Plant Sciences

Permanent URI for this communityhdl:10365/32425

Research from the Department of Plant Sciences. The department website may be found athttps://www.ag.ndsu.edu/plantsciences

Blizzard Watch is the newsletter for the Department of Plant Sciences and can be found at https://hdl.handle.net/10365/28265

Browse

Now showing 1 - 18 of 18

Ascochyta Rabiei in North Dakota: Characterization of the Secreted Proteome and Population Genetics
(North Dakota State University, 2011) Mittal, Nitin
Chickpea is one of the most important leguminous crops grown in regions of southern Europe, Asia, the Middle East, and the United States. Ascochyta blight, caused by Ascochyta rabiei, is the most important foliar disease of chickpea. In favorable conditions, this disease can destroy the entire chickpea field within a few days. In this project the secreted proteins of Ascochyta rabiei have been characterized through one and two-dimensional polyacrylamide gel electrophoresis. This is the first proteomic study of the A. rabiei secretome, and a standardized technique to study the secreted proteome has been developed. A common set of proteins secreted by this pathogen and two isolates that exhibit the maximum and minimum number of secreted proteins when grown in modified Fries and Czapek Dox media have been identified. Population genetic studies of Ascochyta rabiei populations in North Dakota have been conducted using microsatellites and AFLP markers. Population genetic studies have shown that the ascochyta population in North Dakota has not changed genetically in the years 2005, 2006 and 2007, but the North Dakota population is different from the baseline population from the Pacific Northwest. The ascochyta population in North Dakota is a randomly mating population, as shown by the mating type ratio.
Biotic and Abiotic Factors Affecting the Survival of Listeria Monocytogenes in Prairie Pothole Soils and Sediments
(North Dakota State University, 2017) Dusek, Nicholas Stephen
The diversity-invasion relationship states that more diverse communities are more resistant to invasion. Listeria monocytogenes – a gram-positive facultative anaerobe, soil saprotroph, and opportunistic human pathogen – is capable of surviving in a diverse range of habitats, including soil, and several recent studies have shown that the prevalence of L. monocytogenes in soil increases with proximity to surface water. In addition, L. monocytogenes resides frequently in the guts of ruminants and poultry, creating many opportunities for deposition in soil. However, little work has been done to examine the effects of native soil microbiota on the survival of the pathogen. This thesis builds on previous work by examining microbial community diversity in the prairie pothole ecosystem and how it impacts the survival of L. monocytogenes. Results indicate that survival of L. monocytogenes does not seem to differ greatly as an effect of community diversity.
Characterization and Manipulation of the Wheat B Genome
(North Dakota State University, 2017) Zhang, Wei
Common wheat originated from interspecific hybridization of three diploid ancestors followed by spontaneous chromosome doubling. Aegilops speltoides (genome SS) has been controversially considered a possible candidate for the donor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure. The first aim of this study was to characterize the homology between the wheat B genome and the Ae. speltoides S genome. In this study, meiotic pairing for each of the B-S homoeologous pairs was investigated individually. Noticeable homology between chromosomes 1B and 1S was discovered, but not between other homoeologous B-S pairs. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was detected on the long arm of wheat chromosome 1B. The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome. Evidently, Ae. speltoides was involved in the origin of the wheat B genome, but should not be considered an exclusive donor of this genome. Aegilops speltoides and Thinopyrum elongatum (genome EE), two of diploid relatives of wheat, are considered important sources of novel genes for wheat improvement. However, the development of compensating wheat-alien translocations has been limited by laborious cytological analysis. This study aimed to develop an effective procedure of inducing, recovering, and detecting homoeologous recombination in wheat-alien gene introgression lines. Totally, 112 wheat-Ae. speltoides 2B-2S and 87 wheat-Th. elongatum 2B-2E translocation lines were developed through this procedure. Composite bin maps for chromosome 2B as well as homoeologous chromosomes 2S and 2E were constructed by genotyping the translocations using 90K SNP arrays. In addition, genes for resistance to stem rust, tan spot, and SNB on chromosome 2S were physically mapped and incorporated into the wheat genome. Also, an Ae. speltoides-derived deleterious growth gene was physically mapped to the subtelomeric region of chromosome 2S. In summary, the results of the study led to a large number of 2B-2S and 2B-2E recombinants, physically mapped disease and growth-related genes on chromosome 2S, developed novel molecular markers, and optimized chromosome engineering procedures.
