Characterization of Japanese Plum (Prunus salicina) PsMYB10 Alleles Reveals Structural Variation and Polymorphisms Correlating With Fruit Skin Color

Haplotype-resolved genome assembly provides new insights into the genomic origin of purple colour in Prunus mume

Prunus mume, an important ornamental woody plant in the Rosaceae family, contains many interspecific hybridizations. Purple colour is a breeding trait of aesthetic value for P. mume, but little is known about the origin and genetic architecture of this trait. Here we address these issues by producing a haplotype-resolved genome from an interspecific hybrid cultivar of P. mume (M) and P. cerasifera 'Pissardii' (C), named P. mume 'Meiren', followed by a detailed molecular characterization. The final length of the diploid genome is 499.47 Mb, with 250.66 Mb of haplotype M (HM) and 248.79 Mb of haplotype C (HC). Approximately 95.42% (476.61 Mb) of the phased assembly is further anchored to 16 homologous chromosomes. Based on the genomic variation, we identify a 1.8 Mb large-fragmented inversion (INV) on chromosome 1b of HC, which co-segregates with purple colour traits of 'Meiren' inherited from its purple C parent 'Pissardii'. We find that a MYB transcription factor, PmmMYB10.5b, resides at the distal breakpoint of the INV, which displays consistent allele-specific expression (ASE). By directly binding to the promoter of anthocyanin synthetic alleles, PmmMYB10.5b serves as a co-activator to promote anthocyanin accumulation in 'Meiren' organs. Notably, the INV identified in 'Meiren' is generated from 'Pissardii' rather than P. cerasifera, which alters the promoter sequence of PmmMYB10.5b, activates its expression and results in the purple colour trait. Results from this study shed light on the evolutionary origin of purple colour in 'Meiren' and could potentially provide guidance on the genetic improvement of colour traits in ornamental woody plants.

Molecular mechanisms underlying natural deficient and ultraviolet-induced accumulation of anthocyanin in the peel of 'Jinxiu' peach

Peach varieties that differ in red coloration due to varied anthocyanin accumulation result from transcriptional regulation by PpMYB10s, a group of specific R2R3 MYBs. Here we investigated the mechanisms driving a lack of anthocyanin in yellow-skinned 'Jinxiu' peach peel, as well as accumulation induced by UV irradiance. It was found that PpMYB10.1, PpMYB10.2 and PpMYB10.3 were positive regulators of anthocyanin accumulation, but the stimulation by PpMYB10.2 was weak. Low expression of PpMYB10.1 causes natural anthocyanin deficiency in 'Jinxiu' peel. However, the promoter sequences of PpMYB10.1 were identical in 'Jinxiu' and a naturally red-coloured peach 'Hujingmilu'. Therefore, potential negative regulator(s) upstream of PpMYB10.1 were explored. A novel R2R3-MYB repressor termed PpMYB80 was identified through comparative transcriptomic analysis and then functionally confirmed via transiently overexpressing and silencing in peach fruit, as well as transformation in tobacco. PpMYB80 directly binds to the promoter of PpMYB10.1 and inhibits its expression, but does not affect PpMYB10.3. In UV-exposed 'Jinxiu' fruit, expression of PpMYB10.3 was upregulated, while PpMYB10.1 remained low and PpMYB80 enhanced, which results in accumulation of anthocyanin in peel. This study revealed a transcriptional cascade involving PpMYB activators and repressors in regulating basal and UV-induced anthocyanin accumulation in peach peel.

High-density genetic map and quantitative trait loci map of skin color in hawthorn (Crataegus pinnatifida bge. Var. major N.E.Br.)

