Theses and Dissertations at Montana State University (MSU)

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Multi-environment evaluation of winter pea genotypes for winter survival and yield stability
(Montana State University - Bozeman, College of Agriculture, 2024) Poudel, Amrit; Chairperson, Graduate Committee: Kevin McPhee; This is a manuscript style paper that includes co-authored chapters.
Winter pea can be grown as a rotational crop for soil moisture conservation and nutrient recycling in the wheat-growing region of Montana. Development of winter hardy cultivars would increase seed yield and expand the area of adaptation of this crop. Harsh winter conditions present a significant challenge to the production of winter peas. The objective of this study was to screen pea germplasm and breeding lines for winter survival and identify genotypes with good winter hardiness for future crop production. Field trials were conducted to evaluate genotypes at Bozeman, Havre, Huntley, and Moccasin, MT in 2021, 2022, and 2023. These lines included elite winter cultivars and several checks. Winter hardiness was evaluated as the percentage of surviving plants and by agronomic performance including yield. Genotypes were evaluated based on the GGE biplot method. This analysis captured multiple variables including yield, protein content, seed size, and their overall stability across multiple years and locations of study to aid in selecting lines. Differential winter survival was observed across locations and years. Higher winter survival was seen in Bozeman and Havre. Few lines were identified as having high seed yield and stable production over years and locations. Breeding lines had higher mean yield with few good lines having stable production of greater than 2500 kg/ha. Germplasm lines showed better winter survival than breeding lines. Protein content ranged from 20% to 31%. Larger seeds were observed in Moccasin, whereas Havre had the highest protein content. Mega- environment differentiation helped to select specific genotypes based on the trait of interest for a particular environment. Several European and US lines used in the experiments having high winter hardiness record performed better for seed yield and resistance to stress. The lines identified as having high levels of cold tolerance can be used as a prospective genetic resource in pea breeding programs. Genotypes having high and stable seed yield can be considered for release as a variety and made available to producers.
Natural variation in camelina nitrogen responses
(Montana State University - Bozeman, College of Agriculture, 2023) Gautam, Shreya; Chairperson, Graduate Committee: Chengci Chen; Chaofu Lu (co-chair)
Camelina (Camelina sativa L.Crantz) is an oilseed crop with the potential to be planted for biofuel production. It is crucial to select camelina genotypes with higher nitrogen use efficiency (NUE) so that the superior cultivar has higher crop productivity. To select genotypes of camelina that exhibit higher biomass yield and nitrogen use efficiency, two field experiments were conducted in 2021 and 2022 in Sidney, MT with different nitrogen regimes, low (unfertilized) and high (fertilized). Distinct projects were carried out, one of them emphasizing canopy area and normalized difference vegetation index (NDVI), and the other focusing on biomass yield and NUE. The experiments highlighted the response of camelina to nitrogen application and the variation among genotypes. The study identified canopy image analysis effectively differentiated the canopy size and growth rate of camelina genotypes under two nitrogen regimes, demonstrating the influence of nitrogen on camelina growth. The NDVI measurement proved to be useful in evaluating plant health and greenness, offering a time-saving and efficient approach. Additionally, some of the genotypes were identified that exhibited high canopy area, NDVI, and nitrogen use efficiency in both 2021 and 2022, providing potential for enhancing crop productivity. This study reveals the potential to use canopy area, NDVI for biomass yield and nitrogen use efficiency screening in camelina.
Evaluating the genetic and phenotypic responses of Camelina sativa to heat stress
(Montana State University - Bozeman, College of Agriculture, 2023) Smith, Brian Edward; Chairperson, Graduate Committee: Chaofu Lu
Camelina sativa (L.) Crantz is a low-input oilseed crop with a unique fatty acid profile in its seed oil. Camelina oil can be used in biodiesels, jet fuels, and industrial lubricants. Improving the abiotic stress tolerance of camelina is a crucial step for increasing agronomic viability. Climate change is threatening production of camelina with rising global temperatures and shorter growing seasons. Elucidating the phenotypic and genetic responses to high temperatures is essential for successful breeding of heat tolerant camelina varieties. Three experiments were conducted to understand these responses. Two genotypes, Suneson (MT5) and Pryzeth (MT102) were exposed to a transient 14-day heat stress during the reproductive stage and evaluated for agronomic and seed quality traits along the main stem. Next, a mapping population consisting of 257 recombinant inbred lines (RILs) were grown under the same temperature regimes for 14 days beginning at the onset of the reproductive stage. Finally, reproductive tissues undergoing heat stress from two genotypes with contrasting heat responses, RIL23 and RIL167, were examined with RNA sequencing, and the phenotypes along the main stem were compared. From the phenotype evaluation, both MT5 and MT102 were significantly impacted by heat. Both genotypes experienced reductions in seed and pod size, seed weight, and total oil contents. As reported in other oilseed crops, camelina is negatively affected by heat, characterized primarily by lower yield and reduced oil content. The QTL analysis identified several key gene regions with co-located traits on chromosomes 8, 10, and 12. This demonstrates the ability to identify heat-responsive gene regions via phenotyping along the main stem. The transcriptomes of RILs 23 and 167 contrasted in both sampled tissue types, with RIL23 appearing more responsive to heat. Phenotypic analysis of these genotypes confirmed the transcriptional differences, as RIL23 was more resistant for several traits associated with fertility. These studies provide resources and protocols for future studies that may assist in improving the heat-tolerance of camelina.
