Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits

Comparative chloroplast genome analyses of cultivated spinach and two wild progenitors shed light on the phylogenetic relationships and variation

Spinacia is a genus of important leafy vegetable crops worldwide and includes cultivated Spinacia oleracea and two wild progenitors, Spinacia turkestanica and Spinacia tetrandra. However, the chloroplast genomes of the two wild progenitors remain unpublished, limiting our knowledge of chloroplast genome evolution among these three Spinacia species. Here, we reported the complete chloroplast genomes of S. oleracea, S. turkestanica, and S. tetrandra obtained via Illumina sequencing. The three chloroplast genomes exhibited a typical quadripartite structure and were 150,739, 150,747, and 150,680 bp in size, respectively. Only three variants were identified between S. oleracea and S. turkestanica, whereas 690 variants were obtained between S. oleracea and S. tetrandra, strongly demonstrating the close relationship between S. turkestanica and S. oleracea. This was further supported by phylogenetic analysis. We reported a comprehensive variant dataset including 503 SNPs and 83 Indels using 85 Spinacia accessions containing 61 S. oleracea, 16 S. turkestanica, and eight S. tetrandra accessions. Thirteen S. oleracea accessions were derived through introgression from S. turkestanica that acts as the maternal parent. Together, these results provide a valuable resource for spinach breeding programs and improve our understanding of the phylogenetic relationships within Amaranthaceae.

GreeNC 2.0: a comprehensive database of plant long non-coding RNAs

The Green Non-Coding Database (GreeNC) is one of the reference databases for the study of plant long non-coding RNAs (lncRNAs). Here we present our most recent update where 16 species have been updated, while 78 species have been added, resulting in the annotation of more than 495 000 lncRNAs. Moreover, sequence clustering was applied providing information about sequence conservation and gene families. The current version of the database is available at: http://greenc.sequentiabiotech.com/wiki2/Main_Page.

The branchless gene Clbl in watermelon encoding a TERMINAL FLOWER 1 protein regulates the number of lateral branches

A SNP mutation in Clbl gene encoding TERMINAL FLOWER 1 protein is responsible for watermelon branchless. Lateral branching is one of the most important traits, which directly determines plant architecture and crop productivity. Commercial watermelon has the characteristics of multiple lateral branches, and it is time-consuming and labor-costing to manually remove the lateral branches in traditional watermelon cultivation. In our present study, a lateral branchless trait was identified in watermelon material WCZ, and genetic analysis revealed that it was controlled by a single recessive gene, which named as Clbl (Citrullus lanatus branchless). A bulked segregant sequencing (BSA-seq) and linkage analysis was conducted to primarily map Clbl on watermelon chromosome 4. Next-generation sequencing-aided marker discovery and a large mapping population consisting of 1406 F₂ plants were used to further map Clbl locus into a 9011-bp candidate region, which harbored only one candidate gene Cla018392 encoding a TERMINAL FLOWER 1 protein. Sequence comparison of Cla018392 between two parental lines revealed that there was a SNP detected from C to A in the coding region in the branchless inbred line WCZ, which resulted in a mutation from alanine (GCA) to glutamate (GAA) at the fourth exon. A dCAPS marker was developed from the SNP locus, which was co-segregated with the branchless phenotype in both BC₁ and F₂ population, and it was further validated in 152 natural watermelon accessions. qRT-PCR and in situ hybridization showed that the expression level of Cla018392 was significantly reduced in the axillary bud and apical bud in branchless line WCZ. Ectopic expression of ClTFL1 in Arabidopsis showed an increased number of lateral branches. The results of this study will be helpful for better understanding the molecular mechanism of lateral branch development in watermelon and for the development of marker-assisted selection (MAS) for new branchless watermelon cultivars.

Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways

Gramene is an integrated bioinformatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. Originally targeting grasses, Gramene has grown to host annotations for over 90 plant genomes including agronomically important cereals (e.g., maize, sorghum, wheat, teff), fruits and vegetables (e.g., apple, watermelon, clementine, tomato, cassava), specialty crops (e.g., coffee, olive tree, pistachio, almond), and plants of special or emerging interest (e.g., cotton, tobacco, cannabis, or hemp). For some species, the resource includes multiple varieties of the same species, which has paved the road for the creation of species-specific pan-genome browsers. The resource also features plant research models, including Arabidopsis and C4 warm-season grasses and brassicas, as well as other species that fill phylogenetic gaps for plant evolution studies. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. This chapter outlines system requirements for end-users and database hosting, data types and basic navigation within Gramene, and provides examples of how to (1) explore Gramene's search results, (2) explore gene-centric comparative genomics data visualizations in Gramene, and (3) explore genetic variation associated with a gene locus. This is the first publication describing in detail Gramene's integrated search interface-intended to provide a simplified entry portal for the resource's main data categories (genomic location, phylogeny, gene expression, pathways, and external references) to the most complete and up-to-date set of plant genome and pathway annotations.

Nucleotide variation in the phytoene synthase (ClPsy1) gene contributes to golden flesh in watermelon (Citrullus lanatus L.)

A gene controlling golden flesh trait in watermelon was discovered and fine mapped to a 39.08 Kb region on chromosome 1 through a forward genetic strategy, and Cla97C01G008760 (annotated as phytoene synthase protein, ClPsy1 ) was recognized as the most likely candidate gene. Vitamin A deficiency is a worldwide public nutrition problem, and β-carotene is the precursor for vitamin A synthesis. Watermelon with golden flesh (gf, which occurs due to an accumulated abundance of β-carotene) is an important germplasm resource. In this study, a genetic analysis of segregated gf gene populations indicated that gf was controlled by a single recessive gene. BSA-seq (Bulked segregation analysis) and an initial linkage analysis placed the gf locus in a 290-Kb region on watermelon chromosome 1. Further fine mapping in a large population including over 1000 F₂ plants narrowed this region to 39.08 Kb harboring two genes, Cla97C01G008760 and Cla97C01G008770, which encode phytoene synthase (ClPsy1) and GATA zinc finger domain-containing protein, respectively. Gene sequence alignment and expression analysis between parental lines revealed Cla97C01G008760 as the best possible candidate gene for the gf trait. Nonsynonymous SNP mutations in the first exon of ClPsy1 between parental lines co-segregated with the gf trait only among individuals in the genetic population and were not related to flesh color in natural watermelon panels. Promoter sequence analysis of 26 watermelon accessions revealed two SNPs in the cis-acting element sequences corresponding to MYB and MYC2 transcription factors. RNA-seq data and qRT-PCR verification showed that two MYBs exhibited expression trends similar to that of ClPsy1 in the parental lines and may regulate the ClPsy1 expression. Further research findings indicate that the gf trait is determined not only by ClPsy1 but also by ClLCYB, ClCRTISO and ClNCED7, which play important roles in watermelon β-carotene accumulation.

Genome-Wide Identification and Characterization of the Trehalose-6-phosphate Synthetase (TPS) Gene Family in Watermelon (Citrullus lanatus) and Their Transcriptional Responses to Salt Stress

With the increase in watermelon cultivation area, there is an urgent need to explore enzymatic and genetic resources for the sustainable development of watermelon, especially under salt stress. Among the various compounds known, trehalose plays an important role in regulating abiotic stress tolerances in diverse organisms, including plants. Therefore, the present study comprehensively analyzed the trehalose-6-phosphate synthase (TPS) gene family in watermelon. The study analyzed the functional classification, evolutionary characteristics, and expression patterns of the watermelon TPS genes family. Seven ClTPSs were identified and classified into two distinct classes according to gene structure and phylogeny. Evolutionary analysis suggested the role of purifying selection in the evolution of the TPS family members. Further, cis-acting elements related to plant hormones and abiotic stress were identified in the promoter region of the TPS genes. The tissue-specific expression analysis showed that ClTPS genes were widely expressed in roots, stems, leaves, flowers, and fruits, while ClTPS3 was significantly induced under salt stress. The overexpression of ClTPS3 in Arabidopsis thaliana significantly improved salt tolerance. Finally, the STRING functional protein association networks suggested that the transcription factor ClMYB and ClbHLH regulate ClTPS3. Thus, the study indicates the critical role of ClTPS3 in watermelon response to salt stress.

Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits

Spinach is a nutritious leafy vegetable belonging to the family Chenopodiaceae. Here we report a high-quality chromosome-scale reference genome assembly of spinach and genome resequencing of 305 cultivated and wild spinach accessions. Reconstruction of ancestral Chenopodiaceae karyotype indicates substantial genome rearrangements in spinach after its divergence from ancestral Chenopodiaceae, coinciding with high repeat content in the spinach genome. Population genomic analyses provide insights into spinach genetic diversity and population differentiation. Genome-wide association studies of 20 agronomical traits identify numerous significantly associated regions and candidate genes for these traits. Domestication sweeps in the spinach genome are identified, some of which are associated with important traits (e.g., leaf phenotype, bolting and flowering), demonstrating the role of artificial selection in shaping spinach phenotypic evolution. This study provides not only insights into the spinach evolution and domestication but also valuable resources for facilitating spinach breeding.

Spinach is a nutritious leafy vegetable growing worldwide. Here, the authors report a high-quality chromosome-scale reference genome assembly of spinach and genome resequencing of 305 accessions, and provide insights into spinach domestication and the genetic basis of agronomic traits.

CsAGA1 and CsAGA2 Mediate RFO Hydrolysis in Partially Distinct Manner in Cucumber Fruits

A Raffinose family oligosaccharides (RFOs) is one of the major translocated sugars in the vascular bundle of cucumber, but little RFOs can be detected in fruits. Alpha-galactosidases (α-Gals) catalyze the first catabolism step of RFOs. Six α-Gal genes exist in a cucumber genome, but their spatial functions in fruits remain unclear. Here, we found that RFOs were highly accumulated in vascular tissues. In phloem sap, the stachyose and raffinose content was gradually decreased, whereas the content of sucrose, glucose and fructose was increased from pedicel to fruit top. Three alkaline forms instead of acid forms of α-Gals were preferentially expressed in fruit vascular tissues and alkaline forms have stronger RFO-hydrolysing activity than acid forms. By inducible gene silencing of three alkaline forms of α-Gals, stachyose was highly accumulated in RNAi-CsAGA2 plants, while raffinose and stachyose were highly accumulated in RNAi-CsAGA1 plants. The content of sucrose, glucose and fructose was decreased in both RNAi-CsAGA1 and RNAi-CsAGA2 plants after β-estradiol treatment. In addition, the fresh- and dry-weight of fruits were significantly decreased in RNAi-CsAGA1 and RNAi-CsAGA2 plants. In cucurbitaceous plants, the non-sweet motif within the promoter of ClAGA2 is widely distributed in the promoter of its homologous genes. Taken together, we found RFOs hydrolysis occurred in the vascular tissues of fruits. CsAGA1 and CsAGA2 played key but partly distinct roles in the hydrolysis of RFOs.

Highly efficient, genotype-independent transformation and gene editing in watermelon (Citrullus lanatus) using a chimeric ClGRF4-GIF1 gene

Efficient genetic transformation has the potential to advance research and breeding in watermelon (Citrullus lanatus), but regeneration from tissue culture remains challenging. Previous work showed that expressing a fusion of two interacting transcription factors, GROWTH-REGULATING FACTOR4 (GRF4) and GRF-INTERACTING FACTOR1 (GIF1), improved regeneration in wheat (Triticum aestivum). By overexpressing a chimeric fusion of ClGRF4 and ClGIF1, we achieved highly efficient transformation in watermelon. Mutating the mi396 microRNA target site in ClGRF further boosted the transformation efficiency up to 67.27% in a genotype-independent manner. ClGRF4-GIF1 can also be combined with clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) genome editing tools to achieve highly efficient gene editing in watermelon, which we used to successfully create diploid seedless watermelon. This research thus puts forward a powerful transformation tool for future watermelon research and breeding.

Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity

Background

Heterozygous genomes are widespread in outcrossing and clonally propagated crops. However, the variation in heterozygosity underlying key agronomic traits and crop domestication remains largely unknown. Cassava is a staple crop in Africa and other tropical regions and has a highly heterozygous genome.

Results

We describe a genomic variation map from 388 resequenced genomes of cassava cultivars and wild accessions. We identify 52 loci for 23 agronomic traits through a genome-wide association study. Eighteen allelic variations in heterozygosity for nine candidate genes are significantly associated with seven key agronomic traits. We detect 81 selective sweeps with decreasing heterozygosity and nucleotide diversity, harboring 548 genes, which are enriched in multiple biological processes including growth, development, hormone metabolisms and responses, and immune-related processes. Artificial selection for decreased heterozygosity has contributed to the domestication of the large starchy storage root of cassava. Selection for homozygous GG allele in MeTIR1 during domestication contributes to increased starch content. Selection of homozygous AA allele in MeAHL17 is associated with increased storage root weight and cassava bacterial blight (CBB) susceptibility. We have verified the positive roles of MeTIR1 in increasing starch content and MeAHL17 in resistance to CBB by transient overexpression and silencing analysis. The allelic combinations in MeTIR1 and MeAHL17 may result in high starch content and resistance to CBB.

Conclusions

This study provides insights into allelic variation in heterozygosity associated with key agronomic traits and cassava domestication. It also offers valuable resources for the improvement of cassava and other highly heterozygous crops.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-021-02524-7.

The role of watermelon caffeic acid O-methyltransferase (ClCOMT1) in melatonin biosynthesis and abiotic stress tolerance

Melatonin is a pleiotropic signaling molecule that regulates plant growth and responses to various abiotic stresses. The last step of melatonin synthesis in plants can be catalyzed by caffeic acid O-methyltransferase (COMT), a multifunctional enzyme reported to have N-acetylserotonin O-methyltransferase (ASMT) activity; however, the ASMT activity of COMT has not yet been characterized in nonmodel plants such as watermelon (Citrullus lanatus). Here, a total of 16 putative O-methyltransferase (ClOMT) genes were identified in watermelon. Among them, ClOMT03 (Cla97C07G144540) was considered a potential COMT gene (renamed ClCOMT1) based on its high identities (60.00-74.93%) to known COMT genes involved in melatonin biosynthesis, expression in almost all tissues, and upregulation under abiotic stresses. The ClCOMT1 protein was localized in the cytoplasm. Overexpression of ClCOMT1 significantly increased melatonin contents, while ClCOMT1 knockout using the CRISPR/Cas-9 system decreased melatonin contents in watermelon calli. These results suggest that ClCOMT1 plays an essential role in melatonin biosynthesis in watermelon. In addition, ClCOMT1 expression in watermelon was upregulated by cold, drought, and salt stress, accompanied by increases in melatonin contents. Overexpression of ClCOMT1 enhanced transgenic Arabidopsis tolerance against such abiotic stresses, indicating that ClCOMT1 is a positive regulator of plant tolerance to abiotic stresses.

The NAC transcription factor ClNAC68 positively regulates sugar content and seed development in watermelon by repressing ClINV and ClGH3.6

NAC (NAM, ATAF1/2, and CUC2) transcription factors play important roles in fruit ripening and quality. The watermelon genome encodes 80 NAC genes, and 21 of these NAC genes are highly expressed in both the flesh and vascular tissues. Among these genes, ClNAC68 expression was significantly higher in flesh than in rind. However, the intrinsic regulatory mechanism of ClNAC68 in fruit ripening and quality is still unknown. In this study, we found that ClNAC68 is a transcriptional repressor and that the repression domain is located in the C-terminus. Knockout of ClNAC68 by the CRISPR-Cas9 system decreased the soluble solid content and sucrose accumulation in mutant flesh. Development was delayed, germination was inhibited, and the IAA content was significantly decreased in mutant seeds. Transcriptome analysis showed that the invertase gene ClINV was the only gene involved in sucrose metabolism that was upregulated in mutant flesh, and expression of the indole-3-acetic acid-amido synthetase gene ClGH3.6 in the IAA signaling pathway was also induced in mutant seeds. EMSA and dual-luciferase assays showed that ClNAC68 directly bound to the promoters of ClINV and ClGH3.6 to repress their expression. These results indicated that ClNAC68 positively regulated sugar and IAA accumulation by repressing ClINV and ClGH3.6. Our findings provide new insights into the regulatory mechanisms by which NAC transcription factors affect fruit quality and seed development.

