Transposable elements cause the loss of self-incompatibility in citrus

Origin of a self-compatibility associated MITE in Petota and its application in hybrid potato breeding

Hybrid potato breeding offers a promising solution to tackle the challenges in potato breeding. However, most diploids are self-incompatible (SI), which hinders the development of inbred lines. S-locus inhibitor (Sli) is a 'master key' gene capable of conferring self-compatibility (SC) to most of the SI diploids, yet the regulatory mechanism underlying its male gamete-specific expression remains unclear, limiting its breeding potential. This study has uncovered that a miniature inverted-repeat transposable element (Mi-549) within the Sli promoter can affect the methylation pattern of the promoter, thereby regulating the pollen-specific expression of Sli as well as the SC phenotype in diploids. We delved into the origin of Mi-549 within Petota and found that Mi-549 was likely acquired fortuitously in wild Solanum lesteri but was not favored during domestication, probably due to the asexual propagation nature of potato. Although Mi-549 and its impacts on Sli as well as SC are not selected, screening of Mi-549 identified three novel SC accessions that belong to S. lesteri, Solanum neocardenasii and Solanum stenotomum, which enrich the germplasm pool associated with stress and pest resistance and hold significant value for breeding applications.

Unveiling the metaxenia effect and its regulatory mechanism in sucrose synthesis through integration of dominant resources in pear

Breeding efforts have led to numerous superior pear varieties. However, challenges persist in pear cultivation, with limited cultivar diversity and underutilization of local varieties, resulting in an unbalanced industry. Metaxenia offers potential for breeding excellent pear varieties suitable for different ecological conditions. Yet, the precise effects and mechanisms of metaxenia on pear fruit remain unclear. This study examined six pear varieties through artificial pollination with four primary pear varieties ('Cuiguan', 'Chuxialǜ', 'Huangjin', and 'Yuguan'). Eight fruit quality indicators, such as sugar content and sugar-acid ratio, were assessed, and results showed that the choice of pollinating variety significantly affected pear fruit quality. Pollen from 'Huixi' and 'Jinhuazao' resulted in superior fruit quality in 'Cuiguan' pears. Similarly, 'Jinhuazao' and 'Xiyuanbai' outperformed the control group in pollinating 'Chuxialǜ'. Additionally, 'Xiyuanbai' and 'Xipi' improved 'Huangjin' pear quality post-pollination. Cross-pollinating 'Yuguan' with pollen from 'Huixi', 'Xipi', and 'Xiyuanbai' produced hybrid fruits of superior quality. The study also explored metaxenia's impact on sugar metabolism in 'Cuiguan' pears, revealing significant effects on sugar accumulation processes. Further analysis highlighted the regulatory roles of specific genes in sucrose accumulation and degradation within fruits. These findings provide insights into metaxenia's effects on pear fruit appearance, quality, and sucrose content variations, shedding light on underlying mechanisms. The study also offers valuable information for selecting pollinating trees and identifying desirable traits in pear crossbreeding efforts.

The Combination of Start-Codon-Targeted (SCoT) and Falling Stone (FaSt) Transposon-Specific Primers Provides an Efficient Marker Strategy for Prunus Species

A novel primer (FaSt-R) targeting the Prunus-specific Falling Stone (FaSt) non-autonomous transposon was combined with start-codon-targeted (SCoT) primers to assess genetic diversity in 12 cultivars from six Prunus species and 28 cultivars of European plum. Compared to SCoT-only analyses, the SCoT-FaSt combination produced fewer total bands but a higher percentage of polymorphic bands, while maintaining comparable values for polymorphism information content, resolving power, gene diversity, and Shannon's index. SCoT-FaSt markers generated bands across a broader size range, which made gel patterns less dense, enabling the more accurate detection of differentially amplified fragments. Neighbor-joining and principal component analyses confirmed that SCoT-FaSt markers provided sufficient phylogenetic resolution at both interspecific and intraspecific levels. The sequencing of 32 SCoT-FaSt amplicons revealed FaSt elements in 26 fragments, with SCoT primers preferentially annealing to GC-rich exonic and intergenic regions. Seventeen protein-coding and one RNA-coding gene were partially identified, with FaSt elements localized in UTRs and introns of genes with key physiological functions. Comparative analysis indicated a biased distribution of FaSt elements between the Cerasus and Prunus subgenera. In silico findings suggest that FaSt elements are more fragmented in cherry species, potentially contributing to subgeneric divergence. Overall, the SCoT-FaSt marker system is effective for evaluating Prunus genetic diversity, reconstructing phylogenetic relationships, and elucidating the genomic impact of an active Mutator-like transposon.