Characterization and testing of reduced height (RHT) hypomorphs in durum and spring wheat
(Montana State University - Bozeman, College of Agriculture, 2023) Ugrin, Josey Mackinsey; Chairperson, Graduate Committee: Michael J. Giroux
The Reduced Height (Rht) gene in wheat (Triticum aestivum L.) increases yield by partitioning less nutrients to stem elongation and more towards spike development. In hexaploid wheat, the mutations Rht-B1b and Rht-D1b, create high-yielding semi-dwarf varieties. While Rht-B1b and Rht-D1b have been widely adopted due to their ability to increase yield, they also have drawbacks such as smaller seed size and lower protein content. Furthermore, tetraploid durum wheat (Triticum. turgidum L), Rht-B1b creates plants that are shorter than in hexaploid wheat under Northern Great Plains growing conditions. This project aimed to further characterize Rht and to develop a plant height intermediate between current standard-height and semi-dwarf varieties to increase yield in both durum and spring wheat. To create novel Rht alleles, seeds were mutagenized with Ethyl-methanesulfonate (EMS) and mutations were identified. Near-isogenic lines (NILS) were developed for the two Rht-A1 alleles and Rht-B1b-E529K alleles in semi-dwarf (Rht-B1b) and standard height (Rht-B1a) varieties in durum. In spring wheat, NILs were developed for eight Rht-A1 alleles in two high-yielding Montana varieties. These NILS were planted in field trials and plant height and grain traits were measured. Four novel mutations, Rht-A1-E63K, Rht-A1-Q6*, Rht-A1-V55M, and Rht-A1-53T in spring wheat and two mutations in durum, Rht-B1b-E529K and Rht-A1-S50F all had either significantly changed height or grain traits. Along with developing and testing Rht alleles for field trait improvement, we did a study to characterize an Rht stop-codon dosage response in wheat. Previous studies in rice and barley have indicated that a lack of the functional SLR1/SLN1 gene respectively, results in an abnormal growth response characterized by taller height and slender appearance. This effect on Rht function has yet to be tested in wheat. Rht nonsense alleles were created by screening an EMS treated population created using seed of a standard-height Montana variety. We combined mutations creating lines homozygous for single, double, or triple mutations. In field trials, Rht triple mutants exhibited a slender, elongated phenotype with strike heads similar to SLN1 mutants in barley. Differences in height varied for the other crosses but did trend towards increased height with increased Rht-stop mutation dosage.
Leveraging a global spring, 2-row barley population to accelerate the development of superior forage barley varieties for Montana growers
(Montana State University - Bozeman, College of Agriculture, 2021) Hoogland, Traci Janelle; Chairperson, Graduate Committee: Jamie Sherman
As more people around the globe escape poverty, they are eating more meat and dairy products. To support this increased demand for animal products there is an urgent need to develop more sustainable high-quality forage and hay crops for the livestock production industry. Barley (Hordeum vulgare spp. vulgare L.) is considered one of the most drought tolerant of the annual cereals and spring barley has been shown to out yield established perennial forages under drought conditions in central Montana (Cash, Surber, & Wichman, 2006). To accelerate the development of superior forage barley varieties for Montana, the following goals were identified 1) Utilize a genome wide association analysis to find genetic regions related to key forage and agronomic traits, 2) Use statistical modeling to a) examine the relationship between difficult to measure forage traits such as quality and yield, and easy to measure agronomic traits such as flowering time and plant height, b) identify agronomic traits that can be used as proxies for yield and quality in the earliest stages of the breeding program when genetic and phenotypic variability are at their greatest. Through these techniques the importance of variation in timing of plant maturity was identified. Statistical modeling showed that variability in forage yield and quality was observed to be closely related to variability in the timing of heading and soft-dough dates. Plant height was also determined to be of importance especially for biomass yield. Through genome-wide association analysis, novel QTL were discovered in relation to all studied traits. QTL were detected on all seven chromosomes and the majority of forage trait QTL co-located with QTL related to the timing and progression of plant development and maturity. This appeared to indicate that in a population of global barley accessions, the loci with the greatest impact on forage traits may be those containing genes regulating plant development and senescence. This further strengthened the evidence from the modeling study that a relationship exists between the two trait categories: traits for measuring the timing of plant development and forage traits.