Candidate gene analysis of watermelon stripe pattern locus ClSP ongoing recombination suppression

Using two segregating population, watermelon stripe pattern underlying gene ClSP was delimited to a 611.78 Kb region, consisting of four discrete haploblocks and ongoing recombination suppression. Stripe pattern is an important commodity trait in watermelon, displaying diverse types. In this study, two segregating populations were generated for genetic mapping the single dominant locus ClSP, which was finally delimited to a 611.78 Kb interval with suppression of recombination. According to polymorphism sites detected among genotypes, four discrete haploblocks were characterized in this target region. Based on reference genomes, 81 predicted genes were annotated in the ClSP interval, including seven transcription factors namely as candidate No1-No7. Meanwhile, the ortholog gene of cucumber ist responsible for the irregular stripes was considered as candidate No8. Strikingly, gene structures of No1-No5 completely varied from their reference descriptions and subsequently re-annotated. For instance, the original adjacent distribution candidates No2 and No3 were re-annotated as No2_3, while No4 and No5 were integrated as No4_5. Sequence analysis demonstrated the third polymorphism in CDS of re-annotated No4_5 resulting in truncated proteins in non-stripe plants. Furthermore, only No4_5 was down-regulated in light green stripes relative to dark green stripes. Transcriptome analysis identified 356 DEGs between dark green striped and light green striped peels, with genes involved in photosynthesis and chloroplast development down-regulated in light green stripes but calcium ion binding related genes up-regulated. Additionally, 38 DEGs were annotated as transcription factors, with the majority up-regulated in light green stripes, such as ERFs and WRKYs. This study not only contributes to a better understanding of the molecular mechanisms underlying watermelon stripe development, but also provides new insights into the genomic structure of ClSP locus and valuable candidates.

Genetic Resources and Vulnerabilities of Major Cucurbit Crops

The Cucurbitaceae family provides numerous important crops including watermelons (Citrullus lanatus), melons (Cucumis melo), cucumbers (Cucumis sativus), and pumpkins and squashes (Cucurbita spp.). Centers of domestication in Africa, Asia, and the Americas were followed by distribution throughout the world and the evolution of secondary centers of diversity. Each of these crops is challenged by multiple fungal, oomycete, bacterial, and viral diseases and insects that vector disease and cause feeding damage. Cultivated varieties are constrained by market demands, the necessity for climatic adaptations, domestication bottlenecks, and in most cases, limited capacity for interspecific hybridization, creating narrow genetic bases for crop improvement. This analysis of crop vulnerabilities examines the four major cucurbit crops, their uses, challenges, and genetic resources. ex situ germplasm banks, the primary strategy to preserve genetic diversity, have been extensively utilized by cucurbit breeders, especially for resistances to biotic and abiotic stresses. Recent genomic efforts have documented genetic diversity, population structure, and genetic relationships among accessions within collections. Collection size and accessibility are impacted by historical collections, current ability to collect, and ability to store and maintain collections. The biology of cucurbits, with insect-pollinated, outcrossing plants, and large, spreading vines, pose additional challenges for regeneration and maintenance. Our ability to address ongoing and future cucurbit crop vulnerabilities will require a combination of investment, agricultural, and conservation policies, and technological advances to facilitate collection, preservation, and access to critical Cucurbitaceae diversity.

Genome-wide association study reveals the genetic architecture of 27 agronomic traits in tomato

Tomato (Solanum lycopersicum) is a highly valuable fruit crop, and yield is one of the most important agronomic traits. However, the genetic architecture underlying tomato yield-related traits has not been fully addressed. Based on ∼4.4 million single nucleotide polymorphisms obtained from 605 diverse accessions, we performed a comprehensive genome-wide association study for 27 agronomic traits in tomato. A total of 239 significant associations corresponding to 129 loci, harboring many previously reported and additional genes related to vegetative and reproductive development, were identified, and these loci explained an average of ∼8.8% of the phenotypic variance. A total of 51 loci associated with 25 traits have been under selection during tomato domestication and improvement. Furthermore, a candidate gene, Sl-ACTIVATED MALATE TRANSPORTER15, that encodes an aluminum-activated malate transporter was functionally characterized and shown to act as a pivotal regulator of leaf stomata formation, thereby affecting photosynthesis and drought resistance. This study provides valuable information for tomato genetic research and breeding.

Advances in Genomics Approaches Shed Light on Crop Domestication

Crop domestication occurred ~10,000–12,000 years ago when humans shifted from a hunter–gatherer to an agrarian society. Crops were domesticated by selecting the traits in wild plant species that were suitable for human use. Research is crucial to elucidate the mechanisms and processes involved in modern crop improvement and breeding. Recent advances in genomics have revolutionized our understanding of crop domestication. In this review, we summarized cutting-edge crop domestication research by presenting its (1) methodologies, (2) current status, (3) applications, and (4) perspectives. Advanced genomics approaches have clarified crop domestication processes and mechanisms, and supported crop improvement.

An integrated transcriptome and metabolome approach reveals the accumulation of taste-related metabolites and gene regulatory networks during watermelon fruit development

Accumulation patterns and gene regulatory networks of sugars and cucurbitacins and related primary and secondary metabolites during cultivated watermelon 'Cheng Lan' and wild watermelon 'PI 632,751' fruit development were identified. Metabolites are the end products of cellular regulatory processes and play important roles in fruit taste formation. However, comprehensive studies on the accumulation patterns of watermelon fruit metabolites and transcriptional regulatory networks are still scarce. In this study, 451 annotated metabolites were identified at four key fruit developmental stages in wild watermelon 'PI 632,751' and modern cultivated watermelon 'Cheng Lan'. Interestingly, 11 sugars and 25 major primary metabolites were mainly accumulated in 'Cheng Lan' during fruit development, which are considered to be the potential metabolites beneficial to the formation of watermelon taste. Cucurbitacins and the main flavonoids were mainly specifically accumulated in 'PI 632,751', not being considered to be responsible for the taste. Moreover, forty-seven genes involved in carbohydrate metabolism, glycolysis, and TCA cycle were highly expressed in 'Cheng Lan', which was positively correlated with the accumulation of major primary metabolites. Alternatively, seven UDP-glycosyltransferase genes are closely related to the glycosylation of cucurbitacins through co-expression analysis. Our findings established a global map of metabolite accumulation and gene regulation during fruit development in wild and cultivated watermelons and provided valuable information on taste formation in watermelon fruit.

Evolutionary gain of oligosaccharide hydrolysis and sugar transport enhanced carbohydrate partitioning in sweet watermelon fruits

How raffinose (Raf) family oligosaccharides, the major translocated sugars in the vascular bundle in cucurbits, are hydrolyzed and subsequently partitioned has not been fully elucidated. By performing reciprocal grafting of watermelon (Citrullus lanatus) fruits to branch stems, we observed that Raf was hydrolyzed in the fruit of cultivar watermelons but was backlogged in the fruit of wild ancestor species. Through a genome-wide association study, the alkaline alpha-galactosidase ClAGA2 was identified as the key factor controlling stachyose and Raf hydrolysis, and it was determined to be specifically expressed in the vascular bundle. Analysis of transgenic plants confirmed that ClAGA2 controls fruit Raf hydrolysis and reduces sugar content in fruits. Two single-nucleotide polymorphisms (SNPs) within the ClAGA2 promoter affect the recruitment of the transcription factor ClNF-YC2 (nuclear transcription factor Y subunit C) to regulate ClAGA2 expression. Moreover, this study demonstrates that C. lanatus Sugars Will Eventually Be Exported Transporter 3 (ClSWEET3) and Tonoplast Sugar Transporter (ClTST2) participate in plasma membrane sugar transport and sugar storage in fruit cell vacuoles, respectively. Knocking out ClAGA2, ClSWEET3, and ClTST2 affected fruit sugar accumulation. Genomic signatures indicate that the selection of ClAGA2, ClSWEET3, and ClTST2 for carbohydrate partitioning led to the derivation of modern sweet watermelon from non-sweet ancestors during domestication.