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.
Computational Identification, Phylogenetic and Synteny Analysis of Receptor-Like Kinases “RLK” and Receptor-Like Proteins “RLP” in Legumes
(North Dakota State University, 2018) Restrepo Montoya, Daniel
Legumes are considered the second most important family of crop plants after the grass family based on economic relevance. In recent years, the field of legume genomics has expanded due to advancements in high-throughput sequencing and genotyping technologies. To date, no published comparative genomic analysis explores receptor-like kinases “RLK” and receptor-like proteins “RLP” among legume genomes. Evaluating these RLK and RLP should provide a source of new information because extensive genetic and phenotypic studies have already discovered the diverse roles of RLK and RLP in cell development, disease resistance, and stress responses among other functions. This study demonstrates that a computational logical approach for classifying the RLK/RLP in legumes/non-legumes is statistically well supported and can be used in other plant species. The analysis of RLK/RLP of 7 legumes and 3 non-legume species evaluated suggests that about 2% are RLK and less than 1% of the proteins are RLP. The results suggest a dynamic evolution of RLK and RLP in the legume family. In fact, between 66% to 85% of RLK and 83% to 88% of RLP belong to orthologous clusters among the species evaluated. The remaining RLK and RLP proteins are classified as singletons. The ratio of the pairwise synteny blocks of RLK/RLP among legumes shows a 1:1 relationship. The exception is G. max, which shows an approximately 2:1 ratio due to its recent whole genome duplication (G. max vs. the other six legumes). The other legumes show evidence of a similar proportion of plasma membrane proteins among the legume pairwise synteny blocks.
Development of a Molecular Marker to Track APA G40199 Introgression in Common Bean for Bruchid Resistance
(North Dakota State University, 2018) Mazaheri, Lucy
In common bean (Phaseolus vulgaris), the main seed storage pests are the bruchid beetles. Damage done to the seed by the larvae has a large impact on seed quality and yield. Arcelin (ARC), phytohaemagglutinin (PHA), and α-amylase inhibitor (α-AI) are linked seed storage proteins that form the APA locus on chromosome Pv04 and are associated with resistance. A major breeding objective is to introduce bruchid resistance into common bean from a resistant tepary genotype, G40199, by introgressing the resistant APA locus into susceptible common bean backgrounds. Here we developed a molecular marker that tracks the introgression. A set of PCR primers to the α-amylase inhibitor locus amplified a DNA fragment that showed a 45 base pair insertion in the middle of a lectin Leg_b domain. This enhanced locus characterization and insertion/deletion marker may preclude the need for bruchid resistance screening early in the breeding.
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.
Genetic Investigation of Wild Oat with Acetyl-Coa Carboxylase Gene Sequence Variation
(North Dakota State University, 2013) Mehta, Sonali
Wild oat (Avena fatua) is a grass weed species that infests cropland. Common post-emergent herbicides for controlling wild oat are those that inhibit acetyl-CoA carboxylase (ACCase) and acetolactate synthase (ALS). Variation among plastidic ACCase gene sequences of herbicide-susceptible wild oat biotypes USDA96 and KYN119 revealed ACCase gene diversity consistent with possible separate diploid ancestry, with KYN119 more likely to share diploid ancestry with herbicide-resistant UM1. USDA96 wild oat shows low-level tolerance to the ALS-inhibiting herbicide flucarbazone, and the inheritance of this tolerance was studied among F3 families generated from KYN119 and USDA96 reciprocal crosses. Quantitative inheritance was observed at the below-label flucarbazone rate of 1.81 g ai/ha. Some F3 families had higher post-treatment main shoot dry weights than either parent, which may be due to heterosis and/or genetic contributions from both parents. No evidence for association between the Acc1;1 ACCase gene and low-level tolerance to flucarbazone was observed.