The impact of Teosinte branched1 and reduced height mutations in durum wheat
(Montana State University - Bozeman, College of Agriculture, 2021) Brown, McKenna Margaret; Chairperson, Graduate Committee: Michael J. Giroux
Increasing the yield of wheat requires identifying new genetic combinations of alleles by crossing or by creating variation in yield limiting genes. Wheat yield is impacted by tiller number and seeds per tiller, both of which are impacted by the Reduced height (Rht) and Teosinte branched1 (TB1) genes. In this study, durum plants varying for Rht and TB1 alleles created by EMS mutagenesis were studied to determine the impact of each allele upon agronomic and seed traits. Both projects aimed to increase durum yield, one through an increase in tiller number; the other through the development of a plant with height between current full-height and semi-dwarf varieties that can allocate more resources to seed production. The impact of TB1 null alleles were studied alone and together in greenhouse and field trials, along with an RNA sequencing study to determine the impact of TB1 mutation upon global gene expression in developing meristems. TB1 single and double null mutants produced more biomass and tillers per plant, and expression of genes in meristems varied. A screen of wheat varieties grown in Montana identified that several spring and durum wheat varieties contain different TB1 alleles, but none contained TB1 null alleles. Rht experiments included field trials, coleoptile length and gibberellic acid responsiveness assays, and an in-vitro test to determine the impact of each Rht mutation upon binding to Gibberellin Interacting Domain 1 (GID1) that directly influences plant height. It was found that the previously described Rht-B1b-E529K allele reduced both plant height and coleoptile length while two newly characterized Rht mutations had lesser impacts with trends towards intermediate-height plants. The results of this research demonstrate that Rht alleles that alter RHT binding to GID1 and TB1 null alleles may prove useful in increasing durum tillering and optimizing plant height for different growing conditions.
Genetics of seed dormancy in wheat and barley
(Montana State University - Bozeman, College of Agriculture, 2020) Vetch, Justin Michael; Chairperson, Graduate Committee: Michael J. Giroux; Robert N. Stougaard, John M. Martin and Michael J. Giroux were co-authors of the article, 'Revealing the genetic mechanisms of preharvest sprouting' in the journal 'Plant science' which is contained within this dissertation.; Robert N. Stougaard, John M. Martin and Michael J. Giroux were co-authors of the article, 'Allelic impacts of TaPHS1, TaMKK3, and Vp1B3 on preharvest sprouting of northern Great Plains winter wheats' in the journal 'Crop science' which is contained within this dissertation.; Jason G. Walling, Jamie D. Sherman, John M. Martin and Michael J. Giroux were co-authors of the article, 'Mutations in the HvMKK3 AND HvAlaAT1 genes affect barley pre-harvest sprouting and after-ripened seed dormancy' in the journal 'Crop science' which is contained within this dissertation.; Philip L. Bruckner, John M. Martin and Michael J. Giroux were co-authors of the article, 'TAMFT homeologs are associated with preharvest sprouting winter wheat' submitted to the journal ''Crop science' which is contained within this dissertation.
