Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used ...long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions. Hundreds of SV-gene pairs exhibit subtle and significant expression changes, which could broadly influence quantitative trait variation. By combining quantitative genetics with genome editing, we show how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production. In the last example, higher order epistasis among four SVs affecting three related transcription factors allowed introduction of an important harvesting trait in modern tomato. Our findings highlight the underexplored role of SVs in genotype-to-phenotype relationships and their widespread importance and utility in crop improvement.
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•Long-read sequencing of 100 tomato genomes uncovered 238,490 structural variants•Transposons underlie many SVs, and SV hotspots revealed large introgressions•SVs associated with genes are predictive of population-scale changes in expression•New genome assemblies resolved complex breeding QTLs caused by SVs
Comprehensive structural variant identification in tomato genomes allows insight into the evolution and domestication of tomato and serves as a resource for phenotype-directed breeding.
Abstract
The process of plant domestication is often protracted, involving underexplored intermediate stages with important implications for the evolutionary trajectories of domestication traits. ...Previously, tomato domestication history has been thought to involve two major transitions: one from wild Solanum pimpinellifolium L. to a semidomesticated intermediate, S. lycopersicum L. var. cerasiforme (SLC) in South America, and a second transition from SLC to fully domesticated S. lycopersicum L. var. lycopersicum in Mesoamerica. In this study, we employ population genomic methods to reconstruct tomato domestication history, focusing on the evolutionary changes occurring in the intermediate stages. Our results suggest that the origin of SLC may predate domestication, and that many traits considered typical of cultivated tomatoes arose in South American SLC, but were lost or diminished once these partially domesticated forms spread northward. These traits were then likely reselected in a convergent fashion in the common cultivated tomato, prior to its expansion around the world. Based on these findings, we reveal complexities in the intermediate stage of tomato domestication and provide insight on trajectories of genes and phenotypes involved in tomato domestication syndrome. Our results also allow us to identify underexplored germplasm that harbors useful alleles for crop improvement.
Key Message
Six novel fruit weight QTLs were identified in tomato using multiple bi-parental populations developed from ancestral accessions. Beneficial alleles at these loci arose in ...semi-domesticated subpopulations and were likely left behind. This study paves the way to introgress these alleles into breeding programs.
The size and weight of edible organs have been strongly selected during crop domestication. Concurrently, human have also focused on nutritional and cultural characteristics of fruits and vegetables, at times countering selective pressures on beneficial size and weight alleles. Therefore, it is likely that novel improvement alleles for organ weight still segregate in ancestral germplasm. To date, five domestication and diversification genes affecting tomato fruit weight have been identified, yet the genetic basis for increases in weight has not been fully accounted for. We found that fruit weight increased gradually during domestication and diversification, and semi-domesticated subpopulations featured high phenotypic and nucleotide diversity. Columella and septum fruit tissues were proportionally increased, suggesting targeted selection. We developed twenty-one F
2
populations with parents fixed for the known fruit weight genes, corresponding to putative key transitions from wild to fully domesticated tomatoes. These parents also showed differences in fruit weight attributes as well as the developmental timing of size increase. A subset of populations was targeted for QTL-seq, leading to the identification of six uncloned fruit weight QTLs. Three QTLs, located on chromosomes 1, 2 and 3, were subsequently validated by progeny testing. By exploring the segregation of the known fruit weight genes and the identified QTLs, we estimated that most beneficial alleles in the newly identified loci arose in semi-domesticated subpopulations from South America and were not likely transmitted to fully domesticated landraces. Therefore, these alleles could be incorporated into breeding programs using the germplasm and genetic resources identified in this study.
Fruit flavor is defined as the perception of the food by the olfactory and gustatory systems, and is one of the main determinants of fruit quality. Tomato flavor is largely determined by the balance ...of sugars, acids and volatile compounds. Several genes controlling the levels of these metabolites in tomato fruit have been cloned, including
,
,
,
, and
. The aim of this study was to identify any association of these genes with trait variation and to describe the genetic diversity at these loci in the red-fruited tomato clade comprised of the wild ancestor
, the semi-domesticated species
and early domesticated
. High genetic diversity was observed at these five loci, including novel haplotypes that could be incorporated into breeding programs to improve fruit quality of modern tomatoes. Using newly available high-quality genome assemblies, we assayed each gene for potential functional causative polymorphisms and resolved a duplication at the
locus found in several wild and semi-domesticated accessions which caused lower accumulation of lipid derived volatiles. In addition, we explored gene expression of the five genes in nine phylogenetically diverse tomato accessions. In general, the expression patterns of these genes increased during fruit ripening but diverged between accessions without clear relationship between expression and metabolite levels.
