Plant Sciences Doctoral Work
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Browsing Plant Sciences Doctoral Work by Subject "Botany."
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Item Adaptation of Quality Protein Maize (Zea Mays L.) to Northern U.S. Corn Belt(North Dakota State University, 2015) Dong, NaiyuanThere is a need to increase the value of crops and develop the next generation of healthier products. Quality protein maize (Zea mays L.) is an option but has never been adapted to short – season environments. Quality protein maize (QPM) with homozygous embryo and endosperm for mutant allele o2 at the α-zeins regulatory gene opaque-2 shows about 60 to 100% increase in lysine and tryptophan essential amino acids when comparing with non-QPM maize. The objectives of this research were to adapt QPM genotypes to the northern U.S. through the NDSU Early QPM Program, and to evaluate the agronomic potential of early generation QPM lines and hybrids developed by the NDSU maize breeding program for the northern USA. Fifty-four inbred lines, including 47 QPM donor lines from the Iowa State University (ISU) maize breeding program, six experimental lines from the NDSU maize breeding program and one ex-PVP line from industry, were selected to produce 94 early-QPM backcross populations. Based on the earliness, protein content, and amino acid levels of lysine, 218 BC1S2 lines were selected for testcrosses with industry testers. Experiments evaluating testcrosses were arranged in 12 x 12 and 10 x 10 partially balanced lattice designs across three environments in 2013 and 2014. Based on this evaluation, totally 48 S2 lines were selected for further development, 17 of them representing the Stiff Stalk (SS) heterotic group and 31 representing the non-SS-group. Selected lines provided unique advanced inbred lines with hybrid combinations showing not only above average grain yield, dry down, and protein content but also, high levels of lysine, tryptophan, and methionine. The results of this research show, for the first time, the successful adaptation of QPM genotypes to short-season environments. The NDSU maize-breeding program has developed the first high quality maize products through the EarlyQPM and EarlyQPMF (for feedstock) national programs.Item Advanced Cropping Systems for Oil and Biomass Feedstock Production in the Northern Great Plains(North Dakota State University, 2015) Zayas, Alfredo AponteVideo summarizing a Ph.D. dissertation for a non-specialist audience.Item Agronomic Practices that Impact Grain Quality Factors of Durum Wheat (Triticum Turgidum L. Var. Durum Desf.)(North Dakota State University, 2016) Forster, Shana M.Durum wheat is a type of wheat primarily used for pasta production. North Dakota is the leading producer of durum wheat in the US with average yields of 2700 kg ha-1. Durum wheat price discounts are common and occur due to disease, heavy metal contamination, and environmental issues that impact grain quality. Studies were conducted in order to determine how agronomic approaches might impact durum quality. Experiments were conducted in order to determine what impact planting date, cultivar, and seeding rate had on the agronomic performance and quality of end-use traits. In general, a delay in planting date resulted in a significant decrease in yield and test weight for all cultivars. Cultivars differed for many of the end-use traits evaluated such as protein content, falling number, and vitreous kernel. Seeding rate had little impact on the traits evaluated. No combination of planting date and cultivar was identified that consistently resulted in grain marketed as US Grade 1 hard amber durum (HAD), or ‘choice durum’. Cultivar selection remains the best option for maintaining end-use traits. The effect of Zn fertilizer source and placement on grain Cd were evaluated. Treatments evaluated had no negative impact on grain yield or test weight. The foliar application of 1.1 kg Zn ha-1 Zn-EDTA in combination with 33 kg N ha-1 in the form of UAN applied at Feekes 10 growth stage (boot stage) resulted in the lowest grain Cd, and highest grain Zn, Fe and protein and represents an approach of biofortification for durum wheat.Item Agronomic Studies of Forage Brassicas as Full-Season and Cover Crops for Grazing in North Dakota(North Dakota State University, 2017) Teuber Winkler, Osvaldo RobertoAnnual forages represent a good feed resource to extend the grazing season into fall and winter, providing a good quality forage for the livestock, allowing more efficient use of rangeland, and at the same time improving soil properties. Many species in the Brassicaceae family are used as forages for grazing. Forage brassicas are characterized by high forage yield, with high nutritive value, low establishment and harvest cost (direct grazing), while providing many ecosystems services. Forage brassicas can be grown as full season forage crops or as cover crops planted after a grain crop. The objectives of this study were: 1) to identify brassicas species and cultivars with high biomass production and forage quality when grown as full-season and as cover crops in North Dakota; 2) to determine their optimum sowing date, plant density and the response to different N and S fertilization rates. Replicated experiments were conducted at four sites Fargo, Prosper, Carrington and Walcott, ND in 2012-2014. Results indicate swede (Brassica napus L. var. napobrassica) and kale [B.oleraceae L. convar. acephala (DC)] were the highest forage yielding brassicas when established in full-season and turnip [Brassica rapa L. var. rapa (L.) Thell).], cv. ‘Appin’ was the highest yielding sown after August. In full-season brassicas, delaying sowing date reduced total forage yield in all species but did not influence forage quality. In brassicas sown after August, total forage yield decreased significantly only in radish in the second sowing date. Plant density did not have an effect on forage yield or N accumulation averaged across environments and species in full-season forage brassicas. This was different in brassicas sown after August, where the highest forage yield was obtained with the highest plant density (≥200 plants m-2). Kale and swede leaf, root/stem, and dead matter yield increased up to 200 kg N ha-1 in a linear response. Sulfur and the interaction between N and S did not have an effect in forage yield and quality. Both full-season and cover crops forage brassicas have great potential as supplemental high quality forage for grazing in North Dakota.Item Association Mapping and Genetic Diversity Studies of Agronomic and Quality Traits in Durum Wheat [Triticum turgidum L. var. durum (Desf.)](North Dakota State University, 2017) Johnson, MarinaGenetic diversity studies in breeding programs are important to identify parental lines for hybridization and introgression of desirable alleles into elite germplasm. The genetic diversity analysis of 283 North Dakota State University (NDSU) advanced durum wheat breeding lines developed during the last 20 years indicated that the population was structured according to its breeding history. Total genetic diversity analysis (HT = 0.334) showed adequate level of genetic variation. The results will help in breeding efforts to broaden the genetic base and select lines for crossing as well as for genetic and genomic studies to facilitate the combination of desirable alleles. The quantitative nature of important target traits, combined with environmental effects, makes it difficult to bring the desirable improvement in durum wheat to meet the expectations of all the stakeholders involved in the durum wheat industry. With an objective to identify molecular markers for marker-assisted breeding (MAB), the present study attempted to identify marker-trait associations for six agronomic and 29 quality traits using a genome-wide association study (GWAS) mapping approach. The study used two types of phenotypic datasets, a historic unbalanced dataset belonging to a total of 80 environments collected over a period of 16 years and a balanced dataset collected from two environments, to identify the applicability of historic unbalanced phenotypic data for GWAS analysis. A total of 292 QTL were identified for agronomic and quality traits, with 10 QTL showing major effects (R2 >15%). Over 45% of QTL for agronomic and quality traits were present in both the unbalanced and balanced datasets, with about 50% of those present in both environments in the balanced dataset. Genome-wide association mapping studies identified several candidate markers for use in marker-assisted selection (MAS) for height, gluten strength, distribution of small kernels, polyphenol oxidase (PPO) activity, and yield.Item Characterization and Manipulation of the Wheat B Genome(North Dakota State University, 2017) Zhang, WeiCommon wheat originated from interspecific hybridization of three diploid ancestors followed by spontaneous chromosome doubling. Aegilops speltoides (genome SS) has been controversially considered a possible candidate for the donor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure. The first aim of this study was to characterize the homology between the wheat B genome and the Ae. speltoides S genome. In this study, meiotic pairing for each of the B-S homoeologous pairs was investigated individually. Noticeable homology between chromosomes 1B and 1S was discovered, but not between other homoeologous B-S pairs. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was detected on the long arm of wheat chromosome 1B. The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome. Evidently, Ae. speltoides was involved in the origin of the wheat B genome, but should not be considered an exclusive donor of this genome. Aegilops speltoides and Thinopyrum elongatum (genome EE), two of diploid relatives of wheat, are considered important sources of novel genes for wheat improvement. However, the development of compensating wheat-alien translocations has been limited by laborious cytological analysis. This study aimed to develop an effective procedure of inducing, recovering, and detecting homoeologous recombination in wheat-alien gene introgression lines. Totally, 112 wheat-Ae. speltoides 2B-2S and 87 wheat-Th. elongatum 2B-2E translocation lines were developed through this procedure. Composite bin maps for chromosome 2B as well as homoeologous chromosomes 2S and 2E were constructed by genotyping the translocations using 90K SNP arrays. In addition, genes for resistance to stem rust, tan spot, and SNB on chromosome 2S were physically mapped and incorporated into the wheat genome. Also, an Ae. speltoides-derived deleterious growth gene was physically mapped to the subtelomeric region of chromosome 2S. In summary, the results of the study led to a large number