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Background Pistachio ( Pistacia vera ), one of the most important commercial nut crops worldwide, is highly adaptable to abiotic stresses and is tolerant to drought and salt stresses. Results Here, we provide a draft de novo genome of pistachio as well as large-scale genome resequencing. Comparative genomic analyses reveal stress adaptation of pistachio is likely attributable to the expanded cytochrome P450 and chitinase gene families. Particularly, a comparative transcriptomic analysis shows that the jasmonic acid (JA) biosynthetic pathway plays an important role in salt tolerance in pistachio. Moreover, we resequence 93 cultivars and 14 wild P. vera genomes and 35 closely related wild Pistacia genomes, to provide insights into population structure, genetic diversity, and domestication. We find that frequent genetic admixture occurred among the different wild Pistacia species. Comparative population genomic analyses reveal that pistachio was domesticated about 8000 years ago and suggest that key genes for domestication related to tree and seed size experienced artificial selection. Conclusions Our study provides insight into genetic underpinning of local adaptation and domestication of pistachio. The Pistacia genome sequences should facilitate future studies to understand the genetic basis of agronomically and environmentally related traits of desert crops.

Background The genus Pistacia , belonging to the family Anacardiaceae, includes various species that hold ecological, nutritional, and medicinal significance. There is limited information on the morphological and pomological diversity of Pistacia atlantica Desf. subsp. cabulica and subsp. mutica . This study aims to examine this diversity and contribute to the improvement of sustainable use and agricultural practices. Results Morphological and pomological variation of 44 female accessions of P. atlantica (20 of subsp. cabulica and 24 of subsp. mutica ) grown naturally in Mount Taftan, Sistan-va-Baluchestan, Iran, was assessed. One-way ANOVA ( p  <  0.05 ) showed significant differences among the examined genotypes. The coefficient of variation (CV) ranged from 7.60% (kernel thickness) to 167.04% (kernel crispness), with 34 out of 48 traits (70.83%) showing CVs greater than 20%, indicating high variability. The range of leaf-related characters was as follows: leaf length: 87.52–157.80 mm, leaf width: 55.28–121.97 mm, leaflets per leaf: 5–7, petiole length: 25.87–66.91 mm, and petiole diameter: 1.15–2.2 mm. The range of fruit-related characters was as follows: bunchlets per bunch: 10–17, fruit pedicel length: 1.37–7.12 mm, fruit pedicel width: 0.9–1.23 mm, nut length: 5.49–8.23 mm, nut width: 6.19–8.42 mm, nut thickness: 4.39–6.42 mm, and 100-nut weight: 12.36–25.91 g. These variations indicate adaptability and agricultural potential. Most accessions showed moderate growth, intermediate vigor, and branching, optimizing photosynthesis. Leaf and petiole traits vary, reflecting adaptations to environmental conditions. Ripening times span from late September to mid-October, with yield potential mostly intermediate. According to correlation matrix analysis, high positive correlations were found between 100-nut weight and kernel thickness ( r  =  0.708** ), nut length ( r  =  0.764** ), and nut thickness ( r  =  0.603** ), and these correlations are also supported by multiple regression analysis ( β  = 0.47, β  = 0.69, β  = 0.31, P  < 0.00, respectively). According to principal components analysis, the first three principal components (PC1 = 13.39%, PC2 = 9.30%, and PC3 = 9.25%) represented 31.94% of the total variation. The datasets were evaluated together, and the first 14 accessions were detected, including four accessions of subsp. mutica (No. 23, 5, 11, and 16) and 11 accessions of subsp. cabulica (No. 5, 15, 18, 10, 20, 12, 1, 7, 17, and 13), respectively. The accessions 1 and 7 of subsp. cabulica , though among the first 14, fall outside the 95% confidence ellipse in the scatter plot, indicating that they differ significantly from the others in terms of their traits. This suggests they may possess unique characteristics. Conclusions This study highlights the significant morphological and pomological diversity between the P. atlantica subsp. cabulica and subsp. mutica , providing valuable insights for breeding and conservation. The key trait relationships identified through statistical analysis may guide trait selection for better yield and adaptability.

