Genomic analyses of diverse wild and cultivated accessions provide insights into the evolutionary history of jujube

The 'Candidatus phytoplasma ziziphi' effectors SJP1 and SJP2 destabilise the bifunctional regulator ZjTCP7 to modulate floral transition and shoot branching

Phytoplasmic SAP11 effectors alter host plant architecture and flowering time. However, the exact mechanisms have yet to be elucidated. Two SAP11-like effectors, SJP1 and SJP2, from 'Candidatus Phytoplasma ziziphi' induce shoot branching proliferation. Here, the transcription factor ZjTCP7 was identified as a central target of these two effectors to regulate floral transition and shoot branching. Ectopic expression of ZjTCP7 resulted in enhanced bolting and earlier flowering than did the control. Interaction and expression assays demonstrated that ZjTCP7 interacted with the ZjFT-ZjFD module, thereby enhancing the ability of these genes to directly bind to the ZjAP1 promoter. The effectors SJP1 and SJP2 unravelled the florigen activation complex by specifically destabilising ZjTCP7 and ZjFD to delay floral initiation. Moreover, the shoot branching of the ZjTCP7-SRDX transgenic Arabidopsis lines were comparable to those of the SJP1/2 lines, suggesting the involvement of ZjTCP7 in the regulation of shoot branching. ZjTCP7 interacted with the branching repressor ZjBRC1 to enhance suppression of the auxin efflux carrier ZjPIN3 expression. ZjTCP7 also directly bound to and upregulated the auxin biosynthesis gene ZjYUCCA2, thereby promoting auxin accumulation. Our findings confirm that ZjTCP7 serves as a bifunctional regulator destabilised by the effectors SJP1 and SJP2 to modulate plant development.

Transcriptome-referenced association study provides insights into the regulation of oil and fatty acid biosynthesis in Torreya grandis kernel

INTRODUCTION

Torreya grandis is a gymnosperm belonging to Taxodiaceae. As an economically important tree, its kernels are edible and rich in oil with high unsaturated fatty acids, such as sciadonic acid. However, the kernels from different T. grandis landraces exhibit fatty acid and oil content variations.

OBJECTIVES

As a gymnosperm, does T. grandis have special regulation mechanisms for oil biosynthesis? The aim of this study was to dissect the genetic architecture of fatty acid and oil content and the underlying mechanism in T. grandis.

METHODS

We constructed a high integrity reference sequence of expressed regions of the genome in T. grandis and performed transcriptome-referenced association study (TRAS) for 10 fatty acid and oil traits of kernels in the 170 diverse T. grandis landraces. To confirm the TRAS result, we performed functional validation and molecular biology experiments for oil significantly associated genes.

RESULTS

We identified 41 SNPs from 34 transcripts significantly associated with 7 traits by TRAS (-log10 (P) greater than 6.0). Results showed that LOB domain-containing protein 40 (LBD40) and surfeit locus protein 1 (SURF1) may be indirectly involved in the regulation of oil and sciadonic acid biosynthesis, respectively. Moreover, overexpression of TgLBD40 significantly increased seed oil content. The nonsynonymous variant in the TgLBD40 coding region discovered by TRAS could alter the oil content in plants. Pearson's correlation analysis and dual-luciferase assay indicated that TgLBD40 positively enhanced oil accumulation by affecting oil biosynthesis pathway genes, such as TgDGAT1.

CONCLUSION

Our study provides new insights into the genetic basis of oil biosynthesis in T. grandis and demonstrates that integrating RNA sequencing and TRAS is a powerful strategy to perform association study independent of a reference genome for dissecting important traits in T. grandis.

Defence and nutrition synergistically contribute to the distinct tolerance of rice subspecies to the stem borer, Chilo suppressalis

Damage caused by the rice striped stem borer (SSB), Chilo suppressalis (Walker) (Lepidoptera: Pyralidae), is much more severe on indica/xian rice than on japonica/geng rice (Oryza sativa) which matches pest outbreak data in cropping regions of China. The mechanistic basis of this difference among rice subspecies remains unclear. Using transcriptomic, metabolomic and genetic analyses in combination with insect bioassay experiments, we showed that japonica and indica rice utilise different defence responses to repel SSB, and that SSB exploited plant nutrition deficiencies in different ways in the subspecies. The more resistant japonica rice induced patterns of accumulation of methyl jasmonate (MeJA-part of a defensive pathway) and vitamin B1 (VB1-a nutrition pathway) distinct from indica cultivars. Using gene-edited rice plants and SSB bioassays, we found that MeJA and VB1 jointly affected the performance of SSB by disrupting juvenile hormone levels. In addition, genetic variants of key biosynthesis genes in the MeJA and VB1 pathways (OsJMT and OsTH1, respectively) differed between japonica and indica rice and contributed to performance differences; in indica rice, SSB avoided the MeJA defence pathway and hijacked the VB1 nutrition-related pathway to promote development. The findings highlight important genetic and mechanistic differences between rice subspecies affecting SSB damage which could be exploited in plant breeding for resistance.

Systematic exploration of Ziziphus species collection and gene identification influencing physiological traits using genotype-by-sequencing technology

The Ziziphus genus, belonging to the Rhamnaceae family, holds significant economic, nutritional, and medicinal value. However, much remains to be discovered about its diversity and physical characteristics. Factors such as growth, resilience to changes, disease resistance, and unique features contribute to the quality of Ziziphus species. This study aims to investigate the genomes of 200 genotypes from five Ziziphus species: Ziziphus jujuba (Zj), Ziziphus nummularia (Zm), Ziziphus oxyphylla (Zx), Ziziphus mauritiana (Zm), and the cultivated variety Ziziphus jujube var. jujube, collected from Pakistan and China. Our goal is to identify single nucleotide polymorphisms (SNPs) associated with eight different traits and understand the genetic diversity within the selected Ziziphus species and their genotypes. Using high-quality SNPs obtained through genotype-by-sequencing (GBS), we conducted population structure, phylogenetic, and principal coordinates analyses, identifying a total of 10,945 clean SNPs. These genotypes were categorized into two groups, A and B. Natural Ziziphus variants in Pakistan, specifically Z. jujuba and Z. nummularia, exhibited high levels of genetic diversity and polymorphic information content (PIC) of 0.46 and 0.41, respectively, compared to other species. Furthermore, we identified 15 influential candidate genes that play crucial roles in regulating agronomic traits, such as fruit width and diameter, leaf width, plant height, and stem diameter within this group. This study provides valuable insights that can be utilized in Ziziphus breeding efforts.

