinese-cultivated common apricot germplasms possessed much higher genetic diversity than those cultivated in Western countries. We also detected seven migration events among different apricot groups, where 27% of the genome was identified as being introgressed. Remarkably, we demonstrated that these introgressed regions drove the current high level of germplasm diversity in Chinese-cultivated common apricots by introducing different genes related to distinct phenotypes from different cultivated groups. Our results highlight the consideration that introgressed regions may provide an important reservoir of genetic resources that can be used to sustain modern breeding programs.

Genomic and transcriptomic analyses of Citrus sinensis varieties provide insights into Valencia orange fruit mastication trait formation

Valencia orange (Citrus sinensis Osbeck) (VO) is a type of late-ripening sweet orange whose ripening occurs 4 to 5 months later than that of the mid-ripening common sweet orange (CO). Notably, the mastication trait of VO fruit is inferior to that of CO fruit. To date, how inferior pulp mastication trait forms in VO has not been determined. In this study, 13 VO varieties and 12 CO varieties were subjected to whole-genome resequencing. A total of 2.98 million SNPs were identified from 25 varieties, and a SNP molecular marker was developed to distinguish VO and CO. Moreover, 144 and 141 genes identified by selective sweep analysis were selected during VO and CO evolution, respectively. Based on gene functional enrichment analysis, most of the selected VO genes were related to the stress response and lignin biosynthesis. Simultaneously, we comparatively analyzed the transcriptome profiles of peel and pulp tissues among three VO varieties and three CO varieties, and the results demonstrated differences in lignin biosynthesis between VO and CO fruits. Furthermore, coexpression network analysis was performed to identify hub genes of lignin-related and variety-specific networks, which included CsERF74, CsNAC25, CsHSFB3, CsSPL4/13, etc. Overall, this study provides important insights into the mastication trait formation of Valencia orange fruit.

New high-quality peach (Prunus persica L. Batsch) genome assembly to analyze the molecular evolutionary mechanism of volatile compounds in peach fruits

Peach (Prunus persica L. Batsch) is an economically important fruit crop worldwide. Although a high-quality peach genome has previously been published, Sanger sequencing was used for its assembly, which generated short contigs. Here, we report a chromosome-level genome assembly and sequence analysis of Chinese Cling, an important founder cultivar for peach breeding programs worldwide. The assembled genome contained 247.33 Mb with a contig N50 of 4.13 Mb and a scaffold N50 of 29.68 Mb, representing 99.8% of the estimated genome. Comparisons between this genome and the recently published one (Lovell peach) uncovered 685 407 single nucleotide polymorphisms, 162 655 insertions and deletions, and 16 248 structural variants. Gene family analysis highlighted the contraction of the gene families involved in flavone, flavonol, flavonoid, and monoterpenoid biosynthesis. Subsequently, the volatile compounds of 256 peach varieties were quantitated in mature fruits in 2015 and 2016 to perform a genome-wide association analysis. A comparison with the identified domestication genomic regions allowed us to identify 25 quantitative trait loci, associated with seven volatile compounds, in the domestication region, which is consistent with the differences in volatile compounds between wild and cultivated peaches. Finally, a gene encoding terpene synthase, located within a previously reported quantitative trait loci region, was identified to be associated with linalool synthesis. Such findings highlight the importance of this new assembly for the analysis of evolutionary mechanisms and gene identification in peach species. Furthermore, this high-quality peach genome provides valuable information for future fruit improvement.

