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.

Carbohydrate content sucrose, raffinose, and stachyose are one of the important seed quality traits in soybean. However, little is known about the genetics of these quantitative traits. Recombinant inbred lines (RIL) were developed from the interspecific hybridization between a Glycine max breeding line (V71-370) and a Glycine soja plant introduction (PI407162). The 308 RILs, each parent, and one cultivar were arranged in a randomized complete block design with two replications and planted at two locations in Virginia. The main objective of the first part of this research was to devise a quick, economical, and reliable HPLC methodology to determine the amount of sucrose, raffinose, and stachyose in soybean seeds. Concentration of sucrose, raffinose and stachyose are quantitative traits, which are hard to manipulate genetically due to the influence of genotype, environment, and genotype by environment interactions on seed chemical composition. The objectives of the second study were to evaluate agronomic and quality traits over locations and to study correlations among traits. The agronomic traits analyzed in this study included; maturity, plant canopy height, canopy spread, leaflet length, leaflet width, yield, and seed size. Seed quality traits studied were sucrose, raffinose, and stachyose content. Although some correlation coefficients were statistically significant at P<0.001, many were not large enough to be of practical value. A positive correlation was observed between all three sugars. Significant variation was observed among RILs and locations for all traits studied. Genotype by environment interaction was significant for all of the agronomic traits, but was not significant for seed sucrose, stachyose, or raffinose. Maturity, seed size, and sucrose content were highly heritable traits, whereas plant height, canopy spread, yield, leaf length, leaf width, stachyose content, and raffinose content had relatively low broad-sense heritabilities. The RIL population was used to investigate the genetic basis for these agronomic and seed quality traits. Seven out of twenty soybean molecular linkage groups (MLG), A1, A2, E, F, G, I, and M, were selected on the basis of previous research and mapped in this population with restriction fragment length polymorphism (RFLP) and simple sequence repeat (SSR) markers. Five QTL for seed sucrose content, one QTL each for raffinose and stachyose, and one for each agronomic trait except yield and leaflet width, and two QTL each for yield and leaflet width were detected using the Blacksburg data. Four QTL for seed sucrose content, one QTL for raffinose, two QTL for stachyose, one QTL each for plot width and yield and two QTL for leaflet width were detected using the Warsaw data. Several QTL affecting different agronomic traits shared common genomic regions suggesting pleiotropy at some loci. The majority of the seed quality QTL was stable at both locations. Agronomic traits were more environmentally sensitive and no QTL were common to both locations. Epistasis analysis showed interactions between QTL that detected new genomic regions associated with raffinose content. These results suggest that these potential QTL are definitely on the genomic regions of interest and would be more powerful in marker-assisted selection when we find closer markers to each QTL. / Ph. D.

京都大学 / 新制・論文博士 / 博士(農学) / 乙第13519号 / 論農博第2907号 / 新制||農||1096(附属図書館) / 学位論文||R4||N5419(農学部図書室) / 京都大学大学院農学研究科農学専攻 / (主査)教授 中﨑 鉄也, 教授 那須田 周平, 教授 吉田 健太郎 / 学位規則第4条第2項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

Cotton (Gossypium spp.) is the world’s leading textile fiber crop, and an important source of oil and protein. Insufficient candidate gene derived-markers suitable for genetic mapping and limited information on genes that control economically important traits are the major impediments to the genetic improvement of Upland cotton (G. hirsutum L.). The objectives of this study were to develop a SNP marker discovery strategy in tetraploid cotton species, SNP characterization and marker development from fiber initiation and elongation related genes, chromosomal assignment of these genes by SNP marker-based deletion analysis or linkage mapping, and genetic and molecular analysis of mutants affecting cotton fiber development. Phylogenetic grouping and comparision to At- and Dt-genome putative ancestral diploid species of allotetraploid cotton facilitated differentiation between genome specific polymorphisms (GSPs) and marker-suitable locus-specific polymorphisms (LSPs). By employing this strategry, a total of 222 and 108 SNPs were identified and the average frequency of SNP was 2.35% and 1.30% in six EXPANSIN A genes and six MYB genes, respectively. Both gene families showed independent and incongruent evolution in the two subgenomes and a faster evolution rate in Dt-genome than that in At-genome. SNPs were concordantly mapped to different chromsomes, which confirmed their value as candidate gene marker and indicated the reliability of SNP discovery stragey. QTL mapping by two F2 populations developed from fiber mutants detected major QTL which explain 62.8-87.1% of the phenotypic variation for lint percentage or lint index in the vicinity of BNL3482-138 on chromosome 26. Single marker regression analyses indicated STV79-108, which was located to the long arm of chromosome 12 (the known location of N1 and perhaps n2 loci), also had significant association (R2 % value 15.4-30.6) with lint percentage, lint index, embryo protein percentage and micronaire. Additional QTL and significant markers associated with other seed and fiber traits were detected on different chromosomes. Inheritance analysis indicated that both genetic models N1N1n2n2 and n2n2li3lisub>3 could lead to the fiberless phenotype. The observation of fuzzless-short lint phenotype indicated fiber initiation and elongation were controlled by different mechanisms. The penetrance of Li2 gene expression was observed in this study.

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