of 2B-2S and 2B-2E recombinants, physically mapped disease and growth-related genes on chromosome 2S, developed novel molecular markers, and optimized chromosome engineering procedures.Item Characterization of Common Wheat Translocations Carrying Leaf Rust Resistance Genes from Alien Species(North Dakota State University, 2016) Ibrahim, Mohamed SomoLeaf rust caused by Puccinia triticina Erikss may inflict significant yield losses in wheat; however, can be controlled by breeding for increased host resistance. In earlier studies, effective, resistance has been transferred to common wheat from the wild relatives Thinopyrum ponticum (Lr19), Aegilops sharonensis (Lr56), Ae. peregrina (Lr59), and Ae. neglecta (Lr62). Each translocation was subsequently re-engineered by the induction of homoeologous chromosome exchanges with a normal wheat chromosome to remove unneeded alien chromatin. For each gene the 3-8 most promising recombinants that retained the least linkage drag, but could not be differentiated, were identified. This study employed physical and genetic mapping in conjunction with molecular markers and genomic in situ hybridization to identify those recombinants that are best suited for breeding. For each gene, the recombinant with the least alien chromatin that also appeared to be fully compensating was identified and marker loci suitable for marker-assisted selection were suggested.Item Cloning and Characterization of Meiotic Genes Rec8 and Cdc5 and Subcellular Analysis of Kinetochore Orientation in Wheat(North Dakota State University, 2013) Ma, GuojiaMeiosis is a specialized cell division that halves chromosomes and generates haploid gametes in eukaryotes. It is a dynamic cellular process governed by a complex genetic network. Two key players of this network, Rec8 and Cdc5, were cloned and analyzed using comparative genomics and subcellular immunolocalization methodologies in wheat (Triticum turgidum L., genome AABB). TtRec8 and TtCdc5 were localized to group 1 and 5 chromosomes, with two homoeoalleles in sub-genome A and B, respectively. One of the two TtRec8 homoeoalleles, TtRec8-A1, contains 20 exons in a 6.5 kb-genomic DNA fragment, and the coding region encodes 608 amino acids. Two homoeoalleles of TtCdc5 separately encode 1,081 and 1,084 amino acids. The expression profilings of TtRec8 and TtCdc5 were meiotic tissue dominant in LDN, and the highest levels of TtRec8 and TtCdc5 were at interphase through early prophase I and at pachytene stage of meiosis, separately, and then decreased as meiosis proceeded. TtRec8 protein was detected along the entire chromosomes through the early stages of prophase I. Thereafter, TtRec8 protein was mostly removed from the chromosomes. The DNA sequences and conserved domains of TtRec8 and TtCdc5 as well as their kinetics through the meiotic process in LDN were very similar as the cohesion protein Rec8 and polo-like kinase Cdc5 in models, suggesting their specific roles in meiosis. Chromosome pairing (or synapsis) may play a role in kinetochore orientation during meiosis. Special genotypes that contained both paired (bivalents) and unpaired (univalent) chromosomes in the LDN background were constructed to determine the orientation of sister kinetochores in the univalent and bivalent chromosomes in meiosis I. Among the special genotypes included the hybrids from the crosses of the disomic LDN D-genome substitution lines LDN 1D(1B), LDN 2D(2A), LDN 2D(2B), LDN 3D(3A), LDN 4D(4B), LDN 6D(6A), LDN 6D(6B), LDN 7D(7A), and LDN 7D(7B) with LDN, LDN 1D(1A) with rye (Secale cereale L., genome RR) `Gazelle', LDN with Aegilops tauschii (genome DD) RL5286, and LDN 1D(1B) with Ae. tauschii RL5286. All univalents were found amphitelically orientated and all bivalents syntelically orientated at metaphase I, suggesting meiotic pairing mediates kinetochore orientation and subsequently chromosome segregation in LDN.Item Cloning and Characterization of the Iron-Regulated Transporter (IRT) Genes and Their Transcription Factors in Populus(North Dakota State University, 2015) Huang, DanqiongIron deficiency causes chlorosis in many plant species, resulting in yield loss and poor quality. Many tree species including poplar are susceptible to iron deficiency. Trees suffering from iron deficiency often show interveinal chlorotic leaves and in severe cases, branches or an entire tree may die. In this study, two trees of Populus tremula L.‘Erecta’ growing near each other but with contrasting leaf color phenotypes were used to study the causes of chlorosis and the mechanisms of tolerance or susceptibility to iron chlorosis in poplar. A leaf analysis revealed that the iron deficiency tolerant tree (PtG) had a higher level of dry matter content, chlorophyll (a+b), Chl a/b ratio, Zn and Fe content than the iron chlorosis susceptible tree (PtY). A hydroponic culture confirmed the differences in aforementioned physiological parameters between PtG and PtY responding to iron deficiency. Two iron-regulated transporter genes (PtIRT1 and PtIRT3), the native promoter of the PtIRT1 gene (PtIRT1-pro), and two basic helix-loop-helix (bHLH) transcription factors (PtFIT and PtIRO) were cloned and characterized for their responses to iron deficiency in PtG and PtY. Deduced amino acid analysis revealed that PtIRT1, PtIRT3, PtFIT, and PtIRO in PtG were identical to those in PtY. Phylogenetic and putative domain analyses showed that