Browsing by Subject "QTL"
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Item Fine-Mapping, Physiological Evaluation, and Candidate Gene Exploration of an Iron Deficiency Chlorosis Tolerance Locus in Soybean(2020-07) Merry, RyanIron Deficiency Chlorosis (IDC) can be a significant yield limiting nutrient stress in soybean. IDC most frequently occurs in high pH soils that are rich in calcium carbonates, as is common in areas of the Midwestern United States. While several agronomic solutions exist to combat IDC, such as the application of iron chelates at planting, the use of tolerant soybean genotypes remains the most effective method of controlling IDC stress. Breeding for IDC tolerance is common, however little about the genetics of IDC is understood, aside from a major tolerance locus located on Gm03. A tolerance locus was previously discovered through bi-parental and association mapping on Gm05 to a 1.5 megabase region, which in this study was found to be important in elite soybean germplasm and warranted further investigation. Fine-mapping was conducted using heterogeneous inbred families, narrowing the interval to 137 kilobases and 17 genes. A controlled environment assay was developed to analyze the effect of nodulation, pH, and calcium carbonates on soybean genotypes and to assess the expression of Glyma.05g001700, a gene candidate in the fine-mapped region. Glyma.05g001700 was further explored using protein modeling, domain classification, gene homology, haplotype diversity, and overexpression in soybean hairy roots to assess gene function. It was concluded that Glyma.05g001700 is likely involved in iron homeostasis through changes in gene expression driven by a putative TATA box present in the tolerant genotype ‘Fiskeby III’.Item Genetic Analysis Of Whole-Plant Leaf Area, Leaf Shape, And Leaf Venation Branching In Soybean(2020-04) McCoy, ErikIncreasing soybean production to meet growing demand requires closing the current yield gap, and approaching the yield potential through genetic improvement and optimization of cultivars for specific growth conditions. Leaf traits are important targets for improvement and play key roles in the capture and usage and storage of the resources needed for yield production. Leaf area has been shown to be associated with yield through its effect on transpiration and interception of photosynthetically active radiation (PAR). Leaf shape has similar effects on transpiration through boundary layer effects, and also controls the amount of intercepted PAR by altering the canopy structure and the amount of light that penetrates through the canopy. Leaf venation determines the rate of water flow through the plant, and the geometry of vein topology likely has a significant effect on this rate, and therefore the total water transpired by the plant as a whole. Vein branching angles are thought to play a role in hydraulic conductance, and may also act as a structural constraint to leaf area development. While leaf shape in soybean is known to be controlled by the Ln locus, which in addition pleiotropically affects seed size and number, the genetic basis of whole-plant leaf area and venation topology traits are yet to be discovered. Leaf area, shape, and venation topology are closely linked during leaf development, so an understanding of their genetic basis and relationship to one another is critical to the optimization of leaf type for a target environment. The goals of this study are to identify QTL for whole-plant leaf area, leaf shape, and vein branching angle, as well as to quantify and compare the relationships between these traits. A bi-parental SoyNAM population (IA3023 x LG94-1906) consisting of 136 genotypes was grown twice over two years and measurements were taken for whole-plant leaf area, whole-plant dry mass, specific leaf area, leaflet length, leaflet width, leaflet shape, vein branching angle, and leaflet area. QTL mapping and correlation analyses were performed for all of these leaf traits. Novel QTL were identified for whole-plant leaf area and vein branching angle that co-localized with the Ln locus. QTL identified for leaflet length, leaflet width, and leaflet shape also co-localized with the Ln locus as expected, however a second, novel QTL was identified for leaflet length. These results suggest that the Ln locus may contribute to leaf area and vein branching angle determination in addition to leaf shape and seed size/number. Further investigation into the genetic basis of these traits and their interactions will help in developing cultivars with ideal leaf types. A negative correlation between vein branching angle and whole-plant leaf area was found, supporting the hypothesis that larger branching angles constrain leaf area development. Additional study on this