Identification and classification of aromatic rices based on DNA fingerprinting

Aromatic rices are preferred by the consumers all over the world due to its flavour and palatability. Although a large number of these collections are available, little systematic analysis of genetic diversity has been carried out. With the objective of identification and classification of aromatic rice genotypes, RAPD profiling was employed using 58 random decamer primers. Most of these primers (96.5%) detected polymorphism among the genotypes. Of the 465 amplified bands, 314 were polymorphic. Cluster analysis based on Jaccard's similarity coefficient using UPGMA grouped all the traditional tall, photosensitive, low yielding, long grained ‘basmati’ aromatics together. The short grained aromatic cultivars, formed a different cluster with high level of average similarity among themselves. The dendrogram based on 58 primers was highly similar to that based on 10 and 15 primers with matrix correlation (r) of 0.88 and 0.91, respectively. This suggested that a set of 10 primers can be employed for an initial assessment of genetic diversity in a large number of collections. All the rice genotypes included in the study could be distinguished from each other at the level of 19 to 186 polymorphic bands between individuals in pair wise comparison over all the 58 primers. Probability of identical profiles by chance suggested that about 10⁴¹ genotypes can be unambiguously differentiated by RAPD fingerprints obtained by 58 primers. A diagrammatic mode of presentation of DNA fingerprints of the aromatic rices based on 10 of the informative primers was developed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Cytogenetical studies on African rice,Oryza glaberrima Steud. 3. Primary trisomics produced by pollinating autotriploid with diploid

Summary In order to promote cytogenetical studies on Oryza glaberrima (2n=2x=24), I produced primary trisomics in the progeny of the autotriploid. When the autotriploid was pollinated with the diploid, 136F1 seeds (5.8% of the number of spikelets pollinated) were obtained. The numbers of chromosomes of 31 surviving progeny varied from 24 to 28, with plants having 2n=25 occurring at the highest frequency (34.4%). The primary trisomics differed from one another as well as from the normal disomics in many aspects. The differences were attributed to a single extra chromosome in each trisomic type. Nine primary trisomics were classified into 8 types on the basis of morphological and reproductive features. Seeds were obtained from all primary trisomics except for Type D by self pollination, open pollination or pollination with the disomics. I was able to maintain 7 types of primary trisomics by seed propagation. The primary trisomics which are capable of expressing subtle genetic dissimilarities should be useful for studying the relationship between the two cultivated species of rice at the level of individual chromosomes.     

Interspecific cytoplasm substitutions of an Indica strain of Oryza sativa L. and O. Glaberrima Steud

Summary To study differential nucleus-cytoplasm interactions between the two cultivated rice species, Oryza sativa and O. glaberrima, cytoplasmic substitution lines were made by using a glaberrima strain (G) and an Indica strain of sativa (S). The G cytoplasm had no adverse effect on pollen development when combined with the nucleus of S. On the other hand, when the S cytoplasm was combined with the G nucleus, the substitution line showed no seed set because of male sterility although the pollen grains were normally stained with I₂-KI solution. A dominant gene derived from S strain seemed to cause anther indehiscence in the substitution line. Further, a restorer gene (Rf _j)from Akebono of Japonica type was effective on pollen restoration in the male sterile line, suggesting that the S cytoplasm is the same as those of Japonica type in terms of a fertility-restoring system.This paper is Genetic studies of speciation in cultivated rice. 4.     

Cytological observations in some hybrids between the rice species Oryza sativa L. and O. glaberrima Steud.

Summary Several hybrids between Oryza sativa and O. glaberrima and their backcrosses with O. sativa were studied. Their seed sterility was very different; large differences were also observed in the level of pollen sterility and in the earliness of microspore failure. The proportion of aborted embryo sacs was much lower than the rate of sterile male gametophytes. The backcross populations were much more sterile than the corresponding F₁ hybrids. On the base of our observations and according to the literature, we may conclude that genic unbalance is the main cause of sterility of these hybrids, but that physiological factors may also be involved. Thus a restoration of fertility is generally possible by selection. On the other hand, male-sterile lines could be bred from some of these hybrids.     

