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.     

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.     

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     

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.     

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.     

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.     

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.     

Identification of segregation-distortion-neutral alleles to improve pollen fertility of indica-japonica hybrids in rice (Oryza sativa L.)

The genetics of resistance to Ascochyta blight (Ascochyta fabae f. sp. fabae) was studied in two populations of faba bean (Vicia faba). Plants of a resistant population, ILB 752, and a susceptible one, NEB 463, were screened for their reaction to the pathogen and the results were quantified on a scale of 0–5. Crosses were made between plants both within and between accessions and the F₁ and F₂ generations assessed in a field trial 21 and 45 days after inoculation. Disease scores were greater at 45 days than at 21 days and they were not significantly affected by the presence of susceptible spreader rows in part of the trial. ILB 752 carried a major dominant gene conferring resistance while NEB 463 carried the recessive allele for susceptibility. Furthermore, a minority of plants of NEB 463 appeared to carry at least one pair of complementary recessive genes, also conferring resistance. Most of the plants of ILB 752 were homozygous for the dominant resistance gene and a few were heterozygous. Reciprocal crosses behaved identically, indicating the absence of maternal effects in the expression of Ascochyta blight resistance in faba beans. The results show that it is important to confirm the level of heterozygosity for the resistance genes in this partially outbreeding species before crossing is commenced. The major dominant gene for resistance, identified in ILB 752, has clear potential for use in breeding for Ascochyta blight resistance. The minor genes identified in NEB 463 also show the potential for accumulating resistance through mass selection. This revised version was published online in July 2006 with corrections to the Cover Date.     

Identification of quantitative trait loci (QTLs) for the characters of vascular bundles in peduncle related to indica-japonica differentiation in rice (Oryza sativa L.)

The number of vascular bundles in peduncle and the ratio of vascular bundles to primary rachis branches (V/R ratio)distinguishable between indica andjaponica, are the traits associated with the processes of differentiation between indica and japonica inrice (Oryza sativa L.). In this paper a doubled-haploid population derived from the F₁ hybrid of a cross between anindica cultivar and a japonicacultivar was used to map quantitative trait loci(QTLs) controlling numbers of vascular bundles in peduncle, primary rachis branches and the V/R ratio. For vascular bundles, three QTLs were detected and they collectively explained 58.8% of the total variation. Among them, the QTLqVB-8 with the largest effect,located on chromosome 8, individually accounted for 31.1% of the total variation. Two QTLs controlling primary rachis branches, located on chromosome 8and 10 respectively, were identified and they individually explained 10.5% and18.0% of the total variation respectively. Three QTLs for the V/R ratio, mapped on chromosome 1, 2 and 8, respectively,jointly explained 61.3% of the total variation. Of the three QTLs, the QTL qV/R-1 with the largest additive effect,explained 25.3% of the total variation,was located on chromosome 1 and found to be closely linked to the gene sh-2, a major gene underlying grain-shattering ability. In addition, four and two pairs of significant epistatic QTLs were detected for vascular bundles and the V/R ratio,respectively, but none for rachis branches. Our results suggested that the numbers of vascular bundles and primary rachis branches were independently controlled by different polygenic systems, but the two polygenic systems shared a fraction of quantitative trait loci. The present study also demonstrated that the chromosome region carrying the QTL qV/R-1 for the V/R ratio and the gene sh-2 might play an important role in the processes ofindica-japonica differentiation in rice (Oryza sativa L.). This revised version was published online in August 2006 with corrections to the Cover Date.     

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.     

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     

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.     

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.     

Genetic analysis of salt tolerance at seedling and reproductive stages in rice (Oryza sativa)

Salinity is a major abiotic stress that limits rice production across rice areas as high‐yielding modern rice varieties are generally sensitive to salt stress. The study was conducted to deduce heritability and combining ability estimates of rice for various morphological and physiological traits using a 7 × 7 full‐diallel‐cross analysis at seedling and reproductive stages. The salinity stress treatment was 12 dS m^?1 at the seedling stage and 8 dS m^?1 at the reproductive stage. Diallel analysis revealed high for salinity tolerance scores and shoot height, moderate for shoot dry weight and root dry weight and low for Na⁺ and K⁺ concentrations and K⁺/Na⁺ ratio. The low‐to‐moderate narrow‐sense heritability for number of panicles, number of fertile spikelets, grain weight, spikelet fertility and K⁺/Na⁺ ratio suggests a large breeding population and delayed selection for tolerance until later generations. Significant maternal effects indicate that selection of the female parent is very important for desired trait development. The results of this study confirmed that salinity tolerance at the seedling and reproductive stages is regulated by a different set of genes that could be pyramided using different donors to enhance the level of tolerance.     