Fruit skin color is an important trait of the hawthorn tree, which has an important influence on fruit quality. Crataegus pinnatifida Bge. var. Major N.E.Br. Is one of the most widely cultivated varieties in China and has a long history of medicinal use. In recent years, it has attracted the attention of the world due to its nutritional and medicinal values. Skin color is the focus of breeders and food processors. At present, skin color-related genes have still not been mapped. In this study, "Shandong Da Mianqiu" (♀, red skin color), "Da Huang Mianzha" (♂, yellow skin color) and 131 F1 hybrids were used to construct genetic map of hawthorn by RAD-seq, and QTL mapping was performed by combining these features with the hue angle and the observed color. In this study, 13,260 SNP was assigned to 17 linkage groups, with an integrated map covering 2,297.75 cM was constructed. A total of 5 QTLs related to hawthorn skin color were detected on LG1, LG3 and LG15. Whether hue angle or pericarp color acts as phenotype for QTL mapping, the candidate genes include bHLH086, WD repeat regions and Myb-like. bHLH, WD and Myb play an important role in the color regulation of Hawthorn skin color. These results lay a solid foundation for QTL mapping and molecular marker-assisted breeding of hawthorn.

Genetic tapestry of Capsicum fruit colors: a comparative analysis of four cultivated species

KEY MESSAGE

Genome-wide association study of color spaces across the four cultivated Capsicum spp. revealed a shared set of genes influencing fruit color, suggesting mechanisms and pathways across Capsicum species are conserved during the speciation. Notably, Cytochrome P450 of the carotenoid pathway, MYB transcription factor, and pentatricopeptide repeat-containing protein are the major genes responsible for fruit color variation across the Capsicum species. Peppers (Capsicum spp.) rank among the most widely consumed spices globally. Fruit color, serving as a determinant for use in food colorants and cosmeceuticals and an indicator of nutritional contents, significantly influences market quality and price. Cultivated Capsicum species display extensive phenotypic diversity, especially in fruit coloration. Our study leveraged the genetic variance within four Capsicum species (Capsicum baccatum, Capsicum chinense, Capsicum frutescens, and Capsicum annuum) to elucidate the genetic mechanisms driving color variation in peppers and related Solanaceae species. We analyzed color metrics and chromatic attributes (Red, Green, Blue, L*, a*, b*, Luminosity, Hue, and Chroma) on samples cultivated over six years (2015-2021). We resolved genomic regions associated with fruit color diversity through the sets of SNPs obtained from Genotyping by Sequencing (GBS) and genome-wide association study (GWAS) with a Multi-Locus Mixed Linear Model (MLMM). Significant SNPs with FDR correction were identified, within the Cytochrome P450, MYB-related genes, Pentatricopeptide repeat proteins, and ABC transporter family were the most common among the four species, indicating comparative evolution of fruit colors. We further validated the role of a pentatricopeptide repeat-containing protein (Chr01:31,205,460) and a cytochrome P450 enzyme (Chr08:45,351,919) via competitive allele-specific PCR (KASP) genotyping. Our findings advance the understanding of the genetic underpinnings of Capsicum fruit coloration, with developed KASP assays holding potential for applications in crop breeding and aligning with consumer preferences. This study provides a cornerstone for future research into exploiting Capsicum's diverse fruit color variation.

Insights into tissue-specific anthocyanin accumulation in Japanese plum (Prunus salicina L.) fruits: A comparative study of three cultivars

In the present study, three matured Japanese plum cultivars with different colored peel and flesh were selected to mine the key transcription factors regulating anthocyanin formation in tissues. Results showed that PsMYB10 was correlated with structural genes C4H, F3H, and ANS. PsMYB6 could positively regulate C4H (r = 0.732) and accumulated anthocyanins in Sanhua plum's flesh. Sanhua plum has the highest phenolic and anthocyanin contents (10.24 ± 0.37 gallic acid equivalent mg g-1 dry weight (DW) and 68.95 ± 1.03 μg g-1 DW), resulting itself superior biological activity as 367.1 ± 42.9 Trolox equivalent mg g-1 DW in oxygen radical absorbance capacity value and 72.79 ± 4.34 quercetin equivalent mg g-1 DW in cellular antioxidant activity value. The present work provides new insights into the regulatory mechanism of tissue-specific anthocyanin biosynthesis, confirming the pivotal role of anthocyanins in the biological activity of plums, providing essential support for the development of horticultural products enriched with anthocyanins.

