Browsing by Author "Liu, Chaochih"

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    Biological problem solving through computation
    (2023-06) Liu, Chaochih
    As sequencing becomes more and more affordable, data continues to grow exponentially, and dataset sizes utilized in biological studies continue to increase. There is an increasing importance for reproducible research, especially studies that rely heavily on computational analyses. Custom code written for study-specific goals that are well documented and hosted in source code repositories with version control can accelerate future studies with similar data processing or analysis steps. For example, updating the reference genome positions of old genotyping SNPs as new reference genome versions get released is just as important as handling the latest long-read sequencing technologies. In this dissertation, I present multiple computational solutions to address problems relevant to crop improvement. In Chapter 1 of this dissertation, I use whole-genome sequencing data from 11 barley lines derived from sodium azide mutagenesis to characterize the nature of mutations induced by sodium azide to understand the nature of variants that reduce fitness. In this work, careful variant filtering was performed to identify variants generated by the mutagen. In Chapter 2, I investigate 318 Wild Barley Diversity Collection accessions for evidence of introgression from 2,446 domesticated barley. Information on wild accessions showing crop-to-wild introgression can be used to make informed decisions on wild samples to include in downstream applications. Finally, in Chapter 3, I develop a reproducible computational workflow that automates the scoring of crossovers as a phenotype to provide a means to quickly evaluate the amount of crossover rate variation present in any biparental population. Output from the computational workflow can be used to address limitations imposed by linked selection in breeding populations. For all the chapters, all code used for data processing and analyses is stored in public GitHub repositories to speed up the advancement of future research built upon this work.
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    Environmental association identifies candidates for tolerance to low temperature and drought
    (2019-02-11) Lei, Li; Poets, Ana M; Liu, Chaochih; Wyant, Skylar R; Hoffman, Paul J; Carter, Corey K; Trantow, Richard M; Shaw, Brian G; Li, Xin; Muehlbauer, Gary J; Katagiri, Fumiaki; Morrell, Peter L; pmorrell@umn.edu; Morrell, Peter L; University of Minnesota Department of Plant and Microbial Biology; University of Minnesota Department of Agronomy and Plant Genetics
    Barley is cultivated from the equator to the Arctic Circle. The wild progenitor species, Hordeum vulgare ssp. spontaneum, occupies a relatively narrow latitudinal range (~30 - 40˚ N) primarily at low elevation, < 1500 m. Adaptation to the range of cultivation has occurred over ~8,000 years. The genetic basis of this adaptation is amenable to study through environmental association. Using genotyping from 7,864 SNPs in 784 barley landraces, we perform mixed model association analysis relative to bioclimatic variables and analysis of allele frequency differentiation across multiple partitions of the data. Using resequencing data from a subset of the landraces, we test for linkage disequilibrium (LD) between SNPs queried in genotyping and SNPs in neighboring loci. We identify seven loci previously reported to contribute to adaptive differences to flowering time and abiotic stress in barley and four loci previously identified in other plant species. In many cases, patterns of LD are consistent with the causative variant occurring in the immediate vicinity of the queried SNP. The identification of barley orthologs to well characterized genes may provide new understanding of the nature of adaptive variation and could permit a more targeted use of potentially adaptive variants in barley breeding and germplasm improvement.
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    Sodium azide mutagenesis induces a unique pattern of mutations
    (2025-04-18) Liu, Chaochih; Morrell, Peter; Frascarelli, Giulia; Stec, Adrian; Heinen, Shane; Lei, Li; Wyant, Skylar; Legg, Erik; Spiller, Monika; Muehlbauer, Gary; Smith, Kevin; Fay, Justin; chaochih.l@gmail.com; Liu, Chaochih; University of Minnesota Morrell Lab
    This dataset contains genomic variant calls, structural variation data, and phenotypic measurements related to Hordeum vulgare (barley). It includes VCF and BED files from multiple sequencing platforms—10x Genomics, Oxford Nanopore, PacBio, and Illumina featuring raw, filtered, and phased variants. Structural variant calls in BEDPE format and callable/un-callable region lists are provided. Phenotype data from field trials provide spatially adjusted and raw trait values for agronomic characteristics. These data provide insight on genomic diversity, structural variation, and genotype-phenotype associations in barley. The use of multiple sequencing technologies enables cross-validation of variant calls, allowing for high-confidence genome annotation and population genetics studies. The filtered VCFs help isolate biologically relevant mutations, while the callable region data ensure rigorous quality control for variant interpretation. This dataset is being released as it is supporting the associated paper to this research and also to support the broader research community in comparative genomics, evolutionary biology, and crop improvement studies. By making these resources publicly available, we aim to enhance reproducibility, enable novel insights into barley’s genomic architecture, and assist breeding efforts focused on climate resilience and agronomic performance.
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    Variants from "The role of deleterious substitutions in crop genomes"
    (2016-07-26) Kono, Thomas J Y; Fu, Fengli; Mohammadi, Mohsen; Hoffman, Paul J; Liu, Chaochih; Stupar, Robert M; Smith, Kevin P; Tiffin, Peter; Fay, Justin C; Morrell, Peter L; konox006@umn.edu; Kono, Thomas J Y
    SNP calls in protein coding regions were obtained from 15 barley and 8 soybean lines. Non synonymous SNPs were predicted to be deleterious or not using three approaches.