PtIRT1, PtFIT, and PtIRO may function in iron homeostasis, while PtIRT3 may play a role in zinc transport in poplar. The expression of PtIRT1 and PtFIT are root-specific and up-regulated by iron deficiency. The expression of a GUS gene derived by PtIRT1-pro in tobacco was also up-regulated by iron deficiency, but was not root-specific. The expression of PtIRT3 is ubiquitous and up-regulated by iron deficiency, but significantly down-regulated by zinc deficiency. A high correlation in the expression between PtFIT and PtIRT1 was observed in PtG, but not in PtY. Transgenic poplars overexpressing PtIRT1 or PtIRT3 did not have enhanced Fe accumulation; however, an enhanced tolerance to iron deficiency was found in transgenic plants overexpressing PtFIT. The results suggested that the transcription factor PtFIT may be involved in iron deficiency response through regulation of PtIRT1 and PtFIT itself may be regulated by other factors in poplar.Item Determining Optimum Seeding Rates for Diverse Hard Red Spring Wheat (Triticum Aestivum L.) Cultivars(North Dakota State University, 2016) Mehring, Grant HarrySeeding rate for maximum grain yield can differ for diverse hard red spring wheat (HRSW) (Triticum aestivum L.) cultivars and can be derived from a seeding rate response curve. Six groups of HRSW cultivars with combinations of Rht-B, Rht-D, and Ppd-D with two cultivars per group were planted in 2013-2015 at five seeding rates in 23 trials throughout Minnesota (MN) and eastern North Dakota (ND), USA. Seeding rates ranged from 1.59 – 5.55 million seeds ha-1. Planting dates represented optimum and delayed seeding dates. Agronomic measurements for plant height, lodging, stems per plant, protein, and yield were obtained. Stand loss measurements, defined as the amount of viable seeds that did not become established plants, ranged from 11-19% across seeding rates most commonly planted in the region. There was a seeding rate by cultivar interaction for plant height, protein, lodging, stems plant-1, and yield. As seeding rate increased stems per plant consistently decreased and there were large differences in tillering capacity between cultivars. Increased seeding rate caused increased lodging for those cultivars with a capacity to lodge. Seeding rate for maximum yield of the cultivars differed. Combined over all cultivars, the seeding rate for maximum yield increased as the average yield of an environment decreased. An analysis of covariance (ANCOVA) predictive model was built for yield and tillering. The model for yield across all environments was not predictive with a validation R2 of 0.01. However, when only the bottom six yielding environments out of the total 21 environments were used to build a yield model the predictions were more accurate with a validation R2 of 0.44. The model built and validated for tillering was predictive for the validation environments with an R2 of 0.71 for validation environments. Seeding rate trials continue to be useful for producers making seeding rate decisions for a range of agronomic reasons. Additionally, using regression predictions and separate training and validation datasets to predict yield and tillering with HRSW, genetic and geographic predictors show promise for recommending seeding rates for future environments.Item Developing a DNA Fingerprint for Midwest Six-rowed Malting Barley(North Dakota State University, 2012) Lewis, Magan FriskopThe requirements for brewing beer from barley (Hordeum vulgare L.) malt are specific and unique for each brewer. Anheuser-Busch InBev and Miller Coors Brewing Company (MillerCoors) are two major brewers in the United States that target different malt quality profiles for six-rowed barley malt. Two closely related cultivars developed by the University of Minnesota, Robust and Stander, differ greatly in agronomic and malt quality performance. Robust malt fits the requirements of MillerCoors and Stander malt has many of the parameters desired by Anheuser-Busch InBev. The close relationship between these two cultivars increases the chance of recognizing chromosome regions with the genes controlling malt quality traits. A total of 53 doubled-haploid (DH) lines (original population) and the parents from the Robust x Stander cross were grown at eleven locations in North Dakota and one location in Idaho the past six years. An additional 138 Robust x Stander DH lines were generated in 2009 and were evaluated alongside the original DH population in the summer of 2011 at two North Dakota locations. Agronomic data were collected at all locations and cleaned grain samples of the original population from six of the locations were micro-malted at NDSU. Three linkage maps were developed using the original and 191 DH line (entire) populations. The first linkage map was constructed using the original DH population, along with a total of 102 SNP, SSR, and DArT markers. The second and third linkage maps were developed using only 67 SNP markers, with the original and entire Robust x Stander DH population, respectively. The first map was used to identify QTL controlling malt quality and wort carbohydrate traits on chromosomes 4H, 5H, and 6H. The SNP map constructed using the original DH population was used to identify QTL controlling agronomic traits on chromosome 6H. The third map was used to identify QTL controlling agronomic traits on chromosomes 4H and 6H. The ultimate goal for