Horticulture Research

Climate change poses an increasing threat to the cultivation of deciduous fruit trees, placing greater demands on modern pear breeding. Using pear germplasm adapted to diverse environments, we assembled 11 chromosome-level genomes. In combination with 13 publicly accessible pear genomes, we analyzed presence-absence variations (PAVs) and constructed a graph-based pangenome for pear. By performing a PAV-eQTL analysis of the fruit of 123 pear accessions, we identified PAVs significantly associated with expression levels of genes that may be involved in regulating agronomic traits. Population analysis of 268 pear accessions revealed two stop-gained variants in DAM1 of independent origin, which may function in advancing the blooming date and reducing the chilling requirement. We detected complex PAVs at the NOR1 locus, including two copy-number variations and one deletion. These PAVs contributed to the rapid diversification of the NOR1 locus and the fruit development period through regulating ARF5 and other ripening-related genes. We revealed the selection history of the NOR1 locus and developed novel pear individuals that accumulated alleles for low chilling requirement, early blooming date, and short fruit development period. The results provide valuable resources for pear genomics research and offer a guideline for breeding modern pears with climate resilience.

Sweet orange (Citrus sinensis) exhibits limited genetic diversity and high susceptibility to Huanglongbing (HLB). New HLB-tolerant orange-like hybrids are promising alternatives. However, the genetic control of key flavor compounds in oranges remains unknown. Evaluating 179 juice samples, including oranges, mandarins, Poncirus trifoliata and hybrids, distinct volatile compositions were found. A random forest model predicted untrained samples with 78% accuracy and identified 26 compounds crucial for orange flavor. Notably, seven esters--methyl hexanoate, ethyl hexanoate, ethyl 3-hydroxyhexanoate, ethyl octanoate, methyl butanoate, ethyl butanoate, and ethyl 2-methylbutanoate--differentiated orange from mandarin. Cluster analysis showed six esters with shared genetic control. Differential gene expression analysis identified CsAAT1, an alcohol acyltransferase responsible for ester production in orange. Its activity was validated through overexpression assays. A SNP-based DNA marker in the CDS region accurately predicted phenotypes. This study enhances our understanding of orange flavor compounds, their biosynthetic pathways, and expands breeding options for orange-like cultivars.

Tomato fruit ripening is triggered by the demethylation of key genes, which alters their transcriptional levels thereby initiating and propagating a cascade of physiological events. What is unknown, is how these processes are altered when fruit are ripened using postharvest practices to extend shelf-life, as these practices often reduce fruit quality. To address this, postharvest handling-induced changes in the fruit DNA methylome and transcriptome, and how they correlated with ripening speed, and ripening indicators such as ethylene, ABA, and carotenoids, were assessed. This study comprehensively connected changes in physiological events with dynamic molecular changes. Ripening fruit that reached Turning (T) after storage under dark at 20{degrees}C, 12.5{degrees}C, or 5{degrees}C chilling (followed by 20{degrees}C rewarming), were compared to fresh-harvest fruit FHT. Fruit stored at 12.5{degrees}C, had the biggest epigenetic marks and alterations in gene expression, exceeding changes induced by postharvest chilling. Fruit physiological and chronological age were uncoupled at 12.5{degrees}C, as the time-to-ripening was longest. Fruit ripening at 12.5{degrees}C was not climacteric; there was no respiratory or ethylene burst, rather, fruit were high in ABA. Clear differentiation between postharvest-ripened and FHT was evident in the methylome and transcriptome. Higher expression of photosynthetic genes and chlorophyll levels in FHT fruit, pointing to light as influencing the molecular changes in fruit ripening. Finally, correlative analyses of the -omics data putatively identified genes regulated by DNA methylation. Collectively these data improve our interpretation of how tomato fruit ripening patterns are altered by postharvest practices, and long-term are expected to help improve fruit quality.

