Molecular Research Progress on Gametophytic Self-Incompatibility in Rosaceae Species

Abstract

Self-incompatibility (SI) is a complex mechanism that prevents plants from self-fertilizing to preserve and promote genetic variability. The angiosperm species have developed two different SI systems, the sporophytic (SSI) and the gametophytic (GSI) systems. SI is a significant impediment to steady fruit production in fruit tree species of the Rosaceae. In Rosaceae, GSI is genetically regulated via a single locus, named the ‘S-locus’, which includes a minimum of two polymorphic and relatively intercorrelated S genes: a pistil-expressed S-RNase gene and several pollen-expressed SFBB (S-locus F-Box Brothers) or SFB (S haplotype-specific F-box protein). This necessitates the interaction of S-RNases with the male determinants. Although genetic and molecular analyses of S genes have shown that mutations in both pistils and pollen-specific components induce self-compatibility in many species and cultivars, other genes or molecules outside the S-locus can co-participate in the male gamete rejection in GSI. However, we highlight and synthesize the most recent knowledge on different mechanisms of GSI in Rosaceae in this current review.

1. Introduction

Self-incompatibility (SI) is a genetic system that allows angiosperm species’ pistils to reject pollen from the same individual, which hinders the pistil from self-fertilization and allows outcrossing [1]. Genetic studies have revealed that a single multi-allelic gene, S-locus, controls most SI systems. If the haploid pollen has an identical S allele specificity as the diploid pollen receiver, it is not recognized as an authentic pollen (Figure 1). However, previous research has shown that a minimum of two distinct genes regulate the SI phenotypes of the pistil and the pollen, which are pollen and pistil S genes, respectively [2].

The SI system is widespread in angiosperms, including more than 19 orders, 71 families, 250 genera, and around 60% of the species [3]. According to the genetic regulation of the phenotypic pollen self-incompatibility, the mechanism could be sporophytic (SSI) or gametophytic (GSI) [4]. Plant species from Rosaceae, Solanaceae, and Scrophulariaceae exhibit GSI and possess identical molecules, such as S-RNase as the style S determinant [2]. For the pistil to inhibit self-pollen elongation, the RNase activity of the S-RNase (a basic glycoprotein with ribonuclease activity) is essential [5]. In the species of Rosaceae, including almond (Prunus dulcis D. A. Webb) and Japanese apricot (Prunus mume Siebold and Zucc.), chromosome flanking the S-RNase [6] and DNA sequencing as well as transcriptional assessments [7,8] revealed an excellent candidate gene as the pollen S determinant. For instance, the almond pollen S candidate gene has been given the term SFB for S haplotype-specific F-box protein [8], whereas its putative Japanese apricot ortholog has been given the term SLF for the S-locus F-box gene [7]. The pollen S gene is characterized by an expression exclusive to pollen, significant allelic polymorphism, and similar physical proximity to S-RNase. SFB was shown to be physically related to the S-RNase in three additional Prunus species: sweet cherry [Prunus avium (L.)], sour cherry( Prunus cerasus L.) [9], and P. mume [7,10]. As with the hypervariable region RHV of Rosaceae S-RNases, the variable domains (Va and Vb) of SFB [8] are significantly divergent and subjected to evolutionary pressure [11,12]. Subsequently, the feature of SFB found an F-box motif, two variables, and two hypervariable regions [13], thus playing an essential role in the interaction of SFB with S-RNase to inhibit the growth of the pollen tube in a haplotype-specific manner in GSI.

GSI is a genetic process that causes plant species to distinguish between pollen grains that are viable for fertilization and those that are not. Fertilization occurs only whenever the recipient pistil’s S allele differs from any of the pollen’s S alleles [14]. Several fruit species belonging to the Rosaceae exhibit this system, including strawberry (Fragaria x ananassa (Weston) Duchesne ex Rozier) [15], pear (Pyrus communis L.) [16,17], and apple (Malus domestica (Suckow) Borkh.) [18,19], as well as stone fruit trees including P. dulcis [20], apricot (Prunus armeniaca L.) [21,22], and P. mume.

However, it has been revealed that self-compatibility in some species and cultivars results from various factors. Among these are pistil-determinant [23] and pollen-determinant [24,25,26] mutations at the S-locus. In addition, MGST (M-locus-encoded glutathione S-transferase) gene insertion appeared to confer self-compatibility in a sweet cherry cultivar [27]. In contrast, a novel category of the F-box gene unrelated to S-locus has been associated with the P. mume’s self-compatibility [28]. Likewise, a non-S-locus gene (Sli) has been identified in the Solanaceae that breaks self-incompatibility in diploid potatoes [29]. Therefore, this current review addresses the most recent findings regarding the mechanism of SI in Rosaceae, primarily in the Prunus species. Moreover, given the intricacy of the self-incompatibility system, we discussed the various mechanisms of GSI and those associated with its breakdown in related species and cultivars.

This study was conducted by creating unique keywords and tailoring them to the databases based on the goals. We improved the literature search by adding four keyword rounds. As a result, we improved the quality of our evaluation by adding new terms to the growing collection and revising earlier materials.

Round 1:

The term ‘Gametophytic Self-incompatibility’ was employed. Subsequently, we reviewed the results and examined the cited articles. We recognized the necessity for additional word combinations. Consequently, an expanded array of keyword combinations was discerned, grounded in significant techniques and theories. We additionally employed keywords frequently associated with self-incompatibility, like ‘self-sterility, self-fertilization, sexual reproduction’.

Round 2:

During this phase, we employed a Boolean search utilizing the terms ‘gametophytic self-incompatibility’ AND ‘gametophytic’ AND ‘Rosaceae’, ‘self-incompatibility’ AND ‘molecular research progress’, ‘self-sterility’ AND ‘Rosaceae species’, ‘gametophytic Self-incompatibility’ AND ‘molecular research progress’, AND ‘Rosaceae species’ AND ‘adoption’, ‘self-incompatibility’ OR ‘Rosaceae species’ AND ‘Rosaceae species’ AND ‘molecular research progress’, ‘gametophytic’ AND ‘molecular research progress’ AND ‘Rosaceae species’.

Round 3:

Using Google Scholar, SAGE, Emerald, Scopus, and Springer links, we carried out the final phase to identify explicitly published papers containing the terms ‘gametophytic self-incompatibility’, ‘molecular research in Rosaceae species’, ‘self-sterility in Rosaceae species’, and ‘self-incompatibility in Rosaceae species’, as found in either the abstracts or titles without language limitations.

Round 4:

Researchers conducted a comprehensive review of the reference lists of the selected papers to identify any omitted essential publications. The reference lists were compared with the chosen paper. The titles of the published articles were verified via the bibliography, and the papers used for the studies were published between 1996 and 2024.

2. Chronological Exploration of S-Locus Components Related to the Male and Female Components

Amygdaloideae, Rosoideae, and Dryadoideae are the three subfamilies of Rosaceae [30,31,32]. Research on Rosaceae plant self-incompatibility currently focuses mainly on the species of the subfamily Amygdaloideae [31,33], and its mechanism is becoming increasingly evident. However, an S-Locus consisting of at least two linked genes controls gametophytic self-incompatibility (GSI) (Figure 1) in Rosaceae, including the Prunus species [34]; pistil component S-ribonuclease gene (S-RNase gene) and pollen component (s) encode an F-box protein [35]. Meanwhile, self-compatibility in most of these plant species has been reported to be related to alterations in S-locus genes [36].

2.1. The Female or Pistil Determinant—S-RNase

Solanaceous plant species are the most thoroughly researched in the physiology and mechanisms of GSI. First, the Nicotiana alata Link and Otto cDNAs encode glycoproteins co-segregated with S alleles [37,38]. It is abundantly apparent from the predicted amino acid sequence that stylar RNase is involved in the style’s recognition and rejection reaction. Thus, according to some studies, the S allele product in the Solanaceae’s pistil is a very basic glycoprotein with sequence motifs that resemble the fungus RNase T2 active region [39] and Rh [39], which is notorious as S-RNase [5].

