A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits

Unveiling the heterosis pattern of modern maize breeding in Southwest China through population structure and genetic diversity analysis

Maize (Zea mays L.) is an important food crop throughout the world and is also one of the earliest crops to use heterosis. In this study, we evaluated the genetic diversity, population structure, and selective sweep of 100 elite inbred maize lines collected from the current breeding program in Sichuan province, Southwest China, using 5,261,175 high-quality single nucleotide polymorphisms (SNPs). We discovered an abundance of genetic diversities and classified them into four groups. By combining kinship relationships, these groups were further divided into Tropic-local A, Improved-tropic, Tropic-local B, and Improved-local. Genomic differentiation was assessed using Fst values (0.21-0.44) as well as genetic diversity (π = 6.07 × 10-4 - 6.61 × 10-4). We generated 900 (90 × 10) hybrids using 90 and 10 inbred maize lines from 100 diverse maize germplasms. All hybrids were evaluated for 10 traits in three replicate tests across two locations. We found that the patterns of G1 × G3, G1 × G4, G2 × G3, and G3 × G4 exhibited significant heterosis in yield-related traits and have been used in commercial breeding. In addition, we also explored the relationship between 10 traits of hybrid offspring and the number of heterozygous SNP. Under most heterosis modes, the best linear unbiased estimation (BLUE) value of the trait was highly consistent with the trend of deleterious SNPs, but there was a deviation in the G1 × G3 mode. Taken together, the results provide insight into the utilization of the current maize germplasm in Sichuan province to improve hybrid breeding.

Integrated multi-omics analyses provide new insights into genomic variation landscape and regulatory network candidate genes associated with walnut endocarp

Persian walnut (Juglans regia) is an economically important nut oil tree; the fruit has a hard endocarp/shell to protect seeds, thus playing a key role in its evolution, and the shell thickness is an important trait for walnut breeding. However, the genomic landscape and the gene regulatory networks associated with walnut shell development remain to be systematically elucidated. Here, we report a high-quality genome assembly of the walnut cultivar 'Xiangling' and construct a graphic structure pan-genome of eight Juglans species to reveal the genetic variations at the genome level. We re-sequence 285 accessions to characterize the genomic variation landscape. Through genome-wide association studies (GWAS), we identified 19 loci associated with more than 268 loci that underwent selection during walnut domestication and improvement. Multi-omics analyses, including transcriptomics, metabolomics, DNA methylation, and spatial transcriptomics across eleven developmental stages, revealed several candidate genes related to secondary cell biosynthesis and lignin accumulation. This integrated multi-omics approach revealed several candidate genes associated with secondary cell biosynthesis and lignin accumulation, such as UGP, MYB308, MYB83, NAC043, NAC073, CCoAOMT1, CCoAOMT7, CHS2, CESA7, LAC7, COBL4, and IRX12. Overexpression of JrUGP and JrMYB308 in Arabidopsis thaliana confirmed their roles in lignin biosynthesis and cell wall thickening. Consequently, our comprehensive multi-omics findings offer novel insights into walnut genetic variation and network regulation of endocarp development and shell thickness, which enable further genome-informed breeding strategies for walnut cultivar improvement.

Characterizing the Phenolic Compounds in Iron Walnut Oil (Juglans sigillata Dode) Across Chinese Regions

This study examines the chemical composition and antioxidant properties of iron walnut oil (IWO) from different Chinese regions, using ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry for the analysis of phenolic compounds. Regional variations were identified in fatty acid profiles, with elevated α-linolenic acid levels observed in samples from cooler climates (e.g., Liaoning, sample 1) that were 60% higher than in samples from warmer regions (e.g., Sichuan, sample 2). Antioxidant properties, quantified using 1,1-diphenylpicryl phenyl hydrazine (DPPH), 2,2-azinobis-3-ethylbenzothiazoline-6-sulfonate (ABTS), and Ferric ion reducing antioxidant power (FRAP) assays, corresponded to both oil polyphenol content (up to 62.91 mg/kg) and γ-tocopherol concentrations (268.68-525.05 mg/kg). Nineteen phenolic acids and flavonoids were identified, including ellagic acid, gallic acid, p-hydroxybenzoic acid, syringic acid, vanillic acid, quercetin, caffeic acid, ferulic acid, p-coumaric acid, coniferol, and pinoresinol. This comprehensive analysis underscores the nutritional and therapeutic potential of IWO, and delineates the impact of geographic and environmental factors on its quality, providing a scientific foundation for further research and development aimed at enhancing food industry standards and exploring natural product chemistry.

Whole-genome sequencing revealed genetic basis of diterpenoid alkaloid difference in Aconitum vilmorinianum

BACKGROUND

Aconitum is an important medicinal genus widely used in traditional Chinese medicine, which produces types of diterpenoid alkaloids (DA) among different species. We performed whole genome resequencing (WGS) research in Aconitum spp., and wish to find diterpenoid alkaloids related genetic variations.

RESULTS

In this study, we re-sequenced 150 Aconitum vilmorinianum (A. vilmorinianum) including 102 from the cultivation garden and 48 from the wild, as well as nine wild samples of Aconitum weixiense. The intra-population differentiation of A. vilmorinianum was detected by evolutionary tree and population structure inference. We identify 47 DA biosynthesis genes that might be highly associated with the specialization of DA based on whole-genome resequencing. Of 616 significant SNPs and 105 significant InDels among these genes could be developed as polymorphic molecular markers capable of effectively recognizing A. vilmorinianum from A. weixiense. Furthermore, the significant SNPs and InDels were almost homozygous alternates in A. weixiense, whereas they tended to be homozygous references in the A. vilmorinianum.

