Kazumitsu Onishi

Cold tolerance at the early growth stage in wild and cultivated rice

The present study was conducted to understand the pattern of variation and the genetic bases for cold tolerance at the early growth stage in Asian rice. The genetic variation was investigated at the germination, plumule and seedling stages among 57 strains including cultivated rice (Oryza sativa ssp. indica and ssp. japonica) and its wild progenitor (Oryza rufipogon). The significant differentiation of cold tolerance was observed among the taxonomically divided groups. At the germination stage, both indica and japonica subspecies tended to be more tolerant than O. rufipogon, whereas at the plumule and seedling stages, ssp. japonica tended to be more tolerant than ssp. indica and O. rufipogon. Furthermore, in cold tolerance at the plumule stage, the clinal variation across the latitude of origins was observed within O. rufipogon and ssp. japonica, suggesting that the current pattern of variation seems to have been shaped by both their phylogenetic histories and on-going adaptation to the local environments. QTL analysis between O. sativa ssp. japonica (tolerant) and O. rufipogon (susceptible) revealed five putative QTLs for cold tolerance at the plumule and seedling stages but not at the germination stage. Substitution mapping was also carried out to precisely locate the two major QTLs for cold tolerance at the plumule stage, which could be used for improvement of tolerance to cold stress in ssp. indica.

Different patterns of genealogical relationships found in the two major QTLs causing reduction of seed shattering during rice domestication

The three quantitative trait loci (qSH1, qSH3, and qSH4) causing reduction of seed shattering were investigated to examine their relative importance during rice domestication. The qSH1 and qSH4 loci showed a distinct effect on the reduction of shattering, compared with the qSH3 locus. Fine mapping and sequence analysis strongly suggested that the qSH1 and qSH4 loci are the same as the recently reported genes. A non-shattering allele at qSH1 drastically changed the shattering phenotype to a non-shattering phenotype even in the presence of shattering alleles at the qSH3 and qSH4 loci, showing that qSH1 is genetically epistatic to the other loci. The level of the reduction in sequence diversity was compared between the qSH1 and qSH4 regions. The sequence diversity was severely reduced in the qSH1 region of Oryza sativa subsp. japonica compared with that of O. sativa subsp. indica, despite that the level of diversity was similarly reduced at the qSH4 region in the 2 subspecies. Phylogenetic reconstruction based on the combined sequences of the flanking sites showed different patterns in the 2 subspecies. The 2 subspecies formed a single clade with respect to qSH4, whereas they were separated into different lineages with respect to qSH1, suggesting that these loci had different histories during rice domestication.

Sex‐independent transmission ratio distortion system responsible for reproductive barriers between Asian and African rice species

* A sex-independent transmission ratio distortion (siTRD) system detected in the interspecific cross in rice was analyzed in order to understand its significance in reproductive barriers. The S(1) gene, derived from African rice Oryza glaberrima, induced preferential abortion of both male and female gametes possessing its allelic alternative (), from Asian rice O. sativa, only in the heterozygote. * The siTRD was characterized by resolving it into mTRD and fTRD occurring through male and female gametes, respectively, cytological analysis of gametophyte development, and mapping of the S(1) locus using near-isogenic lines. The allelic distribution of the S(1) locus in Asian and African rice species complexes was also analyzed. * The siTRD system involved at least two components affecting male and female gametogeneses, respectively, including a modifier(s) that enhances fTRD. The chromosomal location of the major component causing the mTRD was delimited within an approx. 40 kb region. The S(1) locus induced hybrid sterility in any pairwise combination between Asian and African rice species complexes. * The allelic state of the S(1) locus has diverged between Asian and African rice species complexes, suggesting that the TRD system has a significant role in the reproductive barriers in rice.

Diversification in flowering time due to tandem FT-like gene duplication, generating novel Mendelian factors in wild and cultivated rice.

