Diploid Species Research Articles

Uniparentality: advantages for range expansion in diploid and diploid-autopolyploid species

AbstractUniparental reproduction, the capacity of an individual to produce offspring autonomously, is expected to facilitate range expansion of populations. Paspalum spp. reproduce uniparentally by sexual (self-fertility) and asexual (apomixis) reproduction and biparentally by sexual (self-sterility) reproduction. We evaluated the relationship between contrasting reproductive strategies (uni- and biparentality) and their impact on the colonizing ability and geographical range sizes of populations. We determined the cytotype composition of 16 populations of P. indecorum, P. cromyorhizon, P. pumilum and P. maculosum and assessed the sexual (self-fertile and self-sterile) and apomictic proportions by cyto-embryological analyses, fertility rates and seed flow cytometry. Data obtained regarding reproductive modes were compared to the distribution range of each cytotype and species. Sexual diploids with moderate degrees of self-fertility and mixed pollination syndromes showed wider distribution ranges than self-sterile diploids. In sexual diploids, increased rates of self-fertility relate to larger distribution areas. In agamic complexes, self-fertility reduces the differences in range sizes between biparental diploids and uniparental tetraploids. In such complexes, the range size of diploid cytotypes explains the range size and dispersal of apomictic tetraploids. Thus, uniparental reproduction via self-fertility and apomixis describes patterns of geographical parthenogenesis in South American species.

The Chromosome Number and rDNA Loci Evolution in Onobrychis (Fabaceae).

The evolution of chromosome number and ribosomal DNA (rDNA) loci number and localisation were studied in Onobrychis Mill. Diploid and tetraploid species, as well as two basic chromosome numbers, x = 7 and x = 8, were observed among analysed taxa. The chromosomal distribution of rDNA loci was presented here for the first time using fluorescence in situ hybridisation (FISH) with 5S and 35S rDNA probes. Onobrychis species showed a high polymorphism in the number and localisation of rDNA loci among diploids, whereas the rDNA loci pattern was very similar in polyploids. Phylogenetic relationships among the species, inferred from nrITS sequences, were used as a framework to reconstruct the patterns of basic chromosome number and rDNA loci evolution. Analysis of the evolution of the basic chromosome numbers allowed the inference of x = 8 as the ancestral number and the descending dysploidy and polyploidisation as the major mechanisms of the chromosome number evolution. Analyses of chromosomal patterns of rRNA gene loci in a phylogenetic context resulted in the reconstruction of one locus of 5S rDNA and one locus of 35S rDNA in the interstitial chromosomal position as the ancestral state in this genus.

Rapid large-scale genomic introgression in Arabidopsis suecica via an autoallohexaploid bridge.

Gene flow between species in the genus Arabidopsis occurs in significant amounts, but how exactly gene flow is achieved is not well understood. Polyploidization may be one avenue to explain gene flow between species. One problem, however, with polyploidization as a satisfying explanation is the occurrence of lethal genomic instabilities in neopolyploids as a result of genomic exchange, erratic meiotic behavior, and genomic shock. We have created an autoallohexaploid by pollinating naturally co-occurring diploid Arabidopsis thaliana with allotetraploid Arabidopsis suecica (an allotetraploid composed of A. thaliana and Arabidopsis arenosa). Its triploid offspring underwent spontaneous genome duplication and was used to generate a multigenerational pedigree. Using genome resequencing, we show that 2 major mechanisms promote stable genomic exchange in this population. Legitimate meiotic recombination and chromosome segregation between the autopolyploid chromosomes of the 2 A. thaliana genomes occur without any obvious bias for the parental origin and combine the A. thaliana haplotypes from the A. thaliana parent with the A. thaliana haplotypes from A. suecica similar to purely autopolyploid plants. In addition, we repeatedly observed that occasional exchanges between regions of the homoeologous chromosomes are tolerated. The combination of these mechanisms may result in gene flow leading to stable introgression in natural populations. Unlike the previously reported resynthesized neoallotetraploid A. suecica, this population of autoallohexaploids contains mostly vigorous, and genetically, cytotypically, and phenotypically variable individuals. We propose that naturally formed autoallohexaploid populations might serve as an intermediate bridge between diploid and polyploid species, which can facilitate gene flow rapidly and efficiently.