Several researchers have discovered that core eudicots, including the highly varied Asterid and Rosid lineages, exhibit S-RNase-based GSI [40,41,42,43]. Since S-RNases are used by roughly three-quarters of plant species, the genes controlling RNase-based SI could be molecular homologs (orthologs), wonderfully preserved vestiges of a characteristic that evolved over 100 million years ago in a common ancestor [41,42,43,44,45]. The S-RNase is a secreted extracellular protein with a signal peptide at the N-terminus [46,47,48]; it has no amino acid sequence pattern 4 [49]. These could be the main distinctive characteristics of S-RNase in flowering plants. Some researchers suggest that S-RNase alleles from the same genus prefer to cluster together evolutionarily [12,49,50]. S-RNase mediates the female determinant of the GSI response and has distinctive features. It is primarily expressed in the styles and is highly polymorphic in its sequence [12,34,51,52,53].

The initial clue to cloning Prunus S-RNase came from the N-terminal sequences of the almond S-RNase [54]. The S-RNases have subsequently been cloned based on their N-terminal amino acid sequences in crops such as almond [12] and sweet cherry [55]. Using S-RNase-specific PCR band polymorphisms, the S-genotypes of the major P. mume cultivars were first identified in 2001. The number of isolated S alleles ranged from S₁ to S₇ S-RNases [56]. A study has confirmed a sequence similar to other Prunus S-RNases by isolating full-length cDNAs for S-RNase alleles of a P. mume cultivar named ‘Nanko’ [57]. Recent advanced research progress in the mechanism of self-(in)compatibility in the fieldwork of pomology has identified several hundred S-RNases alleles of Prunus species, which include peach (Prunus persica (L.) Batsch), P. armeniaca, and P. mume, which have approximately more than 15, 58, and 70 S-RNase alleles available, respectively. However, the identified S-genotypes of the cultivars and species of Rosaceae, including the Prunus species (for instance, see Table 1) are valuable and essential in S-RNase-based GSI mechanism study and breeding research programs.

The S-RNase genes are highly divergent, and their features vary according to the species. For instance, the maximum number of introns is usually two in the Prunus species [46,49] and one in the Malus species [26]. Moreover, S-RNase has both conserved and hypervariable regions. Two hypervariable regions (HVa and HVb) and five conserved domains (C1 to C5) have already been found in Solanaceae [58,59]. Whereas in Prunus species, including P. mume, S-RNase gene features comprise only a single hypervariable region known as RHV, which is placed within the conserved regions C2 and C3, and five conserved portions (C1, C2, C3, RC4, and C5) [28]. These are the most significant differences between Prunus S-RNase gene features and those of other species, particularly the Malus species. S-RNase, on the other hand, is the foundation of a S-genotype identification, which is imperative for fruit production and the breeding program of SI species (Table 1).

Table 1. S-genotypes of some species belonging to Rosaceae.

Cultivar/Accession	Latin Name	Origin	S-Genotype	SC/SI	References
Huang Yan	Prunus persica (L.) Batsch	Yunnan	S2S2	SC	[25]
Bai Nian He	Prunus persica (L.) Batsch	Yunnan	S2S2	SC	[25]
Qing Si	Prunus persica (L.) Batsch	Yunnan	S2S2	SC	[25]
Long 1-2-4	Prunus kansuensis Rehder	Gansu	S1S2	SC	[25]
Zhang Bai 5	Prunus kansuensis Rehder	Gansu	S2S2	SC	[25]
Xinjiang Huang Rou	Prunus ferganensis (Kost. and Rjab.) Y.Y.Yao	Xinjiang	S1S2	SC	[25]
Hong Gan Lu	Prunus persica (L.) Batsch	Liaoning	S2S2	SC	[25]
Hun Chun Tao	Prunus persica (L.) Batsch	Jilin	S1S2	SC	[25]
Da Hong Pao	Prunus persica (L.) Batsch	Hubei	S2S2	SC	[25]
Kharfi	Prunus persica (L.) Batsch	Tunisia	S1S2	SC	[60]
Meski	Prunus persica (L.) Batsch	Tunisia	S1S2	SC	[60]
Blanco Mollar	Prunus persica (L.) Batsch	Spain	S1S1	SC	[60]
Rojo Mollar	Prunus persica (L.) Batsch	Spain	S2S2	SC	[60]
Rubby Rich	Prunus persica (L.) Batsch	USA	S1S1	SC	[60]
Spring Lady	Prunus persica (L.) Batsch	USA	S1S1	SC	[60]
Sun Late	Prunus persica (L.) Batsch	USA	S1S2	SC	[60]
Rich May	Prunus persica (L.) Batsch	USA	S1S2	SC	[60]
Tasstour Hamra Tardive	Prunus salicina Lindl.	NA	SfSk	SI	[53]
Ain Bagra1	Prunus salicina Lindl.	NA	SfSc	SI	[53]
Sauvage	Prunus salicina Lindl.	NA	SfSc	SI	[53]
Tasstour Hamra précoce	Prunus salicina Lindl.	NA	SfSg	SI	[53]
Bedri1	Prunus salicina Lindl.	NA	SeSh	SC	[53]
Santa Rosa (C2)	Prunus salicina Lindl.	NA	ScSe	SC	[53]
Mulata	Prunus domestica L.	NA	S2S5S6S7 S12	NA	[53]
President	Prunus domestica L.	NA	S1S5S7S9	NA	[53]
Meski Kbira Kahla	Prunus insititia L.	NA	S6S7S8S10	NA	[53]
Zenou	Prunus insititia L.	NA	S1S2S10 S11	NA	[53]
Bebecou	Prunus armeniaca L.	NA	S6SC	SC	[61]
Castlebrite	Prunus armeniaca L.	NA	S2S2	SC	[61]
Castleton	Prunus armeniaca L.	NA	S1S2	SC	[61]
Orange Red	Prunus armeniaca L.	NA	S6S17	SI	[61]
SEO	Prunus armeniaca L.	NA	S6S17	SI	[61]
Velázquez	Prunus armeniaca L.	NA	S5S20	SI	[61]
Cheyenne	Prunus armeniaca L.	NA	S6S9	SI	[62]
Primaya	Prunus armeniaca L.	NA	S1S6	SI	[62]
Fiamma	Prunus armeniaca L.	NA	ScSc	SC	[21]
Summit	Prunus avium (L.)	NA	S1S2	NA	[63]
Sunburst	Prunus avium (L.)	NA	S3S4	NA	[63]
Emperor Francis	Prunus avium (L.)	NA	S3S4	NA	[63]
Vanda	Prunus avium (L.)	NA	S1S6	NA	[63]
Fragaria viridis 42	Fragaria viridis Weston	NA	SaSb	SI	[15]
Xiyeqing	Prunus mume Siebold and Zucc.	China	S2S15	SI	[64]
Zaohong	Prunus mume Siebold and Zucc.	China	S2S15	SC	[64]
Ruantiaohongmei	Prunus mume Siebold and Zucc.	NA	S14S13	NA	[65]
Xiaoyezhugan	Prunus mume Siebold and Zucc.	NA	S3S33	NA	[65]
Zhonghong	Prunus mume Siebold and Zucc.	NA	S3S24	NA	[65]
Meilinhong	Prunus mume Siebold and Zucc.	NA	S37S1	NA	[65]
Dalongmei	Prunus mume Siebold and Zucc.	NA	S20S30	NA	[65]
Huasu	Pyrus communis L.	NA	S5S108	NA	[66]
Huanghua	Pyrus communis L.	NA	S1S2	NA	[66]
Manfeng	Pyrus communis L.	NA	S3S4	NA	[66]
Yunnan Mali	Pyrus communis L.	NA	S12S51	NA	[66]
Ambrosia	Malus domestica (Suckow) Borkh.	NA	S3S28	NA	[67]
Goodland	Malus domestica Borkh.	NA	S11S55	NA	[67]
Newtown Pippin	Malus domestica (Suckow) Borkh.	NA	S2S7	NA	[67]
Minneiska	Malus domestica (Suckow) Borkh.	NA	S24S55	NA	[67]
Marubakaidou	Malus prunifolia (Willd.) Borkh.	NA	S1S2	NA	[68]
A18	Prunus tenella Batsch	Serbia	S2S3	NA	[69]
A10	Prunus tenella Batsch	Serbia	S1S5	NA	[69]
A18	Prunus tenella Batsch	Serbia	S2S3	NA	[69]
A3	Prunus tenella Batsch	Serbia	S8S9	NA	[69]
A14	Prunus tenella Batsch	Serbia	S2S5	NA	[69]
A17	Prunus tenella Batsch	Serbia	S2S3	NA	[69]
Cigany	Prunus cerasus L.	Azerbaijan	S6m2S9S26S36b2		[70]
Erdi Botermo	Prunus cerasus L.	Azerbaijan	S4S6mS35S36a		[70]
A8	Prunus tenella Batsch	Serbia	S4S9	NA	[69]
A6	Prunus tenella Batsch	Serbia	S7S8	NA	[69]
A9	Prunus tenella Batsch	Serbia	S7S8	NA	[69]
A11	Prunus tenella Batsch	Serbia	S1S5	NA	[69]
A15	Prunus tenella Batsch	Serbia	S6S8	NA	[69]
Muir Beauty	Prunus domestica L.	NA	S10S17	SC	[71]
G45N-35	Prunus domestica L.	NA	S8S14S16	SI	[71]
G40N-34	Prunus domestica L.	NA	S4S7	SI	[71]
Improved French	Prunus domestica L.	NA	S10S12S17	SC	[71]
3-8E-46RR	Prunus domestica L.	NA	S1S3S6S17	SC	[71]
Sutter	Prunus domestica L.	NA	S3S10S12S17	SC	[71]
D3-39	Prunus domestica L.	NA	S6S17	SC	[71]
G16N-19	Prunus domestica L.	NA	S11S14S17	SC	[71]
Zempléni	Prunus spinosa L.	Nagykapos	S12SCSJSQ	SC	[72]
Dabai	Prunus pseudocerasus Lindl.	China	S1S2S5S8	SC	[73]
Taishanganying	Prunus pseudocerasus Lindl.	China	S1S2S4S6	NA	[73]
Satsuma	Prunus salicina Lindl.	USA	SfSh	NA	[74]
Huahongli	Prunus salicina Lindl.	China	SbS8	NA	[74]
Sordum	Prunus salicina Lindl.	Japan	SaSb	NA	[75]
Fenghuali			SdSg	NA	[74]
Pingguoli	Prunus salicina Lindl.	China	S15S116	NA	[76]
Honeyrosa	Prunus salicina Lindl.	Japan	SbSg	SC	[77]
Bullbank	Prunus salicina Lindl.	USA	SKS8	NA	[74]
Daqingke	Prunus salicina Lindl.	China	SeS20	NA	[74]
Huangguli	Prunus salicina Lindl.	China	SeS12	NA	[74]
Wanshuhuanai	Prunus salicina Lindl.	China	S8S9	NA	[74]
Zhengzhouzaoli	Prunus salicina Lindl.	China	S10/32S15	NA	[74]
Sanyueli	Prunus salicina Lindl.	China	S10/32Ssany	NA	[74]
Saozouli	Prunus salicina Lindl.	China	S11S16	NA	[74]

