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Item Identification of Molecular Markers Linked to X-Disease Resistance in Chokecherry(North Dakota State University, 2012) Wang, HongxiaX-disease, caused by phytoplasmas, is one of the destructive diseases in stone fruit trees, causing yield loss and poor fruit quality. So far no effective methods are available to control X-disease. X-disease resistance has been first discovered in chokecherry (Prunus virginiana, 2n=4x=32), which is a native woody species of North America. To identify molecular markers linked to X-disease resistance, simple sequence repeat (SSR) markers were used to construct genetic linkage maps for chokecherry and to identify markers associated with X-disease resistance in chokecherry. In this research, three segregating populations of chokecherry were developed by crossing one X-disease resistant (CL) with three susceptible chokecherry lines (a, c, and d), of which the progenies were 101, 177, and 82, respectively. In order to construct a genetic map for chokecherry, 108 pairs of SSR primers were employed from other Prunus species. Additionally, a set of 246 SSRs were developed from chokecherry sequencing by Roche 454 sequencing technology. A total of 354 pairs of SSR primers were used to screen individuals of all three populations. Two software programs, TetraploidMap and JoinMap, were used to construct linkage map based on single-dose restriction fragments (SDRFs) and two parental linkage maps were generated for each population from both software programs. Bulked segregant analysis (BSA) was applied for identification of X-disease resistance markers. As a result, one SSR marker was found to be linked to the X-disease resistance. The set of 246 chokecherry SSRs was later used to test transferability among another 11 rosaceous species (sour cherry, sweet cherry, wild cherry, peach, apricot, plum, apple, crabapple, pear, june berry, and raspberry). As a result, chokecherry SSR primers can be transferable in Prunus species or other rosaceous species. An average of 63.2% and 58.7% of amplifiable chokecherry primers amplified DNA from cherry and other Prunus species, respectively, while 47.2% of amplifiable chokecherry primers can be transferable to other rosaceous species. The genetic information, including genetic map, disease linked marker, chokecherry sequence, and confirmed transferability of the identified chokecherry SSRs to other species, will benefit the genetic research in Prunus and other rosaceous species.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 Identification of Molecular Markers for Marker-Assisted Selection of Malting Quality and Associated Traits in Barley(North Dakota State University, 2015) Jung, RenataBarley (Hordeum vulgare L.) is one of the most important cereal crops in North Dakota, which ranks second amongst all states for barley production in the United States. Barley is used for the production of malt, which is used for brewing beer. The malting and brewing industries set strict standards for malt quality; yet, determining malt quality of experimental barley lines is very expensive. For this reason, quality is typically determined at the latter stages of the breeding program, resulting in rejection of many genotypes after large investments for agronomic performance, disease resistance, and end-use quality evaluations have occurred. High quality malt cultivars must possess numerous genetically controlled characteristics. This limits the effectiveness of phenotypic selection for malt quality. The use of marker-assisted selection (MAS) may enable breeders to eliminate lines with undesirable traits earlier in the breeding process, reducing costs, and improving genetic gain. In spite of the large number of mapped QTLs, few examples exist in the literature in which QTL analysis and MAS have been applied to the genetic improvement of malting barley. This research was initiated to identify robust marker-trait associations for malting quality, disease resistance, and agronomic traits utilizing genome-wide association mapping of selected NDSU two-rowed lines. Our research successfully identified numerous marker-trait associations for the traits evaluated to be used for MAS to improve the North Dakota State University barley breeding program.