The 'Candidatus Phytoplasma ziziphi' effectors SJP1/2 negatively control leaf size by stabilizing the transcription factor ZjTCP2 in jujube

Phytoplasmas manipulate host plant development to benefit insect vector colonization and their own invasion. However, the virulence factors and mechanisms underlying small-leaf formation caused by jujube witches' broom (JWB) phytoplasmas remain largely unknown. Here, effectors SJP1 and SJP2 from JWB phytoplasmas were identified to induce small-leaf formation in jujube (Ziziphus jujuba). In vivo interaction and expression assays showed that SJP1 and SJP2 interacted with and stabilized the transcription factor ZjTCP2. Overexpression of SJP1 and SJP2 in jujube induced ZjTCP2 accumulation. In addition, the abundance of miRNA319f_1 was significantly reduced in leaves of SJP1 and SJP2 transgenic jujube plants and showed the opposite pattern to the expression of its target, ZjTCP2, which was consistent with the pattern in diseased leaves. Overexpression of ZjTCP2 in Arabidopsis promoted ectopic leaves arising from the adaxial side of cotyledons and reduced leaf size. Constitutive expression of the miRNA319f_1 precursor in the 35S::ZjTCP2 background reduced the abundance of ZjTCP2 mRNA and reversed the cotyledon and leaf defects in Arabidopsis. Therefore, these observations suggest that effectors SJP1 and SJP2 induced small-leaf formation, at least partly, by interacting with and activating ZjTCP2 expression both at the transcriptional and the protein level, providing new insights into small-leaf formation caused by phytoplasmas in woody plants.

Haplotype-resolved T2T reference genomes for wild and domesticated accessions shed new insights into the domestication of jujube

Chinese jujube (Ziziphus jujuba Mill.) is one of the most important deciduous tree fruits in China, with substantial economic and nutritional value. Jujube was domesticated from its wild progenitor, wild jujube (Z. jujuba var. spinosa), and both have high medicinal value. Here we report the 767.81- and 759.24-Mb haplotype-resolved assemblies of a dry-eating 'Junzao' jujube (JZ) and a wild jujube accession (SZ), using a combination of multiple sequencing strategies. Each assembly yielded two complete haplotype-resolved genomes at the telomere-to-telomere (T2T) level, and ~81.60 and 69.07 Mb of structural variations were found between the two haplotypes within JZ and SZ, respectively. Comparative genomic analysis revealed a large inversion on each of chromosomes 3 and 4 between JZ and SZ, and numerous genes were affected by structural variations, some of which were associated with starch and sucrose metabolism. A large-scale population analysis of 672 accessions revealed that wild jujube originated from the lower reaches of the Yellow River and was initially domesticated at local sites. It spread widely and was then independently domesticated at the Shanxi-Shaanxi Gorge of the middle Yellow River. In addition, we identified some new selection signals regions on genomes, which are involved in the tissue development, pollination, and other aspects of jujube tree morphology and fertilization domestication. In conclusion, our study provides high-quality reference genomes of jujube and wild jujube and new insights into the domestication history of jujube.

A natural mutation in the promoter of the aconitase gene ZjACO3 influences fruit citric acid content in jujube

Jujube (Ziziphus jujuba Mill.) is the most economically important fruit tree of the Rhamnaceae and was domesticated from wild or sour jujube (Z. jujuba Mill. var. spinosa Hu). During the process of domestication, there was a substantial reduction in the content of organic acids, particularly malate and citrate, which greatly influence the taste and nutritional value of the fruit. We previously demonstrated that ZjALMT4 is crucial for malate accumulation. However, the mechanism of citrate degradation in jujube remains poorly understood. In the present study, aconitase ZjACO3 was shown to participate in citric acid degradation in the cytoplasm through the GABA pathway. Interestingly, we discovered an E-box mutation in the ZjACO3 promoter (-484A > G; CAAGTG in sour jujube mutated to CAGGTG in cultivated jujube) that was strongly correlated with fruit citrate content; 'A' represented a high-citrate genotype and 'G' represented a low-citrate genotype. We developed and validated an ACO-based Kompetitive allele-specific PCR (KASP) marker for determining citric acid content. Yeast one-hybrid screening, transient dual-luciferase assays, and overexpression analyses showed that the transcription factor ZjbHLH113 protein directly binds to CAGGTG in the promoter of ZjACO3 in cultivated jujube plants, transcriptionally activating ZjACO3 expression, and enhancing citric acid degradation. Conversely, binding ability of the ZjbHLH113 protein to CAAGTG was weakened in sour jujube, thereby promoting citrate accumulation in the fruit. These findings will assist in elucidating the mechanism by which ZjACO3 modulates citrate accumulation in sour jujube and its cultivars.

Comparative analysis of jujube and sour jujube gave insight into their difference in genetic diversity and suitable habitat

Jujube (Ziziphus jujuba var. jujuba Mill.) and sour jujube (Z. jujuba var. spinosa (Bunge) Hu ex H.F.Chow.) are economically, nutritionally, and ecologically significant members of the Rhamnaceae family. Despite their importance, insufficient research on their genetics and habitats has impeded effective conservation and utilization. To address this knowledge gap, we conducted plastome sequencing, integrated distribution data from China, and assessed genetic diversity and suitable habitat. The plastomes of both species exhibited high conservation and low genetic diversity. A new-found 23 bp species-specific Indel in the petL-petG enabled us to develop a rapid Indel-based identification marker for species discrimination. Phylogenetic analysis and dating illuminated their genetic relationship, showing speciation occurred 6.9 million years ago, in a period of dramatic global temperature fluctuations. Substantial variations in suitable climatic conditions were observed, with the mean temperature of the coldest quarter as the primary factor influencing distributions (-3.16°C-12.73°C for jujube and -5.79°C to 4.11°C for sour jujube, suitability exceeding 0.6). Consequently, distinct conservation strategies are warranted due to differences in suitable habitats, with jujube having a broader distribution and sour jujube concentrated in Northern China. In conclusion, disparate habitats and climatic factors necessitate tailored conservation approaches. Comparing genetic diversity and developing rapid species-specific primers will further enhance the sustainable utilization of these valuable species.

