Background Peach (Prunus persica) and almond (P. dulcis) are closely related species within the Prunus genus that exhibit strikingly different fruit characteristics, particularly in mesocarp expansion and ripening behaviour. To investigate the biological processes driving these differences, we performed a comprehensive transcriptomic analysis of fruit development in the peach cultivar 'Earlygold', the almond cultivar 'Texas', and their interspecific F1 hybrid. Fruit samples were collected at three developmental stages that are key in the different ripening behaviour of peach and almond: initial phase of rapid growth (T1), cell expansion and lignification (T2), and ripening (T3).Results Global transcriptome profiling revealed almost identical expression patterns irrespective of the reference genome used for the RNA-seq analysis. We found 4,241, 3,862 and 2,922 DEGs between T1 and T2 in 'Earlygold', 'Texas' and F1 hybrid respectively, with most specific changes (55%, 76.6% and 51.3%) occurring during the first half of fruit development. Between T2 and T3, peach-type fruits continued active transcriptional regulation (2,665 DEGs in 'Earlygold', 2,199 in F1 hybrid), whereas almond showed limited late-stage changes (1,032 DEGs), reflecting its non-ripening phenotype. Enrichment analysis showed conserved cell division and photosynthesis-related genes enriched at T1 at both species. Peach displayed unique enrichment in pathways related to auxin signaling, DNA replication, and cyanogenic compound metabolism whereas almond for abscisic acid- and ethylene-related stress pathways. Allele-specific expression (ASE) analysis in the F1 hybrid revealed 79, 99 and 119 peach-biased ASE genes, and 27, 51 and 77 almond-biased ASE genes at T1, T2 and T3, respectively.Conclusions These findings reveal that peach and almond share conserved early developmental programs but diverge markedly from mid-development. Our data highlight auxin signaling, DNA replication, and ethylene-mediated ripening as central processes driving these developmental differences. The limited number of ASE genes and their parental bias patterns further illuminate cis-regulatory divergence between both species. This study provides new insights into the genetic regulation of fruit development in Prunus species and demonstrates a robust pipeline for cross-species transcriptomic analysis.

Using cultivars based on a single, partly heterozygous, genotype is one of the bases of agriculture, frequently used in seed-propagated species such as vegetables and field crops (F1 hybrid varieties), and in most fruit trees and ornamentals (clonal varieties) that reproduce vegetatively. Producing two inbred lines that fully or partly reconstruct a given high-value heterozygous individual is now possible with the Resynthesis method, which uses molecular markers to select pairs of complementary genotypes in the F2 and subsequent selfing generations. The objective of this paper was to develop a software to facilitate the selection of such complementary pairs from a large number of segregating genotyped individuals. The ResynPy tool we developed screens the genotyping data of a segregating population, originating from selfing a top-performing partly heterozygous individual, and detects pairs of individuals that could produce progeny containing individuals nearly identical to the initial elite genotype. Our software selects candidate pairs of individuals in a small timeframe window with a low memory footprint. ResynPy tool could be part of a breeding toolkit to accelerate breeding programs in any plant species of economic importance capable of producing self-pollinated progeny. ResynPy is a software developed in Python language and is freely available on GitHub (HYPERLINK “ https://github.com/kostasgalexiou/ResynPy/tree/main ”). ResynPy automates the process of individual selection implemented by the Resynthesis method, in a highly efficient manner through parallelization, allowing to plant breeders for detection of pairs of complementary individuals in a selfing population that could be suitable parents to a plant variety with economically important agronomic traits. With ResynPy, breeders are provided with a fast and easy-to-use tool that will aid them to advance their plant breeding programs.

Natural variations are the foundation of crop improvement. However, genomic variability remains largely understudied. Here, we present the full-spectrum integrated panvariome and pangenome of 1,020 peach accessions, including 10.5 million single-nucleotide polymorphisms, insertions, deletions, duplications, inversions, translocations, copy-number variations, transposon-insertion polymorphisms, and presence-absence variations, uncovering 70.6% novel variants and 3,289 novel genes. Analysis of the panvariome recapitulated the global evolutionary history of the peach and identified several novel trait-causally rare variants. We found that landraces and improved accessions encode more genes than the wild accessions, implying gene gains during peach domestication and improvement. Analysis of global introgression patterns revealed their value in phenotype prediction and gene mining, and suggested that the most likely wild progenitor of the domesticated peach is Prunus mira and that almond was involved in the origin of Prunus davidiana. Furthermore, we developed a novel panvariome-based one-step solution for association study, GWASPV, which was used to identify several trait-conferring genes and over 2,000 novel associations.. Collectively, our study reveals new insights into peach evolution and genomic variations, providing a novel method for plant gene mining and important targets for peach breeding.