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 Quantitative Genetic Analysis of 16 Maize Populations Adapted to the Northern U.S. Corn Belt(North Dakota State University, 2013) Laude, TonetteGenetic diversity is essential for genome sequencing and a key contributor to increase frequency of favorable alleles for maize improvement. The objectives of this study were to determine the genetic components, assess the genetic diversity, and propose the heterotic grouping of a large sample of short-season maize populations based on multiple traits. Sixteen maize populations were included in a diallel mating design that followed Gardner-Eberhart Analysis (GEAN) II to estimate variety (vi) and heterosis (hij) genetic effects. The general combining ability (gi) estimates were also determined and used to classify the populations based on their genetic diversity. Data were generated in partially balanced single lattice experiments across North Dakota (ND) locations in 2010, 2011, and 2012. Combined analyses of variance showed significant differences among genotypes. Heterosis effects explained the most among diallel entries sum of squares for grain yield, while vi effects had greater influence on grain quality traits. The gi effects agreed with the genetic effect that had larger contribution to the total among diallel entries sum of squares for various traits. Three groups were formed based on the genetic distances (GD) of the gi estimates. Four heterotic groups were established based on sij estimates for grain yield. Close correspondence was observed between the groups formed using GD and sij. The heterotic grouping among populations agreed with their genetic background information and heterotic group’s specific and general combining ability (HSGCA) estimates. The EARLYGEM 21 populations having exotic background were assigned to a unique heterotic group. The heterotic groups established among these populations will increase breeding efficiency to improve and develop genetically broad-based populations. Inter-population recurrent selection programs can be employed for population crosses with high grain yield and above average grain quality formed by parental populations belonging to different heterotic groups. Intra-population recurrent selection programs can also be established for the parental populations identified with desirable grain quality traits. These populations will serve as unique germplasm sources of short-season diverse inbred lines to produce the next generation of diverse northern U.S. hybrids. New heterotic patterns have been established as a source of new commercially viable single-cross and population hybrids. [Full abstract in document contains symbols]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 Usefulness of Expired Proprietary (Ex-PVP) Maize (Zea Mays L.) Germplasm for U.S. Northern Breeding Programs(North Dakota State University, 2014) Al Bari, Md. AbdullahMaize (Zea mays L.) inbred lines and hybrids are protected by U.S. Patent and/or Plant Variety Protection Act (PVPA). Protection lasts 20 years and it affects breeding access in a highly confidential and competitive market. This research assessed the usefulness of patent expired short-season maize inbred lines. The study was conducted i) to understand the nature of gene action of a short-season maize breeding sample for agronomy and grain quality traits ii) to identify ex-PVP inbred lines and hybrids as potential breeding sources for short-season maize breeding programs for agronomic, grain quality, and nutritional traits iii) to identify and validate heterotic groups of ex-PVP inbreds and NDSU inbred lines, and iv) to identify desirable top heterotic patterns among ex-PVP, industry testers, and NDSU lines. Three North Carolina Mating Design II (NCII) crosses were made including NDSU lines, ex-PVP lines, and top industry testers in the 2010 North Dakota State University (NDSU) Fargo summer nursery and in the 2010 - 2011 NDSU New Zealand winter nursery. Hybrids were planted across six different ND environments in 2011 and 2012 following partially balanced lattice experimental designs. Combining ability analyses were performed following NCII design. Additive and non-additive genetic variances were important for regulating the expression of most traits with the preponderance of additive genetic variance. Our research identified ex-PVP inbred lines PH207, Q381, PHP02, S8324, PHK76, CR1Ht, PHT77, LH205, LH54, and PHJ40 that could be used as breeding sources to increase mostly grain yield. Most of the inbred lines belong to Stiff Stalk (SS), non-SS, or Lancaster backgrounds, although some belong to both SS/non-SS genetic backgrounds. The top heterotic patterns, from our trials, were represented in the following combinations: SS x non-SS, Iodent x SS, SS x Lancaster, Iodent x Lancaster, and SS/non-SS x SS. Our trials suggest most ex-PVP lines are not useful directly in immediate hybrid production for agronomic and grain quality traits. In such a context, improvements in intellectual property and re-thinking of breeding rights access are encouraged to explore more suitable hybrids for short-season maize breeding programs.Item Towards the Development of a Gene-Based Eco-Physiology Model for Common Bean: Genotype by Environment Interactions(North Dakota State University, 2014) Colbert, Raphael WeslyGenotype by environment interactions (GxE) complicate selection in common bean (Phaseolus vulgaris L.). Crop