CONCLUSIONS

Our results discussed the difference in genetic background in A. vilmorinianum compared to A. weixiense and these high-quality DA biosynthesis-associated polymorphic locus provided useful genetic information for discrimination of A. vilmorinianum and could serve as a vehicle to study the mechanism of DA differentiation in Aconitum.

Multi-omics analysis reveals the allelic variation in JrWDRC2A9 and JrGPIAP conferring resistance against anthracnose (Colletotrichum gloeosporioides) in walnut (Juglans regia)

Walnut anthracnose induced by Colletotrichum gloeosporioides is a devastating disease that seriously threatens walnut cultivation. Screening novel resistance genes and exploring the molecular mechanisms are essential for disease-resistant genetic improvement of walnut. We conducted a genome-wide association studies of disease resistance traits based on the relative resistance index and single nucleotide polymorphisms (SNPs) obtained from 182 resequenced walnut accessions and 10 loci and corresponding candidate genes associated with resistance against C. gloeosporioides were identified. Then, through combined transcriptome analysis during C. gloeosporioides infection and qRT-PCR, we identified JrWDRC2A9 in SNP Chr13_36265784 loci and JrGPIAP in SNP Chr07_10106470 loci as two walnut anthracnose resistance genes. The validation of the disease resistance function of transgenic strains indicated that both JrWDRC2A9 and JrGPIAP promote walnut resistance to anthracnose. SNP Chr13_36265784 (A>G) is located in the coding region of JrWDRC2A9 causing a glutamine (JrWDRC2A9HapI) to arginine (JrWDRC2A9HapII). Allelic variation in the WD domain attenuates JrWDRC2A9-mediated resistance against C. gloeosporioides and the binding affinity of JrWDRC2A9 for JrTLP1. On the contrary, the allelic variation caused by SNP Chr07_10106470 (T>G) increased the walnut accessions resistance to C. gloeosporioides by promoting the expression level of JrGPIAP. Functional genomics revealed that JrGPIAP binds to the promoter of JrPR1L and activates its transcription, which is strengthened by the interaction between JrGPIAP and JrEMP24. These findings reveal the allelic variation in JrWDRC2A9 and JrGPIAP conferring resistance against C. gloeosporioides, providing a genetic basis for walnut disease resistance breeding in the future.

Ancient structural variants control sex-specific flowering time morphs in walnuts and hickories

Balanced mating type polymorphisms offer a distinct window into the forces shaping sexual reproduction strategies. Multiple hermaphroditic genera in Juglandaceae, including walnuts (Juglans) and hickories (Carya), show a 1:1 genetic dimorphism for male versus female flowering order (heterodichogamy). We map two distinct Mendelian inheritance mechanisms to ancient (>37 million years old) genus-wide structural DNA polymorphisms. The dominant haplotype for female-first flowering in Juglans contains tandem repeats of the 3' untranslated region of a gene putatively involved in trehalose-6-phosphate metabolism and is associated with increased cis gene expression in developing male flowers, possibly mediated by small RNAs. The Carya locus contains ~20 syntenic genes and shows molecular signatures of sex chromosome-like evolution. Inheritance mechanisms for heterodichogamy are deeply conserved, yet may occasionally turn over, as in sex determination.

Comprehensive Evaluation of Cryptic Juglans Genotypes: Insight from Molecular Markers and Phylogenetic Analysis

Background/Objectives: The current research work aimed to evaluate the cryptic walnut genotypes of the Hazara region in Pakistan by using DNA barcoding and phylogenetic analysis. Methods: Based on morphological traits such as nut size, nut shape, and the number of leaflets, five genotypes were chosen and samples were collected for the current study. For molecular analysis, gDNA was isolated from the fresh leaves, and the five most effective angiosperm-specific markers, ITS2, rbcLa, rbcLc, rpoC1, and UBE3, were utilized. Based on amplification, sequencing, and identification success rates, ITS2 and UBE3 were recorded as the most efficient markers followed by rbcLa, rbcLc, and rpoC1. Results: During phylogenetic analysis, the query genotype-1 based on ITS2 and genotype-2 based on UBE3 clustered with (KF454101.1-Juglans regia) and (KC870919.1-J. regia) with bootstraps of 56 and 100, respectively. Genotype-3 based on rbcla clustered in a major clade with J. regia L., cultivars (MN397935.1 J. regia 'Vina') and (MN397934.1-J. regia 'Serr'), (MN397933.1 J. regia 'Pedro'), (MN397932.1 J. regia 'Lara'), (MN397931.1 J. regia 'Howard'), and (MN397930.1 J. regia 'Hartley') with bootstrap of 100. Meanwhile, genotype-4 and genotype-5 based on rbclc and rpoC1 clustered with (MN397935.1 J. regia 'Vina') and (MN397934.1 J. regia 'Serr'), across the database sequences. To clarify the taxonomic status of cryptic walnut genotypes, it is necessary to combine diverse DNA barcodes. The results of ITS2 and UBE3, followed by rbcL barcoding markers, are promising taxonomic tools for cryptic walnut genotypes in Pakistan. Conclusions: It has been determined that the genotypes of walnuts in the study area are both J. regia L. and its cultivars and that the accuracy of discrimination regarding the genus Juglans L. is greater than 90%. The reported DNA barcodes are recommended for the correct identification and genetic evaluation of Juglans taxa and its population.

Complete mitochondrial genome assembly of Juglans regia unveiled its molecular characteristics, genome evolution, and phylogenetic implications

BACKGROUND

The Persian walnut (Juglans regia), an economically vital species within the Juglandaceae family, has seen its mitochondrial genome sequenced and assembled in the current study using advanced Illumina and Nanopore sequencing technology.

