Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars

Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time

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.

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.

Detection and distribution of two dominant alleles associated with the sweet kernel phenotype in almond cultivated germplasm

Almond [Prunus dulcis Miller (D. A. Webb), syn. Prunus amygdalus L.)] is the major tree nut crop worldwide in terms of production and cultivated area. Almond domestication was enabled by the selection of individuals bearing sweet kernels, which do not accumulate high levels of the toxic cyanogenic glucoside amygdalin. Previously, we showed that the Sweet kernel (Sk) gene, controlling the kernel taste in almond, encodes a basic helix loop helix (bHLH) transcription factor regulating the amygdalin biosynthetic pathway. In addition, we characterized a dominant allele of this gene, further referred to as Sk-1, which originates from a C¹⁰³⁶→T missense mutation and confers the sweet kernel phenotype. Here we provide evidence indicating that the allele further referred to as Sk-2, originally detected in the cultivar "Atocha" and arising from a T⁹⁸⁹→G missense mutation, is also dominantly inherited and confers the sweet kernel phenotype in almond cultivated germplasm. The use of single nucleotide polymorphism (SNP) data from genotyping by sequencing (GBS) for population structure and hierarchical clustering analyses indicated that Sk-2 occurs in a group of related genotypes, including the widespread cultivar "Texas", descending from the same ancestral population. KASP and dual label functional markers were developed for the accurate and high-throughput selection of the Sk-1 and Sk-2 alleles, and the genotyping of a panel of 134 almond cultivars. Overall, our results provide further insights on the understanding of the almond cultivation history. In addition, molecular marker assays and genotypic data presented in this study are expected to be of major interest for the conduction of almond breeding programs, which often need to select sweet kernel individuals in segregant populations.

Susceptibility of Almond (Prunus dulcis) Cultivars to Twig Canker and Shoot Blight Caused by Diaporthe amygdali

Twenty-five almond cultivars were assessed for susceptibility to Diaporthe amygdali, causal agent of twig canker and shoot blight disease. In laboratory experiments, growing twigs were inoculated with four D. amygdali isolates. Moreover, growing shoots of almond cultivars grafted onto INRA 'GF-677' rootstock were used in 4-year field inoculations with one D. amygdali isolate. In both types of experiments, inoculum consisted of agar plugs with mycelium, which were inserted underneath the bark, and the lesion lengths caused by the fungus were measured. Necrotic lesions were observed in the inoculated almond cultivars in both laboratory and field tests, confirming the susceptibility of all evaluated cultivars to all inoculated isolates of D. amygdali. Cultivars were grouped as susceptible or very susceptible according to a cluster analysis. The relationship between some agronomic traits and cultivar susceptibility was also investigated. Blooming and ripening times were found to be relevant variables explaining cultivar performance related to D. amygdali susceptibility. Late and very late blooming and early and medium ripening cultivars were highly susceptible to D. amygdali. Our results may provide valuable information that could assist in ongoing breeding programs of this crop and in the selection of cultivars for new almond plantations.

Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D.A. Webb] cultivar 'Nonpareil'

Almond [Prunus dulcis (Mill.) D.A. Webb] is an economically important, specialty nut crop grown almost exclusively in the United States. Breeding and improvement efforts worldwide have led to the development of key, productive cultivars, including 'Nonpareil,' which is the most widely grown almond cultivar. Thus far, genomic resources for this species have been limited, and a whole-genome assembly for 'Nonpareil' is not currently available despite its economic importance and use in almond breeding worldwide. We generated a 571X coverage genome sequence using Illumina, PacBio, and optical mapping technologies. Gene prediction revealed 49,321 putative genes using MinION Oxford nanopore and Illumina RNA sequencing, and genome annotation found that 68% of predicted models are associated with at least one biological function. Furthermore, epigenetic signatures of almond, namely DNA cytosine methylation, have been implicated in a variety of phenotypes including self-compatibility, bud dormancy, and development of noninfectious bud failure. In addition to the genome sequence and annotation, this report also provides the complete methylome of several almond tissues, including leaf, flower, endocarp, mesocarp, exocarp, and seed coat. Comparisons between methylation profiles in these tissues revealed differences in genome-wide weighted % methylation and chromosome-level methylation enrichment.