Lycorisinsularis (Amaryllidaceae), a new species from eastern China revealed by morphological and molecular evidence.

Lycorisinsularis S.Y.Zhang & J.W.Shao, a new fertile diploid species from coastal provinces in eastern China is described. This new species is most similar to L.sprengeri in morphology and has been misidentified as the latter for a long time. However, it can be distinguished from the latter by the relatively longer perianth tube (1.5‒2.5 cm vs. less than 1.3 cm), a characteristic that was overlooked before. Phylogenetic analysis, based on complete plastid genome, showed that L.insularis is not genetically related to L.sprengeri in the genus. The former was a sister group of L.sanguinea, while the latter was closely related to L.longituba and L.chinensis and they were respectively located on different clades that were separated at the base of the phylogenetic tree. The chromosome number of L.insularis is 2n = 22. At present, as the new species is relatively widely distributed and the wild population can normally reproduce by seeds, we evaluate it as LC (Least Concern) according to criteria of the IUCN Red List.

Fertility, genome stability, and homozygosity in a diverse set of resynthesized rapeseed lines

Rapeseed (Brassica napus, AACC) was formed by hybridization between progenitor species Brassica rapa (AA) and Brassica oleracea (CC). As a result of a limited number of hybridization events between specific progenitor genotypes and strong breeding selection for oil quality traits, rapeseed has limited genetic diversity. The production of resynthesized B. napus lines via interspecific hybridization of the diploid progenitor species B. rapa and B. oleracea is one possible way to increase genetic variation in rapeseed. However, most resynthesized lines produced so far have been reported to be meiotically unstable and infertile, in contrast to established B. napus cultivars. This hinders both maintenance and use of this germplasm in breeding programs. We characterized a large set of 140 resynthesized lines produced by crosses between B. rapa and B. oleracea, as well as between B. rapa and wild C genome species (B. incana, B. hilarionis, B. montana, B. Bourgeaui, B. villosa and B. cretica) for purity (homozygosity), fertility, and genome stability. Self-pollinated seed set, seeds per ten pods as well as percentage pollen viability were used to estimate fertility. SNP genotyping was performed using the Illumina Infinium Brassica 60K array for 116 genotypes, with at least three individuals per line. Most of the material which had been advanced through multiple generations was no longer pure, with heterozygosity detected corresponding to unknown parental contributions via outcrossing. Fertility and genome stability were both genotype-dependent. Most lines had high numbers of copy number variants (CNVs), indicative of meiotic instability, and high numbers of CNVs were significantly associated with reduced fertility. Eight putatively stable resynthesized B. napus lines were observed. Further investigation of these lines may reveal the mechanisms underlying this effect. Our results suggest that selection of stable resynthesized lines for breeding purposes is possible.

Comparative evolutionary dynamics of the 5’cis-regulatory elements (CREs) of miR167 genes in diploid and allopolyploid cotton species

Cotton fiber morphogenesis is tightly regulated by several microRNAs (miRNAs) including miR167 which regulates auxin-signaling through the transcriptional regulation of its target genes during fiber development. To emphasize the evolution of spatiotemporal regulatory attributes of miR167 genes during fiber development, a comparative analysis of 5′cis-regulatory elements (CREs) and coding sequences of miR167 genes from progenitor diploid A2 (G. arboreum), D5 (G. raimondii) species and decedent allopolyploid AD1 (G. hirsutum) and AD2 (G. barbadense) species were performed in an evolutionary framework. Interestingly, different miR167 genes were conserved both in A- and D-subgenomes of AD1 and AD2 species (>90% sequence similarities) and acquired the least variations in gene sequences during allopolyploidy followed by species diversification. However, substantial accumulation of structural variations in 1.5kb long upstream regions exhibited that the regulatory regions had undergone extensive evolutionary changes during cotton evolution in both diploid and allopolyploid species. Several unique CREs could be identified and further classified into development-, light-, organ-, stress- and hormone-responsive motifs with their varied frequencies. Co-expression analyses of miR167 genes and their respective CREs-binding transcription factors (TFs) showed tissue- and developmental stage-specific correlation, especially with bHLH transcription factor (R2 = 0.93) during fiber initiation and elongation stages of AD1 species. The reconstructed gene networks of the most significant predicted TFs with CREs underscored the possible genetic control mechanisms of these factors during fiber development. These observations highlighted that various regulatory motifs were preserved during cotton evolution and may be exploited for future crop improvement programs.