Molecular Mapping of a Pollen Killer Gene S29(t) in Oryza Glaberrima and Co-Linear Analysis with S22 in O. Glumaepatula

Two species in genus Oryza, O. glaberrima and O. glumaepatula, are valuable and potential sources of useful genes of interest for rice improvement. However, the hybrid sterility between O. sativa and these two species is a main reproduction barrier when transferring the favorable traits/genes to mbox{O. sativa.} To overcome it, the nature of hybrid sterility should be understood further. The objective in the report is to map a new hybrid sterility gene as a Mendelian factor from O. glaberrima and analyze the co-linear of hybrid sterility S loci mbox{between} mbox{O. glaberrima} and mbox{O. glumaepatula} via comparative mapping approach. A BC₂F₂ population, derived from a single semi-sterility plant of BC₂F₁ of WAB56-104/ WAB450-11-1-2-P41-HB (WAB450-6) //WAB56-104///WAB56-104 was employed to map this pollen killer in O. glaberrima since WAB450-6 is a progeny of interspecific hybrid between O. sativa and O. glaberrima. A new pollen killer locus, S29(t) in O. glaberrima, was identified and mapped to interval between SSR marker RM7033 (1.1 cM) and RM7562 (1.3 cM) on rice chromosome 2. Comparative mapping indicated that S29(t) closely corresponded to S22 which is also a pollen killer gene in O. glumaepatula and is tightly linked with RFLP marker S910 on the short arm of rice chromosome 2. The good co-linear between S29(t) and S22 implied that there might exist common (orthologous) hybrid sterility loci controlled the reproduction barrier among AA genome species of genus Oryza, which will contribute significantly to our understanding of speciation and operation of hybrid sterility between O. sativa and its AA genome relatives.     

Increasing biodiversity of irrigated rice in Africa by interspecific crossing of Oryza glaberrima (Steud.) × O. sativa indica (L.)

The African rice Oryza glaberrima, traditionally cultivated since more than 3.500 years, is of poor agronomic performance but resistant/tolerant to various stresses and diseases. The introduction of these characters into O. sativa cultivars is difficult since crossing barriers cause spikelet sterility in F1. Backcrossing can restore fertility and recently facilitated the development of fertile O. glaberrima × O. sativa ssp. japonica hybrid progenies for rain fed systems. With the objective to gain access to African rice germplasm for improvement of irrigated rice, crosses were performed with eighteen O. glaberrima and twenty O. sativa ssp. indica accessions. In total about one hundred F1-hybrid grains were obtained. The F1 plants were all completely sterile and backcrossing (BC) to O. sativa was performed in order to restore spikelet fertility. Monitoring of Tog5681 × IR64 hybrid progenies under field conditions revealed a broad genetic diversity within the BC₁ and BC₂ populations. Some BC₁ and BC₂ progeny plants outperformed the O. sativa parent, indicating that the heterozygocity level and complementary gene action after two backcrosses are still sufficient to positively influence plant vigor. Spikelet fertility of progenies was highly variable, but almost complete fertility was already observed within the BC₁F₂ population. High spikelet fertility was preserved in one out of two analyzed BC₁F₃ families and inmost of the BC₂F₃ families. The ability to restore spikelet fertility within few generations and the potential of the genetic diversity present in interspecific progenies facilitates the development of plant types specifically designed for the African irrigated and lowland environment. This revised version was published online in August 2006 with corrections to the Cover Date.     

The indica-japonica classification of Asian rice ecotypes and Japanese lowland and upland rice (Oryza sativa L.)

Summary Rice cultivars (Oryza sativa L.) belonging to five ecotypes (aus, aman, boro, bulu and tjereh) and to two groups of Japanese rice (lowland and upland) are examined with respect to KClO₃ resistance, phenol reaction and apiculus hair length. These characters have been used as available criteria to classify rice into two types indica and japonica, for the last thirty years.The findings of this study are that the aman, boro and tjereh ecotypes should be classified as typical indica; and that the Japanese lowland rice cultivars are mainly typical japonica. Some of the aus, bulu and Japanese upland rice cultivars differ from typical indica and typical japonica, so the respective terms aus type, bulu type and J.u.r. type, are proposed. Aman, boro tjereh and Japanese lowland rice are cultivated in lowland. Some of the aus, bulu and Japanese upland rice cultivars have the characteristics of upland rice. In general, lowland rice cultivars can be clearly classified into indica or japonica, while upland cultivars cannot.Abbreviations Aph dominant gene for apiculus hair length > 0.7 mm - aph recessive gene for apiculus hair length < 0.7 mm - J.u.r. type Japanese upland rice type     

Identification of four genes for stable hybrid sterility and an epistatic QTL from a cross between Oryza sativa and Oryza glaberrima