Crop pests have profoundly deleterious effects on crop yield and food security. However, conventional pest control depends heavily on the utilization of insecticides, which develops strong pesticide resistance and concerns of food safety. Crop and their wild relatives display diverse levels of pest resistance, indicating the feasibility for breeding of pest-resistant crop varieties. In this study, we integrate deep learning (DL)/machine learning (ML) algorithms, plant phenomics and whole genome sequencing (WGS) data to conduct genomic selection (GS) of pest-resistance in grapevine. We employ deep convolutional neural networks (DCNN) to accurately calculate the severity of damage by pests on grape leaves, which achieves a classification accuracy of 95.3% (Visual Geometry Group 16, VGG16, for binary trait) and a correlation coefficient of 0.94 in regression analysis (DCNN with Pest Damage Score, DCNN-PDS, for continuous trait). We apply DL models to predict and integrate phenotype (both binary and continuous) along with WGS data from 231 grape accessions, conducting Genome-Wide Association Studies (GWAS). This analysis detects a total of 69 QTLs, encompassing 139 candidate genes involved in pathways associated with pest resistance, including jasmonic acid (JA), salicylic acid (SA), ethylene, and other related pathways. Furthermore, through the combination with transcriptome data, we identify specific pest-resistant genes, such as ACA12 and CRK3, which play distinct roles in resisting herbivore attacks. Machine learning-based GS demonstrates a high accuracy (95.7%) and a strong correlation (0.90) in predicting the leaf area damaged by pests as binary and continuous traits in grapevine, respectively. In general, our study highlights the power of DL/ML in plant phenomics and GS, facilitating genomic breeding of pest-resistant grapevine.

Apple scab, caused by Venturia inaequalis, remains one of the most damaging diseases in apple orchards, driving intensive pesticide use worldwide. Reducing this dependence requires the deployment of durable resistance, ideally through the combination of major resistance genes (R genes) with quantitative trait loci (QTL) that confer partial and potentially complementary protection. Yet, few apple scab QTLs have been functionally validated, and their underlying mechanisms remain largely unresolved. Here, we refined and functionally described, with transcriptomic data, five resistance QTLs in a biparental population of 1,970 individuals derived from the cross TN 10-8 x Fiesta. Using 43 newly developed KASP markers, QTL locations were substantially precised through high-resolution genotyping and phenotyping with two V. inaequalis isolates exhibiting contrasting virulence. Four QTL (qT1, qF11, qF17, qT13) were validated, while qF3 was not confirmed. Transcriptomic data comparison revealed the expression of candidate genes within the narrowed intervals, including receptor-like proteins in qT1, and RNAi- and signaling-related genes in qF11 and qF17, suggesting a diversified and complementary defense network. These findings refine the genetic architecture of apple scab resistance and suppose the existence of shared molecular pathways between major R gene, such as the well-described Rvi6 gene, and quantitative resistance, with for instance the QTL qT1. The identified loci and markers provide robust tools for marker-assisted and genomic breeding aimed at developing apple cultivars with complementary and potentially durable resistance pathways.

Strawberry aroma is a key component of fruit quality, influencing consumer preferences and playing important ecological roles, including plant defense. However, the genetic basis of volatile organic compound (VOC) biosynthesis remains only partially understood, particularly in the wild woodland strawberry Fragaria vesca, which has enormous potential to uncover genetic diversity within the genus for improving the commercial strawberries. Here, we performed Genome-Wide Association Studies (GWAS) across a diverse European collection of F. vesca accessions. We identified multiple novel candidate genes involved in the biosynthesis of diverse volatile esters, lactones, terpenoids, and methyl ketones. Among them, we characterized FvJMT2, a SABATH family methyltransferase which we found associated with natural variation in benzenoid esters content. Transient expression in Nicotiana benthamiana and strawberry fruit confirmed its role in methyl benzoate biosynthesis, while enzymatic assays demonstrated that FvJMT2 encodes a promiscuous enzyme capable of methylating not only benzoic acid, but also cinnamic, salicylic, and jasmonic acids. Behavioral assays revealed that methyl benzoate at physiologically relevant concentrations significantly reduced the attraction of Drosophila suzukii flies, supporting a dual role of this VOC in both flavor and pest deterrence. Finally, natural variation analyses in wild Fragaria species and F. x ananassa cultivars showed that benzenoid esters have been largely lost in modern cultivars but retained in ancient and wild accessions. Altogether, this study provides novel insights into the genetics and ecological relevance of strawberry volatiles and identifies candidate loci and alleles for future studies.