Cultivation and morphology of jujube (Ziziphus Jujuba Mill.) in the Qi River Basin of Northern China during the Neolithic Period

This transition from gathering to cultivation is a significant aspect of studying early agricultural practices. Fruit trees are an essential component of food resources and have played a vital role in both ancient and modern agricultural production systems. The jujube (Ziziphus jujuba Mill.), with its long history of cultivation in northern China, holds great importance in uncovering the diet of prehistoric humans and understanding the origins of Chinese agricultural civilization. This paper focuses on the domestication of jujube by analyzing the morphology of jujube stones found in three Neolithic sites in northern China's Qi River basin, Zhujia, Wangzhuang, and Dalaidian. The measurements of these jujube kernels are compared with those found in other areas of northern China, as well as modern jujube kernels that were collected. The measurements revealed that the length-to-diameter (L/D) ratio of sour jujube kernels ranged from 1.36 to 1.78, whereas the L/D ratio of cultivated jujube stones varied between 1.96 and 4.23. Furthermore, jujube stones obtained from Zhujia and Wangzhuang sites exhibit pointed ends and possess an elongated oval or narrow oval shape overall, which is indicative of clearly artificial domestication traits. Therefore, this study suggests that jujube was selected and cultivated as an important food supplement in the Qi River basin no later than around 6200 BP.

Quantification of fatty acids in seed oil and important bioactive compounds in Iranian Rosa canina L. ecotypes for potential cosmetic and medicinal uses

Rosa canina L. (Rosaceae), commonly known as the rose hip, is originated from Europe, Africa, and Asia with a long history in medicinal applications. This study aimed to analyze the morphological traits, fatty acids profile, and content of phenolic compounds, anthocyanins, vitamin C, total carotenoid, total phenol, total flavonoid, and antioxidant activity of the fruits of eleven Iranian R. canina ecotypes (RCEs). The highest coefficient of variation was obtained in 1000 seed weight (46.57%). The seed oil varied from 8.08 ± 0.17% to 16.91 ± 0.35%. Linoleic (35.41 ± 0.78% to 49.59 ± 0.96%) and eicosanoic (17.67 ± 0.06% to 25.36 ± 0.54%) acids were the predominant fatty acids in the studied samples. The anthocyanin content in the fruits was ranged from 0.98 ± 0.03 to 4.41 ± 0.04 mg cyanidin 3-glucoside/100 g of dry weight (mg C3G/100 g DW). The high content of vitamin C (103.51 ± 1.24-419.70 ± 3.12 mg/100 g DW), total carotenoid (111.22 ± 0.78-206.98 ± 1.25 mg β-carotene equivalents per g of dry weight (mg β-CARE/g DW)), total phenol (52.87 ± 0.82-104.52 ± 0.23 mg GAE/g DW), and total flavonoid (14.20 ± 0.12-25.18 ± 0.47 mg RE/g DW) were observed in the studied samples. Catechin (20.42 ± 0.47-19.22 ± 0.13 µg/g DW) was the major phenolic compound. The high antioxidant activity in the fruits of the plant was recorded in the studied RCEs (IC50 = 12.54 ± 0.18-26.33 ± 0.13 μg/ml). A significant correlation between some phytochemical compounds (dependent variable) and morphological features (independent variable) was found. Based on our findings, the fruit of the studied ecotypes can be used for future breeding programs and drug development.

Transcriptome Characterization of Pigment-Related Genes in Jujube (Ziziphus Jujuba Mill.) Peel at Different Growth Stages

One of the most important qualities of jujube fruit is its color. Chlorophyll, carotenoid, and anthocyanin all play important roles in the coloring of jujube fruit. However, few studies have focused on the pigment molecular mechanism. In the present study, jujube peels of 'Sanbianhong' in three growth stages were evaluated for their gene expression characteristics and gene regulation related to pigment formation using the transcriptome sequencing analysis. A total of 84.86 Gb of clean data were obtained in the analysis. In the FS1 vs. FS3, FS1 vs. FS5, and FS3 vs. FS5, 4,530, 11,012, and 9,072 differentially expressed genes (DEGs) were identified, respectively. The inter-group screening among the three comparisons yielded 1430 common DEGs. Among these DEGs, 27, 16, and 28 genes were enriched in chlorophyll, carotenoid, and anthocyanin metabolic pathways, respectively. Twelve genes were chosen at random, and the accuracy of the transcriptome data were confirmed using qRT-PCR. The molecular mechanism underlying the pigmentation of jujube fruit was elucidated at the transcriptome level, which would provide a scientific basis for the subsequent functional studies on the color-regulating genes of jujube fruits.

ZjWRKY23 and ZjWRKY40 Promote Fruit Size Enlargement by Targeting and Downregulating Cytokinin Oxidase/Dehydrogenase 5 Expression in Chinese Jujube

Fruit size is crucial for fruit trees, as it contributes to both quality and yield. However, the underlying mechanism of fruit size regulation remains largely unknown. Taking advantage of using a fruit double-sized bud mutant of Chinese jujube, "Jinkuiwang" and its wild type, "Jinsixiaozao", we carried out a comprehensive study on the mechanism of fruit size development in jujube. Using weighted gene coexpression network analyses, a number of candidate regulators for fruit size including those involved in hormonal signaling pathways, transcription factors, and heat shock proteins were identified. A hub gene named cytokinin oxidase/dehydrogenase 5 (ZjCKX5), responsible for cytokinin degradation, was found to play a negative role in regulating fruit size development, and overexpressing ZjCKX5 in tomato and Arabidopsis resulted in much smaller fruits and dwarf plants. Furthermore, another two hub genes, ZjWRKY23 and ZjWRKY40 transcription factors, were found to participate in fruit size regulation by targeting and downregulating the ZjCKX5 expression. Overexpressing ZjWRKY23 or ZjWRKY40 in tomato led to much larger fruits and promoted plant architecture. Based on these results, a molecular framework for jujube fruit size regulation, namely, ZjWRKY-ZjCKX5 module, was proposed. This study provides a new insight into the molecular networks underlying fruit size regulation.