To further understand the nature of hybrid sterility between Oryza sativa and Oryza glaberrima, quantitative trait loci (QTL) controlling hybrid sterility between the two cultivated rice species were detected in BC₁F₁ and advanced backcross populations. A genetic map was constructed using the BC₁F₁ population derived from a cross between WAB450-16, an O. sativa cultivar, and CG14, an O. glaberrima cultivar. Seven main-effect QTLs for pollen and spikelet sterility were detected in the BC₁F₁. Forty-four sterility NILs (BC₆F₁) were developed via successive backcrosses using pollen sterility plants as female and WAB450-16 as the recurrent parent. Seven NILs, in which the target QTL regions were heterozygous while the other QTL regions as well as most of the reminder of the genome were homozygous for the WAB450-16 allele, were selected as the QTL identification materials. BC₇F₁ for the seven NILs showed a continuous variation in pollen and spikelet fertility. The four identified pollen sterility QTLs were located one each on chromosomes 1, 3, 7 and 7. Pollen sterility loci qSS-3 and qSS-7a were on chromosomes 3 and 7, respectively, which coincides with the previously identified S19, and S20, while loci qSS-1 and qSS-7b on chromosomes 1 and 7L appear distinct from all previously reported loci. An epistatic interaction controlling the hybrid sterility was detected between qSS-1 and qSS-7a.     

Genetic divergence among cold tolerant rices (Oryza sativa L.)

Summary Genetic divergence was investigated among 17 rice varieties known to possess some degree of cold tolerance at different growth stages. The 17 varieties and their 102 F₁ hybrids with 6 male testers were studied for isozyme variation at 15 loci, spikelet fertility, and degree of cold tolerance at various stages. Multivariate analyses of the data provided several schemes of divergence based on various sources of evidence. All schemes gave similar results, and separated the varieties into japonica and indica groups. The japonica group displayed specific isozymes, a low F₁ fertility with indica testers, and a high degree of cold tolerance which was expressed in the F₁ progenies. The indica group displayed contrasting specific isozymes, a high F₁ fertility with indica testers, and a moderate to low degree of cold tolerance which was not expressed in the F₁ progenies. One variety, ARC 6000, displayed unique traits in most schemes and was classified into a distinct type based on the isozymes. The results emphasize that cold tolerance is a major trait for classification of rice into two varietal groups and that proper characterization of potential donors is essential in breeding. Isozyme studies are useful tools for this purpose.     

A gametocidal factor of Oryza glaberrima Steud. in O. sativa L.

Summary Recurrent backcrossing has been carried out with a view to transfer a gene for non-glutinous endosperm from two strains of O. glaberrima (Wx _g /Wx _g ) to glutinous japonica and indica varieties (wx/wx) of Oryza sativa. In the course of backcrosses Wx _g /wx segregants were crossed with each of the two glutinous varieties of sativa as the respective recurrent male parent. The wx/wx and Wx _g /wx segregants in the successive generations were consistently fully fertile and semi-sterile, respectively. The semi-sterility of Wx _g /wx plants was attributable to abortion of most of the pollen grains carrying the gene wx. The nucleus but not cytoplasm was related to the semi-sterility. The Wx _g /Wx plants having the gene for non-glutinous endosperm of a glaberrima strain and a japonica variety of sativa were also semi-sterile. Both wx- and Wx-megaspores in the plants heterozygous for the gene Wx _g were deleteriously affected. The results could be explained by assuming that a factor tightly linked with the gene Wx _g of glaberrima sterilizes gametes not carrying it in the heterozygotes and that the gametocidal action is exerted when combined with the sativa nucleus by the recurrent backcross method.     

Variations of the vascular bundle system in Asian rice cultivars

Summary The capacity of vascular bundle system transporting assimilates from source to sink is one of the limiting factors for rice (Oryza sativa L.) yield. Genetic variation in vascular bundle system should be investigated for improvement of transporting efficiency. A total of 531 Asian rice cultivars were studied for vascular bundles in the peduncle and its relation to spike morphology. A few difference was detected for the number of primary rachis branches of the spike among the cultivars from various countries. However, the number of vascular bundles significantly differed among the cultivars; those from Nepal, Bangladesh and India bore more vascular bundles than those from Japan. Therefore, the ratio of vascular bundles to rachis branches (V/R ratio) was nearly 1.0 in cultivars from Japan, while those from Nepal, Bangladesh and India ranged from 1.3 to 2.2. Chinese and Indonesian cultivars incuded two types of high and low V/R ratios. Cultivars with high V/R ratio showed positive reactions to the phenol solution, while those with low V/R ratio were negative reactions, suggesting that the former cultivars are of Indica type and the latter of Japonica type. It was concluded that the relationship between vascular bundles and rachis branches differentiated among the ecotypes of Asian cultivated rice.     

