国立情報学研究所で電子化したコンテンツを使用している。

Soybean (Glycine max [L.] Merr.) cultivars differ in their resistance to sudden death syndrome (SDS). The syndrome is caused by root colonization by Fusarium virguliforme (ex. F. solani f. sp. glycines). Breeding for improve SDS response has proven challenging, possible due to interactions among the 18 known loci for resistance. Four loci for resistance to SDS (cqRfs to cqRfs3) were found clustered within 20 cM of the rhg1 locus underlying resistance to soybean cyst nematode (SCN) on chromosome 18. Another locus on chromosome 20 (cqRfs5) was reported to interact with this cluster. The aims of this study were to compare the inheritance of resistance to SDS in a near isogenic line (NIL) population that was fixed for resistance to SCN but still segregated at 2 of the 4 loci (cqRfs1 and cqRfs) for resistance to SDS on chromosome 18; to examine the interaction with the locus on chromosome 20; and to identify candidate regions underlying quantitative trait loci (QTL). Used were a near isogenic line population derived from residual heterozygosity in an F5:7 recombinant inbred line EF60 1-40; SDS response data from 2 locations and years; four microsatellite markers and six thousand SNP markers. Polymorphic regions were found from 2,788 to 8,938 Kbp on chromosome 18 and 33,100 to 34,943 Kbp on chromosome 20. Both regions were significantly (0.005 < P > 0.0001) associated with resistance to SDS. A fine map was constructed that Mendelized the three loci. Substitution maps suggested the two loci on chromosome 18 were actually 3 loci (cqRfs, cqRfs1 and cqRfs19). Candidate genes for cqRfs19 were identified in a small region of the genome sequence of soybean. An epistatic interaction was inferred where the allele of loci on chromosome 18 determined the value of the locus on chromosome 20. It was concluded that SDS loci are both complex and interacting which may explain the slow progress in breeding for resistance to SDS.

Abstract The genetic basis of large adaptive differences in timing of bud set and frost hardiness between natural populations of Scots pine (Pinus sylvestris L.) was studied with the aid of RAPD markers and quantitative genetic tools. Steep clinal variation was found for both traits among Finnish Scots pine populations, and the differences between populations were found to be largely genetic. QTL mapping with Bayesian analysis revealed four potential QTLs for timing of bud set, and seven for frost hardiness. The QTLs were mostly different between the two traits. The potential QTLs included loci with large effects, and additionally smaller QTLs. The largest QTLs for bud set date accounted for about a fourth of the mean difference between populations. Thus, natural selection during adaptation has resulted in fixation of genes of large effect. This result is in conflict with the classical infinitesimal model, but agrees with the results of Orr (1998), suggesting fixation of large effects during adaptation. The applicability of RAPD and SSCP markers in quantitative genetic studies was also studied. The SSCP technique was found to be efficient in finding polymorphic markers. SSCP polymorphism in coding genes may provide candidate genes for QTL mapping studies. RAPDs were found to be useful for many descriptive analyses, but specific analyses would require more caution.

Abstract The pattern and the genetic basis of variation in courtship song of D. virilis were studied using three different approaches: a candidate gene, a biometrical and a quantitative trait locus (QTL) method. Nucleotide variation in a candidate song gene, no-on-transientA, was analysed both within the species (D. virilis and D. littoralis) and between the species of the D. virilis group. Nucleotide variation showed no signs of selection and there was no association between the nucleotide or repeat length variation in nonA gene region and the song characters of the D. virilis group species. Molecular markers (microsatellites) were isolated for D. virilis and their cross-species amplification was tested in all members of the D. virilis group. Intraspecific variation in D. virilis was studied at the phenotypic level in male song characters and at the genetic level in microsatellites. Significant geographic variation was detected in both levels, grouping the strains according to the main continents of the species' distribution range: America, Asia, Europe and Japan. The strains with most extreme song phenotypes were chosen for further analysis. The inheritance of two courtship song characters, the number of pulses in a pulse train (PN) and the length of a pulse train (PTL) was studied by analysing the means and variances of these characters between parental and reciprocal F1, F2 and backcross males. This biometrical analysis showed the genetic basis of these song characters to be polygenic with significant dominance, epistatic and Y-chromosomal effects on both characters. A subset of these data (F2 generation males) were used to conduct a QTL study with the aid of a recombination linkage map constructed for the microsatellites. Composite interval mapping (CIM) revealed significant QTLs, which were shared in both characters. Altogether, significant QTLs, located on the X, 2nd, 3rd and 4th chromosome, were found to affect PN, whereas only QTLs on the 3rd chromsome was found to affect PTL. The effect of the same QTL on the 3rd chromosome on both characters accounted for 31.8% and 49.1% of the mean difference between the parental strains in PN and PTL, respectively. These results suggest the genetic basis for these song characters is caused mainly by autosomal QTLs with a relatively large effect.