Background Pistachio ( Pistacia vera L.) growth, yield and quality are affected by abiotic stress especially drought. Understanding the strategies that improve dehydration tolerance is essential for developing resistant pistachio rootstocks. In the experiment, nine-month-old saplings of seven clonal interspecies hybrids of Pistacia atlantica × P. integerrima (C1, C2, C16-1, C8-3, C4-2, C9-4 and UCB1) were assessed for growth and physiological responses to water withholding and recovery. Result Water deficit negatively impacted growth parameters, including shoot dry weight, root dry weight and leaf area, in all hybrids; however, the C1 demonstrated relatively minor reductions compared to the other hybrids. Glycine betaine content in leaves increased by 49.4% in C9-4 and 47% in C1, while only 7% and 11% increases were found in the most sensitive clones, C8-3 and C4-2. Notably, C9-4, identified as the most tolerant clone, displayed the highest proline levels, with increases of 29.5% in leaves and 41.5% in roots, in contrast to C8-3, which showed minimal increases of 6% and 11% in leaves and roots, respectively. Clones with higher compatible solutes maintained higher relative water content (RWC), lower osmotic potential and smaller reductions in leaf water potential. RWC declined by just 6% in C9-4, whereas it dropped by 88% in C8-3. Osmotic potentials in C9-4 were − 1.61 MPa in leaves and − 0.271 MPa in roots, while in C8-3, they were − 0.93 MPa and − 0.11 MPa in leaves and roots, respectively. Following recovery, evaluations of growth, physiological traits and visual observations indicated that C8-3 had poor recovery ability. Heatmap and PCA analyses categorized the clones into three groups: “tolerant” (C9-4, C1 and C2), “moderately tolerant” (UCB1) and “sensitive” (C8-3, C4-2 and C16-1). Conclusion The results of this study underscore the significance of osmotic adjustment as a more critical trait compared to growth and stomatal parameters in effectively differentiating tolerant clones from sensitive ones.

Conservation and characterization of germplasm collections are essential for safeguarding agrobiodiversity and supporting breeding programs. A collection of 140 accessions comprising three different Pistacia species, P. integerrima, P. terebinthus, and P. vera, was analyzed using 27 EST-SSR markers. On average, 3.4 alleles per locus, and 28.2% rare alleles were found. Observed heterozygosity (Ho = 0.36) was lower than expected (He = 0.48), while five loci displayed PIC values above 0.50, highlighting their high informativeness. The phylogenetic analysis clearly separated the three species. Among P. vera samples, Nj tree and population structure analysis identified three main sub-groups: Eastern Mediterranean/Middle Eastern accessions, Italian traditional cultivars, and US modern cultivars. The first group showed higher internal variability, reflecting both local diversification and historical genetic exchanges. Through the use of EST-SSR markers, the present study assesses the genetic diversity within the Pistacia collection while highlighting errors due to mislabeling issues. These results confirm the effectiveness of microsatellite markers to provide a framework for the management and exploitation of genetic diversity for breeding and conservation strategies, also in the Pistacia genus.

Background Pistachio ( Pistacia vera L.) is one of the most important commercial nut crops worldwide. It is a salt-tolerant and long-lived tree, with the largest cultivation area in Iran. Climate change and subsequent increased soil salt content have adversely affected the pistachio yield in recent years. However, the lack of genomic/global transcriptomic sequences on P. vera impedes comprehensive researches at the molecular level. Hence, whole transcriptome sequencing is required to gain insight into functional genes and pathways in response to salt stress. Results RNA sequencing of a pooled sample representing 24 different tissues of two pistachio cultivars with contrasting salinity tolerance under control and salt treatment by Illumina Hiseq 2000 platform resulted in 368,953,262 clean 100 bp paired-ends reads (90 Gb). Following creating several assemblies and assessing their quality from multiple perspectives, we found that using the annotation-based metrics together with the length-based parameters allows an improved assessment of the transcriptome assembly quality, compared to the solely use of the length-based parameters. The generated assembly by Trinity was adopted for functional annotation and subsequent analyses. In total, 29,119 contigs annotated against all of five public databases, including NR, UniProt, TAIR10, KOG and InterProScan. Among 279 KEGG pathways supported by our assembly, we further examined the pathways involved in the plant hormone biosynthesis and signaling as well as those to be contributed to secondary metabolite biosynthesis due to their importance under salinity stress. In total, 11,337 SSRs were also identified, which the most abundant being dinucleotide repeats. Besides, 13,097 transcripts as candidate stress-responsive genes were identified. Expression of some of these genes experimentally validated through quantitative real-time PCR (qRT-PCR) that further confirmed the accuracy of the assembly. From this analysis, the contrasting expression pattern of NCED3 and SOS1 genes were observed between salt-sensitive and salt-tolerant cultivars. Conclusion This study, as the first report on the whole transcriptome survey of P. vera , provides important resources and paves the way for functional and comparative genomic studies on this major tree to discover the salinity tolerance-related markers and stress response mechanisms for breeding of new pistachio cultivars with more salinity tolerance.

