Genetic Regulation of Fruit Shape in Horticultural Crops: A Review

Abstract

The shape of fruits is a critical trait affecting the commercial value and consumer acceptance of horticultural crops. Genetic regulation of fruit shape involves complex interactions among multiple genes and environmental factors. This review summarizes recent advances in understanding the genetic mechanisms controlling fruit shape in several key horticultural crops, including tomato, pepper, cucumber, peach, and grape. We present the identification and characterization of genes and quantitative trait loci (QTLs) that influence fruit shape, focusing on the roles of genes such as OVATE, SUN, FAS, LC, ENO, GLOBE, CsSUN, CsFUL1, CsCRC, PpCAD1, PpOFP1, and VvSUN. This review highlights the importance of hormonal pathways, particularly those involving synthesis and concentration of cytokinins and brassinosteroids in shaping fruit morphology, and explores how these genes interact and form regulatory networks that collectively determine the final fruit shape. This knowledge provides a foundation for developing strategies to improve fruit quality and yield through genetic modification and breeding programs.

1. Introduction

Fruit shape is a critical trait in horticultural crops, significantly impacting both the commercial value and consumer preference of fruits. In the context of tomatoes, chili peppers, cucumbers, peaches, and grapes, the shape of the fruit not only affects its aesthetic appeal but also influences handling, storage, and transportation efficiency [1,2,3,4,5]. For example, elongated or uniform-shaped fruits are easier to harvest mechanically (tomatoes, chili peppers, cucumbers, peaches)/process in industry (grapes) and pack for shipping, making them more suitable for large-scale commercial production. From a consumer perspective, fruit shape can be a deciding factor in purchasing decisions, as certain shapes are often associated with specific qualities or uses. For instance, round tomatoes are preferred for fresh consumption, while oblong ones are often used for processing [5]. Similarly, heart-shaped peaches are favored for their novelty and aesthetic appeal, while rounder shapes are preferred for their juiciness and ease of eating [6].

Moreover, fruit shape can impact the nutritional content and flavor profile of the fruit. For example, in cucumbers, the shape can affect the distribution of seeds and the concentration of flavor compounds, which in turn influences the overall eating experience [7]. In grapes, the compactness of the clusters and the shape of individual berries can affect sugar accumulation and juice yield [8].

Fruit shape is regulated by genetic molecular mechanisms and can also be influenced by environmental factors [7], especially temperature, light, and humidity conditions [9]. The genetic mechanisms underlying fruit shape are complex and represent a typical quantitative trait that is controlled by multiple genes [10,11,12,13]. Horticultural crops with fruits as their main edible organs include tomatoes, peppers, cucumbers, peaches, and grapes.

Understanding the genetic basis of fruit shape is crucial for developing cultivars that satisfy the diverse needs of growers and consumers. Advances in genetic research, including the identification of key genes like OVATE, SUN, and CsSUN [10,11,14], are enabling targeted breeding programs to modify fruit shape for enhanced marketability and functionality [15,16]. This genetic manipulation holds significant promise for improving the economic viability of horticultural crops and boosting consumer satisfaction. These developments not only deepen our understanding of plant development but also foster novel breeding strategies to optimize fruit shape, size, and quality. As research advances, we expect to discover new genes and regulatory pathways that will refine our capacity to engineer crops with desirable fruit characteristics.

In this review, to ensure a comprehensive review of the literature, we conducted a systematic search using databases such as PubMed, Scopus, and Web of Science. The search terms included combinations of “fruit morpholog” and the names of the specific crops studied (e.g., “tomato”, “pepper”, “cucumber”, “grape”, “peach”). This review focused on articles published between January 2000 and December 2023. We applied specific inclusion and exclusion criteria to select relevant studies. Inclusion criteria involved the following: (1) research on the genetic regulation of fruit shape and size in tomatoes, peppers, cucumbers, grapes, and peaches; and (2) peer-reviewed primary research articles or reviews. Exclusion criteria included studies that focused solely on non-fruit development aspects or articles without genetics relevant to fruit morphology.

2. Genetic Regulation of Fruit Shape in Horticultural Crops

2.1. Tomato

2.1.1. Overview of Fruit Shape Diversity

Tomatoes (Solanum lycopersicum) are a significant vegetable crop globally, valued not only for their culinary uses but also as a model organism for studying fleshy fruit development due to their relatively simple genetic background and well-characterized traits [17,18]. One of the most visually important traits in tomatoes is fruit shape, which can vary from round to pear-shaped, elongated, and even lobed forms. This diversity in fruit morphology is crucial for consumer preference and marketability, influencing aspects such as packaging and transportation. The genetic basis of these shapes is complex and involves multiple genes and regulatory pathways that work in concert to produce the diverse array of fruit forms observed in modern tomato cultivars.

2.1.2. QTL Mapping and GWAS Analysis

QTL mapping and genome-wide association studies (GWASs) have identified significant loci associated with fruit shape in tomatoes. fs8.1 is a major quantitative trait locus (QTL) controlling the elongated shape of tomato fruits. Grandillo et al. [18] mapped fs8.1 using a backcross population to a region on the short arm of chromosome 8 between markers TG176 and CT92, covering about 20 cM and explaining nearly 27% of the phenotypic variation (fruit shape index) in the backcross population. Sun et al. [19] narrowed down the fs8.1 interval to 3.03 Mb and annotated and analyzed the expression of genes within this region. They identified six genes differentially expressed in the ovaries of fs8.1 and wild-type lines during flowering.