Unraveling a genetic roadmap for improved taste in the domesticated apple

Although taste is an important aspect of fruit quality, an understanding of its genetic control remains elusive in apple and other fruit crops. In this study, we conducted genomic sequence analysis of 497 Malus accessions and revealed erosion of genetic diversity caused by apple breeding and possible independent domestication events of dessert and cider apples. Signatures of selection for fruit acidity and size, but not for fruit sugar content, were detected during the processes of both domestication and improvement. Furthermore, we found that single mutations in major genes affecting fruit taste, including Ma1, MdTDT, and MdSOT2, dramatically decrease malate, citrate, and sorbitol accumulation, respectively, and correspond to important domestication events. Interestingly, Ma1 was identified to have pleiotropic effects on both organic acid content and sugar:acid ratio, suggesting that it plays a vital role in determining fruit taste. Fruit taste is unlikely to have been negatively affected by linkage drag associated with selection for larger fruit that resulted from the pyramiding of multiple genes with minor effects on fruit size. Collectively, our study provides new insights into the genetic basis of fruit quality and its evolutionary roadmap during apple domestication, pinpointing several candidate genes for genetic manipulation of fruit taste in apple.

Genomic basis of high-altitude adaptation in Tibetan Prunus fruit trees

The Great Himalayan Mountains and their foothills are believed to be the place of origin and development of many plant species. The genetic basis of adaptation to high plateaus is a fascinating topic that is poorly understood at the population level. We comprehensively collected and sequenced 377 accessions of Prunus germplasm along altitude gradients ranging from 2,067 to 4,492 m in the Himalayas. We de novo assembled three high-quality genomes of Tibetan Prunus species. A comparative analysis of Prunus genomes indicated a remarkable expansion of the SINE retrotransposons occurred in the genomes of Tibetan species. We observed genetic differentiation between Tibetan peaches from high and low altitudes and that genes associated with light stress signaling, especially UV stress signaling, were enriched in the differentiated regions. By profiling the metabolomes of Tibetan peach fruit, we determined 379 metabolites had significant genetic correlations with altitudes and that in particular phenylpropanoids were positively correlated with altitudes. We identified 62 Tibetan peach-specific SINEs that colocalized with metabolites differentially accumualted in Tibetan relative to cultivated peach. We demonstrated that two SINEs were inserted in a locus controlling the accumulation of 3-O-feruloyl quinic acid. SINE1 was specific to Tibetan peach. SINE2 was predominant in high altitudes and associated with the accumulation of 3-O-feruloyl quinic acid. These genomic and metabolic data for Prunus populations native to the Himalayan region indicate that the expansion of SINE retrotransposons helped Tibetan Prunus species adapt to the harsh environment of the Himalayan plateau by promoting the accumulation of beneficial metabolites.

Resequencing and transcriptomic analysis reveal differences in nitrite reductase in jujube fruit (Ziziphus jujuba Mill.)

BACKGROUND

Jujube is a typical fruit tree species from China. 'Muzao', a cracking-susceptible cultivar, and 'Linhuang No. 1', a cracking-resistant cultivar, were selected in a previous study as contrasting research materials. Whole-genome resequencing and transcriptomic analysis of 'Linhuang No. 1' and 'Muzao' allowed the identification of differentially expressed genes with different gene structures between the two cultivars and could be helpful in explaining the differences and similarities between the two cultivars.

RESULTS

Resequencing identified 664,129 polymorphic variable sites between 'Linhuang No. 1' and 'Muzao'. To determine the genetic relationship among 'Linhuang No. 1', 'Muzao' and the jujube genome reference cultivar 'Dongzao', the characteristic polymorphic variable sites were analysed by principal component analysis. The genetic relationship between 'Linhuang No. 1' and 'Muzao' was closer than that of either variety and 'Dongzao'. Nineteen differentially expressed genes were identified by combining transcriptomic analysis with resequencing analysis. LOC107427052 (encoding a nitrite reductase) was identified by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis for further study. The identified insertion was not in the domain region of the LOC107427052 gene coding sequence (CDS) region and was verified by the finding that the insertion did not affect translation of the protein. The LOC107427052 gene expression levels, nitrite reductase activities and nitrite contents of 'Muzao' were significantly higher than the corresponding values of 'Linhuang No. 1' at the young fruit stage. There was no significant difference in the quantity of the product of nitrite reductase, namely, ammonia, between the two cultivars.

