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Spain is one of the most important producers of fresh apricots (Prunus armeniaca L.). Traditional production was based on several local cultivars with good quality and well adapted to the industry. However, most are susceptible to important viral diseases that affect fruit production and quality. The main viral diseases are sharka (Plum pox virus, PPV) and viruela (Apple chlorotic leaf spot virus, ACLSV). Using foreign resistance sources to PPV, new resistant cultivars have been released. More recently, two new resistance sources to ACLSV have been identified: the Spanish cultivar ‘Mauricio’ and the French cultivar ‘Bergeron’. With the objective of obtaining new genotypes resistant to both diseases simultaneously, two crosses between the apricot selections ‘5–26’ and ‘11–1’ from CEBAS-CSIC (resistant to PPV) and ACLSV-resistant cultivars ‘Mauricio’ and ‘Bergeron’ were achieved, and the descendants were evaluated for resistance to these diseases. Molecular markers were also used to evaluate the genitors and descendants. Results showed that 100% and 75% of seedlings were resistant to PPV and ACLSV, respectively, and 70% were resistant to both diseases simultaneously. In general, no interaction between both viruses was detected, infecting the plant independently. For the first time, apricot plants resistant to PPV and ACLSV simultaneously have been obtained.

lowering time in almond [Prunus dulcis (Miller) Webb] is a complex process involving the chilling and heat requirements’ characteristic and genetic background of each cultivar. During the falling temperatures of autumn, cultivated almond, activate a winter-survival strategy called endodormancy to protect against unfavorably cold temperatures. Chill accumulation allows the progression from almond flower bud endodormancy stage to flower bud ecodormancy regulated by heat accumulation. Major breeding challenges to analyze molecular changes associated to bud dormancy and flowering will be the appropriate phenotyping together with the incorporation of genomic, transcriptomic and epigenetic tools for the development of improved breeding strategies. This chapter reviews the transcriptional changes associated to flower bud dormancy and flowering in almond including DNA sequence motifs, mRNA expression, epigenetic modifications and phytohormone signaling. Inheritance and transmission of flowering time and chilling and heat requirements in almond have been largely studied in almond being polygenic traits with high heritability although a major gene late blooming (Lb) controlling flowering time. In addition, molecular studies at DNA level have confirmed this polygenic nature identifying several genome regions (quantitative trait loci, QTLs) involved. Studies about regulation of gene expression are scarce although several transcription factors have been described as responsible. From the metabolomics point of view, the integrated analysis of the mechanisms of accumulation of cyanogenic glucosides and flowering regulation through transcription factors opens new possibilities in the analysis of this complex trait in almond. Finally, at epigenetic level, DNA methylation assays have been performed

Almond shell hardness is an economically important quality trait that protects the integrity of the kernel. It is directly related with shelling or crack-out percent. In the U.S. and Australian markets, soft to semi-hard shells varieties have been used in the industry, while in the European market, hard shells are dominantly sold and distributed. The origin of a hard shell is from wild almond species. Soft shells in the USA and Australia have been selected for a higher crack-out percent or larger kernel and ease of processing. Here, we examined breeding populations totaling 264 trees that were genotyped with genotyping-by-sequencing (GBS) where shell hardness was measured with a texture analyzer, and shell weight, in-shell weights and shell thickness were measured and crack-out percent was calculated. In a genome-wide association, seven genetic loci were found to be associated with shell hardness, crack-out percent, shell thickness and shell weight. Of these seven, one was shared between multiple traits. Kompetitive allele-specific PCR (KASP) assays were developed and tested in unrelated breeding lines from Australia, Spain, France and Italy. One KASP assay was found to be highly predictive of shell hardness in this diverse panel and can be applied for use in marker-assisted breeding.