Genetics of Wheat Domestication and Septoria Nodorum Blotch Susceptibility in Wheat
(North Dakota State University, 2019) Sharma, Sapna
T. aestivum ssp. spelta Iranian type has long been thought to potentially be the direct non-free threshing hexaploid progenitor. I evaluated a RIL population derived from a cross between CS and Iranian spelta accession P503 to identify loci suppressing free-threshabilty in P503. Identification of QTL associated with threshability in region known to harbor the Tg2A gene, and an inactive tg2D allele supported the hypothesis of Iranian spelta being derived from a more recent hybridization between free-threshing hexaploid and emmer wheat. Parastagonospora nodorum is an important fungal pathogen and secretes necrotrophic effectors that evoke cell death. In this research, a DH population segregating for Snn5 was used to saturate Snn5 region of chromosome 4B with molecular markers. The physical distance between Snn5 flanking markers was narrowed to 1.38 Mb with genetic distance of 2.8 cM. The markers developed in this study will provide a strong foundation for map-based cloning of Snn5.
Genome-Wide Association Mapping of Host Resistance to Stem Rust, Leaf Rust, Tan Spot, and Septoria Nodorum Blotch in Cultivated Emmer Wheat
(North Dakota State University, 2015) Sun, Qun
Cultivated emmer wheat (Triticum turgidum ssp. dicoccum) is a good source of genes for resistance to several major diseases of wheat. The objectives of this study were to use genome-wide association analysis to detect genomic regions in cultivated emmer germplasm harboring novel resistance genes to four wheat diseases: stem rust, leaf rust, tan spot, and Septoria nodorum blotch (SNB). A natural population including 180 cultivated emmer accessions with a high level of geographic diversity was assembled as the association-mapping panel. This cultivated emmer panel was evaluated phenotypically by scoring reactions to stem rust, leaf rust, tan spot, and SNB and was genotyped using a 9K SNP Infinium array. After filtering for missing data points and minor allele frequency (MAF), 4,134 SNPs were used for association analysis using 178 emmer accessions. Based on principle component (PC) analysis, five subpopulations strongly associated with geographic origins were suggested by the first three PCs. Genome-wide association analysis revealed that 222, 42, 146, and 42 SNPs were significantly associated with resistance to stem rust, leaf rust, tan spot, and SNB, respectively, at the significant level of 1 percentile. Among the significant SNPs at the significant level of 0.1 percentile, ten, one, nine, and one co-located with known genes or QTL associated with resistance to the four diseases, respectively. The remaining significant SNPs were located in the genomic regions where no known resistance genes have been identified for the four diseases. This evidence suggests that some of the emmer wheat accessions carry novel genes conferring resistance to the four diseases. Additionally, 14, three, eight, and five LD blocks harboring at least one significant SNP were identified and might harbor putative QTL related to resistance to the four diseases, respectively. These studies provide information about the genomic regions in cultivated emmer that are associated with resistance to stem rust, leaf rust, tan spot, and SNB. Results from these studies provide guidance for selecting emmer accessions when decisions are being made about the parents that will be used for the development of new resistant germplasm and mapping populations for identifying novel genes conferring resistance to major wheat diseases.
