Inheritance and linkage relationship of scent in rice

Summary The inheritance of scent in rice and linkage relationship of genes governing scent with those controlling leaf sheath colour, ripening hull colour and apiculus pigmentation were studied in a cross between Pankaj (nonscented) and Kalabhat (scented) rice cultivars. The scent was identified by leaf analysis.Two dominant complementary genes Sk ₁ and Sk ₂ were found to be responsible for controlling scent. Either of the genes produce mild scent, the presence of both Sk ₁ and Sk ₂ is necessary for production of parental type scent. The genes were independent of other genes controlling leaf sheath colour, ripening hull colour and apiculus pigmentation.     

Studies on the amylose content and gelatinisation temperature in certain local cultivars and induced grain shape mutants in rice

Summary Ninety local cultivars and 124 induced grain shape mutants were screened for their amylose content and gelatinisation temperature as indexed by the alkali disintegration patterns. The amylose content was high in most of the local cultivars and ranged from 19.2 to 32.0% and from 12.3 to 33.2% in the mutants. Wide variation was also observed for the alkali disintegration values and most of the varieties had low alkali values. A positive but low correlation between alkali values and amylose content and a negative correlation between alkali values and protein content was observed. The preliminary studies suggest that the amylose content at different milling levels increased with an increase in the level of milling. Some of the local cultivars and induced mutants were found to be superior with high amylose and high gelatinisation temperature and could be utilized in breeding programmes directed towards improving the cooking quality of high yielding varieties.     

Quantitative chromosome map of a representative indica rice

The somatic chromosomes of standard indica diploid rice, IR 36, were squashed on glass slides and stained with Giemsa. The condensation patterns (CP) of prometaphase chromosomes were quantitatively analysed using CHIAS III software. The relative length and centromeric index (CI) were converted from CHIAS III to numerical data and calculated by EXCEL program. The ideogram based on CP of indica rice was established. There were 2 pairs of satellite chromosomes and the result was confirmed by fluorescence in situ hybridization using 45S rDNA as a probe. This revised version was published online in July 2006 with corrections to the Cover Date.     

A diversity analysis of genetic resources in rice

Summary A total of 1407 japonica and 488 indica accessions representing nine countries were randomly drawn from the International Rice Research Institute catalog of germ plasm resources for an analysis of diversity. The qualitative gene frequencies as well as means and coefficients of variation for quantitative traits for each race and country in general confirmed the widely recognized pattern of indica-japonica differentiation but suggested more overlap than often realized. Use of a diversity index showed indica to be more variable than japonica, but with different countries having similar levels of diversity. A multivariate analysis based on 39 characters showed divergence among countries within each race but with a great amount of overlap in the scatter of individual entries. This study was carried out simply to illustrate some genetic resource analyses and it is therefore discussed in relation to the documentation aspects.     

Inheritance studies of characters associated with floating habit and their linkage relationship in rice

Summary Deep water rice varieties in general have certain peculiar characters which are associated with floating habit. These characters are (i) early nodal differentiation, (ii) nodal rooting, (iii) spreading habit, (iv) awned grains, (v) brown hull colour, (vi) red pericarp (red rice), and (vii) seed dormancy. Inheritance of these characters and linkage relationship of genes governing these characters were studied in a cross between Pankaj (non floating) and Nageribao (floating) rice varieties. Nageribao, a cultivar from Assam possesses these characters.Early nodal differentiation was observed to be controlled by a single dominant gene, designated as Nd. Nodal rooting was controlled by two dominant complementary genes, designated as Nr ₁ and Nr ₂. We found an inhibitory factor for spreading habit and one for brown hull colour in Pankaj; the operation of two dominant duplicate genes An ₁ and An ₂ for controlling awning characters, a single dominant gene Rd for red pericarp colour and a single dominant gene Gd for grain dormancy. Joint segregations between these characters resulted in the assignment of genes in the X linkage group of indica rices with estimated map distances based on the cross-over values. The genes An (awning), Es (spreading habit), Nr (nodal rooting) and Nd (nodal differentiation) were observed to be associated with each other. The gene for red pericarp (Rd) was observed to be linked with the grain dormaney gene Gd.     