this research in years to come is to develop a genetic haplotype that helps distinguish six-rowed barley lines suitable for MillerCoors and Anheuser-Busch InBev.Item Development and Characterization of Wheat Germplasm for Resistance to Stem Rust UG99 in Wheat(North Dakota State University, 2013) Zhang, QijunWorld wheat production is currently threated by stem rust (caused by Puccinia graminis f. sp. tritici) Ug99 race (TTKSK). The ongoing global effort to combat Ug99 is focusing on the identification and deployment of Ug99-resistant genes (Sr) into commercial cultivars. The objectives of this study were to identify TTKSK-effective Sr genes in untapped durum and common wheat germplasm and introgression of TTKSK-effective Sr genes from tetraploid wheat (Triticum turgidium) and Aegilops tauschii into hexaploids through production of synthetic hexaploid wheat (SHW). For identification of TTKSK-effective Sr genes, 177 durum and common wheat cultivars and lines were first evaluated using three highly virulent races TTKSK, TRTTF, and TTTTF and 71 cultivars and lines with TTKSK resistance were identified. The TTKSK-resistant cultivars and lines were then evaluated using six local races and the molecular markers that are diagnostic or tightly linked to the known TTKSK-effective Sr genes. The race specification and marker analysis showed that several previously deployed TTKSK-effective Sr genes such as Sr2, Sr24 and Sr42 were present in some of the cultivars and lines. A number of resistant cultivars and lines derived from wheat relatives such as Thinopyrum ponticum, Th. elongatum, Th. intermedium, and Ae. speltoides may carry novel Sr genes. For SHW development, 200 new SHW lines were developed by crossing 181 tetraploid wheat accessions to 14 Ae. tauschii accessions. Sixty-six of the new SHW lines, 14 previously-developed SHW lines, and their parents were evaluated for resistance to TTKSK, TRTTF, TTTTF and six other races and genotyped using molecular markers linked to the known genes in T. dicoccum and Ae. tauschii. The evaluation data showed that 44 SHW lines were resistant to TTKSK. The race specification and marker analysis showed that Sr2 from T. dicoccum and Sr33 from Ae. tauschii were present in some of the SHW lines and a number of SHW lines have novel genes conferring TTKSK resistance. The durum and wheat cultivars and lines and SHW lines with known and novel Sr genes conferring resistance to TTKSK will be useful resources for improving wheat resistance to TTKSK and other emerging races of stem rust.Item Early-Season Weed Control in Direct-Seeded Onion (Allium Cepa L.)(North Dakota State University, 2012) Loken, James RyanOnion is a poor competitor with early-season broadleaf weeds. In addition, there are no current herbicide labels that allow POST application prior to the onion two-leaf stage in ND and PRE herbicide options provide inconsistent results. Bromoxynil and oxyfluorfen at reduced rates plus adjuvants were evaluated in the greenhouse for common lambsquarters and redroot pigweed control and crop safety when applied to onion prior to the two-leaf stage. Bromoxynil and oxyfluorfen plus methylated seed oil (MSO) or petroleum oil concentrate (POC) had the greatest onion safety compared to other tested adjuvants and provided acceptable weed control 12 d after three sequential applications. 14C-oxyfluorfen absorption was evaluated in the laboratory 24 h after treatment and oxyfluorfen absorption was greatest at 35 C compared to 15 and 25 C. Multiple applications of bromoxynil and oxyfluorfen at reduced rates were further evaluated with MSO or POC in field experiments. Bromoxynil provided 12% better common lambsquarters control and 9 t/ha greater large-grade onion yield than oxyfluorfen. Greater reduced rates resulted in greater common lambsquarters control and reduced common lambsquarters stand density. Common lambsquarters control was 24 to 32% greater when POC or MSO were used, respectively, compared to no adjuvant. Bromoxynil did not reduce onion stand/m as rates increased, but oxyfluorfen reduced onion stand as rates increased. Four or five sequential bromoxynil or oxyfluorfen applications every 7 d resulted in 14 to 19% greater weed control than three sequential applications. Onion stand was severely reduced by PRE herbicide and multiple reduced-rate application combinations.Item Environmental Influence on Cold-Climate Grapevine (Vitis Spp.) Fall Acclimation Response and Fruit Ripening(North Dakota State University, 2016) Stenger, JohnTwo experiments were conducted to determine differences in sensitivity to temperature among cold-climate grapevine genotypes in fall-acclimation response. One experiment utilized a growth chamber to compare grapevine plantlets under reducing photoperiod in two static temperatures through the quantification of seven predictor variables. Reduction models were compared for their effectiveness in interpreting the interaction among cultivars, traits, photoperiodic times, and temperatures. All models identified three similar axes relating the genotypes. Tucker decomposition was better able to separate wild genotypes from hybrids, was more consistent in the subspace defined, and was more readily interpretable, thus was preferred over SVD. Adapted types, V. riparia and ‘Frontenac’, showed increased tip responsiveness to temperature while V. riparia and ‘MN 1131’ more temperature response in