Analysis on the spectra and level of wide-compatibility conferred by three neutral alleles in inter-subspecific hybrids of rice (Oryza sativa L.) using near isogenic lines

Wide‐compatibility varieties are a special class of rice germplasm that is able to produce fertile hybrids when crossed to either indica or japonica subspecies. Previous studies determined the f5 allele from ‘Dular’ (f5‐Du), f6 allele from ‘Dular’ (f6‐Du) and S5 allele from ‘02428’ (S5‐08) as neutral alleles conferring wide‐compatibility. However, the possible extent of the effect of the three neutral alleles has not been fully characterized because of the narrow range of the tester varieties used and the highly complex differentiation in Asian cultivated rice. In this study, we further developed the five near‐isogenic lines with higher recovery rates of the recurrent parent genome, and testcrossed to 14 japonica varieties, which have been widely used in rice breeding programmes in China. The results clearly revealed that all three neutral alleles exhibited substantial effects on spikelet fertility in most of the indica–japonica testcrosses, which indicated that these hybrid sterility loci have been extensively differentiated between indica and japonica varieties. The magnitudes of effects on spikelet fertility averaged over various crosses seem to be similar among the three neutral alleles, with f5‐Du, f6‐Du and S5‐08 alleles increasing spikelet fertility by 15.09%, 13.99% and 14.25%, respectively. The testcrosses involving f5‐Du allele generally showed much smaller variation in pollen fertility than others. The pyramiding lines with two neutral alleles showed a wider spectrum and a higher level of wide compatibility than others, whereas most of the increases in hybrid fertility couldn’t be simply explained by additive effects, suggesting the very complexity of wide compatibility and hybrid sterility. The indica–japonica hybrids involving restorer lines as one of their parents showed much higher pollen fertility (almost normal) and also higher spikelet fertility. The implications of the findings in rice breeding programmes are also discussed.     

SSR analysis of chromosome 8 regions associated with aroma and cooked kernel elongation in Basmati rice

Aroma and cooked kernel elongation (CKE) are the two most important quality traits, which differentiate the highly valued Basmati rice from other rice types. Previous studies on genetic analysis have shown that genes/QTLs for these two traits are linked and present on chromosome number 8. We have evaluated the genetic diversity in 33 rice genotypes representative of the traditional Basmati (TB), cross-bred Basmati derived from indica × Basmati rice crosses and non-Basmati (indica and japonica) rice varieties for chromosome number 8 using 26 SSR markers including a specific marker (SCU-SSR1) for RG28 locus; the results have been compared with whole genome based SSR allelic data. The 26 SSR markers (24 polymorphic and 2 monomorphic) amplified a total of 106 alleles; 21 of these alleles were detected to be unique, present in only one genotype. The number and size of the alleles, and polymorphism information content (PIC) values ranged between 1–8, 87–312 and 0–0.736 bp, respectively. SCU-SSR1 marker amplified a total of three alleles (128, 129 and 130 bp). All the TB varieties except Basmati 217 (129 bp) and 7/13 cross-bred Basmati varieties had the 130 bp allele. Alleles of 129 and 128 bp were present in majority of the indica and japonica varieties, respectively. The average pair-wise Jaccard similarity coefficients for TB, indica and japonica varieties were 0.512, 0.483 and 0.251, respectively. Average similarity coefficient between TB and japonica was higher (0.236) compared to that between TB and indicas (0.150). Genetic relationships as determined by Principal Component Analysis (PCA, NTSYS-pc), PowerMarker tree, and Structure analyses, clearly showed high-level differentiation between TB and indica rice varieties, which formed two distinct clusters. The cross-bred Basmati and japonica rice genotypes were placed between these two clusters. Basmati 217 and Ranbir Basmati were quite divergent from rest of the TB varieties. Some of cross-bred Basmati varieties including Super, CSR30 and kernel were closer to TB. Indica rice varieties, CSR10 (salt tolerant variety) and Pokkali (salt tolerant landrace) formed a separate distinct cluster. The Pritchard structure analysis divided the rice genotypes in four major sub-populations of TB, cross-bred Basmati, indica and japonica (including Ranbir Basmati and Basmati 217) rice varieties. Chromosome 8 data-set showed a positive correlation (Mantel test, r = 0.739) with the allelic data-set for 30 SSR markers well-distributed on 12 rice chromosomes indicating a higher level of similarity between the two. The study demonstrates the distinctness of TB from other rice types (indica and japonica) and also provides several novel markers for differentiation between TB rice supplies from cheaper cross-bred Basmati and long-grain non-Basmati varieties at commercial level.     