Notes. NA = Not Applicable, SI = Self-incompatible, SC = Self-compatible.

Table 1. S-genotypes of some species belonging to Rosaceae.

Cultivar/Accession	Latin Name	Origin	S-Genotype	SC/SI	References
Huang Yan	Prunus persica (L.) Batsch	Yunnan	S2S2	SC	[25]
Bai Nian He	Prunus persica (L.) Batsch	Yunnan	S2S2	SC	[25]
Qing Si	Prunus persica (L.) Batsch	Yunnan	S2S2	SC	[25]
Long 1-2-4	Prunus kansuensis Rehder	Gansu	S1S2	SC	[25]
Zhang Bai 5	Prunus kansuensis Rehder	Gansu	S2S2	SC	[25]
Xinjiang Huang Rou	Prunus ferganensis (Kost. and Rjab.) Y.Y.Yao	Xinjiang	S1S2	SC	[25]
Hong Gan Lu	Prunus persica (L.) Batsch	Liaoning	S2S2	SC	[25]
Hun Chun Tao	Prunus persica (L.) Batsch	Jilin	S1S2	SC	[25]
Da Hong Pao	Prunus persica (L.) Batsch	Hubei	S2S2	SC	[25]
Kharfi	Prunus persica (L.) Batsch	Tunisia	S1S2	SC	[60]
Meski	Prunus persica (L.) Batsch	Tunisia	S1S2	SC	[60]
Blanco Mollar	Prunus persica (L.) Batsch	Spain	S1S1	SC	[60]
Rojo Mollar	Prunus persica (L.) Batsch	Spain	S2S2	SC	[60]
Rubby Rich	Prunus persica (L.) Batsch	USA	S1S1	SC	[60]
Spring Lady	Prunus persica (L.) Batsch	USA	S1S1	SC	[60]
Sun Late	Prunus persica (L.) Batsch	USA	S1S2	SC	[60]
Rich May	Prunus persica (L.) Batsch	USA	S1S2	SC	[60]
Tasstour Hamra Tardive	Prunus salicina Lindl.	NA	SfSk	SI	[53]
Ain Bagra1	Prunus salicina Lindl.	NA	SfSc	SI	[53]
Sauvage	Prunus salicina Lindl.	NA	SfSc	SI	[53]
Tasstour Hamra précoce	Prunus salicina Lindl.	NA	SfSg	SI	[53]
Bedri1	Prunus salicina Lindl.	NA	SeSh	SC	[53]
Santa Rosa (C2)	Prunus salicina Lindl.	NA	ScSe	SC	[53]
Mulata	Prunus domestica L.	NA	S2S5S6S7 S12	NA	[53]
President	Prunus domestica L.	NA	S1S5S7S9	NA	[53]
Meski Kbira Kahla	Prunus insititia L.	NA	S6S7S8S10	NA	[53]
Zenou	Prunus insititia L.	NA	S1S2S10 S11	NA	[53]
Bebecou	Prunus armeniaca L.	NA	S6SC	SC	[61]
Castlebrite	Prunus armeniaca L.	NA	S2S2	SC	[61]
Castleton	Prunus armeniaca L.	NA	S1S2	SC	[61]
Orange Red	Prunus armeniaca L.	NA	S6S17	SI	[61]
SEO	Prunus armeniaca L.	NA	S6S17	SI	[61]
Velázquez	Prunus armeniaca L.	NA	S5S20	SI	[61]
Cheyenne	Prunus armeniaca L.	NA	S6S9	SI	[62]
Primaya	Prunus armeniaca L.	NA	S1S6	SI	[62]
Fiamma	Prunus armeniaca L.	NA	ScSc	SC	[21]
Summit	Prunus avium (L.)	NA	S1S2	NA	[63]
Sunburst	Prunus avium (L.)	NA	S3S4	NA	[63]
Emperor Francis	Prunus avium (L.)	NA	S3S4	NA	[63]
Vanda	Prunus avium (L.)	NA	S1S6	NA	[63]
Fragaria viridis 42	Fragaria viridis Weston	NA	SaSb	SI	[15]
Xiyeqing	Prunus mume Siebold and Zucc.	China	S2S15	SI	[64]
Zaohong	Prunus mume Siebold and Zucc.	China	S2S15	SC	[64]
Ruantiaohongmei	Prunus mume Siebold and Zucc.	NA	S14S13	NA	[65]
Xiaoyezhugan	Prunus mume Siebold and Zucc.	NA	S3S33	NA	[65]
Zhonghong	Prunus mume Siebold and Zucc.	NA	S3S24	NA	[65]
Meilinhong	Prunus mume Siebold and Zucc.	NA	S37S1	NA	[65]
Dalongmei	Prunus mume Siebold and Zucc.	NA	S20S30	NA	[65]
Huasu	Pyrus communis L.	NA	S5S108	NA	[66]
Huanghua	Pyrus communis L.	NA	S1S2	NA	[66]
Manfeng	Pyrus communis L.	NA	S3S4	NA	[66]
Yunnan Mali	Pyrus communis L.	NA	S12S51	NA	[66]
Ambrosia	Malus domestica (Suckow) Borkh.	NA	S3S28	NA	[67]
Goodland	Malus domestica Borkh.	NA	S11S55	NA	[67]
Newtown Pippin	Malus domestica (Suckow) Borkh.	NA	S2S7	NA	[67]
Minneiska	Malus domestica (Suckow) Borkh.	NA	S24S55	NA	[67]
Marubakaidou	Malus prunifolia (Willd.) Borkh.	NA	S1S2	NA	[68]
A18	Prunus tenella Batsch	Serbia	S2S3	NA	[69]
A10	Prunus tenella Batsch	Serbia	S1S5	NA	[69]
A18	Prunus tenella Batsch	Serbia	S2S3	NA	[69]
A3	Prunus tenella Batsch	Serbia	S8S9	NA	[69]
A14	Prunus tenella Batsch	Serbia	S2S5	NA	[69]
A17	Prunus tenella Batsch	Serbia	S2S3	NA	[69]
Cigany	Prunus cerasus L.	Azerbaijan	S6m2S9S26S36b2		[70]
Erdi Botermo	Prunus cerasus L.	Azerbaijan	S4S6mS35S36a		[70]
A8	Prunus tenella Batsch	Serbia	S4S9	NA	[69]
A6	Prunus tenella Batsch	Serbia	S7S8	NA	[69]
A9	Prunus tenella Batsch	Serbia	S7S8	NA	[69]
A11	Prunus tenella Batsch	Serbia	S1S5	NA	[69]
A15	Prunus tenella Batsch	Serbia	S6S8	NA	[69]
Muir Beauty	Prunus domestica L.	NA	S10S17	SC	[71]
G45N-35	Prunus domestica L.	NA	S8S14S16	SI	[71]
G40N-34	Prunus domestica L.	NA	S4S7	SI	[71]
Improved French	Prunus domestica L.	NA	S10S12S17	SC	[71]
3-8E-46RR	Prunus domestica L.	NA	S1S3S6S17	SC	[71]
Sutter	Prunus domestica L.	NA	S3S10S12S17	SC	[71]
D3-39	Prunus domestica L.	NA	S6S17	SC	[71]
G16N-19	Prunus domestica L.	NA	S11S14S17	SC	[71]
Zempléni	Prunus spinosa L.	Nagykapos	S12SCSJSQ	SC	[72]
Dabai	Prunus pseudocerasus Lindl.	China	S1S2S5S8	SC	[73]
Taishanganying	Prunus pseudocerasus Lindl.	China	S1S2S4S6	NA	[73]
Satsuma	Prunus salicina Lindl.	USA	SfSh	NA	[74]
Huahongli	Prunus salicina Lindl.	China	SbS8	NA	[74]
Sordum	Prunus salicina Lindl.	Japan	SaSb	NA	[75]
Fenghuali			SdSg	NA	[74]
Pingguoli	Prunus salicina Lindl.	China	S15S116	NA	[76]
Honeyrosa	Prunus salicina Lindl.	Japan	SbSg	SC	[77]
Bullbank	Prunus salicina Lindl.	USA	SKS8	NA	[74]
Daqingke	Prunus salicina Lindl.	China	SeS20	NA	[74]
Huangguli	Prunus salicina Lindl.	China	SeS12	NA	[74]
Wanshuhuanai	Prunus salicina Lindl.	China	S8S9	NA	[74]
Zhengzhouzaoli	Prunus salicina Lindl.	China	S10/32S15	NA	[74]
Sanyueli	Prunus salicina Lindl.	China	S10/32Ssany	NA	[74]
Saozouli	Prunus salicina Lindl.	China	S11S16	NA	[74]

