Xiaoxuan Wang

Genomic analyses provide insights into the history of tomato breeding

The histories of crop domestication and breeding are recorded in genomes. Although tomato is a model species for plant biology and breeding, the nature of human selection that altered its genome remains largely unknown. Here we report a comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions. We provide evidence that domestication and improvement focused on two independent sets of quantitative trait loci (QTLs), resulting in modern tomato fruit ∼100 times larger than its ancestor. Furthermore, we discovered a major genomic signature for modern processing tomatoes, identified the causative variants that confer pink fruit color and precisely visualized the linkage drag associated with wild introgressions. This study outlines the accomplishments as well as the costs of historical selection and provides molecular insights toward further improvement.

Rewiring of the Fruit Metabolome in Tomato Breeding

Humans heavily rely on dozens of domesticated plant species that have been further improved through intensive breeding. To evaluate how breeding changed the tomato fruit metabolome, we have generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes from hundreds of tomato genotypes. The combined results illustrate how breeding globally altered fruit metabolite content. Selection for alleles of genes associated with larger fruits altered metabolite profiles as a consequence of linkage with nearby genes. Selection of five major loci reduced the accumulation of anti-nutritional steroidal glycoalkaloids in ripened fruits, rendering the fruit more edible. Breeding for pink tomatoes modified the content of over 100 metabolites. The introgression of resistance genes from wild relatives in cultivars also resulted in major and unexpected metabolic changes. The study reveals a multi-omics view of the metabolic breeding history of tomato, as well as provides insights into metabolome-assisted breeding and plant biology.

The Tomato Hoffman's Anthocyaninless Gene Encodes a bHLH Transcription Factor Involved in Anthocyanin Biosynthesis That Is Developmentally Regulated and Induced by Low Temperatures.

Anthocyanin pigments play many roles in plants, including providing protection against biotic and abiotic stresses. Many of the genes that mediate anthocyanin accumulation have been identified through studies of flowers and fruits; however, the mechanisms of genes involved in anthocyanin regulation in seedlings under low-temperature stimulus are less well understood. Genetic characterization of a tomato inbred line, FMTT271, which showed no anthocyanin pigmentation, revealed a mutation in a bHLH transcription factor (TF) gene, which corresponds to the ah (Hoffmans anthocyaninless) locus, and so the gene in FMTT271 at that locus was named ah. Overexpression of the wild type allele of AH in FMTT271 resulted in greater anthocyanin accumulation and increased expression of several genes in the anthocyanin biosynthetic pathway. The expression of AH and anthocyanin accumulation in seedlings was shown to be developmentally regulated and induced by low-temperature stress. Additionally, transcriptome analyses of hypocotyls and leaves from the near-isogenic lines seedlings revealed that AH not only influences the expression of anthocyanin biosynthetic genes, but also genes associated with responses to abiotic stress. Furthermore, the ah mutation was shown to cause accumulation of reactive oxidative species and the constitutive activation of defense responses under cold conditions. These results suggest that AH regulates anthocyanin biosynthesis, thereby playing a protective role, and that this function is particularly important in young seedlings that are particularly vulnerable to abiotic stresses.

Inducible Positive Mutant Screening System to Unveil the Signaling Pathway of Late Blight Resistance

Late blight is the most devastating potato disease and it also causes serious yield loss in tomato. Several disease resistance genes (R genes) to late blight have been cloned from potato in the past decade. However, the resistance mechanisms remain elusive. Tomato and potato belong to the botanical family Solanaceace and share remarkably conserved genome structure. Since tomato is a model system in genetic and plant pathology research, we used tomato to develop a powerful mutant screening system that will greatly facilitate the analysis of the signaling pathway of resistance to Phytophthora infestans. First we proved that the R3a transgenic tomatoes developed specific hypersensitive cell death response (HR) to P. infestans strains carrying the corresponding avirulence gene Avr3a, indicating that the signaling pathway from the R3a-Avr3a recognition to HR is conserved between potato and tomato. Second, we generated transgenic tomatoes carrying both R3a and Avr3a genes, with the latter under the control of a glucocorticiod-inducible promoter. Dexamethasone induced expression of Avr3a and resulted in localized HR. This versatile system can be used to construct a mutant library to screen surviving mutants whose resistance signal transduction was interrupted, providing the basis to identify key genes involved in the resistance to late blight in Solanaceae.

A putative R3 MYB repressor is the candidate gene underlying atroviolacium, a locus for anthocyanin pigmentation in tomato fruit

Fine-mapping of the atv locus identifies a putative R3 MYB repressor SLMYBATV as its candidate gene. We present a model of the anthocyanin gene regulation network in the peel of tomato fruit.

