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Persian or English walnut (Juglans regia L.), the walnut species cultivated for nut production, is one of the oldest food sources known and is grown worldwide in temperate areas. France is the 7th leading producer as of 2016 with 39 kt. Deciphering walnut genetic diversity and structure is important for efficient management and use of genetic resources. In this work, 253 worldwide accessions from the INRA walnut germplasm collection, containing English walnut and several related species, were genotyped using 13 SSR (Single Sequence Repeat) markers selected from the literature to assess diversity and structure. Genetic diversity parameters showed a deficiency of heterozygotes and, for several SSRs, allele-specificities among the accessions tested. Principal Coordinate Analysis (PCoA) showed the 253 accessions clustered in largely in agreement with the existing botanical classification of the genus. Among the 217 J. regia accessions, two main clusters, accessions from Eastern Europe and Asia, and accessions from Western Europe and America, were identified using STRUCTURE software. This was confirmed by Principal Coordinate Analysis and supported by Neighbor-Joining tree construction using DARwin software. Moreover, a substructure was found within the two clusters, mainly according to geographical origin. A core collection containing 50 accessions was selected using the maximum length sub-tree method and prior knowledge about their phenotype. The present study constitutes a preliminary population genetics overview of INRA walnut genetic resources collection using SSR markers. The resulting estimations of genetic diversity and structure are useful for germplasm management and for future walnut breeding programs.

Background Walnut kernels contain a large amount of unsaturated fatty acids, such as linoleic acid and linolenic acid, which are essential fatty acids for humans and have important effects on growth and health. The main function of fatty acid desaturase (FAD), which is widely distributed in organisms, is to remove hydrogen from carbon chains in the biosynthesis of unsaturated fatty acids to generate C=C bonds. Results By performing a series of bioinformatics analysis, 24 members of the JrFAD gene family were identified from the genome database of walnut, and then compared with the homologous genes from Arabidopsis . Phylogenetic analysis showed that JrFADs were classified into four subfamilies: the SAD desaturase subfamily, Δ7/Δ9 desaturase subfamily, Δ12/ω-3 desaturase subfamily and “front-end” desaturase subfamily. Meanwhile, the expression of fatty acid synthesis genes in walnut kernels at different developmental stages was analysed by transcriptome sequencing, with expression of JrFAD3-1 , which encodes an enzyme involved in linolenic acid synthesis, being particularly prominent. The relative expression level of JrFAD3-1 changed dramatically with the kernel development stages and exhibited a Bell-Shaped Curve. A significant positive correlation was observed between the expression of JrFAD3-1 during 70–100 DAF (Days after flowering) and the content of alpha-linolenic acid during 100–130 DAF, with a correlation coefficient of 0.991. Additionally, JrFAD3-1 was proved closely related to homologous genes in Betula pendula and Corylus heterophylla , indicating that the conserved structure of FADs is consistent with classical plant taxonomy. Conclusion Twenty-four members JrFADs in walnut were identified and classified into four subfamilies. JrFAD3-1 may play significant roles in the biosynthesis of polyunsaturated fatty acids in walnut.

Background Almond ( Prunus dulcis ) is one of the most important nut crops cultivated worldwide, valued for its nutritional content and economic significance. Local landraces, particularly those from ecologically diverse regions, harbor valuable genetic variation that can be exploited in breeding programs. This study aimed to assess the morphological, biochemical, and molecular diversity of local almond genotypes collected from a natural population located along the Türkiye–Syria border. Results Eighteen promising genotypes were evaluated using morphometric traits, biochemical composition, and SSR markers. Nut weight ranged from 1.50 g to 2.18 g, kernel weight from 0.59 g to 1.50 g, and kernel ratio from 16.43 to 54.99%, indicating considerable phenotypic variation. Genotype G11 stood out with a high kernel weight (> 1.2 g), soft shell, and the highest kernel ratio (54.99%). Oil content varied across genotypes, with G2 having the highest (56.25%) and G15 the lowest (45.85%), and an overall average of 51.50%. Molecular analysis using 16 SSR markers revealed a high polymorphism rate (99.4%), reflecting substantial genetic variability. Principal coordinate analysis (PCoA) and UPGMA clustering distinguished genetically diverse individuals, while STRUCTURE analysis grouped the genotypes into two main genetic clusters. Conclusions The high morphological, biochemical, and molecular diversity observed in this almond population highlights the importance of the conservation of local genetic resources. Genotypes such as G11 and G2 show strong potential for use in breeding programs due to their favorable nut quality and oil content. Future work will focus on field evaluations of these genotypes under standard cultivation to assess their agronomic performance.