CRISPR genome editing has shown tremendous potential in genetic improvement of citrus. So far, citrus genome editing has been conducted using juvenile tissues resulting in genome-edited citrus plants that require multiple years before they can produce flowers and fruit. Here we tested whether citrus genome editing via mature tissue transformation can overcome such a hurdle. CsLOB1 is a susceptibility gene for citrus canker caused by Xanthomonas citri subsp. citri (Xcc). The transcription activator-like effector PthA4 of Xcc activates CsLOB1 by binding to the effector-binding element in its promoter (EBEpthA4-CsLOBP). In Valencia sweet orange, two CsLOB1 promoter alleles are present: TI CsLOBP, and TII CsLOBP. We specifically utilized a CRISPR/Cas9 construct (GFP-p1380N-Cas9/sgRNA:CsLOBP2) targeting EBEpthA4 in TI CsLOBP but not TII CsLOBP to test genome editing efficacy and off-target mutations. GFP-p1380N-Cas9/sgRNA:CsLOBP2 function was first validated using Xcc-facilitated agroinfiltration in Valencia leaves. The construct was subsequently introduced into Valencia mature internodal stem segments via Agrobacterium-mediated transformation, generating three independent transgenic lines (#V2, #V3 and #V5). Targeted mutations in EBEpthA4-TI CsLOBP were detected in all three lines with mutation frequencies of 100%, 21.43% and 41.94% in #V2, #V3 and #V5, respectively, while no mutations were detected in TII CsLOBP. Infection with Xcc{Delta}pthA4:dCsLOB1.3, carrying a designer TALE that specifically activates TI CsLOBP, resulted in reduced canker symptoms in #V2. Importantly, all three EBEpthA4-TI CsLOBP edited lines flowered within 15 months. In sum, these results demonstrate that CRISPR/Cas9-mediated genome modification through mature citrus transformation can achieve high genome editing efficacy and overcome the juvenility.

Softening is a hallmark of ripening in fleshy fruits, and has both desirable and undesirable implications for texture and postharvest stability. Accordingly, the timing and extent of ripening and associated textural changes are key targets for improving fruit quality through breeding. Previously, we identified a large effect locus associated with harvest date and firmness in apple (Malus domestica) using genome-wide association studies (GWAS). Here, we present additional evidence that polymorphisms in or around a transcription factor gene, NAC18.1, may cause variation in these traits. First, we confirmed our previous findings with new phenotype and genotype data from [~]800 apple accessions. In this population, we compared a genetic marker within NAC18.1 to markers targeting three other firmness-related genes currently used by breeders (ACS1, ACO1, and PG1), and found that the NAC18.1 marker was the strongest predictor of both firmness at harvest and firmness after three months of cold storage. By sequencing NAC18.1 across 18 accessions, we revealed two predominant haplotypes containing the single nucleotide polymorphism (SNP) previously identified using GWAS, as well as dozens of additional SNPs and indels in both the coding and promoter sequences. NAC18.1 encodes a protein with high similarity to the NON-RIPENING (NOR) transcription factor, a regulator of ripening in tomato (Solanum lycopersicum). To test whether these genes are functionally orthologous, we introduced both NAC18.1 transgene haplotypes into the tomato nor mutant and showed that both haplotypes complement the nor ripening deficiency. Taken together, these results indicate that polymorphisms in NAC18.1 may underlie substantial variation in apple firmness through modulation of a conserved ripening program.

Fruit shape is a key horticultural trait shaped by conserved genetic pathways and hormonal interactions, yet the mechanisms underlying shape diversity in fleshy fruits remain incompletely understood. Studies in model species such as Arabidopsis thaliana, tomato, and rice have established Ovate Family Proteins (OFPs) as central regulators of organ morphology through their interactions with brassinosteroid (BR) and gibberellin (GA) pathways and cytoskeleton dynamics. Here, we combine phylogenetic, transcriptomic, and co-expression network analysis to investigate fruit shape regulation in peach and apple, two major Rosaceae crops. We show that flat and oblong phenotypes are associated with distinct OFP expression patterns and with coordinated changes in hormone-related modules, revealing conserved OFP-hormone-cytoskeleton regulatory circuits. Flat shapes were linked to the activation of flat-associated OFPs in the absence of brassinosteroid signalling, whereas oblong shapes were associated with the activation of elongation-related OFPs under brassinosteroid-responsive conditions. Our findings extend current models of fruit morphology by providing species-specific mechanistic insight into OFP-mediated regulation in Rosaceae, offering a refined framework for breeding fruit shape.