RESULTS

The 1,007,576 bp mitogenome of J. regia consisted of three circular chromosomes with a 44.52% GC content encoding 39 PCGs, 47 tRNA, and five rRNA genes. Extensive repetitive sequences, including 320 SSRs, 512 interspersed, and 83 tandem repeats, were identified, contributing to genomic complexity. The protein-coding sequences (PCGs) favored A/T-ending codons, and the codon usage bias was primarily shaped by selective pressure. Intracellular gene transfer occurred among the mitogenome, chloroplast, and nuclear genomes. Comparative genomic analysis unveiled abundant structure and sequence variation among J. regia and related species. The results of selective pressure analysis indicated that most PCGs underwent purifying selection, whereas the atp4 and ccmB genes had experienced positive selection between many species pairs. In addition, the phylogenetic examination, grounded in mitochondrial genome data, precisely delineated the evolutionary and taxonomic relationships of J. regia and its relatives. We identified a total of 539 RNA editing sites, among which 288 were corroborated by transcriptome sequencing data. Furthermore, expression profiling under temperature stress highlighted the complex regulation pattern of 28 differently expressed PCGs, wherein NADH dehydrogenase and ATP synthase genes might be critical in the mitochondria response to cold stress.

CONCLUSIONS

Our results provided valuable molecular resources for understanding the genetic characteristics of J. regia and offered novel perspectives for population genetics and evolutionary studies in Juglans and related woody species.

Resistant risk and resistance mechanism of florylpicoxamid in Colletotrichum gloeosporioides isolated from Chinese walnut

Colletotrichum gloeosporioides is the causal pathogen for the devastating walnuts anthracnose. A novel quinone inside inhibitor (QiI) fungicide florylpicoxamid has strong inhibitory efficacy against C. gloeosporioides. This study looked into the resistance risk and mechanism of C. gloeosporioides to florylpicoxamid. The basal level sensitivity of C. gloeosporioides isolates (n = 102) to florylpicoxamid was established with an average 50% mycelial growth inhibition concentration (EC50) value of 0.069 ± 0.035 μg/mL. Six stable florylpicoxamid-resistant mutants with resistance factors of >1000 were produced. The fitness of every mutant was much lower than that of their parental isolates. In general, the resistance risk of C. gloeosporioides to florylpicoxamid would be moderate. Molecular docking results revealed that the amino acid substitutions A37V, and S207L in CgCytb lead to a reduction in the binding affinity between florylpicoxamid and CgCytb, indicating that these two mutations (S207L and A37V in CgCytb) indeed confer florylpicoxamid resistance in C. gloeosporioides. These findings offer a fresh viewpoint on the mechanism underlying QiI fungicide resistance and could support the prudent application of florylpicoxamid in the future to combat walnut anthracnose.

Species divergence and environmental adaptation of Picea asperata complex at the whole genome level

To study the interspecific differentiation characteristics of species originating from recent radiation, the genotyping-by-sequencing (GBS) technique was used to explore the kinship, population structure, gene flow, genetic variability, genotype-environment association and selective sweeps of Picea asperata complex with similar phenotypes from a genome-wide perspective. The following results were obtained: 14 populations of P. asperata complex could be divided into 5 clades; P. wilsonii and P. neoveitchii diverged earlier and were more distantly related to the remaining 6 spruce species. Various geological events have promoted the species differentiation of P. asperata complex. There were four instances of gene flow among P. koraiensis, P. meyeri, P. asperata, P. crassifolia and P. mongolica. The population of P. mongolica had the highest level of nucleotide diversity, and P. neoveitchii may have experienced a bottleneck recently. Genotype-environment association found that a total of 20,808 genes were related to the environmental variables, which enhanced the adaptability of spruce in different environments. Genes that were selectively swept in the P. asperata complex were primarily associated with plant stress resistance. Among them were some genes involved in plant growth and development, heat stress, circadian rhythms and flowering. In addition to the commonly selected genes, different spruce species also displayed unique genes subjected to selective sweeps that improved their adaptability to different habitats. Understanding the interspecific gene flow and adaptive evolution of Picea species is beneficial to further understanding the species relationships of spruce and can provide a basis for studying spruce introgression and functional genomics.

New insights into the evolution and local adaptation of the genus Castanea in east Asia

Chestnut plants (Castanea) are important nut fruit trees worldwide. However, little is known regarding the genetic relationship and evolutionary history of different species within the genus. How modern chestnut plants have developed local adaptation to various climates remains a mystery. The genomic data showed that Castanea henryi first diverged in the Oligocene ~31.56 million years ago, followed by Castanea mollissima, and the divergence between Castanea seguinii and Castanea crenata occurred in the mid-Miocene. Over the last 5 million years, the population of chestnut plants has continued to decline. A combination of selective sweep and environmental association studies was applied to investigate the genomic basis of chestnut adaptation to different climates. Twenty-two candidate genes were associated with temperature and precipitation. We also revealed the molecular mechanism by which CmTOE1 interacts with CmZFP8 and CmGIS3 to promote the formation of non-glandular trichomes for adaptation to low temperature and high altitudes. We found a significant expansion of CER1 genes in Chinese chestnut (C. mollissima) and verified the CmERF48 regulation of CmCER1.6 adaptation to drought environments. These results shed light on the East Asian chestnut plants as a monophyletic group that had completed interspecific differentiation in the Miocene, and provided candidate genes for future studies on adaptation to climate change in nut trees.