The number of locules also affects the shape and size of the fruit, controlled by quantitative trait loci (QTLs). Most of the phenotypic variation is explained by two major QTLs, fasciated (fas) and locule number (lc), which interact with each other. Fas is located on chromosome 11, and partial loss of function of the FAS protein changes or reduces its function, resulting in an increase in the number of locules in tomato fruits [20]. Xu et al. [21] further demonstrated that the fas locus responsible for the increase in tomato fruit size during domestication is caused by a regulatory mutation in SlCLV3 (CLAVATA3). This locus is a 294 kb inversion with breakpoints located in the first intron of the YABBY transcription factor and 1 kb upstream of the start codon of SlCLV3. This leads to partial loss of SlCLV3 expression and an increase in the number of locules, causing the fruit to become larger. lc is located on chromosome 2 and is encoded by the tomato ortholog of WUSCHEL (WUS). Two single nucleotide polymorphisms (SNPs) 1080 bp downstream of WUS result in an increase in the number of locules in tomato fruits [20].

In large-fruited tomato germplasm, fruit size is influenced by flat and globe shapes. Twenty-three advanced selections from the cross between Fla. 8000 and Fla. 8111B were genotyped using a genome-wide SNP array. A single locus on the upper arm of chromosome 12, named GLOBE, was identified as associated with fruit shape. In an F₂ population of 238 plants and 69 recombinant inbred lines, the GLOBE locus was further refined to a 392-kilobase region. A survey of various germplasms from multiple breeding programs confirmed that this locus broadly explains the flat/globe shape variation. A single base insertion in an exon of the Solyc12g006860 gene, which encodes a brassinosteroid hydroxylase, was found to completely segregate with fruit shape across all tested populations [22].

2.1.3. Key Genes Involved in Fruit Shape and Functional Analysis

OVATE: This gene is a growth inhibitor that belongs to the OVATE family of proteins (OFP). Due to a single nucleotide mutation (G→T), which causes a premature stop codon, tomato fruit shape changes from round to pear-shaped [11]. OVATE interacts with Tonneau1 recruiting motif (TRM) to regulate cell division patterns during ovary development, thereby altering tomato fruit shape [23]. TRM influences organ shape along the medial–lateral and proximal–distal growth axes, and the TRM-OFP regulatory complex can jointly regulate tomato fruit shape [5]. Wu et al. [24] constructed near-isogenic lines (NILs) of OVATE and confirmed that OVATE affects ovary elongation before flowering, leading to elongation at the proximal end of the fruit. Additionally, OVATE can alter seed shape. Seeds from the OVATE NILs are significantly shorter in length but wider compared to the wild type (LA1589), indicating a trend toward smaller seed size [25].

SUN: This gene is a positive regulator of plant growth, coding for a member of the IQ67 domain (IQD) family. Due to a 24.7 kb gene duplication mediated by the transposable element Rider (from chromosome 10 to chromosome 7), the copy number of SUN increases, resulting in elongated tomato fruits [10]. In a round-fruited background, overexpression of SUN under the 35S promoter leads to extremely elongated fruit shape. SUN does not control fruit weight but mediates the redistribution of fruit mass, increasing longitudinal cell divisions while decreasing transverse ones [26]. Morphological and histological analyses indicated that fs8.1 affects reproductive organ elongation mainly by increasing the number of cells in the proximal–distal direction, and fs8.1 fruits also show increased weight compared to wild-type fruits. Wang et al. [27] conducted expression analysis of flower buds at different developmental stages in wild-type and near-isogenic lines of sun, ovate, and fs8.1. Their results showed that the SUN gene has a stronger impact on transcriptome data than OVATE and fs8.1. SUN alters the expression of genes involved in auxin biosynthesis, signaling, and polar transport, suggesting that SUN may regulate ovary/fruit shape by changing the expression of auxin-related genes early in ovary development.

Locules: Rodríguez et al. [28] used CRISPR/Cas9 genome editing technology to confirm that the SlWUS-SlCLV3 model in tomato fruits can influence fruit size by regulating the number of locules, and the regulatory elements lc and fas show synergistic effects. lc is caused by a gain-of-function mutation in SlWUS, while fas is caused by a partial loss-of-function mutation in SlCLV3. Tomato varieties containing lc or fas and lc and fas mutant alleles carry fruits with multiple locules [29]. Additionally, the CLE9 homolog of CLV3 in tomatoes can also bind to WUS. Mutations in cle9 can enhance the phenotype of clv3 mutants. Aguirre et al. [30] analyzed the cis-regulatory gene Slclv3Pro-Slwuslc-SlCLE9 and its relationship with tomato fruit size, finding that saturated dose-dependent epistatic interactions may be widespread. Different allelic states of redundant paralogs can affect the form of dose-dependent relationships, revealing saturated dose dependency and allele-specific interactions. This epistatic phenomenon at the cis-regulatory level can directly affect the number of locules and thus the size of tomato fruits. Apart from these genes, there are others that can control the shape of tomato fruits, such as the ld (lobedness degree) gene. Its genetic determinant is located on chromosome 11, and ld6 on chromosome 6 plays a modifying role, regulating the degree of lobing in tomato fruits. These two epistatic QTLs explain approximately 61% of the variation, while ld6 on chromosome 8 explains about 17% of the variation [31]. SlMYB1 (MYB transcription factor) can also regulate the shape of tomato fruits, making them smoother or flatter [32]. Knockout of the repressor SlMYB3R3 can alter the pattern of cell division during the ovary stage, leading to elongated tomato fruits [33].

