Elias M. Elias - Thesis Committee

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Analysis and Identification of QTL for Resistance to Sclerotinia Sclerotiorum in Pea (Pisum sativum L.)
(North Dakota State University, 2018) Ashtari Mahini, Rahil
White mold caused by Sclerotinia sclerotiorumi s one of the most devastating diseases infecting field pea (Pisum sativum L.) which causes severe yield loss worldwide. Population 17 (Lifter/ PI240515), and Population 19 (PI169603/ Medora) were developed by single seed descent and screened by greenhouse evaluation and detached stem assay to identify potential sources of white mold resistance. Twenty-two partial resistant inbred lines were identified with short internode which met at least two resistance criteria based on lesion expansion inhibition (LEI) and nodal transmission inhibition (NTI). To find SNPs (single nucleotide polymorphism) responsible for white mold resistance, Populations 17 and 19 were genotyped using GBS (genotyping by sequencing) methodology and analyzed with the GBS-SNP-CROP pipeline. Linkage maps were constructed for each population and a composite map based on shared SNPs between the two populations was also generated. Nineteen QTL were identified as contributing to resistance to white mold. Seventeen were associated with LEI and two were associated with NTI. The QTL responsible for lesion expansion on LG VII were duplicated in the short internode subset of both populations. Partially resistant inbred lines and QTL responsible for white mold resistance identified in this study can be useful as resources for resistance to S. sclerotiorum in further experiments aimed at developing resistant cultivars.
Association Studies on Pre-Germination Flooding Tolerance and Cell Wall Components Related to Plant Architecture in Dry Bean
(North Dakota State University, 2018) Walter, Katelynn
Dry bean breeding programs have made significant advances in combating both abiotic and biotic stresses as well as improving plant architectural traits via selective breeding. Flooding can cause complete crop loss in dry bean. On the other hand, breeding for an upright architecture in dry bean has been a breeding target in several programs. However, the stem cell wall components underlying this change have yet to be studied. This research focused on analyzing the cell wall components that might be involved in dry bean architecture as well as pre-germination flooding tolerance in dry bean. For the plant architecture study, two significant genomic regions were identified on Pv07 and Pv08 associated with lignin accumulation in dry bean. For the pre-germination flooding study, one unpigmented seed coat genotype (Verano) and three pigmented seed coat genotypes (Indeterminate Jamaica Red, Durango, and Midnight) had germination rates similar to that of the tolerant check.
Rust Resistance in the Guatemalan Climbing Bean Germplasm Collection
(North Dakota State University, 2017) Montejo Domínguez, Luz de Maria Albertina
Common bean is the main source of protein, fiber, and iron for Guatemalan's poorest households; however, bean rust can cause up to 100% yield losses. There is limited information about bean rust in Guatemala, especially at mid-altitude highlands. During 2015, 23 bean rust samples were collected in the Western Guatemalan Highlands and 17 isolates where characterized, as a result, races 63-1 and 31-1 were identified. Those were used to evaluate rust resistance by using 372 Guatemalan climbing beans. In total, 82% of accessions were resistant to race 63-1, 86% to race 31-1, and 90% to race 20-3. Based on GWAS results (78,754 SNPs) the Pv02 (38.13 Mb-38.22Mb) and Pv04 (379 kb) regions were associated with resistance to race 20-3. The Pv10 (10.71-10.68 Mb and 11.09 Mb) and Pv04 (1.42 MB) regions control resistance to race 63-1. And, the Pv04 (39.28 Mb) and Pv02 (35.92 Mb) control resistance to race 31-1.
Delayed Harvest Affects Quality of Durum Wheat
(North Dakota State University, 2017) Cabas-Lühmann, Patricia Alejandra
Harvest can be delayed for many reasons. This research was conducted to determine the effect of delayed harvest on grain and semolina quality of durum wheat (Triticum turgidum L. ssp. durum [Desf.] Husn.). Twelve durum cultivars were planted in eight-row plots with four replicates at three environments. Two rows were harvested at four harvest times that were spaced about one week apart. The trend for all cultivars was for an increase in percent of large kernels, kernel brightness, 1000-kernel weight, and semolina gluten index with delayed harvest, while grain yield, test weight, kernel vitreousness, falling number, grain yellow pigment, and semolina yellowness and wet gluten content generally decreased. At all environments ‘Carpio’ tended to have high yields and ‘Strongfield’ low yields. ‘Carpio’ and ‘Joppa’ had the highest yellow pigment content and very strong gluten. In conclusion, grain and semolina quality generally declined with delayed harvest but varied with cultivar.