relationship in soybean and other crops may prove this connection spans across species, and can be a useful target in breeding for ideal leaf types.Item Genetics of Rust Resistance in a Wheat Nested Association Mapping Population(2017-10) Manan, FazalWheat is an important food crop in many parts of the world, but its genetic diversity has been eroded due to intense selection in breeding programs. To increase genetic diversity in the Minnesota wheat breeding program, a nested association mapping population was developed by crossing 25 exotic accessions selected from the USDA-ARS Spring Wheat Core Collection with RB07, a Minnesota cultivar selected as the common parent because it has wide adaptation in the region. Virulent races of the stem rust (Puccinia graminis f. sp. tritici, Pgt), leaf rust (P. triticina, Pt), and stripe rust (P. striiformis f. sp. tritici, Pst) pathogens threaten the wheat crop in the region. Thus, the objective of this thesis was to elucidate the genetics of rust resistance in select families of the Minnesota Nested Association Mapping Population (MNAMP) based on qualitative (chi-square tests of Mendelian gene models) and quantitative (quantitative trait loci (QTL) mapping with 66,685 single nucleotide polymorphic markers) genetic analyses. Four families segregated for resistance to the widely virulent Pgt races of TTKSK, TRTTF, and TTKST. One to five Mendelian genes and five to 19 QTL conferred stem rust resistance in individual families. One family segregated for resistance to Pt race TFBGQ with Lr21 virulence. One Mendelian gene and two QTL controlled resistance to this pathogen race. Three families segregated for resistance to the Pst races PSTv-37 and PSTv-40. Three to five Mendelian genes and two to 12 QTL conferred resistance to these races in individual families. Rust resistant progeny identified from the MNAMP will be useful for enhancing the resistance of wheat to the three rust diseases.Item Identification and Characterization of Important Quantitative Trait Loci for Soluble Solids and Titratable Acidity for Germplasm in the University of Minnesota Apple Breeding Program(2020-12) Miller, BayleeApple fruit acidity and sweetness are two of the major trait components involved in apple seedling sensory evaluation. Published studies have alluded to some of the genetic components of apple fruit acidity and sweetness, but few have included an array of germplasm relevant to the University of Minnesota apple breeding program. With the release and subsequent frequent use of ‘Honeycrisp’ and ‘Minneiska’ apple cultivars as parents at the University of Minnesota, the germplasm set deviates from other breeding programs. In order to increase breeding efficiency and increase overall quality of apple seedlings, this study describes the genetic components of apple fruit acidity and sweetness and provides breeding insights to negate the creation of undesirable apple seedlings. This study uses data from 2010 to 2018 to characterize a wide but relevant array of germplasm, using six major families, three of which have ‘Honeycrisp’ as a parent, and three of which have ‘Minneiska’ as a parent. Three major loci associated with variation in titratable acidity content on linkage groups 1, 8, and 16, and two loci associated with variation in soluble solids content on linkage groups 1 and 13 were identified, and haplotypes were characterized for each locus. The conclusions from this study provide insights for designing crosses that create seedlings with desirable ranges of acidity and sweetness characteristics.Item Identification of Quantitative Trait Loci for Resistance to White Mold in Soybeans via Genome-Wide Association and Linkage Mapping(2022-06) Mayta, JuanWhite mold disease in soybeans is one of the most important causes of yield losses in the northern regions of the United States and Canada. Host resistance continues to be the most viable tactic for managing white mold; however, progress is slow due to laborious phenotyping techniques that are difficult to replicate and the polygenic nature of the white mold resistance trait. Breeding for white mold resistance will be significantly facilitated by improved screening methods and the use of molecular markers. In this work, we developed and validated a phenotyping method using spray mycelium and inoculated sorghum in two field environments. Using this methodology, a collection of 230 F5:12 recombinant inbred lines derived from the Minsoy x Noir1 cross and 280 diverse PIs and cultivars were phenotyped for white mold resistance in two field environments. Additionally, both populations were phenotyped in the greenhouse using the cut stem method. Five breeding lines and one PI with resistance levels similar to the current resistant check S19-90 were identified. This