This work presents two new almond cultivars obtained by the Centro de Edafología y Biología Aplicada del Segura (CEBAS)–Consejo Superior de Investigaciones Científicas (CSIC) Almond Breeding Program: Florida and Alaska. Both are self-compatible and soft-shelled with a kernel percentage higher than 50%. ‘Florida’ is early blooming (like ‘Nonpareil’), whereas ‘Alaska’ is extra late (more than 2 weeks later than ‘Nonpareil’). Both are very productive and have attractive kernels. ‘Florida’ has an extra-early ripening date (∼3 d before ‘Nonpareil’) and ‘Alaska’ is intermediate (∼2 weeks later than ‘Nonpareil’). From a chemical point of view, ‘Florida’ is very similar to ‘Nonpareil’, and ‘Alaska’ stands out for its high fat content (60%), which is unusual for American cultivars. ‘Florida’ could play a role in the traditional warm areas of ‘Nonpareil’, whereas ‘Alaska’ is an attractive cultivar for colder areas with a higher risk of frost

This book brings together the latest information on almond genomics and transcriptomics, with a particular focus on cutting-edge findings, tools, and strategies employed in genome sequencing and analysis with regard to the most important agronomic traits. Cultivated almond [(Prunus dulcis (Miller) D. A. Webb, syn. Prunus amygdalus Batsch., Amygdalus communis L., Amygdalus dulcis Mill.)] is a tree crop producing seeds of great economic interest, and adapted to hot and dry climates. Domesticated in Southeast Asia, its small diploid genome and phenotypic diversity make it an ideal model to complement genomics studies on peach, generally considered to be the reference Prunus species. Both represent consanguineous species that evolved in two distinct environments: warmer and more humid in the case of peach, and colder and xerophytic for almond. The advent of affordable whole-genome sequencing, in combination with existing Prunus functional genomics data, has now made it possible to leverage the novel diversity found in almond, providing an unmatched resource for the genetic improvement of this species

Endodormancy in temperate fruit trees like Prunus is a protector state that allows the trees to survive in the adverse conditions of autumn and winter. During this process, plants accumulate chill hours. Flower buds require a certain number of chill hours to release from endodormancy, known as chilling requirements. This step is crucial for proper flowering and fruit set, since incomplete fulfillment of the chilling requirements produces asynchronous flowering, resulting in low quality flowers, and fruits. In recent decades, global warming has endangered this chill accumulation. Because of this fact, many agrochemicals have been used to promote endodormancy release. One of the first and most efficient agrochemicals used for this purpose was hydrogen cyanamide. The application of this agrochemical has been found to advance endodormancy release and synchronize flowering time, compressing the flowering period and increasing production in many species, including apple, grapevine, kiwi, and peach. However, some studies have pointed to the toxicity of this agrochemical. Therefore, other nontoxic agrochemicals have been used in recent years. Among them, Erger R + Activ Erger R and Syncron R + NitroActive R have been the most popular alternatives. These two treatments have been shown to efficiently advance endodormancy release in most of the species in which they have been applied. In addition, other less popular agrochemicals have also been applied, but their efficiency is still unclear. In recent years, several studies have focused on the biochemical and genetic variation produced by these treatments, and significant variations have been observed in reactive oxygen species, abscisic acid (ABA), and gibberellin (GA) levels and in the genes responsible for their biosynthesis. Given the importance of this topic, future studies should focus on the discovery and development of new environmentally friendly agrochemicals for improving the modulation of endodormancy release and l

Flower bud dormancy in temperate fruit tree species, such as almond [Prunus dulcis (Mill.) D.A. Webb], is a survival mechanism that ensures that flowering will occur under suitable weather conditions for successful flower development, pollination and fruit set. Dormancy is divided into three sequential phases: paradormancy, endodormancy and ecodormancy. During the winter, buds need cultivar-specific chilling requirements (CRs) to overcome endodormancy and heat requirements to activate the machinery to flower in the ecodormancy phase. One of the main factors that enables the transition from endodormancy to ecodormancy is transcriptome reprogramming. In this work, we therefore monitored three almond cultivars with different CRs and flowering times by RNA sequencing during the endodormancy release of flower buds and validated the data by quantitative real-Time PCR in two consecutive seasons. We were thus able to identify early and late flowering time candidate genes in endodormant and ecodormant almond flower buds associated with metabolic switches, transmembrane transport, cell wall remodeling, phytohormone signaling and pollen development. These candidate genes were indeed involved in the overcoming of the endodormancy in almond. This information may be used for the development of dormancy molecular markers, increasing the efficiency of temperate fruit tree breeding programs in a climate-change context.