Wampee (Clausena lansium) is an economically significant subtropical fruit tree widely cultivated in Southern China. High-quality genomic resources are unavailable, but they are essential for functional genomics and germplasm enhancement of wampee. Here, we provide a chromosome-level genome sequence for the wampee cultivar JinFeng and a population genomic analysis of 266 accessions. The 297.1 Mb wampee genome, containing nine chromosomes with a scaffold N50 of 29.2 Mb and encoding 23,468 protein-coding genes, showed a significant improvement over the previous version. We dissected the wampee population structure and genetic differentiation in China using population genomic analysis, which detected 110 and 671 genes under a selective sweep associated with sour and sweet wampee evolution in domesticated clones, respectively. Homozygous non-synonymous single nucleotide polymorphisms are likely associated with fruit flavor differentiation. A genome-wide association study identified 220 remarkable marker-trait associations for total acid content, harboring 289 genes encoding transcription factors, transporters, and enzymes involved in sugar and acid metabolism, which are potentially useful for sour and sweet taste development in wampee fruit. Furthermore, the ethylene response factor family gene ClERF061 and the SWEET family gene ClSWEET7 were identified. Linkage assessment between the relative expression levels of ClERF061 or ClSWEET7 and the total acid/total sugar contents implied their potential involvement in sugar-acid metabolism in wampee fruits. High-quality genome resources are valuable for expediting wampee research and genome-assisted breeding.

It is crucial to understand domestication to unravel the evolutionary processes that shape the divergence of populations. Differences in life-history traits have probably led to marked differences in the mode and speed of evolution between trees and annuals, particularly the extent of crop-wild gene flow during domestication. Apple is an iconic tree and major fruit crop grown worldwide. The contribution of wild apple species to the genetic makeup of the cultivated apple genome remains a topic of intense investigations. We used population genomics in combination with SNPs to investigate the contributions of the two known wild apple relatives, Malus sylvestris and Malus sieversii, and a supposed contributor, Malus baccata, to European and Chinese rootstock and dessert genomes, with a focus on the extent of wild-crop gene flow during apple domestication. We showed that the European dessert and rootstock apples form a specific gene pool, whereas the Chinese dessert and rootstock apples were a mixture of three wild gene pools. Coalescent-based inferences and gene flow estimates indicated that M. baccata is an additional contributor to the genome of both European and Chinese cultivated apples through wild-to-crop introgressions. We also confirmed previous results on the contribution of M. sylvestris to the cultivated apple genome, and provided insights into the origin of the apple rootstock. This study further demonstrates the role of gene flow during apple domestication, as seen in other woody perennials, and show that domestication of the apple tree involved several wild apple species.

Orphan genes and transcription factor genes (TFs) are pervasive across genomes, play pivotal roles as regulators in a myriad of biological processes. Despite their ubiquity, the evolutionary trajectories and functional divergence of these genes remain largely unexplored. Theaceae family, encompassing the economically and culturally significant tea plant, presents a unique opportunity to study these dynamics. Here, we decoded a nearly complete, chromosome-scale reference genome of Stewartia gemmata spanning 2.95 Gb. This study is enhanced by integrating the genome of S. gemmata, an early-diverging species within Theaceae, crucial for phylogenomic analyses and understanding the functional dynamics of orphan genes in this family. Our analysis confirmed the absence of a recent specific whole-genome duplication (WGD) event, with tandem duplications emerging as the predominant mechanism for gene duplication at ancestral nodes within Theaceae. By conducting an extensive comparative genomics analysis across 13 Theaceae and comparing these with a wide array of eukaryotic and prokaryotic proteins, we identified 37,618 orphan genes and 25,884 TFs in Theaceae. Interestingly, some orphan genes appear to have ancient origins in tea plant ancestors, suggesting relatively early origins with frequent gains and losses, conversely, many others seem more specific and recent. Notably, the orphan genes are characterized by shorter lengths, fewer exons and functional domains than TFs, implying relatively simpler functional roles. These orphan genes demonstrate diverse cellular localization and functions as predicted by GO/KEGG analysis, and are implicated in environmental response and flavor formation in tea plants. This study not only sheds light on the distinct evolutionary histories and functional divergences between orphan genes and TFs in Theaceae, but also contributes to our understanding of the genetic complexity and adaptability of this economically and culturally valuable plant family. Short summary: The nearly complete genome of an early-diverging species Stewartia gemmata and phylogenomic studies provide insights into new gene evolution in Theaceae.

