Biomedical subjects

Yoshihiro Matsuoka

Publications and source records attributed to Yoshihiro Matsuoka.

10 recordsLinked to original sources

PubMed2005

Genealogical use of chloroplast DNA variation for intraspecific studies of Aegilops tauschii Coss.

Intraspecific patterns of chloroplast DNA variation was studied in Aegilops tauschii Coss., the D-genome progenitor of bread wheat. Nucleotide sequences of ten chloroplast microsatellite loci were analyzed for 63 accessions that cover the central part of the species distribution. As is often the case with nuclear microsatellites, those of chloroplasts of Ae. tauschii bear complex mutations. Several types of mutations other than change in the microsatellite repeat number were found, including base substitutions and length mutations in flanking regions. In total, eight mutations were present in the flanking regions of four loci. Most mutations in the flanking regions of microsatellite repeats are associated with biallelic polymorphisms. Phylogeographic analyses showed that such biallelic polymorphisms are useful to investigate intraspecific patterns of monophyletic lineage divergence. In contrast, most microsatellite repeat sites are multiallelic, variable within intraspecific lineages, and useful to compare degrees of genetic diversity between lineages. These findings show that the chloroplast genome harbors evolutionary variations informative for intraspecific studies of Ae. tauschii and can be analyzed by genealogical approaches.

Afghanistan↗

PubMed2005

Genetic diversity and population structure of teosinte.

The teosintes, the closest wild relatives of maize, are important resources for the study of maize genetics and evolution and for plant breeding. We genotyped 237 individual teosinte plants for 93 microsatellites. Phylogenetic relationships among species and subspecific taxa were largely consistent with prior analyses for other types of molecular markers. Plants of all species formed monophyletic clades, although relationships among species were not fully resolved. Phylogenetic analysis indicated that the Mexican annual teosintes divide into two clusters that largely correspond to the previously defined subspecies, Z. mays ssp. parviglumis and ssp. mexicana, although there are a few samples that represent either evolutionary intermediates or hybrids between these two subspecies. The Mexican annual teosintes show genetic substructuring along geographic lines. Hybridization or introgression between some teosintes and maize occurs at a low level and appears most common with Z. mays ssp. mexicana. Phylogeographic and phylogenetic analyses of the Mexican annual teosintes indicated that ssp. parviglumis diversified in the eastern part of its distribution and spread from east to west and that ssp. mexicana diversified in the Central Plateau of Mexico and spread along multiple paths to the north and east. We defined core sets of collections of Z. mays ssp. mexicana and ssp. parviglumis that attempt to capture the maximum number of microsatellite alleles for given sample sizes.

Alleles↗

PubMed2005

An analysis of genetic diversity across the maize genome using microsatellites.

How domestication bottlenecks and artificial selection shaped the amount and distribution of genetic variation in the genomes of modern crops is poorly understood. We analyzed diversity at 462 simple sequence repeats (SSRs) or microsatellites spread throughout the maize genome and compared the diversity observed at these SSRs in maize to that observed in its wild progenitor, teosinte. The results reveal a modest genome-wide deficit of diversity in maize relative to teosinte. The relative deficit of diversity is less for SSRs with dinucleotide repeat motifs than for SSRs with repeat motifs of more than two nucleotides, suggesting that the former with their higher mutation rate have partially recovered from the domestication bottleneck. We analyzed the relationship between SSR diversity and proximity to QTL for domestication traits and observed no relationship between these factors. However, we did observe a weak, although significant, spatial correlation for diversity statistics among SSRs within 2 cM of one another, suggesting that SSR diversity is weakly patterned across the genome. Twenty-four of 462 SSRs (5%) show some evidence of positive selection in maize under multiple tests. Overall, the pattern of genetic diversity at maize SSRs can be explained largely by a bottleneck effect with a smaller effect from selection.

DNA, Plant↗

PubMed2004

Durum wheat as a candidate for the unknown female progenitor of bread wheat: an empirical study with a highly fertile F1 hybrid with Aegilops tauschii Coss.