Genomic Analysis of Domestication-Related Traits and Stem Rust Resistance in Tetraploid Wheat
(North Dakota State University, 2017) Saini, Jyoti
Modern durum and common wheat cultivars were developed from ancient wheat ancestors by natural and artificial selection of agronomic and domestication traits, which ultimatey decreased their genetic diversity and made them more susceptible to various biotic and abiotic stresses. At present, new sources of resistance need to be introgressed into future wheat cultivars to combat the effect of the disease stem rust caused by the biotrophic fungal pathogen Puccinia graminis f.sp. tritici (Pgt). In this dissertation, I first analyzed the domestication-related traits in a tetraploid recombinant inbred line (RIL) population developed from a cross between the durum wheat line Rusty and the cultivated emmer accession PI 193883 (referred to as the RP883 population). Second, the RP883 population and a double haploid (DH) population (referred to as the LP749 population) derived from a cross between the durum cultivar Lebsock and the Triticum. turgidium ssp. carthlicum accession PI 94749, and nine durum wheat cultivars were screened with Pgt races TMLKC, TTKSK, TRTTF, and TTTTF. Domestication-related trait analysis in the RP883 population showed vernalization (Vrn-A1) and domestication (Q) genes had a pleiotrophic effect on spike length, spikelet per spike, spike compactness, and threshability. Additionally, an interaction and dosage effect of three free-threshing trait governing loci, teneacious glume Tg2A and Tg2B, and q, revealed that mutation in all three loci are required to attain complete free threshability. The stem rust analysis done in the RP883 population showed two Sr gene regions conferring resistance against TMLKC, TTKSK, and TRTTF: one novel gene region on chromosome 2BL (Sr883) and likely a new allele or gene residing in close proximity to the Sr13 gene on 6AL. The second stem rust study using the LP749 population and nine durum wheat cultivars showed that most likely the U.S. durum germplasm carries the four major Sr genes, Sr7a (4AL), Sr8155B1 (6AS), Sr13 (6AL), and likely Sr9e (2BL) against TTKSK, TRTTF, and TTTTF. In conclusion, results obtained from this domestication study provide knowledge about different stages in wheat evolution. Both stem rust studies revealed genetic diversity in the tetraploid wheat gene pool and indicate their utility in future breeding programs.
Genomic and Molecular Characterization of Pyrenphora teres f. teres
(North Dakota State University, 2019) Wyatt, Nathan Andrew
Pyrenophora teres f. teres is the causal agent of net form net blotch of barley. P. teres f. teres is prevalent globally across all barley growing regions and globally is the most devastating foliar disease of barley. Though economically important, the molecular mechanism whereby P. teres f. teres causes disease is poorly understood and investigations into these mechanisms have been hindered by a lack of genomic resources. To set a genomic foundation for P. teres f. teres the reference isolate 0-1 was sequenced and assembled using PacBio single molecule real-time (SMRT) sequencing and scaffolded into 12 chromosomes to provide the first finished genome of P. teres f. teres. High confidence gene models were generated for the reference genome of isolate 0-1 using a combination of pure culture and in planta RNA sequencing. An additional four P. teres f. teres isolates were sequenced and assembled to the same quality as the reference isolate 0-1 and used in a comparative genomic study. Comparisons of the five P. teres f. teres isolates showed a two-speed genome architecture with the genome being partitioned into core and accessory genomic compartments. Accessory genomic compartments clustered in sub-telomeric regions of the P. teres f. teres genome with a majority of previously identified quantitative trait loci (QTL) associated with avirulence/virulence being spanned by these accessory regions. Using these genomic resources, with a bi-parental mapping population and a natural population for QTL analysis and genome wide association study (GWAS), respectively, we identified a candidate gene for the previously mapped AvrHar. QTL analysis identified a locus extending off the end of P. teres f. teres chromosome 5 and GWAS analysis identified significant associations with a gene encoding a small secreted protein. The candidate AvrHar gene was validated using CRISPR-Cas9-RNP gene disruption in parental isolates 15A and 0-1. Disruption of AvrHar in isolate 15A did not result in a phenotypic change while disruption of the 0-1 allele resulted in a complete loss of pathogenicity. This is the first identification of an effector from P. teres f. teres validated using CRISPR-Cas9-RNP gene editing.