Pecan is a tree nut crop native to the United States and Mexico, with a global market of over 2 billion USD. Nut size has been the most important target trait for crop improvement during the very limited breeding cycles. However, relatively little is known about the molecular basis of pecan nut ontogeny and the mechanisms underlying pecan nut sizing. Besides nut size, pecan fruit faces myriad physiological disorders throughout the growing season, making knowledge of essential genes at each growth stage a necessary first step in developing new cultivars and management practices to overcome these issues. To develop a deeper understanding of pecan fruit development and identify candidate genes underlying the large fruit phenotype, a time-course transcriptomic study of pecan fruit in two genotypes, ‘Mahan’ and ‘Tiny Tim’, was conducted. Weighted Gene-Coexpression Network Analysis (WGCNA) was employed to group transcripts into functional clusters, and hub transcripts were identified through module correlation analysis to select those that are potential drivers of these functional clusters. Modules related to cell wall biosynthesis, cell wall organization, and inositol metabolism in ‘Mahan’, and proteolysis and abscisic acid response in ‘Tiny Tim’ were found to be potentially associated with nut size.

Background European Hazelnut ( Corylus avellana L.) is a high-value, understudied crop that exhibits a large diversity of traits. Commercial production relies on a small number of globally grown varieties. Advancing hazelnut breeding requires a comprehensive understanding of its genetic diversity and its association with valuable traits. Here, we used genotyping-by-sequencing to sequence 316 hazelnut varieties, retaining 282 samples and 44,757 single nucleotide polymorphisms (SNPs) after quality control. This collection was used to study genetic diversity, identify genomic loci under selection, and describe genome-wide association with nut traits, i.e. nut size, perimeter and caliber. Results We uncovered three genetic clusters and five ancestral populations, with Eurasian varieties (Türkiye, Azerbaijan, and Georgia) being the most distinct and European and U.S. populations showing higher admixture. We identified four loci under positive selection in Eurasian varieties, including one within Cav06g02620 (probable calcium uniporter) on chromosome 6. We also characterized the nut morphology of 151 genotyped varieties, leading to the identification of ten SNPs associated with nut traits. Conclusions While functional validation of candidate genes and the use of a larger population are important for future analysis, our findings provide a basis for exploring the genetics of quantitative traits in hazelnut, supporting breeding and conservation efforts.

Background Walnut is an oilseed tree species and an ecologically important woody tree species that is rich in oil and nutrients. In light of differences in the lipid content, fatty acid composition and key genes expression patterns in different walnut varieties, the key gene regulatory networks for lipid biosynthesis in different varieties of walnuts were intensively investigated. Results The kernels of two walnut varieties, ‘Xilin 3’ (X3) and ‘Xiangling’ (XL) were sampled at 60, 90, and 120 days post-anthesis (DPA) to construct 18 cDNA libraries, and the candidate genes related to oil synthesis were identified via sequencing and expression analysis. A total of 106 differentially expressed genes associated with fatty acid biosynthesis, fatty acid elongation, unsaturated fatty acid biosynthesis, triglyceride assembly, and oil body storage were selected from the transcriptomes. Weighted gene co-expression network analysis (WGCNA), correlation analysis and quantitative validation confirmed the key role of the FAD3 (109002248) gene in lipid synthesis in different varieties. Conclusions These results provide valuable resources for future investigations and new insights into genes related to oil accumulation and lipid metabolism in walnut seed kernels. The findings will also aid future molecular studies and ongoing efforts to genetically improve walnut.