their relative active growth to tissue maturation compared with marginal types including ‘Marquette’. Overall, it seems at least one strategy for temperature adaptive response is required in addition to early onset of acclimation for successful adaptation to the Northern Plains Region. In a second study, mature plants of three locally important cultivars were evaluated under five environmental conditions for similar acclimation traits along with fruit maturation traits under naturally decreasing photoperiod and temperature regimes. Reductions of phenotypic and temperature trends lead to a correlation between axes contrasting investigated years. Unique responses to temperature reduction were found in all cultivars, while ‘Marquette’ was additionally more responsive under temperature increases as it reverted to an active growth state. These alterations were speculated to be caused by differential partitioning of phloem resources within the plant through control of stomatal conductance. Lastly, a unique genotype was discovered. The genotype was determinate in both growth and reproduction in contrast to the indeterminate vining growth habit that defines members of Vitis. The natural mutant may have use in research on plant reproductive and vegetative growth regulation. Overall, insight was gained into the contrasts among acclimation processes within Vitis hybrids, and the use of growth chamber based evaluations of V. riparia derived progeny for background selection may lead to more rapid introgression of adaptive traits into favorable quality backgrounds in cold-climate Vitis breeding.Item Genetic and Physiological Relationships between Oat Grain Quality Components(North Dakota State University, 2013) Dorcinvil, RonaldThe use of oats for human consumption is increasing every day due to the health benefits of oat products. With the objective to study relationships among factors affecting oat grain quality, two Recombinant Inbred Lines (RIL) mapping populations (`ND030299' x `ND991151' and `ND030299' x `Souris') have been used in this study. The two populations with their parents and three check cultivars were evaluated in a square lattice design in 2008 and 2009 at two North Dakota locations. Data were recorded on the following agronomic traits: grain yield, test weight, 1000 kernel weight, thin kernels, heading date, and plant height. Chemical and grain physical analysis were performed for â-glucan, oil, and groat percentage. A total of 4975 SNP markers were assessed on the two populations using a 32-bead chip platform developed by Illumina. QTLs for agronomic and grain physical traits were mapped and characterized in the two populations using Windows QTL Cartographer. Grain yield was positively correlated with test weight, thin kernels, plant height, â-glucan content, and associated negatively with 1000 kernel weight. Thirty linkage groups using 1168 polymorphic markers were formed for population 05021, whereas population 05026 comprised 33 linkage groups using 1024 polymorphic markers. The 30 linkage groups of population 05021 contained from 3 to 62 markers, and varied in size from 15.8 to 225.3 cM for a total map size of 2601.7 cM. The 33 linkage groups of population 05026 comprised from 2 to 42 markers, and varied in size from 2.3 to 143.2 cM for a total map size of 1174.2 cM. Nineteen genomic regions on 14 linkage groups were significantly associated with agronomic and grain chemical traits in the population 05021. Fourteen genomic regions on 12 linkage groups were identified for agronomic traits in the population 05026. The same genomic region on LG 05021-16 was associated with thin kernels, test weight, 1000 kernel weight, and oil content. LG 05026-19 loci, from position 23.7 to 47 cM, had strong effects on heading date, plant height, and grain yield. The QTLs consistently detected across environments and between the two populations could serve as starting points for marker-assisted selection.Item Genetic Diversity and Genome-Wide Association Mapping of Agronomic, Disease Resistance, and Quality Traits in Barley Accessions from Ethiopia, Icarda, and the U.S.(North Dakota State University, 2015) Daba, Sintayehu DebebePlant breeding is a dynamic process that incorporates new germplasm to introduce genetic variation. Knowledge gained from genetic diversity studies and identification of potentially useful germplasm is critical for efficiently utilizing these new materials for breeding program. Linkage disequilibrium (LD), diversity, and association mapping analyses in barley (Hordeum vulgare L.) were done using a mapping panel that included Ethiopian landraces, and cultivars and breeding lines from the Ethiopian, ICARDA, and NDSU breeding programs. LD decayed within 10 to 20 cM in the mapping panel and large proportions of unlinked loci were found to have large LD estimates, indicating that factors other than linkage contributed to LD. Diversity analyses using phenotypic data and molecular markers indicated that the mapping panel was highly structured according to spike row-type, geographic origin, and breeding history; thus, accounting for population structure and familial relatedness was crucial for association analyses. Comparison of the four models (Naïve, P, K, and P+K) indicated that the P+K model is the best model for the current mapping panel. The genome-wide association study (GWAS) identified 94 QTL for 14 agronomic and