Genetics of stem elongation ability in rice (Oryza sativa L.)

Summary The genetics of stem elongation ability in rice was studied in parents, F₁, F₂ and backcross generations of six crosses. Segregation analysis indicated dominance for stem elongation ability. Estimation of genetic parameters under epistatic model indicated more than one locus control stem elongation ability and both additive and nonadditive gene effects were important. Epistatic effects were predominant over additive and dominance effects with an important role of duplicate type of epistasis. The occurrence of significant additive and additive x additive types of genetic variation and the moderately high broad sense heritability indicated the possibility of selection for an increased manifestation of stem elongation ability.     

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.     

Effects of cytoplasm on heterosis and combining ability for agronomic traits in rice (Oryza sativa L.)

Summary Effect of sterilizing (WA) cytoplasm on heterosis and combining ability for days to flowering, plant height and grain yield in rice was studied in 70 crosses and their reciprocals produced by 10 cytoplasmic male sterile (A), their maintainer (B) and seven restorer (R) lines following line x tester design. The materials consisting of 140 hybrids (70 A/R and their reciprocal 70 R/B) plus 17 parental lines (10 B + 7 R) were evaluated under six environments, created by growing in three fields with different fertilizer doses (0, 60, 120 kg N/ha) and 2 seasons (dry and wet) during 1986 at IRRI farm. Reciprocal cross effect (A/R vs R/B) were highly significant for all the three traits. Interaction of reciprocal cross effects with environments were also highly significant for yield and days to flowering. Cytoplasmic effect for yield, days to flowering and plant height were estimated by comparing A/R and R/B combination and testing the significance of difference with LSD value. In order to avoid confounding effect of spikelet sterility on yields, twenty crosses showing normal spikelet fertility were selected. Both positive and negative cytoplasmic effects were observed for the three traits. The effects were modified by environments, except for plant height. Heterosis for all three traits was also affected by cytoplasm, however, manifestation of cytoplasmic effects was higher for heterosis for days to flower than in heterosis for yield and plant height. Effect of cytoplasm was more pronounced on general combining ability effects of parents than specific combining ability effects of crosses. Among the parents two CMS lines A4 (IR54752A) and A8 (IR22107-113-3-3A) and two R lines: R2 (IR46) and R7 (IR9761-19-1) showed consistent positive effect of cytoplasm on general combining ability. These lines have given several good heterotic combinations. The study indicated the usefulness of evaluating diverse cytoplasmic sources in various nuclear genotypes bred for hybrid rice breeding program.     

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 analysis of mesocotyl length and its relationship with other agronomic characters in rice (Oryza sativa L.)

Summary Mesocotyl length is an important character in promoting seedling emergence of direct-seeded rice. Genetic analysis of rice mesocotyl length was conducted using a six parent diallel cross. Generation mean analysis was carried out on parents (P), F1, F2 and backcrosses (B) of three crosses to complement the genetic information from the diallel analysis. Both analyses demonstrated the presence of significant additive and dominance effects. Duplicate type of non-allelic interaction was detected by the generation mean analysis and two crosses showed significant negative dominance gene effect. Dominance was partial and the narrow sense heritability estimate for mesocotyl length was high, indicating the preponderance of the additive effects.Mesocotyl length was negatively but weakly correlated with the coleoptile length and length of the second internode L2. There was no correlation between mesocotyl length and other mature plant characters such as plant height and internode lengths L₁, (L₁ being the peduncle with subsequent internodes to the base of the plant). Selection for mesocotyl length can therefore be carried out independent of these plant characters and semidwarf rice varieties with long mesocotyl can be developed.     

Anther and pollen grain culture of rice (Oryza sativa L.)

Summary Factors favouring callus proliferation and subsequent regeneration of plants from pollen grains of rice anthers (Oryza sativa L., cvx. Bahia, Girona, Balilla × Sollana and Sequial) were determined. Cultivar differences in response were found, such as a high rate of haploid plant regeneration.In addition, isolated pollen grain culture was used to induce tissue proliferation outside the anther walls. The frequency of callus formation from isolated pollen grains was very low. It was necessary to preculture the anthers before pollen grain separation, in order to accomplish a successful development later. Root differentiation was observed in some of the obtained callus.     

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.     

Wide compatibility in rice (Oryza sativa L.)

