Hiroko Morishima

Genomic regions affecting seed shattering and seed dormancy in rice

Abstract Non-shattering of the seeds and reduced seed dormancy were selected consciously and unconsciously during the domestication of rice, as in other cereals. Both traits are quantitative and their genetic bases are not fully elucidated, though several genes with relatively large effects have been identified. In the present study, we attempted to detect genomic regions associated with shattering and dormancy using 125 recombinant inbred lines obtained from a cross between cultivated and wild rice strains. A total of 147 markers were mapped on 12 rice chromosomes, and QTL analysis was performed by simple interval mapping and composite interval mapping. For seed shattering, two methods revealed the same four QTLs. On the other hand, for seed dormancy a number of QTLs were estimated by the two methods. Based on the results obtained with the intact and de-hulled seeds, QTLs affecting hull-imposed dormancy and kernel dormancy, respectively, were estimated. Some QTLs detected by simple interval mapping were not significant by composite interval mapping, which reduces the effects of residual variation due to the genetic background. Several chromosomal regions where shattering QTLs and dormancy QTLs are linked with each other were found. This redundancy of QTL associations was explained by ”multifactorial linkages” followed by natural selection favoring these two co-adapted traits.

VARIATIONS IN THE BREEDING SYSTEMS OF A WILD RICE, ORYZA PERENNIS

An important factor determining the genetic structure and evolutionary dynamics of a population is its breeding system. I t differs among plant species as has been surveyed by Fryxell (1957) but its variation within a species is little known. Oryza perennis Moench is distributed throughout the tropical countries of the world, and comprises many varieties or forms with different propagation habits. They can be divided into four main geographical groups or races, Asian, American, African, and Oceanian, distinguished by characterassociation patterns and F1 sterility relationships, though not by single characters (the writers’ unpublished data). The Asian race tends to differentiate into perennial (perennis or bdunga) and annual (spontanea or fatua) types, though there are many intermediates (Morishima et a]., 1961), and the perennial type may be the progenitor of cultivated rice, 0. sativa L. (Oka and Chang, 1962; Oka, 1964). The Oceanian race also seems to contain perennial and annual types. The African race, called 0. perennis subsp. barthii, is highly rhizomatous, while the American race, comprising a Cuban form called 0. cubensis Ekman and other South American forms, appears to vary from perennial to annual. In contrast, another cultivated species, 0. glaberrima Steud., and its wild progenitor, 0. breviligulata A. Chev. et Roehr., endemic to West Africa, are wholly annuals (Morishima et al., 1963). To investigate how the variation in the breeding system of 0. perennis is related to that in the mode of adaptation, the writers made a survey of breeding characters of various strains. Data for 0. pa-

Genetic characterization of weedy rice (Oryza sativa L.) based on morpho-physiology, isozymes and RAPD markers

Abstract Weedy rice (Oryza sativa L.) is an important resource for breeding and for studying the evolution of rice. The present study was carried out to identify the genetic basis of the weedy rices distributed in various countries of the world. One hundred and fifty two strains of weedy rice collected from Bangladesh, Brazil, Bhutan, China, India, Japan, Korea, Nepal, Thailand and the USA were tested for variations in six morpho-physiological characteristics and in 14 isozyme loci. Twenty six weedy strains selected from the above materials were assayed for the Est-10 locus, six RAPD loci of the nuclear genome, and one chloroplast locus. From the results of multivariate analysis based on the morpho-physiological characteristics and the isozymes, weedy rice strains were classified into indica and japonica types, and each type was further divided into forms resembling cultivated and wild rice. Thus, four groups designated as I, II, III and IV were identified. Weedy strains of group I (indica-type similar to cultivars) were distributed mostly in temperate countries, group II (indica-type similar to wild rice) in tropical countries, group III (japonica-type similar to cultivars) in Bhutan and Korea, group IV ( japonica-type similar to wild rice) in China and Korea. In group I, classified as indica, several strains showed japonica-specific RAPD markers, while some others had japonica cytoplasm with indica-specific RAPD markers in a heterozygous state at several loci. One weedy strain belonging to group II showed a wild rice-specific allele at the Est-10 locus. However, in groups III and IV, no variation was ound either for the markers on Est-10 or for the RAPD loci tested. Judging from this study, weedy rice of group I might have originated at least partly from gene flow between indica and japonica, whereas that of group II most probably originated from gene flow between wild and cultivated indica rice. Weedy rice of group III is thought to have originated from old rice cultivars which had reverted to a weedy form, and that of group IV from gene flow between japonica cultivars and wild rice having japonica backgrounds.