CONCLUSIONS

The present study was the first to explore the differences between different jujube cultivars ('Linhuang No. 1' and 'Muzao') by combining genome resequencing and transcriptomics. LOC107427052 (encoding a nitrite reductase) was characterized by KEGG enrichment analysis. The insertion in the CDS region of the LOC107427052 gene provides a new direction for the study of nitrogen metabolism in jujube. Our study has laid a foundation for the comparative analysis of nitrite metabolism between the jujube cultivars 'Linhuang No. 1' and 'Muzao'.

Diversity and Relationships among Neglected Apricot (Prunus armeniaca L.) Landraces Using Morphological Traits and SSR Markers: Implications for Agro-Biodiversity Conservation

Apricot (Prunus armeniaca L.) is an economically important tree species globally cultivated in temperate areas. Italy has an ample number of traditional varieties, but numerous landraces are abandoned and at risk of extinction because of increasing urbanization, agricultural intensification, and varietal renewal. In this work, we investigated the morphological and genetic diversity present in an ex-situ collection of 28 neglected varieties belonging to the so-called "Vesuvian apricot". Our aim was to understand the level of diversity and the possible link between the promotion of specific fruit types (e.g., by public policies) and the intraspecific variation in apricot. The combination of five continuous and seven categorical traits allowed us to phenotypically distinguish the varieties; while fruit quality-related attributes displayed high variation, both apricot size and skin colour were more uniform. The twelve fluorescent-based Simple Sequence Repeats (SSRs) markers identified cultivar-specific molecular profiles and revealed a high molecular diversity, which poorly correlated with that described by the morphological analysis. Our results highlighted the complementary information provided by the two sets of descriptors and that DNA markers are necessary to separate morphologically related apricot landraces. The observed morphological and genetic differences suggest a loss of diversity influenced by maintenance breeding of specific pomological traits (e.g., skin colour and size). Finally, our study provided evidence to recommend complementary strategies to avoid the loss of diversity in apricot. Actions should pivot on both the promotion of easily identified premium products and more inclusive biodiversity-centred on-farm strategies.

Population-scale peach genome analyses unravel selection patterns and biochemical basis underlying fruit flavor

A narrow genetic basis in modern cultivars and strong linkage disequilibrium in peach (Prunus persica) has restricted resolution power for association studies in this model fruit species, thereby limiting our understanding of economically important quality traits including fruit flavor. Here, we present a high-quality genome assembly for a Chinese landrace, Longhua Shui Mi (LHSM), a representative of the Chinese Cling peaches that have been central in global peach genetic improvement. We also map the resequencing data for 564 peach accessions to this LHSM assembly at an average depth of 26.34× per accession. Population genomic analyses reveal a fascinating history of convergent selection for sweetness yet divergent selection for acidity in eastern vs. western modern cultivars. Molecular-genetics and biochemical analyses establish that PpALMT1 (aluminum-activated malate transporter 1) contributes to their difference of malate content and that increases fructose content accounts for the increased sweetness of modern peach fruits, as regulated by PpERDL16 (early response to dehydration 6-like 16). Our study illustrates the strong utility of the genomics resources for both basic and applied efforts to understand and exploit the genetic basis of fruit quality in peach.

Low levels of genetic differentiation with isolation by geography and environment in populations of Drosophila melanogaster from across China

The fruit fly, Drosophila melanogaster, is a model species in evolutionary studies. However, population processes of this species in East Asia are poorly studied. Here we examined the population genetic structure of D. melanogaster across China. There were 14 mitochondrial haplotypes with 10 unique ones out of 23 known from around the globe. Pairwise F_ST values estimated from 15 novel microsatellites ranged from 0 to 0.11, with geographically isolated populations showing the highest level of genetic uniqueness. STRUCTURE analysis identified high levels of admixture at both the individual and population levels. Mantel tests indicated a strong association between genetic distance and geographical distance as well as environmental distance. Full redundancy analysis (RDA) showed that independent effects of environmental conditions and geography accounted for 62.10% and 31.58% of the total explained genetic variance, respectively. When geographic variables were constrained in a partial RDA analysis, the environmental variables bio2 (mean diurnal air temperature range), bio13 (precipitation of the wettest month), and bio15 (precipitation seasonality) were correlated with genetic distance. Our study suggests that demographic history, geographical isolation, and environmental factors have together shaped the population genetic structure of D. melanogaster after its introduction into China.