Population-scale peach genome analyses unravel selection patterns and biochemical basis underlying fruit flavor

A narrow genetic basis in modern cultivars and strong linkage disequilibrium in peach (Prunus persica) has restricted resolution power for association studies in this model fruit species, thereby limiting our understanding of economically important quality traits including fruit flavor. Here, we present a high-quality genome assembly for a Chinese landrace, Longhua Shui Mi (LHSM), a representative of the Chinese Cling peaches that have been central in global peach genetic improvement. We also map the resequencing data for 564 peach accessions to this LHSM assembly at an average depth of 26.34× per accession. Population genomic analyses reveal a fascinating history of convergent selection for sweetness yet divergent selection for acidity in eastern vs. western modern cultivars. Molecular-genetics and biochemical analyses establish that PpALMT1 (aluminum-activated malate transporter 1) contributes to their difference of malate content and that increases fructose content accounts for the increased sweetness of modern peach fruits, as regulated by PpERDL16 (early response to dehydration 6-like 16). Our study illustrates the strong utility of the genomics resources for both basic and applied efforts to understand and exploit the genetic basis of fruit quality in peach.

Identification and QTL Analysis of Flavonoids and Carotenoids in Tetraploid Roses Based on an Ultra-High-Density Genetic Map

Roses are highly valuable within the flower industry. The metabolites of anthocyanins, flavonols, and carotenoids in rose petals are not only responsible for the various visible petal colors but also important bioactive compounds that are important for human health. In this study, we performed a QTL analysis on pigment contents to locate major loci that determine the flower color traits. An F1 population of tetraploid roses segregating for flower color was used to construct an ultra-high-density genetic linkage map using whole-genome resequencing technology to detect genome-wide SNPs. Previously developed SSR and SNP markers were also utilized to increase the marker density. Thus, a total of 9,259 markers were mapped onto seven linkage groups (LGs). The final length of the integrated map was 1285.11 cM, with an average distance of 0.14 cM between adjacent markers. The contents of anthocyanins, flavonols and carotenoids of the population were assayed to enable QTL analysis. Across the 33 components, 46 QTLs were detected, explaining 11.85-47.72% of the phenotypic variation. The mapped QTLs were physically clustered and primarily distributed on four linkage groups, namely LG2, LG4, LG6, and LG7. These results improve the basis for flower color marker-assisted breeding of tetraploid roses and guide the development of rose products.

Genetic and Pre- and Postharvest Factors Influencing the Content of Antioxidants in Cucurbit Crops

Cucurbitaceae is one of the most economically important plant families, and includes some worldwide cultivated species like cucumber, melons, and squashes, and some regionally cultivated and feral species that contribute to the human diet. For centuries, cucurbits have been appreciated because of their nutritional value and, in traditional medicine, because of their ability to alleviate certain ailments. Several studies have demonstrated the remarkable contents of valuable compounds in cucurbits, including antioxidants such as polyphenols, flavonoids, and carotenoids, but also tannins and terpenoids, which are abundant. This antioxidant power is beneficial for human health, but also in facing plant diseases and abiotic stresses. This review brings together data on the antioxidant properties of cucurbit species, addressing the genetic and pre- and postharvest factors that regulate the antioxidant content in different plant organs. Environmental conditions, management, storage, and pre- and postharvest treatments influencing the biosynthesis and activity of antioxidants, together with the biodiversity of this family, are determinant in improving the antioxidant potential of this group of species. Plant breeding, as well as the development of innovative biotechnological approaches, is also leading to new possibilities for exploiting cucurbits as functional products.

Domestication of Crop Metabolomes: Desired and Unintended Consequences

The majority of the crops and vegetables of today were domesticated from their wild progenitors within the past 12 000 years. Considerable research effort has been expended on characterizing the genes undergoing positive and negative selection during the processes of crop domestication and improvement. Many studies have also documented how the contents of a handful of metabolites have been altered during human selection, but we are only beginning to unravel the true extent of the metabolic consequences of breeding. We highlight how crop metabolomes have been wittingly or unwittingly shaped by the processes of domestication, and highlight how we can identify new targets for metabolite engineering for the purpose of de novo domestication of crop wild relatives.

A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons

Wild relatives or progenitors of crops are important resources for breeding and for understanding domestication. Identifying them, however, is difficult because of extinction, hybridization, and the challenge of distinguishing them from feral forms. Here, we use collection-based systematics, iconography, and resequenced accessions of Citrullus lanatus and other species of Citrullus to search for the potential progenitor of the domesticated watermelon. A Sudanese form with nonbitter whitish pulp, known as the Kordofan melon (C. lanatus subsp. cordophanus), appears to be the closest relative of domesticated watermelons and a possible progenitor, consistent with newly interpreted Egyptian tomb paintings that suggest that the watermelon may have been consumed in the Nile Valley as a dessert by 4360 BP. To gain insights into the genetic changes that occurred from the progenitor to the domesticated watermelon, we assembled and annotated the genome of a Kordofan melon at the chromosome level, using a combination of Pacific Biosciences and Illumina sequencing as well as Hi-C mapping technologies. The genetic signature of bitterness loss is present in the Kordofan melon genome, but the red fruit flesh color only became fixed in the domesticated watermelon. We detected 15,824 genome structural variants (SVs) between the Kordofan melon and a typical modern cultivar, "97103," and mapping the SVs in over 400 Citrullus accessions revealed shifts in allelic frequencies, suggesting that fruit sweetness has gradually increased over the course of watermelon domestication. That a likely progenitor of the watermelon still exists in Sudan has implications for targeted modern breeding efforts.

Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce

Lettuce (Lactuca sativa) is an important vegetable crop worldwide. Cultivated lettuce is believed to be domesticated from L. serriola; however, its origins and domestication history remain to be elucidated. Here, we sequenced a total of 445 Lactuca accessions, including major lettuce crop types and wild relative species, and generated a comprehensive map of lettuce genome variations. In-depth analyses of population structure and demography revealed that lettuce was first domesticated near the Caucasus, which was marked by loss of seed shattering. We also identified the genetic architecture of other domestication traits and wild introgressions in major resistance clusters in the lettuce genome. This study provides valuable genomic resources for crop breeding and sheds light on the domestication history of cultivated lettuce.

Loquat (Eriobotrya japonica (Thunb.) Lindl) population genomics suggests a two-staged domestication and identifies genes showing convergence/parallel selective sweeps with apple or peach

Crop domestication and evolution represent key fields of plant and genetics research. Here, we re-sequenced and analyzed whole genome data from 51 wild accessions and 53 representative cultivars of Eriobotrya japonica, an important semi-subtropical fruit crop. Population genomics analysis suggested that modern cultivated E. japonica experienced a two-staged domestication fitting the "marginality model," being initially domesticated in west-northern Hubei province from a mono-phylogenetic wild progenitor, then refined mainly in Jiangsu, Zhejiang and Fujian provinces of China. Cultivated E. japonica has experienced little reduction in genome-wide nucleotide polymorphism compared with wild forms. Genes responsible for sugar biosynthesis were enriched in regions harboring putative selective sweeps. An approach based on co-clustering into gene families and evaluating chromosome colinearity of orthologous and paralogous genes was used to identify convergent/parallel selective sweeps among different crops. Specifically, more than one hundred of orthologs and paralogs undergoing selective sweeps were identified between loquat, apple and peach, among which 14 encoded "UDP glycosyltransferase 1." In sum, the study not only provided valuable information for breeding of E. japonica, but also enriched knowledge of crop domestication.