Differentiation of perennial and annual types due to habitat conditions in the wild riceOryza perennis

Populations of the common wild rice of AsiaO. rufipogonGriff. (=Oryza perennisMoench) were studied with regard to interrelations between life-history traits and habitat conditions. They showed a perennial-annual continuum and differed in reproductive allocation and many other traits. Perennial populations were found in deep swamps, while annual populations were in shallower, temporary swamps which were parched in the dry season. The perennial and annual types tended to be in association with other perennial and annual plants, respectively, suggesting their niche differentiation. Intermediate perennial-annual populations were in communities with a high species diversity. In one population, plants growing on the periphery of the swamp were of annual and those in deeper center were of perennial type. Another population seemed to be differentiated into an annual and an intermediate type in accordance with different degrees of habitat disturbance. The small genetic distances found between the sub-populations suggested their differentiation within a gene pool.

Population genetic structure of wild rice Oryza glumaepatula distributed in the Amazon flood area influenced by its life-history traits

Wild plant species develop their own way of living to adapt to the specific environment of their habitats. Their life‐history traits strongly affect the genetic structure of the population. The wild species Oryza glumaepatula Steud. growing in the Amazon basin seems to have characteristic life‐history traits suited for the flood condition. At the vegetative growth stage, the culms frequently break at internodes. With no roots anchoring on the ground, plant bodies floating in the water move downriver by water current and wind. To examine the association between the life‐history traits and genetic population structure of Amazonian O. glumaepatula, we analysed allozyme variability at 29 loci of 16 enzymes using 37 populations from five regions. Allozymes were not so variable (total gene diversity HE = 0.044) compared with Asian wild rice, O. rufipogon Griff. The bottleneck effect and rare opportunity of interspecies gene flow may prevent the development of allozyme variability. Population genotypes tended to be differentiated among geographically isolated regions. Observed heterozygosities were much lower than expected heterozygosities, or gene diversity (HO = 0.003 for whole population) and FIS over polymorphic loci was 0.931, indicating that O. glumaepatula has developed an inbreeding system. But, the intrapopulation gene diversity (HS) was higher than interpopulation gene diversity (DST), as generally observed in outbreeding populations. The migration ability of O. glumaepatula makes long‐distance seed dispersal possible. This might have led to frequent gene flow among populations.

PHENETIC SIMILARITY AND PHYLOGENETIC RELATIONSHIPS AMONG STRAINS OF ORYZA PERENNIS , ESTIMATED BY METHODS OF NUMERICAL TAXONOMY

The relationship between taxa can be estimated from different viewpoints: (a) comparison of characters ranging from protein structure to outward appearance (phenetics, if overall similarity is considered), (b) crossability, meiotic chromosome behavior, fertility and other features of hybrids, (c) ecological and distributional features, and so on. These represent different aspects of relationship between existing taxa, but do not necessarily indicate phylogeny. The advances in numerical taxonomy, however, have inevitably tempted workers to consider the possibility of deduction of phylogeny by numerical evaluation of information obtained from existing organisms (Doolittle and Blomback, 1964; Camin and Sokal, 1965; Wilson, 1965; Throckmorton, 1965; Fitch and Margoliash, 1967; Cavalli-Sforza and Edwards, 1967; Horne, 1967). Oryza perennis Moench is a wild species distributed in swampy habitats throughout the humid tropics, and is a complex of different forms. Usually its strains are classified into Asian, African and American forms or groups (I. R. R. I. 1964, p. 251252). The taxonomy and nomenclature of this species have been a matter of controversy among taxonomists; Tateoka (1963) considered the African form as a distinct species, 0. barthii A. Chev., and called other forms 0. rufipogon Griff., while Henderson (1964) considered all three forms as subspecies of 0. perennis. The present writer takes the latter view. The Asian annual form has become known under various names, for instance, 0. sativa f. spontanea Roschev. or 0. sativa var. fatua Prain or 0. rufipogon subsp. rufipogon. It is considered here as a form of 0. perennis, since the strains of the Asian group show a continuous array of intergrades between perennial and annual types (Morishima et al., 1961). Further, the present work suggests that certain strains from New Guinea and Australia may be considered as a new, Oceanian, form. The various strains all have the same number of chromosomes (n = 12), and can be hybridized with one another. The F1 hybrids show no disturbance in meiotic chromosome pairing, but show sterilities of varying degrees and some other deteriorative phenomena (Chu et al., 1969). The strains are adapted to different kinds of ecological niches and differ in their breeding system (Oka and Morishima, 1967). We initiated studies of this species because its Asian perennial form was considered to be the progenitor of cultivated rice, Oryza sativa L. (Oka and Chang, 1962; Oka, 1964). For a systematic investigation of variations within 0. perennis, data for various characters of the strains and their F1 sterility relationships were analyzed by methods of numerical taxonomy. This paper deals with the methods and results, distinguishing between the phenetic and phylogenetic standpoints. An attempt was made to introduce a relative time scale into the diagram showing the hypothesized phylogenetic relationships of the strains.