Genomic evidence for evolutionary history and local adaptation of two endemic apricots: Prunus hongpingensis and P. zhengheensis

Apricot, belonging to the Armeniaca section of Rosaceae, is one of the economically important crop fruits that has been extensively cultivated. The natural wild apricots offer valuable genetic resources for crop improvement. However, some of them are endemic, with small populations, and are even at risk of extinction. In this study we unveil chromosome-level genome assemblies for two southern China endemic apricots, Prunus hongpingensis (PHP) and P. zhengheensis (PZH). We also characterize their evolutionary history and the genomic basis of their local adaptation using whole-genome resequencing data. Our findings reveal that PHP and PZH are closely related to Prunus armeniaca and form a distinct lineage. Both species experienced a decline in effective population size following the Last Glacial Maximum (LGM), which likely contributed to their current small population sizes. Despite the observed decrease in genetic diversity and heterozygosity, we do not observe an increased accumulation of deleterious mutations in these two endemic apricots. This is likely due to the combined effects of a low inbreeding coefficient and strong purifying selection. Furthermore, we identify a set of genes that have undergone positive selection and are associated with local environmental adaptation in PHP and PZH, respectively. These candidate genes can serve as valuable genetic resources for targeted breeding and improvement of cultivated apricots. Overall, our study not only enriches our comprehension of the evolutionary history of apricot species but also offers crucial insights for the conservation and future breeding of other endemic species amidst rapid climate changes.

A haplotype-resolved genome provides insight into allele-specific expression in wild walnut (Juglans regia L.)

Wild germplasm resources are crucial for gene mining and molecular breeding because of their special trait performance. Haplotype-resolved genome is an ideal solution for fully understanding the biology of subgenomes in highly heterozygous species. Here, we surveyed the genome of a wild walnut tree from Gongliu County, Xinjiang, China, and generated a haplotype-resolved reference genome of 562.99 Mb (contig N50 = 34.10 Mb) for one haplotype (hap1) and 561.07 Mb (contig N50 = 33.91 Mb) for another haplotype (hap2) using PacBio high-fidelity (HiFi) reads and Hi-C technology. Approximately 527.20 Mb (93.64%) of hap1 and 526.40 Mb (93.82%) of hap2 were assigned to 16 pseudochromosomes. A total of 41039 and 39744 protein-coding gene models were predicted for hap1 and hap2, respectively. Moreover, 123 structural variations (SVs) were identified between the two haplotype genomes. Allele-specific expression genes (ASEGs) that respond to cold stress were ultimately identified. These datasets can be used to study subgenome evolution, for functional elite gene mining and to discover the transcriptional basis of specific traits related to environmental adaptation in wild walnut.

Integrated metabolomic and transcriptomic dynamic profiles of endopleura coloration during fruit maturation in three walnut cultivars

BACKGROUND

The color of endopleura is a vital factor in determining the economic value and aesthetics appeal of nut. Walnuts (Juglans) are a key source of edible nuts, high in proteins, amino acids, lipids, carbohydrates. Walnut had a variety endopleura color as yellow, red, and purple. However, the regulation of walnut endopleura color remains little known.

RESULTS

To understand the process of coloration in endopleura, we performed the integrative analysis of transcriptomes and metabolomes at two developmental stages of walnut endopleura. We obtained total of 4,950 differentially expressed genes (DEGs) and 794 metabolites from walnut endopleura, which are involved in flavonoid and phenolic biosynthesis pathways. The enrichment analysis revealed that the cinnamic acid, coniferyl alcohol, naringenin, and naringenin-7-O-glucoside were important metabolites in the development process of walnut endopleura. Transcriptome and metabolome analyses revealed that the DEGs and differentially regulated metabolites (DRMs) were significantly enriched in flavonoid biosynthesis and phenolic metabolic pathways. Through co-expression analysis, CHS (chalcone synthase), CHI (chalcone isomerase), CCR (cinnamoyl CoA reductase), CAD (cinnamyl alcohol dehydrogenase), COMT (catechol-Omethyl transferase), and 4CL (4-coumaroyl: CoA-ligase) may be the key genes that potentially regulate walnut endopleura color in flavonoid biosynthesis and phenolic metabolic pathways.

CONCLUSIONS

This study illuminates the metabolic pathways and candidate genes that underlie the endopleura coloration in walnuts, lay the foundation for further study and provides insights into controlling nut's colour.

A Multiplex PCR System of Novel Microsatellite Loci for Population Genetic Application in Walnuts

Multiplex polymerase chain reaction (PCR) of microsatellite loci allows for simultaneous amplification of two or more pairs of primers in a single PCR reaction; hence, it is cost and time effective. However, very few attempts have been reported in non-model species. In this study, by combining a genome-based de novo development and cross-species application approach, a multiplex PCR system comprising 5 PCR reactions of 33 microsatellites consisting of 26 novel genomic and 7 literature-sourced loci was tested for polymorphisms, cross-species transferability, and the ability to assess genetic diversity and population structure of three walnut species (Juglans spp.). We found that the genome-based approach is more efficient than other methods. An allelic ladder was developed for each locus to enhance consistent genotyping among laboratories. The population genetic analysis results showed that all 33 loci were successfully transferred across the three species, showing high polymorphism and a strong genetic structure. Hence, the multiplex PCR system is highly applicable in walnut species. Furthermore, we propose an efficient pipeline to characterize and genotype polymorphic microsatellite loci. The novel toolbox developed here will aid future ecology and evolution studies in walnut and could serve as a model for other plant species.

Physiological and transcriptomic analyses of response of walnuts (Juglans regia) to Pantoea agglomerans infection

Introduction

Walnut blight is a serious bacterial disease that affects the yield and quality of walnuts. Pantoea agglomerans is one of the main causative agents of walnut blight. However, there have been few studies on the response of walnuts to P. agglomerans infection.

