Selecting the superior late-leafing genotypes of Persian walnut (Juglans regia L.) using morphological and pomological evaluations

BACKGROUND

Late-spring frost is one of the major factors limiting and reducing yield of Persian walnut (Juglans regia L.) in temperate regions, including Iran. Therefore, in the present study, seedling-originated genotypes of walnut were investigated to identify late-leafing genotypes with high-quality kernels for direct cultivation in orchards or as parents in breeding programs. In the first step, the variation of the selected trees was investigated in terms of traits related to phenology, vegetation, and fruit. In the second step, late-leafing trees were identified and their traits related to kernel quality were investigated to identify superior genotypes.

RESULTS

Strong variabilities were exhibited among the studied genotypes based on the traits recorded. The genotypes showed high variation based on dates of leafing, full male flowering date, and full female flowering date, including very early, early, moderate, and late. After recording the leafing date, 21 late-leaf genotypes were identified and evaluated to select the superiors among them in terms of kernel quantity and quality. Among them, the values of nut-related traits ranged as follows: nut length: 30.12-49.74 mm, nut width: 29.31-37.17 mm, nut weight: 8.77-16.47 g, and shell thickness: 1.15-2.25 mm. The values of kernel-related traits ranged as follows: kernel length: 22.35-35.73 mm, kernel width: 21.79-29.03 mm, kernel weight: 3.22-8.17 g, and kernel percentage: 35.08-53.95%.

CONCLUSIONS

According to the ideal values and situations of commercial characteristics of walnut, twelve promising late-leafing genotypes (No. 9, 13, 32, 33, 72, 77, 78, 82, 83, 86, 92, and 98) were identified and are recommended for cultivation in orchards.

Unravelling the genetic diversity and population structure of common walnut in the Iranian Plateau

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.

Population-genomic analyses reveal bottlenecks and asymmetric introgression from Persian into iron walnut during domestication

Background

Persian walnut, Juglans regia, occurs naturally from Greece to western China, while its closest relative, the iron walnut, Juglans sigillata, is endemic in southwest China; both species are cultivated for their nuts and wood. Here, we infer their demographic histories and the time and direction of possible hybridization and introgression between them.

Results

We use whole-genome resequencing data, different population-genetic approaches (PSMC and GONE), and isolation-with-migration models (IMa3) on individuals from Europe, Iran, Kazakhstan, Pakistan, and China. IMa3 analyses indicate that the two species diverged from each other by 0.85 million years ago, with unidirectional gene flow from eastern J. regia and its ancestor into J. sigillata, including the shell-thickness gene. Within J. regia, a western group, located from Europe to Iran, and an eastern group with individuals from northern China, experienced dramatically declining population sizes about 80 generations ago (roughly 2400 to 4000 years), followed by an expansion at about 40 generations, while J. sigillata had a constant population size from about 100 to 20 generations ago, followed by a rapid decline.

Conclusions

Both J. regia and J. sigillata appear to have suffered sudden population declines during their domestication, suggesting that the bottleneck scenario of plant domestication may well apply in at least some perennial crop species. Introgression from introduced J. regia appears to have played a role in the domestication of J. sigillata.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-022-02720-z.

Advances in Rootstock Breeding of Nut Trees: Objectives and Strategies

The production and consumption of nuts are increasing in the world due to strong economic returns and the nutritional value of their products. With the increasing role and importance given to nuts (i.e., walnuts, hazelnut, pistachio, pecan, almond) in a balanced and healthy diet and their benefits to human health, breeding of the nuts species has also been stepped up. Most recent fruit breeding programs have focused on scion genetic improvement. However, the use of locally adapted grafted rootstocks also enhanced the productivity and quality of tree fruit crops. Grafting is an ancient horticultural practice used in nut crops to manipulate scion phenotype and productivity and overcome biotic and abiotic stresses. There are complex rootstock breeding objectives and physiological and molecular aspects of rootstock-scion interactions in nut crops. In this review, we provide an overview of these, considering the mechanisms involved in nutrient and water uptake, regulation of phytohormones, and rootstock influences on the scion molecular processes, including long-distance gene silencing and trans-grafting. Understanding the mechanisms resulting from rootstock × scion × environmental interactions will contribute to developing new rootstocks with resilience in the face of climate change, but also of the multitude of diseases and pests.