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.     

Trisomic genetic analysis of aroma in three Japanese native rice varieties (Oryza sativa L.)

Information on the genetics of aroma in rice facilitates breeding and selection of new aromatic varieties with high yield and good quality. Objective of the present study was to make clear the number of genes controlling aroma, and the allelism of aroma genes and the location of aroma gene(s) on the chromosome in three Japanese native aromatic rice varieties (Kabashiko, Shiroikichi and Henroyori). Lack of leaf aroma in all F₁ plants of non-aromatic/aromatic crosses indicated the recessive nature of aroma, and the segregation ratios (3:1) of non-aromatic to aromatic plants in its F₂ populations from Nipponbare/aromatic varieties crosses revealed that each of the three aromatic varieties contains a single recessive gene for aroma. Through trisomic analysis, the segregation of non-aromatic and aromatic plants in all F₂ populations from the crosses between trisomics lines NT8, with an extra chromosome 8, and aromatic varieties deviated significantly from disomic segregation of 3:1 ratios, and fitted to trisomic segregation, however, in other F₂ populations derived from other 7 types of trisomic F₁ plants, the segregation ratios of non-aromatic to aromatic were 3:1, indicating that the single recessive aroma gene was located on chromosome 8 in three aromatic varieties. This revised version was published online in July 2006 with corrections to the Cover Date.     

Inheritance of aroma in rice

Summary Inheritance of an aroma was worked out in crosses between Brimful from Nepal as an aromatic rice and leading Japanese varieties Koshihikari and Nipponbare as non-aromatic ones. The F₂ pattern of segregation for aroma to non-aroma was 3:13 indicating one dose gene for aroma and one dose inhibitor gene in two crosses. This ratio was confirmed by genetic behavior of F₃ populations.     

Inheritance of salt tolerance in rice

Summary The genetic behavior of salt tolerance was studied in artificially salinized conditions at the International Rice Research Institute.Divergent selection, carried out at a salinity level where the ECe was 15.2 mmhos/cm at 25 C in F₃ lines from two crosses confirmed the effects of salt tolerance on F₄ progeny with realized heritability values of 0.39 and 0.62, respectively.In a cross between two tolerant cultivars there was clear over-dominance for tolerance, despite the high environmental fluctuation which resulted in a low genetic response as indicated by a low but significant repeatability of 0.20–0.25, and many progeny lines more tolerant than the parents were recovered. The superior tolerance of these progenies compared to the parents was confirmed subsequently at 3 different salt levels. In the same experiment a cross between tolerant and susceptible cultivars produced some progeny of comparable tolerance with tolerant sources.In a 6×6 diallel cross experiment with two tolerant, moderate, and susceptible varieties each, both general and specific combining ability were significant.The findings indicate the possibility of breeding rices more tolerant than existing tolerant cultivars through cumulative crosses of tolerant cultivars. Further improvement can be attained by crossing highly tolerant lines with donors of good agronomic traits and pest and disease resistance.     

Inheritance of grain threshability in rice

Summary Inheritance of grain threshability was studied in a cross between two indica rice varieties. Hard threshability was found to be completely dominant over easy threshability. The segregation pattern indicated threshability to be monogenically controlled.     

Linkage of genes for anthocyanin pigmentation in rice (Oryza sativa L.)

