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Background The widely cultivated pepper ( Capsicum spp.) is one of the most diverse vegetables; however, little research has focused on characterizing the genetic diversity and relatedness of commercial varieties grown in China. In this study, a panel of 92 perfect single-nucleotide polymorphisms (SNPs) was identified using re-sequencing data from 35 different C. annuum lines. Based on this panel, a Target SNP-seq genotyping method was designed, which combined multiplex amplification of perfect SNPs with Illumina sequencing, to detect polymorphisms across 271 commercial pepper varieties. Results The perfect SNPs panel had a high discriminating capacity due to the average value of polymorphism information content, observed heterozygosity, expected heterozygosity, and minor allele frequency, which were 0.31, 0.28, 0.4, and 0.31, respectively. Notably, the studied pepper varieties were morphologically categorized based on fruit shape as blocky-, long horn-, short horn-, and linear-fruited. The long horn-fruited population exhibited the most genetic diversity followed by the short horn-, linear-, and blocky-fruited populations. A set of 35 core SNPs were then used as kompetitive allele-specific PCR (KASPar) markers, another robust genotyping technique for variety identification. Analysis of genetic relatedness using principal component analysis and phylogenetic tree construction indicated that the four fruit shape populations clustered separately with limited overlaps. Based on STRUCTURE clustering, it was possible to divide the varieties into five subpopulations, which correlated with fruit shape. Further, the subpopulations were statistically different according to a randomization test and F st statistics. Nine loci, located on chromosomes 1, 2, 3, 4, 6, and 12, were identified to be significantly associated with the fruit shape index ( p  < 0.0001). Conclusions Target SNP-seq developed in this study appears as an efficient power tool to detect the genetic diversity, population relatedness and molecular breeding in pepper. Moreover, this study demonstrates that the genetic structure of Chinese pepper varieties is significantly influenced by breeding programs focused on fruit shape.

Jujube ( Ziziphus jujuba Mill.), belonging to the Rhamnaceae family, is gaining increasing prominence as a perennial fruit crop with significant economic and medicinal values. Here, we conduct de novo assembly of four reference-grade genomes, encompassing one wild and three cultivated jujube accessions. We present insights into the population structure, genetic diversity, and genomic variations within a diverse collection of 1059 jujube accessions. Analyzes of the jujube pan - genome, based on our four assemblies and four previously released genomes, reveal extensive genomic variations within domestication-associated regions, potentially leading to the discovery of a candidate gene that regulates flowering and fruit ripening. By leveraging the pan-genome and a large-scale resequencing population, we identify two candidate genes involved in domestication traits, including the seed-setting rate, the bearing-shoot length and the leaf size in jujube. These genomic resources will accelerate evolutionary and functional genomics studies of jujube. Jujube is a perennial fruit crop with significant economic and medicinal values. Here, the author report genome assemblies of four jujube accessions, construct pan-genome together with four previously published genomes, and generate resequencing data to reveal genetic basis of domestication traits.

Background Prunus sibirica L. is one of the most pivotal eco-economic tree species in China’s arid and semi-arid areas. The phenomenon of physiological fruit drop in P. sibirica L. is severe, and understanding fruit growth patterns and drop characteristics is crucial for high-quality cultivar production. However, there are few reports on P. sibirica fruit development and physiological fruit drop. Results In this study, we investigated the characteristics of fruit development, vegetative bud outgrowth, and fruit abscission, and explored the dynamic features of sugar metabolism in different tissues during physiological fruit drop and its relationship with fruit drop. The results showed that the fruit and vegetative bud outgrowth of the “Shanxing No. 1” variety exhibited an S-shaped growth pattern with three physiological stages. The flower and fruit drop of “Shanxing No. 1” lasted for about 70 days with an 89.73% total drop rate and three abscission peaks, which could be divided into the flower abscission stage mainly caused by pistil abortion, rapid fruitlet abscission stage, mainly caused by carbohydrate competition between the fruit and vegetative bud outgrowth; and slow fruit abscission stage mostly related to seed abortion. The perspective of the vegetative buds removal experiment further proved the competition between fruitlet and vegetative bud outgrowth simultaneously. During physiological fruit drop, the sugar contents and activities of sucrose metabolism enzymes in different tissues showed regular changes, corresponding to the dynamic law of fruit drop. Sucrose metabolism was mainly dominated by decomposition, and the enzymes involved in sucrose decomposition played a significant role. Acid invertase and sucrose synthase (decomposition direction) were the key enzymes regulating fruit abscission in P. sibirica L. Conclusions These results laid a foundation for revealing the physiological characteristics and physiological mechanism of P. sibirica L. fruit development, and also provided a theoretical basis for high-quality and high-yield cultivation of P. sibirica L.