Notes. NA = Not Applicable, SI = Self-incompatible, SC = Self-compatible.

2.2. Male or Pollen Determinant—SFB Genes

The discovery and identification of S-RNase in Solanaceae species [5] facilitated the detection of the pollen S gene termed SFB in many species of Rosaceae, including sweet cherry [9,78] and Japanese apricot [7,10]. Prunus S-locus domains have been sequenced using genome walking, leading to the identification of S-RNase [6]. The genomic regions of almond S-RNase have undergone DNA sequencing and transcriptional investigations, revealing polymorphic and non-polymorphic S-locus F-box genes called SFB for the S haplotype-specific F-box protein gene and SLF for the S-locus F-box [8,79]. The SFB exhibits traits such as high allelic polymorphism, specific pollen expression, and physical proximity to the S-RNase. During the investigation, the same S-RNase gene found in SC and SI of the cherry species P. cerasus and P. avium was discovered in the cherry S-locus [9]. Prunus pollen-specific S genes usually have at least two ‘SFB’ and ‘SLF’ with relatively different structures. The pollen SFB gene from P. mume is named PmSFB. Together, all these supported the hypothesis that the male component in Prunus species GSI is SFB. Many Prunus SFB alleles are currently accessible, such as peach, apricot, Japanese apricot [80], and sweet cherry for SI study purposes (Table 2). Moreover, it should be underlined that due to the progress of research on the physiology and mechanism of self-(in)compatibility, which has occurred in the framework of horticulture in general and particularly in fruit production, this could be used in the improvement of breeding and productivity of fruit trees.

However, pollen-specific S gene ‘SFB’ has an intron in the untranslated region, compared to Plantaginaceous and Solanaceous SFLs, which do not have this. In Prunus species, SLFs/SLFLs belonging to the S-locus contain the domains of the F-box motif and FBA [25]. As previously mentioned in the introduction section, SFB exhibits two variable (V1 and V2) and two hypervariable (HVa and HVb) domains [13,60], which seemed hydrophilic or at least moderately hydrophobic, implying they may be displayed on the surface and play a significant role in the allele specificity of the interaction mechanism with S-RNase for the recognition response of non-self/self-S-RNases [25,81]. For instance, in protein interaction tests between S-RNases and different domains of SFB, the S-RNases did not interact with the SFB F-box region. In contrast, they interacted with the whole sequence and its variable and hypervariable regions [25] (Figure 2).

Table 2. SFB alleles or genotypes of some species belonging to Rosaceae.

