Plant Sciences Doctoral Work

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Evaluation of Pea Protein and Modified Pea Protein as Egg Replacers
(North Dakota State University, 2012) Hoang, Hieu Duy
Native yellow pea (Pisum sativum) protein isolates (PPIs) showed good foaming and emulsifying properties but a poor gelling characteristic. However, this can be corrected by Transglutaminase (TGase) treatment. PPIs were obtained using alkaline extraction method in which extracting pH, precipitating pH, flour–to–water ratio, and extraction time were optimized to obtain maximum yields and least change in protein functionalities. Extraction pH of 10.0, precipitating pH of 4.3, flour–to–water ratio of 1:6, and 30 minute extraction time were found to be optimum values for pea protein extraction. SDS–PAGE gels showed that the PPI had a very similar protein molecular weight profile as its original flour. TGase treatment was applied on PPIs at different pH levels from 4.3 to 7.0. The SDS–PAGE and RVA tests showed that treatment at pH 6.0 provided the best overall functionality. Large molecular weight (MW) proteins (~ 90,000 Da) and medium MW proteins (~50,000 – 80,000 Da) were the main substrates for TGase catalyzed reaction whereas most low MW the proteins (< 45,000 Da) were not involved. RVA results indicated that treatments at pH 6.0 and 7.0 had the highest viscosities but the treatment at pH 6.0 had better stability and consistency. Functionality tests indicated that modified PPIs possessed a better viscosity profile than the native PPIs but no improvement in gelling capacity and only minor impact on foaming and emulsifying properties. PPIs performance greatly depended on their final pHs. The foaming capacity, foaming stability, and emulsion capacity were significantly improved when the final pH of PPIs was adjusted from 4.3 to 7.0. The overall sensory evaluation results suggested that TGase–treated PPIs and PPIs were not yet able to replace egg in the cake system. Only PPI can replace egg in the cookie system. TGase–treated samples had a lower acceptability due to an “off–taste” and a “strange” flavor. Future work, therefore, should study TGase combined with other treatments to further improve PPIs functionalities. Purification should be integrated into extraction process and other food systems should also be included to extent the scope and role of modified PPIs in food industry.
Identification of Molecular Markers Linked to X-Disease Resistance in Chokecherry
(North Dakota State University, 2012) Wang, Hongxia
X-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.
Early-Season Weed Control in Direct-Seeded Onion (Allium Cepa L.)
(North Dakota State University, 2012) Loken, James Ryan
Onion 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.
Physicochemical Properties of Commercial Gums and their Effects on Processing and Cooking Quality of Nontraditional Pasta
(North Dakota State University, 2012) Sandhu, Gurleen Kaur
Processing characteristics and quality of pasta made from durum flour and semolina and the physicochemical properties of commercial gums and their effects on processing and cooking quality of nontraditional pasta was investigated. An initial experiment was conducted using semolina and durum flour fortified with nontraditional ingredients (soy flour or oat flour, 10% w/w) and xanthan, guar or locust bean gums (2% w/w). A second set of experiments were conducted to determine the effect of commercial source of food gums on their effect on the processing and cooking quality of nontraditional pasta. Proper hydration of nontraditional ingredient blends was more easily achieved with durum flour than semolina. This was attributed to the smaller particle size of durum flour compared to semolina. Nontraditional ingredients tended to over hydrate semolina resulting in large aggregates that adhered to metal surfaces, all of which made mixing and pasta processing difficult. Initially, dough strength was greater with durum flour than with semolina, but semolina had better dough stability over time. Soy and oat flours reduced dough strength. Xanthan and guar gums increased dough stability, particularly with durum flour. Pasta made with durum flour generally had greater cooking loss and lower cooked firmness than pasta made from semolina. Soy and oat flours reduced cooked firmness and increased cooking loss. Guar and locust bean gums did not affect cooking quality of pasta. Xanthan gum increased cooked firmness of pasta. Samples of each gum were obtained from three different commercial vendors. For each food gum, samples varied in bulk density, molecular weight, viscosity in distilled water and the magnitude of effect on dough strength with commercial source. The effect of xanthan, guar and locust gums on hydration, dough strength, and cooking quality was not affected by commercial source. The magnitude of the increase in dough strength caused by xanthan and guar gums varied among their respective commercial sources.
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.