Due to limited local knowledge regarding the optimal harvest time for this non-native variety, a two-year study (2021–2022) was conducted using a randomized complete block design with four blocks. This study aimed to determine the ideal harvest time based on quantitative and qualitative fruit characteristics in saveh, which has a semi-arid climate. Twelve similarly sized trees were selected for each orchard, and fruits were harvested at three-time intervals: 155 days after flowering (DAF) (September 27), 170 DAF (October 12), and 185 DAF (October 27). Ten fruits from four sides of the tree canopy were collected and analyzed for physical and biochemical properties. The results showed that harvest time significantly affected fruit weight, aril weight, and juice percentage positively, while it negatively impacted rind percentage. The first harvest date yielded the lowest quantitative and qualitative traits, with incomplete skin and aril coloration. By the third harvest, pomegranate fruits exhibited the highest total soluble solids (17.76 °Brix), pH (3.41), and anthocyanin content (32.56 mg/L), along with the lowest total phenols (17.28 mg GAE/L), antioxidant capacity (79.78%), and titratable acidity (1.11%), resulting in the highest flavor or ripening index (16.31). In addition, cracking rates increased substantially, reaching 30.25% by the third harvest, compared to negligible levels of 20.72% by the second harvest. Juice percentage and aril weight improved significantly with delayed harvest, peaking on October 27. These findings suggest that October 12–27 is the optimal harvest window for superior fruit quality while considering the risk of fruit cracking. This study provides practical insights into harvest timing for maximizing the marketability and nutritional value of ‘Wonderful’ pomegranates in semi-arid climates.

Variation in cucumber (Cucumis sativus L.) fruit size and shape is highly quantitative, implicating interplay of multiple components. Recent studies have identified numerous fruit size and shape quantitative trait loci (QTL); however, underlying factors remain to be determined. We examined ovary and fruit development of two sequenced cucumber genotypes with extreme differences in fruit size and shape, Chinese Long ‘9930’ (CL9930), and pickling type ‘Gy14’. Differences were observed in several independent factors that can influence size and shape: ovule number, rate and period of cell division in longitudinal and cross section in ovaries and fruit, timing and rate of fruit expansion in length and diameter, and cell shape. Level and timing of expression of select fruit growth stage marker genes and candidate fruit size gene homologs associated with cucumber fruit size and shape QTL were examined from 5-day pre-anthesis to 20-day post-pollination. Our results indicate that variation in fruit size and shape results from differences in cell number and shape in longitudinal and cross section, driven in turn by differences in orientation, timing, and duration of cell division and expansion, both pre- and post-anthesis, and suggest candidate genes contributing to determination of cucumber fruit size and shape.