Citrus is one of the most important tree crops worldwide and citrus production is threatened by Huanglongbing (HLB), a devasting citrus disease caused by Candidatus Liberibacter. HLB is a pathogen-triggered immune disease, in which the pathogen initiates systemic and chronic immune responses including the excessive production of reactive oxidative species, which subsequently lead to cell death of phloem tissues and HLB disease symptoms. Here, we identified putative genetic determinants of HLB pathogenicity by integrating citrus genomic resources to characterize the pan-genome of accessions that differ in their response to HLB. Genome-wide association mapping and analysis of allele-specific expression between susceptible, tolerant, and resistant accessions further refined candidates underlying the response to HLB. To enable these analyses we first developed a phased diploid assembly of Citrus sinensis Newhall genome and produced resequencing data for 91 citrus accessions that differ in their response to HLB. These data were combined with previous resequencing data from 356 sequenced accessions for genome-wide association mapping of the HLB response. Genes with HLB pathogenicity were associated with the host immune response, ROS production, and antioxidants. Overall, this study has provided a significant recourse of citrus genomic data and we have identified candidate genes to be further explored to understand the genetic determinants of HLB pathogenicity and to generate HLB resistant/tolerant citrus varieties.

The pear (Pyrus spp.) is a remarkable fruit, well known for its diverse flavors, textures, culinary versatility, and global horticultural importance. However, the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored. Here, we de novo assembled and annotated the genomes of the maternal (PsbM) and paternal (PsbF) lines of the hybrid Yuluxiang pear and constructed the first pear pangenome of 1.15Gb by combining these two genomes with five previously published pear genomes. Using the constructed pangenome, we identified 21,224 gene PAVs and 1,158,812 SNPs in the non-reference genome that were absent in the PsbM reference genome. Compared with SNP markers, we found that PAV-based analysis provides additional insights into the pear population structure. In addition, we also revealed that some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations. Moreover, our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the gene PsbMGH3.1 potentially enhances sepal shedding in Xuehuali which is vital for pear quality. This research helps further capture the genetic diversity of pear populations and provides valuable genomic resources for accelerating pear breeding.

Cultivated strawberry (Fragaria x ananassa) has a brief history of less than 300 years, beginning with the hybridization of octoploids F. chiloensis and F. virginiana. Here we explored the genomic signatures of this history using whole-genome sequences of 289 wild, heirloom and modern varieties. Four non-admixed wild octoploid populations were identified, with recurrent introgression among the sympatric populations. The proportion of F. virginiana ancestry increased by 20% in modern varieties over initial hybrids, and the proportion of F. chiloensis subsp. pacifica rose from 0 to 3.4%. Effective population size rapidly declined during early breeding. Meanwhile, divergent selection for distinct environments reshaped wild allelic origins in 21 out 28 chromosomes. Despite 20 breeding cycles since the initial hybridization, more than half of loci underlying yield and fruit size are still not under selection. These insights add clarity to the domestication and breeding history of what is now the most widely cultivated fruit in the world.

Tomato wild relatives are valuable genetic resources for trait discovery and understanding the genetic basis of fruit metabolism and quality. Yet, only a fraction of naturally occurring variation has been exploited. Here, we performed metabolite profiling of two large Backcross Inbred Line populations derived from crosses between the wild species S. pennellii accession LA5240 (Lost) and cultivated genotypes LEA (determinate) and TOP (indeterminate), including [~]1400 and [~]500 lines, respectively. High-resolution mapping identified enormous metabolic quantitative trait loci (mQTL), including a new locus on chromosome 12 associated with fruit sucrose accumulation that harbours INVERTASE INHIBITOR 3 (SlINVINH3) protein. Comparative analysis indicated that SlINVINH3 is highly expressed in wild S. pennellii 0716 fruit, whereas a six-amino acid deletion is present in its coding sequence compared with S.pennellii LA5240 and S. lycopersicum. We further demonstrated that in SlINVINH3-overexpressing tomato plants, only the S. pennellii LA5240 allele led to increased sucrose, accompanied by reduced fructose and glucose levels. Furthermore, the large population size enabled us to assess the epistatic interactions, with approximately 40% of interactions being more-than-additive and 60% less-than-additive. Our results demonstrate the power of permanent exotic populations to reveal hidden metabolic diversity and provide an approach for improving fruit quality through targeted breeding and metabolic engineering.