Background Pistachio ( Pistacia vera L.) is one of the most important nut crops in the world. There are about 11 wild species in the genus Pistacia, and they have importance as rootstock seed sources for cultivated P. vera and forest trees. Published information on the pistachio genome is limited. Therefore, a genome survey is necessary to obtain knowledge on the genome structure of pistachio by next generation sequencing. Simple sequence repeat (SSR) markers are useful tools for germplasm characterization, genetic diversity analysis, and genetic linkage mapping, and may help to elucidate genetic relationships among pistachio cultivars and species. Results To explore the genome structure of pistachio, a genome survey was performed using the Illumina platform at approximately 40× coverage depth in the P. vera cv. Siirt. The K-mer analysis indicated that pistachio has a genome that is about 600 Mb in size and is highly heterozygous. The assembly of 26.77 Gb Illumina data produced 27,069 scaffolds at N50 = 3.4 kb with a total of 513.5 Mb. A total of 59,280 SSR motifs were detected with a frequency of 8.67 kb. A total of 206 SSRs were used to characterize 24 P. vera cultivars and 20 wild Pistacia genotypes (four genotypes from each five wild Pistacia species) belonging to P. atlantica, P. integerrima, P. chinenesis, P. terebinthus, and P. lentiscus genotypes. Overall 135 SSR loci amplified in all 44 cultivars and genotypes, 41 were polymorphic in six Pistacia species. The novel SSR loci developed from cultivated pistachio were highly transferable to wild Pistacia species. Conclusions The results from a genome survey of pistachio suggest that the genome size of pistachio is about 600 Mb with a high heterozygosity rate. This information will help to design whole genome sequencing strategies for pistachio. The newly developed novel polymorphic SSRs in this study may help germplasm characterization, genetic diversity, and genetic linkage mapping studies in the genus Pistacia .

Background Pistachio ( Pistacia vera L.) is a dioecious species that has a long juvenility period. Therefore, development of marker-assisted selection (MAS) techniques would greatly facilitate pistachio cultivar-breeding programs. The sex determination mechanism is presently unknown in pistachio. The generation of sex-linked markers is likely to reduce time, labor, and costs associated with breeding programs, and will help to clarify the sex determination system in pistachio. Results Restriction site-associated DNA (RAD) markers were used to identify sex-linked markers and to elucidate the sex determination system in pistachio. Eight male and eight female F 1 progenies from a Pistacia vera L. Siirt × Bağyolu cross, along with the parents, were subjected to RAD sequencing in two lanes of a Hi-Seq 2000 sequencing platform. This generated 449 million reads, comprising approximately 37.7 Gb of sequences. There were 33,757 polymorphic single nucleotide polymorphism (SNP) loci between the parents. Thirty-eight of these, from 28 RAD reads, were detected as putative sex-associated loci in pistachio. Validation was performed by SNaPshot analysis in 42 mature F 1 progenies and in 124 cultivars and genotypes in a germplasm collection. Eight loci could distinguish sex with 100% accuracy in pistachio. To ascertain cost-effective application of markers in a breeding program, high-resolution melting (HRM) analysis was performed; four markers were found to perfectly separate sexes in pistachio. Because of the female heterogamety in all candidate SNP loci, we report for the first time that pistachio has a ZZ/ZW sex determination system. As the reported female-to-male segregation ratio is 1:1 in all known segregating populations and there is no previous report of super-female genotypes or female heteromorphic chromosomes in pistachio, it appears that the WW genotype is not viable. Conclusion Sex-linked SNP markers were identified and validated in a large germplasm and proved their suitability for MAS in pistachio. HRM analysis successfully validated the sex-linked markers for MAS. For the first time in dioecious pistachio, a female heterogamety ZW/ZZ sex determination system is suggested.

Long non-coding RNAs (lncRNAs) play crucial roles in regulating gene expression in response to plant stresses. Given the importance regulatory roles of lncRNAs, providing methods for predicting the function of these molecules, especially in non-model plants, is strongly demanded by researchers. Here, we constructed a reference sequence for lncRNAs in P. vera ( Pistacia vera L.) with 53220 transcripts. In total, we identified 1909 and 2802 salt responsive lncRNAs in Ghazvini, a salt tolerant cultivar, after 6 and 24 h salt treatment, respectively and 1820 lncRNAs in Sarakhs, a salt sensitive cultivar, after 6 h salt treatment. Functional analysis of these lncRNAs by several hybrid methods, revealed that salt responsive NAT-related lncRNAs associated with transcription factors, CERK1, LEA, Laccase genes and several genes involved in the hormone signaling pathways. Moreover, gene ontology (GO) enrichment analysis of salt responsive target genes related to top five selected lncRNAs showed their involvement in the regulation of ATPase, cation transporter, kinase and UDP-glycosyltransferases genes. Quantitative real-time PCR (qRT-PCR) experiment results of lncRNAs, pre-miRNAs and mature miRNAs were in accordance with our RNA-seq analysis. In the present study, a comparative analysis of differentially expressed lncRNAs and microRNA precursors between salt tolerant and sensitive pistachio cultivars provides valuable knowledge on gene expression regulation under salt stress condition.