Flowering in Persian walnut: patterns of gene expression during flower development

BACKGROUND

Flower development and sufficient fruit set are important parameters with respect to walnut yield. Knowledge about flowering genes of fruit trees can help to conduct better molecular breeding programs. Therefore, this study was carried out to investigate the expression pattern of some flowering genes (FT, SOC1, CAL, LFY and TFL1) in Persian walnut (cv. Chandler) during the growing season and winter dormancy.

RESULTS

The results showed that walnut flower induction and initiation in Shahmirzad, Iran occurred in early June and late September, respectively. After meeting chilling and heat requirement, flower differentiation and anthesis occurred in late-March and mid-April to early-May, respectively. Study of flowering gene expression showed that the expression of the FT gene increased in three stages including before breaking of bud dormancy, from late March to late April (coincided with flower differentiation and anthesis) and from late May to mid-June (coincided with flower induction). Like FT, the expression of SOC1 gene increased during flower induction and initiation (mid-May to early-August) as well as flower anthesis (mid-April to early-May). LFY and CAL genes as floral meristem identity genes are activated by FT and SOC1 genes. In contrast with flowering stimulus genes, TFL1 showed overexpression during winter dormancy which prevented flowering.

CONCLUSION

The expression of FT gene activated downstream floral meristem identity genes including SOC1, CAL and LFY which consequently led to release bud dormancy as well as flower anthesis and induction. Also, TFL1 as a flowering inhibitor gene in walnut showed overexpression during the bud dormancy. Chilling accumulation reduced TFL1 gene expression and increased the expression of flowering genes which ultimately led to overcome dormancy.

Wound healing effects of Persian walnut (Juglans regia L.) green husk on the incision wound model in rats

Walnut green husk (WGH) has been mentioned as a wound-healing agent in traditional Iranian medicine. Although previous studies indicated that WGH is a good source of pharmaceutical ingredients, they did not assess its wound healing activity; so the present study set out the scientific validation of the wound healing potential of the Persian walnut. Total phenolic content, reducing power, DPPH, and nitric oxide scavenging activity of aqueous ethanol extract of WGH was evaluated. Forty-eight male Wistar albino rats were divided into four groups of 12 each. An incision wound was created on the dorsal region of each rat. WGH extract (20% w/w), WGH burnt residues (20% w/w), Eucerin, and Phenytoin ointments were used in each group. Wound length, contraction percentage, and histopathological evaluations were recorded on days 3, 7, 10, and 14. Total phenolic content and EC₅₀ values of reducing power, DPPH and nitric oxide scavenging activity of the WGH extract were 61.34 ± 0.64 mg/g dry extract, 0.95 ± 0.02 mg/mL, 0.35 ± 0.01 mg/mL, and 0.28 ± 0.01 mg/mL, respectively. Treated animals with WGH extract showed significantly (p ≤ 0.05) better results for physical and pathological parameters compared to the control group; overall, WGH extract showed better results than WGH burnt residues. The present study indicated that the WGH aqueous ethanol extract has a promising potential for wound healing in the animal model and could be a valuable resource for developing new wound-healing medicines for humans.

The walnut genetic resources of INRA: chronological phenotypic data and ontology

OBJECTIVES

Persian walnut (Juglans regia L.), the walnut species cultivated for nut production, is grown worldwide in temperate areas. In this work, chronological phenotypic data have been collected regarding a part of the walnut genetic resources of the French National Institute for Agricultural Research (INRA) of Bordeaux. Using a well described ontology, these data have been collected in order to assess the phenotypic variations among the accessions, and to better manage the germplasm collection. These data can also be helpful for any breeding program as they provide a clear phenotypic characterization of the main cultivars.

DATA DESCRIPTION

This paper introduces a dataset collected for 150 J. regia accessions for a period from 1965 to 2016, and for 3 observation sites, released as comma separated value spreadsheet. It includes observations about phenological traits (e.g. flowering dates), traits related to in-shell walnut (e.g. weight and size), and traits related to kernel (e.g. color). It can be used by other researchers particularly for multi-site phenological studies in the context of climate change since climate data files are also available. In addition, a complete walnut ontology was deposited in this repository and can assist to standardize the management of any walnut germplasm collection.