The impaired biosynthetic networks in defective tapetum lead to male sterility in watermelon

Heterosis has been widely applied in watermelon breeding, because of the higher resistance and yield of hybrid. As the basis of heterosis utilization, genic male sterility (GMS) is an important tool for facilitating hybrid seed production, while the detailed mechanism in watermelon is still largely unknown. Here, we report a spontaneous mutant Se18 exhibited complete male sterility due to the uniquely multilayered tapetum and the un-meiotic pollen mother cells during pollen development. Using TMT based quantitative proteomic analyses, a total of 348 differentially abundant proteins (DAPs) were detected with the overwhelming majority down-regulated in mutant Se18. By analyzing the putative orthologs/homologs of Arabidopsis GMS related genes, the biosynthesis and transport of sporopollenin and tryphine precursors were predictably altered in mutant compared to its sibling wild type. Moreover, the general phenylpropanoid pathway as well as its related metabolisms was also expectably impaired in mutant, coincident with the pale yellow petals. Notably, some key transcriptional factors regulating tapetum development, together with their down-regulated targets, offered potentially valuable candidates regarding of male sterility. Collectively, the disrupted regulatory networks underlying male sterility of watermelon was proposed, which provide novel insights into genetic mechanism of male reproductive process and rich gene resources for future research. SIGNIFICANCE: Watermelon is an importantly economical cucurbit crop worldwide, with high nutritional value. Although several male sterile mutants have been identified in watermelon, the underlying molecular mechanism is poorly elucidated. Comparative cytological analysis revealed that the defective development of tapetum was responsible for male sterility in mutant Se18. Combined with the morphological comparison, male floral buds at 2.0-2.5 mm in diameter were confirmed with no obvious phenotypic differences but distinct cytological defects, which were in turn sampled for TMT based proteomic analyses. Referring to functionally characterized GMS related genes, the genetic pathway DYT1-TDF1-AMS-MS188-MS1 regulating tapetum development, together with some downstream targets, were considerably altered in mutant Se18. Moreover, enrichment analyses illustrated the general phenylpropanoid related metabolisms, as well as the biosynthesis and transport of sporopollenin and tryphine precursors, were significantly disrupted in defective anther development. Collectively, the proposed regulatory networks in watermelon not only contribute to a better understanding of molecular mechanisms underlying male sterility, but also provide valuable GMS related candidates for future researches.

Building a cluster of NLR genes conferring resistance to pests and pathogens: the story of the Vat gene cluster in cucurbits

Most molecularly characterized plant resistance genes (R genes) belong to the nucleotide-binding-site-leucine-rich-repeat (NLR) receptor family and are prone to duplication and transposition with high sequence diversity. In this family, the Vat gene in melon is one of the few R genes known for conferring resistance to insect, i.e., Aphis gossypii, but it has been misassembled and/or mispredicted in the whole genomes of Cucurbits. We examined 14 genomic regions (about 400 kb) derived from long-read assemblies spanning Vat-related genes in Cucumis melo, Cucumis sativus, Citrullus lanatus, Benincasa hispida, Cucurbita argyrosperma, and Momordica charantia. We built the phylogeny of those genes. Investigating the paleohistory of the Vat gene cluster, we revealed a step by step process beginning from a common ancestry in cucurbits older than 50 my. We highlighted Vat exclusively in the Cucumis genera, which diverged about 20 my ago. We then focused on melon, evaluating a minimum duplication rate of Vat in 80 wild and cultivated melon lines using generalist primers; our results suggested that duplication started before melon domestication. The phylogeny of 44 Vat-CDS obtained from 21 melon lines revealed gain and loss of leucine-rich-repeat domains along diversification. Altogether, we revealed the high putative recognition scale offered in melon based on a combination of SNPs, number of leucine-rich-repeat domains within each homolog and number of homologs within each cluster that might jointly confer resistance to a large pest and pathogen spectrum. Based on our findings, we propose possible avenues for breeding programs.

Proteomic Analysis of Fusarium oxysporum-Induced Mechanism in Grafted Watermelon Seedlings

Grafting can improve the resistance of watermelon to soil-borne diseases. However, the molecular mechanism of defense response is not completely understood. Herein, we used a proteomic approach to investigate the molecular basis involved in grafted watermelon leaf defense against Fusarium oxysporum f.sp. niveum (FON) infection. The bottle gourd rootstock-grafted (RG) watermelon seedlings were highly resistant to FON compared with self-grafted (SG) watermelon plants, with a disease incidence of 3.4 and 89%, respectively. Meanwhile, grafting significantly induced the activity of pathogenesis-related proteases under FON challenge. Proteins extracted from leaves of RG and SG under FON inoculation were analyzed using two-dimensional gel electrophoresis. Thirty-nine differentially accumulated proteins (DAPs) were identified and classified into 10 functional groups. Accordingly, protein biosynthetic and stress- and defense-related proteins play crucial roles in the enhancement of disease resistance of RG watermelon seedlings, compared with that of SG watermelon seedlings. Proteins involved in signal transduction positively regulated the defense process. Carbohydrate and energy metabolism and photosystem contributed to energy production in RG watermelon seedlings under FON infection. The disease resistance of RG watermelon seedlings may also be related to the improved scavenging capacity of reactive oxygen species (ROS). The expression profile of 10 randomly selected proteins was measured using quantitative real-time PCR, among which, 7 was consistent with the results of the proteomic analysis. The functional implications of these proteins in regulating grafted watermelon response against F. oxysporum are discussed.

QTL associated with gummy stem blight resistance in watermelon

We identified QTLs associated with gummy stem blight resistance in an interspecific F_2:3 Citrullus population and developed marker assays for selection of the loci in watermelon. Gummy stem blight (GSB), caused by three Stagonosporopsis spp., is a devastating fungal disease of watermelon (Citrullus lanatus) and other cucurbits that can lead to severe yield losses. Currently, no commercial cultivars with genetic resistance to GSB in the field have been reported. Utilizing GSB-resistant cultivars would reduce yield losses, decrease the high cost of disease control, and diminish hazards resulting from frequent fungicide application. The objective of this study was to identify quantitative trait loci (QTLs) associated with GSB resistance in an F_2:3 interspecific Citrullus mapping population (N = 178), derived from a cross between Crimson Sweet (C. lanatus) and GSB-resistant PI 482276 (C. amarus). The population was phenotyped by inoculating seedlings with Stagonosporopsis citrulli 12178A in the greenhouse in two separate experiments, each with three replications. We identified three QTLs (ClGSB3.1, ClGSB5.1 and ClGSB7.1) associated with GSB resistance, explaining between 6.4 and 21.1% of the phenotypic variation. The genes underlying ClGSB5.1 includes an NBS-LRR gene (ClCG05G019540) previously identified as a candidate gene for GSB resistance in watermelon. Locus ClGSB7.1 accounted for the highest phenotypic variation and harbors twenty-two candidate genes associated with disease resistance. Among them is ClCG07G013230, encoding an Avr9/Cf-9 rapidly elicited disease resistance protein, which contains a non-synonymous point mutation in the DUF761 domain that was significantly associated with GSB resistance. High throughput markers were developed for selection of ClGSB5.1 and ClGSB7.1. Our findings will facilitate the use of molecular markers for efficient introgression of the resistance loci and development of GSB-resistant watermelon cultivars.

Comparative Metabolomic Profiling of Citrullus spp. Fruits Provides Evidence for Metabolomic Divergence during Domestication

Watermelon (Citrullus lanatus) is one of the most nutritional fruits that is widely distributed in the whole world. The nutritional compositions are mainly influenced by the genotype and environment. However, the metabolomics of different domestication status and different flesh colors watermelon types is not fully understood. In this study, we reported an extensive assessment of metabolomic divergence in the fruit flesh among Citrullus sp. and within Citrullus sp. We demonstrate that metabolic profiling was significantly different between the wild and cultivated watermelons, the apigenin 6-C-glucoside, luteolin 6-C-glucoside, chrysoeriol C-hexoside, naringenin C-hexoside, C-pentosyl-chrysoeriol O-hexoside, and sucrose are the main divergent metabolites. Correlation analysis results revealed that flavonoids were present in one tight metabolite cluster. The main divergent metabolites in different flesh-colored cultivated watermelon fruits are p-coumaric acid, 2,3-dihydroflavone, catechin, N-(3-indolylacetyl)-l-alanine, 3,4-dihydroxycinnamic acid, and pelargonidin o-hexoside. A total of 431 differentially accumulated metabolites were identified from pairwise comparative analyses. C. lanatus edible-seed watermelon (cultivars) and C. mucosospermus (wild) have similar fruit metabolic profiles and phenotypic traits, indicating that edible-seed watermelon may be a relative of wild species and a relatively primitive differentiation type of cultivated watermelon. Our data provide extensive knowledge for metabolomics-based watermelon improvement of Citrullus fruits meet their enhanced nutritive properties or upgraded germplasm utility values.