No description available.

Development of winter wheat (Triticum aestivum L.) cultivars capable of more efficient uptake and utilization of applied nitrogen (N) has the potential to increase grower profitability and reduce negative environmental consequences associated with N lost from the plant-soil system. The first study sought to evaluate genotypic variation for N use efficiency (NUE) and identify lines consistently expressing high or low NUE under two or more N rates in a total of 51 N-environments. The results indicated that significant genotype by N rate interactions were frequently observed when trials utilized at least three N rates and identified wheat lines with high and stable yield potential that varied in performance under low N conditions. In addition, NUE was associated with above-ground biomass at physiological maturity were found to be both highly heritable across multiple N supplies. In the second study, two bi-parental mapping populations having a common low ('Yorktown') and two high (VA05W-151 and VA09W-52) NUE parents were characterized to dissect the genetics underlying N response. The populations were evaluated in eight N-environments and genotyped using single-nucleotide polymorphism data derived from a genotyping-by-sequencing protocol to identify quantitative trait loci (QTL) associated with high NUE. Six QTL for NUE were identified on chromosomes 1D, 2D, 4A, 6A, 7A, and 7D that were associated with N use efficiency. The QTL on 2D and 4A co-localized with known loci governing photoperiod sensitivity and resistance to Fusarium head blight (caused by the fungal pathogen Fusarium graminearum Schwabe), respectively. Three of the identified QTL (6A, 7A, and 7D) were associated with NUE in previous investigations, while the QTL on 1D was novel. The final experiment employed a small panel of soft red winter wheat lines to study the effects of photoperiod alleles on chromosome 1D (Ppd-D1) on yield-related traits under three or five N rates that were variably split over two growth stages in eight environments. The results validated the effect of a photoperiod sensitive allele (Ppd-D1b) that was associated with increased grain yield across N rates in half of the Virginia testing environments and under low N rates in all Ohio testing sites at the expense of grain N content. Yield advantages conferred by the Ppd-D1b allele were attributable to increased floret fertility and kernel number per spike. The findings from these studies have direct application for winter wheat breeding programs targeting NUE improvements. / Doctor of Philosophy / Wheat (Triticum aestivum L.) products account for a significant percentage of the total dietary calories and protein consumed globally. To meet production demands, wheat requires efficient nitrogen (N) management to ensure continued grower profitability and to reduce negative environmental impacts of N lost from agricultural systems. This dissertation sought to evaluate variation among wheat lines for N use efficiency (NUE), assess the performance of wheat lines under multiple N supplies, validate traits that are associated with NUE, investigate the role of photoperiod sensitivity genes on N response, and identify regions of the wheat genome associated with high N use efficiency. These studies were conducted using panels of winter wheat lines grown under two or more N conditions over a combined 32 location-years. Results of Chapter I identified variation in cultivar response to N rates was more frequently observed when a greater number of N rates were used in trials of wheat N response. The first chapter also identified variation among wheat lines for NUE and identified lines that consistently produce high grain yields over N-location-years. In addition, above-ground biomass at physiological maturity was found to be strongly associated with grain yield under all N rates and was highly heritable in both studies. Chapter II utilized a combination of genetic and observable trait data to perform genetic analysis in two bi-parental populations grown in eight Nlocation-years. The study identified reproducible and significant genetic markers associated with NUE for application in wheat breeding programs. Upon analysis of photoperiod sensitive versus insensitive wheat lines in Chapter III, photoperiod sensitive wheat lines had a significant yield advantage under N-limited conditions in Ohio and across N treatments in half of the Virginia testing location-years. This resulted from an increased number of kernels per spike and fertile florets in photoperiod sensitive wheat lines. Results from this dissertation suggest that active breeding and selection for N response may be achieved through the employment of high NUE genes and the continued identification of adapted high NUE wheat parental lines.