ENO: Researchers identified ENO as a tomato fruit size regulator that may control WUSCHEL gene expression to limit stem cell proliferation in a flower-specific manner. A natural 85 bp deletion in the promoter of ENO leads to decreased expression of this gene and increased locule number 34. During tomato domestication, naturally occurring cis-regulatory mutations in the CLAVATA-WUSCHEL signaling pathway increased fruit size by enlarging meristems, resulting in flowers with extra organs and larger fruits. Mutations in ENO lead to larger, multilocular fruits by expanding the floral meristem size. Genetic analyses revealed that ENO works synergistically with mutations in LOCULE NUMBER (encoding SlWUS) and FASCIATED (encoding SlCLV3), key players in the evolution of fruit size during domestication [34].

GLOBE: CRISPR/Cas9 knockout experiments confirmed that a brassinosteroid hydroxylase (Solyc12g006860) is responsible for the GLOBE locus [22]. In silico analysis of 595 wild and domesticated accessions indicated that the mutant allele of GLOBE arose late in tomato domestication. Fruit measurements in three genetic backgrounds showed that GLOBE affects fruit size, shape attributes, pedicel length/width, and susceptibility to weather damage. The mutant allele of GLOBE is largely recessive for most traits except fruit size, where it exhibits an additive effect [22].

Recently, researchers recently also found that zinc finger protein (SlPZF1) and NAC transcription factor (NOR-like1) play important roles in regulating fruit size by regulating endoreduplication, cell layer number, and cell area in tomato [35]. Additionally, cytokinins (CKs) can regulate fruit size. This study demonstrates that reducing endogenous active CK levels through the overexpression of the CK-inactivating enzyme gene AtCKX2 in tomato fruit tissues leads to smaller fruit size and reduced pericarp thickness compared to wild-type fruits. The decrease in pericarp thickness and single fruit weight in transgenic plants was primarily due to a reduced number of cells, indicating decreased cell division [36]. The BR-signaling mutant displayed a dwarf phenotype, with reduced vegetative growth, fruit size, and weight. Microscopic and transcriptional analysis of the abs1 mutant fruits revealed that reduced cell size and number were responsible for these phenotypic differences [37].

2.1.4. Future Directions for Research

Future research will further explore how OVATE and SUN genes interact with other regulatory factors to modulate the shape and size of tomato fruits. Additionally, gaining a deeper understanding of how FAS and LC genes influence locule numbers and their underlying molecular mechanisms will be another important direction. Through these studies, scientists can better understand the regulatory network of fruit development and develop new breeding strategies to optimize the shape and yield of tomato fruits. Additionally, investigating the interactions between hormonal pathways, such as auxin, cytokinin, and brassinosteroids, could help elucidate their contributions to fruit development. Finally, incorporating multi-omics approaches and phenotyping technologies could accelerate breeding programs aimed at enhancing desirable fruit traits.

2.2. Chili Pepper

2.2.1. Overview of Fruit Shape Diversity

Chili peppers (Capsicum spp.) are notable for their diverse fruit shapes, which include screw peppers, lantern peppers, string peppers, conical peppers, and bullhorn peppers [38]. The variability in fruit morphology is a critical determinant of visual quality, influencing market grading and consumer preferences. As members of the Solanaceae family, chili peppers share a close phylogenetic relationship with tomatoes, having diverged relatively recently. This close relationship results in a high degree of genomic collinearity, suggesting that homologous genes controlling fruit shape in tomatoes may also play significant roles in shaping chili pepper fruit morphology [39].

2.2.2. QTL Mapping and GWAS Analysis of Pepper Fruit Shape Genes

Borovsky and Paran [40] constructed mapping populations from round and slender chili peppers and identified a major QTL, fs10, on chromosome 10, explaining 68% of the phenotypic variation in fruit shape index. Tissue analysis revealed that fs10 affects fruit elongation by controlling cell expansion and replication. fs10 was localized to a 5 Mbp region containing the direct ortholog of the tomato gene SlOFP20, which inhibits fruit elongation. VIGS-mediated silencing of the chili pepper homolog CaOFP20 led to increased fruit length in two independent backgrounds. CaOFP20 showed differential expression in fs10 near-isogenic lines and in round and elongated fruit germplasms, suggesting that CaOFP20 acts as an inhibitor of fruit elongation and is the most likely candidate gene for fs10. Cao et al. [41]. detected strong overlapping GWAS signals on chromosome 3 related to chili fruit shape index, length, and diameter, naming the locus fsi. The most significant SNP for fsi overlapped with previously mapped QTLs for fruit shape and length (fs-3.1, fl-3.2) [42] and matched the SNP location determined by Colonna et al. [43]. The SNP caused a non-synonymous Ile340Thr (ATT→ACT) mutation in the Capana03g002426 gene, encoding a TRM protein, which is a regulator of fruit shape in tomatoes and cucumbers [41]. Capana03g002426 (TRM25) is expressed early in chili fruit development, and functional mutations in TRM25 may regulate chili fruit shape [41].