Validation of Molecular Markers Associated with Grain Cadmium in Durum Wheat (Triticum turgidum L. var. durum Desf.)
(North Dakota State University, 2016) Salsman, Evan Lee
Durum wheat is capable of accumulating cadmium, a toxic heavy metal, in the grain at levels that have been deemed unsafe. Previous studies have identified genetic variation in durum wheat that can be exploited to create low Cd cultivars. In this study, six KASP markers were validated on 4,178 durum wheat samples from preliminary and advanced yield trials grown in 2013 and 2014 at Langdon, Minot, and Williston, North Dakota. One marker on chromosome 5B was polymorphic in all crosses between high and low Cd parents and had r² values ranging from 0.38-0.85. Two other markers on the same chromosome predicted similar levels of variation in many trials; however these were not polymorphic in all populations. Two markers linked to the grain Cd locus on chromosome 5B are suitable for marker assisted selection due to the more widely shared polymorphism of one and the closer linkage distance of the other.
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, Marina
Genetic 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.
Molecular Mapping of Fusarium Head Blight Resistance in Two Adapted Spring Wheat Cultivars
(North Dakota State University, 2015) ElDoliefy, Ahmed ElFatih Amin
Releasing bread wheat (Triticum aestivum) cultivars with resistance to Fusarium head blight (FHB) disease can be endangered by narrowing the variation in genetic sources. However, resistance to FHB rely on five different types. FHB resistance types I, II, III, IV and V were assessed in field and greenhouse under multiple locations and years experiment’s combination. In our study, the genetic of FHB resistance in two widely cultivated hard red spring wheat varieties (‘Glenn’ and ‘Parshall’) were dissected. The specific objectives of the study were to generate recombinant inbred lines (RIL) populations, phenotypic assessment for FHB resistance, different informative genotypic marker data, genetic map, and finally QTL analysis. For Glenn/MN00216-4 (GM) population, 112 RIL were developed; while for Parshall/Reeder (PR) population, 110 RIL were developed. The RIL, checks and the two parents were evaluated for five FHBrelated and one agronomic-related traits over two to six environments in North Dakota, Minnesota, and South Dakota. Two genetic maps were developed covering 2,229 cM of length using 645 DArT markers for GM population, and 470.4 cM length using 154 DArT/SNP combined markers for PR population. Composite interval mapping identified 37 QTL for the GM population, and 10 QTL for the PR population. Results showed that Glenn lacks the major consistent (Fhb1 and Fhb5A) QTL from the Chinese source Sumai3, while acquired (Fhb2). Parshall proved to be domestic with no exotic resistance background, though it acquired similar genomic regions to Fhb2 of Sumai3. PR genome contains five major QTL including three novel QTL with multiple FHB resistance and two with stable effect (1AS and 4BL) across at least two environments. Along with these previously identified QTL for FHB resistance, in both populations, new QTL were also identified such as Fhb-1B1L.c and 7D1S.b in Glenn, and Fhb.5AL, 7AS and 4BL in Parshall. In conclusion, our study added to the wheat genome, two genetic maps, new QTL for FHB resistance and two germplasms with new recombination for QTL and/or resistance sources. Finally, Glenn and Parshall can be of great importance if implemented in wheat enhancement and molecular assisted breeding programs nationally and internationally.
Uncovering the Genetic Basis and Characters Association of Wheat Spike-Related, Agronomic and Quality Traits
(North Dakota State University, 2014) Echeverry-Solarte, Morgan
Modern wheat (Triticum aestivum L.) cultivars are characterized by having spikes with fusiform architecture and rachis nodes with one spikelet. However, genotypes with supernumerary spikelets (SS) in which rachis nodes have more than one spikelet exist in nature. Although this may be a promising trait that increases yield components, detailed knowledge about the molecular basis of SS trait and their influence on other wheat traits is still lacking. In the present study, a population of 163 recombinant inbred lines (RILs) derived from an elite line and an exotic line with SS was used to identify QTL for SS and other wheat traits. The RILs, seven checks and the two parents were evaluated for seven SS-related, 10 spike-related, 10 agronomic, and eight quality traits over four to six environments in North Dakota. A genetic map of 3,114.2 cM of length with an average distance of 4.6 cM between any two marker loci was developed using 159 RIL and 939 DArT markers. Composite interval mapping identified 221 QTL, out of which 29% were consistent QTL and 19% were major QTL. Most of the QTL were located on the B-genome (44%) followed by the A-genome (37%) and D-genome (19%). The exotic parent with SS contributed 48% of alleles that increased phenotypic values of the traits suggesting the possibility of enriching the breeding germplasm with genes from this genotype. Seven consistent QTL with epistatic interaction were associated to the SS. QSS.ndsu-2D, a major QTL for SS, was co-located in a cluster of QTL on 2DS demonstrating either pleiotropic effect or closely linkage with 19 QTL for other wheat traits. Similarly, a major QTL associated with glume pubescences (QPP.ndsu-1A.1) was co-located on 1AS with seven QTL for other wheat traits. Major and consistent QTL are targets for further marker assisted selection in wheat breeding programs and/or for research projects aiming of gene cloning.