Increasing marker density results in better map coverage and efficiency of genetic analysis. Here, we resequenced a large (N = 235) F1 progeny from two distant peach cultivars, ‘Zhongyou Pan #9’ and ‘September Free’, and constructed two parental maps (1:1 segregations) and one combined map (1:2:1 segregations) with 134 277 SNPs. Markers with the same genotype for all individuals studied were grouped in bins and a unique genotype for each bin was inferred to avoid mapping problems derived from erroneous data. The total genetic distance of the two parental maps was 431.9 and 594.2 cM with a short mean distance, 0.9 cM, between contiguous bins (groups of markers with the same genotype) and high collinearity with the peach genome. The genetics of eight fruit-related traits was analyzed for 2 years, allowing the positions of two major genes, fruit shape (S) and flesh adhesion to the stone (F), to be established, along with nine quantitative trait loci (QTLs) for quantitative traits including fruit soluble solids concentration, titratable acidity, weight, maturity date, and flesh color (yellow to orange). We developed a machine learning-based linear model to assess flesh color, which proved more efficient than physical colorimetric parameters (L, a*, b*), detecting consistent QTLs. Based on map position, gene expression patterns, and function, candidate genes were identified. Overall, our results provide two new elements: ultra-high-density maps with resequencing data to enhance mapping resolution and phenotyping strategies based on machine learning models that improve the quality of quantitative measurements to help understand the genetic control of key fruit quality traits.

Almond breeding is increasingly focusing on kernel quality. However, unlike other agronomic traits, the genetic basis of physical and chemical kernel quality traits has been poorly investigated. To address this gap, we conducted a QTL mapping of these traits to enhance our understanding of their genetic control. We phenotyped fruit samples from an F1 population derived from the cross between ‘Marcona’ and ‘Marinada’ for up to four years, using conventional and image analysis methods. Additionally, the 91 individuals of the population were genotyped with the almond Axiom™ 60K SNP array, and high-density linkage maps were constructed. These analyses identified several genomic regions of breeding interest. For example, two regions on chromosome one were found to contain QTLs for kernel shape and dimension, while another region at the end of the same chromosome contained QTLs for kernel fatty acid composition. Notably, QTLs for kernel symmetry and kernel shoulder, reported for the first time in this study, were also mapped on chromosome one. These QTLs will serve as a foundation for developing molecular markers linked to kernel physical and chemical quality traits in almonds, facilitating the integration of marker-assisted selection into breeding programs.

SUMMARY:Pedigree-based analyses' prime role is to unravel relationships between individuals in breeding programs and germplasms. This is critical information for decoding the genetics underlying main inherited traits of relevance, and unlocking the genotypic variability of a species to carry out genomic selections and predictions. Despite the great interest, current lineage visualizations become quite limiting in terms of public display, exploration, and tracing of traits up to ancestral donors. PERSEUS is a user-friendly, intuitive, and interactive web-based tool for pedigree visualizations represented as directed graph networks distributed using a force-repulsion method. The visualizations do not only showcase individual relationships among accessions, but also facilitate a seamless search and download of phenotypic traits along the pedigrees. PERSEUS is a promising tool for breeders and scientists, advantageous for evolutionary, genealogy, and diversity analyses among related accessions and species.AVAILABILITY AND IMPLEMENTATION:PERSEUS is freely accessible at https://bioinformatics.cragenomica.es/perseus and GitHub code is available at https://github.com/aranzana-lab/PERSEUS.

Peach is a model for Prunus genetics and genomics, however, identifying and validating genes associated to peach breeding traits is a complex task. A gene coexpression network (GCN) capable of capturing stable gene-gene relationships would help researchers overcome the intrinsic limitations of peach genetics and genomics approaches and outline future research opportunities. In this study, we created four GCNs from 604 Illumina RNA-Seq libraries. We evaluated the performance of every GCN in predicting functional annotations using an algorithm based on the 'guilty-by-association' principle. The GCN with the best performance was COO300, encompassing 21 956 genes. To validate its performance predicting gene function, we performed two case studies. In case study 1, we used two genes involved in fruit flesh softening: the endopolygalacturonases PpPG21 and PpPG22. Genes coexpressing with both genes were extracted and referred to as melting flesh (MF) network. Finally, we performed an enrichment analysis of MF network and compared the results with the current knowledge regarding peach fruit softening. The MF network mostly included genes involved in cell wall expansion and remodeling, and with expressions triggered by ripening-related phytohormones, such as ethylene, auxin, and methyl jasmonate. In case study 2, we explored potential targets of the anthocyanin regulator PpMYB10.1 by comparing its gene-centered coexpression network with that of its grapevine orthologues, identifying a common regulatory network. These results validated COO300 as a powerful tool for peach and Prunus research. This network, renamed as PeachGCN v1.0, and the scripts required to perform a function prediction analysis are available at https://github.com/felipecobos/PeachGCN.

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.