Cultivar /Accession	Latin Name	Origin	SFB Alleles-or Genotype	SC/SI	References
Meiguili	Prunus salicina Lindl.	NA	PsSFB-c/PsSFB-e	NA	[82]
Nvgelei	Prunus salicina Lindl.	NA	PsSFB-c/PsSFB-h	NA	[82]
Daqiandi	Prunus mume Siebold and Zucc.	Nanjing	PmSFB2/ PmSFB22	NA	[83]
Huangjiazuanshi	Prunus salicina Lindl.	NA	PsSFB-e/PsSFB-h	NA	[82]
Heibaoshi	Prunus salicina Lindl.	NA	PsSFB-b/PsSFB-h	NA	[82]
Nanko	Prunus mume Siebold and Zucc.	NA	PmSFB1/PmSFB7	SI	[10]
Younai	Prunus salicina Lindl.	NA	PsSFB-f/PsSFB-h	NA	[82]
Huangpili	Prunus salicina Lindl.	NA	PsSFB-f/PsSFB-7	NA	[82]
Dalizhong	Prunus mume Siebold and Zucc.	Nanjing	PmSFB7/PmSFB14	NA	[83]
Ozarkpremier	Prunus salicina Lindl.	NA	PsSFB-a/PsSFB-f	NA	[82]
Qiuji	Prunus salicina Lindl.	NA	PsSFB-b/PsSFB-h	NA	[82]
Xiangjiaoli	Prunus salicina Lindl.	NA	PsSFB-e/PsSFB-10	NA	[82]
Orleans-171	Prunus avium (L.)	NA	PaSFB7/ PaSFB10	SI	[84]
Zaohong	Prunus mume Siebold and Zucc.	Nanjing	PmSFB2/PmSFB15	SC	[28]
Katy	Prunus armeniaca L.	NA	Par-SFB8/ Par-SFB1	SC	[85]
Jiangjishantao (Wild peach)	Prunus davidiana (Carrière) Franch.	NA	PdSFB1/ PdSFB2	NA	[86]
Hongding	Prunus mume Siebold and Zucc.	Zhejiang	SFB18/SFB42	NA	[80]
Fupinggansutao	Prunus kansuensis Rehder	NA	PkSFB1/ PkSFB2	NA	[86]
Dabai	Prunus pseudocerasus Lindl.	China	PpsSFB1/PpsSFB5	SC	[73]
Taishanganying	Prunus pseudocerasus Lindl.	China	PpsSFB1/PpsSFB4/PpsSFB6	SC	[73]
Wickson	Prunus salicina Lindl.	NA	PsSFBk/SFBf	NA	[87]
Black Diamond	Prunus salicina Lindl.	NA	PsSFBe/SFBh	NA	[87]
Royal-Zee	Prunus salicina Lindl.	NA	PsSFBc/SFBe	NA	[87]
Songold	Prunus salicina Lindl.	NA	PsSFBh/SFBk	NA	[87]
Methely	Prunus salicina Lindl.	NA	PsSFBb/SFBg	NA	[87]
Shiro	Prunus salicina Lindl.	NA	PsSFBg/SFBf	NA	[87]
Golfrose	Prunus salicina Lindl.	NA	PsSFBb/SFBc	NA	[87]
Newyorker	Prunus salicina Lindl.	NA	PsSFBe/SFBk	NA	[87]

Notes. NA = Not Applicable.

Table 2. SFB alleles or genotypes of some species belonging to Rosaceae.

Cultivar /Accession	Latin Name	Origin	SFB Alleles-or Genotype	SC/SI	References
Meiguili	Prunus salicina Lindl.	NA	PsSFB-c/PsSFB-e	NA	[82]
Nvgelei	Prunus salicina Lindl.	NA	PsSFB-c/PsSFB-h	NA	[82]
Daqiandi	Prunus mume Siebold and Zucc.	Nanjing	PmSFB2/ PmSFB22	NA	[83]
Huangjiazuanshi	Prunus salicina Lindl.	NA	PsSFB-e/PsSFB-h	NA	[82]
Heibaoshi	Prunus salicina Lindl.	NA	PsSFB-b/PsSFB-h	NA	[82]
Nanko	Prunus mume Siebold and Zucc.	NA	PmSFB1/PmSFB7	SI	[10]
Younai	Prunus salicina Lindl.	NA	PsSFB-f/PsSFB-h	NA	[82]
Huangpili	Prunus salicina Lindl.	NA	PsSFB-f/PsSFB-7	NA	[82]
Dalizhong	Prunus mume Siebold and Zucc.	Nanjing	PmSFB7/PmSFB14	NA	[83]
Ozarkpremier	Prunus salicina Lindl.	NA	PsSFB-a/PsSFB-f	NA	[82]
Qiuji	Prunus salicina Lindl.	NA	PsSFB-b/PsSFB-h	NA	[82]
Xiangjiaoli	Prunus salicina Lindl.	NA	PsSFB-e/PsSFB-10	NA	[82]
Orleans-171	Prunus avium (L.)	NA	PaSFB7/ PaSFB10	SI	[84]
Zaohong	Prunus mume Siebold and Zucc.	Nanjing	PmSFB2/PmSFB15	SC	[28]
Katy	Prunus armeniaca L.	NA	Par-SFB8/ Par-SFB1	SC	[85]
Jiangjishantao (Wild peach)	Prunus davidiana (Carrière) Franch.	NA	PdSFB1/ PdSFB2	NA	[86]
Hongding	Prunus mume Siebold and Zucc.	Zhejiang	SFB18/SFB42	NA	[80]
Fupinggansutao	Prunus kansuensis Rehder	NA	PkSFB1/ PkSFB2	NA	[86]
Dabai	Prunus pseudocerasus Lindl.	China	PpsSFB1/PpsSFB5	SC	[73]
Taishanganying	Prunus pseudocerasus Lindl.	China	PpsSFB1/PpsSFB4/PpsSFB6	SC	[73]
Wickson	Prunus salicina Lindl.	NA	PsSFBk/SFBf	NA	[87]
Black Diamond	Prunus salicina Lindl.	NA	PsSFBe/SFBh	NA	[87]
Royal-Zee	Prunus salicina Lindl.	NA	PsSFBc/SFBe	NA	[87]
Songold	Prunus salicina Lindl.	NA	PsSFBh/SFBk	NA	[87]
Methely	Prunus salicina Lindl.	NA	PsSFBb/SFBg	NA	[87]
Shiro	Prunus salicina Lindl.	NA	PsSFBg/SFBf	NA	[87]
Golfrose	Prunus salicina Lindl.	NA	PsSFBb/SFBc	NA	[87]
Newyorker	Prunus salicina Lindl.	NA	PsSFBe/SFBk	NA	[87]

Notes. NA = Not Applicable.

3. Research Achievements on Self-(in)Compatibility Mechanism Understanding and Perspectives in Fruit Tree Species

3.1. Self-Compatibility Mutation, S-RNase Recognition System

Self-incompatibility impedes self-pollination in plants. Most herbaceous or annual crops lost their self-incompatibility features during domestication or evolution and became self-compatible (SC). In contrast, most fruit species and/or cultivars have retained their SI to date. This may be due to their reproductive issues and their long generation time and size [88]. The genetic mechanism of this phenomenon has, for a long time, intrigued the interest of horticultural researchers. However, mutations have been found to confer SC in several of these fruit plants’ species and cultivars [27,61,89,90,91]. In the S-locus, the S-RNase gene mutations that result in S-RNase failure are proven to induce SC in Solanaceae and Rosaceae [10]. For instance, in Prunus, SC is imparted via limited S-RNase transcription, which results in low S-RNase accumulation in the female component [10]. Hence, it was assumed that a low expression of S-RNase or its absence in the female component conferring SC is a fundamental and widespread characteristic of S-RNase-based GSI.

All notorious Solanaceous and Plantaginaceous pollen part mutations (PPMs) are related to an antagonistic interaction, such as two distinct pollen S alleles in a single pollen grain [23,92,93]. Alterations that interrupt pollen S (SLF) function in the Solanaceous and Plantaginaceous species families have not yet been identified. Thus, it is assumed that they confer either SI or lethality, whereas these alterations interrupt pollen S (SFB) function in Prunus species, resulting in SC [21,23,24,94]. As noted previously, only SFB and SCF/SLFL recognize S-RNase in SC pollen tubes, indicating that SFB and SLFL are the prominent participants in the polyubiquitination of S-RNases in Prunus species [95]. Likewise, using a yeast two-hybrid system as well as in vitro ubiquitination tests, it was revealed that SLFL is a component of the SCF complex in S-RNase recognition that is already absorbed in the pollen tubes, and their polyubiquitination in peach (a common self-compatible Prunus species) was investigated [25]. However, following S-RNase absorption in the pollen tubes, auto-S-RNase could be recognized and protected by SFB; the SLFL proteins could not target S-RNase due to their lack of recognition. As a result of the SFB mutation, auto-S-RNase lost its protection; SLFL detected and targeted auto-S-RNase during polyubiquitination, resulting in its breakdown, followed by pollen tube elongation and fertilization achievement [25]. Consistently, in previous studies, authors have reported the presence of Prunus species’ self-incompatible S haplotype mutant versions in self-compatible peaches, involved in their self-compatibility. The mutated determinants of pollen (SFB gene) are encoded by haplotypes S1 and S2 and encode the mutated determinants of pollen (SFB gene), and the function of S-RNase, or the determinant of the pistil, is disrupted in peach [96]. Therefore, in most Prunus species, particularly peach, self-compatibility is more closely associated with mutations in S-locus genes than other factors. In addition, it is difficult to rule out the possibility that mutations producing or affecting sex functions result from hybridization.