Radiation Hybrid Fine Mapping of Two Fertility-Related Genes: Marking the Path to Wheat Hybrids
(North Dakota State University, 2012) Bassi, Filippo Maria
Over one billion people, more than 1/9th of the global population, are undernourished. Feeding the ever increasing population has to be the most important goal of plant sciences. Since cultivated areas are not likely to increase, I will need to produce more with what is available. This can be summarized in one word: yield. Unfortunately, wheat’s yield is expected to increase only 1.13% by 2019, a prediction that if converted into reality will likely indicate that I failed to cope with the world demographic increase. A new strategy to revolutionize wheat production is required, and some believe that this change might be represented by wheat hybrids. Achieving adequate commercial production of wheat hybrids has the potential to nearly double the yield of one of the world’s most important staple food. The first fundamental step toward this goal is to develop feasible methodologies to sterilize the male part of the complete wheat flowers. Two fertility-related genes are the primary target of this study, namely the species cytoplasm specific on chromosome 1D, and the desynaptic locus on chromosome 3B. This dissertation summarizes the important achievements obtained toward the cloning of the two loci by means of radiation hybrid functional analysis. Radiation hybrid is a technique that employs radiation to create genetic diversity along the targeted chromosome. Chapter 1 explains in details how this methodology can be applied to plants. The use of radiation hybrid mapping permitted creating a comprehensive map of wheat chromosome 3B, as discussed in Chapter 2, and then expanded the mapping information to identify the 2 Mb location of the desynaptic locus desw2, as discussed in Chapter 3. A similar approach on chromosome 1D allowed first to pinpoint the location of the species cytoplasm specific gene to a region of 2 Mb, as discussed in Chapter 4, and then ultimately to find a strong candidate for this locus, as discussed in Chapter 5. Now that the molecular locations of these genes have been unraveled by this study, their sequence can be streamlined into transformation to ultimately produce female wheat plants, and consequently hybrids.
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.
Quantitative Genetic Analysis of 16 Maize Populations Adapted to the Northern U.S. Corn Belt
(North Dakota State University, 2013) Laude, Tonette
Genetic 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]
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.
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.
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.
Characterization of Edible Bean Flours: Properties and Functionality
(North Dakota State University, 2013) Simons, Courtney W.
Consumption of pulses is considered part of a healthy diet. Therefore, the opportunity exists for development of new pulse-based ingredients. However, a better understanding of their properties is necessary. The compositional and functional properties will vary depending on the bean type, their physical form (pre-cooked, raw flour, starch or protein fractionates) and growing location. In this study, edible bean flours (pinto, navy, black and small red) were subjected to extrusion cooking to produce snacks and texturized high-protein flour. The extrudates were studied to determine the effect of extrusion on the physical, physicochemical, chemical, sensory, and digestibility properties. Texturized high-protein flour was used in a bread formulation study. Finally, a preliminary study of location effect on production of grassy compounds, e.g. hexanal and hexanol, in pinto beans was conducted to determine importance of growing environment on flavor development during storage. The results of these studies showed that bean flours generally had excellent extrusion properties (good expansion and texture). However, pre-cooked flours had much lower expansion and textural integrity compared to raw bean flours and starch fractionates. Nutritional content (protein, total starch, fiber and ash) of flours were generally retained after extrusion. Lipids and resistant starch (RS) however were significantly reduced. Significant reduction in RS resulted in snacks having high glycemic index. Extrudates had 20% lower raffinose content suggesting reduced potential for flatulence after extrusion processing. Sensory evaluation of pinto, navy and black bean snacks indicated good overall acceptability. Pinto bean high-starch fraction differed in composition and functionality (viscosity and thermal properties) compared to its raw whole flour and extruded form. Adding 5% texturized pinto bean protein to bread increased its lysine content by 50%; without significantly affecting bread quality. A significant statistical interaction between growing location and storage time on hexanol and hexanal concentrations was observed for pinto beans grown in Forest River, Johnstown and Hatton North Dakota. This Dissertation will help processors understand the potential for beans as a food ingredient. Applications may include use in breads and other baked products, extruded puffed snacks, pasta, and soups. Bean flours can improve nutritional quality and provide unique functionality to food systems.