Loquat (Eriobotrya japonica (Thunb.) Lindl) population genomics suggests a two-staged domestication and identifies genes showing convergence/parallel selective sweeps with apple or peach

Crop domestication and evolution represent key fields of plant and genetics research. Here, we re-sequenced and analyzed whole genome data from 51 wild accessions and 53 representative cultivars of Eriobotrya japonica, an important semi-subtropical fruit crop. Population genomics analysis suggested that modern cultivated E. japonica experienced a two-staged domestication fitting the "marginality model," being initially domesticated in west-northern Hubei province from a mono-phylogenetic wild progenitor, then refined mainly in Jiangsu, Zhejiang and Fujian provinces of China. Cultivated E. japonica has experienced little reduction in genome-wide nucleotide polymorphism compared with wild forms. Genes responsible for sugar biosynthesis were enriched in regions harboring putative selective sweeps. An approach based on co-clustering into gene families and evaluating chromosome colinearity of orthologous and paralogous genes was used to identify convergent/parallel selective sweeps among different crops. Specifically, more than one hundred of orthologs and paralogs undergoing selective sweeps were identified between loquat, apple and peach, among which 14 encoded "UDP glycosyltransferase 1." In sum, the study not only provided valuable information for breeding of E. japonica, but also enriched knowledge of crop domestication.

Exaptation Traits for Megafaunal Mutualisms as a Factor in Plant Domestication

Megafaunal extinctions are recurring events that cause evolutionary ripples, as cascades of secondary extinctions and shifting selective pressures reshape ecosystems. Megafaunal browsers and grazers are major ecosystem engineers, they: keep woody vegetation suppressed; are nitrogen cyclers; and serve as seed dispersers. Most angiosperms possess sets of physiological traits that allow for the fixation of mutualisms with megafauna; some of these traits appear to serve as exaptation (preadaptation) features for farming. As an easily recognized example, fleshy fruits are, an exaptation to agriculture, as they evolved to recruit a non-human disperser. We hypothesize that the traits of rapid annual growth, self-compatibility, heavy investment in reproduction, high plasticity (wide reaction norms), and rapid evolvability were part of an adaptive syndrome for megafaunal seed dispersal. We review the evolutionary importance that megafauna had for crop and weed progenitors and discuss possible ramifications of their extinction on: (1) seed dispersal; (2) population dynamics; and (3) habitat loss. Humans replaced some of the ecological services that had been lost as a result of late Quaternary extinctions and drove rapid evolutionary change resulting in domestication.

The Draft Genome of a Flat Peach (Prunus persica L. cv. '124 Pan') Provides Insights into Its Good Fruit Flavor Traits

The flat peach has become more and more popular worldwide for its fruit quality with relatively low acidity, high sugar content and rich flavor. However, the draft genome assembly of flat peach is still unavailable and the genetic basis for its fruit flavor remains unclear. In this study, the draft genome of a flat peach cultivar '124 Pan' was assembled by using a hybrid assembly algorithm. The final assembly resulted in a total size of 206 Mb with a N50 of 26.3 Mb containing eight chromosomes and seven scaffolds. Genome annotation revealed that a total of 25,233 protein-coding genes were predicted with comparable gene abundance among the sequenced peach species. The phylogenetic tree and divergence times inferred from 572 single copy genes of 13 plant species confirmed that Prunus ferganensis was the ancestor of the domesticated peach. By comparing with the genomes of Prunus persica (Lovell) and Prunus ferganensis, the expansion of genes encoding enzymes involved in terpene biosynthesis was found, which might contribute to the good fruit flavor traits of '124 Pan'. The flat peach draft genome assembly obtained in this study will provide a valuable genomic resource for peach improvement and molecular breeding.