Unraveling the Genetics of Seed Dormancy in Barley Using Genome-Wide Association and Biparental Mapping
(North Dakota State University, 2013) Correa-Morales, Ana Maria
Seed dormancy is the delay or inability of viable seeds to germinate under favorable conditions. The differential expression of dormancy levels in barley (Hordeum vulgare L.) seeds impacts malt quality. While dormant genotypes are required to avoid the incidence of preharvest-sprouting, genotypes with low dormancy are needed for uniform germination of seeds during malting. The objective of this study was to determine the genetic basis underlying seed dormancy in spring barley using genome-wide association mapping (AM) and linkage mapping. A panel of 3,072 elite U.S. spring barley breeding lines from eight breeding programs participating in the USDA-NIFA Barley Coordinated Agricultural Project and 193 F1-derived doubled-haploid lines from the cross `Stander'/ `Robust' were used to map QTL controlling seed dormancy. The AM panel and the doubled-haploid population were genotyped with SNP markers using the Illumina Golden Gate assay. Four mixed linear models that controlled population structure and kinship were used for the AM analyses, while composite interval mapping was used for the analysis of the biparental population. Our results confirmed the existence of marker-trait associations delineating two QTL regions in the long arm of chromosome 5H (5HL) using the AM panel, and a large effect QTL in the same region using the biparental population. The locations and effects of these marker-trait associations are congruent with previously mapped QTL for seed dormancy and demonstrate the two mapping methods effectively targeted the same genetic regions on the barley genome and provide insights about the genetics of seed dormancy.
Total Yellow Pigment Content and Oxidative Stress Level during Kernel Development
(North Dakota State University, 2013) Dobrydina, Marina N.
The focus of this research was to determine the effects of cultivar and environment on levels of total yellow pigment content and oxidative stress during grain development and in semolina and pasta. Lipoxygenase activity increased just before and declined after physiological maturity, while change in malondialdehyde content in the kernel mirrored that of yellow pigment and declined with maturity. After grain reached physiological maturity, levels of lipoxygenase activity, malondialdehyde content and yellow pigment content per kernel were lowest in 2011, while polyphenol oxidase activity was lowest in 2010. Lipoxygenase activity and yellow pigment content decreased after milling and processing, whereas malondialdehyde content decreased after milling but increased with processing. No lipoxygenase activity was detected after processing. Stereomicroscopy and scanning electron microscopy were used to observe anatomical and morphological changes that occurred as durum wheat caryopsis progressed from anthesis to final desiccation.
Genetic and Physiological Relationships between Oat Grain Quality Components
(North Dakota State University, 2013) Dorcinvil, Ronald
The 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.
Identification of Quantitative Trait Loci Associated with a Low Cadmium Uptake Gene in Durum Wheat (Triticum Turgidum L. Var. Durum)
(North Dakota State University, 2013) AbuHammad, Wesam Ali
The main objective of durum wheat breeding is to identify lines that are low in Cadmium accumulation by using linkage mapping. 178 recombinant inbred lines (RILs) derived from across between Grenora × Haurani were used to identify QTL for Cadmium (Cd) tolerance. A total of 1,132 polymorphic loci (1,111 SNP and 21SSR loci) were used for linkage map analysis. Among these, 330 (29 percent) markers were successfully integrated into the linkage maps at a LOD score of 3.0. The linkage map had a total genetic distance of 720.2 cM with an average distance of 2.2 cM between adjacent markers distributed on 14 chromosomes. Quantitative trait loci analysis was conducted using composite interval mapping (CIM). A Single putative QTL associated with Cd uptake was detected on Chromosome 5B. This QTL increased Cd uptake by the presence of alleles from Grenora. The additive effect of the Grenora allele was 0.02 mg/kg. The variation in Cd accumulation explained by this QTL (r2) was 54.3 percent. Association mapping was also used to analyze two durum wheat collections consisting of advanced breeding lines from the North Dakota wheat breeding program to discover markers associated with the amount of Cd accumulated in the grains. For the 2009 collection, one major QTL that explains 3 percent of phenotypic variation was identified on Chromosome 2B at 7.25 cM which could cosegregate with a height locus identified earlier. For the 2010 collection, one QTL that explains 34 percent of phenotypic variation was identified on Chromosome 5B at 165.7cM and one other at 178.3cM that explains 27 percent of phenotypic variation. Because of the complexity of Cd accumulation in wheat grains, the identification of additional QTL will require a better coverage of markers and a larger collection of genotypes. This will help breeding for low Cd using MAS.