Summary The inheritance of anthocyanin pigmentation and the interrelationship between genes governing anthocyanin pigmentation in different parts of the rice plant and genes governing panicle density were studied in the cross Suma × Wanar-1. A ratio of 45 pigmented: 19 non pigmented was realised for anthocyanin accumulation in sheath, nodal ring, internode, leaf tip, leaf margin and apiculus whereas a ratio of 3 normal:1 laxy was observed for panicle density. Pleiotropic action of a basic gene (A) and each of the two complementary duplicate genes (P _a or P _b) was detected. A linkage group of genes localising pigment in six plant parts was identified, the sequence of genes being P _nr-P _lm-P _la-P _a-P _sh-P _in. This may form part of the III S _p group of Misro et al. (1966), in which case the genes P _nr and P _la are proposed to be additions to this group.     

A linkage group in rice (Oryza sativa L.) involving anti-inhibitory genes

Summary Inheritance studies of purple pigmentation in T-160 x AC-177 revealed that purple colour in the coleoptile is based on four genes (Pc ₁ , Pc₂, I-Pc, Ai-Pc), in the internode on two genes (Pin _a1 , Pin _a2 ), in the junctura on three genes (Pja, Pjb ₁ , Pjb ₂ ) and in the apiculus on three genes (Pa, I-P, Ai-P). For panicle density monogenic segregation (Lx) was obtained. Linkage was established between the genes for the apiculus (Pa and Ai-P), panicle density (Lx), the internode (Pin _a ), the coleoptile (Ai-Pc) and the junctura (Pja), in that sequence. This linkage group forms part of the IV mp group of Misro et al. (1966) which corresponds to the g group of japonica.The two anti-inhibitory genes Ai-Pg and Ai-Pau of the linkage group Ai-Pg=Ai-Pc=Ai-Pau reported earlier (Dhullappanavar et al., 1975) are also allotted to the IV linkage group of Misro et al. (1966) since Ai-Pc is placed in that group in the present studies.     

Genetic characteristics of Korean weedy rice (Oryza sativa L.) by RFLP analysis

Summary The genetic characteristics and classification of 24 strains of Korean weedy rice, two strains of foreign red rice, three Japonica cultivars, one Tongil cultivar and one Indica cultivar (Oryza sativa L.) were investigated at the DNA level using the restriction fragment length polymorphism (RFLP) method. Eighty-three random combinations between six restriction enzymes and forty genomic DNA probes (RG# and KR#) were assayed. Thirty-seven (92.5%) out of the forty probes used showed polymorphisms among the 31 accessions assayed. A high level of polymorphism was found between short and long grain type Korean weedy rices, whereas fewer polymorphisms were presented among strains within each grain type. A dendrogram summarizing genetic similarity coefficients among thirty-one accessions was constructed based on their DNA polymorphisms. The Korean weedy rice strains were classified into two groups identical to the short and long grain types classified by morphological and physiological characters. From the RFLP analysis, it was deduced that the short grain strains of Korean weedy rice belonged to Japonica, while the long grain strains were closer to Indica than to Japonica, and were differentiated into a local ecotype surviving in the growth conditions in the southern part of the Korean peninsula.     

Genetic analysis of the response to day length in rice

Summary Inheritance of time-to-flowering, plant height, tiller number, spikelet number and flag leaf area was studied under day lengths of 10 and 14 hours in a diallel cross of six rice varieties. Early flowering was dominant to late in both environments but the varieties flowering early in one environment were late flowering in the other. Analysis of F₁ and F₂ data from the cross of Heenati-310 x IR-8 suggested a digenic control of early flowering in short days with complementary interaction. It is considered that while relatively few genes control time-to-flowering in rice a previous proposal that separate genes for time-to-flowering and photoperiod sensitivity exist is unnecessary on present evidence. Whereas culm length, tiller number and flag leaf area were increased by longer days, the number of spikelets per panicle was reduced. The length of the panicle was little affected by changing environment, and throughout certain characters and varieties, such as tiller number in I-geo-tze, were more stable than others. Varietal crosses of Heenati-310 x IR-8 and Tainan x MI-273(m) appeared to give high yield potential.     