In an earlier study, the extracted DNA from leaves and styles of SC and SI P. dulcis accessions were subjected to the DNA bisulfite modification treatment known as ‘MethylEasy’. Sf-RNase PCR amplification was successfully performed using fifteen specific primers designed to be situated in the upstream section of Sf-RNase. No change was detected in Sf-RNase introns in the acquired sequences. However, in the upstream region of the Sf-RNases (5′-flanking region) of SC cultivars, four cytosine residues could not be converted to thymine, indicating the presence of methylation [97]. In every instance, these methylated cytosine CG and CNG forms were present, with adenine as the N nucleotide. Previous research suggests that DNA methylation could be a controller component to inhibit gene expression [98]. This suggestion lends credence to the notion that the observed variations are not ‘anomalies’ but distinct features of the exact underlying mechanism. It is also reported that essential roles are played by histone proteins and epigenetic changes to DNA bases in the control of gene transcription, genome stability, biological processes, and chemical alteration of the DNA to activate or inactivate the gene [99]. According to the findings, it is proposed that these regulatory aspects may have emerged as an active control mechanism for Sf-RNase expression and then conferred the SC in some cultivars of P. dulcis. Consequently, epigenetic alterations could offer new prospects for cultivar improvement, specifically molecular breeding for the generation of SC cultivars with fruit production advantages compared to SI cultivars (Table 3).

It has been revealed that, using S-RNase gene-specific PCR and genomic DNA blot studies, empirically known SC cultivars of P. mume shared an S-RNase, termed Sf-RNase. A segregation study supported the co-segregation of Sf-RNase and SC [100]. However, changes between the amino acid sequences produced from Sf-RNase and other SI S-RNases signify that pollen S could be involved in the SC in the Sf haplotype [101]. DNA methylation in similar Sf-RNase had been found to confer SC in some almond cultivars. The mutation in SFBf, which results in mutant SC pollen, is identical to that of sweet cherry SFB4’, as indicated by DNA sequence analysis [94]. The SFBf coding region contains a 6.8 kb insertion in the center, which results in transcripts for an abnormal SFB that lacks the C-terminal half, which is known to include putatively S-specific hypervariable domains [94]. Since the Sf haplotype provides SC in P. mume, a genetic marker for SC in this species was established. Sf-RNase-specific PCR bands were effectively produced using a primer pair set derived from the Sf-RNase unique sequence’s second intron [102]. Additionally, loop-mediated isothermal amplification (LAMP) primers designed from a 6.8 kb insertion fragment sequence were developed to determine the Sf haplotype [103]. Thus, during the SC breeding program for main Prunus species, especially in Japanese apricot production regions, which are widely distributed and significant economic fruit crops in temperate areas. At the earliest phases of development, Sf-carrying SC individuals could be identified using the well-established Sf-typing technology.

‘Currot’ (S_CS_C) and ‘Canino’ (S₂S_C) are two SC cultivars of apricots that share the naturally occurring SC haplotype. Sequence analysis revealed that while the SC S-RNase gene is unaffected, the SFBc gene contains a 358 bp insertion, producing a shortened protein. This genetic variation is related to SI breakdown [104,105]. Moreover, they revealed new F-box genes expressing a hitherto undescribed protein with substantial sequence homology to Prunus SFB proteins [7,8,104]. However, the evidence excludes them as the source of S-heteroallelic pollen (S-locus) or the pollen-part mutation [104]. A study compared two Japanese apricot cultivars with different phenotypes, including SC and SI [28]. Mutation insertion or deletion has not been found in nucleotides and amino acid sequences of S-RNases and SFBs alleles. Moreover, the alleles of the SFBs and S-RNases have been primarily expressed in the pollen and pistils, respectively, with similar expression levels in both SC and SI cultivars. However, they discovered new F-box genes in a P. mume SC cultivar identical to those previously identified in apricot [28,104], which could be related to the SC system in the mentioned cultivar [28]. In contrast, PPMs have been identified as the cause of SC in P. mume [24,94]. These findings support the hypothesis that S-locus components and S-locus-independent variables are necessary for GSI study in Prunus. Furthermore, we proposed that the factors leading to SC conferring in plants could vary widely across plant families, species, and even cultivars, such as in the case of the Japanese apricot.

Table 3. Mutations and genetic variations cause the breakdown of self-incompatibility in Rosaceae species.

Accessions/ Cultivars	Latin Name	Affected Part at the S-Locus	Gene/ Allele	Types of the Mutation and Genetic Variations	References
Currot	Prunus armeniaca L.	Pollen	SFB(c)	An insertion of 358 bp	[104]
Canino	Prunus armeniaca L.	Pollen	SFB(c)	An insertion of 358 bp	[104]
Fiamma	Prunus armeniaca L.	Pollen	SFB	Insertion of a transposable element at a position +904 to 1261 bp in SFB	[21]
Orihime	Prunus mume Siebold and Zucc.	Pollen	SFBf	An insertion of 6.8 Kbp in the middle of the SFBf coding region	[81,94]
Cristobalina	Prunus avium (L.)	Outside S-locus	MGST	Insertion of a transposon-like sequence in MGST promoter region	[27]
Feicheng Hong Li 6	Prunus persica L. Batsch	Pollen	SFB4m	An insertion of 4949 bp fragment	[25]
Guang He Tao	Prunus mira Koehne	Pollen	SFB2m	An insertion of 5 bp in SFB2m sequence	[25]
Xinjiang Huang Rou	Prunus kansuensis Rehder	Pollen	SFB1m	An insertion of 155 bp Insertion in SFB1m sequence	[25]
ErdiB-termo	Prunus cerasus L.	Style	S6-Nasem	An insertion of 2600 bp upstream in S6-RNase	[106]
Osa-N-jisseiki	Pyrus pyrifolia (Burm.f.) Nakai	Style	S4-RNase	Deletion of a 236 kb region	[107]
Yanzhuang	Pyrus × bretschneideri Rehder	Style	S21-RNase	The residue of glycine-to-valine mutation in the conserved region C2 inhibits RNase activity of mutated S-RNase. This substitution breakdowns self-incompatibility in some plants	[108]
Unknown	Fragaria nilgerrensis Schlecht. ex J.Gay	Style	S-RNase	Loss of S-RNase	[109]
Wild Fragaria vesca V4	Fragaria vesca L.	Style	S-RNase	Loss of S-RNase	[109]
Unknown	Fragaria iinumae Makino	Style	S-RNase	Loss of S-RNase	[109]
Fragaria vesca 41	Fragaria vesca L.	Style	S-RNase	Loss of S-RNase	[15]
Fragaria nilgerrensis 45	Fragaria nilgerrensis Schlecht. ex J.Gay	Style	S-RNase	Loss of S-RNase	[15]
Fragaria mandshurica 43	Fragaria mandshurica Staudt	Style	S-RNase	Loss of S-RNase	[15]
Benihoppe	Fragaria × ananassa (Weston) Duchesne ex Rozier	Style	S-RNase	Loss of S-RNase	[15]
Blanquerna	Prunus dulcis D. A. Webb	Style	Sf-RNase	DNA methylation in Sf -RNase (epigenetic changes in several cytosine residues were detected in a fragment of 4700 bp of the 5′ upstream region)	[97]
Soleta	Prunus dulcis D. A. Webb	Style	Sf-RNase	DNA methylation in Sf -RNase (epigenetic changes in several cytosine residues were detected in a fragment of 4700 bp of the 5′ upstream region)	[97]

Table 3. Mutations and genetic variations cause the breakdown of self-incompatibility in Rosaceae species.