'Candidatus Phytoplasma ziziphi' Changes the Metabolite Composition of Jujube Tree Leaves and Affects the Feeding Behavior of Its Insect Vector Hishimonus hamatus Kuoh

Hishimonus hamatus Kuoh is a leafhopper species native to China that feeds on Chinese jujube leaves. This leafhopper species has been verified to transmit jujube witches' broom (JWB) disease, caused by phytoplasma, a fatal plant pathogen, which belongs to the phytoplasma subgroup 16SrV-B. The transmission of JWB phytoplasma largely relies on the feeding behavior of piercing-sucking leafhoppers. However, the specific mechanisms behind how and why the infection of JWB influences the feeding behavior of these leafhoppers are not fully understood. To address this, a study was conducted to compare the feeding patterns of H. hamatus when feeding JWB-infested jujube leaves to healthy leaves using the electrical penetration graph (EPG) technique. Then, a widely targeted metabolome analysis was performed to identify differences in the metabolite composition of JWB-infected jujube leaves and that of healthy jujube leaves. The results of EPG analyses revealed that when feeding on JWB-infected jujube leaves, H. hamatus exhibited an increased frequency of phloem ingestion and spent longer in the phloem feeding phase compared to when feeding on healthy leaves. In addition, the results of metabolomic analyses showed that JWB-infected leaves accumulated higher levels of small-molecular carbohydrates, free amino acids, and free fatty acids, as well as lower levels of lignans, coumarins and triterpenoids compared to healthy leaves. The above results indicated that the H. hamatus preferentially fed on the phloem of infected leaves, which seems to be linked to the transmission of the JWB phytoplasma. The results of metabolomic analyses partially imply that the chemical compounds might play a role in making the infected leaves more attractive to H. hamatus for feeding.

Jujube witches' broom phytoplasmas inhibit ZjBRC1-mediated abscisic acid metabolism to induce shoot proliferation

Jujube witches' broom (JWB) phytoplasmas parasitize the sieve tubes of diseased phloem and cause an excessive proliferation of axillary shoots from dormant lateral buds to favour their transmission. In previous research, two JWB effectors, SJP1 and SJP2, were identified to induce lateral bud outgrowth by disrupting ZjBRC1-mediated auxin flux. However, the pathogenesis of JWB disease remains largely unknown. Here, tissue-specific transcriptional reprogramming was examined to gain insight into the genetic mechanisms acting inside jujube lateral buds under JWB phytoplasma infection. JWB phytoplasmas modulated a series of plant signalling networks involved in lateral bud development and defence, including auxin, abscisic acid (ABA), ethylene, jasmonic acid, and salicylic acid. JWB-induced bud outgrowth was accompanied by downregulation of ABA synthesis within lateral buds. ABA application rescued the bushy appearances of transgenic Arabidopsis overexpressing SJP1 and SJP2 in Col-0 and ZjBRC1 in the brc1-2 mutant. Furthermore, the expression of ZjBRC1 and ABA-related genes ZjHB40 and ZjNCED3 was negatively correlated with lateral main bud outgrowth in decapitated healthy jujube. Molecular evidence showed that ZjBRC1 interacted with ZjBRC2 via its N-terminus to activate ZjHB40 and ZjNCED3 expression and ABA accumulation in transgenic jujube calli. In addition, ZjBRC1 widely regulated differentially expressed genes related to ABA homeostasis and ABA signalling, especially by binding to and suppressing ABA receptors. Therefore, these results suggest that JWB phytoplasmas hijack the ZjBRC1-mediated ABA pathways to stimulate lateral bud outgrowth and expansion, providing a strategy to engineer plants resistant to JWB phytoplasma disease and regulate woody plant architecture to promote crop yield and quality.

Virus-Induced Gene Silencing (VIGS) in Chinese Jujube

Virus-induced gene silencing (VIGS) is a fast and efficient method for assaying gene function in plants. At present, the VIGS system mediated by Tobacco rattle virus (TRV) has been successfully practiced in some species such as cotton and tomato. However, little research of VIGS systems has been reported in woody plants, nor in Chinese jujube. In this study, the TRV-VIGS system of jujube was firstly investigated. The jujube seedlings were grown in a greenhouse with a 16 h light/8 h dark cycle at 23 °C. After the cotyledon was fully unfolded, Agrobacterium mixture containing pTRV1 and pTRV2-ZjCLA with OD₆₀₀ = 1.5 was injected into cotyledon. After 15 days, the new leaves of jujube seedlings showed obvious photo-bleaching symptoms and significantly decreased expression of ZjCLA, indicating that the TRV-VIGS system had successfully functioned on jujube. Moreover, it found that two injections on jujube cotyledon could induce higher silencing efficiency than once injection. A similar silencing effect was then also verified in another gene, ZjPDS. These results indicate that the TRV-VIGS system in Chinese jujube has been successfully established and can be applied to evaluate gene function, providing a breakthrough in gene function verification methods.

Comparative Anatomical and Transcriptomics Reveal the Larger Cell Size as a Major Contributor to Larger Fruit Size in Apricot

Fruit size is one of the essential quality traits and influences the economic value of apricots. To explore the underlying mechanisms of the formation of differences in fruit size in apricots, we performed a comparative analysis of anatomical and transcriptomics dynamics during fruit growth and development in two apricot cultivars with contrasting fruit sizes (large-fruit Prunus armeniaca 'Sungold' and small-fruit P. sibirica 'F43'). Our analysis identified that the difference in fruit size was mainly caused by the difference in cell size between the two apricot cultivars. Compared with 'F43', the transcriptional programs exhibited significant differences in 'Sungold', mainly in the cell expansion period. After analysis, key differentially expressed genes (DEGs) most likely to influence cell size were screened out, including genes involved in auxin signal transduction and cell wall loosening mechanisms. Furthermore, weighted gene co-expression network analysis (WGCNA) revealed that PRE6/bHLH was identified as a hub gene, which interacted with 1 TIR1, 3 AUX/IAAs, 4 SAURs, 3 EXPs, and 1 CEL. Hence, a total of 13 key candidate genes were identified as positive regulators of fruit size in apricots. The results provide new insights into the molecular basis of fruit size control and lay a foundation for future breeding and cultivation of larger fruits in apricot.

