Biology subjects

van der Knaap, E.

Publications and source records attributed to van der Knaap, E..

4 recordsLinked to original sources

bioRxiv2022

Genomic characterization of a wild-like tomato accession found in Arizona; a northward migration story

Tomato domestication history has been revealed to be a highly complex story. A major contributor to this complexity is an evolutionary intermediate group (Solanum lycopersicum var. cerasiforme (Alef.) Voss; SLC) between the cultivated tomato (Solanum lycopersicum var. lycopersicum L.; SLL) and its wild relative (Solanum pimpinellifolium L.; SP). SLC includes accessions with a broad spectrum of genomic and phenotypic characteristics. Some of the SLC accessions were previously hypothesized to be spreading northward from South America into Mesoamerica and that migration probably entailed reversal to wild-like phenotypes such as smaller fruits. Prior to this study, the northernmost confirmed extension of the SLC was limited to northern Mexico. In this study, we employed genomic methods to investigate the origin of a wild-like tomato found in a garden in Scottsdale Arizona, USA. The so-called "Arizona tomato" featured a vigorous growth habit and carried small fruits weighing 2-3 grams. Our phylogenomic analyses revealed the identity of the Arizona tomato as a member of the Mexican SLC population (SLC MEX). To our knowledge, this is the first report of an SLC accession, confirmed using genomics, growing spontaneously in Arizona. This finding could have implications for conservation biology as well as agriculture.

plant biology↗

bioRxiv2021

The evolutionary dynamics of genetic mutational load throughout tomato domestication history

Understanding the evolution of deleterious mutations through domestication has fascinated evolutionary biologists and breeders alike. Some domesticated organisms have been reported to accumulate deleterious mutations, i.e. radical amino acid changes, through their domestication history ("cost of domestication"). However, more recent evidence paints a more complex picture of this phenomenon in different domesticated organisms. In this study, we used genomic sequences of 253 tomato accessions to investigate the evolution of deleterious mutations and genomic structural variants (SVs) through tomato domestication history. Specifically, we used phylogeny-based methods to identify deleterious mutations in the cultivated tomato as well as its closely related semi-wild and wild populations. We also explored a potential correlation between deleterious mutations and SVs. To create a functional link between deleterious alleles and phenotypes of interest for tomato breeding, we also conducted Genome-wide Association Studies (GWAS) on several fruit volatiles. Our results implicate a downward trend, throughout tomato domestication history, in diversity of most alleles, regardless of their functional impact. This suggests that demographic factors, such as bottleneck events and inbreeding, have reduced overall genetic diversity, leading to lower deleterious load and SVs as well as loss of some beneficial alleles during tomato domestication. We also detected an increase in proportions of nonsynonymous and deleterious alleles (relative to synonymous and neutral nonsynonymous alleles, respectively) during the initial stage of tomato domestication in Ecuador, although the final stage of tomato domestication in Mexico did not seem to involve such an increase. However, deleterious alleles in cultivated tomato seem to be more frequent than expected by neutral theory of molecular evolution. Additionally, for all tomato populations, we found a higher proportion of deleterious mutations in genomic regions impacted by SVs. Our analyses also revealed frequent deleterious alleles in several well-studied tomato genes, probably involved in response to biotic and abiotic stress as well as fruit development and flavor regulation. Also, through genome-wide association studies (GWAS), we discovered deleterious alleles associated with two volatiles: isobutyl acetate, which is important for tomato fruit flavor, and methyl salicylate, involved in disease resistance and regulating flowering time. To provide a practical guide for breeding experiments, we created TomDel, a public searchable database of 21,162 deleterious alleles identified in this study (https://github.com/hrazif/TomDel-0.1)

genomics↗

bioRxiv2021

Large-scale comparative small RNA analyses reveal genomic structural variants in driving expression dynamics and differential selection pressures on distinct small RNA classes during tomato domestication

Tomato has undergone extensive selections during domestication. Recent progress has shown that genomic structural variants (SVs) have contributed to gene expression dynamics during tomato domestication, resulting in changes of important traits. Here, through comprehensive analyses of small RNAs (sRNAs) from nine representative tomato accessions, we demonstrate that SVs substantially contribute to the dynamic expression of the three major classes of plant sRNAs: microRNAs (miRNAs), phased secondary short interfering RNAs (phasiRNAs), and 24-nt heterochromatic siRNAs (hc-siRNAs). Changes in the abundance of phasiRNAs and 24-nt hc-siRNAs likely contribute to the alteration of mRNA gene expression during tomatos recent evolution, particularly for genes associated with biotic and abiotic stress tolerance. We also observe that miRNA expression dynamics are associated with imprecise processing, alternative miRNA-miRNA* selections, and SVs. SVs mainly affect the expression of less-conserved miRNAs that do not have established regulatory functions or low abundant members in highly expressed miRNA families, highlighting different selection pressures on miRNAs compared to phasiRNAs and 24-nt hc-siRNAs. Our findings provide insights into plant sRNA evolution as well as SV-based gene regulation during crop domestication. Furthermore, our dataset provides a rich resource for mining the sRNA regulatory network in tomato.

plant biology↗

bioRxiv2021

Haplotype analyses reveal novel insights into tomato history and domestication to show long-distance migrations and latitudinal adaptations

A novel haplotype-based approach that uses Procrustes analysis and automatic classification was used to provide further insights into tomato history and domestication. Agrarian societies domesticated species of interest by introducing complex genetic modifications. For tomatoes, two species, one of which had two botanical varieties, are thought to be involved in its domestication: the fully wild Solanum pimpinellifolium (SP), the wild and semi-domesticated S. lycopersicum var. cerasiforme (SLC) and the cultivated S. l. var. lycopersicum (SLL). The Procrustes approach showed that SP evolved into SLC during a gradual migration from the Peruvian deserts to the Mexican rainforests and that Peruvian and Ecuadorian SLC populations were the result of more recent hybridizations. Our model was supported by independent evidence, including ecological data from the accession collection site and morphological data. Furthermore, we showed that photosynthesis-, and flowering time-related genes were selected during the latitudinal migrations.

evolutionary biology↗