Background Walnut ( Juglans regia L.) breeding programs aim to develop new genotypes that exhibit superior agronomic traits, including high yield, improved nut quality, and favorable phenological traits. One of the primary methods used in these programs is hybridization, which involves controlled crosses between selected parent varieties. In reciprocal cross, understanding the genetic contributions of both maternal and paternal parents is crucial, as these contributions significantly influence the phenotypic traits of the resulting progeny. This knowledge allows breeders to predict and select genotypes that best meet the desired breeding objectives, ultimately enhancing agricultural productivity and sustainability. Results This study analyzed the pomological traits of F1 plants derived from four different hybrid combinations: Pedro × Maraş 18, Pedro × Sütyemez 1, Maraş 18 × Pedro, and Sütyemez 1 × Pedro. The assessment focused on key nut traits, including nut length, nut diameter, nut weight, kernel weight, and kernel percentage. Statistical analyses revealed significant variations in these traits among the hybrid combinations, with these differences determined at the p  < 0.05 significance level. Kernel weight exhibited the highest coefficient of variation (CV = 33.63%), indicating substantial variability in this trait among the hybrids. Nut diameter had the lowest variability (CV = 12.82%), suggesting greater consistency across the hybrid combinations. Other traits, such as nut weight, nut length, and kernel percentage, showed intermediate levels of variability, with CVs of 27.33%, 13.45%, and 18.59%, respectively. The study found that maternal parents played a more partially dominant role in determining nut traits in most hybrid combinations. However, when Sütyemez 1 and Maraş 18 were used as maternal parents, their influence on the inheritance of some nut traits was relatively greater than the other parent variety (Pedro). Conclusion The findings emphasize the crucial role of parent selection in walnut hybridization breeding programs, with parental effects being relatively prominent in influencing pomological traits, underscoring the need for careful selection of maternal parents to achieve the desired outcomes. Among the varieties studied, Pedro, Maraş 18, and Sütyemez 1 were identified as promising parent genotypes for improving key nut traits. The variability observed in traits such as kernel and nut weights suggests potential for further selection and genetic improvement. This variation highlights the genetic diversity present in the studied hybrids, which can be effectively utilized in breeding efforts. These results not only contribute to the improvement of walnut varieties but also have broader implications for global walnut production, providing valuable guidance for breeding programs aiming to improve nut quality in walnut hybridization programs.

Background In many parts of the world, including Iran, walnut ( Juglans regia L.) production is limited by late-spring frosts. Therefore, the use of late-leafing walnuts in areas with late-spring frost is the most important method to improve yield. In the present study, the phenotypic diversity of 141 seedling genotypes of walnut available in the Senejan area, Arak region, Markazi province, Iran was studied based on morphological traits to obtain superior late-leafing genotypes in the cropping seasons of 2022 and 2023. Results Based on the results of the analysis of variance, the studied genotypes showed a significant variation in terms of most of the studied morphological and pomological traits. Therefore, it is possible to choose genotypes for different values ​​of a trait. Kernel weight showed positive and significant correlations with leaf length ( r  = 0.32), leaf width ( r  = 0.33), petiole length ( r  = 0.26), terminal leaflet length ( r  = 0.34), terminal leaflet width ( r  = 0.21), nut length ( r  = 0.48), nut width ( r  = 0.73), nut weight ( r  = 0.83), kernel length ( r  = 0.64), and kernel width ( r  = 0.89). The 46 out of 141 studied genotypes were late-leafing and were analyzed separately. Among late-leafing genotypes, the length of the nut was in the range of 29.33–48.50 mm, the width of the nut was in the range of 27.51–39.89 mm, and nut weight was in the range of 8.18–16.06 g. The thickness of shell was in the range of 1.11–2.60 mm. Also, kernel length ranged from 21.97–34.84 mm, kernel width ranged from 21.10–31.09 mm, and kernel weight ranged from 3.10–7.97 g. Conclusions Based on important and commercial traits in walnut breeding programs, such as nut weight, kernel weight, kernel percentage, kernel color, and ease of kernel removal from nuts, 15 genotypes, including no. 92, 91, 31, 38, 33, 18, 93, 3, 58, 108, 16, 70, 15, 82, and 32 were superior and could be used in walnut breeding programs in line with the introduction of new cultivars and the revival of traditional walnut orchards to commercialize them.

