シミュレーションと栽培試験を用いた植物育種におけるゲノミックセレクションの可能性評価

学位の種別: 課程博士審査委員会委員 : (主査)東京大学准教授 岩田 洋佳, 東京大学教授 二宮 正士, 東京大学教授 岸野 洋久, 東京大学特任准教授 藤本 優, 筑波大学教授 大澤 良University of Tokyo(東京大学

Potential of Genomic Selection in Mass Selection Breeding of an Allogamous Crop: An Empirical Study to Increase Yield of Common Buckwheat

To evaluate the potential of genomic selection (GS), a selection experiment with GS and phenotypic selection (PS) was performed in an allogamous crop, common buckwheat (Fagopyrum esculentum Moench). To indirectly select for seed yield per unit area, which cannot be measured on a single-plant basis, a selection index was constructed from seven agro-morphological traits measurable on a single plant basis. Over 3 years, we performed two GS and one PS cycles per year for improvement in the selection index. In GS, a prediction model was updated every year on the basis of genotypes of 14,598–50,000 markers and phenotypes. Plants grown from seeds derived from a series of generations of GS and PS populations were evaluated for the traits in the selection index and other yield-related traits. GS resulted in a 20.9% increase and PS in a 15.0% increase in the selection index in comparison with the initial population. Although the level of linkage disequilibrium in the breeding population was low, the target trait was improved with GS. Traits with higher weights in the selection index were improved more than those with lower weights, especially when prediction accuracy was high. No trait changed in an unintended direction in either GS or PS. The accuracy of genomic prediction models built in the first cycle decreased in the later cycles because the genetic bottleneck through the selection cycles changed linkage disequilibrium patterns in the breeding population. The present study emphasizes the importance of updating models in GS and demonstrates the potential of GS in mass selection of allogamous crop species, and provided a pilot example of successful application of GS to plant breeding

Codon pairs of the HIV-1 vif gene correlate with CD4+T cell count

Background: the human APOBEC3G (A3G) protein activity is associated with innate immunity against HIV-1 by inducing high rates of guanosines to adenosines (G-to-A) mutations (viz., hypermutation) in the viral DNA. If hypermutation is not enough to disrupt the reading frames of viral genes, it may likely increase the HIV-1 diversity. To counteract host innate immunity HIV-1 encodes the Vif protein that binds A3G protein and form complexes to be degraded by cellular proteolysis.Methods: Here we studied the pattern of substitutions in the vif gene and its association with clinical status of HIV-1 infected individuals. To perform the study, unique vif gene sequences were generated from 400 antiretroviral-naive individuals.Results: the codon pairs: 78-154, 85-154, 101-157, 105-157, and 105-176 of vif gene were associated with CD4+ T cell count lower than 500 cells per mm(3). Some of these codons were located in the (81)LGQGVSIEW(89) region and within the BC-Box. We also identified codons under positive selection clustered in the N-terminal region of Vif protein, between (WKSLVK26)-W-21 and (YRHHY44)-Y-40 regions (i.e., 31, 33, 37, 39), within the BC-Box (i.e., 155, 159) and the Cullin5-Box (i.e., 168) of vif gene. All these regions are involved in the Vif-induced degradation of A3G/F complexes and the N-terminal of Vif protein binds to viral and cellular RNA.Conclusions: Adaptive evolution of vif gene was mostly to optimize viral RNA binding and A3G/F recognition. Additionally, since there is not a fully resolved structure of the Vif protein, codon pairs associated with CD4+ T cell count may elucidate key regions that interact with host cell factors. Here we identified and discriminated codons under positive selection and codons under functional constraint in the vif gene of HIV-1.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Japan Society for the Promotion of Science (SPS KAKENHI)Universidade Federal de São Paulo, Dept Med, São Paulo, BrazilUniv Tokyo, Grad Sch Agr & Life Sci, Tokyo, JapanFed Univ Para, Inst Biotechnol, BR-66059 Belem, Para, BrazilUniv Vigo, Dept Biochem Genet & Immunol, Bioinformat & Mol Evolut Lab, Vigo 36310, SpainUniversidade Federal de São Paulo, Dept Med, São Paulo, BrazilFAPESP: 06/50109-5Japan Society for the Promotion of Science (SPS KAKENHI): 19300094Web of Scienc

Rapid genotyping with DNA micro-arrays for high-density linkage mapping and QTL mapping in common buckwheat (Fagopyrum esculentum Moench)