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.     

Mapping of QTLs for leaf developmental behavior in rice (Oryza sativa L.)

Leaf developmental behavior in rice (Oryza sativa L.) is one of the important agronomic characteristics, which not only determines vegetative growth but also influences grain yield. This study was conducted to identify quantitative trait loci (QTLs) for total number of leaves (TNL), days to the emergence of flag-leaf (DEF) and the leaf emergence rates (LER) on main stem, which mainly represent leaf developmental behavior, using recombinant inbred lines (RILs) derived from a cross between a japonica variety, Asominori and an indica variety, IR24, cultivated in 2001 and 2002. The transgressive segregations in both parental directions and continuous variations of all three tested traits were observed. Significant correlations among these traits were detected. A total of fourteen QTLs for leaf development behavior were detected with 289 RFLP markers. Six QTLs controlling TNL were mapped to chromosomes 3, 5, 6, 8, 9, 12, and accounted for 5.615.7% of the total phenotypic variations, and three QTLs for DEF were mapped to chromosome 3, 6, 8 and accounted for 10.735.4% of total phenotype variation and five QTLs for LER were mapped to chromosome 1(two QTLs), 2, 4, 9 and explained 6.217.5% of phenotype variation. The identification of QTLs for leaf developmental behavior in rice may be useful for selection of fast growing genotype before heading using maker-assisted selection.     

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.     

A new dominant earliness character of CMS line Zaoxian A and its application value in rice (Oryza sativa L.)

Summary A distant cross between a maintainer Zhenshan 97B and an early maturing F₂ palnt of O. longistaminata x O. rufipogon was made in 1985, and a new CMS line Zaoxian A was bred in 1989 through continuous backcross of new maintainer plants derived from the distant cross to the leading CMS line Zhenshan 97A. Several experiments were carried out in Sichuan during 1990–1992, to analyze the inheritance of earliness of Zaoxian A and its application value to hybrid rice production. The results showed that Zaoxian A was as early-maturing as Zhenshan 97A, the earliness of Zaoxian A was incompletely dominant to the lateness of restorer lines, and was different from the earliness of Zhenshan 97A which was suppressed by the lateness of restorer lines. The F₁ hybrids between Zaoxian A and late maturing restorers combined the early maturity and high yielding capacity, and significantly outyielded the provincial and national checks with same or longer growth duration, because the larger genetic distance between early and late maturing ecotypes remained unchanged and the new earliness could express in F₁ generation. Therefore, the new dominant earliness character of Zaoxian A could enhance the regional and seasonal adaptability of rice. It is also valuable to hybrid rice production and the formation of new cropping systems with high yielding capacity and high economical profit.     

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.     

The inheritance of nitrate content in lettuce (Lactuca sativa L.)

Summary The inheritance of nitrate content in lettuce was analysed using 16 F₂ populations and three F₃ populations. Frequency distributions of nitrate content in F₂ and F₃ populations were unimodal and symmetrical, indicating a quantitative inheritance. Both significant positive and negative deviations of the F₂ mean from the mid-parent value were found, indicating dominance or epistasis. Deviations towards low nitrate content were more frequent than deviations in the other direction. Estimates of heritabilities for nitrate content in the F₂ populations ranged from 18% to 69% and were in most cases above 50%. Crosses between low nitrate cultivars did not have lower estimates of heritability in the F₂ than crosses between cultivars with larger differences in nitrate content. In one case a genotype x experiment interaction for nitrate content of parental cultivars was found.Three F₃ populations of crosses between cultivars with low nitrate content were analysed. Estimates of heritabilities for F₃ line means ranged from 78% to 91% and estimates of the genetic standard deviation of nitrate content in unselected advanced generations ranged from 0.24–0.33 g kg^–1. The estimates of heritabilities and of genetic variation in advanced generations offer good prospects of selection of low nitrate genotypes in lettuce. A comparison of efficiency of selection in the F₂ generation and F₃ line selection is made.