Loss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes. However, in almond, little is known about the genetic variability in current breeding stocks, although several cases of inbreeding depression have been reported. To gain insights into the genetic structure in modern breeding programs worldwide, marker-verified pedigree data of 220 almond cultivars and breeding selections were analyzed. Inbreeding coefficients, pairwise relatedness, and genetic contribution were calculated for these genotypes. The results reveal two mainstream breeding lines based on three cultivars: “Tuono”, “Cristomorto”, and “Nonpareil”. Descendants from “Tuono” or “Cristomorto” number 76 (sharing 34 descendants), while “Nonpareil” has 71 descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.041, with 14 genotypes presenting a high inbreeding coefficient, over 0.250. Breeding programs from France, the USA, and Spain showed inbreeding coefficients of 0.075, 0.070, and 0.037, respectively. According to their genetic contribution, modern cultivars from Israel, France, the USA, Spain, and Australia trace back to a maximum of six main founding genotypes. Among the group of 65 genotypes carrying the Sf allele for self-compatibility, the mean relatedness coefficient was 0.125, with “Tuono” as the main founding genotype (24.7% of total genetic contribution). The results broaden our understanding about the tendencies followed in almond breeding over the last 50 years and will have a large impact into breeding decision-making process worldwide. Increasing current genetic variability is required in almond breeding programs to assure genetic gain and continuing breeding progress.

Prunus species are important crops in temperate regions. In these regions, drought periods are predicted to occur more frequently due to climate change. In this sense, to reduce the impact of climate warming, obtaining new tolerant/resistant cultivars and rootstocks is a mandatory goal in Prunus breeding. Therefore, the current study assembled three Prunus species including almond, (P. dulcis Mill D.A. Webb), apricot (P. armeniaca L.) and peach (P. persica L.) to model the temporal effects of drought. A hybrid peach × almond and a wild almond-relative species Prunus webbii were also included in the study. Physiological traits associated with photosynthetic activity, leaf water status, and chlorophyll content were assessed under three watering treatments. Results showed that effects of time, genotype, and treatment interact significantly in all traits. In addition, results confirmed that P. webbii have a greater tolerance to drought than commercial rootstocks. However, “Real Fino” apricot showed the fastest recovery after re-irrigation while being one of the most affected cultivars. In addition, from the better response to these watering treatments by the almond genotypes, two different trends were observed after re-irrigation treatment that clearly differentiate the response of the almond cultivar “Garrigue” from the rest of Prunus genotypes. A better characterization of the short-term drought response in Prunus, an accurate and more efficient evaluation of the genotype effect was obtained from the use of mixed models considering appropriate variance–covariance structures. Although the advantages of these approaches are rarely used in Prunus breeding, these methodologies should be undertaken in the future by breeders to increase efficiency in developing new breeding materials.

In this study, the control of eco- and endo-dormancy release led to the modulation of the flowering time in almond (Prunus dulcis (Mill.) D.A. Webb). The study was performed in almond cultivars with contrasting flowering times: the extra-early flowering cultivar Desmayo Largueta and the ultra-late cultivar Tardona. Temperature control in the “Autumn”, “Winter” and “Spring” chambers successfully delayed the flowering time in Desmayo Largueta. Advance flowering in the cultivar Tardona was limited, however, even with the application of sufficient chill in the Winter chamber. The ecodormancy period and the heat accumulation for flowering were not stable among cultivars, even though the heat accumulation was generally high, in accordance with that accumulated in field conditions. The heat requirements of the early cultivar Desmayo Largueta were lower than those of the ultra-late cultivar Tardona. We observed a decreasing pattern in ecodormancy along treatments that was probably related to the temperature in the Spring chamber. Finally, flowering and fruit set were highly variable, and these parameters were more dependent on the cultivar assayed than on the treatment applied. Although the ripening time under our experimental conditions was earlier than the phenological dates observed in the field, the flowering time delayed the ripening time in the case of the extra-early cultivar Desmayo Largueta. The fruit weight increased in the last treatments, whereas the kernel/fruit ratio decreased, as the kernel weight did not vary significantly along treatments. The results obtained show that flowering time can be modulated by temperature control and that other uncontrolled factors, such as photoperiod, can be involved in the control of endodormancy release and flowering time, especially in late flowering cultivars.