Ma et al. [44] constructed a genetic linkage map using an F₂ population and detected multiple QTLs related to fruit shape. Only five QTLs—ftl2.1 (fruit length), ftd2.1 (fruit diameter), fts1.1 (fruit shape), ftw2.1 (fruit weight), and lcn1.1 (locule number)—were consistently detected in both F₂ and F_2:3 populations. lcn1.1 was mapped between markers HM1112 and EPMS709, with a genetic distance of 3.18 cM. Functional annotation and expression analysis identified Capana01g004285, encoding the BREVIS RADIX (BRX) protein, as a candidate gene. VIGS of CaBRX reduced the number of locules and affected the expression of genes related to flower and locule development, suggesting that CaBRX plays a crucial role in locule number development, which in turn influences fruit shape. Liu et al. [45] scanned for QTLs related to fruit length and width in a near-isogenic line population derived from a cross between bird’s eye pepper and sweet pepper. They identified QTLs on chromosome 3, qFL3.1 (69.9–78.4 Mb), and qFWD3.1 (64.9–73.6 Mb), with LOD scores greater than 10.

2.2.3. Key Genes Involved in Fruit Shape and Functional Analysis

Chili peppers display a diverse range of fruit shapes, including screw peppers, lantern peppers, string peppers, conical peppers, and bullhorn peppers. Fruit shape is a critical trait for evaluating the visual quality and market grading of chili peppers. Chili peppers and tomatoes belong to the same Solanaceae family, share a relatively recent divergence time, and have a close phylogenetic relationship, preserving a high degree of collinearity between their genomes. Both crops produce fleshy fruits, and homologs of genes controlling tomato fruit shape may play a role in determining pepper fruit shape.

Tsaballa et al. [38] cloned the CaOvate gene in chili peppers, which is homologous to the OVATE gene in tomatoes. Relative quantitative expression analysis showed higher expression levels of CaOvate in round-shaped fruits. Virus-induced gene silencing (VIGS) of CaOvate in round-shaped chili peppers led to increased fruit length and a change in fruit shape to more elongated, suggesting that CaOvate is involved in regulating chili fruit shape. Razo-Mendivil et al. [46] performed transcriptome analysis on Chiltepin (wild type) and Serrano (cultivated type) peppers at 20 days after flowering and at the red ripe stage. They found enrichment of homologous genes related to tomato fruit shape. In Chiltepin peppers, OVATE gene expression was higher, while in Serrano peppers, expression levels were lower. OVATE and a homolog of the tomato FAS gene were clustered together. FAS mutations in tomatoes result in larger fruits. The round and smaller size of Chiltepin fruits may be related to OVATE and FAS genes.

2.2.4. Future Directions for Research

Future research should focus on the intricate interactions between the CaOvate gene and other regulatory factors to elucidate their collective role in modulating chili pepper fruit shape. Additionally, exploring the functional mechanisms underlying the identified QTLs and their relationships with the expression of related genes will be essential. Understanding the regulatory networks that govern fruit development in chili peppers may lead to new breeding strategies that optimize fruit characteristics such as shape, size, and market appeal. Enhanced insights into these genetic pathways could ultimately contribute to improved agricultural practices and the development of cultivars that meet consumer demands.

2.3. Cucumber

2.3.1. Overview of Fruit Shape Diversity

Fruit shape is one of the most critical agronomic traits in cucumber, significantly impacting both its market value and yield. Throughout the domestication and diversification processes, cucumber fruit has evolved into various shapes, from spherical to elongated forms. This diversity in fruit morphology is governed by a complex interplay of genetic and environmental factors, making fruit shape a target for breeding programs aiming to improve cucumber quality and productivity. Studies have revealed that different fruit shapes arise from changes in cell division, cell expansion, and the number of carpels in cucumber fruits. By analyzing the genetic basis of these phenotypes, researchers aim to understand how such traits evolved and how they can be further manipulated to improve agricultural outcomes.

2.3.2. QTL Mapping and GWAS Analysis

Quantitative trait locus (QTL) mapping and genome-wide association studies (GWASs) have been instrumental in identifying regions of the genome associated with cucumber fruit shape. Li et al. [47] used F₂, F₃, and near-isogenic line populations for linkage and association analyses, narrowing down the region controlling the variation in the number of carpels in cucumber to a 16 kb interval on chromosome 1. CsCLV3 is a strong candidate gene for the Cn locus. Pan et al. [13] used round-fruited WI7239 and elongated-fruited WI7238 as parental lines to construct F₂ and F3 populations, detecting QTLs related to fruit size on chromosomes 1 and 2, FS1.2 and FS2.1. Fine-mapping revealed that CsSUN is a candidate gene for FS1.2, which is a homolog of the tomato fruit shape gene SUN, with a 161 bp deletion in the first exon of CsSUN in round-fruited cucumbers. Xin et al. [48] identified a cucumber mutant, sf1, with short fruits due to inhibited cell division. By crossing this mutant with long-fruited cucumbers and constructing an F₂ population, they mapped a locus on chromosome 2 encoding a RING-type E3 ligase, SF1. A G→A mutation at the 230th amino acid position changed Arg (R) to Lys (K), enhancing the ubiquitination and degradation of SF1, leading to accumulation of the ethylene biosynthetic rate-limiting enzyme ACS2 (1-aminocyclopropane-1-carboxylate synthase 2), which results in excessive ethylene production and shortened fruit length. This suggests that fine-tuning ethylene homeostasis can regulate cucumber fruit elongation.