Chromosome-level genome assembly of Fragaria pentaphylla using PacBio and Hi-C technologies.

Fragaria pentaphylla, a wild diploid quinquefoliolate species of Fragaria, is native to Southwest China. It has two morphs of red and white fruit color in nature and has characteristics of unique fragrance and resistance, which made it not only a valuable breeding material but also a potential model plant for molecular function researches. Here, we generate a high-quality chromosome-level genome assembly of a F. pentaphylla accession, BAAFS-FP039 employing a combination of PacBio Long-Read Sequencing, Illumina Short-Read Sequencing, and Hi-C Sequencing. The assembled genome contained 256.74 Mb and a contig N50 length of 32.38 Mb, accounting for 99.9% of the estimated genome (256.77 Mb). Based on Hi-C data, seven pseudo-chromosomes of F. pentaphylla-FP039 genome were assembled, covering 99.39% of the genome assembly. The genome was composed of 44.61% repetitive sequences and 29,623 protein-coding genes, 97.62% of protein-coding genes could be functionally annotated. Phylogenetic and chromosome syntenic analysis revealed that F. pentaphylla-FP039 was closely related to F. nubicola. This high-quality genome could provides fundamental molecular resources for evolutionary studies, breeding efforts, and exploring the unique biological characteristics of F. pentaphylla.

Identification and Characterization of Wheat-Aegilops comosa 7M (7A) Disomic Substitution Lines with Stripe Rust and Powdery Mildew Resistance.

Aegilops comosa (MM, 2n = 2x = 14), an important diploid species from the wheat tertiary gene pool, contains many unique genes/traits of potential use for wheat breeding, such as disease resistance. In this study, three sister lines, NAL-32, NAL-33, and NAL-34, were identified from a wheat-A. comosa distant cross using fluorescence in situ hybridization, simple sequence repeat markers, and PCR-based unique gene markers combined with single nucleotide polymorphism (SNP) array analysis. Genetically, NAL-32 contained neither an alien nor translocation chromosome, whereas NAL-33 and NAL-34 had disomic 7M (7A) substitution chromosomes but differed in the absence or presence of the 1BL/1RS translocation chromosomes, respectively. The absence of 7A in NAL-33 and NAL-34 and the unusual 1B in the latter were verified by wheat 55K SNP arrays. The two 7M (7A) substitution lines had similar levels of resistance to stripe rust and powdery mildew, but better than that of NAL-32 and their common wheat parents, suggesting that the stripe rust and powdery mildew resistance of NAL-33 and NAL-34 were derived from the 7M of A.comosa. This research provides important bridge materials that can potentially be used for transferring stripe rust and powdery mildew resistance.

Autopolyploid inheritance and a heterozygous reciprocal translocation shape chromosome genetic behavior in tetraploid blueberry (Vaccinium corymbosum).