Mitochondrial Sequence Diversity Among Alloplasmic and Euplasmic Triticum Species
(North Dakota State University, 2013) Noyszewski, Andrzej Krzysztof
Four mitochondrial genomes of Triticum species were sequenced and annotated: 1) (lo) durum mitochondrial genome, which is an alloplasmic line with Triticum longissimum(SS) cytoplasm and T. turgidum (AABB) nucleus, 2) T. longissimum, 3) T. turgidum and 4) T. tauschii (DD). Comparison showed major differences in atp6, nad9, nad6, rps19-p, cob and cox2 genes among all four species. Additionally, species-specific ORFs were also identified. A single nucleotide polymorphism search within known genes showed that the alloplasmic line differs from the two parental lines by six nucleotides in the cox3, mttB, rps2, rps4 and rps13 genes. We were able to recognize mitochondrial heteroplasmy based on single nucleotide variation (SNV) and regions of high SNV density within a given species. Structural differences between T. turgidum, (lo) durum and T. longissimum mitochondrial genomes were observed; however, conserved gene blocks and gene pairs among these species were identified. Three possible recombination events in gene blocks I, V and VI were recognized. We observed differences in the alloplasmic line, compared to its parental lines in: sequence, predicted genes, single nucleotide polymorphism (SNP) and genome structure. These facts support the hypothesis of the accelerated evolution of the mitochondrial genome when transferred into alien nuclear background. We also found that major gene changes recognized here appear to be common among Triticum species. Based on sequence assembly, we report full mitochondrial sequence of T. turgidum. We recognized 40 SNP differences compared to the T. aestivum mitochondrial genome, where 5 SNPs were found in known mitochondrial genes: rps1, rps2, cox3 and ccmFN. The T. longissimum and T. tauschii share highly similar genomes in structure and content, different only at the level of SNVs. A method to establish phylogenetic relationships based on mitochondrial genome sequence is proposed using differences in reference assembly with a common mitochondrial backbone sequence. We confirm conservation of the mitochondrial gene content within Triticum species. These results create background to explore the role of mitochondrial genes in conditioning nuclear cytoplasmic incompatibility in a wide range of Triticum alloplasmic lines and also deepen our understanding of evolutionary relationships that exist in the Triticum genus.
Cloning and Characterization of Meiotic Genes Rec8 and Cdc5 and Subcellular Analysis of Kinetochore Orientation in Wheat
(North Dakota State University, 2013) Ma, Guojia
Meiosis 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.
Selection of Dry Bean Genotypes Adapted for Drought Tolerance in the Northern Great Plains
(North Dakota State University, 2013) Linares, Angela M.
Drought stress is a production constraint that growers face in the Northern Great Plains. This research was conducted to (1) assess the differences in seed yield due to drought within each one of the three most important dry bean market classes grown in the region (pinto, navy, and black), (2) estimate the genetic gain and progress over time due to the use of improved dry bean cultivars from 1981 to 2011, (3) evaluate the `Buster'/SER 22 recombinant inbred line population under drought conditions and identify loci associated with drought tolerance that could be used in Marker Assisted Selection (MAS) in the future. Results showed that, on average, drought stress can reduce seed yield by 35% in North Dakota. Seed yield in black cultivars can be reduced as much as 36% in dryland when compared to irrigated conditions, followed by navy and pinto with 35 and 32% of seed yield reduction, respectively. Data over 26 years showed yield gains of 15, 14, and 11kg ha-1 yr-1 for pinto, black, and navy beans under dryland conditions, respectively, while yield reductions were observed under irrigated conditions. Results will help to design strategic plans toward the genetic improvement of dry beans for the region. On the other hand, quantitative trait loci (QTL) were detected for seed yield, 100-seed weight, days to maturity, days to flower, and leaf temperature. The genetic map had a length of 778.4 cM and was based on 378 single nucleotide polymorphism (SNP) markers. Transgressive segregation was also observed for all phenotypes under study. Some of the QTL identified could be useful for selection purposes under optimal, irrigated, and drought conditions.
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.
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. Abdullah
Maize (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.
Towards the Development of a Gene-Based Eco-Physiology Model for Common Bean: Genotype by Environment Interactions
(North Dakota State University, 2014) Colbert, Raphael Wesly
Genotype 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.
Radiation Hybrid Mapping of Barley Chromosome 3H
(North Dakota State University, 2014) Mazaheri, Mona
Assembly of the barley (Hordeum vulgare L.) genome requires high resolution maps for aligning contig-based physical maps along chromosomes. Genetic maps lack accurate information on the physical position of almost half of the barley genome located in recombination-poor regions. Radiation hybrid (RH) mapping is an alternative approach, which is based on radiation-induced chromosomal deletions. In this study, an RH population for barley chromosome 3H was developed. Genotyping 373 3H-RH lines with 113 markers resulted in an RH map with an average resolution of 2.22 Kb. Compared to an analogous genetic map, the 3H-RH map resolution was 9.53-X higher, reaching to >262.40-X better resolution in the centromeric region. We suggest that RH maps would facilitate assembly of the barley genome. For future RH studies of the barley genome, an optimum genotyping platform, consisting of 400,536 barley-specific repeat junction markers (RJMs), was developed.
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.

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