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.     

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 analysis of ratooning ability of rice (Oryza sativa L.)

Summary Genetic analysis of generation means of F₁, F₂, F₃, F₄, and the parental populations of the cross IR10154-23-3-3A/IR15795-232-3-3-2 for ratooning ability was conducted. Good ratooning ability is a recessive trait. The parents differed by at least two pairs of major genes for ratooning ability. A large proportion of transgressive segregants in F₂ suggested that the expression of ratooning ability is influenced not only by major genes but also by modifiers. Broad-sense heritability estimates computed by different methods ranged from 0.66 to 0.88. Narrow-sense heritability by the F₄–F₃ regression method was 0.39. The heritability estimates were 0.42 and 0.33 by the variance component method. The prevalence of additive x additive type of gene effects along with prominent additive effects imply some scope for selection in the segregating generations. However, non-additive type of gene action also affects the expression of ratooning ability.     

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.     

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.     

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.     

Amylose synthesis capacity of the three Wx genes of wheat cv. Chinese Spring

The Wx locus controls amylose synthesis in the cereal endosperm. Hexaploid wheat (Triticum aestivum L.) has the three Wx loci on chromosomes 7A ( Wx-A1), 4A (Wx-B1) and 7D (Wx-D1). To verify the effects of null alleles on reducing amylose content and determine the amylose synthesis capacity of each Wx gene independently and accurately, we produced eight possible types of recombinant lines carrying different null alleles at the Wx loci under the ‘Chinese Spring’ genetic background. Amylose content varied from 0% of the waxy ‘Chinese Spring’ to 25% of the ‘Chinese Spring’ normal type. The reducing effect of the single null alleles was the largest in Wx-B1b, and there was no significant difference between Wx-A1b and Wx-D1b. More than 3% reductions in amylose content were detected in the double null types. The results of the double null lines further demonstrated that for the capacity of amylose synthesis, Wx-B1a predominates and produces 21–22% amylose, followed by Wx-D1a (20–21%) and Wx-A1a (15–18%). These significant differences were partly correlated with variation in the amounts of the Wx proteins produced by different Wx genes. However, comparisons of the double null lines with the single null or normal lines indicated that amylose content was not linearly proportional to the number of the Wx genes, suggesting that the Wx genes act in an epistatic manner. This revised version was published online in July 2006 with corrections to the Cover Date.     

A major gene for low temperature germinability in rice (Oryza sativa L.)

Low temperature-induced retardation of seedling growth is a common problem in temperate rice-growing areas, at high altitudes of tropical and sub-tropical areas, and in areas with a cold irrigation water supply. Studies on low temperature germinability have revealed complex inheritance of the trait. The purpose of this study was to identify the gene(s) for low temperature germinability using Italica Livorno as a donor parent. The frequency distributions for the germination rate at 15 °C in the F₂ and BC₁F₁ populations showed continuous segregation, suggesting that low temperature germinability was under polygenic control. Since some lines in the BC₁F₁ population showed vigorous low temperature germinability similar to that of Italica Livorno, backcrosses until the BC₅F₁ generation was carried out using Hayamasari as the recurrent parent. Clear segregations of low temperature germinability were observed in the BC₅F₁ and BC₅F₂ populations. The distribution of low temperature germinability fitted a single-gene segregation, indicating that a single dominant gene with a large effect was transferred to Hayamasari. This gene is tentatively symbolized as Ltg(t). Low temperature germinability of near isogenic lines for Ltg(t) was similar to that of Italica Livorno. Ltg(t) should greatly contribute to the improvement and manipulation of low temperature germinability in rice breeding programs. This revised version was published online in August 2006 with corrections to the Cover Date.     

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.     

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     

The effect of the Waxy locus (Granule Bound Starch Synthase) on pasting curve characteristics in specialty rices (Oryza sativa L.)