S-Locus Genotyping in Japanese Plum by High Throughput Sequencing Using a Synthetic S-Loci Reference Sequence

Self-incompatibility in Prunus species is governed by a single locus consisting of two highly multi-allelic and tightly linked genes, one coding for an F-box protein-i.e., SFB in Prunus- controlling the pollen specificity and one coding for an S-RNase gene controlling the pistil specificity. Genotyping the allelic combination in a fruit tree species is an essential procedure both for cross-based breeding and for establishing pollination requirements. Gel-based PCR techniques using primer pairs designed from conserved regions and spanning polymorphic intronic regions are traditionally used for this task. However, with the great advance of massive sequencing techniques and the lowering of sequencing costs, new genotyping-by-sequencing procedures are emerging. The alignment of resequenced individuals to reference genomes, commonly used for polymorphism detection, yields little or no coverage in the S-locus region due to high polymorphism between different alleles within the same species, and cannot be used for this purpose. Using the available sequences of Japanese plum S-loci concatenated in a rosary-like structure as synthetic reference sequence, we describe a procedure to accurately genotype resequenced individuals that allowed the analysis of the S-genotype in 88 Japanese plum cultivars, 74 of them are reported for the first time. In addition to unraveling two new S-alleles from published reference genomes, we identified at least two S-alleles in 74 cultivars. According to their S-allele composition, they were assigned to 22 incompatibility groups, including nine new incompatibility groups reported here for the first time (XXVII-XXXV).

Chromosome-Level Assembly of Flowering Cherry (Prunus campanulata) Provides Insight into Anthocyanin Accumulation

The flowering cherries (genus Prunus, subgenus Cerasus) are popular ornamental trees in China, Japan, Korea, and elsewhere. Prunus campanulata Maxim. is an important species of flowering cherry native to Southern China, which is also distributed in Taiwan, the Ryukyu Islands of Japan, and Vietnam. It produces bell-shaped flowers with colors ranging from bright pink to crimson during the Chinese Spring Festival from January to March each year. We selected the P. campanulata cultivar "Lianmeiren", with only 0.54% of heterozygosity, as the focus of this study, and generated a high-quality chromosome-scale genome assembly of P. campanulata by combining Pacific Biosciences (PacBio) single-molecule sequencing, 10× Genomics sequencing, and high-throughput chromosome conformation capture (Hi-C) technology. We first assembled a 300.48 Mb genome assembly with a contig N50 length of 2.02 Mb. In total, 28,319 protein-coding genes were predicted from the genome, 95.8% of which were functionally annotated. Phylogenetic analyses indicated that P. campanulata diverged from a common ancestor of cherry approximately 15.1 million years ago. Comparative genomic analyses showed that the expanded gene families were significantly involved in ribosome biogenesis, diterpenoid biosynthesis, flavonoid biosynthesis, and circadian rhythm. Furthermore, we identified 171 MYB genes from the P. campanulata genome. Based on the RNA-seq of five organs at three flowering stages, expression analyses revealed that the majority of the MYB genes exhibited tissue-specific expression patterns, and some genes were identified as being associated with anthocyanin accumulation. This reference sequence is an important resource for further studies of floral morphology and phenology, and comparative genomics of the subgenera Cerasus and Prunus.

An LTR retrotransposon in the promoter of a PsMYB10.2 gene associated with the regulation of fruit flesh color in Japanese plum