Hexaploid bread wheat was derived from a hybrid cross between a cultivated form of tetraploid Triticum wheat (female progenitor) and a wild diploid species, Aegilops tauschii Coss. (male progenitor). This cross produced a fertile triploid F1 hybrid that set hexaploid seeds. The identity of the female progenitor is unknown, but various cultivated tetraploid Triticum wheats exist today. Genetic and archaeological evidence suggests that durum wheat ( T. turgidum ssp. durum) may be the female progenitor. In previous studies, however, F1 hybrids of durum wheat crossed with Ae. tauschii consistently had low levels of fertility. To establish an empirical basis for the theory of durum wheat being the female progenitor of bread wheat, we crossed a durum wheat cultivar that carries a gene for meiotic restitution with a line of Ae. tauschii. F1 hybrids were produced without using embryo rescue techniques. These triploid F1 hybrids were highly fertile and spontaneously set hexaploid F2 seeds at the average selfed seedset rate of 51.5%. To the best of our knowledge, this is the first example of the production of highly fertile F1 hybrids between durum wheat and Ae. tauschii. The F1 and F2 hybrids are both similar morphologically to bread wheat and have vigorous growth habits. Cytological analyses of F1 male gametogenesis showed that meiotic restitution is responsible for the high fertility of the triploid F1 hybrids. The implications of these findings for the origin of bread wheat are discussed.

Crops, Agricultural↗

PubMed2003

Directional evolution for microsatellite size in maize.

Directional evolution in microsatellites is the tendency for microsatellites either to increase or to decrease in size over time between populations. We analyzed 99 microsatellite loci in a sample of 193 maize plants representing the entire pre-Columbian range of this crop for evidence of directional evolution. We took advantage of the known phylogeographic history of maize with the independent movement of maize from its ancestral location in Mexico to North and South America. We show that there is an increase in the average allele size of microsatellites in the geographically derived North and South American groups relative to the ancestral Mexican group. We also show that there is a negative correlation between average allele size and altitude in all three groups. Directional evolution in maize microsatellites can be explained by changes in the mutation rate over time and space, changes in the degree of mutational bias to a larger allele, demographic differences between the ancestral and geographically derived populations, and/or scenarios involving selection on microsatellite size. The occurrence of directional evolution for microsatellite size indicates that the estimation of population parameters with microsatellite data in maize should be done with caution.

Alleles↗

PubMed2002

A single domestication for maize shown by multilocus microsatellite genotyping.

There exists extraordinary morphological and genetic diversity among the maize landraces that have been developed by pre-Columbian cultivators. To explain this high level of diversity in maize, several authors have proposed that maize landraces were the products of multiple independent domestications from their wild relative (teosinte). We present phylogenetic analyses based on 264 individual plants, each genotyped at 99 microsatellites, that challenge the multiple-origins hypothesis. Instead, our results indicate that all maize arose from a single domestication in southern Mexico about 9,000 years ago. Our analyses also indicate that the oldest surviving maize types are those of the Mexican highlands with maize spreading from this region over the Americas along two major paths. Our phylogenetic work is consistent with a model based on the archaeological record suggesting that maize diversified in the highlands of Mexico before spreading to the lowlands. We also found only modest evidence for postdomestication gene flow from teosinte into maize.

Genes, Plant↗

PubMed2002

Whole chloroplast genome comparison of rice, maize, and wheat: implications for chloroplast gene diversification and phylogeny of cereals.