disease resistance traits; and 145 QTL for 11 malt and grain quality traits. Association mapping of agronomic and disease resistance traits identified six photoperiod related loci (Ppd_H1, HvFT4, HvGI, HvFT2, HvCO2, and HvCO1) and one vernalization-related locus (VRN-H1) for days to heading, one semi-dwarf locus (sdw3) for plant height, and four resistance loci (Rrs1, Rrs15, rpt.k and rpt.r). The largest number of QTL for malt and grain quality traits was detected in chromosome 5H, followed by chromosome 7H. QTL for malt and grain quality traits were mapped near the Hor1, Hor2, Upg2, Dor4, Ltp1, Amy1, and Amy2 loci. Several unique QTL were identified in the ICARDA and NDSU accessions, with the NDSU materials having the favorable marker genotypes. These regions could be useful to the Ethiopian breeding program for improving malt quality. The current study indicated that association mapping provided useful tool to identify QTL for several traits simultaneously. Because the QTL had small effect and distributed across the genome, genome selection may be warranted for improving these traits.Item Genetics of Drought Tolerance in Hard Red Spring Wheat in the Northern United States of America(North Dakota State University, 2017) Al Rabbi, S. M. HisamDrought affects about 50% of wheat (Triticum aestivum L.) globally and is a major threat for sustainable wheat production. This dissertation discusses three studies carried out to dissect drought tolerance in hard red spring wheat (HRSW) in the northern United States of America (USA). The first study used a bi-parental mapping approach with a recombinant inbred line (RIL) population developed from a cross between a drought-tolerant cultivar, ‘Reeder’ (PI613586), and a drought-susceptible cultivar, ‘Albany.’ The RILs were evaluated in different locations in North Dakota (ND) over three years. Data were collected on plant height (PH), days to heading (DH), yield (YLD), test weight (TW), and thousand kernel weight (TKW). A high-density genetic map was constructed using Illumina’s Infinium 90K single nucleotide polymorphism (SNP) genotypic data. In the second study, the same RIL population was evaluated for PH, DH, YLD, TKW, number of tillers (TIL), number of spikes (SPK), canopy dry weight (CDW), and wilting score (WS) in the greenhouse rather than the field. The third study used association mapping (AM) approach with an association panel comprised of ≥350 genotypes which were evaluated for PH, DH, YLD, TW, and TKW in different locations in ND. The bi-parental mapping study identified a total of 38 QTL each in the field and the greenhouse experiment. Among those, a total of six and eight QTL respectively, were identified under drought conditions. A total of five and eight QTL respectively were identified for both control and drought conditions. Besides this, the bi-parental mapping study identified six QTL for Drought susceptibility index (DSI) in the greenhouse experiment. In contrast, AM study identified a total of 69 QTL where 16 QTL were identified under drought conditions and 50 QTL were identified under both drought and control conditions. Further, 12 genomic regions associated with drought tolerance were repeated across two and sometimes all three studies. Ten novel QTL on chromosomes 2D, 3D, 4A, 4D, 5B, 7A, and 7B were identified. The QTL identified exclusively under drought conditions, under both drought and normal conditions and for DSI could be helpful for developing drought-tolerant wheat cultivars through marker-assisted selection (MAS).Item Genetics of End-Use Quality Characteristics in Spring Wheat (Triticum Aestivum L.)(North Dakota State University, 2017) Mohajeri Naraghi, SepehrWheat (Triticum aestivum L.) is one of the most important crops consumed by humans around the world. Improving the end-use quality traits is one of the major objectives in wheat breeding programs. However, little is known about the genomic regions controlling these traits. Discovering the genetic architecture underlying important end-use quality traits can accelerate breeding via marker-assisted selection (MAS) in addition to providing genomic and biological information. Therefore, for this dissertation, a quantitative trait loci (QTL) mapping and a genome-wide association study (GWAS) were conducted to identify QTL for 16 end-use quality traits, including the grain protein content, flour extraction rate, eight mixograph-related parameters, and six baking-related properties. A population of 127 recombinant inbred lines (RILs) from a cross between Glenn (PI-639273) and Traverse (PI-642780) was developed for the QTL mapping study, and an association panel of 355 elite spring wheat lines was used for the GWAS study. The phenotyping of these traits was performed in nine environments in North Dakota, USA, over a three-year period. The genotyping for both the RIL population and association panel was conducted using the wheat Illumina iSelect 90K SNP assay. A total of 76 additive QTL (A-QTL) and 73 digenic epistatic QTL (DE-QTL) were found for the 16 end-use quality traits in the QTL mapping study. These QTL were distributed across all wheat chromosomes except chromosome 3D. Overall, 12 stable major A-QTL and three stable DE-QTL were identified for the end-use quality traits in the QTL mapping study, indicating that both A-QTL and DE-QTL played an important role in controlling end-use quality traits. In