Genetic analysis of mixed models of fruit sugar-acid fractions in a cross between jujube (Ziziphus jujuba Mill.) and wild jujube (Z. acido jujuba)

Chinese jujube (Ziziphus jujuba Mill.), an economically significant species in the Rhamnaceae family, is a popular fruit tree in Asia. The sugar and acid concentrations in jujube are considerably higher than those in other plants. Due to the low kernel rate, it is extremely difficult to establish hybrid populations. Little is known about jujube evolution and domestication, particularly with regard to the role of the sugar and acid components of jujube. Therefore, we used cover net control as a hybridization technique for the cross-breeding of Ziziphus jujuba Mill and 'JMS2' and (Z. acido jujuba) 'Xing16' to obtain an F₁ population (179 hybrid progeny). The sugar and acid levels in the F₁ and parent fruit were determined by HPLC. The coefficient of variation ranged from 28.4 to 93.9%. The sucrose and quinic acid levels in the progeny were higher than those in the parents. The population showed continuous distributions with transgressive segregation on both sides. Analysis by the mixed major gene and polygene inheritance model was performed. It was found that glucose is controlled by one additive-dominant major gene and polygenes, malic acid is controlled by two additive-dominant major genes and polygenes, and oxalic acid and quinic acid are controlled by two additive-dominant-epistatic major genes and polygenes. The results of this study provide insights into the genetic predisposition and molecular mechanisms underlying the role of sugar acids in jujube fruit.

Resequencing of Rosa rugosa accessions revealed the history of population dynamics, breed origin, and domestication pathways

BACKGROUND

Rosa rugosa is a shrub that originated in China and has economic and ecological value. However, during the development of R. rugosa, the genetic background was chaotic, and the genetic structure among different wild populations was unclear, as well as wild and cultivated accessions. Here, we report whole-genome resequencing of wild and cultivated R. rugosa accessions.

RESULTS

A total of 19,041,284 SNPs were identified in 188 R. rugosa accessions and 3 R. chinensis accessions by resequencing. Population genetic analysis revealed that cultivated and wild groups were separated very early. All R. rugosa accessions were divided into 8 categories based on genetic structure: (1) Weihai, Yantai, and Liaoning category, (2) Jilin category, and (3) Hammonasset category (above three are wild); (4) traditional varieties, (5) hybrids between R. rugosa and R. chinensis, (6) Zizhi Rose, (7) Kushui Rose, (8) hybrids between R. rugosa and R. multiflora. We found that the heterozygosity and genetic diversity of wild accessions were generally lower than those of cultivated individuals. The genes that were selected during cultivation were identified, and it was found that these genes were mainly related to environmental adaptation and growth.

CONCLUSIONS

The Jilin population was the oldest population and later migrated to Liaoning and then migrated to Yantai and Weihai by sea regression in the Bohai Basin. The Hammonasset naturalized population probably originated from the Jilin population and then experienced separate differentiation. The long-term asexual reproduction pattern of R. rugosa decreased genetic diversity in the wild population. During R. rugosa cultivation, the ancestors of the Jilin population were involved in breeding traditional varieties, after which almost no wild individuals were engaged in breeding. However, in recent decades, cross breeding of R. rugosa started the utilization of wild germplasms. In comparison, some other species play important roles in variety formation. Few genes related to economic traits were selected, suggesting no directional domestication in the R. rugosa cultivation process.

Triterpenoids in Jujube: A Review of Composition, Content Diversity, Pharmacological Effects, Synthetic Pathway, and Variation during Domestication

Chinese jujube (Ziziphus jujuba Mill.) and its wild ancestor, sour jujube (Z. acidojujuba C.Y. Cheng & M.J. Liu), is a Ziziphus genus in the Rhamnaceae family. ZJ and ZA are rich in a variety of active ingredients, with triterpenoids being a unique active ingredient, which are present in the fruit, leaves, branches, and roots. More than 120 triterpenoids have been identified in ZJ and ZA, and have various biological activities. For example, betulinic and ursolic acids have anticancer, antioxidant, antibacterial and antiviral activities. ceanothic, alphitolic, and zizyberanalic acids possess anti-inflammatory activities. The MVA pathway is a synthetic pathway for triterpenoids in ZJ and ZA, and 23 genes of the MVA pathway are known to regulate triterpene synthesis in ZJ and ZA. In order to better understand the basic situation of triterpenoids in ZJ and ZA, this paper reviews the types, content dynamic changes, activities, pharmacokinetics, triterpenoid synthesis pathways, and the effects of domestication on triterpenoids in ZJ and ZA, and provides some ideas for the future research of triterpenoids in ZJ and ZA. In addition, there are many types of ZJ and ZA triterpenoids, and most of the studies on their activities are on lupane- and ursane-type triterpenes, while the activities of the ceanothane-type and saponin are less studied and need additional research.

Effects of harpin and carbendazim on antioxidant accumulation in young jujube leaves

Jujube leaf tea is a functional beverage that soothes the nerves. In this study, we evaluated the effects of carbendazim and harpin on disease index, biomass accumulation, H2O2, antioxidant contents, and phenyl alanine ammonia lyase (PAL) activity in young jujube leaves. Compared to harpin, carbendazim decreased the disease index and induced higher H2O2 content. Additionally, the pesticide reduced young leaf biomass accumulation. In contrast, harpin increased vitamin C, glutathione, total phenolics, and total antioxidant capacity in young leaves compared to carbendazim. Compared with the control, harpin enhanced the PAL activity. Carbendazim residues were present in treated leaves for 14 days. Our study findings provide a method for improving jujube leaf tea quality from a pesticide utilization perspective.

Genomic C-Value Variation Analysis in Jujube (Ziziphus jujuba Mill.) in the Middle Yellow River Basin

Chinese jujube (Ziziphus jujuba Mill.) originated in the Yellow River basin (YRB) of the Shanxi-Shaanxi region. The genomic C-value is a crucial indicator for plant breeding and germplasm evaluation. In this study, we used flow cytometry to determine the genomic C-values of jujube germplasms in the YRB of the Shanxi-Shaanxi region and evaluated their differences in different sub-regions. Of the 29 sub-regions, the highest and lowest variations were in Linxian and Xiaxian, respectively. The difference between jujube germplasms was highly significant (F = 14.89, p < 0.0001) in Linxian. Cluster analysis showed that both cluster 2 and 4 belonged to Linxian, which were clearly separated from other taxa but were cross-distributed in them. Linxian County is an important gene exchange center in the YRB of the Shanxi-Shaanxi region. Principal component analysis showed that cluster 1 had low genomic C-values and single-fruit weights and cluster 2 had high genomic C-values and vitamin C contents. The genomic C-value was correlated with single-fruit weight and vitamin C content. In addition, the genomic C-value was used to predict fruit agronomic traits, providing a reference for shortening the breeding cycle and genetic diversity-related studies of jujube germplasm.