S-RNase evolution in self-incompatibility: Phylogenomic insights into synteny with Class I T2 RNase genes

S-RNases are essential in the gametophytic self-incompatibility (GSI) system of many flowering plants, where they act as stylar-S determinants. Despite their prominence, the syntenic genomic origin and evolutionary trajectory of S-RNase genes in eudicots have remained largely unclear. Here, we performed large-scale phylogenetic and microsynteny network analyses of T2 RNase genes across 130 angiosperm genomes, encompassing 35 orders and 56 families. S-like RNase genes in Cucurbitaceae species phylogenetically grouped with functionally characterized S-RNases in various species. Additionally, Cucurbitaceae S-like RNase genes showed conserved synteny with Class I T2 RNase genes. From this, we inferred that the well-characterized S-RNase genes (belonging to Class III-A genes) and Class I T2 RNase genes (located on duplicated genomic blocks) likely derived from the gamma triplication event shared by core eudicots. Additionally, we identified frequent lineage-specific gene transpositions of S-RNases and S-like RNases across diverse angiosperm lineages, including Rosaceae, Solanaceae, and Rutaceae families, accompanied by a significant increase in transposable element activity near these genes. Our findings delineate the genomic origin and evolutionary path of eudicot S-RNase genes, enhancing our understanding of the evolution of the S-RNase-based GSI system.

Recurrent excision of a hAT-like transposable element in CmAPRR2 leads to the "shooting star" melon phenotype

The external appearance of fruit commodities is an essential trait that has profound effects on consumer preferences. A natural melon variety, characterized by an uneven and patchy arrangement of dark green streaks and spots on the white-skinned rind, resembles shooting stars streaking across the sky; thus, this variety is called "Shooting Star" (SS). To investigate the mechanism underlying the SS melon rind pattern, we initially discovered that the variegated dark green color results from chlorophyll accumulation on the white skin. We then constructed a segregation population by crossing a SS inbred line with a white rind (WR) inbred line and used bulk segregant analysis (BSA) revealed that the SS phenotype is controlled by a single dominant gene, CmAPRR2, which has been previously confirmed to determine dark green coloration. Further genomic analysis revealed a hAT-like transposable element (TE) inserted in CmAPRR2. This TE in CmAPRR2 is recurrently excised from rind tissues, activating the expression of CmAPRR2. This activation promotes the accumulation of chlorophyll, leading to the variegated dark green color on the rind, and ultimately resulting in the SS rind phenotype. Therefore, we propose that the SS phenotype results from the recurrent excision of the hAT-like TE in CmAPRR2.

Alternative splicing and deletion in S-RNase confer stylar-part self-compatibility in the apple cultivar 'Vered'

Although self-incompatibility in apples (Malus × domestica Borkh.) is regulated by a single S-locus with multiple S-haplotypes that comprise pistil S (S-RNase) and pollen S genes, it is not desirable in commercial orchards because it requires cross-pollination to achieve stable fruit production. Therefore, it is important to identify and characterize self-compatible apple cultivars. However, little is known about self-compatibility (SC) and its underlying molecular mechanisms in apples. In this study, we discovered that 'Vered', an early maturing and low chilling-requiring apple cultivar, exhibits stable SC, which was evaluated via self-pollination tests. The S-genotype of 'Vered' was designated as S24S39sm. Results of genetic analysis of selfed progeny of 'Vered' revealed that SC is associated with the S39sm-haplotype, and molecular analyses indicated that it is caused by alternative splicing and a 205-bp deletion in S39sm-RNase. These events induce frameshifts and ultimately produce the defective S39sm-RNase isoforms that lack their C-terminal half. These results enabled us to develop a 117-bp DNA marker that can be used to assist in the selection of self-compatible apples with the dysfunctional S39sm-RNase. Thus, analysis of 'Vered' provided insights into the molecular mechanism of the very rare trait of natural stylar-part SC. Moreover, 'Vered' is a valuable genetic resource for breeding cultivars with SC and/or low chilling requirement in apple. Our findings contribute to a better understanding of self-compatible molecular mechanisms in apple and provide for the accelerated breeding of self-compatible apple cultivars.