Understanding chromosome recombination behavior in polyploidy species is key to advancing genetic discoveries. In blueberry, a tetraploid species, the line of evidences about its genetic behavior still remain poorly understood, owing to the inter-specific, and inter-ploidy admixture of its genome and lack of in depth genome-wide inheritance and comparative structural studies. Here we describe a new high-quality, phased, chromosome-scale genome of a diploid blueberry, clone W85. The genome was integrated with cytogenetics and high-density, genetic maps representing six tetraploid blueberry cultivars, harboring different levels of wild genome admixture, to uncover recombination behavior and structural genome divergence across tetraploid and wild diploid species. Analysis of chromosome inheritance and pairing demonstrated that tetraploid blueberry behaves as an autotetraploid with tetrasomic inheritance. Comparative analysis demonstrated the presence of a reciprocal, heterozygous, translocation spanning one homolog of chr-6 and one of chr-10 in the cultivar Draper. The translocation affects pairing and recombination of chromosomes 6 and 10. Besides the translocation detected in Draper, no other structural genomic divergences were detected across tetraploid cultivars and highly inter-crossable wild diploid species. These findings and resources will facilitate new genetic and comparative genomic studies in Vaccinium and the development of genomic assisted selection strategy for this crop.

Applications of In Vitro Tissue Culture Technologies in Breeding and Genetic Improvement of Wheat.

Sources of new genetic variability have been limited to existing germplasm in the past. Wheat has been studied extensively for various agronomic traits located throughout the genome. The large size of the chromosomes and the ability of its polyploid genome to tolerate the addition or loss of chromosomes facilitated rapid progress in the early study of wheat genetics using cytogenetic techniques. At the same time, its large genome size has limited the progress in genetic characterization studies focused on diploid species, with a small genome and genetic engineering procedures already developed. Today, the genetic transformation and gene editing procedures offer attractive alternatives to conventional techniques for breeding wheat because they allow one or more of the genes to be introduced or altered into an elite cultivar without affecting its genetic background. Recently, significant advances have been made in regenerating various plant tissues, providing the essential basis for regenerating transgenic plants. In addition, Agrobacterium-mediated, biolistic, and in planta particle bombardment (iPB) gene delivery procedures have been developed for wheat transformation and advanced transgenic wheat development. As a result, several useful genes are now available that have been transferred or would be helpful to be transferred to wheat in addition to the current traditional effort to improve trait values, such as resistance to abiotic and biotic factors, grain quality, and plant architecture. Furthermore, the in planta genome editing method will significantly contribute to the social implementation of genome-edited crops to innovate the breeding pipeline and leverage unique climate adaptations.

Chromosome painting reveals inter-chromosomal rearrangements and evolution of subgenome D of wheat.

Aegilops species represent the most important gene pool for breeding bread wheat (Triticum aestivum). Thus, understanding the genome evolution, including chromosomal structural rearrangements and syntenic relationships among Aegilops species or between Aegilops and wheat, is important for both basic genome research and practical breeding applications. In the present study, we attempted to develop subgenome D-specific fluorescence in situ hybridization (FISH) probes by selecting D-specific oligonucleotides based on the reference genome of Chinese Spring. The oligo-based chromosome painting probes consisted of approximately 26 000 oligos per chromosome and their specificity was confirmed in both diploid and polyploid species containing the D subgenome. Two previously reported translocations involving two D chromosomes have been confirmed in wheat varieties and their derived lines. We demonstrate that the oligo painting probes can be used not only to identify the translocations involving D subgenome chromosomes, but also to determine the precise positions of chromosomal breakpoints. Chromosome painting of 56 accessions of Ae. tauschii from different origins led us to identify two novel translocations: a reciprocal 3D-7D translocation in two accessions and a complex 4D-5D-7D translocation in one accession. Painting probes were also used to analyze chromosomes from more diverse Aegilops species. These probes produced FISH signals in four different genomes. Chromosome rearrangements were identified in Aegilops umbellulata, Aegilops markgrafii, and Aegilops uniaristata, thus providing syntenic information that will be valuable for the application of these wild species in wheat breeding.

Chromosomal instability and phenotypic variation in a specific lineage derived from a synthetic allotetraploid wheat.