A comparative plastomic analysis of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow and implication of the origin of Chinese jujube

Comparative plastomics can be used to explicitly dissect various types of plastome variation. In the present study, the plastome variation pattern of Ziziphus jujuba var. spinosa (also called sour jujube) and its phylogenomic relationship with Chinese jujube were investigated. Plastomes of 21 sour jujube individuals were sequenced and assembled. The length of the sour jujube plastomes ranged between 159399 and 161279 bp. The plastomes exhibited collinearity of structure, gene order and content. The most divergent regions were located in the intergenic spacers, such as trnR-UCU-atpA and psbZ-trnG-UCC. Sliding window analysis demonstrated that the sequence variation among the sour jujube plastomes was relatively low. Sixty-two to 76 SSRs with 4 motif types were identified in the sour jujube plastomes with a predominant motif type of A/T. Three protein-coding genes exhibited higher nonsynonymous/synonymous substitution ratios, indicating that these genes may undergo positive selection. A total of 80 SNPs were detected and 1266 potential RNA editing sites of 23 protein-coding genes were predicted. In the phylogenomic tree constructed, sour jujube has a sister relationship to Chinese jujube, which indicates that Chinese jujube may have originated or been domesticated from sour jujube. The present study explicitly investigated the individual-level plastome variation of sour jujube and provides potential valuable molecular markers for future genetic-related study of this lineage.

Integrated microRNA and transcriptome profiling reveals the regulatory network of embryo abortion in jujube

Hybridization is an important approach to the production of new varieties with exceptional traits. Although the kernel rate of wild jujube (Ziziphus jujuba Mill. var. spinosa Hu.) is generally high, that of cultivated jujube (Z. jujuba Mill.) is low, greatly hampering the jujube breeding process. However, the mechanism by which this trait changed during jujube domestication remains unclear. Here, we explored the potential regulatory network that governs jujube embryo abortion using correlation analysis of population traits, artificial pollination, sugar content measurements and multi-omics analysis. The results showed that embryo abortion was an important reason for the low kernel rate of cultivated jujube, and kernel rate was negatively correlated with edible rate. Twenty-one days after pollination was a critical period for embryo abortion. At this time, the sugar content of cultivated 'Junzao' kernels decreased significantly compared with that of the pulp, but sugar content remained relatively stable in kernels of wild 'Suanzao'. A total of 1142 differentially expressed genes targeted by 93 microRNAs (miRNAs) were identified by transcriptome, miRNA and degradome sequencing, and may be involved in the regulation of embryo abortion during kernel development. Among them, DELLA protein, TCP14 and bHLH93 transcription factors have been shown to participate in the regulation of embryonic development. Our findings suggest that carbohydrate flow between different tissues of cultivated jujube exhibits a bias toward the pulp at 21 days after pollination, thereby restricting the process of kernel development. This information enhances our understanding of the embryo abortion process and reveals miRNA-target gene pairs that may be useful for molecular-assisted breeding.

Exchanges of economic plants along the land silk road

BACKGROUD

The greatest contribution of the Silk Road is to communicate among different countries and nationalities, and promote two-way cultural exchanges between the East and the West. We now have clearer understanding about how material civilization and religious culture of Central Asia and West Asia spread eastward along the Land Silk Road. However, there is controversial about how crops migrate along the Land Silk Road.

RESULTS

We summarize archaeology, genetics, and genomics data to explore crop migration patterns. Of the 207 crops that were domesticated along the Land Silk Road, 19 for which genomic evidence was available were selected for discussion.

CONCLUSIONS

There were conflicting lines of evidence for the domestication of Tibetan barley, mustard, lettuce, buckwheat, and chickpea. The main reasons for the conflicting results may include incomplete early knowledge, record differences in different period, sample sizes, and data analysis techniques. There was strong evidence that Tibetan barley, barley, wheat, and jujube were introduced into China before the existence of the Land Silk Road; and mustard, lettuce, buckwheat, chickpea, alfalfa, walnut, cauliflower, grape, spinach, apple, cucumber, mulberry, and pea spread to China via trade and human migration along the Land Silk Road.

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.

Genetic diversity and population dynamic of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow in Central China

Phylogeographic research concerning Central China has been rarely conducted. Population genetic and phylogeography of Ziziphus jujuba var. spinosa (also called sour jujube) were investigated to improve our understanding of plant phylogeographic patterns in Central China. Single-copy nuclear gene markers and complete chloroplast genome data were applied to 328 individuals collected from 21 natural populations of sour jujube in China. Nucleotide variation of sour jujube was relatively high (π = 0.00720, θ _w = 0.00925), which resulted from the mating system and complex population dynamics. Analysis of molecular variation analysis revealed that most of the total variation was attributed to variation within populations, and a high level of genetic differentiation among populations was detected (F _st = 0.197). Relatively low long-distance dispersal capability and vitality of pollen contributed to high genetic differentiation among populations. Differences in the environmental conditions and long distance among populations further restricted gene flow. Structure clustering analysis uncovered intraspecific divergence between central and marginal populations. Migrate analysis found a high level of gene flow between these two intraspecific groups. Bayesian skyline plot detected population expansion of these two intraspecific groups. Network and phylogeny analysis of chloroplast haplotypes also found intraspecific divergence, and the divergence time was estimated to occur at about 55.86 Ma. Haplotype native to the Loess Plateau was more ancient, and multiple glacial refugia of sour jujube were found to locate at the Loess Plateau, areas adjacent to the Qinling Mountains and Tianmu Mountains. Species distribution model analysis found a typical contraction-expansion model corresponding to the Quaternary climatic oscillations. In the future, the distribution of sour jujube may shift to high-latitude areas. This study provides new insights for phylogeographic research of temperate plant species distributed in Central China and sets a solid foundation for the application of the scientific management strategy of Z. jujuba var. spinosa.

Composition and environmental interpretation of the weed communities in the main planting base of jujube (Ziziphus jujuba Mill. cv. 'LingwuChangzao'), Ningxia province of China

Background

Ziziphus jujuba Mill. cv. 'LingwuChangzao' is a traditional jujube cultivar in northwest China. It is of great significance to explore the weed community composition and environmental characterization for the ecological control and comprehensive management of weeds in jujube orchards. In this article, a total of 37 species were recorded in 40 sample plots (1 m × 1 m). Moreover, fourteen environmental indicators to characterize the spatial locations, climate and soil nutrient characteristics of the plant communities were adopted.

Methodology

Through the two-way indicator species analysis (TWINSPAN) quantity classification and canonical correspondence analysis (CCA) ranking methods, the types of weed communities in the main planting base of jujube 'LingwuChangzao' and the main environmental factors affecting the change and distribution of weed types were analyzed.