Japanese plums exhibit wide diversity of fruit coloration. The red to black hues are caused by the accumulation of anthocyanins, while their absence results in yellow, orange or green fruits. In Prunus, MYB10 genes are determinants for anthocyanin accumulation. In peach, QTLs for red plant organ traits map in an LG3 region with three MYB10 copies (PpMYB10.1, PpMYB10.2 and PpMYB10.3). In Japanese plum the gene copy number in this region differs with respect to peach: there are at least three copies of PsMYB10.1, with the expression of one of them (PsMYB10.1a) correlating with fruit skin color. The objective of this study was to determine a possible role of LG3-PsMYB10 genes in the natural variability of the flesh color trait and to develop a molecular marker for marker-assisted selection (MAS). We explored the variability within the LG3-PsMYB10 region using long-range sequences obtained in previous studies through CRISPR-Cas9 enrichment sequencing. We found that the PsMYB10.2 gene was only expressed in red flesh fruits. Its role in promoting anthocyanin biosynthesis was validated by transient overexpression in Japanese plum fruits. The analysis of long-range sequences identified an LTR retrotransposon in the promoter of the expressed PsMYB10.2 gene that explained the trait in 93.1% of the 145 individuals analyzed. We hypothesize that the LTR retrotransposon may promote the PsMYB10.2 expression and activate the anthocyanin biosynthesis pathway. We propose for the first time the PsMYB10.2 gene as candidate for the flesh color natural variation in Japanese plum and provide a molecular marker for MAS.

An efficient CRISPR-Cas9 enrichment sequencing strategy for characterizing complex and highly duplicated genomic regions. A case study in the Prunus salicina LG3-MYB10 genes cluster

BACKGROUND

Genome complexity is largely linked to diversification and crop innovation. Examples of regions with duplicated genes with relevant roles in agricultural traits are found in many crops. In both duplicated and non-duplicated genes, much of the variability in agronomic traits is caused by large as well as small and middle scale structural variants (SVs), which highlights the relevance of the identification and characterization of complex variability between genomes for plant breeding.

RESULTS

Here we improve and demonstrate the use of CRISPR-Cas9 enrichment combined with long-read sequencing technology to resolve the MYB10 region in the linkage group 3 (LG3) of Japanese plum (Prunus salicina). This region, which has a length from 90 to 271 kb according to the P. salicina genomes available, is associated with fruit color variability in Prunus species. We demonstrate the high complexity of this region, with homology levels between Japanese plum varieties comparable to those between Prunus species. We cleaved MYB10 genes in five plum varieties using the Cas9 enzyme guided by a pool of crRNAs. The barcoded fragments were then pooled and sequenced in a single MinION Oxford Nanopore Technologies (ONT) run, yielding 194 Mb of sequence. The enrichment was confirmed by aligning the long reads to the plum reference genomes, with a mean read on-target value of 4.5% and a depth per sample of 11.9x. From the alignment, 3261 SNPs and 287 SVs were called and phased. A de novo assembly was constructed for each variety, which also allowed detection, at the haplotype level, of the variability in this region.

CONCLUSIONS

CRISPR-Cas9 enrichment is a versatile and powerful tool for long-read targeted sequencing even on highly duplicated and/or polymorphic genomic regions, being especially useful when a reference genome is not available. Potential uses of this methodology as well as its limitations are further discussed.

Research Progress on Genetic Basis of Fruit Quality Traits in Apple (Malus × domestica)

Identifying the genetic variation characteristics of phenotypic traits is important for fruit tree breeding. During the long-term evolution of fruit trees, gene recombination and natural mutation have resulted in a high degree of heterozygosity. Apple (Malus × domestica Borkh.) shows strong ecological adaptability and is widely cultivated, and is among the most economically important fruit crops worldwide. However, the high level of heterozygosity and large genome of apple, in combination with its perennial life history and long juvenile phase, complicate investigation of the genetic basis of fruit quality traits. With continuing augmentation in the apple genomic resources available, in recent years important progress has been achieved in research on the genetic variation of fruit quality traits. This review focuses on summarizing recent genetic studies on apple fruit quality traits, including appearance, flavor, nutritional, ripening, and storage qualities. In addition, we discuss the mapping of quantitative trait loci, screening of molecular markers, and mining of major genes associated with fruit quality traits. The overall aim of this review is to provide valuable insights into the mechanisms of genetic variation and molecular breeding of important fruit quality traits in apple.