Methods

In this study, the soluble sugar, photosynthesis, antioxidant enzyme activities, and secondary metabolites were measured, and the transcriptomic analysis was performed to determine the response of walnut tissue cultures to P. agglomerans infection.

Results

After pathogen inoculation, the soluble sugar content decreased, and photosynthesis was inhibited. Antioxidant enzyme (superoxide dismutase and peroxidase) activities and secondary metabolites (phenol and flavonoid) contents increased, especially in the early stages of inoculation. Transcriptomic analysis revealed that the phenylpropanoid biosynthesis pathway is induced after infection, and pathogen infection promotes ABA and ethylene signal transduction and inhibits auxin signaling. In addition, SA and JA-related gene expression was altered after inoculation with P. agglomerans, and the FLS- and calcium-mediated disease resistance signaling pathways were activated. Furthermore, our results suggested an involvement of the R-protein RPM-mediated disease resistance pathway in the response of walnuts to bacterial infections.

Discussion

Our findings indicated that phenylpropanoid biosynthesis, hormone signal transduction, and plant-pathogen interaction have key roles in pathogenic inoculation, which provide insights into the molecular mechanisms in the response of walnuts to P. agglomerans infection.

A chromosome-level genome assembly provides insights into Cornus wilsoniana evolution, oil biosynthesis, and floral bud development

Cornus wilsoniana W. is a woody oil plant with high oil content and strong hypolipidemic effects, making it a valuable species for medicinal, landscaping, and ecological purposes in China. To advance genetic research on this species, we employed PacBio together with Hi-C data to create a draft genome assembly for C. wilsoniana. Based on an 11-chromosome anchored chromosome-level assembly, the estimated genome size was determined to be 843.51 Mb. The N50 contig size and N50 scaffold size were calculated to be 4.49 and 78.00 Mb, respectively. Furthermore, 30 474 protein-coding genes were annotated. Comparative genomics analysis revealed that C. wilsoniana diverged from its closest species ~12.46 million years ago (Mya). Furthermore, the divergence between Cornaceae and Nyssaceae occurred >62.22 Mya. We also found evidence of whole-genome duplication events and whole-genome triplication γ, occurring at ~44.90 and 115.86 Mya. We further inferred the origins of chromosomes, which sheds light on the complex evolutionary history of the karyotype of C. wilsoniana. Through transcriptional and metabolic analysis, we identified two FAD2 homologous genes that may play a crucial role in controlling the oleic to linoleic acid ratio. We further investigated the correlation between metabolites and genes and identified 33 MADS-TF homologous genes that may affect flower morphology in C. wilsoniana. Overall, this study lays the groundwork for future research aimed at identifying the genetic basis of crucial traits in C. wilsoniana.

Reference genome of California walnut, Juglans californica, and resemblance with other genomes in the order Fagales

Juglans californica, California walnut, is a vulnerable small tree that is locally abundant but restricted to woodland and chaparral habitats of Southern California threatened by urbanization and land use change. This species is the dominant species in a unique woodland ecosystem in California. It is one of 2 endemic California walnut species (family Juglandaceae). The other species, Northern California black walnut (J. hindsii), has been suggested controversially to be a variety of J. californica. Here, we report a new, chromosome-level assembly of J. californica as part of the California Conservation Genomics Project (CCGP). Consistent with the CCGP common methodology across ~150 genomes, we used Pacific Biosciences HiFi long reads and Omni-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises 137 scaffolds spanning 551,065,703 bp, has a contig N50 of 30 Mb, a scaffold N50 of 37 Mb, and BUSCO complete score of 98.9%. Additionally, the mitochondrial genome has 701,569 bp. In addition, we compare this genome with other existing high-quality Juglans and Quercus genomes, which are in the same order (Fagales) and show relatively high synteny within the Juglans genomes. Future work will utilize the J. californica genome to determine its relationship with the Northern California walnut and assess the extent to which these 2 endemic trees might be at risk from fragmentation and/or climate warming.

Plant genome resequencing and population genomics: Current status and future prospects

Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.

Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement

BACKGROUND

During domestication and subsequent improvement plants were subjected to intensive positive selection for desirable traits. Identification of selection targets is important with respect to the future targeted broadening of diversity in breeding programmes. Rye (Secale cereale L.) is a cereal that is closely related to wheat, and it is an important crop in Central, Eastern and Northern Europe. The aim of the study was (i) to identify diverse groups of rye accessions based on high-density, genome-wide analysis of genetic diversity within a set of 478 rye accessions, covering a full spectrum of diversity within the genus, from wild accessions to inbred lines used in hybrid breeding, and (ii) to identify selective sweeps in the established groups of cultivated rye germplasm and putative candidate genes targeted by selection.

RESULTS

Population structure and genetic diversity analyses based on high-quality SNP (DArTseq) markers revealed the presence of three complexes in the Secale genus: S. sylvestre, S. strictum and S. cereale/vavilovii, a relatively narrow diversity of S. sylvestre, very high diversity of S. strictum, and signatures of strong positive selection in S. vavilovii. Within cultivated ryes we detected the presence of genetic clusters and the influence of improvement status on the clustering. Rye landraces represent a reservoir of variation for breeding, and especially a distinct group of landraces from Turkey should be of special interest as a source of untapped variation. Selective sweep detection in cultivated accessions identified 133 outlier positions within 13 sweep regions and 170 putative candidate genes related, among others, to response to various environmental stimuli (such as pathogens, drought, cold), plant fertility and reproduction (pollen sperm cell differentiation, pollen maturation, pollen tube growth), and plant growth and biomass production.

CONCLUSIONS

Our study provides valuable information for efficient management of rye germplasm collections, which can help to ensure proper safeguarding of their genetic potential and provides numerous novel candidate genes targeted by selection in cultivated rye for further functional characterisation and allelic diversity studies.