Results

The weed communities within the study area were divided into 15 types by the TWINSPAN classification. There were significant differences in soil factors to the species diversity indices of the weed communities, the diversity of weed communities was negatively correlated with available potassium, whereas positively correlated with soil water content. The CCA results showed that community structure and spatial distribution of weed communities were affected by soil water content, total potassium, soil organic carbon, total phosphorus, total nitrogen. Our results can be used as a reference for orchard weed management and provide a theoretical basis for weed invasion control and creating a higher biodiversity in arable land under the background of environmental change.

Iminodisuccinic acid enhances antioxidant and mineral element accumulation in young leaves of Ziziphus jujuba

Jujube leaf tea, which is made from the young leaves of Ziziphus jujuba, is a novel functional herb tea or infusion that inhibits the central nervous system. In the current study, the effects of iminodisuccinic acid (IDS), as a metal complexing agent, on mineral element content, oxidative damage, antioxidant enzyme activities, and antioxidant accumulation in the young and mature leaves of Z. jujuba were investigated. Results demonstrated that foliar fertilization with ionic (FeCl2 and ZnCl2) and chelated (Fe-IDS and Zn-IDS) fertilizers could drastically enhance iron and zinc contents, coupled with increased vitamin C level, glutathione accumulation, total phenolic content, and total antioxidant capacity (evaluated based on the Fe3+ reducing power of leaf extracts), compared with the control, particularly in young leaves. However, chelated fertilizers considerably reduced the chlorophyll level, H2O2 content, and lipid peroxidation rate than ionic fertilizers, particularly in young leaves. Compared with the control, chelated fertilizers induced greater superoxide dismutase and catalase activities, particularly in young leaves. Moreover, decreased enzyme activities were observed in the ionic fertilizer-treated leaves compared with the control-treated leaves. Thus, using a chelating agent could improve the accumulation of mineral elements and antioxidants in young leaves by reducing metal-mediated reactive oxygen species toxicity.

Pan-Genome Analysis Reveals the Abundant Gene Presence/Absence Variations Among Different Varieties of Melon and Their Influence on Traits

Melon (Cucumismelo L.) is an important vegetable crop that has been subjected to domestication and improvement. Several varieties of melons with diverse phenotypes have been produced. In this study, we constructed a melon pan-genome based on 297 accessions comprising 168 Mb novel sequences and 4,325 novel genes. Based on the results, there were abundant genetic variations among different melon groups, including 364 unfavorable genes in the IMP_A vs. LDR_A group, 46 favorable genes, and 295 unfavorable genes in the IMP_M vs. LDR_M group. The distribution of 709 resistance gene analogs (RGAs) was also characterized across 297 melon lines, of which 603 were core genes. Further, 106 genes were found to be variable, 55 of which were absent in the reference melon genome. Using gene presence/absence variation (PAV)-based genome-wide association analysis (GWAS), 13 gene PAVs associated with fruit length, fruit shape, and fruit width were identified, four of which were located in pan-genome additional contigs.

Jujube metabolome selection determined the edible properties acquired during domestication

Plants supply both food and medicinal compounds, which are ascribed to diverse metabolites produced by plants. However, studies on domestication-driven changes in the metabolome and genetic basis of bioactive molecules in perennial fruit trees are generally lacking. Here, we conducted multidimensional analyses revealing a singular domestication event involving the genomic and metabolomic selection of jujube trees (Ziziphus jujuba Mill.). The genomic selection for domesticated genes was highly enriched in metabolic pathways, including carbohydrates and specialized metabolism. Domesticated metabolome profiling indicated that 187 metabolites exhibited significant divergence as a result of directional selection. Malic acid was directly selected during domestication, and the simultaneous selection of specialized metabolites, including triterpenes, consequently lead to edible properties. Cyclopeptide alkaloids (CPAs) were specifically targeted for the divergence between dry and fresh cultivars. We identified 1080 significantly associated loci for 986 metabolites. Among them, 15 triterpenes were directly selected at six major loci, allowing the identification of a homologous cluster containing seven 2,3-oxidosqualene cyclases (OSCs). An OSC gene was found to contribute to the reduction in the content of triterpenes during domestication. The complete pathway for synthesizing ursolic acid was dissected by integration of the metabolome and transcriptome. Additionally, an N-methyltransferase involved in the biosynthesis of CPA and responsible for inter-cultivar content variation was identified. The present study promotes our understanding of the selection process of the global metabolome subsequent to fruit tree domestication and facilitates the genetic manipulation of specialized metabolites to enhance their edible traits.

Chromosome-scale assembly and population diversity analyses provide insights into the evolution of Sapindus mukorossi

Sapindus mukorossi is an environmentally friendly plant and renewable energy source whose fruit has been widely used for biomedicine, biodiesel, and biological chemicals due to its richness in saponin and oil contents. Here, we report the first chromosome-scale genome assembly of S. mukorossi (covering ~391 Mb with a scaffold N50 of 24.66 Mb) and characterize its genetic architecture and evolution by resequencing 104 S. mukorossi accessions. Population genetic analyses showed that genetic diversity in the southwestern distribution area was relatively higher than that in the northeastern distribution area. Gene flow events indicated that southwest species may be the donor population for the distribution areas in China. Genome-wide selective sweep analysis showed that a large number of genes are involved in defense responses, growth and development, including SmRPS2, SmRPS4, SmRPS7, SmNAC2, SmNAC23, SmNAC102, SmWRKY6, SmWRKY26, and SmWRKY33. We also identified several candidate genes controlling six agronomic traits by genome-wide association studies, including SmPCBP2, SmbHLH1, SmCSLD1, SmPP2C, SmLRR-RKs, and SmAHP. Our study not only provides a rich genomic resource for further basic research on Sapindaceae woody trees but also identifies several economically significant genes for genomics-enabled improvements in molecular breeding.