Salinity substantially affects plant growth and crop productivity worldwide. Plants adopt several biochemical mechanisms including regulation of antioxidant biosynthesis to protect themselves against the toxic effects induced by the stress. One-year-old pistachio rootstock exhibiting different degrees of salinity tolerance were subjected to sodium chloride induced stress to identify genetic diversity among cultivated pistachio rootstock for their antioxidant responses, and to determine the correlation of these enzymes to salinity stress. Leaves and roots were harvested following NaCl-induced stress. The results showed that a higher concentration of NaCl treatment induced oxidative stress in the leaf tissue and to a lesser extent in the roots. Both tissues showed an increase in ascorbate peroxidase, superoxide dismutase, catalase, glutathione reductase, peroxidase, and malondialdehyde. Responses of antioxidant enzymes were cultivar dependent, as well as temporal and dependent on the salinity level. Linear and quadratic regression model analysis revealed significant correlation of enzyme activities to salinity treatment in both tissues. The variation in salinity tolerance reflected their capabilities in orchestrating antioxidant enzymes at the roots and harmonized across the cell membranes of the leaves. This study provides a better understanding of root and leaf coordination in regulating the antioxidant enzymes to NaCl induced oxidative stress.

Background Based on our previous studied on different provenances of Pistacia chinensis , some accessions with high quality and quantity of seed oils has emerged as novel source of biodiesel. To better develop P. chinensis seed oils as woody biodiesel, a concurrent exploration of oil content, FA profile, biodiesel yield, and fuel properties was conducted on the seeds from 5 plus germplasms to determine superior genotype for ideal biodiesel production. Another vital challenge is to unravel mechanism that govern the differences in oil content and FA profile of P. chinensis seeds across different accessions. FA biosynthesis and oil accumulation of oil plants are known to be highly controlled by the transcription factors. An integrated analysis of our recent transcriptome data, qRT-PCR detection and functional identification was performed as an attempt to highlight LEC1/WRI1-mediated transcription regulatory mechanism for high-quality oil accumulation in P. chinensis seeds. Results To select ideal germplasm and unravel high oil accumulative mechanism for developing P. chinensis seed oils as biodiesel, five plus trees (accession PC-BJ/PC-AH/PC-SX/PC-HN/PC-HB) with high-yield seeds were selected to assess the variabilities in weight, oil content, FA profile, biodiesel yield and fuel property, revealing a variation in the levels of seed oil (50.76–60.88%), monounsaturated FA (42.80–70.72%) and polyunsaturated FA (18.78–43.35%), and biodiesel yield (84.98–98.15%) across different accessions. PC-HN had a maximum values of seed weight (26.23 mg), oil (60.88%) and biodiesel yield (98.15%), and ideal proportions of C18:1 (69.94%), C18:2 (17.65%) and C18:3 (1.13%), implying that seed oils of accession PC-HN was the most suitable for ideal biodiesel production. To highlight molecular mechanism that govern such differences in oil content and FA profile of different accessions, a combination of our recent transcriptome data, qRT-PCR detection and protein interaction analysis was performed to identify a pivotal role of LEC1/WRI1-mediated transcription regulatory network in high oil accumulation of P. chinensis seeds from different accessions. Notably, overexpression of PcWRI1 or PcLEC1 from P. chinensis seeds in Arabidopsis could facilitate seed development and upregulate several genes relevant for carbon flux allocation (plastidic glycolysis and acetyl-CoA generation), FA synthesis, TAG assembly and oil storage, causing an increase in seed oil content and monounsaturated FA level, destined for biodiesel fuel property improvement. Our findings may present strategies for better developing P. chinensis seed oils as biodiesel feedstock and bioengineering its high oil accumulation. Conclusions This is the first report on the cross-accessions assessments of P. chinensis seed oils to determine ideal accession for high-quality biodiesel production, and an effective combination of PcWRI1 or PcLEC1 overexpression, morphological assay, oil accumulation and qRT-PCR detection was applied to unravel a role of LEC1/WRI1-mediated regulatory network for oil accumulation in P. chinensis seeds, and to highlight the potential application of PcWRI1 or PcLEC1 for increasing oil production. Our finding may provide new strategies for developing biodiesel resource and molecular breeding.