The Solanaceae or "nightshade" family is an economically important group with remarkable diversity. To gain a better understanding of how the unique biology of the Solanaceae relates to the family's ...small RNA (sRNA) genomic landscape, we downloaded over 255 publicly available sRNA data sets that comprise over 2.6 billion reads of sequence data. We applied a suite of computational tools to predict and annotate two major sRNA classes: (1) microRNAs (miRNAs), typically 20- to 22-nucleotide (nt) RNAs generated from a hairpin precursor and functioning in gene silencing and (2) short interfering RNAs (siRNAs), including 24-nt heterochromatic siRNAs typically functioning to repress repetitive regions of the genome via RNA-directed DNA methylation, as well as secondary phased siRNAs and trans-acting siRNAs generated via miRNA-directed cleavage of a polymerase II-derived RNA precursor. Our analyses described thousands of sRNA loci, including poorly understood clusters of 22-nt siRNAs that accumulate during viral infection. The birth, death, expansion, and contraction of these sRNA loci are dynamic evolutionary processes that characterize the Solanaceae family. These analyses indicate that individuals within the same genus share similar sRNA landscapes, whereas comparisons between distinct genera within the Solanaceae reveal relatively few commonalities.
The study of hybridization in aquatic plants is complicated by rarity of flower production, absence of roots, and asexuality. Elatine is a cosmopolitan genus of aquatic flowering plants with about 25 ...species worldwide. Historically, there has been little concern regarding hybridization in the genus due to the prevalence of autogamy (i.e. self-pollination), which potentially limits xenogamous pollen transfer among the species. Two morphologically complex species (Elatine hexandra and E. americana) are the only known polyploids in the genus. In previous phylogenetic analyses, both species resolved incongruently in gene trees obtained from nuclear (ITS) versus plastid (matK/trnK and rbcL) regions. Suspecting that the phylogenetic incongruence might be a consequence of past hybridization events, we tested that hypothesis by conducting an additional phylogenetic analysis of Elatine, which incorporated sequences from a low copy nuclear gene (phyC). Elatine hexandra and E. americana were the only Elatine species exhibiting intraspecific polymorphic sites, i.e. heterozygosity, in phyC. Allele specific amplification enabled us to resolve these polymorphisms for inclusion in a phylogenetic analysis along with the monomorphic phyC sequences within species obtained for the remaining Elatine species. The phyC tree confirmed that both polyploids probably are allopolyploids, in a pattern consistent with the placement of the putative parental taxa in previous phylogenetic analyses of ITS, matK/trnK, and rbcL sequence data. The distributions of E. americana and E. hexandra, along with their potential parental species, are consistent with the proposed hybrid origins for the polyploids and provide additional clues on their geographic regions of origin.
Elatine rotundifolia was described in 2008 from Ecuador as a new species because of its unique morphology and geographical distribution. However, an examination of type material for E. rotundifolia ...suggested to us initially that this taxon had been assigned incorrectly to Elatine, despite some superficial similarity to that genus. This possibility was investigated using morphological and molecular data. We found that E. rotundifolia differed from other members of Elatine by several vegetative and reproductive features, which indicated a distant alliance closer to Lindemiaceae (Lamiids; Asterids) rather than Elatinaceae (Fabids; Superrosids). We then conducted a phylogenetic analysis of DNA sequences from the internal transcribed spacer region, which included isotype material of E. rotundifolia, as well as various representatives of Elatinaceae, Lindemiaceae, and other angiosperm clades. The molecular data resolved E. rotundifolia among several accessions of Micranthemum (Lindemiaceae) in a position quite remote phylogenetically from accessions of Bergia and Elatine (Elatinaceae). From these results, we conclude that the name E. rotundifolia refers to a taxon that was misplaced in Elatine, and represents instead a member of Micranthemum (Lindemiaceae), and possibly is synonymous with the aquatic species M. umbrosum. Elatine rotundifolia de Ecuador fue descrita en 2008 como una nueva especie debido a su morfología y distribución geográfica única. Sin embargo, un examen de material tipo para E. rotundifolia nos sugirió inicialmente que este taxón había sido asignado incorrectamente a Elatine, a pesar de cierta semejanza superficial a ese género. Investigamos esta posibilidad utilizando datos morfológicos y moleculares. Encontramos que E. rotundifolia difirió de otros miembros de Elatine por varias características vegetativas y reproductivas, lo que indicó una alianza distante más cerca de Lindemiaceae (Lamiids; Asteridae) en lugar de Elatinaceae (Fabids; Superrosids). Entonces realizamos un análisis filogenético de las secuencias de ADN de la región espaciadora transcrita interna, que incluyó material de isotipo de E. rotundifolia, así como diversos representantes de Elatinaceae, Lindemiaceae, y otros clados de angiospermas. Los datos moleculares resolvieron E. rotundifolia entre varias accesiones de Micranthemum (Lindemiaceae) en una posición muy alejada filogenéticamente de accesiones de Bergia y Elatine (Elatinaceae). A partir de estos resultados, concluimos que el nombre E. rotundifolia se refiere a un taxón que fue mal clasificado en Elatine, y en cambio representa un miembro de Micranthemum (Lindemiaceae), y posiblemente es sinónimo de la especie acuática M. umbrosum.