Hintergrund: Die Berlin Fat Mouse Inzuchtlinie (BFMI) ist ein Modell für Adipositas und das metabolische Syndrom. Diese Studie zielte darauf ab, genetische Varianten zu identifizieren, die mit dem gestörten Glukosestoffwechsel assoziiert sind, indem die fettleibigen Linien BFMI861-S1 und BFMI861-S2 verwendet wurden, die genetisch eng verwandt sind, sich aber in mehreren Merkmalen unterscheiden. BFMI861-S1 ist insulinresistent und speichert ektopisches Fett in der Leber, während BFMI861-S2 insulinsensitiv ist. Methoden: Die QTL-Analyse wurde in zwei fortgeschrittenen Intercross-Linien (AIL) in der Generation durchgeführt. Eine AIL wurde aus der Kreuzung BFMI861-S1 x BFMI861-S2 und die zweite AIL aus der Kreuzung BFMI861-S1 x BFMI861-B6N erhalten. Für beide AILs wurden Phänotypen über 25 bzw. 20 Wochen gesammelt. Zur Priorisierung von positionellen Kandidatengenen wurden Gesamtgenomsequenzierung und Genexpressionsdaten der Elternlinien verwendet. Ergebnisse: Für den AIL BFMI861-S1 x BFMI861-S2 wurden überlappende QTL für das Gonadenfettgewebegewicht und die Blutglukosekonzentration auf Chromosom (Chr) 3 (95,8–100,1 Mb) und für das Gonadenfettgewebegewicht, Lebergewicht und Blut nachgewiesen Glukosekonzentration auf Chr 17 (9,5–26,1 Mb). Für die AIL BFMI861-S1 x BFMI861-B6N zeigte ein hochsignifikanter QTL auf Chromosom (Chr) 1 (157–168 Mb) einen Zusammenhang mit dem Lebergewicht. Ein QTL für das Körpergewicht nach 20 Wochen wurde auf Chr 3 (34,1 – 40 Mb) gefunden, der sich mit einem QTL für das scAT-Gewicht überlappte. In einem multiplen QTL-Mapping-Ansatz wurde ein zusätzliches QTL, das das Körpergewicht bei 16 Wochen beeinflusste, auf Chr 6 (9,5–26,1 Mb) identifiziert. Schlussfolgerungen: Die QTL-Kartierung zusammen mit einem detaillierten Priorisierungsansatz ermöglichte es uns, Kandidatengene zu identifizieren, die mit Merkmalen des metabolischen Syndroms in beiden AILs assoziiert sind. / Background: The Berlin Fat Mouse Inbred line (BFMI) is a model for obesity and the metabolic syndrome. This study aimed to identify genetic variants associated with the impaired glucose metabolism using the obese lines BFMI861-S1 and BFMI861-S2, which are genetically closely related, but differ in several traits. BFMI861-S1 is insulin resistant and stores ectopic fat in the liver, whereas BFMI861-S2 is insulin sensitive. Methods: QTL-analysis was performed in two advanced intercross lines (AIL) in generation. One AIL obtained from the cross BFMI861-S1 x BFMI861-S2 and the second AIL from the cross BFMI861-S1 x BFMI861-B6N. For both AILs phenotypes were collected over 25 and 20 weeks, respectively. For prioritization of positional candidate genes whole genome sequencing and gene expression data of the parental lines were used. Results: For the AIL BFMI861-S1 x BFMI861-S2 overlapping QTL for gonadal adipose tissue weight and blood glucose concentration were detected on chromosome (Chr) 3 (95.8-100.1 Mb), and for gonadal adipose tissue weight, liver weight, and blood glucose concentration on Chr 17 (9.5-26.1 Mb). For the AIL BFMI861-S1 x BFMI861-B6N one highly significant QTL on chromosome (Chr) 1 (157–168 Mb) showed an association with liver weight. A QTL for body weight at 20 weeks was found on Chr 3 (34.1 – 40 Mb) overlapping with a QTL for scAT weight. In a multiple QTL mapping approach, an additional QTL affecting body weight at 16 weeks was identified on Chr 6 (9.5-26.1 Mb). Conclusions: QTL mapping together with a detailed prioritization approach allowed us to identify candidate genes associated with traits of the metabolic syndrome in both AILs.