Summary Wide compatible varieties (WCVs) show normal spikelet fertility in crosses with Indica and Japonica rice varieties. Crosses of Indica and Japonica varieties frequently show high spikelet sterility which prevents exploitation of heterosis for grain yield. We screened 41 rice varieties for the wide compatibility trait by crossing each with three Indica and three Japonica testers. Varieties giving fertile F₁ hybrids with both groups of testers were classified as WCVs. Seven varieties viz., BPI-76 (Indica); N 22; Lambayeque-1 and Dular (Aus); Moroberekan, Palawan and Fossa HV (Japonicas), were identified as WCVs. The frequency of WCVs was higher among Aus and Japonicas. The wide compatibility trait in varieties: Dular and Moroberekan was controlled by a single dominant gene linked with the Est-2 and Amp-3 loci (mean recombination 32.0%). Est-2 and Amp-3 showed complete linkage. Pgi-2 was found to be linked with Est-2 and Amp-3 (mean recombination 16.1%). Est-2 and Amp-3, showed a tighter linkage with C ⁺ (mean recombination 4.1%). Pgi-2 showed a lower linkage with C ⁺ (mean recombination 17.3%). The recombination values between the WC gene in Dular and C ⁺ was much higher than those reported in Japan for the WC gene (S₅ ⁿ) from Ketan Nangka. It is possible that the WC gene from Dular is different from that in Ketan Nangka. Linkage intensities with the WC gene were not strong enough to be of use for indirect selection for the wide compatibility trait. A search for a more closely linked isozyme or DNA marker was proposed.     

Random amplified polymorphic DNA analysis of Australian rice (Oryza sativa L.) varieties

Summary The genetic relationships between rice varieties were analysed by using the polymerase chain reaction (PCR), with arbitrary oligonucleotide primers in the random amplified polymorphic DNA (RAPD) method. PCR with 22 arbitrary primers applied to 37 varieties produced 144 useful markers, of which 67% were polymorphic. Thus, with selected primers sufficient polymorphism could be detected to allow identification of individual varieties. Visual examination of electrophoresis gels and analysis of banding patterns confirmed that commercial Australian and USA lines and their relatives were very closely related, with similarity indices of 88–97%. Three varieties originating from more distant geographical centres were easily distinguished, producing variety-specific amplification profiles and expressing a lower similarity index of 80% to all other varieties tested. PCR offers a potentially simple, rapid and reliable method for rice genotype identification and recognition of lines that could contribute genetic diversity to new commercial varieties.Abbreviations PCR Polymerase Chain Reaction - RAPD Random Amplified Polymorphic DNA     

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.     

QTL analysis of seed dormancy in rice (Oryza sativa L.)

Effective cumulative temperature (ECT) after heading would be a more reasonable parameter for seed sampling of pre-harvest sprouting/seed dormancy (SD) tests in segregating populations than the days after flowering. SD is an important agronomic trait associated with grain yielding, eating quality and seed quality. To identify genomic regions affecting SD at different grain-filling temperatures, and to further examine the association between SD and ECT during grain-filling, 127 double haploid (DH) lines derived from a cross between ZYQ8 (indica)/JX17 (japonica) by anther culture were analyzed. The quantitative trait loci (QTLs) and their digenic epistasis for SD were identified using a molecular linkage map of this population. A total of four putative QTLs for SD (qSD-3, qSD-5, 6 and 11) were detected on chromosomes 3, 5, 6 and 11, together explaining 41.4% of the phenotypic variation. Nine pairs of digenic epistatic loci were associated with SD on all but chromosome 9, and their contributions to phenotypic variation varied from 2.87%–8.73%. The SD QTL on chromosome 3 was identical to the QTLs found in other mapping populations with different genetic backgrounds, which could be a desirable candidate for gene cloning and marker-assisted selection in rice breeding.     

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     

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.     

Inheritance of amylose content in rice (Oryza sativa L.)

Summary The inheritance of low and very low amylose contents in six rice crosses and their reciprocals was studied by single grain analysis of parents F₁, F₂, B₁ and B₂ seeds. To minimize the environmental effects, the seeds of all generations of all crosses were produced in a single season. The results indicated different dosage effects in different crosses. One major gene was found to govern a difference of 6–12% in amylose content in low and intermediate amylose parents. Very low amylose content was similarly found to be governed by one major gene in crosses between very low- and low-amylose content parents. Minor genes and modifiers also seem to play some role. In the cross between two low amylose parents differing by about 2.5% in amylose content, the differences appeared to be controlled by some minor genes and modifiers. The selection program in different crosses has been suggested.     

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.     

Analysis of ATPase and succinic dehydrogenase in F1 hybrids of rice (Oryza sativa L.)

Summary Activities of ATPase and succinic dehydrogenase were assessed in three F₁ hybrids of rice and their parental lines during boot leaf stage, flowering, on 10th and 20th days after flowering. ATPase activity showed increase at the flowering and on 20th day after flowering. Succinic dehydrogenase activity continued to rise till 10th day after flowering and declined on 20th day after flowering. Hybrids with high yield were generally endowed with more positive heterosis for these two enzymes. Correlation coefficient of grain yield per panicle was significantly positive with ATPase activity at all the stages studied. Heterosis for ATPase activity might serve a reliable criterion for the selection of efficient F₁ combinations.     