The transfer of a gene for glutinous endosperm to Oryza glaberrima Steud. From a japonica variety of O. sativa L.

Summary In common rice, Oryza sativa L. (n=12), the gene Am for non-glutinous is dominant over the gene am for glutinous. In African rice, O. glaberrima Steud. (n=12), no spontaneous glutinous strain has been found, but recently a glutinous strain of glaberrima was induced by EMS-treatment.The interspecific cytoplasm substitution line with sativa cytoplasm and glaberrima nucleus is male sterile. It has been confirmed that the complete restoration of pollen fertility in this male sterile line is attributed to a single dominant nuclear gene Rf _j.Trial to transfer gene am from sativa to glaberrima was commenced with backcrosses of the F₁ hybrid (glutinous sativa cv. Iwai-mochi × glaberrima ) to glaberrima type plants of the substitution line homozygous for Rf _j,using the latter as the pollen parent. At the B₁ step, highly fertile glaberrima type Am/am plants were obtained. Thereafter plants of this type were backcrossed to normal glaberrima as the recurrent pollen parent to complete the nuclear substitution. It was confirmed that the EMS-induced glutinous character of glaberrima was a monogenic recessive and that the same gene controls the expression of glutinous character in the different rice species, sativa and glaberrima.     

Genetic studies on the interspecific cytoplasm substitution lines of an Asian perennial strain of Oryza rufipogon Griff. and O. glaberrima Steud.

Summary It is shown that the restorer gene Rf _j extracted from the Japanese rice variety Akebono is effective on pollen restoration in the cytoplasm substitution line having the nucleus of Oryza glaberrima and japonica or indica cytoplasm of O. sativa, and is of the sporophytic type.The Asian perennial type of the wild rice species O. rufipogon is considered to be the progenitor of O. sativa. Two substitution lines having the cytoplasm of a perennial strain of O. rufipogon from Sri Lanka and the nucleus of O. glaberrima with or without the gene Rf _j in homozygous condition have been bred by means of successive backcrosses. These lines have now reached the BC₅ generation. Plants of the lines resemble morphologically the recurrent parent, but do not show pollen restoration, indicating that the cytoplasm of the rufipogon strain induced male sterility and that the gene Rf _j does not act as the restorer.     

Effects of low temperature storage on the pollen of Brassica campestris,B. oleracea and B. napus

Summary Four indica cultivars viz. Kalinga-I, Ptb. 10, IR 27280-13-3-3-3 and Co. 41 were found to possess male sterile cytoplasm with fertility restoring genes while the cultivar Krishna was found to maintain the male sterility in all the cases. All the plants in the F₁ of Kalinga-I × Krishna were observed to be completely male sterile and continued to show complete pollen sterility in subsequent backcross generations when backcrossed with recurring pollen parent, Krishna. Thus, it was posible to develop a new cytoplasmic-genetic male sterile line in indica rice (Krishna A) with Kalinga-I male sterile cytoplasm and this male sterile cytoplasm was found to be genetically different from others. Further, the newly developed male sterile line (Krishna A) was observed to be tolerant for low temperature at seedling stage.     

Photoperiod insensitivity gene essential to the varieties grown in the northern limit region of paddy rice (Oryza sativa L.) cultivation

Summary The release of extremely early maturing varieties has made it possible to cultivate rice in Hokkaido (NL45-42°) in Japan, the northern limit region of paddy rice cultivation. Until then, rice cultivation in this region has been impracticable due to the climate condition, especially short summer and long-day more than 15 hours during summer. Experiment results confirmed that the success of rice cultivation in this area depends on raising photoperiod insensitivity varieties with short basic vegetative growth period. Moreover, in this study, the genetic factors controlling the photoperiod insensitivity of Hokkaido varieties were analyzed by using 8 kinds of tester lines for three loci, E1, E2, and E3, controlling photoperiod sensitivity. It was found out that all the varieties examined carry el, a photoperiod insensitivity allele of E1 locus, but as for the other loci, E2 and E3, the existence of plural alleles were recognized. We have already clarified that almost all the japonica-type varieties grown in Japan (except Hokkaido) and Taiwan carry E1 bringing about strong photoperiod sensitivity. Accordingly, it can be concluded that el is the gene essential to Hokkaido varieties: the interchange of E1 with e1 enabled rice cultivation under long-day condition.     