material is adapted to the Upper Midwest and could be used as potential donor germplasm to improve resistance to white mold. Linkage mapping analysis was performed on the Minsoy x Noir1 population using a set of 957 SSR and SNP markers. Four markers showed significant associations with white mold resistance on Chromosomes 6, 7, 8, and 12 (LOD>3), explaining 45% of the variability. Marker Satt567 on chromosome 7 is a new white mold resistance QTL, explaining 17% of the variability. Genome-wide association (GWAS) was performed using 1,536 SNP markers. Five QTLs showed significant associations with white mold resistance (FDR, qvalue≤0.1). The identified QTLs correspond to two regions on chromosome 19 and one region on chromosome 14. Of particular interest is marker BARC-039375-07306 on the short arm of chromosome 19; this marker corresponds with a major QTL associated with canopy architecture in soybeans. A second region on chromosome 19 consists of three markers positioned between 47,988,748 and 48,229,536 bp. Among these three markers, BARC-007569-00135 was the most significant and consistent across environments. Phenotypic variation explained by all significant markers was 13%. The QTLs on chromosome 19 were identified in field experiments, whereas the QTL on chromosome 14 resulted from the greenhouse evaluation.Item QTL mapping and GWAS identify sources of iron deficiency chlorosis and canopy Wilt Tolerance in the Fiskeby III X Mandarin (Ottawa) soybean population(2015-01) Butenhoff, Karl JosephAbiotic stresses are a major yield limiting component in soybean production that producers cannot directly control. Therefore, an increase in the understanding of how different abiotic stresses affect soybean, and the identification of sources of tolerance to these stresses will be critical for the continued increase of soybean productivity well into the future. Here I present three separate, but related, studies analyzing iron deficiency chlorosis and drought tolerance in several soybean populations. For the first and second studies, the objectives were to (i) characterize the Fiskeby III X Mandarin (Ottawa) recombinant inbred line (RIL) population for its tolerance to iron deficiency chlorosis (IDC) and drought; (ii) identify quantitative trait loci (QTL) via composite interval mapping for iron deficiency chlorosis and canopy wilt in the RIL population; and (iii) identify co-localization of abiotic stress QTL and putative candidate genes for iron deficiency chlorosis tolerance and delayed canopy wilt. Iron chlorosis and canopy wilt scores were significantly different across the three years tested between the RILs as well as the parents of the population. Fiskeby III consistently scored better than Mandarin (Ottawa) for tolerance to iron chlorosis and canopy wilt in all three years. Two QTL were discovered, one on chromosome five and one on chromosome six, that together accounted for approximately 25 percent of the phenotypic variation for IDC. Two QTL were also identified for canopy wilt, one on chromosome six and one on chromosome 12, that together accounted for approximately 13 percent of the phenotypic variation. The two QTL identified on chromosome six co-localized to the same confidence interval. Several previously identified QTL co-localized with the identified IDC and canopy wilt QTL in this study. In addition, a potential candidate gene was identified on chromosome five that may play a role in the soybean IDC response. The third study was undertaken to potentially validate the QTL identified for IDC in the first study in two independent soybean populations. The objectives of this study were to (i) utilize association mapping to detect markers significantly associated with IDC in two independent populations, (ii) compare significant identified markers with the QTL regions identified in the bi-parental RIL population, and (iii) validate the major QTL identified on chromosome five in the RIL population. Association mapping identified 12 significant markers that accounted for 27.2 percent and 8.9 percent of the phenotypic variation for IDC in the two populations, respectively. These markers co-localized with several known iron related QTL and genes. A significant cluster of 11 markers on chromosome five co-localized with the major IDC QTL identified in the bi-parental Fiskeby III X Mandarin (Ottawa) population. A second potential candidate gene was identified in this QTL region that may be related to IDC in soybean.Item QTL mapping of iron deficiency chlorosis tolerance in soybean using connected populations(2014-03) Jones, Ilene LouiseSoybean iron deficiency chlorosis or IDC is a yield limiting, abiotic stress condition common to calcareous soil types present in the Upper Midwest. Complex interactions among soil