models can play a valuable role by helping plant breeding programs to better understand GxE. The objectives of this study were to evaluate agronomic, morphological, and phenotypic traits of a recombinant inbred lines population derived from the inter-gene pool cross [Jamapa (Mesoamerican) x Calima (Andean); RIJC] across five environments and generate data to validate a gene based eco-physiology model using an independent population (RISR) from the cross of Stampede x Redhawk. Field trials were conducted across North Dakota, Florida, Puerto Rico, Colombia (Popayan and Palmira), and Nebraska from 2011 to 2013. Resolvable row-column designs and RCBD with three replications and two-row plots were used to evaluate the populations. Analysis of variance was performed using the PROC MIXED procedure of SAS. Genotype main effect and GxE interaction (GGE) biplots were assessed for seed yield components and RISR were compared to the RIJC population. The results suggested different mega-environments depending on the trait of interest. Locations relatively more homogenous can be clustered and North Dakota usually stands alone. The biplots allowed detecting stable genotypes or subsets which were best adapted to mega-environments. Moderate to high narrow-sense heritability estimates (0.55 to 0.87, 0.25 to 0.76 and 0.56 to 0.69 for phenological traits, seed yield components and other agronomic traits, respectively), were observed suggesting various traits such as flowering time, physiological maturity, seeds per pod, plant height, among others, may be used as selection criteria to improve common bean. The populations responded relatively more similar for most of the traits assessed in North Dakota. However means across locations for RIJC differ significantly from RISR grown alone in North Dakota. Seed yield losses for RISR population in drought conditions were 54.3% and 59.0% in 2012 and 2013, respectively. This study will help developing the next generation gene-based crop model along with a high-resolution linkage map and identification of potential candidate genes controlling various traits. Ideal genotypes suited for specific mega-environments can be designed. These new techniques should shorten the cycle needed to develop superior varieties by implementing efficient early generation selection.Item Screening of the USDA Core Collection of Common Bean for Reaction to Halo Blight and Identification of Genomic Regions Associated with Resistance(North Dakota State University, 2016) Ghising, KiranWith only three sources of resistance currently known to race 6 of Pseudomonas syringae pv. phaseolicola (Burkholder) (Psp) which causes halo blight, an important bacterial disease of common bean, there is an urgent need to identify additional sources of resistance. Therefore, 283 accessions of common bean from the USDA-NPGS core collection were evaluated for resistance to race 6 of Psp under greenhouse conditions. Using unifoliate leaf inoculation method, a total of 13% of accessions were resistant. Five of these accessions, PI 201329, PI 309810, PI 310826, PI 319592, and PI 533259, displayed the highest levels of resistance with mean halo blight score of 1.1. Unifoliate vs trifoliate inoculation methods were also evaluated. Significantly higher mean (4.0) and range (1.0-7.0) of halo blight severity was observed at trifoliate stage compared to unifoliate stage, 2.0 and 1.0-2.4, respectively. A significant positive but weak correlation (r2=0.17) of halo blight severity between trifoliate and pod inoculation methods within an individual plant suggests that disease resistance may be controlled by independent genes prevalent at each plant developmental stage. Halo blight severity observed in trifoliate leaves and pods under greenhouse condition was later validated under field condition. Significantly higher mean disease score and range of 4.7 and 2.3-7.1 were reported at pod stage compared to 3.6 and 2.0-6.6, respectively, at trifoliate stage. However, PI 313217 showed consistent resistant reaction across all plant development stages, i.e., unifoliate, trifoliate, and pod, under both field and greenhouse conditions. A significant but weak correlation (r2=0.21) between halo blight severity in trifoliate leaves and pods under field condition confirmed the greenhouse results. To identify genomic regions associated with resistance to race 6 of Psp, genome-wide association mapping study (GWAS) was employed using 197 accessions and 4707 single nucleotide polymorphism (SNP) markers. Three significant regions were identified, of which two novel regions in Pv04 and one in Pv05 controlled for 19% of the phenotypic variation. The significant SNPs could be used in marker assisted selection (MAS) for the improvement of common bean breeding program with focus on resistance to race 6 of Psp.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.