Regeneration and genetic transformation of Spanish rice cultivars using mature embryos

To establish a plant regeneration system from embryogenic callus derived from mature rice embryos, the addition of aminoacids and the effect of two macronutrient solutions MSD and N6D to the basal callus induction medium was tested in three Spanish varieties, Senia, Tebre and Bahia. Aminoacids enhanced the production of embryogenic callus in Tebre and Senia whereas in the case of Bahia, embryogenic callus, which gave rise to a high rate of differentiated shoots, was induced without aminoacids. The macronutrient solution had also to be adjusted for each variety. Pre-regeneration treatment with ABA significantly improved the regeneration rate in all media tested, independently of the media in which the embryogenic callus were induced. In a comparison of growth regulators, BA yielded more shoots than Kin in all varieties whereas the effect of the auxins NAA or IAA was dependent on the variety. Transgenic plants from the three varieties were obtained via an Agrobacterium tumefaciens transformation system, using the optimised culture media. This revised version was published online in July 2006 with corrections to the Cover Date.     

RFLP/AFLP mapping of a brown planthopper (Nilaparvata lugens Stål) resistance gene Bph1 in rice

We have constructed a linkage map of the rice brown planthopper (BPH)resistance gene, Bph1. RFLP and AFLP markers were selected by thebulked segregant analysis and used in the mapping study of 262 F₂sthat were derived from a cross of `Tsukushibare', a susceptible japonica cultivar, and `Norin-PL3', an authentic japonicaBph1-introgression line. Twenty markers were mapped within a 28.9-cMregion containing the Bph1 locus on the long arm of rice chromosome12. Combining the result of segregation analysis of BPH resistance by themass seedling test and that of the markers, the Bph1 locus wasmapped within a 5.8-cM region between two flanking markers. The closestAFLP markers, em5814N and em2802N, was at 2.7 cM proximal to theBph1 locus. Together with the previously constructed high-resolutionmap of bph2 locating the locus at ca. 10 cM proximal to the Bph1 locus, this improved version of the linkage map would facilitatepyramiding these two important BPH resistance genes.     

Mapping and genetic analysis of two fertility restorer loci in the wild-abortive cytoplasmic male sterility system of rice (Oryza sativa L.)

Hybrid varieties developed by making use of the wild abortive cytoplasmic male sterility system account for 90% of hybrid rice produced. Previous inheritance studies have established that the fertility restoration in this system is controlled by two major loci, but the chromosomal locations of the fertility restorer (Rf) loci have yet to be resolved. In this study we determined the genomic locations of the two Rf loci by their linkage to molecular markers. The Rf gene containing regions were identified by surveying two bulks, made of 30 highly fertile and 46 highly sterile plants from a large F₂ population of the cross between Zhenshan 97A and Minghui 63, with RFLP markers covering the entire rice genome. The survey identified two likely Rf gene containing regions, located on chromosomes 1 and 10 respectively. This was confirmed by ANOVA using a large random sample from the same F₂ population and also with a genome-wide QTL analysis of a test-cross population. The results also showed that both loci have major effects of almost complete dominance on fertility restoration and the effect of the locus on chromosome 10 is larger than the one on chromosome 1. The two loci acted as a pair of classical duplicate genes; a single dominant allele at one of the two loci would suffice to restore the fertility to normal or nearly normal. Closely linked markers identified in this study may be used for marker assisted selection in hybrid rice breeding programs. This revised version was published online in July 2006 with corrections to the Cover Date.     