LncRNA109897-JrCCR4-JrTLP1b forms a positive feedback loop to regulate walnut resistance against anthracnose caused by Colletotrichum gloeosporioides

Walnut anthracnose induced by Colletotrichum gloeosporioides is a disastrous disease that severely restricts the development of the walnut industry in China. Long non-coding RNAs (lncRNAs) are involved in adaptive responses to disease, but their roles in the regulation of walnut anthracnose resistance response are not well defined. In this study, transcriptome analysis demonstrated that a C. gloeosporioides-induced lncRNA, lncRNA109897, located upstream from the target gene JrCCR4, upregulated the expression of JrCCR4. JrCCR4 interacted with JrTLP1b and promoted its transcriptional activity. In turn, JrTLP1b induced the transcription of lncRNA109897 to promote its expression. Meanwhile, transient expression in walnut leaves and stable transformation of Arabidopsis thaliana further proved that lncRNA, JrCCR4, and JrTLP1b improve the resistance of C. gloeosporioides. Collectively, these findings provide insights into the mechanism by which the lncRNA109897-JrCCR4-JrTLP1b transcriptional cascade regulates the resistance of walnut to anthracnose.

Genome-wide characterization and development of SSR markers for genetic diversity analysis in northwestern Himalayas Walnut (Juglans regia L.)

In the present study, we designed and validated genome-wide polymorphic SSR markers (110 SSRs) by mining the walnut genome. A total of 198,924 SSR loci were identified. Among these, successful primers were designed for 162,594 (81.73%) SSR loci. Dinucleotides were the most predominant accounting for 88.40% (175,075) of total SSRs. The SSR frequency was 377.312 SSR/Mb and it showed a decreasing trend from dinucleotide to octanucleotide motifs. We identified 20 highly polymorphic SSR markers and used them to genotype 72 walnut accessions. Over all, we obtained 118 alleles that ranged from 2 to 12 with an average value of 5.9. The higher SSR PIC values indicate their robustness in discriminating walnut genotypes. Heat map, PCA, and population structure categorized 72 walnut genotypes into 2 distinct clusters. The genetic variation within population was higher than among population as inferred by analysis of molecular variance (AMOVA). For walnut improvement, it is necessary to have a large repository of SSRs with high discriminative power. The present study reports 150,000 SSRs, which is the largest SSR repository for this important nut crop. Scientific communities may use this repository for walnut improvement such as QTL mapping, genetic studies, linkage map construction, and marker-assisted selection.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03563-6.

Establishment of Agrobacterium-mediated transformation system to Juglans sigillata Dode 'Qianhe-7'

An efficient genetic transformation system is of great significance for verifying gene function and improving plant breeding efficiency by gene engineering. In this study, a stable Agrobacterium mediated genetic transformation system of Juglans sigillata Dode 'Qianhe-7' was investigated using callus and negative pressure-assisted and ultrasonic-assisted transformation selection. The results showed that the axillary shoot leaves were suitable to induce callus and the callus proliferation rate could reach 516.27% when induction calli were cultured on DKW medium containing 0.5 mg L^-1 indole-3-butyric acid, 1.2 mg L^-1 2,4-dichlorophenoxyacetic acid and 0.5 mg L^-1 kinetin for 18 d. In addition, negative pressure infection was the optimal infection method with the lowest browning rate (0.00%), high GFP conversion rate (16.67%), and better growth status. To further prove the feasibility of this genetic transformation system, the flavonol synthetase (JsFLS₅) gene was successfully transformed into the into leaf-derived callus of 'Qianhe-7'. JsFLS₅ expression and the content of total flavonoids in transformed callus were improved significantly compared with the untransformed callus, which proved that we had an efficient and reliable genetic transformation system using leaf-derived callus of Juglans sigillata.

Systematical Characterization of the AT-Hook Gene Family in Juglans regia L. and the Functional Analysis of the JrAHL2 in Flower Induction and Hypocotyl Elongation

AT-hook motif nuclear localization (AHL) proteins play essential roles in various plant biological processes. Yet, a comprehensive understanding of AHL transcription factors in walnut (Juglans regia L.) is missing. In this study, 37 AHL gene family members were first identified in the walnut genome. Based on the evolutionary analysis, JrAHL genes were grouped into two clades, and their expansion may occur due to segmental duplication. The stress-responsive nature and driving of developmental activities of JrAHL genes were revealed by cis-acting elements and transcriptomic data, respectively. Tissue-specific expression analysis showed that JrAHLs had a profound transcription in flower and shoot tip, JrAHL2 in particular. Subcellular localization showed that JrAHL2 is anchored to the nucleus. Overexpression of JrAHL2 in Arabidopsis adversely affected hypocotyl elongation and delayed flowering. Our study, for the first time, presented a detailed analysis of JrAHL genes in walnut and provided theoretical knowledge for future genetic breeding programs.