Identification and characterisation of resistance gene analogues from wild Chinese Vitis species

Summary Generating a collection of resistance gene analogues (RGAs) is an initial step towards the isolation of plant disease resistance genes. Based on the two conserved motifs in the nucleotide-binding site leucine-rich repeat (NBS-LRR) domain from previously cloned plant resistance genes, degenerate oligonucleotide primers were designed and used to isolate RGAs from five wild Chinese Vitis species: V. quinquangularis ‘83-4-96’, V. bashanica ‘Xunyang-8’, V. davidii ‘Tangwei’, V. yeshanensis ‘Yanshan’, and V. bryoniifolia ‘Anlin-3’. A total of 55 RGAs with uninterrupted open reading frames were obtained and further assembled within each species into 26 distinct RGAs. These RGAs were classified into six distinct families. Their deduced amino acid sequences contained the conserved motifs characteristic of NBS-LRR resistance genes. However, the sequences of the identified RGAs were very divergent from each other. The low ratio of non-synonymous to synonymous substitutions, and non-detectable recombination events within families, indicate that the NBS regions of Vitis RGAs are under purifying selection rather than diversifying selection. Furthermore, all the RGAs identified in this study were grouped into the non-Toll/Interleukin 1 receptor (TIR)-type of NBS-LRR resistance genes, based on phylogenetic analysis with other known plant R genes.

Fine mapping and molecular marker development of anthocyanin absent , a seedling morphological marker for the selection of male sterile 10 in tomato

Seedling morphology plays an important role in plant breeding via marker-assisted selection. The tomato (Solanum lycopersicum) mutant, anthocyanin absent (aa), presents a green hypocotyl during the seedling stage. This trait has been utilized in marker-assisted selection of male sterile 10 (ms 10) at the seedling stage because their corresponding loci are closely linked on chromosome 2. However, the genetic basis of aa has not been ascertained to date. In the present study, aa was fine-mapped to a 96.3-kb region on chromosome 2 that contained 14 putative genes. Thereinto, Solyc02g081340, which encodes a putative glutathione S-transferase, was thereby designated SlGSTAA. Phylogenetic analysis suggested that SlGSTAA was closely related to PhAN9, which is required for anthocyanin sequestration in petunia (Petunia hybrida). Real-time quantitative reverse transcription PCR analysis showed that the expression of the SlGSTAA gene was barely detected in aa mutants. Sequencing revealed that there was a 3.4-kb deletion in the aa region, where the SlGSTAA gene was apparently deleted. A codominant insertion/deletion marker was developed in line with the deletion to differentiate homozygous wild-type, heterozygous, and homozygous aa mutant genotypes. The findings of the present study may facilitate the functional analysis of the SlGSTAA gene and marker-assisted selection of aa and ms 10 in tomato.

Fine mapping of a major QTL controlling early flowering in tomato using QTL-seq

Abstract: Early flowering is one of the major earliness traits in tomato and is also an important agronomical trait in crop plants; thus, this trait is important for plant breeding and crop improvement. With the innovation of rapid and cost-effective technologies, quantitative trait locus (QTL)-seq has become the preferred method of performing QTL identification. In the present study, we identified a candidate QTL of an early flowering trait in tomato (Solanum lycopersicum) using QTL-seq. Two DNA pools of the extreme phenotype of the F2 progeny from crosses between the ‘Bone MM’ cultivar (early flowering, P1) and ‘071-440’ cultivar (late flowering, P2) were bulked for sequencing and an alignment analysis. We observed 220 single nucleotide polymorphism markers, seven candidate QTLs, and genes that may be associated with early flowering located between 1.6 and 71.8 Mb on chromosome 1. Using traditional QTL analysis, the location of one QTL was confirmed in the physical region between 23.5 and 25.3 Mb, which corresponded to the region identified using QTL-seq, and was referred to as EF1 (Solyc01g017060). A real-time quantitative reverse transcription polymerase chain reaction analysis showed that EF1 was the most highly expressed among the candidate genes and significantly expressed in early flowering parents and furthermore, we found that EF1, which had a similar sequence to the Ycf2 gene, may relate to the early flowering phenotype.

Fine Mapping of a Gene (ER4.1) that Causes Epidermal Reticulation of Tomato Fruit and Characterization of the Associated Transcriptome.

The hydrophobic cuticle that covers the surface of tomato (Solanum lycopersicum) fruit plays key roles in development and protection against biotic and abiotic stresses, including water loss, mechanical damage, UV radiation, pathogens, and pests. However, many details of the genes and regulatory mechanisms involved in cuticle biosynthesis in fleshy fruits are not well understood. In this study, we describe a novel tomato fruit phenotype, characterized by epidermal reticulation (ER) of green fruit and a higher water loss rate than wild type (WT) fruit. The ER phenotype is controlled by a single gene, ER4.1, derived from an introgressed chromosomal segment from the wild tomato species S. pennellii (LA0716). We performed fine mapping of the single dominant gene to an ~300 kb region and identified Solyc04g082540, Solyc04g082950, Solyc04g082630, and Solyc04g082910as potential candidate genes for the ER4.1 locus, based on comparative RNA-seq analysis of ER and WT fruit peels. In addition, the transcriptome analysis revealed that the expression levels of genes involved in cutin, wax and flavonoid biosynthesis were altered in the ER fruit compared with WT. This study provides new insights into the regulatory mechanisms and metabolism of the fruit cuticle.