Revealing the Genetic Components Responsible for the Unique Photosynthetic Stem Capability of the Wild Almond Prunus arabica (Olivier) Meikle

Almond [Prunus dulcis (Mill.) D. A. Webb] is a major deciduous fruit tree crop worldwide. During dormancy, under warmer temperatures and inadequate chilling hours, the plant metabolic activity increases and may lead to carbohydrate deficiency. Prunus arabica (Olivier) Meikle is a bushy wild almond species known for its green, unbarked stem, which stays green even during the dormancy period. Our study revealed that P. arabica green stems assimilate significantly high rates of CO₂ during the winter as compared to P. dulcis cv. Um el Fahem (U.E.F.) and may improve carbohydrate status throughout dormancy. To uncover the genetic inheritance and mechanism behind the P. arabica stem photosynthetic capability (SPC), a segregated F1 population was generated by crossing P. arabica to U.E.F. Both parent's whole genome was sequenced, and SNP calling identified 4,887 informative SNPs for genotyping. A robust genetic map for U.E.F. and P. arabica was constructed (971 and 571 markers, respectively). QTL mapping and association study for the SPC phenotype revealed major QTL [log of odd (LOD) = 20.8] on chromosome 7 and another minor but significant QTL on chromosome 1 (LOD = 3.9). As expected, the P. arabica allele in the current loci significantly increased the SPC phenotype. Finally, a list of 64 candidate genes was generated. This work sets the stage for future research to investigate the mechanism regulating the SPC trait, how it affects the tree's physiology, and its importance for breeding new cultivars better adapted to high winter temperatures.

Characterization of Sweet Almond Oil Content of Four European Cultivars (Ferragnes, Ferraduel, Fournat, and Marcona) Recently Introduced in Morocco

This study concerns the characterization of oil content and quality indices for almond cultivars (Marcona (Mr), Fournat (Fn), Ferragnes (Fg), and Ferraduel (Fd)) recently introduced into marginal agricultural areas in eastern Morocco. These verities are known for their rusticity and late flowering stage. The analyzed almond oils showed low acidity and peroxide values ranging, respectively, from 0.32 to 0.36% and 1.88 to 3.18 meq O₂/kg. Fatty acid (FA) profile revealed a predominance of the unsaturated FA represented essentially by the oleic (56.64-64.03%) and linoleic FA (24.57-29.80%). Triacylglycerol (TAG) analysis allowed the determination of eleven species with a remarkable dominance of trioleylglycerol (OOO: 30%) and dioleyllinoleoylglcerol (OOL: 27.25%). Regarding the minor compounds, the results showed that the total phenol content ranges between 85.33 and 141.66 mg/kg. Concerning the tocopherol content, the studied oils showed richness in these secondary metabolites (408.99-491.77 mg/kg) with a dominance of α-tocopherol. In comparison to their homologues in the Mediterranean area, the evaluated almond oils demonstrated a slight superiority in terms of quality, in particular, to those produced in Spain.

Variability of Chemical Profile in Almonds (Prunus dulcis) of Different Cultivars and Origins

Almonds show a great variability in their chemical composition. This variability is a result of the existence of a diverse range of almond cultivars, the self-incompatibility of most almond cultivars, and the heterogeneous harvesting conditions found around the different locations where almons are grown. In the last years, the discrimination among almond cultivars has been the focal point of some research studies to avoid fraud in protected geographical indications in almond products and also for selecting the best cultivars for a specific food application or the most interesting ones from a nutritional point of view. In this work, a revision of the recent research works related to the chemical characterization and classification of almond cultivars from different geographical origins has been carried out. The content of macronutrients, tocopherols, phytosterols, polyphenols, minerals, amino acids, and volatile compounds together with DNA fingerprint have been reported as possible cultivar and origin markers. The analysis of the results showed that no individual almond compound could be considered a universal biomarker to find differences among different almond cultivars. Hence, an adequate selection of variables or the employment of metabolomics and the application of multivariate statistical techniques is necessary when classification studies are carried out to obtain valuable results. Meanwhile, DNA fingerprinting is the perfect tool for compared cultivars based on their genetic origin.