Elatine rotundifolia was described in 2008 from Ecuador as a new species because of its unique morphology and geographical distribution. However, an examination of type material for E. rotundifolia ...suggested to us initially that this taxon had been assigned incorrectly to Elatine, despite some superficial similarity to that genus. This possibility was investigated using morphological and molecular data. We found that E. rotundifolia differed from other members of Elatine by several vegetative and reproductive features, which indicated a distant alliance closer to Linderniaceae (Lamiids; Asterids) rather than Elatinaceae (Fabids; Superrosids). We then conducted a phylogenetic analysis of DNA sequences from the internal transcribed spacer region, which included isotype material of E. rotundifolia, as well as various representatives of Elatinaceae, Linderniaceae, and other angiosperm clades. The molecular data resolved E. rotundifolia among several accessions of Micranthemum (Linderniaceae) in a position quite remote phylogenetically from accessions of Bergia and Elatine (Elatinaceae). From these results, we conclude that the name E. rotundifolia refers to a taxon that was misplaced in Elatine, and represents instead a member of Micranthemum (Linderniaceae), and possibly is synonymous with the aquatic species M. umbrosum.
The cosmopolitan genus Elatine (Elatinaceae) includes about 25 aquatic species of mostly diminutive aquatic plants, whose relationships have not been evaluated using a phylogenetic approach. The ...taxonomic study of this group has been complicated by the small stature of the plants, their minute reproductive structures, and their cosmopolitan distribution. Consequently, much uncertainty exists with respect to species delimitations, their geographical distributions, and interspecific relationships. To clarify the infrageneric classification of Elatine and to provide insights on interspecific relationships within the genus, we conducted a phylogenetic study of nearly all (24) of the currently recognized species using both morphological and molecular data. The tree topology obtained based on morphological data (including vegetative and reproductive characters) was less-resolved than the trees based on molecular data, derived from either nuclear (ITS) or two plastid regions (matK/trnK and rbcL). However, the tree topology obtained from combined morphological and molecular data was well resolved and placed the morphologically distinctive E. alsinastrum as the sister group of the remaining species, which fell within two major clades: a clade of 4-merous-flowered species and a clade of 3-merous species, within which was embedded a subclade of 2-merous species. Although a number of topological differences occurred between the ITS and plastid tree topologies, significant incongruence was observed only for the placements of E. americana and E. hexandra, possibly resulting from reticulate evolution. Bergia, the sister genus of Elatine, comprises larger species, which often are mostly helophytic but never truly aquatic. Ancestral state reconstructions based on the ITS tree indicated that a morphological reduction series (in stature and floral merosity) exists among Elatine species, which is best explained as a consequence of adaptation to their aquatic life. These phylogenetic analyses also have helped to clarify the infrageneric classification of the genus and to provide a better understanding of the natural and nonindigenous distributions of the species. The new monotypic section Elatine sect. Cymifera, including E. brochonii, is described.
Previous taxonomic studies of Elatine, a group of mostly annual aquatic plants, were based only on morphological data. Thus, a comprehensive study using modern molecular techniques would seem ...necessary in order to gain further insights on the systematics of the genus. Throughout my dissertation project, I have evaluated morphological and molecular data to provide insights on the taxonomy and evolutionary history of the Elatine species. In chapter 1 of this dissertation, I review the previous taxonomic studies on Elatine and summarize the approaches I have taken throughout this dissertation project to achieve a better understanding of the systematics of Elatine. Chapter 2 provides the first comprehensive phylogenetic hypothesis for Elatine, which I have reconstructed using morphological data. As part of that analysis, I have examined the microscopic seed characteristics of 55 Elatine accessions using scanning electron microscopy (SEM). In chapter 3, I test the morphologically based phylogeny described in chapter 2 by comparing it to topologies derived from a molecular phylogenetic reconstruction using DNA sequences obtained from several gene regions that have been used in previous taxonomic studies conducted in closely related families. In chapter 4, I discuss the potential role of hybridization within the genus based on the results of DNA sequence data that I obtained from a low-copy gene region (phyC). In chapter 5, I synthesize the novel morphological and molecular evidence provided throughout my dissertation to refine taxonomic circumscriptions of the species and then provide a practical taxonomic key to all Elatinespecies worldwide.
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