Accessions/ Cultivars	Latin Name	Affected Part at the S-Locus	Gene/ Allele	Types of the Mutation and Genetic Variations	References
Currot	Prunus armeniaca L.	Pollen	SFB(c)	An insertion of 358 bp	[104]
Canino	Prunus armeniaca L.	Pollen	SFB(c)	An insertion of 358 bp	[104]
Fiamma	Prunus armeniaca L.	Pollen	SFB	Insertion of a transposable element at a position +904 to 1261 bp in SFB	[21]
Orihime	Prunus mume Siebold and Zucc.	Pollen	SFBf	An insertion of 6.8 Kbp in the middle of the SFBf coding region	[81,94]
Cristobalina	Prunus avium (L.)	Outside S-locus	MGST	Insertion of a transposon-like sequence in MGST promoter region	[27]
Feicheng Hong Li 6	Prunus persica L. Batsch	Pollen	SFB4m	An insertion of 4949 bp fragment	[25]
Guang He Tao	Prunus mira Koehne	Pollen	SFB2m	An insertion of 5 bp in SFB2m sequence	[25]
Xinjiang Huang Rou	Prunus kansuensis Rehder	Pollen	SFB1m	An insertion of 155 bp Insertion in SFB1m sequence	[25]
ErdiB-termo	Prunus cerasus L.	Style	S6-Nasem	An insertion of 2600 bp upstream in S6-RNase	[106]
Osa-N-jisseiki	Pyrus pyrifolia (Burm.f.) Nakai	Style	S4-RNase	Deletion of a 236 kb region	[107]
Yanzhuang	Pyrus × bretschneideri Rehder	Style	S21-RNase	The residue of glycine-to-valine mutation in the conserved region C2 inhibits RNase activity of mutated S-RNase. This substitution breakdowns self-incompatibility in some plants	[108]
Unknown	Fragaria nilgerrensis Schlecht. ex J.Gay	Style	S-RNase	Loss of S-RNase	[109]
Wild Fragaria vesca V4	Fragaria vesca L.	Style	S-RNase	Loss of S-RNase	[109]
Unknown	Fragaria iinumae Makino	Style	S-RNase	Loss of S-RNase	[109]
Fragaria vesca 41	Fragaria vesca L.	Style	S-RNase	Loss of S-RNase	[15]
Fragaria nilgerrensis 45	Fragaria nilgerrensis Schlecht. ex J.Gay	Style	S-RNase	Loss of S-RNase	[15]
Fragaria mandshurica 43	Fragaria mandshurica Staudt	Style	S-RNase	Loss of S-RNase	[15]
Benihoppe	Fragaria × ananassa (Weston) Duchesne ex Rozier	Style	S-RNase	Loss of S-RNase	[15]
Blanquerna	Prunus dulcis D. A. Webb	Style	Sf-RNase	DNA methylation in Sf -RNase (epigenetic changes in several cytosine residues were detected in a fragment of 4700 bp of the 5′ upstream region)	[97]
Soleta	Prunus dulcis D. A. Webb	Style	Sf-RNase	DNA methylation in Sf -RNase (epigenetic changes in several cytosine residues were detected in a fragment of 4700 bp of the 5′ upstream region)	[97]

3.2. Modifiers and Genetic Factors Involving in Self-(in)-Compatibility Regulation

Different complex genetic mechanisms are involved in S-RNase-based GSI systems [48,110]. However, SI evidence depends not only on S-locus main factors (pistil S gene and pollen S gene) but also on modulator genes involved in complex mechanisms [111]. Since discovering the first non-S-site modifiers in Solanaceae [112,113], many non-S-site modifiers have been increasingly identified in Rosaceae. These modifier genes have been found in broad types of signal transduction systems, including calcium signaling [111,114,115], reactive oxygen species [116], hormone signaling [117], phosphoinositide signaling [118,119], and biochemical metabolic processes [110,120,121,122,123]. They could have variable effects on the occurrence of self-incompatibility. The apple pollen ABC transporter MdABCF can let S-RNase penetrate the pollen tube [124]; the calcium-regulating factor MdCBL5 may interact with S-RNase to regulate pollen tube growth and is impacted by S-RNase. In the S-RNase regulation seen in Ref. [114], MdMVG, an actin-binding protein (ABP) expressed in pollen tubes, can directly bind to self-S-RNase and restrict its cleavage of F-actin, disrupt the equilibrium of the F-actin cycle, and inhibit self-pollen tube growth [125].

S-RNase penetrates the apple pollen tube, induces the accumulation of jasmonic acid, and afterward motivates the defensive protein MdD1 to bind with the active site of S-RNase and restrict its action. Before molecular recognition, decreasing or restricting S-RNase cytotoxicity is crucial to enable normal pollen tube elongation [126]. A ParMDO gene, which encodes a disulfide-like A oxidoreductase, is sited in the nearly 134 Kb region of the M site of chromosome 3 of P. armeniaca and is involved in SI response (disulfide bond A-like oxidoreductase). Self-compatible variants or alleles of the ParMDO gene have 358 bp MITE transposon insertion and lost function [127]. The insertion of the promoter of the MGST gene at the M site induced SC in the sweet cherry cultivar ‘Cristobalina’. Notably, the enzyme and the encoded product of the ParMDO gene-encoding glutathione S-transferase belong to the thioredoxin superfamily [27]. Matsumoto and Tao [95] revealed that the MGST and DnaJ proteins from sweet cherry are subunits of the SCF complex involved in the SI system.

On the other hand, the serine/threonine kinase protein has been recently reported to be involved in pollen tube recognition of the non-self- and self-S-RNase protein reaction of GSI in almonds [128]. Similarly, GLABROUS1 enhancer-binding protein-like (GEBPL) is implicated in pollen–pistil interactions in the GSI system in P. dulcis [129]. The above information indicates that, in addition to the main factors related to the S-locus, several kinds of factors unrelated to this locus are involved in the mechanisms of the GSI.

3.3. Overview of Molecular Recognition Mechanism between Pollen and Pistil Determinants Genes

Non-self-S-RNase toxicity is acknowledged by male-determinant (SFB/SFBBs/SLFs according to the species) factor F-box protein after entering. The ubiquitin system (Ubiquitin-proteasome system (UPS)) has been associated with self-incompatibility reactions because F-box protein is an E3 or SCF complex element of the ubiquitin ligase implicated in the ubiquitination and degradation of proteins in fruit tree species [130]. Concerning the mechanism via which S-RNase enters pollen cells and interacts with male determinants, there seem to be two hypotheses or models explaining the discrepancies between the effects of male determinant mutations and hetero-S haplotype diploid pollen. The ubiquitinated protein system is used to detoxify non-self-S-RNases in pollen tubes, as well as a model of non-self-collaborative recognition (cooperative non-self-recognition) and one-factor self-recognition models (self-recognition) [48,131]. Multiple non-self F-box (SFB/SFBBs/SLFs) male determinants collaborate to distinguish S-RNase and degrade its toxicity based on the non-self-cooperative recognition model. In contrast, a single F-box male component detects S-RNase. According to the single-factor self-recognition model, it does not degrade the toxicity of the S-RNase inhibitory protein, enabling its toxicity to be exerted.