Fruit color is an important trait in peach from the point of view of consumer preference, nutritional content, and diversification of fruit typologies. Several genes and phenotypes have been described for peach flesh and skin color, and although peach color knowledge has increased in the last few years, some fruit color patterns observed in peach breeding programs have not been carefully described. In this work, we first describe some peach mesocarp color patterns that have not yet been described in a collection of commercial peach cultivars, and we also study the genetic inheritance of the red dots present in the flesh (RDF) and red color around the stone (CAS) in several intra- and interspecific segregating populations for both traits. For RDF, we identified a QTL at the beginning of G5 in two intraspecific populations, and for CAS we identified a major QTL in G4 in both an intraspecific and an interspecific population between almond and peach. Finally, we discuss the interaction between these QTLs and some other genes previously identified in peach, such as dominant blood flesh (DBF), color around the stone (Cs), subacid (D) and the maturity date (MD), and the implications for peach breeding. The results obtained here will help peach germplasm curators and breeders to better characterize their plant materials and to develop an integrated system of molecular markers to select these traits.

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.

Domestication drastically changed crop genomes, fixing alleles of interest and creating different genetic populations. Genome-wide association studies (GWASs) are a powerful tool to detect these alleles of interest (and so QTLs). In this study, we explored the genetic structure as well as additive and non-additive genotype-phenotype associations in a collection of 243 almond accessions. Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups, all formed by accessions with a common origin. One of these groups was formed exclusively by Spanish accessions, while the rest were mainly formed by accessions from China, Italy, France, and the USA. These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases: Asiatic, Mediterranean, Californian, and southern hemisphere. In total, we found 13 independent QTLs for nut weight, crack-out percentage, double kernels percentage, and blooming time. Of the 13 QTLs found, only one had an additive effect. Through candidate gene analysis, we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage, Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage, and Prudul26A000954 as a candidate gene for the QTL found in blooming time. Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding.

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.

Almost a decade after the publication of the genome of a double-haploid genotype from the 'Lovell' peach rootstock, knowledge on the peach and other Prunus genetics has enormously increased, and its applications for breeding have been pushed further forward. Currently there are 29 Prunus de novo sequences available in the genome database for Rosaceae, additionally showing the already known high synteny between all Prunus genomes. More than 60 Prunus major genes, mostly from peach or peach x almond crosses, have been identified, mapped and some of them cloned or have strong candidates responsible for their phenotypic variation. Marker-assisted selection has been integrated as an efficient approach to help breeders, based on the development of tightly linked markers to the genes involved in main characters under selection. New marker-based breeding approaches have been proposed: marker-assisted introgression, for fast introgression of new alleles or genes coming from exotic sources, that has already been successfully implemented. Resynthesis, a strategy to obtain peach lines that, maintaining the basic trait architecture of a top cultivar, can integrate new alleles or genes of interest with non-transgenic approaches, is underway. New tools for phenotypic and genetic analysis have recently been developed, including a multi-site peach reference population (RefPop) and a complete collection of peachalmond introgression lines. Together, they promise a deeper understanding of peach genetics, with the expected consequences of increased peach fruit quality, productivity, and resilience to the potentially devastating effects of climate change.

Pedigree relationships used for research or in commercial breeding programs are often unknown or uncertain. Nevertheless, a detailed and contrasted pedigree information is crucial to understand the genetics of simply and quantitatively inherited traits and to plan appropriate crosses for breeding new cultivars. Even though peach [Prunus persica (L.) Batsch] has been used in the last decades as a model species for Rosaceae crops, an automated and extensive pedigree reconstruction encompassing the cultivars with most historical and commercial relevance has not been created to this date. Here we present the pedigree reconstruction of peach lines and cultivars using complete genotypic data and partial historic information based on a metaheuristic approach. We also present the ongoing prospect of a user-friendly web application to easily access and visualize these pedigree networks. The web would be of great use for breeders and scientist to identify the genotypes that have contributed most to the genetic variation of the cultivated accessions, and to trace back donors of relevant traits, among other uses.

Based on detailed maps, DNA sequences and phenotypic data, there is a great deal of information on the genetics and genomics of 'Earlygold', a historical peach cultivar from the US. The F-2 between 'Texas' almond and 'Earlygold' peach (T x E) was used to construct the first saturated peach linkage map that later became the reference map for the Prunus genus. This population and the first backcross ('Texas' x 'Earlygold') x 'Earlygold' (T1E) yielded information on QTLs for a large number of agronomic traits, and T1E is being used as the basis for constructing a set of introgression lines of 'Texas' fragments into the 'Earlygold' background, currently in progress. This paper describes the construction of a high-density SNP map for 'Earlygold' using an F-2 population, and the QTL analysis of 24 traits. Results of maps and QTLs are compared with those from the 'Earlygold' parent of the TN map, using the same set of markers and characters. Results show major differences between the two progenies in terms of numbers of markers mapped and the capability of detecting QTLs, with a large increase in the resolution of maps and QTLs when using the F-2 progeny compared to the TN pseudo-testcross. In addition, we provide data on leaf senescence color, studied for the first time in peach, with two consistent QTLs located in the same position as other color-related genes and QTLs.

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.