addition to the QTL mapping study, a total of 91 significant marker–trait associations (MTA) were identified for the end-use quality traits in the GWAS study. These MTA were distributed across all wheat chromosomes except chromosome 4D. Overall, the current study identified multiple novel stable QTL that could be used in MAS for end-use quality trait improvement in wheat breeding programs.Item Genome-Wide Association Mapping of Host Resistance to Stem Rust, Leaf Rust, Tan Spot, and Septoria Nodorum Blotch in Cultivated Emmer Wheat(North Dakota State University, 2015) Sun, QunCultivated emmer wheat (Triticum turgidum ssp. dicoccum) is a good source of genes for resistance to several major diseases of wheat. The objectives of this study were to use genome-wide association analysis to detect genomic regions in cultivated emmer germplasm harboring novel resistance genes to four wheat diseases: stem rust, leaf rust, tan spot, and Septoria nodorum blotch (SNB). A natural population including 180 cultivated emmer accessions with a high level of geographic diversity was assembled as the association-mapping panel. This cultivated emmer panel was evaluated phenotypically by scoring reactions to stem rust, leaf rust, tan spot, and SNB and was genotyped using a 9K SNP Infinium array. After filtering for missing data points and minor allele frequency (MAF), 4,134 SNPs were used for association analysis using 178 emmer accessions. Based on principle component (PC) analysis, five subpopulations strongly associated with geographic origins were suggested by the first three PCs. Genome-wide association analysis revealed that 222, 42, 146, and 42 SNPs were significantly associated with resistance to stem rust, leaf rust, tan spot, and SNB, respectively, at the significant level of 1 percentile. Among the significant SNPs at the significant level of 0.1 percentile, ten, one, nine, and one co-located with known genes or QTL associated with resistance to the four diseases, respectively. The remaining significant SNPs were located in the genomic regions where no known resistance genes have been identified for the four diseases. This evidence suggests that some of the emmer wheat accessions carry novel genes conferring resistance to the four diseases. Additionally, 14, three, eight, and five LD blocks harboring at least one significant SNP were identified and might harbor putative QTL related to resistance to the four diseases, respectively. These studies provide information about the genomic regions in cultivated emmer that are associated with resistance to stem rust, leaf rust, tan spot, and SNB. Results from these studies provide guidance for selecting emmer accessions when decisions are being made about the parents that will be used for the development of new resistant germplasm and mapping populations for identifying novel genes conferring resistance to major wheat diseases.Item Genomic Analysis of Domestication-Related Traits and Stem Rust Resistance in Tetraploid Wheat(North Dakota State University, 2017) Saini, JyotiModern durum and common wheat cultivars were developed from ancient wheat ancestors by natural and artificial selection of agronomic and domestication traits, which ultimatey decreased their genetic diversity and made them more susceptible to various biotic and abiotic stresses. At present, new sources of resistance need to be introgressed into future wheat cultivars to combat the effect of the disease stem rust caused by the biotrophic fungal pathogen Puccinia graminis f.sp. tritici (Pgt). In this dissertation, I first analyzed the domestication-related traits in a tetraploid recombinant inbred line (RIL) population developed from a cross between the durum wheat line Rusty and the cultivated emmer accession PI 193883 (referred to as the RP883 population). Second, the RP883 population and a double haploid (DH) population (referred to as the LP749 population) derived from a cross between the durum cultivar Lebsock and the Triticum. turgidium ssp. carthlicum accession PI 94749, and nine durum wheat cultivars were screened with Pgt races TMLKC, TTKSK, TRTTF, and TTTTF. Domestication-related trait analysis in the RP883 population showed vernalization (Vrn-A1) and domestication (Q) genes had a pleiotrophic effect on spike length, spikelet per spike, spike compactness, and threshability. Additionally, an interaction and dosage effect of three free-threshing trait governing loci, teneacious glume Tg2A and Tg2B, and q, revealed that mutation in all three loci are required to attain complete free threshability. The stem rust analysis done in the RP883 population showed two Sr gene regions conferring resistance against TMLKC, TTKSK, and TRTTF: one novel gene region on chromosome 2BL (Sr883) and likely a new allele or gene residing in close proximity to the Sr13 gene on 6AL. The second stem rust study using the LP749 population and nine durum wheat cultivars showed that most likely the U.S. durum germplasm carries the four major Sr genes, Sr7a (4AL), Sr8155B1 (6AS), Sr13 (6AL), and likely Sr9e (2BL) against TTKSK, TRTTF, and TTTTF. In conclusion, results obtained from this domestication study provide knowledge about different stages in wheat evolution. Both stem rust studies revealed genetic diversity in the tetraploid wheat gene pool and indicate their utility in future breeding programs.
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