Montana producers have many biotic and abiotic stresses to contend with. One of interest to avoid is preharvest sprouting (PHS), which is the precocious germination of grains before harvest. PHS affected grain is discounted at the elevator, resulting in grain being unsuitable for many foods and direct losses to producers. PHS is not widespread every year in Montana but in some years causes large economic loss. Although PHS is a response to environmental cues it is largely controlled by genetics. Genes that control seed dormancy are the most likely candidate genes for PHS resistance and the series of studies presented in this dissertation examine the impact of several genes upon small grain PHS susceptibility. The studies used several methods to assess PHS susceptibility and determine which alleles of individual genes were present. The methods included seed dormancy screening assays, alpha amylase enzyme activity analysis, falling numbers analysis, genotyping by direct sequencing and via use of various markers, RNA-sequencing, and gene expression analysis. The first study served as a PHS susceptibility survey and provides PHS tolerance information on MT grown wheat varieties. This study also found that of the three most reported PHS associated genes (TaMFT 3A, TaMKK3 4A, and TaVp1 3B), only TaMFT 3A was associated with PHS in Montana winter wheats, even though the previously reported variation was observed in all three genes. The second study looked at PHS susceptibility among current and historically grown barley varieties. It was found that malt varieties vary greatly in their susceptibility to PHS with the top grown AMBA recommended varieties among the most susceptible. It was also found that a previously unstudied mutation in the HvMKK3 gene is associated with PHS susceptibility. Interestingly, HvMKK3 and HvAlaAT1 affect dormancy at different time points in grain maturity indicating dormancy may be tailored to a specific timeframe (high dormancy at harvest with rapid decay of dormancy after harvest). The final study revisited winter wheat PHS and found that the TaMFT 3B and 3D homeologs are associated with PHS which has not been shown to date.
Hybridization and invasiveness in Eurasian watermilfoil (Myriophyllum spicatum): is prioritizing hybrids in management justified?
(Montana State University - Bozeman, College of Agriculture, 2021) Hoff, Hannah Katherine; Chairperson, Graduate Committee: Ryan Thum; Ryan A. Thum was a co-author of the article, 'Hybridization and invasiveness in Eurasian watermilfoil (Myriophyllum spicatum): is prioritizing hybrids in management justified?' submitted to the journal 'Invasive plant science and management' which is contained within this thesis.
Hybridization can play an important role in the evolution of invasiveness. Eurasian watermilfoil (Myriophyllum spicatum L.) is a widespread aquatic invasive plant species that hybridizes with native northern watermilfoil (Myriophyllum sibiricum Kom.). Previous studies have found mixed evidence for whether hybrid watermilfoil (Myriophyllum spicatum x sibiricum) and pure M. spicatum differ in vegetative growth rate and herbicide response. While several studies have emphasized variation in these traits among M. spicatum x sibiricum genotypes, variation within M. spicatum has not been considered. Therefore, it is unclear how important genetic variation within M. spicatum, versus between M. spicatum and M. spicatum x sibiricum, is in influencing invasive traits and management outcomes. If M. spicatum x sibiricum genotypes are always more invasive than M. spicatum genotypes, simply distinguishing taxa may be sufficient for identifying lake management priorities; however, if significant phenotypic overlap is observed between taxa, distinguishing individual genotypes may be important for tailoring management strategies. We performed replicated trials of a vegetative growth and 2,4-D assay to measure clonal variation in growth rate and herbicide response of M. spicatum and M. spicatum x sibiricum. Our results indicate that M. spicatum x sibiricum exhibits higher average vegetative growth than M. spicatum, whether or not it is treated with 2,4-D. We did not observe interactions between taxon and treatment or between genotype and treatment. Despite differences between M. spicatum and M. spicatum x sibiricum in average vegetative growth, there was substantial overlap between taxa. For example, we found that the fastest-growing genotype of pure M. spicatum did not differ significantly in average growth from the fastest-growing M. spicatum x sibiricum genotype. The potential for overlap between these invasive Myriophyllum taxa suggests that distinguishing and characterizing genotypes may be more informative for management than simply distinguishing between M. spicatum and M. spicatum x sibiricum.
Creating rust resistance in wheat via modification of host genes
(Montana State University - Bozeman, College of Agriculture, 2020) Nyamesorto, Bernard Mensah; Chairperson, Graduate Committee: Li Huang; Hongtao Zhang and Li Huang were co-authors of the article, 'Wheat MYC4 transcriptional factor gene modification enhanced host resistance against rust pathogens' which is contained within this dissertation.; Dissertation contains an article of which Bernard Mensah Nyamesorto is not the main author.
