Browsing by Subject "SNP"
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Item Genetic Diversity, Structure, and Cold Hardiness of Invasive Knotweed (Fallopia spp.) in Minnesota(2022-04) Drazan, DallasKnotweed (Fallopia spp.) is an herbaceous perennial from East Asia that was brought to Europe and North America and, despite control efforts, subsequently spread aggressively on both continents. Knotweed are known to cause structural damage, riverbank destabilization, and outcompete native species thus reducing biodiversity. Two experiments were conducted: a controlled freezing chamber study to quantify the rhizome cold hardiness of the knotweed complex and whole genome sequencing (DArTseq) of 1,249 individuals from North America, Europe, and Asia with a focus on Minnesotan populations used to measure genetic diversity, population structure, species composition, and indirectly measure asexual and sexual dispersal of knotweed. Fallopia japonica and F. sachalinensis were found to be cold hardy to -10°C and F. xbohemica to -9°C. Minnesota knotweed are genetically diverse and spread both sexually and asexually with the hybrid F. xbohemica being the most prevalent taxon in Minnesota.Item Haplotype-Based Selection Signature Analysis Using University Of Minnesota And Us Contemporary Holstein Cattle(2015-11) Yang, JingArtificial selection in dairy cattle since 1964 has achieved steady increase in milk production that was accompanied by unintended declines in fertility. We conducted selection signature analysis to identify genome changes due to the forty years of selection using direct comparison of 45,878 SNPs between Holstein cattle unselected since 1964 and contemporary Holsteins. The Holstein genome had a landscape change from the unselected to the elite contemporary Holsteins. About 31% of the genome was affected by the forty years of selection, and 230 regions had highly significant changes in long-range allele frequencies and genotypic heterozygosity. From these 230 regions, 197 genes with documented fertility functions mostly in mice and humans were identified, leading to the hypothesis that the unintended declines in fertility since 1964 was due to hitchhiking of selection by negative effects of fertility genes. The female-male ratio of the 197 fertility genes is approximately 5:4, indicating that the fertility problems in the contemporary Holstein population likely was due to decreased fertility in both females and males. The elite Holsteins were more heterozygous than their contemporaries in all thirty regions where the elite cows and their contemporaries had significant heterozygosity differences, including seven regions in or near large clusters of olfactory receptors, zinc fingers, cationic amino acid transporters, sialic acid-binding Ig-like genes, vomeronasal receptors, keratin genes, EMR2 receptors, and transfer RNA’s.Item Maize Mo17 SNPs(2018-07-11) Zhou, Peng; zhoux379@umn.edu; Zhou, Peng; University of Minnesota Springer LabGenome resequencing of Mo17 was done as part of the bioMAP project (REF). 477 million 100bp paired-end reads were generated for Mo17 giving an average of 95x coverage. Reads were first trimmed by Trimmomatic (Bolger et al. 2014) and mapped to the maize B73 genome AGPv4 (Jiao et al. 2017) using BWA-MEM (Li and Durbin 2010). PCR duplicates were marked and removed using GATK (McKenna et al. 2010). Variants were called by GATK haplotypecaller and filtered using different filters for SNPs: (QD > 2, FS < 60, MQ > 40, MQRankSum > -12.5, ReadPosRankSum > -8, SOR < 4) and for InDels: (QD > 2, FS < 200, ReadPosRankSum > -20, SOR < 10). Moreover, variants located in regions with unusually high coverage (DP > Mean + 2*SD) and heterozygous calls (GT == '0/1') were also removed. The final variant file containing 8.04 million variants with 164 thousand CDS variants was deposited in DRUM.Item Molecular diversity, linkage disequilbrium and genetic mapping in East Africa wheat(2013-04) Macharia, Godwin Kamau.Despite recognition as key bread wheat producers in sub-Saharan Africa, for decades Ethiopia and Kenya have relied on imports to meet local consumption needs. The challenges posed by pests and diseases as exemplified by repeated attacks by the Russian Wheat Aphid, and the new highly virulent race TTKSK (Ug99) of stem rust, have been strong yield barriers. To change this trend, it is important that breeding populations that combine desirable alleles for yield, disease, and pest resistance are developed followed by selection, promotion and adoption of superior cultivars. In the first chapter of this thesis, SNP- based characterization of population structure and diversity in a comprehensive panel of 297, mainly East Africa lines are described. Four to seven subpopulations were identified largely consistent with line breeding era. The oldest East Africa germplasm was found to be most diverse based on several summary statistics. Present day germplasm including that in commercial production was associated with relatively high allelic diversity too. Methods used to detect signatures of past selection successfully identified outlier SNPs possibly under positive selection which could have played an important role in increasing the adaptive range of bread wheat in East Africa. Long range linkage disequilibrium consistent with past observations for this species, was detected and is described in chapter two. Over 50 QTL for adult plant resistance (APR) to stem, leaf and stripe rusts are reported from mixed model association mapping. Similarly, APR previously observed in the cultivar Kenya- Nyangumi was dissected leading to the detection of 15 minor QTL across all rusts. These results are presented in chapter three. In chapter four, results for high and low molecular weight glutenin subunit alleles, puroindoline proteins, grain hardness and other bread making quality-determining traits that were characterized amongst 216 Ethiopia and Kenya bread wheat lines are discussed.