Background This study assessed the effects of auxin analog, para-chlorophenoxyacetic acid (pCPA), on fruit set and development in Micro-Tom tomato (TOMJPF00001) via phenotypic, biochemical, metabolomic, and transcriptomic analyses. Results pCPA treatment significantly ( p  < 0.05) reduced floral abscission, increased fruit set and yield, while impacting fruit morphology, ripening, sugar content, organoleptic properties, and phytohormone profiles. Metabolomic profiling revealed 836 differentially accumulated metabolites (DAMs). Among these, several phenylpropanoid-related DAMs (isoferulic acid, 6-methylcoumarin, naringenin, hesperetin 5-O-glucoside, quercetin, and dihydrokawain) were upregulated in immature green, mature green, and breaker fruits, but downregulated in red ripe fruits following pCPA application. Transcriptome analysis yielded 35,501 differentially expressed genes (DEGs), including 740 novel genes, with growth stage-specific expression patterns observed in phenylpropanoid, carotenoid, and flavonoid biosynthetic pathways. Particularly, pCPA treatment downregulated chitinase ( Soly04g072000.3 ) and acidic endochitinase ( Soly05g050130.3 ), potentially enhancing fruit firmness through cell wall stabilization. Reduced accumulation of alpha-L-arabinofuranosidase ( Soly10g077080.2 ) and a UDP-glucose 6-dehydrogenase family protein ( Soly06g069550.1 ) further supported this observation. In red ripe fruits, pCPA decreased organic acids (malic and citric acids), sugars (fructose, glucose and sucrose), soluble solids (TSS/brix), amino acids (aspartic acid, phenylalanine, valine) and nucleotide (uracil, cytosine) levels, correlating with altered sensory attributes. pCPA also influenced lipid biosynthesis in mature green fruits and consistently downregulated sucrose across all developmental stages, suggesting impacts on carbohydrate metabolism. Furthermore, pCPA treatment altered the expression of genes related to carbohydrate metabolism, including beta-amylase ( Soly08g007130.3 ), ADP-glucose pyrophosphorylase ( Soly07g056140.3 ), and beta-glucosidase ( Soly11g071640.2 ). pCPA-induced alterations in fruit development were correspondingly susceptible to alternative splicing patterns. Conclusions These findings provide insights into the molecular mechanisms underlying pCPA-induced changes in tomato fruit set and development, offering valuable information for optimizing horticultural breeding practices and strategies.

Immature citruses are an important resource for the pharmaceutical industry due to their high levels of metabolites with health benefits. In this study, we used untargeted liquid chromatography–mass spectrometry (LC-MS) metabolomics to investigate the changes associated with fruit size in immature citrus fruits in the first weeks of growth. Three orange cultivars (Citrus sinensis ‘Navel’, Citrus sinensis ‘Valencia’, and Citrus sinensis ‘Valencia Late’) and a mandarin (Citrus reticulata Blanco ‘Fremont’) were separated into eight fruit sizes, extracted, and analyzed. Statistical analyses revealed a distinct separation between the mandarin and the oranges based on 56 metabolites, with an additional separation between the ‘Navel’ orange and the ‘Valencia’ and ‘Valencia Late’ oranges based on 21 metabolites. Then, metabolites that evolved significantly with fruit size growth were identified, including 40 up-regulated and 31 down-regulated metabolites. This study provides new insights into the metabolite modifications of immature Citrus sinensis and Citrus reticulata in the first weeks of growth and emphasizes the significance of including early sampled fruits in citrus maturation studies.

The health-promoting effects of phenolic compounds depend on their bioaccessibility from the food matrix and their consequent bioavailability. We carried out a randomized crossover pilot clinical trial to evaluate the matrix effect (raw flesh and juice) of ‘Ataulfo’ mango on the bioavailability of its phenolic compounds. Twelve healthy male subjects consumed a dose of mango flesh or juice. Blood was collected for six hours after consumption, and urine for 24 h. Plasma and urine phenolics were analyzed by electrochemical detection coupled to high performance liquid chromatography (HPLC-ECD). Five compounds were identified and quantified in plasma. Six phenolic compounds, plus a microbial metabolite (pyrogallol) were quantified in urine, suggesting colonic metabolism. The maximum plasma concentration (Cmax) occurred 2–4 h after consumption; excretion rates were maximum at 8–24 h. Mango flesh contributed to greater protocatechuic acid absorption (49%), mango juice contributed to higher chlorogenic acid absorption (62%). Our data suggests that the bioavailability and antioxidant capacity of mango phenolics is preserved, and may be increased when the flesh is processed into juice.