The domestication process in grapevine facilitated the fixation of desired traits. The vegetative propagation of grapevines through cuttings has allowed for easier preservation of these genotypes compared to sexual reproduction. Nonetheless, even with vegetative propagation, different phenotypes often emerge within the same vineyard due to potential genetic somatic mutations in the genome. These mutations, however, are not the sole factors influencing phenotype. Alongside somatic variations, epigenetic variation has been proposed as pivotal player in regulating phenotypic variability acquired during domestication. The emergence of these epialleles might have significantly influenced grapevine domestication over time. This study aims to investigate the impact of the domestication process on the methylation patterns in cultivated grapevines. Reduced-representation bisulphite sequencing was conducted on 18 cultivated and wild accessions. Results revealed that cultivated grapevines exhibited higher methylation levels than their wild counterparts. Differential Methylation Analysis between wild and cultivated grapevines identified a total of 9955 differentially methylated cytosines, of which 78% where hypermethylated in cultivated grapevines. Functional analysis shows that core methylated genes (those consistently methylated in wild and cultivated accessions) are associated to stress response and terpenoid/isoprenoid metabolic processes. While genes presenting differential methylation are associated with proteins targeting to the peroxisome, ethylene regulation, histone modifications, and defense response. Additionally, our findings reveal that environmentally induced DNA methylation patterns are, at least partially, guided by the region of origin of wild grapevine accessions. Collectively, our results shed light on the pivotal roles that epialleles might have played throughout the domestication history of grapevines.

Climate change increasingly threatens global Capsicum (pepper) production. Accelerating the deployment of climate-resilient cultivars requires effective use of genetic diversity conserved in genebanks. We implement a "turbocharging" strategy in Capsicum by integrating genome-wide association studies and genomic prediction in a core collection (n = 423), followed by genomic prediction across the global collection (n = 10,250) using the core as a training population. We generated genomic estimated breeding values (GEBVs) for 31 high-accuracy traits (r > 0.5) encompassing hyperspectral phenotypes (heat/control), agronomic performance (heat/control) and fruit quality. To enhance accessibility and decision-making, we developed a large language model (LLM) integrated application that enables flexible, preference-based selection of candidates. By narrowing the parental decision space, this framework streamlines screening of large germplasm collections while balancing climate resilience, quality attributes and market demands. Our approach provides a scalable decision-support system to accelerate climate-resilient Capsicum breeding and maximize global genetic resources.

Inhibitors of acetohydroxyacid synthase, the common enzyme of branched-chain amino acid biosynthesis, were applied to ripening apple (Malus xdomestica Borkh.), banana (Musa spp.), and flowering quince (Chaenomeles xsuperba) fruits to discern the contribution of newly synthesized precursors to branched-chain ester formation. After treatment, anteiso- and iso-branched-chain volatiles (i.e., those related to isoleucine, and valine and leucine, respectively) were observed to universally decrease in content. Fruits recovered production following exogenous feeding of branched-chain -ketoacids. Furthermore, apple and banana fruits were capable of metabolizing all three branched-chain -ketoacids to esters. Among free amino acids, only the branched-chain amino acids with correspondingly reduced branched-chain esters had a lesser concentration following treatment with inhibitor. Our results ultimately reject the hypothesis that anteiso- and iso-branched-chain esters are derived from preexisting amino acids and instead support the hypothesis that these esters are the product of de novo precursor biosynthesis. The novel use of these inhibitors also allowed for further investigation of branched-chain volatile biosynthesis, the citramalate synthase pathway, and the importance of precursor availability in fruits. Notably, in Valery banana fruit, ethyl acetate and butyl acetate were found to be dependent on acetohydroxyacid synthase activity for production whereas 1-methylbutyl acetate and 1-methylbutyl butanoate (sec-branched-chain esters) were not. Inhibitor usage on apples also allowed for a sensory study that found that humans can discern the absence of 2-methylbutyl and 2-methylbutanoate esters in apple fruit. Additionally, a population genetics analysis found that there is selection pressure against apples that lack these esters.

Starch is the primary carbohydrate reserve in potato (Solanum tuberosum L.) tubers and a critical determinant of their industrial value. The rate of starch degradation during postharvest storage directly influences key traits such as endodormancy (ED) duration and cold-induced sweetening (CIS), which affect sprouting behavior. In this study, we used CRISPR/Cas9 genome editing to knockout StAMY23, a gene encoding -amylase involved in starch breakdown. stamy23 plants exhibited higher yield and extended tuber ED postharvest, without significantly altering CIS or starch granule content. To further reduce CIS, we knockout StAMY23 in VACUOLAR INVERTASE knockout (stvinv) backgrounds, generating stamy23/stvinv double-knockouts plants. These lines showed significantly reduced CIS, prolonged ED, and elevated starch content, along with altered starch granule content. Collectively, our findings demonstrate that simultaneous downregulation of StAMY23 and StVINV can additively enhance desirable postharvest traits, providing a promising strategy for improving potato storage quality through precision genome editing.