A new genomic tool for walnut (Juglans regia L.): development and validation of the high-density Axiom™ J. regia 700K SNP genotyping array

Over the last 20 years, global production of Persian walnut (Juglans regia L.) has grown enormously, likely reflecting increased consumption due to its numerous benefits to human health. However, advances in genome-wide association (GWA) studies and genomic selection (GS) for agronomically important traits in walnut remain limited due to the lack of powerful genomic tools. Here, we present the development and validation of a high-density 700K single nucleotide polymorphism (SNP) array in Persian walnut. Over 609K high-quality SNPs have been thoroughly selected from a set of 9.6 m genome-wide variants, previously identified from the high-depth re-sequencing of 27 founders of the Walnut Improvement Program (WIP) of University of California, Davis. To validate the effectiveness of the array, we genotyped a collection of 1284 walnut trees, including 1167 progeny of 48 WIP families and 26 walnut cultivars. More than half of the SNPs (55.7%) fell in the highest quality class of 'Poly High Resolution' (PHR) polymorphisms, which were used to assess the WIP pedigree integrity. We identified 151 new parent-offspring relationships, all confirmed with the Mendelian inheritance test. In addition, we explored the genetic variability among cultivars of different origin, revealing how the varieties from Europe and California were differentiated from Asian accessions. Both the reconstruction of the WIP pedigree and population structure analysis confirmed the effectiveness of the Applied Biosystems™ Axiom™ J. regia 700K SNP array, which initiates a novel genomic and advanced phase in walnut genetics and breeding.

The Phytogeographic History of Common Walnut in China

Common walnut (Juglans regia L.) is an economically important hardwood tree species cultivated worldwide for its high quality wood and edible nuts. It is generally accepted that after the last glaciation J. regia survived and grew in almost completely isolated stands in Asia, and that ancient humans dispersed walnuts across Asia and into new habitats via trade and cultural expansion. The history of common walnut in China is a matter of debate, however. We estimated the genetic diversity and spatial genetic structure of 31 walnut populations sampled across its Chinese range using 22 microsatellite markers (13 neutral and 9 non-neutral). Using historical data and population genetic analysis, including approximate Bayesian analysis (ABC), we reconstructed the demographic history of J. regia in China. The genetic data indicated the likely presence of J. regia in glacial refugia in the Xinjiang province (Northwest China), Northeastern China (Beijing, Shandong, and Changbai Mountains), Central China (Qinling and Baishan Mountains and Xi'an), and Southwestern China (Tibet, Yunnan, Guizhou, and Sichuan provinces). Based on DIY-ABC analysis, we identified three ancient lineages of J. regia in China. Two lineages (subpopulation A and subpopulation B+C) diverged about 2.79 Mya, while Southwestern China, and Qinling and Baishan Mountains lineages diverged during the Quaternary glaciations (about 1.13 Mya). Remnants of these once-distinct genetic clusters of J. regia may warrant ecological management if they are to be retained as in situ resources. A population size expansion in Northeastern China was detected in the last five centuries. The present distribution of walnut in China resulted from the combined effects of expansion/contraction from multiple refugia after the Last Glacial Maximum and later human exploitation.

Evaluation of genetic variability among "Early Mature" Juglans regia using microsatellite markers and morphological traits

Limiting the juvenile phase and reducing tree size are the two main challenges for breeders to improve most fruit crops. Early maturation and dwarf cultivars have been reported for many fruit species. “Early mature” and low vigor walnut genotypes were found among seedlings of Persian walnut. Nine microsatellite markers were used to evaluate genetic diversity among “Early Mature” Persian walnut accessions and provide a comparison with “normal growth” accessions. Six maturation related characteristics were also measured in “Early Mature” samples. Phenotypic traits and diversity indices showed relatively high levels of genetic diversity in “Early Mature” seedlings and indicated high differentiation between individuals. Seedling height, the most diverse phenotypic trait, has an important role in the clustering of “Early Mature” accessions. The “Early Mature” type had higher number of alleles, number of effective allele, and Shannon index compared to the “Normal Growth” group. The two types of studied walnuts had different alleles, with more than half of produced alleles specific to a specific group. “Early Mature” and “Normal Growth” walnuts had 27 and 17 private alleles, respectively. Grouping with different methods separated “Early Mature” and “Normal Growth” samples entirely. The presence of moderate to high genetic diversity in “Early Mature” walnuts and high genetic differentiation with “Normal Growth” walnuts, indicated that “Early Mature” walnuts were more diverse and distinct from “Normal Growth” samples. Moreover, our results showed SSR markers were useful for differentiating between “Early Mature” and “Normal Growth” walnuts. A number of identified loci have potential in breeding programs for identification of “Early Mature” walnuts at the germination phase.