Genomic analyses of diverse wild and cultivated accessions provide insights into the evolutionary history of jujube

The Chinese jujube (Ziziphus jujuba Mill.), a member of the Rhamnaceae family, is an important perennial fruit tree crop of substantial economic, ecological and nutritional value, and is also used as a traditional herbal medicine. Here, we report the resequencing of 493 jujube accessions, including 202 wild and 291 cultivated accessions at >16× depth. Our population genomic analyses revealed that the Shanxi-Shaanxi area of China was jujube's primary domestication centre and that jujube was then disseminated into East China before finally extending into South China. Divergence events analysis indicated that Ziziphus acidojujuba and Ziziphus jujuba diverged around 2.7 Mya, suggesting the interesting possibility that a long pre-domestication period may have occurred prior to human intervention. Using the large genetic polymorphism data set, we identified a 15-bp tandem insertion in the promoter of the jujube ortholog of the POLLEN DEFECTIVE IN GUIDANCE 1 (POD1) gene, which was strongly associated with seed-setting rate. Integrating genome-wide association study (GWAS), transcriptome data, expression analysis and transgenic validation in tomato, we identified a DA3/UBIQUITIN-SPECIFIC PROTEASE 14 (UBP14) ortholog, which negatively regulate fruit weight in jujube. We also identified candidate genes, which have likely influenced the selection of fruit sweetness and crispness texture traits among fresh and dry jujubes. Our study not only illuminates the genetic basis of jujube evolution and domestication and provides a deep and rich genomic resource to facilitate both crop improvement and hypothesis-driven basic research, but also identifies multiple agriculturally important genes for this unique perennial tree fruit species.

Developmental transcriptome profiling uncovered carbon signaling genes associated with almond fruit drop

Almond is one of the most featured nut crops owing to its high nutritional value. However, due to three different waves of flower and fruitlet drop, fruit drop is a major concern for growers. In this study, we carried out a time-course transcriptome analysis to investigate gene expression differences between normal and abnormal fruitlet development. By de novo assembly analysis, we identified 33,577 unigenes and provided their functional annotations. In total, we identified 7,469 differentially expressed genes and observed the most apparent difference between normal and abnormal fruits at 12 and 17 days after flowering. Their biological functions were enriched in carbon metabolism, carbon fixation in photosynthetic organisms and plant hormone signal transduction. RT-qPCR validated the expression pattern of 14 representative genes, including glycosyltransferase like family 2, MYB39, IAA13, gibberellin-regulated protein 11-like and POD44, which confirmed the reliability of our transcriptome data. This study provides an insight into the association between abnormal fruit development and carbohydrate signaling from the early developmental stages and could be served as useful information for understanding the regulatory mechanisms related to almond fruit drop.

Preliminary Identification of Key Genes Controlling Peach Pollen Fertility Using Genome-Wide Association Study

Previous genetic mapping helped detect a ~7.52 Mb putative genomic region for the pollen fertility trait on peach Chromosome 06 (Chr.06), which was too long for candidate gene characterization. In this study, using the whole-genome re-sequencing data of 201 peach accessions, we performed a genome-wide association study to identify key genes related to peach pollen fertility trait. The significant association peak was detected at Chr.06: 2,116,368 bp, which was in accordance with the previous genetic mapping results, but displayed largely improved precision, allowing for the identification of nine candidate genes. Among these candidates, gene PpABCG26, encoding an ATP-binding cassette G (ABCG) transporter and harboring the most significantly associated SNP (Single Nucleotide Polymorphism) marker in its coding region, was hypothesized to control peach pollen fertility/sterility based on the results of gene function comparison, gene relative expression, and nucleotide sequence analysis. The obtained results will help us to understand the genetic basis of peach pollen fertility trait, and to discover applicable markers for pre-selection in peach.