chemical and physical properties within these calcareous soils limit the amount of ferrous iron available to soybean plants. The subsequent nutrient deficiency leads to the classic chlorotic phenotype characterized by interveinal yellowing of new growth trifoliates. IDC is responsible for yield losses up to 0.8 Mg ha-1 amounting to an estimated economic loss of $120 million per annum. To mitigate yield losses, growers prefer to plant IDC tolerant cultivars; however, IDC tolerant cultivars have been known to yield less on non-chlorotic soils. In order to improve IDC tolerance without an associated reduction in yield, we evaluated yield and IDC performance using a network of 13 F4-derived recombinant inbred line (RIL) populations connected by common parents. Chlorosis severity was evaluated using two methods: visual chlorosis ratings and remote sensing via normalized difference vegetative index (NDVI) values collected from the GreenSeeker® RT100 System. NDVI values correlated strongly with visual chlorosis ratings with the largest negative Pearson's correlation coefficient of -0.89 (p-value < 0.0001) captured at the V4 growth stage. NDVI values collected at V4 were moderately correlated to yield with a Pearson's correlation coefficient of -0.61 (p-value < 0.0001), indicating that IDC tolerant lines yield less than IDC susceptible lines on non-chlorotic soils. Co-localization of IDC and yield QTL detected on linkage groups A1/5, J/16, and L/19 confirm that the correlations are in part due to genetically linked loci or pleiotropic effects of a single locus.Item The Road From Variants To Traits: How Regulatory Variants Affect Gene Expression & Organismal Phenotypes(2024-03) Renganaath, KaushikNature hosts an incredible amount of diversity and beneath such diversity lies fascinating genetics that we have spent years trying to decode. Differences in our DNA sequences lead to variation in organismal traits. Most of these variants have been found to reside in noncoding portions of the genome, implying that a lot of organismal trait variation arises from variation in gene expression levels. Advances in sequencing technology have over the years allowed us to map hundreds of genomic loci underlying gene expression variation, and these loci are called expression quantitative trait loci (eQTLs). These eQTLs are of two types, local and trans, depending on their proximity to the genes they regulate. Local eQTLs regulate expression of genes in close genomic proximity while trans eQTLs regulate distant genes. Today, we possess a vast catalog of eQTLs across multiple taxa. Yet, we don’t fully understand the mechanisms by which eQTLs affect organismal traits. In this dissertation, I computationally dissect the mechanisms connecting genetic variation, gene expression and organismal traits in yeast Saccharomyces cerevisiae. As the first eukaryotic organism to have its genome fully sequenced, S.cerevisiae has over the years been a workhorse for understanding the genetics underlying complex traits. We today have comprehensive sets of QTLs underlying traits like gene expression and growth in yeast that account for most of heritable variation in these traits, allowing us to investigate the mechanisms by which eQTLs lead to organismal trait variation. In this dissertation, I characterize causal variants underlying local eQTLs in yeast (Chapter II) and the mechanisms by which eQTLs influence growth in different conditions (Chapter III). My work unravels fundamental principles by which eQTLs influence complex organismal traits.Item Shoot apical meristem architecture in maize: Diversity, genetic control, and its relationship to adult plant morphology(2014-07) Thompson, Addie MayThe maize shoot apical meristem (SAM) contains a pool of undifferentiated stem cells that produce all above-ground plant organs. Previous studies of the SAM have focused mainly on analysis of mutants conferring visible phenotypes. Though these approaches indicated the effect of genotype on SAM size, this represents the first work to characterize natural diversity in SAM architecture and its genetic control, as well as its relationship to adult plant traits. A time course of SAM growth throughout vegetative development was conducted to assess growth over time, resulting in the description of three phases of growth: initial proliferation, slower growth, and rapid expansion before transition. The results also indicated that 14 days after planting was the most appropriate time point for subsequent measurements. Quantitative trait loci for meristem traits (height, width, midpoint width, arc length, L1 arc cell number, plastochron internode, height:width ratio, volume, cell size) were mapped in the intermated B73 x Mo17 recombinant inbred line population. Distinct control of