Doctor of Philosophy / Department of Agronomy / Allan K. Fritz / Heat stress is one of the major environmental constraints for wheat production worldwide. High temperature during grain filling in wheat leads to a significant reduction in yield. In this research, three different projects were completed. The first project was to study cytoplasmic effects on heat tolerance in wheat, where ten different alloplasmic lines of wheat were backcrossed with four different wheat varieties: „Karl 92‟, „Ventnor‟, „U1275‟ and „Jagger‟. The nuclear genome of the alloplasmic lines was substituted by backcrossing six times using the recurrent parents as males. During the fifth and/or fourth backcross, reciprocal crosses were made to develop NILs (Near Isogenic Lines) for cytoplasm. Sixty-eight NILs and their parents were evaluated in growth chambers for post-anthesis heat tolerance. Plants were grown in the greenhouse and placed under heat stress for 14 days starting at 10 days after anthesis. Growth chambers were maintained at 35°/30°C for heat stress and the greenhouse was maintained at 20°/15°C as the optimum temperature. Effects of high temperature on chlorophyll content and Fv/Fm (a chlorophyll fluorescence measuring parameter) were found to be significant. Cytoplasms 1, 4, 5, 8, 9 and10 provided greater tolerance in one or more nuclear backgrounds. These results indicated that cytoplasmic effects can contribute to heat tolerance of wheat. The second project focused on identification of quantitative trait loci (QTL) for thylakoid membrane damage (TMD), SPAD chlorophyll content (SCC) and plasma membrane damage (PMD), as these traits are found to be associated with resistance to heat stress and contributes to relatively stable yield under high temperature. A RIL (Recombinant Inbred line) population of a cross between winter wheat cultivars „Ventnor‟ and „Karl 92‟ was evaluated using two different temperature regimes (20°/15°C, 36°/30°C) imposed at ten days after anthesis. The aforementioned traits were evaluated and associated with various molecular markers (SSR, AFLP and SNP). The putative QTL associated are localized on chromosomes 6A, 7A, 1B, 2B and 1D and have the potential to be used in marker assisted selection for improving heat tolerance in wheat. In the third project, a transgenic approach to increase grain fill during high temperatures was investigated. Grain fill is reduced at temperatures above 25°C in wheat partly due to the inactivity of soluble starch synthase. We isolated a soluble starch synthase gene from rice that has the potential to overcome this deficiency during high temperatures and placed it behind both a constitutive promoter and an endosperm-specific promoter. Transgene expression and the effects of the transgene expression on grain yield-related traits for four generations (T0, T1, T2 and T3) were monitored. The results demonstrated that even after four generations, the transgene was still expressed at high levels, and transgenic plants produced grains of greater seed weight than Bobwhite control plants under the same environmental conditions. Thousand-seed weight under high temperatures increased 21-34% in T2 and T3 transgenic plants when compared to the non-transgenic control plants. In addition, the duration of photosynthesis was longer in transgenic wheat than in non-transgenic controls. Our study demonstrated that expression of rice soluble starch synthase gene in wheat can improve wheat yield under heat stress conditions.

The goal of this project was to determine the genetic architecture of water-use efficiency (WUE) for foxtail pine, which included genomic loci, and effect sizes of this trait. Foxtail pine is a subalpine endemic conifer that inhabits two distinct regional populations separated by 500 km in the mountains of California. In order to achieve this goal, a robust linkage map containing thousands of genetic markers was created using four megagametophyte arrays ranging in size from approximately 70 to 95 megagametophytes. Quantitative trait loci (QTL) discovered for WUE were mapped along the linkage map using linear mixed models and five half-sibling families grown in a common garden. Effect sizes of these QTL were tested for differences between the two regional populations of foxtail pine.

Master of Science / Division of Biology / Michael A. Herman / Caenorhabditis elegans are free-living bacterivorous nematodes that naturally consume bacteria as food source. As an excellent genetic model, C. elegans has proven to be a successful system to study innate immune responses to human pathogens, which resulted in identification of many evolutionarily conserved defense pathways. Most of these studies examined innate immune pathway mutants in a single genetic background in response to monoculture of human pathogens that worms might not necessarily encounter in the wild. While this has led to the successful genetic dissection of these defense pathways, in order to fully understand their biological functions, the relevant ecological and evolutionary context needs to be taken into account. The bacterial environment C. elegans naturally encounter is likely to be highly heterogeneous. While many bacteria are mainly considered as dietary resource for worms, some could be potential pathogens. Worms thus constantly face the challenge to defend against the pathogens mixed in the food. Stenotrophomonas maltophilia is one such bacterium. S. maltophilia is a ubiquitous bacterium that has been found associated with native nematodes. But it can also cause nosocomial infections in human, especially in immune-compromised individuals. Due to its natural resistance to multiple antibiotics, it has been emerging as an opportunistic human pathogen. Our lab isolated a S. maltophilia strain, JCMS, which was found being pathogenic to C. elegans. Both C. elegans strains, N2 (Bristol, England) and CB4856 (Hawaii), showed decreased survivorship when fed on S. maltophilia JCMS compared to E. coli OP50. However, more interestingly, the specific responses towards bacteria are different between strains. This indicates that survivorship of C. elegans is determined by not only genetic and environmental factors, but also genotype by environment (G×E) interactions (GEI). In order to identify the underlying genetic basis, we mapped quantitative trait loci (QTL) in a N2×CB4856 recombinant inbred panel for the survivorship in response to E. coli OP50 and S. maltophilia JCMS.