Newly formed plant allopolyploids usually have meiosis defect, resulting in chromosomal instability manifested as variation in chromosome number and/or structure. However, not all nascent allopolyploids are equally unstable. The wheat group (Aegilops/Triticum) contains 13 diploid species with distinct genome types. Many of these species can be artificially hybridized to produce viable but sterile inter-specific/intergeneric F1 hybrids, which can generate fertile synthetic allotetraploid wheats after whole genome doubling. Compared with synthetic allotetraploid wheats that contain genome combinations of AADD and S*S*DD (S* refers to related S genomes of a different species), those containing an S*S*AA genome are significantly more stable. However, robustness of the relative stability of S*S*AA genomes is unknown, nor are the phenotypic and fitness consequences during occurrences of secondary chromosomal instability. Here, we report a specific lineage originated from a single individual plant of a relatively stable synthetic allotetraploid wheat with genomes SlSlAA (Sl and A subgenomes were from Ae. longissima and T. urartu, respectively) that showed a high degree of transgenerational chromosomal instability. Both numerical chromosome variation (NCV) and structural chromosome variation (SCV) occurred widely. While substantial differences in frequencies of both NCV and SCV were detected across the different chromosomes, only NCV frequencies were significantly different between the two subgenomes. We found that NCVs and SCVs occurred primarily due to perturbed meiosis, allowing formation of multivalents and univalents as well as homoeologous exchanges. Thus, the combination of NCVs and SCVs affected multiple phenotypic traits, particularly those related to reproductive fitness.

Rychc Confers Extreme Resistance to Potato virus Y in Potato.

The Potato virus Y (PVY) is responsible for huge economic losses for the potato industry worldwide and is the fifth most consequential plant virus globally. The main strategies for virus control are to limit aphid vectors, produce virus-free seed potatoes, and breed virus-resistant varieties. The breeding of PVY-resistant varieties is the safest and most effective method in terms of cost and environmental protection. Rychc, a gene that confers extreme resistance to PVY, is from S. chacoense, which is a wild diploid potato species that is widely used in many PVY-resistant breeding projects. In this study, Rychc was fine mapped and successfully cloned from S. chacoense accession 40-3. We demonstrated that Rychc encodes a TIR-NLR protein by stably transforming a diploid susceptible cultivar named AC142 and a tetraploid potato variety named E3. The Rychc conferred extreme resistance to PVYO, PVYN:O and PVYNTN in both of the genotypes. To investigate the genetic events occurring during the evolution of the Rychc locus, we sequenced 160 Rychc homologs from 13 S. chacoense genotypes. Based on the pattern of sequence identities, 160 Rychc homologs were divided into 11 families. In Family 11 including Rychc, we found evidence for Type I evolutionary patterns with frequent sequence exchanges, obscured orthologous relationships and high non-synonymous to synonymous substitutions (Ka/Ks), which is consistent with rapid diversification and positive selection in response to rapid changes in the PVY genomes. Furthermore, a functional marker named MG64-17 was developed in this study that indicates the phenotype with 100% accuracy and, therefore, can be used for marker-assisted selection in breeding programs that use S. chacoense as a breeding resource.

The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome.

Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. Brassica carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.

Leaf proteome reveals the alterations in photosynthesis and defense-related proteins between potato tetraploid cultivars and diploid wild species

Potato (Solanum tuberosum L.) as the important food crop worldwide has abundant morphological and genetic diversity. To understand the underlying molecular mechanisms determining phenotypic differences in wild species and cultivated potato, a comparative proteomics approach was applied to analyze leaf proteome alteration among three tetraploid cultivars and three diploid wild species using two-dimensional gel electrophoresis (2-DE). Quantitative image analysis showed a total of 47 protein spots with significantly altered abundance (>3-fold, P < 0.05), and 45 differentially abundant proteins were identified by MALDI-TOF/TOF MS. These proteins exhibited both the qualitative and quantitative changes. Most of them were involved in photosynthesis, cell defense and rescue, protein biosynthesis, which might exhibit the main differences between tetraploid cultivars and diploid wild species. The photosynthesis and protein biosynthesis-related proteins were up-regulated or only present in tetraploid cultivars, suggesting the higher photosynthetic efficiency and more newly synthesized peptides. It might contribute to some superior traits of tetraploid cultivars, such as larger leaf size, greater growth vigor, better tuber yield and quality. However, some cell defense and rescue-related proteins, especially the pathogenesis-related proteins and antioxidant enzymes, were up-regulated or only present in diploid wild species. It might be responsible for stronger resistance to diseases and pests or tolerance to environmental stresses in diploid wild species. This study would provide valuable information for the underlying molecular mechanisms of potato genetic diversity, and help in developing strategies for the utilization of wild species for potato improvement.