Pan et al. [49] constructed near-isogenic lines related to cucumber fruit length and identified a QTL, FS5.2, located within a 95.5 kb physical distance on chromosome 5. Morphological and cytological analyses indicated that FS5.2 mainly regulates cucumber fruit shape by modulating cell division and expansion mediated by auxin. The authors speculated that the CRABS CLAW homolog CsCRC in Arabidopsis thaliana might be a key candidate gene for FS5.2. Subsquently, Che et al. [50] performed fine-mapping of the QTL FS5.2 on chromosome 5 using near-isogenic line populations, ultimately narrowing down the interval to 44.6 kb. This interval contains the CRABS CLAW homolog CsCRC. A single nucleotide polymorphism (G→A) in CsCRC is associated with the variation in fruit length regulated by FS5.2.

Xie et al. [51] identified a spherical fruit mutant in an EMS-mutagenized cucumber population. MutMap analysis narrowed down the candidate gene interval to a 6.47 Mb range on chromosome 2, which includes the previously reported FS2.1 locus. A single nucleotide mutation (C→A) causes a truncated protein in the CsTRM5 homolog of the tomato fruit shape gene SlTRM5 (CsaV3_2G013800). Knockout of this gene results in significantly shorter fruit lengths in cucumber. CsTRM5 regulates cucumber fruit shape by affecting cell division orientation and expansion, with ABA being involved in the cell expansion process. Zhang et al. [52] identified a short fruit mutant, sf4, in an EMS-mutagenized population. This phenotype is controlled by a recessive gene. The sf4 locus is located within a 116.7 kb genomic region between markers GCSNP75 and GCSNP82 on chromosome 1. The candidate gene, Csa1G665390, has a G to A mutation at the end of the 21st intron, changing the splice site GT-AG to GT-AA, resulting in a 42 bp base deletion in the 22nd exon. This gene encodes OGT (O-linked N-acetylglucosamine transferase). Although no studies have yet confirmed a relationship between OGT and fruit elongation, CsSF4 may promote fruit growth by activating gibberellin signaling through O-GlcNAc (O-linked N-acetylglucosamine) glycosylation inhibition of DELLA protein function.

2.3.3. Key Genes Involved in Fruit Shape and Functional Analysis

Zhao et al. [53] identified an SNP (3393C/A) in the CsFUL1 (FRUITFULL-like MADS-box) gene in cucumber lines. Knockout of CsFUL1A led to further elongation of cucumber fruits, while overexpression of CsFUL1A resulted in significantly shorter fruit lengths. CsFUL1A binds to the CArG-box in the promoter region of the cell division and expansion regulator CsSUP (SUPERMAN), suppressing its expression. Additionally, CsFUL1A inhibits the expression of auxin transporter proteins PIN1 (PIN-FORMED1) and PIN7, reducing auxin accumulation in the fruit. This indicates that CsFUL1A regulates cucumber fruit length by inhibiting CsSUP and others. Zhang et al. [54] identified a homolog of HDC1 (Histone Deacetylase Complex 1) called SF2 in short-fruited cucumber mutants. SF2 is enriched in meristematic tissues and inhibits cell proliferation by targeting the biosynthesis and metabolism of cytokinins and polyamines, thereby controlling the length of cucumber fruits.

The number of carpels also affects cucumber fruit shape, size, and intrinsic quality, making it an important trait in cucumber fruits. Che et al. [55] found that interference with CsCLV3 or overexpression of CsWUS both lead to an increase in the number of carpels in cucumbers. Both genes have negative and positive regulatory roles in the variation in carpel numbers, respectively. CsWUS can directly bind to the promoter of CsCLV3 to activate its expression, while CsFUL1A can directly bind to the promoter of CsWUS to stimulate its expression. Auxin participates in the change in the number of carpels through the interaction of CsARF14 and CsWUS.

Subsquently, Che et al. [50] found that CsCRCA is present in a few short or round fruit phenotypes of semi-wild cucumbers from Xishuangbanna. Overexpression of CsCRCG can restore the short fruit phenotype caused by CsCRCA, and silencing of CsCRC can reduce cucumber fruit length. The auxin response protein gene CsARP1 is a downstream target of CsCRC and promotes fruit elongation mainly through cell expansion.