Plant-ImputeDB: an integrated multiple plant reference panel database for genotype imputation

Genotype imputation is a process that estimates missing genotypes in terms of the haplotypes and genotypes in a reference panel. It can effectively increase the density of single nucleotide polymorphisms (SNPs), boost the power to identify genetic association and promote the combination of genetic studies. However, there has been a lack of high-quality reference panels for most plants, which greatly hinders the application of genotype imputation. Here, we developed Plant-ImputeDB (http://gong_lab.hzau.edu.cn/Plant_imputeDB/), a comprehensive database with reference panels of 12 plant species for online genotype imputation, SNP and block search and free download. By integrating genotype data and whole-genome resequencing data of plants from various studies and databases, the current Plant-ImputeDB provides high-quality reference panels of 12 plant species, including ∼69.9 million SNPs from 34 244 samples. It also provides an easy-to-use online tool with the option of two popular tools specifically designed for genotype imputation. In addition, Plant-ImputeDB accepts submissions of different types of genomic variations, and provides free and open access to all publicly available data in support of related research worldwide. In general, Plant-ImputeDB may serve as an important resource for plant genotype imputation and greatly facilitate the research on plant genetic research.

Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape

BACKGROUND

Structural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic variation, yet the impacts of SVs remain largely unexplored in crops.

RESULTS

Here, we generate a high-quality de novo genome assembly for a flat-fruit peach cultivar and produce a comprehensive SV map for peach, as a high proportion of genomic sequence is occupied by heterozygous SVs in the peach genome. We conduct population-level analyses that indicate SVs have undergone strong purifying selection during peach domestication, and find evidence of positive selection, with a significant preference for upstream and intronic regions during later peach improvement. We perform a SV-based GWAS that identifies a large 1.67-Mb heterozygous inversion that segregates perfectly with flat-fruit shape. Mechanistically, this derived allele alters the expression of the PpOFP2 gene positioned near the proximal breakpoint of the inversion, and we confirm in transgenic tomatoes that PpOFP2 is causal for flat-fruit shape.

CONCLUSIONS

Thus, beyond introducing new genomics resources for peach research, our study illustrates how focusing on SV data can drive basic functional discoveries in plant science.

Metabolome and Transcriptome Integration Reveals Insights Into Flavor Formation of 'Crimson' Watermelon Flesh During Fruit Development

Metabolites have been reported as the main factor that influences the fruit flavor of watermelon. But the comprehensive study on the dynamics of metabolites during the development of watermelon fruit is not up-to-date. In this study, metabolome and transcriptome datasets of 'Crimson' watermelon fruit at four key developmental stages were generated. A total of 517 metabolites were detected by ultrahigh-performance liquid chromatography-electrospray ionization-tandem mass spectrometry and gas chromatography-solid-phase microextraction-mass spectrometry. Meanwhile, by K-means clustering analysis, the total differentially expressed genes were clustered in six classes. Integrating transcriptome and metabolome data revealed similar expression trends of sugars and genes involved in the glycolytic pathway, providing molecular insights into the formation of taste during fruit development. Furthermore, through coexpression analysis, we identified five differentially expressed ADH (alcohol dehydrogenase) genes (Cla97C01G013600, Cla97C05G089700, Cla97C01G001290, Cla97C05G095170, and Cla97C06G118330), which were found to be closely related to C9 alcohols/aldehydes, providing information for the formation of fruit aroma. Our findings establish a metabolic profile during watermelon fruit development and provide insights into flavor formation.

QTL Mapping for Leaf Area of Tea Plants (Camellia sinensis) Based on a High-Quality Genetic Map Constructed by Whole Genome Resequencing

High-quality genetic maps play important roles in QTL mapping and molecular marker-assisted breeding. Tea leaves are not only important vegetative organs but are also the organ for harvest with important economic value. However, the key genes and genetic mechanism of regulating leaf area have not been clarified. In this study, we performed whole-genome resequencing on "Jinxuan," "Yuncha 1" and their 96 F1 hybrid offspring. From the 1.84 Tb of original sequencing data, abundant genetic variation loci were identified, including 28,144,625 SNPs and 2,780,380 indels. By integrating the markers of a previously reported genetic map, a high-density genetic map consisting of 15 linkage groups including 8,956 high-quality SNPs was constructed. The total length of the genetic map is 1,490.81 cM, which shows good collinearity with the genome. A total of 25 representative markers (potential QTLs) related to leaf area were identified, and there were genes differentially expressed in large and small leaf samples near these markers. GWAS analysis further verified the reliability of QTL mapping. Thirty-one pairs of newly developed indel markers located near these potential QTLs showed high polymorphism and had good discrimination between large and small leaf tea plant samples. Our research will provide necessary support and new insights for tea plant genetic breeding, quantitative trait mapping and yield improvement.

Contributions of African Crops to American Culture and Beyond: The Slave Trade and Other Journeys of Resilient Peoples and Crops

There is a general unawareness of food crops indigenous to the African continent that have contributed to Western culture. This under-appreciation is particularly relevant in the current context of societal movements to end historic racism and value the contributions of peoples of African origin and African skin colors. Lack of awareness of the contributions of Africa's crops has negative practical consequences, including inadequate investments in preserving and maximizing the use of crop diversity to facilitate breeding. This paper provides an overview and analysis of African crops that have made significant contributions to the United States and globally, and/or hold potential in the twenty-first century. The paper specifically discusses watermelon, coffee, kola, rooibos, oil palm, shea, cowpea/black eyed pea, leafy greens, okra, yam, sorghum, pearl millet, finger millet, teff, and fonio. The review focuses on the intersection of these crops with racialized peoples, with a particular focus on African-Americans starting with slavery. The analysis includes the sites of domestication of African crops, their historical migration out of Africa, their sociocultural contributions to cuisines and products around the world, their uses today, and the indigenous knowledge associated with traditional cultivation and landrace selection. The untapped potential of local genetic resources and indigenous agronomic strategies are also described. The review demonstrates that African crops played an important role in the development of American cuisine, beverages and household products. Many of these crops are nutritious, high value and stress tolerant. The paper concludes that African crops hold significant promise in improving the resiliency of global food production systems, to mitigate climate change and alleviate food insecurity and rural poverty, especially in dry regions of the world. It is hoped that this review contributes to teaching the next generation of agriculturalists, food scientists and international development professionals about the valuable contributions of Africa's resilient crops and peoples.

Resequencing of 297 melon accessions reveals the genomic history of improvement and loci related to fruit traits in melon

Domestication and improvement are two important stages in crop evolution. Melon (Cucumis melo L.) is an important vegetable crop with wide phenotypic diversity in many horticultural traits, especially fruit size, flesh thickness and aroma, which are likely the results of long-term extensive selection during its evolution. However, selective signals in domestication and improvement stages for these remarkable variations remain unclear. We resequenced 297 wild, landrace and improved melon accessions and obtained 2 045 412 high-quality SNPs. Population structure and genetic diversity analyses revealed independent and two-step selections in two subspecies of melon: ssp. melo and ssp. agrestis during melon breeding. We detected 233 (~18.35 Mbp) and 159 (~17.71 Mbp) novel potential selective signals during the improvement stage in ssp. agrestis and spp. melo, respectively. Two alcohol acyltransferase genes (CmAATs) unique to the melon genome compared with other cucurbit crops may have undergone stronger selection in ssp. agrestis for the characteristic aroma as compared with other cucurbits. Genome-wide association analysis identified eight fruit size and seven flesh thickness signals overlapping with selective sweeps. Compared with thin-skinned ssp. agrestis, thick-skinned ssp. melo has undergone a stronger selection for thicker flesh. In most melon accessions, CmCLV3 has pleiotropic effects on carpel number and fruit shape. Findings from this study provide novel insights into melon crop evolution, and new tools to advance melon breeding.