Expression of thermosensitive genic male sterility in rice under varying temperature situations

Response of thermosensitive genic male sterility in rice to varying temperature situations was studied by using four TGMS lines. In three sets of maximum, minimum and their combined temperatures, it was observed that maximum temperature played a predominant role in influencing sterility/fertility of TGMS lines under the combined regimes. Expression of a TGMS gene was found to be influenced by the genetic background of the recipient lines. Exposure for more than 8 hours of 32 ^°C was found necessary to induce complete male sterility in indica TGMS lines: IR68945-4-33-4-14 and IR68949-11-5-31 while, more than 4 hours of such exposure was enough to induce sterility in case of their japonica donor Norin PL 12. Sudden interruption with 27 ^°C even for 2 hours under the sterility inducing regime of 32/24 ^°C could induce partial fertility in the line IR68945-4-33-4-14. However, the line ID 24 remained completely sterile even with 10 hours of interruption with 27 ^°C. An interruption with lower temperature of 27 ^°C for 4 hours for even one day induced partial fertility in IR68945-4-33-4-14. The period of four to eight days after panicle initiation was the stage most sensitive to temperature variations. Hybrid rice breeders need to develop numerous genetically diverse TGMS lines, which possess critical sterility inducing temperature of 28 ^°C and are not affected by sudden interruptions with a lower temperature for few hours daily for a couple of days. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic analysis of a CSR10 (indica) × Taraori Basmati F3 population segregating for salt tolerance using ISSR markers

Segregation for salinity tolerance and ISSR markers based molecular polymorphism were investigated in a F₃ plant population raised via single-seed descent method from a cross between salt-tolerant indica rice variety CSR10 and salt-susceptible premium traditional Basmati rice variety Taraori Basmati HBC19. A total of 130 F₃plants were evaluated individually for salinity tolerance on 1–9 scale on the basis of seedling growth parameters; the average score ranged between 1.7 to 8.3. Frequency distribution curve obtained using the salinity tolerance data of F₃ population and a chi-square analysis, showed a good fit to a normal distribution. Eleven plants each in the category of salt-tolerant and salt-susceptible were selected from the segregating F₃ population for ISSR marker analysis. A total of 149 bands (4–11 bands per primer) ranging from 200 to 3530 bp were scored for the two rice varieties and the selected CSR10 × HBC19 segregating F₃ plants using 26 ISSR primers. Of these, 89 were monomorphic and 60 were polymorphic. Of the 60 polymorphic bands,36 and 20 bands were specific to CSR10 andHBC19 respectively. The remaining four bands were amplified using UBC primers 810,848, 853 and 886 and present in only some of the CSR10 × HBC19 F₃ plants. Notably, ISSR primers with dinucleotide repeat motif and 5'-anchored end amplified more number of bands (7.0 bands/primer) compared to3'-anchored dinucleotide primers (5.4bands/primer), but 3'-anchored dinucleotide primers revealed higher level of polymorphism (2.6 polymorphic bands/primer) compared to 5'-anchoreddinucleotide primers (1.43 polymorphic bands/ primer). While distribution of majority of the polymorphic bands were more or less in the expected ratios in salt-tolerant and/or salt-sensitive F₃segregating plants, but some of the bands amplified using UBC ISSR primers 823, 825,826, 849, 853, 864, 866 and 884 showed highly skewed distribution. Such polymorphic bands stand greater chances of having a linkage with the genes/ QTLs for salinity tolerance and shall be the target for further studies. This revised version was published online in July 2006 with corrections to the Cover Date.     

Italian rice varieties: historical data, molecular markers and pedigrees to reveal their genetic relationships

Two molecular marker approaches [amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR)] were employed to study genomic relationship among 96 rice cultivars. These included most of the best reputed Italian accessions. AFLP produced 461 fragments, 248 (53%) of which were polymorphic, SSR produced four to 11 alleles in the 12 genomic loci investigated. Genomic similarity was estimated independently for the two molecular marker techniques. Both AFLP and SSR dendrograms agree in splitting the cultivars into two main clusters: a small one, comprising four exotic accessions, and a larger one which could be split into four subgroups. These were also analysed on the basis of historical and pedigree information. This is the first report on the application of DNA polymorphism analysis to reveal genomic relationship among cultivated Italian rice germplasm. Results will be useful for breeding programmes.