Intermediate perennial-annual populations ofOryza perennis found in Thailand and their evolutionary significance

To reexamine the mode of variations in adaptive mechanisms in the Asian form ofOryza perennis, the breeding behavior of natural populations was observed at eight sites selected in Thailand. One population consisted of seedlings only (annual), and five consisted of ratooned plants only (perennial), while two others were mixtures of both. The annual population had a larger number of buried seeds at the habitat than had the others. In the habitat of the annual population, annual species were predominant, while perennial populations tended to coexist with perennial species. The annual population was in a temporary swamp, while perennial populations were found at sites more deeply inundated in the rainy season and retaining moisture in the dry season. This indicated the role of water stress in conditioning the reproductive strategy.Observations of character variations among plants from those populations in a uniform condition proved that the seedling population was of an annual type while those performing mixed sexual and asexual propagations were of an intermediate perennial-annual type. Isoenzymic variations controlled by alleles at two known loci indicated that the two intermediate populations were highly polymorphic and heterozygous. One of them consisted of nine separate clumps which differed in their characteristics. On the basis of these observations, the dynamics of differentiation of this species in adaptive strategy is discussed. It is further suggested that the intermediate perennial-annual type is probably the wild progenitor ofO. sativa.

The extinction of genetic resources of Asian wild rice, Oryza rufipogon Griff.: A case study in Thailand

Natural populations of wild rice, Oryza rufipogon Griff., are now threatened with the disturbance of their natural habitats by various human activities. To obtain basic information on genetic erosion or loss of genetic diversity in wild rice, we investigated how environmental changes of habitat affected the genetic structure of its natural population at a study site in the central plain of Thailand. During 10 years from 1985 to 1994, the wild-rice population at this site was seriously destroyed and fragmented. Using two sets of seed sample collected in 1985 and 1994 from the same population, allozyme variability at 17 loci of 11 enzymes were examined. Isozyme genotypes of mother plants of seed samples were estimated by the segregation in each progeny, and we calculated genetic parameters for the population. Gene diversity severely decreased in the 1994 sample compared with the 1985 sample. It is supposed that declining and fragmentation of the wild rice population, which happened during the 10 years, caused loss of genetic variability and forced the habitually outbreeding plants to inbreed, accelerating a reduction in gene variability. Pgi1-1 allele which was common in Indica rice cultivars of this region was found in the wild rice plants growing at the side of rice fields. Probably, introgression has occurred between wild and cultivated rice plants, and consequently the intrinsic nature of wild rice was gradually blurred by cultivar genes. We must realize that the genetic erosion of wild rice is rapidly proceeding and that an action for their conservation in natural environment, so called in situ conservation, is urgently needed.

Phylogenetic differentiation of cultivated rice, XXIII. Potentiality of wild progenitors to evolve the Indica and Japonica types of rice cultivars

SummaryStudies of intermediate wild-cultivated plants suggested that the Indica-Japonica differentiation of cultivars of Oryza sativa L. has taken place with the domestication of wild plants. The wild progenitor, which is considered to be the Asian form of O. perennisMoench, shows no trace of differentiation into two such types as the Indica and Japonica. To elucidate the potentiality of the wild progenitor to evolve the two types when domesticated, the selfed progenies from an Indica × wild and a japonica × wild cross were examined with regard to three characters known to be useful for distinguishing between the two types. The data showed that Japonica-like plants were derived from the Indica × wild cross and Indica-like plants from the Japonica × wild cross. The Indica-Japonica differentiation was considered to have resulted from selection of incipient domesticates having such potentiality under different climatic conditions; the dynamics was discussed.

COMPARISON OF MODES OF EVOLUTION OF CULTIVATED FORMS FROM TWO WILD RICE SPECIES, ORYZA BREVILIGULATA AND O. PERENNIS

Oryza breviligulata A. Cheval. et Roehr., growing wild in West Africa, is genetically closely related to 0. glaberrima Steud., which is cultivated by the native people of the same region. 0. stapfii Roschev., also found in West Africa, can be regarded as synonymous with 0. breviligulata, as will be pointed out later. These species form an endemic group distinct from the common cultivated rice, 0. sativa L. and the wild species closely related to it, 0. perennis Moench. They can be distinguished from 0. sativa and 0. perennis by short, roundish ligules and other characters, and their F1 hybrids with the latter two species, though they show no disturbance in chromosome pairing, are highly sterile (Morinaga and Kuriyama, 1957; Nezu et al., 1960; etc.). Another wild form occurring in Africa, 0. barthii A. Cheval., is considered by us as an African variety of 0. perennis which can be distinguished from Asian and American forms of the same species by the remarkable rhizome development (Chatterjee, 1948; Sampath and Rao, 1951; Sampath, 1961) . The above rice species may for the sake of simplicity be divided into two series, Series Glaberrima comprising 0. glaberrima and 0. breviligulata, and Series Sativa comprising 0. sativa and 0. perennis. This paper deals mainly with the comparison of the two series regarding the mode of evolution of cultivated forms. Regarding the phylogenetic relationships in Series Sativa, a number of systematic and cytogenetic studies have been made (Chatterjee, 1951; Sampath and Rao,