height- and width-related traits via several small-effect loci, as well as a lack of overlap with known meristem genes, was detected. One locus was validated using near-isogenic lines. Candidate genes were identified by correlating expression in the shoot apex with meristem traits across the population. To assess natural diversity and the impact of heterosis on maize SAM architecture, a set of 27 diverse inbreds and several of their F1 crosses were examined. This revealed that B73 and P39 were among the tallest outliers for SAM height and CML277 was the shortest. Heterosis was observed for meristem traits in several crosses of diverse inbreds to Mo17; some showed dominant effects. Only P39 exhibited heterosis with B73, demonstrating unique alleles contributing to the extreme heights observed in these inbreds. Recombinant inbred populations derived from crosses of P39 and CML277 inbreds to B73 were also used for mapping. Here, a few large-effect loci were identified that affected many meristem traits; most overlapped with known SAM-related genes. Genetic control was shown to be population-dependent. Architecture traits in the meristem were correlated with several adult plant traits, including flowering time, indicating potential shared regulatory mechanisms.Item Transcriptome analysis of wheat and barley near-isogenic line pairs carrying contrasting alleles for different Fusarium head blight resistance QTLs.(2009-06) Jia, HaiyanFusarium head blight (FHB), caused primarily by Fusarium graminearum, is a major disease problem on wheat and barley around the world. Grain yield and quality are reduced due to infection and the accumulation of trichothecene mycotoxins such as deoxynivalenol (DON). Previously, quantitative trait loci (QTL) conferring FHB resistance and reduced DON accumulation have been identified on wheat and barley chromosomes. A major FHB resistance QTL (Fhb1) was identified on wheat chromosome 3BS. Two major QTLs associated with reduced FHB severity have been detected on barley chromosome 2H Bin 8 and 2H Bin 10, which are associated with heading date and spike type, respectively. A QTL associated with reduced deoxynivalenol (DON) accumulation was identified on chromosome 3H Bin 6. Near-isogenic line (NIL) pairs carrying the resistant and susceptible allele for a wheat QTL and three barley QTL were used to examine DON concentration, fungal biomass and transcript accumulation during F. graminearum infection. Based on the disease phenotypes, transcript accumulation data, and comparative analysis of the wheat and barley host response to F. graminearum infection, we developed an integrated model for the wheat and barley-F. graminearum interactions. In addition, gene transcripts that are differentially expressed in the NIL pairs during infection provide a set of genes that may play a role in FHB resistance.Item Using High-Throughput Phenotyping To Investigate The Genetic Bases Of Quantitative Traits In Hybrid Wine Grape (Vitis Spp.)(2019-04) Underhill, AnnaHigh-throughput phenotyping methods have gained popularity in the plant sciences due to their potential to more quickly collect data, reduce human error, and investigate plant characteristics in new ways. In grapes, many economically important traits are quantitative, varying across a spectrum and displaying diverse phenotypes. Though rating scales exist for such traits, their usefulness can be limited by their ability to capture variation across populations; additionally, they require judgement that can vary based on the individual scoring the trait. Automated systems can be used to remedy these issues, eliminating subjectivity and more fully describing phenotypic variation. In these experiments, a semi-automated image analysis system was used to evaluate fruit cluster compactness and berry color in a multispecies hybrid wine grape (Vitis spp.) population. First, color-based image segmentation was used to isolate components of the fruit cluster morphology. Berry color was quantified using several different color spaces, and a MATLAB program was written to measure several morphological components to evaluate cluster compactness. Both color and compactness traits were used to perform quantitative trait loci (QTL) mapping, where associations between the traits and genetic regions were identified. Known QTL for berry color on chromosome 2 were identified, along with several minor QTL associated with color and anthocyanin content. Image-derived traits were associated with known QTL such as the chromosome 9 rachis length QTL, and also identified other regions of interest relating to cluster compactness. Altogether, these projects demonstrate the advantages of high-throughput phenotyping methods and their ability to identify new variation among quantitative traits.