2.3.4. Future Directions for Research

Future research on cucumber fruit shape will likely focus on identifying the downstream effectors of known genes such as CsSUN, CsFUL1A, and SF2. Understanding how these genes interact with hormonal signals like auxin and ethylene will be crucial in uncovering the regulatory networks controlling fruit shape. For instance, fine-tuning ethylene homeostasis could offer new avenues for manipulating fruit elongation. In addition, further exploration of genes such as CsCRC and CsTRM5, which regulate fruit shape by modulating cell division and expansion, will be valuable. These genes may hold the key to understanding the precise molecular mechanisms underlying cucumber fruit morphology. Additionally, the role of ABA and other phytohormones in these processes will require further investigation, as these hormones are implicated in cell expansion and division. Moreover, research will focus on developing advanced genetic tools and technologies to perform functional validation of candidate genes identified through QTL mapping and GWASs. Understanding how these genes are regulated at the transcriptional and post-translational levels, as well as their interactions with environmental factors, will pave the way for the development of high-yield, high-quality cucumber varieties tailored to specific market demands.

2.4. Peach

2.4.1. Overview of Fruit Shape Diversity

Peach is an important fruit crop and, due to its small genome and short juvenile period, is considered a model species for comparative and functional genomics research in the Rosaceae family [56]. The fruit shape of peaches plays a significant role in determining their marketability, with the two primary phenotypes being flat (doughnut-shaped) and round. The shape diversity in peaches arises from variations in genetic and chromosomal structures, leading to differences in fruit development, particularly during the phases of cell division and expansion. Among the most studied forms is the distinction between flat and round fruit types, which are controlled by genes on chromosome 6, though different peach lines may show variations in the specific genes and loci involved. The flat fruit shape is prevalent in several peach cultivars, making it an important subject of study in both breeding programs and genetic research [57].

2.4.2. QTL Mapping and GWAS Analysis

Quantitative trait locus (QTL) mapping and genome-wide association studies (GWASs) have been pivotal in identifying the genetic regions responsible for peach fruit shape. The shape of peach fruit is mainly flat (Donut Peach) or oval shape (Flaming Fury Series, Hale Haven). Cao et al. [58] used high-throughput resequencing technology to perform a whole-genome association study (GWAS) on 129 peach germplasm resources for fruit shape and other agronomic traits. Fluorescence quantitative expression analysis combined with GWAS results showed that a single base mutation (A/T) in the fifth intron of the PpCAD1 (constitutively activated cell death 1) gene, located at approximately 25 Mb on chromosome 6, is highly associated with peach fruit shape variations. Flat fruits exhibit an A/T or A/A genotype, while round fruits have a T/T genotype. The A/T single nucleotide polymorphism (SNP) co-segregates with the flat fruit trait. Guan et al. [59], based on structural variations (SVs) in flat peach chromosomes, conducted a GWAS study using 149 peach samples and discovered that a 1.67 Mb heterozygous inversion on chromosome 6 is the cause of flat fruit variation. This inversion was formed through a non-homologous end-joining (NHEJ) mechanism and accompanied by two misrepair events (a 2 bp deletion (AG/TC) and a 1 bp insertion (G/C)). Additionally, the inversion altered the expression of the PpOFP2 gene near the proximal breakpoint by upregulating its expression, leading to flat fruit shape.

López-Girona et al. [60] also identified a gene on chromosome 6 that controls the flat peach fruit shape. This gene is a homolog of leucine-rich repeat receptor-like kinase (LRRRLK) and exhibits a 10 kb deletion approximately 400 kb upstream that co-segregates with the flat fruit trait. Functionally, this gene complements the function of the key regulator CLAVATA2, which controls the size of the stem cell population. Tan et al. [61] confirmed that an SNP (A/T) at approximately 26 Mb on chromosome 6 is associated with fruit shape differences. Genes adjacent to this A/T polymorphism and haplotypes carrying the T allele may determine the flat fruit shape of peaches. Loss of heterozygosity (LOH) events that eliminate haplotypes carrying the T allele may be the cause of the alteration in wild-type flat peach fruit shape.

Cirilli et al. [62] detected a major locus-regulating fruit shape at the telomere of chromosome 5 and the proximal end of chromosome 6. Both loci explained the phenotypic variation in fruit longitudinal shape. Zhou et al. [63] found that a chromosomal inversion 1.7 Mb downstream of the S locus is the cause of flat peach fruit formation. The proximal and distal breakpoints of the inversion contain a three-base (ACA) deletion and a two-base (GA) insertion, respectively. Near the proximal breakpoint, there is a gene encoding an OVATE family protein, PpOFP1 (Prupe.6G290900). The chromosomal inversion activates the transcription of PpOFP1 early in flat fruit development, inhibiting vertical fruit growth. PpOFP1 interacts with the fruit elongation activator PpTRM17, suggesting the existence of a gene regulatory network (OFP-TRM) controlling peach fruit shape.

2.4.3. Key Genes Involved in Fruit Shape and Functional Analysis

The functional roles of these genes have been extensively studied through genetic and molecular approaches. For instance, previous studies have shown that CAD1 is involved in cell death, pollen germination, and pollen tube elongation in Arabidopsis thaliana and is a subunit of the highly conserved metabolic switch AMPK (5′-AMP-activated protein kinase). PpCAD1 primarily functions during the cell expansion phase of peach fruit development [58]. In flat peaches, structural variations such as a 1.67 Mb inversion on chromosome 6 disrupt the expression of PpOFP2, leading to the characteristic flat fruit shape by altering cell expansion dynamics during fruit growth. PpOFP1 is another essential gene that has been functionally validated through mutant analysis. It interacts with the fruit elongation activator PpTRM17 to regulate vertical fruit growth. The interaction between OFP proteins and TRM (TONNEAU1 recruiting motif) proteins suggests that a regulatory gene network (OFP-TRM) plays a significant role in modulating peach fruit shape [63]. Additionally, research has demonstrated that mutations or deletions in a homolog of the LRR-RLK gene, located approximately 400 kb upstream of the flat fruit shape-controlling region, contribute to shape variation. This gene regulates the size of the stem cell population and thus controls the overall growth and morphology of the fruit [60].