Background Early stages of fruit development from initial set through exponential growth are critical determinants of size and yield, however, there has been little detailed analysis of this phase of development. In this study we combined morphological analysis with 454 pyrosequencing to study transcript level changes occurring in young cucumber fruit at five ages from anthesis through the end of exponential growth. Results The fruit samples produced 1.13 million ESTs which were assembled into 27,859 contigs with a mean length of 834 base pairs and a mean of 67 reads per contig. All contigs were mapped to the cucumber genome. Principal component analysis separated the fruit ages into three groups corresponding with cell division/pre-exponential growth (0 and 4 days post pollination (dpp)), peak exponential expansion (8dpp), and late/post-exponential expansion stages of growth (12 and 16 dpp). Transcripts predominantly expressed at 0 and 4 dpp included homologs of histones, cyclins, and plastid and photosynthesis related genes. The group of genes with peak transcript levels at 8dpp included cytoskeleton, cell wall, lipid metabolism and phloem related proteins. This group was also dominated by genes with unknown function or without known homologs outside of cucurbits. A second shift in transcript profile was observed at 12-16dpp, which was characterized by abiotic and biotic stress related genes and significant enrichment for transcription factor gene homologs, including many associated with stress response and development. Conclusions The transcriptome data coupled with morphological analyses provide an informative picture of early fruit development. Progressive waves of transcript abundance were associated with cell division, development of photosynthetic capacity, cell expansion and fruit growth, phloem activity, protection of the fruit surface, and finally transition away from fruit growth toward a stage of enhanced stress responses. These results suggest that the interval between expansive growth and ripening includes further developmental differentiation with an emphasis on defense. The increased transcript levels of cucurbit-specific genes during the exponential growth stage may indicate unique factors contributing to rapid growth in cucurbits.

Background Expansins (EXPs) facilitate non-enzymatic cell wall loosening during several phases of plant growth and development including fruit growth, internode expansion, pollen tube growth, leaf and root development, and during abiotic stress responses. In this study, the spatial and temporal expression patterns of C. annuum α- EXPANSIN ( CaEXPA ) genes were characterized. Additionally, fruit-specific CaEXPA expression was correlated with the rate of cell expansion during bell pepper fruit development. Results Spatial expression patterns revealed that CaEXPA13 was up-regulated in vegetative tissues and flowers, with the most abundant expression in mature leaves. Expression of CaEXPA4 was associated with stems and roots. CaEXPA3 was expressed abundantly in flower at anthesis suggesting a role for CaEXPA3 in flower development. Temporal expression analysis revealed that 9 out of the 21 genes were highly expressed during fruit development. Of these, expression of six genes, CaEXPA5 , CaEXPA7 , CaEXPA12 , CaEXPA14 CaEXPA17 and CaEXPA19 were abundant 7 to 21 days after anthesis (DAA), whereas CaEXPA6 was strongly expressed between 14 and 28 DAA. Further, this study revealed that fruit growth and cell expansion occur throughout bell pepper development until ripening, with highest rates of fruit growth and cell expansion occurring between 7 and 14 DAA. The expression of CaEXPA14 and CaEXPA19 positively correlated with the rate of cell expansion, suggesting their role in post-mitotic cell expansion-mediated growth of the bell pepper fruit. In this study, a ripening specific EXP transcript, CaEXPA9 was identified, suggesting its role in cell wall disassembly during ripening. Conclusions This is the first genome-wide study of CaEXPA expression during fruit growth and development. Identification of fruit-specific EXPAs suggest their importance in facilitating cell expansion during growth and cell wall loosening during ripening in bell pepper. These EXPA genes could be important targets for future manipulation of fruit size and ripening characteristics.