For genetic studies and genomics-assisted breeding, particularly of minor crops, a genotyping system that does not require a priori genomic information is preferable. Here, we demonstrated the potential of a novel array-based genotyping system for the rapid construction of high-density linkage map and quantitative trait loci (QTL) mapping. By using the system, we successfully constructed an accurate, high-density linkage map for common buckwheat (Fagopyrum esculentum Moench); the map was composed of 756 loci and included 8,884 markers. The number of linkage groups converged to eight, which is the basic number of chromosomes in common buckwheat. The sizes of the linkage groups of the P1 and P2 maps were 773.8 and 800.4 cM, respectively. The average interval between adjacent loci was 2.13 cM. The linkage map constructed here will be useful for the analysis of other common buckwheat populations. We also performed QTL mapping for main stem length and detected four QTL. It took 37 days to process 178 samples from DNA extraction to genotyping, indicating the system enables genotyping of genome-wide markers for a few hundred buckwheat plants before the plants mature. The novel system will be useful for genomics-assisted breeding in minor crops without a priori genomic information

Voltammetric determination of 1-nitropyrene using silver solid amalgam electrode in miniaturized detection cell

Jindřich Karásek, diplomová práce KATA 2010 Abstract Meniscus-modified silver solid amalgam electrode was used in miniaturized detection cell. It was constructed for determination of various analytes in decreased volume using 1-nitropyrene as a model analyte. Working electrode was placed together with reference (Ag/AgCl/3 mol.l-1 KCl) and Pt wire auxiliary electrode in miniaturized voltammetric cell, using 120 µl of base electrolyte for measurements. The oxygen was removed from measured solutions by addition of saturated solution of sodium sulphite. Base electrolyte was composed of methanol and Britton - Robinson buffer pH12,0 in the ratio of 7:3. Determination was optimized for DC voltammetry and differential pulse voltammetry. Limits of quantitation were comparable of about 4.10-6 mol.l-1 in both cases. The methods showed reproducible results with relative standard deviation <3.65 % (n = 10)

Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice

Abstract Root system architecture plays a crucial role in nutrient and water absorption during rice production. Genetic improvement of the rice root system requires elucidating its genetic control. Genome-wide association studies (GWASs) have identified genomic regions responsible for rice root phenotypes. However, candidate gene prioritization around the peak region often suffers from low statistical power and resolution. Transcriptomics enables other statistical mappings, such as transcriptome-wide association study (TWAS) and expression GWAS (eGWAS), which improve candidate gene identification by leveraging the natural variation of the expression profiles. To explore the genes responsible for root phenotypes, we conducted GWAS, TWAS, and eGWAS for 12 root phenotypes in 57 rice accessions using 427,751 single nucleotide polymorphisms (SNPs) and the expression profiles of 16,901 genes expressed in the roots. The GWAS identified three significant peaks, of which the most significant peak responsible for seven root phenotypes (crown root length, crown root surface area, number of crown root tips, lateral root length, lateral root surface area, lateral root volume, and number of lateral root tips) was detected at 6,199,732 bp on chromosome 8. In the most significant GWAS peak region, OsENT1 was prioritized as the most plausible candidate gene because its expression profile was strongly negatively correlated with the seven root phenotypes. In addition to OsENT1, OsEXPA31, OsSPL14, OsDEP1, and OsDEC1 were identified as candidate genes responsible for root phenotypes using TWAS. Furthermore, a cis-eGWAS peak SNP was detected for OsDjA6, which showed the eighth strongest association with lateral root volume in the TWAS. The cis-eGWAS peak SNP for OsDjA6 was in strong linkage disequilibrium (LD) with a GWAS peak SNP on the same chromosome for lateral root volume and in perfect LD with another SNP variant in a putative cis-element at the 518 bp upstream of the gene. These candidate genes provide new insights into the molecular breeding of root system architecture

Prediction accuracy attained through selection cycles.

<p>Results of the discrete GS in a population derived from a single bi-parental cross of Koshihikari × Hatsushimo: red line. Results of the bulked GS: green line. Results of each subpopulation in the island model GS: blue lines.</p

Genotypic values attained through selection cycles.

<p>Maximum of the true genotypic values among selected plants. (a) Solid lines show results of the discrete GS breeding. Dashed lines represent the maximum value of genotypic values in F₆ population derived from a single cross. Red and blue lines respectively represent the results of Koshihikari × Hatsushimo and the results of the best population in each simulation trial. (b) Red, green, and blue lines respectively present results of the discrete GS of Koshihikari × Hatsushimo population, one of the bulked GS, and one of the island-model GS.</p

Summary of the simulation results from three GS breeding procedures.

<p>Summary of the simulation results from three GS breeding procedures.</p