2.4.4. Future Directions for Research

Future research in the field of peach fruit shape will likely focus on deepening our understanding of the molecular mechanisms that control flat and round fruit phenotypes. One of the key areas of exploration will be the further functional validation of candidate genes such as PpCAD1, LRRRLK, and PpOFP1. Gene-editing technologies, such as CRISPR/Cas9, will play a pivotal role in experimentally verifying the roles of these genes and their contributions to fruit morphology. In addition, studies will focus on elucidating the regulatory pathways that link chromosomal structural variations, such as the 1.67 Mb inversion, with changes in gene expression. Understanding how these structural changes disrupt normal gene function and lead to flat fruit shapes will be crucial. Researchers will also investigate the interaction between OVATE family proteins (e.g., PpOFP1 and PpOFP2) and their downstream effectors, such as PpTRM17, to reveal the comprehensive gene regulatory network that shapes peach fruit morphology. Moreover, there is potential for research to explore the effects of environmental factors on the expression of fruit shape-related genes, offering insights into how external conditions might influence genetic pathways. With advanced genomics tools and molecular breeding technologies, scientists aim to improve peach varieties by fine-tuning fruit shape and size, ultimately enhancing both yield and consumer preferences.

2.5. Grape

2.5.1. Overview of Fruit Shape Diversity

Grape cultivation has a long history (more than 3000 years) and is used for various purposes, including fresh consumption (table grape), wine making (wine grapes), drying, and juice production. The fruit shape of table grapes plays an essential role in determining their visual quality and market appeal. While grape berries vary widely in size, color, and flavor, fruit shape has become a key trait for breeding programs aimed at improving their commercial value. Understanding the genetic basis of fruit shape is essential for developing cultivars that meet the diverse needs of growers and consumers. Flat or oval-shaped peaches, for instance, have gained popularity due to their unique aesthetic appeal and perceived ease of consumption, aligning with market trends favoring convenience and novelty. Unlike many other crops, the research on grape fruit shape is still in its early stages compared to other fruit-bearing plants such as tomatoes. However, it has been found that grape fruit shape is controlled by multiple quantitative trait loci (QTLs), with molecular studies increasingly relying on comparative genomics. Researchers often use genes identified in tomato and other fruit crops as a reference point to study the genetic regulation of grape fruit morphology. The complex genetic basis of grape fruit shape involves a wide array of regulatory pathways as well as key genes.

2.5.2. QTL Mapping and GWAS Analysis

QTL mapping and genome-wide association studies (GWASs) have made significant contributions to identifying the genetic loci responsible for grape fruit shape. Liang et al. [64] resequenced 472 grape accessions to analyze genetic variation at single-base resolution across the entire genome, identifying five genomic loci associated with fruit shape. Zhang et al. [65] used whole-genome association analysis combined with parameters related to different grape fruit shapes to study genes controlling fruit shape, detecting 122 single nucleotide positions significantly associated with fruit shape traits. Candidate gene analysis suggested associations with LRR receptor serine/threonine-protein kinases, transcription factors (GATA transcription factor 23-like, transcription factor VIP1, transcription initiation factor TFIID, MADS-box 6), ubiquitin ligases (F-box protein SKIP19 and RING finger protein 44), and plant hormones (indole-3-acetamide synthase GH3.6 and ethylene-responsive transcription factor ERF061). Some genes were found to control multiple traits, indicating that grape fruit shape is subject to the cooperative regulation of several genes [66].

2.5.3. Key Genes Involved in Fruit Shape and Functional Analysis

A growing body of research has begun to identify several key genes that play an essential role in determining the shape of grape fruits. Among these is VvSUN, a gene from the SUN/IQ67 domain (IQD) family, which is considered a homolog of the tomato SUN gene involved in controlling fruit elongation. VvSUN localizes to both the plasma membrane and chloroplasts, suggesting that it has a broader function beyond shaping the fruit, possibly influencing growth processes regulated by auxin pathways during early fruit development [64]. The VvSUN gene plays a central role in the auxin signaling pathway, which is crucial for regulating cell division and elongation during early fruit growth stages. By modulating auxin distribution, VvSUN promotes elongation, thus contributing to the final shape of the grape. Localization studies have shown that VvSUN interacts with the plasma membrane and chloroplasts, indicating its involvement in cellular signaling and metabolic processes [66]. Another important gene associated with grape fruit shape is SRK2A (serine/threonine-protein kinase), located on chromosome 7. A non-synonymous mutation (C→T) in this gene was identified in a whole-genome resequencing study of 472 grape accessions. This mutation affects the protein-coding region, potentially altering the function of the SRK2A protein and influencing fruit shape [65]. Other genes implicated in grape fruit morphology include transcription factors such as GATA transcription factor 23-like, VIP1, and MADS-box 6, all of which play regulatory roles in various growth and developmental processes. Additionally, genes involved in ubiquitin-mediated protein degradation, like F-box protein SKIP19 and RING finger protein 44, are also considered key regulators of fruit shape, highlighting the complexity of genetic control [65].