Starch structure and functionality have a significant impact on the utilization of cereal grains as food and feed. Starch viscosity characteristics are used to characterize rice cooking, processing and eating quality. In order to examine the genetics of viscosity characteristics, we developed molecular markers for five of the major enzymes involved in starch synthesis in the endosperm: granule bound starch synthase, soluble starch synthase, rice branching enzymes 1 and 3 and starch debranching enzyme. These markers were polymorphic in a cross between specialty rice varieties of diverging amylose content and viscosity characteristics. Our results indicate that the Waxy locus, encoding the gene for granule bound starch synthase, has a significant effect on peak viscosity, hot paste viscosity, cool paste viscosity, breakdown and setback viscosity. We estimate that the tightly linked (5–10 cm)locus for starch synthase may have a lesser, additive effect. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic Variation for Salinity Tolerance in Pakistani Rice (Oryza sativa L.) Germplasm

Soil salinity is one of the major production constraints. Development and planting of salt‐tolerant varieties can reduce yield losses due to salinity. We screened 185 rice genotypes at germination stage in petri dishes under control, 50, 100 and 150 mm salt stress, and at seedling stage in Yoshida's hydroponic nutrient solution under control, 50 and 100 mm salt stress. At germination stage, 15 genotypes including Nona Bokra, Sonahri Kangni, 7421, 7423 and 7467, whereas at seedling stage, 28 genotypes including Nona Bokra, Jajai‐77, KSK‐133, KSK‐282, Fakhr‐e‐Malakand, Pakhal, IR‐6, Khushboo‐95, Shahkar and Shua‐92 were found salt tolerant. Basmati‐370, Mushkan, Homo‐46 and accessions 7436, 7437 and 7720 were sensitive to salinity at both germination and seedling stage. We further screened a subset of 33 salt‐tolerant and salt‐sensitive genotypes with SSR markers. Four SSR markers (RM19, RM171, RM172 and RM189) showed significant association with two or more of the studied traits under 50, 100 and 150 mm salt stress. These markers may be further tested for their potential in marker‐assisted selection. The salt‐tolerant genotypes identified in this study may prove useful in the development of salt‐tolerant rice varieties in adapted genetic background.     

Trisomic analysis of a strong photoperiod-sensitivity gene E1 in rice (Oryza sativa L.)

Recent genetic analyses on heading-time of rice indicated that almost all the well-adapted varieties in the temperate zone carry a strong photoperiod-sensitivity gene E1, a dominant allele of E1 locus. In order to identify the chromosome on which E1 is located, a trisomic analysis was made using two primary trisomic series originating from the japonica varieties, Nipponbare and Kinmaze, respectively. The Nipponbare and Kinmaze series were crossed with heading-time tester lines, EG0 and EG3, respectively, both of which did not carry the E1. The F2 populations for chromosome 1, 2, and 3 could not be analyzed due to lack of seed. All the other F2 populations showed distinct segregation into early-type and late-type plants caused by the E1 locus segregation, which suggested that the trisomic analysis for E1 locus could be efficiently made. Both disomic and trisomic groups in the F2 population from the cross of the trisomic line for chromosome 7 × EG0 showed a segregation ratio significantly different at the 1% level from a ratio of 1 [e1e1; early]: 3 [E1e1, E1E1; late]. This suggested that E1 was located on chromosome 7. Subsequently, the linkage analysis was made using three morphological marker genes on chromosome 7. It was recognized that E1 was linked to rfs (rolled fine strip gene) and slg (slender glume gene) with recombination values of 16.3 ± 5.88 and 9.1 ± 4.72%, respectively. From these results, it can be concluded that E1 is most likely to be located on chromosome 7. This revised version was published online in July 2006 with corrections to the Cover Date.     

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.     

Genetic analysis of methionine content in indica-japonica hybrid rice (Oryza sativa L.) at different grain developmental stages

Genetics of methionine content in indica-japonica hybrid rice (Oryza sativa L.) was studied in 35 F₁ hybrids derived from crossing 7 male-sterile indica rice cultivars with 5 restorer japonica rice cultivars. Two genetic models and their corresponding statistical methods for quantitative traits of triploid endosperm in cereal crops were used for the analysis. One is the unconditional model, which refers to the analysis of cumulative measurements along the developmental stages, while another is the conditional model, which relates to analysis throughout the developmental stages. Results showed that methionine content of indica-japonica hybrid rice was controlled by expression of triploid endosperm nuclear genes, cytoplasm genes, diploid maternal plant nuclear genes, and their genotype-environment interaction effects. Dominant effects were important at the first three developmental stages, while additive effects were important at the next two stages of grain development under both unconditional and conditional analyses. With regard to the components of heritability, maternal and cytoplasm general heritabilities and their environmental interaction heritabilities were important. It was suggested that enhancing methionine content could be more efficient when selection is based on maternal plants in early breeding generations.