The complex structure of a single Mendelian factor widespread in the Asian cultivated rice (Oryza sativa) and its wild progenitor (Oryza rufipogon) that caused diverse phenotypes in the timing of flowering under natural field conditions was investigated in near isogenic lines. These near isogenic lines showed differences in flowering time despite all eight accessions collected from tropical regions possessing a recessive gene allelic to the se‐pat gene. Fine mapping in two of these near‐isogenic lines revealed that cultivated (Patpaku) and wild (W593) accessions had three and two linked quantitative trait loci (QTL) in the candidate regions, respectively, showing that Patpaku and W593 possessed linked QTLs with different effects in addition to the commonly‐observed recessive gene (se‐pat). Molecular dissection suggested that the tandemly duplicated FT‐like genes (Hd3a and RFT1) could be the candidate genes for these QTLs. Interestingly, the linked QTLs differed in their epistases, degree of dominance, and genotype × environment interactions. The nucleotide sequences showed that RFT1 has diverged more rapidly than Hd3a during rice evolution, suggesting phenotypic diversification of the two genes. Phylogenetic analysis implied that the se‐pat+ alleles might have emerged in different lineages within O. sativa. The present results strongly suggest that nucleotide divergence and shuffling of the linked QTLs by recombination might have created novel Mendelian factors that probably contribute to responding to local environments.

The Evolution of Sex-Independent Transmission Ratio Distortion Involving Multiple Allelic Interactions at a Single Locus in Rice

Transmission ratio distortion (TRD) is frequently observed in inter- and intraspecific hybrids of plants, leading to a violation of Mendelian inheritance. Sex-independent TRD (siTRD) was detected in a hybrid between Asian cultivated rice and its wild ancestor. Here we examined how siTRD caused by an allelic interaction at a specific locus arose in Asian rice species. The siTRD is controlled by the S6 locus via a mechanism in which the S6 allele acts as a gamete eliminator, and both the male and female gametes possessing the opposite allele (\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(S_{6}^{\mathrm{a}}\) \end{document}) are aborted only in heterozygotes (\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(S_{6}/S_{6}^{\mathrm{a}}\) \end{document}). Fine mapping revealed that the S6 locus is located near the centromere of chromosome 6. Testcross experiments using near-isogenic lines (NILs) carrying either the S6 or \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(S_{6}^{\mathrm{a}}\) \end{document} alleles revealed that Asian rice strains frequently harbor an additional allele (\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(S_{6}^{\mathrm{n}}\) \end{document}) the presence of which, in heterozygotic states (\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(S_{6}/S_{6}^{\mathrm{n}}\) \end{document} and \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(S_{6}^{\mathrm{a}}/S_{6}^{\mathrm{n}}\) \end{document}), does not result in siTRD. A prominent reduction in the nucleotide diversity of S6 or \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(S_{6}^{\mathrm{a}}\) \end{document} carriers relative to that of \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(S_{6}^{\mathrm{n}}\) \end{document} carriers was detected in the chromosomal region. These results suggest that the two incompatible alleles (S6 and \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(S_{6}^{\mathrm{a}}\) \end{document}) arose independently from \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(S_{6}^{\mathrm{n}}\) \end{document} and established genetically discontinuous relationships between limited constituents of the Asian rice population.

Transgressive segregation due to linked QTLs for grain characteristics of rice

SummaryIt has been theoretically proposed that multiple linked quantitative trait loci (QTLs) play a role in the accumulation of hidden variation within and between populations. In this study, the genetic bases for grain characteristics were examined by comparing two accessions representing the two rice subspecies by QTL analysis. Grain dimensions are known to be quantitative traits and to be diagnostic between these two subspecies. To enhance the power to detect QTL with small effects, after transferring a segment of chromosome 6 from an Indica type into a Japonica type of rice by repeated backcrosses, the introgressed segment was dissected by making recombinant inbred lines (RILs) which were expected to have different sizes of the introgressed segment in the same genetic background. The resulting RILs showed distinct transgression of the grain characteristics examined. Multiple QTLs controlling each of the length and breadth of seeds were detected on the introgressed segment, and showed positive and negative additive effects as well as epistatic interactions. The present study confirmed that transgressive segregation resulted from a breakdown of linkage and that the detection of QTLs was highly dependent upon the genetic effects of the neighboring QTLs, indicating the need for caution in interpreting QTL effects.

Complex genetic nature of sex-independent transmission ratio distortion in Asian rice species: the involvement of unlinked modifiers and sex-specific mechanisms