Comparative Analysis of Transposable Elements in the Genomes of Citrus and Citrus-Related Genera

Transposable elements (TEs) significantly contribute to the evolution and diversity of plant genomes. In this study, we explored the roles of TEs in the genomes of Citrus and Citrus-related genera by constructing a pan-genome TE library from 20 published genomes of Citrus and Citrus-related accessions. Our results revealed an increase in TE content and the number of TE types compared to the original annotations, as well as a decrease in the content of unclassified TEs. The average length of TEs per assembly was approximately 194.23 Mb, representing 41.76% (Murraya paniculata) to 64.76% (Citrus gilletiana) of the genomes, with a mean value of 56.95%. A significant positive correlation was found between genome size and both the number of TE types and TE content. Consistent with the difference in mean whole-genome size (39.83 Mb) between Citrus and Citrus-related genera, Citrus genomes contained an average of 34.36 Mb more TE sequences than Citrus-related genomes. Analysis of the estimated insertion time and half-life of long terminal repeat retrotransposons (LTR-RTs) suggested that TE removal was not the primary factor contributing to the differences among genomes. These findings collectively indicate that TEs are the primary determinants of genome size and play a major role in shaping genome structures. Principal coordinate analysis (PCoA) of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) identifiers revealed that the fragmented TEs were predominantly derived from ancestral genomes, while intact TEs were crucial in the recent evolutionary diversification of Citrus. Moreover, the presence or absence of intact TEs near the AdhE superfamily was closely associated with the bitterness trait in the Citrus species. Overall, this study enhances TE annotation in Citrus and Citrus-related genomes and provides valuable data for future genetic breeding and agronomic trait research in Citrus.

The Identification and Analysis of the Self-Incompatibility Pollen Determinant Factor SLF in Lycium barbarum

Self-incompatibility is a widespread genetic mechanism found in flowering plants. It plays a crucial role in preventing inbreeding and promoting outcrossing. The genes that control self-incompatibility in plants are typically determined by the S-locus female determinant factor and the S-locus male determinant factor. In the Solanaceae family, the male determinant factor is often the SLF gene. In this research, we cloned and analyzed 13 S2-LbSLF genes from the L. barbarum genome, which are located on chromosome 2 and close to the physical location of the S-locus female determinant factor S-RNase, covering a region of approximately 90.4 Mb. The amino acid sequence identity of the 13 S2-LbSLFs is 58.46%, and they all possess relatively conserved motifs and typical F-box domains, without introns. A co-linearity analysis revealed that there are no tandemly repeated genes in the S2-LbSLF genes, and that there are two pairs of co-linear genes between S2-LbSLF and the tomato, which also belongs to the Solanaceae family. A phylogenetic analysis indicates that the S2-LbSLF members can be divided into six groups, and it was found that the 13 S2-LbSLFs are clustered with the SLF genes of tobacco and Petunia inflata to varying degrees, potentially serving as pollen determinant factors regulating self-incompatibility in L. barbarum. The results for the gene expression patterns suggest that S2-LbSLF is only expressed in pollen tissue. The results of the yeast two-hybrid assay showed that the C-terminal region of S2-LbSLFs lacking the F-box domain can interact with S-RNase. This study provides theoretical data for further investigation into the functions of S2-LbSLF members, particularly for the identification of pollen determinant factors regulating self-incompatibility in L. barbarum.