Diploid Wheats: Are They Less Immunogenic for Non-Celiac Wheat Sensitive Consumers?

Non-celiac wheat sensitivity (NCWS) is a clinical entity induced by the ingestion of gluten that leads to intestinal and/or extraintestinal symptoms, and is diagnosed when celiac disease and wheat allergy have been ruled out. In addition to gluten, other grains’ components, including amylase trypsin inhibitors (ATIs) and fermentable short-chain carbohydrates (FODMAPs), may trigger symptoms in NCWS subjects. Several studies suggest that, compared with tetraploid and hexaploid modern wheats, ancient diploid wheats species could possess a lower immunogenicity for subjects suffering from NCWS. This review aims to discuss available evidence related to the immunological features of diploid wheats compared to common wheats, and at outlining new dietary opportunities for NCWS subjects.

Developing New Cultivars of Prunus × Rossica Erem. And Clonal Rootstocks at the Krymsk Experiment Breeding Station

Abstract The paper considers the possibilities of expanding the assortment of plum cultivars in world production by hybridising large-fruited myrobalan plum (Prunus cerasifera Ehrh.) cultivars with those of Japanese plum (Prunus salicina Lindl.) and other diploid stone fruit species. Because of many years of breeding work in Russia, cultivars of a new hybridogenous species Prunus × rossica Erem. (Russian plum) have been created, which can ensure a stable supply of fresh fruit from late June to September and complement the assortment of common plum cultivars. A description is given for the best adaptive, high-yielding cultivars with good taste and high canning qualities — ‘Kubanskaya Kometa’, ‘Globus’, ‘Gek’, ‘Iyulskaya Roza’, ‘Dynnaya’, ‘Kolonnovidnaya’, and ‘Podarok Sad-Gigantu’. The efficiency of their cultivation using intensive technologies and own-rooted plants, as well as clonal rootstocks bred at the Krymsk Station, has been shown. It is recommended to carry out intensive cultivation of Russian plum using medium vigorous rootstocks like Kuban 86, Evrika 99, Zarevo, Fortuna and dwarf rootstocks VVA 1, Best, Upryamets and VSV 1.

Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species.

Opposing changes in the abundance of satellite DNA and long terminal repeat (LTR) retroelements are the main contributors to the variation in genome size and heterochromatin amount in Arachis diploids. The South American genus Arachis (Fabaceae) comprises 83 species organized in nine taxonomic sections. Among them, section Arachis is characterized by species with a wide genome and karyotype diversity. Such diversity is determined mainly by the amount and composition of repetitive DNA. Here we performed computational analysis on low coverage genome sequencing to infer the dynamics of changes in major repeat families that led to the differentiation of genomes in diploid species (x = 10) of genus Arachis, focusing on section Arachis. Estimated repeat content ranged from 62.50 to 71.68% of the genomes. Species with different genome composition tended to have different landscapes of repeated sequences. Athila family retrotransposons were the most abundant and variable lineage among Arachis repeatomes, with peaks of transpositional activity inferred at different times in the evolution of the species. Satellite DNAs (satDNAs) were less abundant, but differentially represented among species. High rates of evolution of an AT-rich superfamily of satDNAs led to the differential accumulation of heterochromatin in Arachis genomes. The relationship between genome size variation and the repetitive content is complex. However, largest genomes presented a higher accumulation of LTR elements and lower contents of satDNAs. In contrast, species with lowest genome sizes tended to accumulate satDNAs in detriment of LTR elements. Phylogenetic analysis based on repetitive DNA supported the genome arrangement of section Arachis. Altogether, our results provide the most comprehensive picture on the repeatome dynamics that led to the genome differentiation of Arachis species.