QTL Analysis for Fusarium Head Blight Resistance in Tunisian-Derived Durum Wheat Populations
(North Dakota State University, 2014) Pirseyedi, Seyed Mostafa
Durum (2n=4x=28; AABB) wheat is the grain of choice for the production of high-quality pasta products. Fusarium spp. are causal pathogens for Fusarium Head Blight (FHB). Limited host resistance to this disease exists among adapated durum cultivars. The use of Tunisian-derived durum lines for integration of FHB resistance in cultivars was evaluated. The genetic characterization of FHB resistance was evaluated, and markers assosciated with FHB resistance are presented in two populations. Two backcross inbred line (BIL) populations derived from cross between a resistant durum genotype `Tunisian 108' and susceptible durum wheat cultivars `Ben' and `Lebsock' were screened to identify QTL for FHB resistance. Analysis of variance showed significant effect of genotypes on FHB severity and incidence despite high level of interaction between environment and genotypes. A total of 329 and 331 DArT and microsatellite markers covered a distance of 1887.6 and 1748 cM in two populations respectively. Composite interval mapping using two linkage maps and the phenotypic data revealed 11 different FHB resistance QTL on seven different chromosomes (1A, 1B, 2B, 3B, 5A, 5B, and 7B) in Tunisian/Ben derived population and 15 different FHB resistant QTL on seven different chromosomes (1A, 1B, 3A, 3B, 4A, 5A, and 6B) in population derived from cross between Tunisian/Lebsock. At least two novel QTL were identified on chromosome 2B (Qfhb.ndsu-2B) 4A (Qfhs.ndsu-4A) in Tunisian/Ben//Ben and Tunisian/Lebsock//Lebsock population respectively. Location of the two FHB resistance QTL on chromosome 1B and two QTL on 5A were identical in both populations. Owing to cumulative effects of resistance QTL, high level of transgressive segregation was observed in both populations. Our finding revealed an alternative tetraploid FHB resistance source from Tunisian genomic background that can be utilized with associated markers for wheat geremplasm enhancement.
Comparative Population Genetics of Fusarium Graminearum and Novel Sources of Resistance to Fusarium Head Blight in Spring Wheat
(North Dakota State University, 2013) Puri, Krishna Datta
Fusarium graminearum is the major causal agent of Fusarium head blight (FHB) in cereal crops. The fungus produces several types of trichothecenes [Deoxynivalenol (DON) and its acetylated derivatives, 3-acetyldeoxynivalenol (3ADON) and 15-acetyldeoxynivalenol (15ADON), and nivalenol (NIV)]. Characterization of 123 isolates collected during 1980 to 2000 (old collection), and 43 isolates collected in 2008 (new collection) from North Dakota revealed that 15ADON producing isolates were predominant (98%) in the old collection while the 3ADON producing isolates accounted for 43% in the new collection. Further, evaluation showed that the 3ADON isolates caused a higher disease severity and accumulated more DON in spring wheat than the 15ADON isolates. The 3ADON also exhibited higher DON in rice culture, and produced more spores on agar media. Population genetic analyses revealed a significant genetic differentiation between the two populations. To elucidate the transcriptomic differences between the two populations in vitro and in planta, RNA-sequencing was used. The in vitro gene expression comparison identified 479 up- and 801 down- regulated genes in the 3ADON population compared to 15ADON population. The in planta pair-wise comparisons between the two populations revealed 185, 89, and 62 unique genes to 3ADON at 48, 96 and 144 hours after inoculation (HAI), respectively. In a different study, population genetic analysis was conducted on 160 isolates collected in 2008 and 2009 from a FHB disease nursery located in China. All isolates analyzed were F. asiaticum except one (F. avenaceum). Of the 159 isolates, 79% were NIV producing, 18% were 15ADON and 3% were 3ADON. The two populations grouped based on year of collection exhibited low genetic differentiation (Fst = 0.032). To identify new sources of FHB resistance, 71 wheat accessions of diverse origins were re-evaluated for FHB severity and haplotyped using seventeen DNA markers associated with known resistance quantitative trait loci (QTL). Twenty two accessions had a haplotype different from all known sources used, suggesting that they may carry novel loci for FHB resistance. In conclusion, the information obtained in this study could have an impact on development of effective disease management measures and on improvement of FHB resistance in wheat.