Linkage studies in rice (Oryza sativa L.): Flowering,growth habit and pigmentation

Summary Genetic analysis of ten characters in a rice cross M 18 × T979 revealed the interaction of duplicate, complimentary, inhibitory and anti-inhibitory genes in conditioning pigment in eight characters and in determining flowering and growth habit. The action of genes and their interactions indicated by complex ratios for all the ten characters are claimed to be the first reports. pleiotropic action of two complementary genes and four duplicate genes has been detected. Two linkage groups, one with three genes (Ai-Plg-Ai-Pau-Pja) and the other with nine genes (Plg_a-Pin_a-Er_a-Ef_a-I-Plg-Pg₁-Pn₁-Pr₁-Pnr₁) have been constituted. The three-gene group is tentatively placed in the IV mp group and the other with nine genes is assigned to the X fh group. As a result of the present investigation Ai-Plg is an addition to the IV mp group and Plg_a, Pin_a, Er_a, I-Plg, Pg₁, Pn₁ Pr₁ and Pnr₁ are contributions to the X fh group.     

Yield of F1, F2 and F3 hybrids of rice (Oryza sativa L.)

Summary Yield and yield components of F₁ hybrids were studied in three experiments at 30×30 cm spacings and in one experiment at 15×15 cm spacings. In the 30×30 cm experiments, 10 of the 41 hybrids tested significantly outyielded their high parents. However, only 2 hybrids significantly outyielded the best cultivar: one hybrid yielded 23 % and the other 16 % more than their respective check cultivars. The four hybrids in the 15×15 cm experiment yielded only 59 to 92% as much as their high parents.In areas where rice is transplanted at relatively wide spacings, the observed levels of F₁ heterosis in selected hybrids may be sufficient to warrant production of hybrid rice, if enough hybrid seed can be produced. For direct-seeding at the high rates normal in the USA, the relatively small levels of heterosis and the difficulties of hybrid seed production preclude use of F₁ hybrid rice cultivars at present.None of 19 bulk F₂ and F₃ hybrids in two experiments yielded significantly more than its high parent. Similarly, none of the 12 mixtures included in one experiment yielded significantly more than its high parent. On the basis of yield alone, using bulk F₂ or F₃ or simple mixture populations is not merited.Contribution from the Western Region, Agricultural Research Service, U.S. Department of Agriculture, and the Department of Agronomy and Range Science, University of California, Davis, California 95616.     

Molecular tagging of a gene for resistance to brown planthopper in rice (Oryza sativa L.)

An introgression line derived from an interspecific cross between Oryzasativa and Oryza officinalis, IR54741-3-21-22 was found to beresistant to an Indian biotype of brown planthopper (BPH). Genetic analysisof 95 F₃ progeny rows of a cross between the resistant lineIR54741-3-21-22 and a BPH susceptible line revealed that resistance wascontrolled by a single dominant gene. A comprehensive RAPD analysisusing 275 decamer primers revealed a low level of (7.1%) polymorphismbetween the parents.RAPD polymorphisms were either co-dominant (6.9%), dominant forresistant parental fragments (9.1%) or dominant for susceptible parentalfragments (11.6%). Of the 19 co-dominant markers, one primer,OPA16, amplified a resistant parental band in the resistant bulk and asusceptible parental band in the susceptible bulk by bulked segregantanalysis. RAPD analysis of individual F₂ plants with the primerOPA16 showed marker-phenotype co-segregation for all, with only onerecombinant being identified. The linkage between the RAPD markerOPA16₉₃₈ and the BPH resistance gene was 0.52 cM in couplingphase. The 938 bp RAPD amplicon was cloned and used as a probe on122 Cla I digested doubled haploid (DH) plants from aIR64xAzucena mapping population for RFLP inheritance analysis and wasmapped onto rice chromosome 11. The OPA16₉₃₈ RAPD markercould be used in a cost effective way for marker-assisted selection of BPHresistant rice genotypes in rice breeding programs.     

Anther culture of tropical japonica × indica hybrids of rice (Oryza sativa L.)

Summary Nine japonica × indica F1 hybrids of rice involving 6 indica and 3 japonica tropical varieties, were large scale anther cultured. The frequency of callusing anthers averaged 18.7%. The microspore-derived calli produced green plants with a mean frequency of 8.7%. Albino plants represented 61% of the shoot forming calli. Monitoring of the green and albino plant regenerating capabilities of calli arising between week 4 and week 8 of incubation of the anthers showed no increase of the albino/green ratio and a slow decrease of the shoot forming ability of the transferred calli after the sixth week of culture. Spontaneous doubled haploids (SDH) represented 46% of the regenerated green plants in 4 hybrids. However, a high frequency of partially sterile regenerants was noticed among 132 SDH plants generated from a hybrid.