Identification and Genomic Analysis of Stagonospora Nodorum Blotch Susceptibility Genes in Wheat
(North Dakota State University, 2014) Shi, Gongjun
Parastagonospora nodorum is a necrotrophic fungal pathogen that causes the disease Stagonospora nodorum blotch (SNB) on wheat. The fungus produces necrotrophic effectors (NEs), that when recognized by corresponding host genes, cause cell death leading to disease. A novel NE, designated SnTox7, was identified from culture filtrates of isolate Sn6 of P. nodorum. SnTox7 is a small protein with estimated size less than 30 kDa. The interaction between SnTox7 and its corresponding host sensitivity gene, Snn7, explained 33% of the disease variation among a segregating F2 population. The Snn7 gene governs sensitivity to SnTox7 and was delineated to a 2.7 cM interval on the long arm of wheat chromosome 2D. Another host sensitivity gene Snn3- B1, conferring sensitivity to SnTox3, was previously mapped on the short arm of wheat chromosome 5B. Forty-four molecular markers were added to the genetic map to saturate the Snn3-B1 gene region. High-resolution mapping of the Snn3-B1 locus in 5,600 gametes delineated the gene to a 1.5 cM interval. The closely linked markers should be very useful for marker-assisted selection against Snn3-B1. A third host gene, Snn1, confers sensitivity to the NE Tox1. Snn1 was isolated through map-based cloning, and its structure, expression and allelic diversity were further characterized. A bacterial artificial chromosome (BAC) contig of about 2.5 Mb in size was identified to span the Snn1 locus through screening of Chinese Spring chromosome arm 1BS minimum tiling path (MTP) pools. Additional markers developed from BAC end sequences (BESs) delineated the Snn1 gene to a physical segment consisting of four BAC clones. Sequencing and bioinformatic analysis of these clones led to the identification of seven candidate genes. Six of the seven candidates were excluded through critical recombinants. The seventh gene, a cell wall-associated kinase (WAK), was verified as Snn1 through comparative sequence analysis with ethylmethane sulfonate (EMS)-induced mutants. The Snn1 transcription profile showed that it was regulated by light and possibly circadian rhythms. These results demonstrate that P. nodorum can hijack multiple host pathways driven by different classes of genes that typically confer resistance to biotrophic pathogens, thus demonstrating the surprisingly intricate nature of plant-necrotrophic pathogen interactions.
Identification and Introgression of Novel Genes for Stem Rust Ug99 Resistance from Relative Species of Wheat
(North Dakota State University, 2017) Gill, Baljeet K.
Wheat stem rust, caused by Puccinia graminis Pers.: Pers f. sp. tritici Eriks. & E. Henn. (Pgt), is a destructive disease that can cause severe yield losses in wheat. A new Pgt race Ug99 (TTKSK), which was first identified in Uganda in 1998, has overcome many important stem rust resistance (Sr) genes. There is an ongoing world-wide need to identify new and effective resources of resistance. The objectives of this study were to transfer the Ug99-effective Sr genes from wheat-grass species Thinopyrum junceum to hexaploid wheat through chromosome engineering and to identify and map new Sr genes from tetraploid wheat Triticum turgidum ssp. carthlicum. A wheat ‘Chinese Spring’ (CS) –Th. junceum disomic addition line, HD3505, was identified to be resistant to Pgt races in the Ug99 race group. We transferred the Sr gene from HD3505 into CS through chromosome engineering. I identified three BC2F1 plants with reduced Th. junceum chromatin (BG2133, BG5136, and BG2161) carrying the stem rust resistance. This new gene is located on a wheat group-4 chromosome based on the molecular data. To identify and map the new Sr genes in tetraploid wheat, a population of 190 recombinant inbred lines was developed from a cross between T. turgidum ssp. carthlicum (PI 387696) and susceptible durum wheat line Rusty. This population was screened with TTKSK, TRTTF, and TMLKC and genotyped using the wheat 90K iSelect array. A major QTL was identified and mapped to the genomic region harboring the Sr13 locus on 6AL. Molecular markers for Sr13, including BE403950, CK207347 and KASPSr13, indicated that resistance in PI 387696 was due to the Sr13 gene. But evaluation of genetic stocks carrying Sr13 with specific races at different temperature conditions indicated that resistance in PI 387696 is due to new allelic form of Sr13 or due to other novel Sr gene close to Sr13 locus. The marker validation showed that two newly-developed STARP markers Xrwgsnp6 and Xrwgsnp7 can be used for marker-assisted selection of Sr13 in wheat breeding programs. The novel genes or alleles identified in this research provide resistance against TTKSK and other emerging Pgt races and they can be used in wheat improvement.