Transmission ratio distortion (TRD), in which one allele is transmitted more frequently than the opposite allele, is presumed to act as a driving force in the emergence of a reproductive barrier. TRD acting in a sex-specific manner has been frequently observed in interspecific and intraspecific hybrids across a broad range of organisms. In contrast, sex-independent TRD (siTRD), which results from preferential transmission of one of the two alleles in the heterozygote through both sexes, has been detected in only a few plant species. We previously reported an S6 locus-mediated siTRD, in which the S6 allele from an Asian wild rice strain (Oryza rufipogon) was transmitted more frequently than the S6a allele from an Asian cultivated rice strain (O. sativa) through both male and female gametes in heterozygous plants. Here, we report on the effect of a difference in genetic background on S6 locus-mediated siTRD, based on the analysis using near-isogenic lines and the original wild strain as a parental strain for crossing. We found that the degree of TRD through the male gametes varied depending on the genetic background of the female (pistil) plants. Despite the occurrence of TRD through both male and female gametes, abnormality was detected in ovules, but not in pollen grains, in the heterozygote. These results suggest the involvement of unlinked modifiers and developmentally distinct, sex-specific genetic mechanisms in S6 locus-mediated siTRD, raising the possibility that siTRD driven by a single locus may be affected by multiple genetic factors harbored in natural populations.

Effects of acclimation on chilling tolerance in Asian cultivated and wild rice

Tolerance to low temperature can be enhanced by pre-exposure to low, non-harmful temperatures, a process known as acclimation. The effects of acclimation on chilling tolerance in species from tropical and subtropical regions are not well understood. Therefore, we investigated whether acclimation improved chilling tolerance at the plumule and seedling stages in Asian rice. A comparison of the effect of acclimation between chilling tolerance scores from a tolerant (A58) and a susceptible (W107) strain demonstrated that acclimation enhances chilling tolerance especially in the tolerant strain, indicating that considerable genetic variation in acclimation capacity exists. The genetic variation in chilling tolerance in acclimated plants was investigated using 57 strains derived from cultivated (Oryza sativa L. ssp. japonica and ssp. indica) and wild (O. rufipogon Griff.) rice. The genetic differentiation of the japonica and indica subspecies of cultivated rice with regard to chilling tolerance was more prominent in the presence than in the absence of acclimation. Furthermore, latitudinal clines for chilling tolerance were observed in both acclimated plumules and seedlings of wild rice, whereas without acclimation, a latitudinal cline was observed only at the plumule stage. This suggests that acclimation capacity, as well as intrinsic chilling tolerance, might contribute to local adaptation. QTLs involved in acclimated chilling tolerance at the plumule stage are different from those involved in intrinsic chilling tolerance. The present results indicate that the maximum genetic potential for chilling tolerance is achieved by acclimation, giving cautions for evaluation of genetic resources in rice.

Developmental Fates of Axillary Buds as a Major Determinant for the Pattern of Life History in Lolium

Abstract The architecture of a grass population is determined by the spatial distribution and morphology of tillers. The demographic and phase changes of tillers were compared between an annual-like (Progrow) and perennial (Ruanui) lines of Loliumspecies. We investigated the developmental fate of axillary buds for 57 weeks after germination (WAG) under a constant condition. In general, a high production of seeds is positively correlated with the annual habit in plants. A high production of seeds was highly associated with % reproductive tillers in annual¬like Progrow, which resulted from the death of non-reproductive or vegetative tillers before heading. However, no such tendency was observed in perennial Ruanui. This showed that the death of tillers is genetically regulated to contribute to the maximum success in fitness depending on the longevity. In addition, % reproductive tillers was distinctly reduced during the following regrowth in Ruanui, suggesting that a phase change in the tiller system took places during the growth. Microscopic observations of quiescent axillary buds showed that a phase change from reproductive to vegetative occurred at maturity in Ruanui but not in Progrow. As a result, numerous ears developed in Ruanui plants only when they were vernalized after first maturation (30 WAG), showing that the vernalized state gradually diminishes with time in Ruanui. Thus, the present results confirmed that the differential regulation in the develop¬mental fate of axillary buds actually plays a role for determining the pattern of life history in Lolium.

Genetic architecture underlying the evolutionary change of competitive ability in Asian cultivated and wild rice

ABSTRACT Breeding of competitive cultivars has long been fraught with difficulty owing to limited knowledge of the genetic basis of competitive ability. In this study, we examined the diversity of competitive ability in Asian rice and the genetic basis of this variation. Cultivated strains and wild perennial strains have higher competitive ability than wild annual strains. Quantitative trait locus (QTL) analysis of competitive ability for three weed species was conducted in the cross between cultivated and wild annual strains, and three QTLs for general competitive ability (GCA) were identified. GCA-QTLs conferred higher competitive ability by the cultivated rice alleles and were co-located with QTLs for plant architecture and root growth, detected in the same mapping population. Furthermore, a significant change in GCA was achieved by accumulation and epistatic interaction of three QTLs. Further studies on the genetic control of competitive ability would facilitate the breeding of competitive cultivars in rice.