The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening

Snake gourd (Trichosanthes anguina L.), which belongs to the Cucurbitaceae family, is a popular ornamental and food crop species with medicinal value and is grown in many parts of the world. Although progress has been made in its genetic improvement, the organization, composition, and evolution of the snake gourd genome remain largely unknown. Here, we report a high-quality genome assembly for snake gourd, comprising 202 contigs, with a total size of 919.8 Mb and an N50 size of 20.1 Mb. These findings indicate that snake gourd has one of the largest genomes of Cucurbitaceae species sequenced to date. The snake gourd genome assembly harbors 22,874 protein-coding genes and 80.0% of the genome consists of repetitive sequences. Phylogenetic analysis reveals that snake gourd is closely related to sponge gourd but diverged from their common ancestor ~33-47 million years ago. The genome sequence reported here serves as a valuable resource for snake gourd genetic research and comparative genomic studies in Cucurbitaceae and other plant species. In addition, fruit transcriptome analysis reveals the candidate genes related to quality traits during snake gourd fruit development and provides a basis for future research on snake gourd fruit development and ripening at the transcript level.

Regulatory network of fruit ripening: current understanding and future challenges

Fruit ripening is a developmental process that is spatio-temporally tuned at multiple levels. Molecular dissections of the mechanisms underlying the ripening process have revealed a network encompassed by hormones, transcriptional regulators, epigenomic modifications and other regulatory elements that directly determine fruit quality and the postharvest commodity of fresh produce. Many studies have addressed the important roles of ethylene, abscisic acid (ABA) and other hormones in regulating fruit ripening. Recent studies have shown that some spontaneous mutants for tomato transcription factors (TFs) have resulted from loss-of-function or dominant-negative mutations. Unlike in DNA methylation variation, the histone mark H3K27me3 may be conserved and prevents the transcriptional feedback circuit from generating autocatalytic ethylene. These observations of a network of partially redundant component indicate the need to improve our current understanding. Here, we focussed on the recent advances and future challenges in investigations of the molecular mechanisms of fruit ripening. We also identified several issues that still need to be addressed in future studies.

Divergence of defensive cucurbitacins in independent Cucurbita pepo domestication events leads to differences in specialist herbivore preference

Crop domestication and improvement often concurrently affect plant resistance to pests and production of secondary metabolites, creating challenges for isolating the ecological implications of selection for specific metabolites. Cucurbitacins are bitter triterpenoids with extreme phenotypic differences between Cucurbitaceae lineages, yet we lack integrated models of herbivore preference, cucurbitacin accumulation, and underlying genetic mechanisms. In Cucurbita pepo, we dissected the effect of cotyledon cucurbitacins on preference of a specialist insect pest (Acalymma vittatum) for multiple tissues, assessed genetic loci underlying cucurbitacin accumulation in diverse germplasm and a biparental F₂ population (from a cross between two independent domesticates), and characterized quantitative associations between gene expression and metabolites during seedling development. Acalymma vittatum affinity for cotyledons is mediated by cucurbitacins, but other traits contribute to whole-plant resistance. Cotyledon cucurbitacin accumulation was associated with population structure, and our genetic mapping identified a single locus, Bi-4, containing genes relevant to transport and regulation - not biosynthesis - that diverged between lineages. These candidate genes were expressed during seedling development, most prominently a putative secondary metabolite transporter. Taken together, these findings support the testable hypothesis that breeding for plant resistance to insects involves targeting genes for regulation and transport of defensive metabolites, in addition to core biosynthesis genes.

Soil inoculation of Trichoderma asperellum M45a regulates rhizosphere microbes and triggers watermelon resistance to Fusarium wilt

Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. niveum (FON) is a soil-borne disease that seriously limits watermelon production. In the present study, Trichoderma asperellum (T. asperellum) M45a was shown to be an effective biocontrol agent against FW. In a pot experiment, the application of 10⁵ cfu/g of T. asperellum M45a granules had an improved control effect on FW during the blooming period (up to 67.44%) in soils subjected to five years of continuous cropping with watermelon, while the average length of watermelon vines was also significantly improved (P < 0.05). Additionally, the acid phosphatase (ACP), cellulase (CL), catalase (CAT), and sucrase (SC) activities in the M45a-inoculation group were significantly higher than those in the control (CK) group, and transformation of the soil nutrients (total N, NO3-N, and available P) was significantly increased. Moreover, T. asperellum M45a inoculation reduced fungal diversity, increased bacterial diversity and especially enhanced the relative abundance of plant growth-promoting rhizobacteria (PGPR), such as Trichoderma, Sphingomonas, Pseudomonas, Actinomadura, and Rhodanobacter. Through functional prediction, the relative abundance of ectomycorrhiza, endophytes, animal pathotrophs, and saprotrophs in the fungal community was determined to be significantly lower than that observed in the M45a-treated soil. Correlation analysis revealed that Sphingomonas, Pseudomonas, and Trichoderma had the most differences in terms of microorganism abundance, and these differences were positively correlated with ACP, CL, CAT, and SC. These findings provide guidance for the use of fungicides to achieve microecological control of FW in continuously cropped watermelon plots.

Improving Horticultural Crops via CRISPR/Cas9: Current Successes and Prospects

Horticultural crops include a diverse array of crops comprising fruits, vegetables, nuts, flowers, aromatic and medicinal plants. They provide nutritional, medicinal, and aesthetic benefits to mankind. However, these crops undergo many biotic (e.g., diseases, pests) and abiotic stresses (e.g., drought, salinity). Conventional breeding strategies to improve traits in crops involve the use of a series of backcrossing and selection for introgression of a beneficial trait into elite germplasm, which is time and resource consuming. Recent new plant breeding tools such as clustered regularly interspaced short palindromic repeats (CRISPR) /CRISPR-associated protein-9 (Cas9) technique have the potential to be rapid, cost-effective, and precise tools for crop improvement. In this review article, we explore the CRISPR/Cas9 technology, its history, classification, general applications, specific uses in horticultural crops, challenges, existing resources, associated regulatory aspects, and the way forward.

Unlocking the relationships among population structure, plant architecture, growing season, and environmental adaptation in Henan wheat cultivars

BACKGROUND

Ecological environments shape plant architecture and alter the growing season, which provides the basis for wheat genetic improvement. Therefore, understanding the genetic basis of grain yield and yield-related traits in specific ecological environments is important.

RESULTS

A structured panel of 96 elite wheat cultivars grown in the High-yield zone of Henan province in China was genotyped using an Illumina iSelect 90 K SNP assay. Selection pressure derived from ecological environments of mountain front and plain region provided the initial impetus for population divergence. This determined the dominant traits in two subpopulations (spike number and spike percentage were dominance in subpopulation 2:1; thousand-kernel weight, grain filling rate (GFR), maturity date (MD), and fertility period (FP) were dominance in subpopulation 2:2), which was also consistent with their inheritance from the donor parents. Genome wide association studies identified 107 significant SNPs for 12 yield-related traits and 10 regions were pleiotropic to multiple traits. Especially, GY was co-located with MD/FP, GFR and HD at QTL-ple5A, QTL-ple7A.1 and QTL-ple7B.1 region. Further selective sweep analysis revealled that regions under selection were around QTLs for these traits. Especially, grain yield (GY) is positively correlated with MD/FP and they were co-located at the VRN-1A locus. Besides, a selective sweep signal was detected at VRN-1B locus which was only significance to MD/FP.

CONCLUSIONS

The results indicated that extensive differential in allele frequency driven by ecological selection has shaped plant architecture and growing season during yield improvement. The QTLs for yield and yield components detected in this study probably be selectively applied in molecular breeding.