2.5.4. Future Directions for Research

The future of grape fruit shape research will likely focus on unraveling the complex genetic interactions that govern this trait. While considerable progress has been made in identifying key loci and candidate genes, further functional validation of these genes is required to fully understand their roles. Techniques such as CRISPR/Cas9 gene editing could be used to manipulate genes like VvSUN and SRK2A to experimentally verify their effects on fruit shape, which could lead to the development of new grape varieties with improved visual qualities and market appeal. Additionally, more research is needed to explore the role of plant hormones, particularly how hormones like gibberellins, auxins, and cytokinins interact with key fruit shape regulatory genes. Understanding these interactions will help breeders fine-tune fruit morphology to meet specific industry needs, such as wine-making or fresh consumption. Future studies may also focus on exploring the downstream pathways regulated by genes such as VvSUN and SRK2A, as well as identifying new genes through forward genetics approaches. By combining genomic tools, molecular biology techniques, and advanced breeding methods, researchers can continue to improve grape fruit shape, ultimately enhancing the productivity and commercial value of grape crops.

3. Concluding Remarks and Future Perspectives

The genetic regulation of fruit shape is a rapidly evolving field with significant implications for crop improvement and agricultural productivity. Recent advances have identified key genes such as OVATE, SUN, FAS, and LC in tomatoes, CaOvate and fs10 in chili peppers, CsSUN, CsFUL1A, and CsCRC in cucumbers, PpCAD1 and LRRRLK homologs in peaches, and VvSUN in grapes (Supplemental Table S1). These discoveries provide valuable insights into the molecular mechanisms underlying fruit development and offer promising avenues for developing new breeding strategies.

Future research will delve deeper into the interactions between these genes and other regulatory factors, aiming to optimize fruit shape and yield. Comparative studies across species will help uncover conserved regulatory pathways that govern fruit shape. Integrating multi-omics technologies and gene-editing tools will enable a more comprehensive understanding of the complex regulatory networks involved in fruit shape development. Future research for understanding the genetic regulation of fruit shape in crops such as tomato, chili pepper, cucumber, peach, and grape will focus on several key areas:

(1)

Elucidating gene function and regulatory networks: With the application of gene-editing technologies like CRISPR/Cas9, scientists will further explore the specific functions of genes such as OVATE, SUN, FAS, and LC, as well as how they interact with other genes to regulate fruit shape. CRISPR/Cas9 enables the generation of allelic variants and expression variants by either introducing targeted mutations or modifying gene regulatory elements, thus offering insights into gene dosage effects and gene regulation. For example, in tomatoes, CRISPR has been used to investigate how OVATE interacts with TONNEAU1 recruiting motif (TRM) proteins, modulating cell division patterns and ultimately influencing fruit elongation and shape. By creating specific allelic variants of OVATE, researchers can study how different mutations affect fruit morphology, from minor changes in cell division to dramatic shifts in fruit shape.

(2)

Comparative studies across species: Given that tomato and chili pepper belong to the Solanaceae family and share similar genetic backgrounds, future studies will compare homologous genes across these crops to uncover general rules governing fruit shape regulation. For instance, comparing the CaOvate gene in chili peppers with the OVATE gene in tomatoes in terms of regulatory mechanisms and exploring similarities between the CsSUN gene in cucumbers and the SUN gene in tomatoes.

(3)

Integrating multi-omics technologies: To gain a more comprehensive understanding of the genetic regulation of fruit shape, future research will combine transcriptomics, proteomics, and metabolomics, among other omics technologies, using systems biology approaches to decipher regulatory networks. For example, by analyzing transcriptome data from different developmental stages of fruits to reveal patterns of gene expression and their relationship with fruit shape.

(4)

Developing new breeding strategies: Based on a deep understanding of gene function and regulatory networks, scientists will develop new gene-editing tools and breeding methods to precisely improve crop varieties, cultivating new cultivars according to consumer request and market request and superior quality. For instance, using gene-editing techniques to precisely control the expression of genes related to fruit shape, enabling customized breeding of fruit shape.

(5)

In the study of fruit morphology across crops like tomatoes, peppers, cucumbers, grapes, and peaches, several key genes consistently emerge as crucial regulators. Genes such as OVATE, SUN, FAS, and LC are involved in the control of fruit shape, size, and development in tomatoes and other Solanaceae crops. For example, SUN modulates fruit elongation, while OVATE represses cell elongation and alters fruit shape in multiple crops. Additionally, genes related to meristem size control, like FAS (which regulates carpel number and fruit size), have broad applications for improving fruit traits across species. By targeting these common genes, significant advancements can be made in improving fruit size, shape, and overall yield in a variety of horticultural crops. CRISPR/Cas9 technologies will be instrumental in fine-tuning these genes, allowing for the development of crops with optimized fruit characteristics and improved market quality.