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Browsing by Author "Kono, Thomas"

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    The role of deleterious substitutions in crop genomes
    (2016-10) Kono, Thomas
    Historically, it has been postulated that populations carry genetic variants with deleterious effects as segregating variation. Recent advances in DNA resequencing technology allow a new view on this topic, providing a way to identify segregating molecular sequence variants that alter sites that show constrained evolution. Targeted identification and removal of such segregating variants has been proposed as a novel path for improving agronomic performance in plant breeding programs. In this dissertation, I present a brief review of deleterious variation, and why it may be important to plant breeding. Then, I present a tool for classifying single nucleotide polymorphisms into functional classes using public sequence databases. Next, I present a survey of potentially deleterious alleles segregating in two crop species, and a software package that implements a likelihood ratio test for sequence constraint and deleterious prediction. Finally, I present an examination of the contribution of potentially deleterious alleles to yield in a barley breeding experimental population. While potentially deleterious alleles themselves do not explain a larger proportion of phenotypic variation than non- deleterious alleles, genomic prediction of phenotypes may be improved by examining informative subsets of sequence variants, rather than with genomewide markers.
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    Whole Genome Assembly and Annotation of Northern Wild Rice (Zizania palustris L.), a North American Grain
    (2021-07-23) Haas, Matthew W; Kono, Thomas; Macchietto, Marissa; Millas, Reneth; McGilp, Lillian; Shao, Mingqin; Duquette, Jacques; Hirsch, Candice N; Kimball, Jennifer A; jkimball@umn.edu; Kimball, Jennifer A; University of Minnesota Cultivated Wild Rice Breeding and Genetics Lab
    Northern Wild Rice (NWR; Zizania palustris L.) is an aquatic grass native to North America that is notable for its nutritious grain. This is an important species with ecological, cultural, and agricultural significance, specifically in the Great Lakes region of the United States. Using long- and short-range sequencing, Hi-C scaffolding, and RNA-seq data from eight tissues, we generated a whole genome de novo assembly and annotation of NWR. The assembly is 1.29 Gb, highly repetitive (~76.0%), and contains 46,421 protein-coding genes. Comparative analyses revealed conservation of large syntenic blocks with Oryza sativa L., which were used to identify putative seed shattering genes. Estimates of divergence times revealed the Zizania genus diverged from Oryza ~26-30 million years ago (MYA), while NWR and Zizania latifolia diverged from one another ~6-8 MYA. Comparative genomics revealed evidence of a whole genome duplication in NWR ~5.3 MYA after the NWR-Z. latifolia speciation event. This high-quality genome assembly and annotation provides is a valuable resource for comparative genomics in the Oryzeae tribe and provides an important resource for future conservation and breeding efforts of NWR.