Genetic characterization of rainfed upland New Rice for Africa (NERICA) varieties

A total of 18 rainfed upland New Rice for Africa (NERICA) varieties were categorized as the heavy panicle and low tillering types and early heading, in compared with 32 different varieties. These chromosome components were clarified using 243 SSR markers which showed polymorphism among NERICA varieties and their parents, CG 14 (O. glaberrima Steud.) and one of the recurrent parents, WAB-56-104 (O. sativa L.). NERICA varieties were classified into three groups, which corresponded with these parents’ continuation including two exceptions, NERICAs 14 and 17, by a cluster analysis using polymorphism data of SSR markers and 14 differential markers among them were selected to classify NERICA varieties. However, three groups: NERICAs, 3 and 4, NERICAs, 8, 9 and 11 and NERICAs, 15 and 16 were not distinguishable. Association analysis was carried out for characterization of NERICA varieties by using SSR markers genotype and phenotype of agronomic traits. A total of 131 quantitative trait loci between SSR markers and 11 agronomic traits were detected. The characteristics of early maturity and heavy panicle of upland NERICA varieties were succeeded from Asian rice varieties and the characteristics of high dry matter production and late heading were introduced from CG 14 and the other varieties.     

Studies on the distribution of complementary genes causing F1 weakness in common rice and its wild relatives. 2. Distribution of two complementary genes,Hwc-1 and Hwc-2 gene in native cultivars and its wild relatives of tropical Asia

Summary Distribution of two complementary genes Hwc-1 and Hwc-2 causing F₁ weakness was examined using 159 native rice cultivars and 30 strains of wild relatives collected from various sites of tropical Asia including the Himalayan foothills. Hwc-1 is carried by a Peruvian cultivar, Jamaica, a tester cultivar of this experiment. It was not found in the tested cultivars and strains. Hwc-2 was widely distributed in the Japonica types tested. No wild strains had either Hwc-1 or Hwc-2. Hwc-2 was infrequent in the Japonica types collected from Southern Asian countries. Hwc-2 was estimated to be indigenous to the Japonica types, may be linked with certain gene(s) related to adaptation.     

Inheritance of scent in rice

Summary Inheritance of scent in rice and its association with pigmented characters were studied in T-141 × K-44-1. Four complementary genes appeared to control scent, one of them showing linkage with a complementary gene for glume colour and a supplementary gene for red pigment in apiculus. This group formed part of V (Prp)linkage group of Misro et al. (1966) in which case Pg and P were additions.Pl.480 Project on linkage maps in rice.     

Genetic studies on the interspecific cytoplasm substitution lines of japonica varieties of Oryza sativa L. and O. glaberrima Steud.

Summary Interspecific cytoplasm substitution lines of Oryza sativa and O. glaberrima, i.e. (sativa)-glaberrima and (glaberrima)-sativa, have been bred by means of successive backcrosses, using three japonica varieties of sativa and two glaberrima strains.In all the six substitution lines with the cytoplasm of the glaberrima strains, the fertility increased with succeeding backcrosses, and eventually completely fertile plants whith the characteristics of the parental japonica variety appeared. This indicates that the glaberrima cytoplasm exerted no effect on the genome manifestation of these japonica varieties. Of the five substitution lines with the cytoplasm of each of the japonica varieties, four lines produced male sterile (M.S.) plants only in the backcross generations. In the remaining substitution line with the cytoplasm of the japonica variety Akebono, there was simultaneous segregation for male sterile (M.S.) and pollen fertile plants bearing indehiscent anthers (ID.M.F.) in the backcross generations. In the compulsively selfed progeny of ID.M.F. plants, pollen fertile plants with dehiscent anthers (D.M.F.) occurred with M.S- and ID.M.F. plants. Morphologically, these three types were supposed to have the same genetic background as the glaberrima parent. It was established that D.M.F.-and ID.M.F. plants were homozygous and heterozygous for a dominant nuclear gene restoring pollen fertility, respectively, and the M.S. plants and the two glaberrima strains used in this study carried a recessive gene for pollen sterility in homozygous condition. The restorer gene was assumed to derive from the japonica variety Akebono. The expression of the restorer gene was of the sporophytic type. The pollen sterility of the substitution lines that possessed the cytoplasm of the japonica varieties was of cytoplasmon-genic nature.