Genetic and Molecular Mechanisms Conferring Heat Stress Tolerance in Tomato Plants

Climate change is a major threat to global food security. Changes in climate can directly impact food systems by reducing the production and genetic diversity of crops and their wild relatives, thereby restricting future options for breeding improved varieties and reducing the ability to adapt crops to future challenges. The global surface temperature is predicted to rise by an average of 0.3°C during the next decade, and the Paris Agreement (Paris Climate Accords) aims to limit global warming to below an average of 2°C, preferably to 1.5°C compared to pre-industrial levels. Even if the goal of the Paris Agreement can be met, the predicted rise in temperatures will increase the likelihood of extreme weather events, including heatwaves, making heat stress (HS) a major global abiotic stress factor for many crops. HS can have adverse effects on plant morphology, physiology, and biochemistry during all stages of vegetative and reproductive development. In fruiting vegetables, even moderate HS reduces fruit set and yields, and high temperatures may result in poor fruit quality. In this review, we emphasize the effects of abiotic stress, especially at high temperatures, on crop plants, such as tomatoes, touching upon key processes determining plant growth and yield. Specifically, we investigated the molecular mechanisms involved in HS tolerance and the challenges of developing heat-tolerant tomato varieties. Finally, we discuss a strategy for effectively improving the heat tolerance of vegetable crops.

Integrative Morphological, Physiological, Proteomics Analyses of Jujube Fruit Development Provide Insights Into Fruit Quality Domestication From Wild Jujube to Cultivated Jujube

Jujube (Ziziphus jujuba) was domesticated from wild jujube (Z. jujuba var. spinosa). Here, integrative physiological, metabolomic, and comparative proteomic analyses were performed to investigate the fruit expansion and fruit taste components in a jujube cultivar 'Junzao' and a wild jujube 'Qingjiansuanzao' with contrasting fruit size and taste. We revealed that the duration of cell division and expansion largely determined the final fruit size, while the intercellular space in the mesocarp dictated the ratio of mesocarp volume in mature fruits. The high levels of endogenous gibbereline3 (GA) and zeatin in the growing fruit of 'Junzao' were associated with their increased fruit expansion. Compared with 'Junzao,' wild jujube accumulated lower sugars and higher organic acids. Furthermore, several protein co-expression modules and important member proteins correlated with fruit expansion, sugar synthesis, and ascorbic acid metabolism were identified. Among them, GA20OX involved in GA biosynthesis was identified as a key protein regulating fruit expansion, whereas sucrose-6-phosphate synthase (SPS) and neutral invertase (NINV) were considered as key enzymes promoting sugar accumulation and as major factors regulating the ratio of sucrose to hexose in jujube fruits, respectively. Moreover, the increase of Nicotinamide adenine dinucleotide-Malate dehydrogenase (NAD-MDH) activity and protein abundance were associated with the malic acid accumulation, and the high accumulation of ascorbic acid in wild jujube was correlated with the elevated abundance of GalDH, ZjAPXs, and MDHAR1, which are involved in the ascorbic acid biosynthesis and recycling pathways. Overall, these results deepened the understanding of mechanisms regulating fruit expansion and sugar/acids metabolisms in jujube fruit.

Jujube witches' broom phytoplasma effectors SJP1 and SJP2 induce lateral bud outgrowth by repressing the ZjBRC1-controlled auxin efflux channel

Comprehensively controlling phytoplasma-associated jujube witches' broom (JWB) disease is extremely challenging for the jujube industry. Although the pathogenesis of phytoplasma disease has been highlighted in many plant species, the release of lateral buds from dormancy under JWB phytoplasma infection has not been characterized in woody perennial jujube. Here, two 16SrV-B group phytoplasma effectors, SJP1 and SJP2, were experimentally determined to induce witches' broom with increased lateral branches. In vivo interaction and subcellular localization analyses showed that both SJP1 and SJP2 were translocated from the cytoplasm to the nucleus to target the CYC/TB1-TCP transcription factor ZjBRC1. The N- and C-terminal coiled-coil domains of SJP1 and SJP2 were required for the TCP-binding ability. ZjBRC1 bound directly to the auxin efflux carrier ZjPIN1c/3 promoters and down-regulated their expression to promote the accumulation of endogenous auxin indole-3-acetic acid in jujube calli. Furthermore, JWB phytoplasma infection suppressed ZjBRC1 accumulation and induced ZjPIN1c/3 expression to stimulate lateral bud outgrowth. Therefore, SJP1 and SJP2 stimulate lateral bud outgrowth, at least partly, by repressing the ZjBRC1-controlled auxin efflux channel in jujube, representing a potential strategy for comprehensive phytoplasma-associated disease control and a resource for gene editing breeding to create new cultivars with varying degrees of shoot branching.

Resequencing and transcriptomic analysis reveal differences in nitrite reductase in jujube fruit (Ziziphus jujuba Mill.)

BACKGROUND

Jujube is a typical fruit tree species from China. 'Muzao', a cracking-susceptible cultivar, and 'Linhuang No. 1', a cracking-resistant cultivar, were selected in a previous study as contrasting research materials. Whole-genome resequencing and transcriptomic analysis of 'Linhuang No. 1' and 'Muzao' allowed the identification of differentially expressed genes with different gene structures between the two cultivars and could be helpful in explaining the differences and similarities between the two cultivars.

RESULTS

Resequencing identified 664,129 polymorphic variable sites between 'Linhuang No. 1' and 'Muzao'. To determine the genetic relationship among 'Linhuang No. 1', 'Muzao' and the jujube genome reference cultivar 'Dongzao', the characteristic polymorphic variable sites were analysed by principal component analysis. The genetic relationship between 'Linhuang No. 1' and 'Muzao' was closer than that of either variety and 'Dongzao'. Nineteen differentially expressed genes were identified by combining transcriptomic analysis with resequencing analysis. LOC107427052 (encoding a nitrite reductase) was identified by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis for further study. The identified insertion was not in the domain region of the LOC107427052 gene coding sequence (CDS) region and was verified by the finding that the insertion did not affect translation of the protein. The LOC107427052 gene expression levels, nitrite reductase activities and nitrite contents of 'Muzao' were significantly higher than the corresponding values of 'Linhuang No. 1' at the young fruit stage. There was no significant difference in the quantity of the product of nitrite reductase, namely, ammonia, between the two cultivars.

CONCLUSIONS

The present study was the first to explore the differences between different jujube cultivars ('Linhuang No. 1' and 'Muzao') by combining genome resequencing and transcriptomics. LOC107427052 (encoding a nitrite reductase) was characterized by KEGG enrichment analysis. The insertion in the CDS region of the LOC107427052 gene provides a new direction for the study of nitrogen metabolism in jujube. Our study has laid a foundation for the comparative analysis of nitrite metabolism between the jujube cultivars 'Linhuang No. 1' and 'Muzao'.