Monitoring Apricot (Prunus armeniaca L.) Ripening Progression through Candidate Gene Expression Analysis

This study aimed at the monitoring of the apricot (Prunus armeniaca L.) ripening progression through the expression analysis of 25 genes related to fruit quality traits in nine cultivars with great differences in fruit color and ripening date. The level of pigment compounds, such as anthocyanins and carotenoids, is a key factor in food taste, and is responsible for the reddish blush color or orange skin and flesh color in apricot fruit, which are desirable quality traits in apricot breeding programs. The construction of multiple linear regression models to predict anthocyanins and carotenoids content from gene expression allows us to evaluate which genes have the strongest influence over fruit color, as these candidate genes are key during biosynthetic pathways or gene expression regulation, and are responsible for the final fruit phenotype. We propose the gene CHS as the main predictor for anthocyanins content, CCD4 and ZDS for carotenoids content, and LOX2 and MADS-box for the beginning and end of the ripening process in apricot fruit. All these genes could be applied as RNA markers to monitoring the ripening stage and estimate the anthocyanins and carotenoids content in apricot fruit during the ripening process.

Assembly of the Complete Mitochondrial Genome of Chinese Plum (Prunus salicina): Characterization of Genome Recombination and RNA Editing Sites

Despite the significant progress that has been made in the genome sequencing of Prunus, this area of research has been lacking a systematic description of the mitochondrial genome of this genus for a long time. In this study, we assembled the mitochondrial genome of the Chinese plum (Prunus salicina) using Illumina and Oxford Nanopore sequencing data. The mitochondrial genome size of P. salicina was found to be 508,035 base pair (bp), which is the largest reported in the Rosaceae family to date, and P. salicina was shown to be 63,453 bp longer than sweet cherry (P. avium). The P. salicina mitochondrial genome contained 37 protein-coding genes (PCGs), 3 ribosomal RNA (rRNA) genes, and 16 transfer RNA (tRNA) genes. Two plastid-derived tRNA were identified. We also found two short repeats that captured the nad3 and nad6 genes and resulted in two copies. In addition, nine pairs of repeat sequences were identified as being involved in the mediation of genome recombination. This is crucial for the formation of subgenomic configurations. To characterize RNA editing sites, transcriptome data were used, and we identified 480 RNA editing sites in protein-coding sequences. Among them, the initiation codon of the nad1 gene confirmed that an RNA editing event occurred, and the genomic encoded ACG was edited as AUG in the transcript. Combined with previous reports on the chloroplast genome, our data complemented our understanding of the last part of the organelle genome of plum, which will facilitate our understanding of the evolution of organelle genomes.

PpMYB36 Encodes a MYB-Type Transcription Factor That Is Involved in Russet Skin Coloration in Pear (Pyrus pyrifolia)

Fruit color is one of the most important external qualities of pear (Pyrus pyrifolia) fruits. However, the mechanisms that control russet skin coloration in pear have not been well characterized. Here, we explored the molecular mechanisms that determine the russet skin trait in pear using the F₁ population derived from a cross between russet skin ('Niitaka') and non-russet skin ('Dangshansu') cultivars. Pigment measurements indicated that the lignin content in the skin of the russet pear fruits was greater than that in the non-russet pear skin. Genetic analysis revealed that the phenotype of the russet skin pear is associated with an allele of the PpRus gene. Using bulked segregant analysis combined with the genome sequencing (BSA-seq), we identified two simple sequence repeat (SSR) marker loci linked with the russet-colored skin trait in pear. Linkage analysis showed that the PpRus locus maps to the scaffold NW_008988489.1: 53297-211921 on chromosome 8 in the pear genome. In the mapped region, the expression level of LOC103929640 was significantly increased in the russet skin pear and showed a correlation with the increase of lignin content during the ripening period. Genotyping results demonstrated that LOC103929640 encoding the transcription factor MYB36 is the causal gene for the russet skin trait in pear. Particularly, a W-box insertion at the PpMYB36 promoter of russet skin pears is essential for PpMYB36-mediated regulation of lignin accumulation and russet coloration in pear. Overall, these results show that PpMYB36 is involved in the regulation of russet skin trait in pear.