A major challenge to resistance breeding in bread wheat (Triticum aestivum L.) is limited genetic diversity. The traditional approach to combating this problem is introgression of resistant genes from other closely related species into elite but susceptible cultivars. This strategy is often associated with linkage drag. Moreover, pathogens continue to evolve into different and more virulent forms (races) that overcome these resistant genes in a process called resistance breakdown. A typical example is the outbreak of Ug99, a novel African stem rust pathotype that exhibited virulence against numerous stem rust resistance genes. Creating resistance within wheat's own genome is a panacea to the challenges surrounding the traditional method. Biotrophic plant pathogens such as wheat rusts are known to manipulate host genes as a means of overcoming host defense response and acquiring nutrients. Central to wheat-rust interactions is highly sophisticated immune repertoire consisting of diverse signal perception and intracellular signaling pathways which are regulated by transcriptional regulators and co-factors. Unfortunately, pathogen effector proteins also take advantage of host plant genes (so called pathogen susceptible host genes) including transcriptional mechanisms. Hence editing the genes targeted by these pathogens in wheat is a valuable means of creating host resistance that has been neglected. We conducted these studies to identify host genes targeted by rust pathogens through bioinformatics approaches including transcriptome analysis which showed that wheat NPR1 genes (transcriptional regulator) and MYC4 and MY21 (transcription factors) are negatively involved compatible wheat-rust interactions. Subsequently, when these genes were down regulated in susceptible Chinese Spring using Barley Mosaic Virus Induced Gene Silencing (BSMV) assay, the silenced plants became resistant to rust pathogens. Loss-of-function mutations created in these homeologs via Ethyl methanesulfonate mutagenesis conferred resistant to rust pathogens. Consequently, this study led to the development of new rust resistance germplasms.
Improving malt barley agronomics via allelic selection of senescence and flowering time controlling genes
(Montana State University - Bozeman, College of Agriculture, 2020) Alptekin, Burcu; Chairperson, Graduate Committee: Andreas M. Fischer; Dylan Mangel, Duke Pauli, Tom Blake, Jennifer Lachowiec, Traci Hoogland, Andreas Fischer and Jamie Sherman were co-authors of the article, 'Combined effects of glycine-rich RNA binding protein and a NAC transcription factor extend grain fill duration and improve malt barley agronomic performance' submitted to the journal 'Theoretical and applied genetics' which is contained within this thesis.; Dylan Mangel, Duke Pauli, Tom Blake, Jennifer Lachowiec, Jamie Sherman and Andreas Fischer were co-authors of the article, 'Dissecting the effects of senescence-regulating HvNAM1 and HvNAM2 transcription factors on malt barley agronomics' submitted to the journal 'Molecular breeding' which is contained within this thesis.; Dylan Mangel, Duke Pauli, Tom Blake, Hannah Turner, Jennifer Lachowiec, Jamie Sherman and Andreas Fischer were co-authors of the article, 'Allelic selection of senescence and flowering time controlling genes confers malt extract stability' submitted to the journal 'Journal of the American Society of Brewing Chemists' which is contained within this thesis.
Malt barley (Hordeum vulgare L.) is a high-profit crop for farmers; yet, its production raises challenges that need to be addressed. The standards for grain quality in malt barley are stringent, and the rejection of non-qualified grains by maltsters is the leading cause of revenue loss for malt barley producers. Rejection is mainly due to high grain protein content and low kernel plumpness which both cause significant problems in the malting process. While proper growing practices can improve malt quality, the industry requires genotypes that have more stable malt quality. Therefore, understanding the molecular mechanisms associated with grain quality can be applied to improve selection of superior malt varieties. A considerable volume of literature has suggested that regulation of whole-plant senescence and flowering processes in cereals have direct influences on grain yield and quality parameters. The central question in this dissertation examined whether malt barley agronomic and end use quality can be improved by the selection of varying alleles for genes associated with plant development. With this purpose, two whole-plant senescence-regulating NAM, ATAF and CUC (NAC) transcription factors, HvNAM1 and HvNAM2, and a flowering-time controlling Glycine-Rich RNA Binding Protein (HvGR-RBP1) were studied. Molecular markers for selection of alleles from varieties 'Karl' (with consistently low grain protein) and 'Lewis' were developed, and an advanced-generation malt barley breeding population was genotyped. Statistical analysis of growth parameters from this population showed that selection of HvNAM1 'Karl', HvNAM2 'Karl' and HvGR-RBP1 'Lewis' alleles ensures a longer grain filling period in malt barley. Plants with prolonged grain filling also exhibited increased kernel plumpness and test weight. Additionally, selection of 'Karl' alleles for both NAC genes decreased grain protein content ensuring grain quality for malting. The improvement of grain characteristics correlated with improved malt phenotypes, for example a ~2% increase in malt extract, and improvement in other malt characteristics such as beta-glucan content and alpha-amylase activity was observed. Overall, these data show that molecular genetics and allelic selection for genes controlling plant development is promising for advancing malt quality. Research performed here has a direct potential for improving the profits for malt barley producers.

Theses and Dissertations at Montana State University (MSU)

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