Global Transcriptomic Analyses Provide New Insight into the Molecular Mechanisms of Endocarp Formation and Development in Iron Walnut (Juglans sigillata Dode)

Iron walnut (Juglans sigillata Dode) is a native species in southwestern China that exhibits variation in both fruit morphology and shell thickness. However, the underlying molecular processes controlling hardened endocarp development in walnut has not yet been reported. Here, we generated transcriptional profiles of iron walnut endocarp at three developmental stages using “Dapao”, the most common commercial variety. Using pairwise comparisons between these three stages, a total of 8555 non-redundant differentially expressed genes (DEGs) were identified, and more than one-half of the total DEGs exhibited significant differential expression in stage I as compared with stage II or stage III, suggesting that the first stage may ultimately determine the final characteristics of the mature walnut shell. Furthermore, in the clustering analysis of the above DEGs, 3682, 2349, and 2388 genes exhibited the highest expression in stages I, II, and III, respectively. GO enrichment analysis demonstrated that the major transcriptional variation among the three developmental stages was caused by differences in cell growth, plant hormones, metabolic process, and phenylpropanoid metabolism. Namely, using the tissue-specific expression analysis and a gene co-expression network, we identified MADS-box transcription factor JsiFBP2 and bHLH transcription factor JsibHLH94 as candidate regulators of endocarp formation in the early stage, and JsiNAC56 and JsiMYB78 might play key roles in regulating the lignification process of endocarp in the late stage. This study provides useful information for further research to dissect the molecular mechanisms governing the shell formation and development of iron walnut.

Impact of intercropping grass on the soil rhizosphere microbial community and soil ecosystem function in a walnut orchard

The intercropping of grass in orchards has beneficial effects on soil properties and soil microbial communities and is an important soil management measure for improving orchard productivity and land-use efficiency. However, few studies have explored the effects of grass intercropping on rhizosphere microorganisms in walnut orchards. In this study, we explored the microbial communities of clear tillage (CT), walnut/ryegrass (Lolium perenne L.) (Lp), and walnut/hairy vetch (Vicia villosa Roth.) (Vv) intercropping system using MiSeq sequencing and metagenomic sequencing. The results revealed that the composition and structure of the soil bacterial community changed significantly with walnut/Vv intercropping compared to CT and walnut/Lp intercropping. Moreover, the walnut/hairy vetch intercropping system had the most complex connections between bacterial taxa. In addition, we found that the soil microorganisms of walnut/Vv intercropping had a higher potential for nitrogen cycling and carbohydrate metabolism, which may be related to the functions of Burkholderia, Rhodopseudomonas, Pseudomonas, Agrobacterium, Paraburkholderia, and Flavobacterium. Overall, this study provided a theoretical basis for understanding the microbial communities associated with grass intercropping in walnut orchards, providing better guidance for the management of walnut orchards.

Pan-genome and transcriptome analyses provide insights into genomic variation and differential gene expression profiles related to disease resistance and fatty acid biosynthesis in eastern black walnut (Juglans nigra)

Walnut (Juglans) species are used as nut crops worldwide. Eastern black walnut (EBW, Juglans nigra), a diploid, horticultural important woody species is native to much of eastern North America. Although it is highly valued for its wood and nut, there are few resources for understanding EBW genetics. Here, we present a high-quality genome assembly of J. nigra based on Illumina, Pacbio, and Hi-C technologies. The genome size was 540.8 Mb, with a scaffold N50 size of 35.1 Mb, and 99.0% of the assembly was anchored to 16 chromosomes. Using this genome as a reference, the resequencing of 74 accessions revealed the effective population size of J. nigra declined during the glacial maximum. A single whole-genome duplication event was identified in the J. nigra genome. Large syntenic blocks among J. nigra, Juglans regia, and Juglans microcarpa predominated, but inversions of more than 600 kb were identified. By comparing the EBW genome with those of J. regia and J. microcarpa, we detected InDel sizes of 34.9 Mb in J. regia and 18.3 Mb in J. microcarpa, respectively. Transcriptomic analysis of differentially expressed genes identified five presumed NBS-LRR (NUCLEOTIDE BINDING SITE-LEUCINE-RICH REPEAT) genes were upregulated during the development of walnut husks and shells compared to developing embryos. We also identified candidate genes with essential roles in seed oil synthesis, including FAD (FATTY ACID DESATURASE) and OLE (OLEOSIN). Our work advances the understanding of fatty acid bioaccumulation and disease resistance in nut crops, and also provides an essential resource for conducting genomics-enabled breeding in walnut.

523, Beni Mellal, Morocco, Bouda S, Ennahli S, Hafida H, Laboratory of Biotechnologies and Valorization of Plant Gnetic Resources, University of Sultan Moulay Slimane, Faculty of Sciences and Techniques, P.B. 523, Beni Mellal, Morocco, Departement of Horticulture and Viticulture, National School of Agriculture, Meknes, Morocco, Laboratory of Development and Safety of Food Products, Faculty of Sciences and Techniques, University of Sultan Moulay Slimane Beni Mellal, Morocco. THE WALNUT - CONSTRAINTS AND ADVANTAGES FOR A SUSTAINABLE DEVELOPMENT

The Persian walnut or English walnut (Juglans regia L.) is a commonly grown species for nut production and noble wood. The nut is one of the oldest food and traditional medicine sources. The native and commercial walnut genotypes present a large diversity that differ widely in nut productivity and quality. However, genetic erosion poses a serious threat to this tree. Several researches of walnut genetic diversity are being carried out utilizing morphological, biochemical, and molecular approaches in order to select superior walnut cultivars of different agroclimatic areas to increase nut production and quality. Genetic resource evaluation and agrodiversity conservation have a major role in ensuring food security for future generations through a continuous supply of new rootstocks and improved cultivars.