The molecular recognition of fruit trees is analogous and falls under non-self-cooperative recognition [132]. Once S-RNase penetrates the pollen tube, the male-determining factor F-box protein recognizes it. Non-self-S-RNase is ubiquitinated and tagged for degradation by the 26S proteasome mechanism. At the same time, self-S-RNase is withheld, which is attributable to the toxicity and cessation of average pollen tube growth [25,108,126,133]. S haplotypes encode several SLFs/SFBBs throughout this process, and each SLF/SFBB recognizes a single or many non-self-S-RNases. Subsequently, the 26S proteasome ubiquitinates and degrades it, enabling non-self-pollen tubes to grow and complete fertilization. When recognizing SLF/SFBBs of self-S-RNase, if the S haplotype is present, self-S-RNase will not be degraded via proteasomal degradation and has a toxic function; hence, the pollen tube ceases. S-RNase ubiquitination is controlled by the SCF complex, composed of F-box, Skp1/SSK1, Cullin1 (Cul1), and Rbx1, an E3 ubiquitin ligase, in which the F-box is the detection or recognition constituent of the SCF complex, which helps determine the selectivity of substrate binding, whereas Skp1 functions as a connector between the F-box and the F-box and the Cul1 protein, and Cul1 and Rbx1 compose the catalytic scaffold core [123,134]. Therefore, non-self-S-RNase is recognized and ubiquitinated in the ubiquitination degradation system. In the self-recognition approach, the common General Inhibitor (GI) of pollen expression cannot specifically connect or bind to all S-RNases in the pollen tube. In the situation of affinity, SFB cannot recognize the non-self-S-RNase, the non-self-S-RNase has been restricted via GI, and its toxicity is terminated. However, in case of incompatibility, according to Yamane and Tao [26], SFB can distinguish the self-S-RNase/GI complex, provoke GI polyubiquitination degradation, and release toxic S-RNase, resulting in the degeneration of the self-pollen tube (Figure 3).

4. Approaches Used for Self-Compatible Cultivar Breeding and Improvement

In blooming plants, it is typical for the emergence of many strategies and mechanisms to avoid self-fertilization and promote outcrossing, thus limiting the adverse effects of inbreeding. Gymnosperms and angiosperms have developed physical barriers between the male and female reproductive parts, such as dioecy, monoecy, dichogamy, and floral heteromorphy, to prevent autogamy [135]. However, in the angiosperm, including the species of the Rosaceae, SI has been the most widespread mechanism of inbreeding and its consequences [1,136]. A set of environmental and agroecological factors is, notably, the scarcity of suitable wind at the appropriate time for pollination as well as the insufficiency of pollination insects or vectors. Together, these cause a low fertilization rate of SI species and cultivars. This low fertilization rate reduces their productivity, the yield of the orchards, and the pomological quality of the fruits, leading to the reduction of producers’ income. Therefore, elucidating the mechanisms of SI/SC and improving SC cultivars has interested researchers and breeders. The application of the techniques of classical breeding and conventional breeding, such as in vitro plant selection, controlled crossing, molecular markers, metabolomics, proteomics, and transcriptomics, eases the detection of the significant agronomical features regulating the critical genes of interest in backward as well as forward breeding [137,138,139]. Classic and conventional approaches each have advantages and disadvantages. However, researchers have combined both methods in breeding programs for cultivar enhancement.

4.1. Classical Breeding Techniques

Classical breeding techniques have long served as the mainstay of plant species and accession cultivar development with suitable and desirable features. The hybridization of different cultivars, accessions, or germplasms of the species of Rosaceae, including stone fruit tree species as well as Prunus species, can be used via these techniques to combine the agronomical traits of interest, such as fruit quality, self-compatibility, and good yield [140,141,142]. Consequently, by repeatedly selecting and assessing progenies, breeders have a chance and the opportunity to acquire and improve cultivars containing self-compatibility phenotypes and genotypes. For instance, self-compatibility has been transferred into cultivars of almonds from peach and wild almonds [143]. Breeders can also generate Prunus species cultivars with self-compatibility features via the combination of conventional breeding methods and classical breeding techniques. Combining these classical techniques with modern tools, including molecular markers and biotechnological advancements, may accelerate the breeding process and increase the general efficacy of developing self-compatible cultivars of the species of the Rosaceae. Classical breeding requires patience and may only be successful after several generations.

4.2. Conventional Breeding Approaches

Excellent alternatives are needed to enhance Rosaceae species, including the Prunus genus. Several approaches, such as marker-assisted selection (MAS) methods and gene transformation technologies, are successfully used in enhancing Rosaceae species to produce higher yields and higher-quality fruits and nuts. Applying these techniques is a rapid and efficient means of saving time during crop improvement.

4.2.1. Marker-Assisted Selection

MAS has emerged as a promising approach to achieving desirable traits in plant species with molecular markers to allow breeders to develop crops quickly and efficiently with specific characteristics. MAS is used to characterize germplasm, diversity analysis, trait stacking, gene pyramiding, multi-trait introgression, and the genetic purity of various species of crops; these markers have been widely utilized in plant breeding [144]. The self-compatible allele S4 marker was implemented via MAS in sweet cherry [145]. Similarly, in apricot, the self-compatible genotypes were screened using a high-resolution melting analysis (HRMA) based on MAS [21]. Determining or identifying these alleles carries self-compatibility, which involves genotyping the offspring of cultivars or accessions. A set of trait-associated SNP (single nucleotide polymorphism) markers can be used to detect these variations. Consequently, fewer resources such as expertise and time will be needed for field use, maintenance, and long-term germplasm resource assessment. In summary, MAS is a useful tool for selecting Rosaceae species and cultivars and their accessions with self-compatibility features. These traits associated with the generated SNP markers help breeders select these plant germplasms effectively.

4.2.2. Gene Transformation Technologies

Gene transformation technologies represent a targeted approach to modify or regulate genes in the plant’s DNA molecule to provide self-compatible cultivars. In sweet cherry species, the irradiation technique generated S genes that were self-compatible cultivars. It was revealed that the irradiation of S genes caused mutations that made the related species self-compatible [146]. On the other hand, the transgenic strategy to create SC has not yet been used in Prunus plant species because of challenges with genetic modification in this genera. Therefore, using antisense aligonucleotides against the pollen genes, the self-compatible cultivars of Prunus species have been produced [147]. Some breeding methods include the classic breeding of Rosaceae species generally, and Prunus species particularly take many years. Genetic modification technology has the potential to make it easier to develop self-compatible Prunus cultivars successfully in a short time.

4.2.3. Genome Editing Technologies

Plant biotechnology in agriculture has been undergoing profound changes due to genome engineering. The recently developed gene editing methods make it more straightforward, faster, and more accurate than ever for improving crop species with desired agronomical traits [148]. Editing genes via the CRISPR/Cas9 system has developed into a strategy commonly used in many cultivated plant species to generate cultivars with specific features such as self-compatibility [149]. For instance, in potatoes, the CRISPR/Cas9 system has been successfully applied to selectively silence S-RNase genes to break down SI, creating SC cultivars of potato species [150,151]. There are challenges in producing SC cultivars in Prunus species via the transgenic method; genome editing is essential in enabling precise modifications that are made to target specific genes contained throughout the Prunus species genome without the addition of any foreign DNA, which can be an alternative for scientists to be used in order to generate SC cultivars in Prunus species. For example, since CRISPR/Cas9 technology can induce mutations for specific agronomical feature enhancement [152], it has been previously reported that PPMs or style part mutations caused SC in most stone fruits. They suggest that the CRISPR/Cas9 system can be successfully used to create SC cultivars in Prunus species.

5. Conclusions

Self-incompatibility is a major challenge in fruit production. Researchers have conducted a number of investigations throughout the years to understand the mechanism underlying self-incompatibility in the Rosaceae species. Hence, breeders have developed some SC cultivars. For instance, in recent years, there has been a prominent focus on the discovery and molecular characterization of S-determinants and the mechanism of the loss of SI in certain cultivars. Characterizing natural SC mutants adds to our understanding of the GSI process. Among these, some S-locus gene mutants confer self-compatibility and other molecules or factors outside of the S-locus to co-participate in the complex mechanism of S-RNase degradation, pollen tube growth, or rejection. Hence, discovering natural SC mutants adds to our understanding of GSI genetic regulation and molecular modulation. Furthermore, a conventional breeding technique was used to generate SC Prunus cultivars. We expect that such insights in this review will offer a reference for researchers in future research, thus understanding the GSI mechanism and producing self-compatible cultivars via significant and appropriate breeding approaches to contribute to increasing the fruit production of Rosaceae species as well as to increase farmers’ incomes.