Browsing by Author "Hasing, Tomas"

Now showing 1 - 4 of 4
  • Thumbnail Image
    Extensive phenotypic diversity in the cultivated Florist’s Gloxinia, Sinningia speciosa (Lodd.) Hiern, is derived from the domestication of a single founder population
    Hasing, Tomas; Rinaldi, Elijah; Manrique, Silvia; Colombo, Lucia; Haak, David C.; Zaitlin, David; Bombarely, Aureliano (Wiley, 2019-08-19)
    Domesticated plants are essential for agriculture and human societies. Hence, understanding the processes of domestication will be crucial as we strive for more efficient crops and improvements to plants that benefit humankind in other ways. Here, we study the ornamental plant Sinningia speciosa, and reveal that despite the incredible variety found in domesticated varieties (e.g., in flower colour and form), they are all derived from a single founder population near Rio de Janeiro, Brazil. Knowledge of the domestication of horticultural plants is scarce and given its small, low‐complexity genome, and ease of cultivation, we suggest that S. speciosa is a good model for studying genomic variation during domestication.
  • Thumbnail Image
    K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology
    Ziarsolo, Peio; Hasing, Tomas; Hilario, Rebeca; Garcia-Carpintero, Victor; Blanca, Jose; Bombarely, Aureliano; Cañizares, Joaquin (2021-03-25)
    Background K-seq, a new genotyping methodology based on the amplification of genomic regions using two steps of Klenow amplification with short oligonucleotides, followed by standard PCR and Illumina sequencing, is presented. The protocol was accompanied by software developed to aid with primer set design. Results As the first examples, K-seq in species as diverse as tomato, dog and wheat was developed. K-seq provided genetic distances similar to those based on WGS in dogs. Experiments comparing K-seq and GBS in tomato showed similar genetic results, although K-seq had the advantage of finding more SNPs for the same number of Illumina reads. The technology reproducibility was tested with two independent runs of the tomato samples, and the correlation coefficient of the SNP coverages between samples was 0.8 and the genotype match was above 94%. K-seq also proved to be useful in polyploid species. The wheat samples generated specific markers for all subgenomes, and the SNPs generated from the diploid ancestors were located in the expected subgenome with accuracies greater than 80%. Conclusion K-seq is an open, patent-unencumbered, easy-to-set-up, cost-effective and reliable technology ready to be used by any molecular biology laboratory without special equipment in many genetic studies.
  • Thumbnail Image
    siRNAs regulate DNA methylation and interfere with gene and lncRNA expression in the heterozygous polyploid switchgrass
    Yan, Haidong; Bombarely, Aureliano; Xu, Bin; Frazier, Taylor P.; Wang, Chengran; Chen, Peilin; Chen, Jing; Hasing, Tomas; Cui, Chenming; Zhang, Xinquan; Zhao, Bingyu Y.; Huang, Linkai (2018-07-24)
    Background Understanding the DNA methylome and its relationship with non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), is essential for elucidating the molecular mechanisms underlying key biological processes in plants. Few studies have examined the functional roles of the DNA methylome in grass species with highly heterozygous polyploid genomes. Results We performed genome-wide DNA methylation profiling in the tetraploid switchgrass (Panicum virgatum L.) cultivar ‘Alamo’ using bisulfite sequencing. Single-base-resolution methylation patterns were observed in switchgrass leaf and root tissues, which allowed for characterization of the relationship between DNA methylation and mRNA, miRNA, and lncRNA populations. The results of this study revealed that siRNAs positively regulate DNA methylation of the mCHH sites surrounding genes, and that DNA methylation interferes with gene and lncRNA expression in switchgrass. Ninety-six genes covered by differentially methylated regions (DMRs) were annotated by GO analysis as being involved in stimulus-related processes. Functionally, 82% (79/96) of these genes were found to be hypomethylated in switchgrass root tissue. Sequencing analysis of lncRNAs identified two lncRNAs that are potential precursors of miRNAs, which are predicted to target genes that function in cellulose biosynthesis, stress regulation, and stem and root development. Conclusions This study characterized the DNA methylome in switchgrass and elucidated its relevance to gene and non-coding RNAs. These results provide valuable genomic resources and references that will aid further epigenetic research in this important biofuel crop.
  • Thumbnail Image
    Whole-Genome Resequencing of Seven Eggplant (Solanum melongena) and One Wild Relative (S. incanum) Accessions Provides New Insights and Breeding Tools for Eggplant Enhancement
    Gramazio, Pietro; Yan, Haidong; Hasing, Tomas; Vilanova, Santiago; Prohens, Jaime; Bombarely, Aureliano (2019-10-08)
    Whole-genome resequencing provides information of great relevance for crop genetics, evolution, and breeding. Here, we present the first whole-genome resequencing study using seven eggplant (Solanum melongena) and one wild relative (Solanum incanum) accessions. These eight accessions were selected for displaying a high phenotypic and genetic diversity and for being the founder parents of an eggplant multiparent advanced generation intercrosses population. By resequencing at an average depth of 19.8x and comparing to the high-quality reference genome "67/3" over 10 million high-reliable polymorphisms were discovered, of which over 9 million (84.5%) were single nucleotide polymorphisms and more than 700,000 (6.5%) InDels. However, while for the S. melongena accessions, the variants identified ranged from 0.8 to 1.3 million, over 9 million were detected for the wild S. incanum. This confirms the narrow genetic diversity of the domesticated eggplant and suggests that introgression breeding using wild relatives can efficiently contribute to broadening the genetic basis of this crop. Differences were observed among accessions for the enrichment in genes regulating important biological processes. By analyzing the distribution of the variants, we identified the potential footprints of old introgressions from wild relatives that can help to unravel the unclear domestication and breeding history. The comprehensive annotation of these eight genomes and the information provided in this study represents a landmark in eggplant genomics and allows the development of tools for eggplant genetics and breeding.