Domestication and selection footprints in Persian walnuts (Juglans regia)

Walnut (Juglans) species are economically important hardwood trees cultivated worldwide for both edible nuts and high-quality wood. Broad-scale assessments of species diversity, evolutionary history, and domestication are needed to improve walnut breeding. In this study, we sequenced 309 walnut accessions from around the world, including 55 Juglans relatives, 98 wild Persian walnuts (J. regia), 70 J. regia landraces, and 86 J. regia cultivars. The phylogenetic tree indicated that J. regia samples (section Dioscaryon) were monophyletic within Juglans. The core areas of genetic diversity of J. regia germplasm were southwestern China and southern Asia near the Qinghai-Tibet Plateau and the Himalayas, and the uplift of the Himalayas was speculated to be the main factor leading to the current population dynamics of Persian walnut. The pattern of genomic variation in terms of nucleotide diversity, linkage disequilibrium, single nucleotide polymorphisms, and insertions/deletions revealed the domestication and selection footprints in Persian walnut. Selective sweep analysis, GWAS, and expression analysis further identified two transcription factors, JrbHLH and JrMYB6, that influence the thickness of the nut diaphragm as loci under selection during domestication. Our results elucidate the domestication and selection footprints in Persian walnuts and provide a valuable resource for the genomics-assisted breeding of this important crop.

Interspecific Gene Flow and Selective Sweeps in Picea wilsonii, P. neoveitchii and P. likiangensis

Genome-wide single nucleotide polymorphism (SNP) markers were obtained by genotyping-by-sequencing (GBS) technology to study the genetic relationships, population structure, gene flow and selective sweeps during species differentiation of Picea wilsonii, P. neoveitchii and P. likiangensis from a genome-wide perspective. We used P. jezoensis and P. pungens as outgroups, and three evolutionary branches were obtained: P. likiangensis was located on one branch, two P. wilsonii populations were grouped onto a second branch, and two P. neoveitchii populations were grouped onto a third branch. The relationship of P. wilsonii with P. likiangensis was closer than that with P. neoveitchii. ABBA-BABA analysis revealed that the gene flow between P. neoveitchii and P. wilsonii was greater than that between P. neoveitchii and P. likiangensis. Compared with the background population of P. neoveitchii, the genes that were selected in the P. wilsonii population were mainly related to plant stress resistance, stomatal regulation, plant morphology and flowering. The genes selected in the P. likiangensis population were mainly related to plant stress resistance, leaf morphology and flowering. Selective sweeps were beneficial for improving the adaptability of spruce species to different habitats as well as to accelerate species differentiation. The frequent gene flow between spruce species makes their evolutionary relationships complicated. Insight into gene flow and selection pressure in spruce species will help us further understand their phylogenetic relationships and provide a scientific basis for their introduction, domestication and genetic improvement.

Metabolome genome-wide association study provides biochemical and genetic insights into natural variation of primary metabolites in sesame

Plants' primary metabolites are of great importance from the survival and nutritional perspectives. However, the genetic bases underlying the profiles of primary metabolites in oilseed crops remain largely unclear. As one of the main oilseed crops, sesame (Sesamum indicum L.) is a potential model plant for investigating oil metabolism in plants. Therefore, the objective of this study is to disclose the genetic variants associated with variation in the content of primary metabolites in sesame. We performed a comprehensive metabolomics analysis of primary metabolites in 412 diverse sesame accessions using gas chromatography-mass spectrometry and identified a total of 45 metabolites, including fatty acids, monoacylglycerols (MAGs), and amino acids. Genome-wide association study unveiled 433 significant single-nucleotide polymorphism loci associated with variation in primary metabolite contents in sesame. By integrating diverse genomic analyses, we identified 10 key candidate causative genes of variation in MAG, fatty acid, asparagine, and sucrose contents. Among them, SiDSEL was significantly associated with multiple traits. SiCAC3 and SiKASI were strongly associated with variation in oleic acid and linoleic acid contents. Overexpression of SiCAC3, SiKASI, SiLTPI.25, and SiLTPI.26 in transgenic Arabidopsis and Saccharomyces cerevisiae revealed that SiCAC3 is a potential target gene for improvement of unsaturated fatty acid levels in crops. Furthermore, we found that it may be possible to breed several quality traits in sesame simultaneously. Our results provide valuable genetic resources for improving sesame seed quality and our understanding of oilseed crops' primary metabolism.

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.

Metabolome and Transcriptome Profiling Unveil the Mechanisms of Polyphenol Synthesis in the Developing Endopleura of Walnut (Juglans regia L.)

Walnut (Juglans regia L.) is an important woody nut tree species, and its endopleura (the inner coating of a seed) is rich in many polyphenols. Thus far, the pathways and essential genes involved in polyphenol biosynthesis in developing walnut endopleura remain largely unclear. We compared metabolite differences between endopleura and embryo in mature walnuts, and analyzed the changes of metabolites in endopleura at 35, 63, 91, 119, and 147 days after pollination (DAP). A total of 760 metabolites were detected in the metabolome, and the polyphenol contents in endopleura were higher than those in embryos. A total of 15 types of procyanidins, 10 types of kaempferol glycosides, and 21 types of quercetin glycosides that accumulated during endopleura development were identified. The analysis of the phenylpropane metabolic pathway showed that phenylalanine was gradually transformed into proanthocyanidins and other secondary metabolites with the development of endopleura. A total of 49 unigenes related to polyphenol synthesis were identified by transcriptome analysis of endopleura. The expression patterns of PAL, C4H, 4CL, CHS, CHI, F3H, LDOX, and ANR were similar, and their expression levels were highest in endopleura at maturity. Transcriptome and metabolome analysis showed that endopleura rapidly synthesized and accumulated polyphenols during maturation. Moreover, the transcription factor MYB111 played an important role in synthesizing polyphenols in endopleura, and its expression pattern was positively correlated with the accumulation pattern of quercetin, kaempferol, and proanthocyanidins. MYB111 was co-expressed with NAP, NAC, ATR1, and other genes related to cell senescence and abiotic stress response. Our study analyzed the composition and molecular synthesis mechanism of polyphenols in walnut endopleura, and provided new perspectives and insights regarding the nutritional research of walnut nuts.