Development and Characterization of Wheat Germplasm for Resistance to Stem Rust UG99 in Wheat
(North Dakota State University, 2013) Zhang, Qijun
World 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.
Developing a DNA Fingerprint for Midwest Six-rowed Malting Barley
(North Dakota State University, 2012) Lewis, Magan Friskop
The 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.
Whole-Wheat Flour Milling and the Effect of Durum Genotypes and Traits on Whole-Wheat Pasta Quality
(North Dakota State University, 2017) Deng, Lingzhu
An ultra-centrifugal mill was evaluated by determining the effect of mill configuration and seed conditioning on particle size distribution and quality of whole-wheat (WW) flour. Ultra-centrifugal mill configured with rotor speed of 12,000 rpm, screen aperture of 250 μm, and seed conditioning moisture of 9% resulted in a fine WW flour where 82% of particles were <150 μm, starch damage was 5.9%, and flour temperature was below 35°C. The single-pass and multi-pass milling systems were evaluated by comparing the quality of WW flour and the subsequent WW spaghetti they produced. Two single-pass mill configurations for an ultra-centrifugal mill were used (fine grind: 15,000 rpm with 250 μm mill screen aperture and coarse grind: 12,000 rpm with 1,000 μm mill screen aperture) to direct grind durum grain or to regrind millstreams from roller milling to make WW flour and WW spaghetti. Particle size, starch damage, and pasting properties were similar for direct fine grind WW flour and multi-pass reconstituted flour:fine bran blend and for direct coarse grind WW flour and multi-pass reconstituted semolina:coarse bran blend. Semolna:fine bran or semolina:coarse bran blends made spaghetti with high cooked firmness, while spaghetti made from direct coarse grind or from semolina:fine bran or coarse bran blends had low cooking loss. Nineteen durum wheat (Triticum turgidum L. var. durum) cultivars and 17 breeding lines grown at 19 environments in North Dakota were evaluated for physical and cooking qualities of WW and traditional spaghetti. Of the 36 genotypes evaluated, 21 and 3 genotypes produced good and poor qualities of WW and traditional spaghettis, respectively, while other 12 genotypes produced good traditional spaghetti but produced poor quality WW spaghetti. These data indicate the need to select genotypes specifically for their WW pasta quality. Raw material traits (grain, semolina and WW flour characteristics) were evaluated to identify raw material traits capable of predicting WW spaghetti quality. Grain protein content had significant positive correlation with cooking quality of WW spaghetti. Stepwise multiple regressions showed grain protein content and mixogram break-time and wet gluten were the predominant characteristics in predicting cooking quality of WW spaghetti.
Genetics of End-Use Quality Characteristics in Spring Wheat (Triticum Aestivum L.)
(North Dakota State University, 2017) Mohajeri Naraghi, Sepehr
Wheat (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.
Genetic Characterization of Dormancy in Durum Wheat
(North Dakota State University, 2012) Dilawari, Mridull
Two populations derived by crossing LDN x LDN Dic-3A (Population I) and LDN x LDN Dic-3B (Population II) were genetically characterized for the seed dormancy present on chromosome 3A and 3B of durum wheat. The genes for seed dormancy in these two populations were contributed by the wild parent T. dicoccoides. Although the populations showed transgressive segregants for both dormant as well as nondormant parent, the populations were similar to the dormant parent at Langdon and Prosper 2006 field locations for Population I and at Langdon 2007 and Autumn greenhouse season for Population II. Genotypic and phenotypic analysis over the combined populations showed an environmental effect on expression of the trait. Different QTL were identified for both field and greenhouse season for the population derived from the cross between LDN x LDN Dic-3A. Five QTL for seed dormancy were identified on chromosome 3A for the QTL analysis performed over combined field locations. One QTL ranging between marker interval Xcfa2193 and Xcfd2a was consistently present for the 30 day period of seed germination and was also found to be linked to red grain color trait. The QTL analysis performed on the population derived from the cross between LDN x LDN Dic-3B identified only one major QTL on the long arm of chromosome 3B between the marker interval Xbarc84 and Xwmc291. This QTL was consistently present for all the field and spring greenhouse season for the seed germination period of 30 days. The QTL x E effect was also observed for this QTL, however it was very small.
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. Hisam
Drought 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).

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