Localization shift of a sugar transporter contributes to phloem unloading in sweet watermelons

Unloading sugar from sink phloem by transporters is complex and much remains to be understood about this phenomenon in the watermelon fruit. Here, we report a novel vacuolar sugar transporter (ClVST1) identified through map-based cloning and association study, whose expression in fruit phloem is associated with accumulation of sucrose (Suc) in watermelon fruit. ClVST1⁹⁷ knockout lines show decreased sugar content and total biomass, whereas overexpression of ClVST1⁹⁷ increases Suc content. Population genomic and subcellular localization analyses strongly suggest a single-base change at the coding region of ClVST1⁹⁷ as a major molecular event during watermelon domestication, which results in the truncation of 45 amino acids and shifts the localization of ClVST1⁹⁷ to plasma membranes in sweet watermelons. Molecular, biochemical and phenotypic analyses indicate that ClVST1⁹⁷ is a novel sugar transporter for Suc and glucose efflux and unloading. Functional characterization of ClVST1 provides a novel strategy to increase sugar sink potency during watermelon domestication.

Mapping a Partial Andromonoecy Locus in Citrullus lanatus Using BSA-Seq and GWAS Approaches

The sexual expression of watermelon plants is the result of the distribution and occurrence of male, female, bisexual and hermaphrodite flowers on the main and secondary stems. Plants can be monoecious (producing male and female flowers), andromonoecious (producing male and hermaphrodite flowers), or partially andromonoecious (producing male, female, bisexual, and hermaphrodite flowers) within the same plant. Sex determination of individual floral buds and the distribution of the different flower types on the plant, are both controlled by ethylene. A single missense mutation in the ethylene biosynthesis gene CitACS4, is able to promote the conversion of female into hermaphrodite flowers, and therefore of monoecy (genotype MM) into partial andromonoecy (genotype Mm) or andromonoecy (genotype mm). We phenotyped and genotyped, for the M/m locus, a panel of 207 C. lanatus accessions, including five inbreds and hybrids, and found several accessions that were repeatedly phenotyped as PA (partially andromonoecious) in several locations and different years, despite being MM. A cosegregation analysis between a SNV in CitACS4 and the PA phenotype, demonstrated that the occurrence of bisexual and hermaphrodite flowers in a PA line is not dependent on CitACS4, but conferred by an unlinked recessive gene which we called pa. Two different approaches were performed to map the pa gene in the genome of C. lanatus: bulk segregant analysis sequencing (BSA-seq) and genome wide association analysis studies (GWAS). The BSA-seq study was performed using two contrasting bulks, the monoecious M-bulk and the partially andromonoecious PA-bulk, each one generated by pooling DNA from 20 F2 plants. For GWAS, 122 accessions from USDA gene bank, already re-sequenced by genotyping by sequencing (GBS), were used. The combination of the two approaches indicates that pa maps onto a genomic region expanding across 32.24-36.44 Mb in chromosome 1 of watermelon. Fine mapping narrowed down the pa locus to a 867 Kb genomic region containing 101 genes. A number of candidate genes were selected, not only for their function in ethylene biosynthesis and signalling as well as their role in flower development and sex determination, but also by the impact of the SNPs and indels differentially detected in the two sequenced bulks.

Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression

Melon exhibits substantial natural variation especially in fruit ripening physiology, including both climacteric (ethylene-producing) and non-climacteric types. However, genomic mechanisms underlying such variation are not yet fully understood. Here, we report an Oxford Nanopore-based high-grade genome reference in the semi-climacteric cultivar Harukei-3 (378 Mb + 33,829 protein-coding genes), with an update of tissue-wide RNA-seq atlas in the Melonet-DB database. Comparison between Harukei-3 and DHL92, the first published melon genome, enabled identification of 24,758 one-to-one orthologue gene pairs, whereas others were candidates of copy number variation or presence/absence polymorphisms (PAPs). Further comparison based on 10 melon genome assemblies identified genome-wide PAPs of 415 retrotransposon Gag-like sequences. Of these, 160 showed fruit ripening-inducible expression, with 59.4% of the neighboring genes showing similar expression patterns (r > 0.8). Our results suggest that retrotransposons contributed to the modification of gene expression during diversification of melon genomes, and may affect fruit ripening-inducible gene expression.

Genomes on Canvas: Artist's Perspective on Evolution of Plant-Based Foods

How can we trace the evolution of our plant-based food through time? Here, we will discuss the advantages and disadvantages of using historical paintings to map the history of modern fruits, vegetables, legumes, grains, nuts, and seeds, and explain how the general public can contribute to such studies.

The Chromosome-Scale Genome of Melon Dissects Genetic Architecture of Important Agronomic Traits

Comparative and evolutionary genomics analyses are the powerful tools to provide mechanistic insights into important agronomic traits. Here, we completed a chromosome-scale assembly of the "neglected" but vital melon subspecies Cucumis melo ssp. agrestis using single-molecule real-time sequencing, Hi-C, and an ultra-dense genetic map. Comparative genomics analyses identified two targeted genes, UDP-sugar pyrophosphorylase and α-galactosidase, that were selected during evolution for specific phloem transport of oligosaccharides in Cucurbitaceae. Association analysis of transcriptome and the DNA methylation patterns revealed the epigenetic regulation of sucrose accumulation in developing fruits. We constructed the melon recombinant inbred lines to uncover Alkaline/Neutral Invertase (CINV), Sucrose-Phosphatase 2 (SPP2), α-galactosidase, and β-galactosidase loci related to sucrose accumulation and an LRR receptor-like serine/threonine-protein kinase associated with gummy stem blight resistance. This study provides essential genomic resources enabling functional genomics studies and the genomics-informed breeding pipelines for improving the fruit quality and disease resistance traits.

Recommendations for Choosing the Genotyping Method and Best Practices for Quality Control in Crop Genome-Wide Association Studies

High-throughput genotyping boosts genome-wide association studies (GWAS) in crop species, leading to the identification of single-nucleotide polymorphisms (SNPs) associated with economically important traits. Choosing a cost-effective genotyping method for crop GWAS requires careful examination of several aspects, namely, the purpose and the scale of the study, crop-specific genomic features, and technical and economic matters associated with each genotyping option. Once genotypic data have been obtained, quality control (QC) procedures must be applied to avoid bias and false signals in genotype–phenotype association tests. QC for human GWAS has been extensively reviewed; however, QC for crop GWAS may require different actions, depending on the GWAS population type. Here, we review most popular genotyping methods based on next-generation sequencing (NGS) and array hybridization, and report observations that should guide the investigator in the choice of the genotyping method for crop GWAS. We provide recommendations to perform QC in crop species, and deliver an overview of bioinformatics tools that can be used to accomplish all needed tasks. Overall, this work aims to provide guidelines to harmonize those procedures leading to SNP datasets ready for crop GWAS.

Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of nonclassic domestication

The genetic architecture of quantitative traits is determined by both Mendelian and polygenic factors, yet classic examples of plant domestication focused on selective sweep of newly mutated Mendelian genes. Here we report the chromosome-level genome assembly and the genomic investigation of a nonclassic domestication example, bitter gourd (Momordica charantia), an important Asian vegetable and medicinal plant of the family Cucurbitaceae. Population resequencing revealed the divergence between wild and South Asian cultivars about 6,000 y ago, followed by the separation of the Southeast Asian cultivars about 800 y ago, with the latter exhibiting more extreme trait divergence from wild progenitors and stronger signs of selection on fruit traits. Unlike some crops where the largest phenotypic changes and traces of selection happened between wild and cultivar groups, in bitter gourd large differences exist between two regional cultivar groups, likely reflecting the distinct consumer preferences in different countries. Despite breeding efforts toward increasing female flower proportion, a gynoecy locus exhibits complex patterns of balanced polymorphism among haplogroups, with potential signs of selective sweep within haplogroups likely reflecting artificial selection and introgression from cultivars back to wild accessions. Our study highlights the importance to investigate such nonclassic example of domestication showing signs of balancing selection and polygenic trait architecture in addition to classic selective sweep in Mendelian factors.