Transcriptomic and Metabolomic Analyses Provide Insights into the Formation of the Peach-like Aroma of Fragaria nilgerrensis Schlecht. Fruits.

Fragaria nilgerrensis Schlecht. is a wild diploid strawberry species. The intense peach-like aroma of its fruits makes F. nilgerrensis an excellent resource for strawberry breeding programs aimed at enhancing flavors. However, the formation of the peach-like aroma of strawberry fruits has not been comprehensively characterized. In this study, fruit metabolome and transcriptome datasets for F. nilgerrensis (HA; peach-like aroma) and its interspecific hybrids PA (peach-like aroma) and NA (no peach-like aroma; control) were compared. In total, 150 differentially accumulated metabolites were detected. The K-means analysis revealed that esters/lactones, including acetic acid, octyl ester, δ-octalactone, and δ-decalactone, were more abundant in HA and PA than in NA. These metabolites may be important for the formation of the peach-like aroma of F. nilgerrensis fruits. The significantly enriched gene ontology terms assigned to the differentially expressed genes (DEGs) were fatty acid metabolic process and fatty acid biosynthetic process. Twenty-seven DEGs were predicted to be associated with ester and lactone biosynthesis, including AAT, LOX, AOS, FAD, AIM1, EH, FAH, ADH, and cytochrome P450 subfamily genes. Thirty-five transcription factor genes were predicted to be associated with aroma formation, including bHLH, MYB, bZIP, NAC, AP2, GATA, and TCP family members. Moreover, we identified differentially expressed FAD, AOS, and cytochrome P450 family genes and NAC, MYB, and AP2 transcription factor genes that were correlated with δ-octalactone and δ-decalactone. These findings provide key insights into the formation of the peach-like aroma of F. nilgerrensis fruits, with implications for the increased use of wild strawberry resources.

Integrative analysis of the metabolome and transcriptome provides novel insights into the mechanisms of flavonoid biosynthesis in Camellia lanceoleosa

Flavonoids, the effective material basis for the anti-thrombotic, anti-myocardial ischemia, and anti-dementia drug system framework, are one class of the main bioactive compounds in tea-oil Camellia. However, the molecular mechanism of the transcription regulation of flavonoid biosynthesis in tea-oil Camellia has not been fully investigated. Camellia lanceoleosa (C. lanceoleosa) is a diploid species of section Oleifera with genomic information, which has high value in scientific research and application. To comprehend the molecular mechanism of flavonoid biosynthesis in C. lanceoleosa, five different tissues (roots, stems, leaves, flower buds, and seeds) were used to perform an integrated analysis of the metabolome and transcriptome. Overall, 1,437 metabolites were identified and quantified, among which 488 common metabolites and 92 tissue-specific metabolites were detected in different tissues of C. lanceoleosa. Notably, the most abundant metabolite class was the flavonoids in the detected tissues of C. lanceoleosa. Furthermore, the differential metabolites and genes were also mainly enriched in flavonoid biosynthesis. A total of 145 differentially accumulated flavonoids and 65 differentially expressed structural genes were found within the biosynthesis of flavonoid in C. lanceoleosa. The expression patterns of most genes were consistent with the flavonoid accumulation patterns in the corresponding pathways. Using weighted gene coexpression network analysis, five gene modules and several candidate hub genes involved in flavonoid biosynthesis were investigated in different tissues of C. lanceoleosa, these genes included differentially expressed structural genes (PAL, CHS, DFR, and ANR) and transcription factors (bHLHs, MYBs, WRKYs, NACs, and SPL6). These results provide useful genetic resources for studying the molecular insights into the regulatory network of flavonoid biosynthesis in C. lanceoleos.