The fully sequenced chloroplast genomes of maize (subfamily Panicoideae), rice (subfamily Bambusoideae), and wheat (subfamily Pooideae) provide the unique opportunity to investigate the evolution of chloroplast genes and genomes in the grass family (Poaceae) by whole-genome comparison. Analyses of nucleotide sequence variations in 106 cereal chloroplast genes with tobacco sequences as the outgroup suggested that (1) most of the genic regions of the chloroplast genomes of maize, rice, and wheat have evolved at similar rates; (2) RNA genes have highly conservative evolutionary rates relative to the other genes; (3) photosynthetic genes have been under strong purifying selection; (4) between the three cereals, 14 genes which account for about 28% of the genic region have evolved with heterogeneous nucleotide substitution rates; and (5) rice genes tend to have evolved more slowly than the others at loci where rate heterogeneity exists. Although the mechanism that underlies chloroplast gene diversification is complex, our analyses identified variation in nonsynonymous substitution rates as a genetic force that generates heterogeneity, which is evidence of selection in chloroplast gene diversification at the intrafamilial level. Phylogenetic trees constructed with the variable nucleotide sites of the chloroplast genes place maize basal to the rice-wheat clade, revealing a close relationship between the Bambusoideae and Pooideae.

Chloroplasts↗

PubMed2002

Rate and pattern of mutation at microsatellite loci in maize.

Microsatellites are important tools for plant breeding, genetics, and evolution, but few studies have analyzed their mutation pattern in plants. In this study, we estimated the mutation rate for 142 microsatellite loci in maize (Zea mays subsp. mays) in two different experiments of mutation accumulation. The mutation rate per generation was estimated to be 7.7 x 10(-4) for microsatellites with dinucleotide repeat motifs, with a 95% confidence interval from 5.2 x 10(-4) to 1.1 x 10(-3). For microsatellites with repeat motifs of more than 2 bp in length, no mutations were detected; so we could only estimate the upper 95% confidence limit of 5.1 x 10(-5) for the mutation rate. For dinucleotide repeat microsatellites, we also determined that the variance of change in the number of repeats (sigma(m)2) is 3.2. We sequenced 55 of the 73 observed mutations, and all mutations proved to be changes in the number of repeats in the microsatellite or in mononucleotide tracts flanking the microsatellite. There is a higher probability to mutate to an allele of larger size. There is heterogeneity in the mutation rate among dinucleotide microsatellites and a positive correlation between the number of repeats in the progenitor allele and the mutation rate. The microsatellite-based estimate of the effective population size of maize is more than an order of magnitude less than previously reported values based on nucleotide sequence variation.

Alleles↗

PubMed2002

Plasmon analysis of Triticum (wheat) and Aegilops. 2. Characterization and classification of 47 plasmons based on their effects on common wheat phenotype.

This article comprises our final remarks on the phenotypic effects of alien plasmons on common wheat. Twenty-one vegetative, reproductive, and seed characters of 551 alloplasmic lines of 12 common wheat genotypes with 46 alloplasmons, and as the control, their euplasmic lines were investigated. Effects of genotype, plasmon, and their interaction had high statistical significance for all the characters investigated, whereas phenotypic variations attributable to the alien plasmons were relatively small. Individual plasmon types are characterized by their primary effects on 21 characters. Genotype x plasmon effects on two representative characters, heading date and plant height, are described in detail. Cluster and principal component analyses of the phenotypic effects of the 47 plasmons yielded 22 groups. The relationships between these phenotype-based groups and those defined by molecular differences in organellar genomes were examined. A significant correlation was found with some explainable discrepancies. For efficient plasmon identification, use of six of the present 12 genotypes is proposed. The key for plasmon classification is provided. Our findings indicate that alien plasmons may be of limited value in future wheat breeding, but that the plasmon diversity that exists in Triticum and Aegilops species is of great significance for understanding the evolution of these genera.

Analysis of Variance↗

PubMed2002

[Mucinous adenocarcinoma of the renal pelvis in the horseshoe kidney: a case report].

A 41-year-old man with macroscopic hematuria and abdominal fullness was referred to our hospital. Computed tomography (CT) revealed a left renal pelvic tumor in the horseshoe kidney. We performed left heminephrectomy and ureterectomy. The pathological diagnosis was the mucinous adenocarcinoma in the renal pelvis. He received postoperative adjuvant chemotherapy (CAP therapy). He died of retroperitoneal recurrence 8 months postoperatively. In the literature we found 95 cases of primary adenocarcinoma in the renal pelvis including our case.

Adenocarcinoma, Mucinous↗