Macadamia nuts are one of the most important economic food items in the world. Pericarp thickness and flavonoid composition are the key quality traits of Macadamia nuts, but the underlying mechanism of pericarp formation is still unknown. In this study, three varieties with significantly different pericarp thicknesses, namely, A38, Guire No.1, and HAES 900, at the same stage of maturity, were used for transcriptome analysis, and the results showed that there were significant differences in their gene expression profile. A total of 3837 new genes were discovered, of which 1532 were functionally annotated. The GO, COG, and KEGG analysis showed that the main categories in which there were significant differences were flavonoid biosynthesis, phenylpropanoid biosynthesis, and the cutin, suberine, and wax biosynthesis pathways. Furthermore, 63 MiMYB transcription factors were identified, and 56 R2R3-MYB transcription factors were clustered into different subgroups compared with those in Arabidopsis R2R3-MYB. Among them, the S4, S6, and S7 subgroups were involved in flavonoid biosynthesis and pericarp formation. A total of 14 MiMYBs’ gene expression were verified by RT-qPCR analysis. These results provide fundamental knowledge of the pericarp formation regulatory mechanism in macadamia nuts.

Background Common walnut ( Juglans regia L.) has a long cultivation history, given its highly valuable wood and rich nutritious nuts. The Iranian Plateau has been considered as one of the last glaciation refugia and a centre of origin and domestication for the common walnut. However, a prerequisite to conserve or utilize the genetic resources of J. regia in the plateau is a comprehensive evaluation of the genetic diversity that is conspicuously lacking. In this regard, we used 31 polymorphic simple sequence repeat (SSR) markers to delineate the genetic variation and population structure of 508  J. regia individuals among 27 populations from the Iranian Plateau. Results The SSR markers expressed a high level of genetic diversity ( H O = 0.438, and H E = 0.437). Genetic differentiation among the populations was moderate ( F ST = 0.124), and genetic variation within the populations (79%) significantly surpassed among populations (21%). The gene flow ( N m = 1.840) may have remarkably influenced the population genetic structure of J. regia , which can be attributed to anthropological activities and wind dispersal of pollen. The STRUCTURE analysis divided the 27 populations into two main clusters. Comparing the neighbor-joining and principal coordinate analysis dendrograms and the Bayesian STRUCTURE analysis revealed the general agreement between the population subdivisions and the genetic relationships among the populations. However, a few geographically close populations dispersed into different clusters. Further, the low genetic diversity of the Sulaymaniyah (SMR) population of Iraq necessitates urgent conservation by propagation and seedling management or tissue culture methods; additionally, we recommend the indispensable preservation of the Gonabad (RGR) and Arak (AKR) populations in Iran. Conclusions These results reflected consistent high geographical affinity of the accession across the plateau. Our findings suggest that gene flow is a driving factor influencing the genetic structure of J. regia populations, whereas ecological and geological variables did not act as strong barriers. Moreover, the data reported herein provide new insights into the population structure of J. regia germplasm, which will help conserve genetic resources for the future, hence improving walnut breeding programs’ efficiency.