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.
Protein-ligand Docking Application and Comparison using Discovery Studio and AutoDock
(North Dakota State University, 2017) Wang, Qi
Protein-ligand docking is a structure-based computational method, which is used to predict the small molecule binding modes and binding affinities with protein receptors. The goals of this study are to compare the docking performances of different software and apply the docking method to predict how protein fatty acid desaturase 1 (FADS1) interact with ligands. Two docking software, Discovery Studio and AutoDock, are used for docking comparison of 195 protein-ligand complexes from PDBind dataset. AutoDock performs a little bit better than Discovery Studio on the docking percentage, which is the percent of the docked complexes out of 195. On the other hand, Discovery Studio has a higher accuracy (successfully docked complexes, within 5 RMSD of the native complex structures) than AutoDock. The interaction between FADS1 and Sesamin shows a similar pattern comparing to the interaction between a homolog of FADS1 and a ligand shown in a PDB structure (PDB id 1EUE).
Unraveling the Genetic Architecture of Agronomic Traits and Developing a Genome Wide InDel Panel in Common Bean (Phaseolus vulgaris)
(North Dakota State University, 2015) Mafimoghaddam, Samira
Common bean (Phaseolus vulgaris) is an economically important legume. The agronomic characteristics of this crop such as days to flower, growth habit and seed yield affect breeding strategies. However, little is known about the genomic regions controlling these traits. Therefore, discovering the genetic architecture underlying important agronomic traits can accelerate breeding via marker assisted selection (MAS) in addition to providing genomic and biological information. Genome wide association studies (GWAS) are currently the method of choice to find the genomic regions associated with traits of interest using a population of unrelated individuals. It takes advantage of the historic recombinations that exist in the population to map the traits at a higher resolution. The availability of a reference genome in common bean has paved the way for higher throughput and more accurate genomic research including the discovery of new knowledge and development of new tools. In the first experiment we conducted GWAS using a panel of 280 diverse genotypes from the Middle American gene pool and about 15,000 SNPS with minor allele frequency of 5% and greater to map seven important agronomic traits in common bean. We were able to detect known and new genomic regions with strong candidate genes associated with these traits. In the second experiment we used sequence data from 19 genotypes from different bean market classes to develop a panel of insertion-deletion (InDel) markers that can be used for MAS as well as other genetic and genomic studies. These user-friendly, cost-effective, and co-dominant markers were tested for their efficiency and application. They demonstrated utility in a medium throughput genetic map construction and diversity analysis.
Variation in Core and Accessory Parts of Genome of Escherichia Coli Isolated from Soil from Riparian Areas in New York State
(North Dakota State University, 2016) Maistrenko, Oleksandr
Escherichia coli is commensal bacteria and is a symbiont of the digestive system of vertebrates. Due to frequent deposition of E. coli into extrahost habitats (soil, water), approximately half of its population exists as free living organisms. It is unclear what genome-wide variation stands behind adaptation for extrahost habitat. This thesis applies a genome-wide association study approach to find genetic variation in core and accessory parts of genome of E. coli that is associated with 1) forest or agricultural field soil habitats and 2) with survival phenotype in soil microcosm. Gene composition analysis suggests that pan-genome of environmental E. coli is unlimited. Core and accessory genome contained variation associated with survival phenotype and with forest or field habitat.

Browse

Browsing Plant Sciences by browse.metadata.program "Genomics and Bioinformatics"