QTLs identification of crude fat content in brown rice and its genetic basis analysis using DH and two backcross populations

Fat content is a concern for the enhancement of rice for eating, cooking, and storage qualities. To clarify its genetic mechanism, a double haploid (DH) population derived from anther hybrid F₁ of Zhenshan 97B (indica) and Wuyujing 2 (japonica) and two backcross F₁ (BCF₁) populations, which came from the DH lines backcrossing to two parents, were used to scan quantitative trait loci (QTLs) and dissect gene effects for the crude fat content (CFC) in brown rice. Fourteen QTLs were resolved, distributing on chromosomes 1, 3, and 5–9. Three loci were detected repeatedly in two populations, DH or BCF₁. Among these loci, a major QTL, qCFC5, flanking markers RM87 and RM334, was located on chromosome 5, which was detected simultaneously among three populations. The main QTLs had a major role in controlling CFC in brown rice and were modified by several mini-effect QTLs and epistatic affection. Wenjun Liu and Jing Zeng are contributed equally to this paper.     

Fine mapping of qSS‐9, a major and stable quantitative trait locus,for seed storability in rice (Oryza sativa L.)

Seed storability in rice (Oryza sativa L.) is an important agronomic trait. We previously showed a quantitative trait locus of seed storability, qSS‐9, on chromosome 9 in a backcross population of ‘Koshihikari’ (japonica) / ‘Kasalath’ (indica) // ‘Koshihikari’. In this study, fine mapping of the chromosomal location of qSS‐9 was performed. Effect of ‘Kasalath’ allele of qSS‐9 was validated using a chromosome segment substitution line, SL36, which harboured the target quantitative trait loci (QTL) from ‘Kasalath’ in the genetic background of ‘Nipponbare’ under different ageing treatments in different environments. Subsequently, an F₂ population from a cross between ‘Nipponbare’ and SL36 was used for fine mapping of qSS‐9. Simultaneously, four subnear isogenic lines (sub‐NILs) that represented different recombination breakpoints across the qSS‐9 region were developed from F₃ progeny. Finally, the qSS‐9 locus was located between the Indel markers Y10 and Y13, which delimit a region of 147 kb in the ‘Nipponbare’ genome. These results provide a springboard for map‐based cloning of qSS‐9 and possibilities for breeding rice varieties with strong seed storability.     

Mapping quantitative trait loci conferring blast resistance in upland indica rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

A genetic analysis of blast resistance in upland rice variety is very crucial. In this study, we performed a linkage mapping of quantitative trait loci (QTLs) for blast resistance using an advanced backcross population from a cross between Way Rarem (susceptible indica variety) and Oryzica Llanos 5 (durable resistant indica variety). A transgressive segregation was observed in the advanced backcross population of Way Rarem//Oryzica Llanos 5. A total of 16 QTLs have been identified along chromosomes 1, 3, 5, 6, 7, 8, 9, and 11 against eight blast pathogen isolates. Each QTL accounted from 11.31 to 45.11% of the variation in blast resistance. Most QTLs showed race specificity, demonstrating the small effect of such QTLs. Unexpectedly, several superior blast resistance alleles were contributed by Way Rarem, the susceptible-recurrent parent. Among eight candidate defense response genes detected in several loci, a single gene (oxalate oxidase) present on chromosome 3 was found to be associated with blast resistance in upland indica rice. Ultimately, these advanced backcross lines with resistance to blast tagged by markers might be useful for pyramiding blast resistance alleles in upland rice.     

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

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

Sterility in the rice hybrids and its significance

The degree of sterility resulting in F₁ hybrids has been used by several workers while considering the relative affinity between the different varieties and sub-species within a species and that between different species. The authors contend that sterility cannot be used as a criterion and present spikelet sterility data in F₁ hybrids of inter-varietal, inter-subspecific and interspecific crosses in the cultivated rices to support this contention. They conclude that the evolution of the three sub-species (viz., japonica, javanica and indica) may have taken place independent of each other from the various ecotypes of the putative species Oryza perennis through introgression although the possibility of the indica giving rise to japonica on the one hand and the javanica on the other cannot be altogether ruled out.The consequences of such a mode of evolution are discussed and the possibility of the existence of a slightly different set of linkage groups in indica rices compared with that of japonica rices is suggested.     

Fingerprinting temperate <Emphasis Type="Italic">japonica</Emphasis> and tropical <Emphasis Type="Italic">indica</Emphasis> rice genotypes by comparative analysis of DNA markers

This paper describes the relative efficiency of three marker systems, RAPD, ISSR, and AFLP, in terms of fingerprinting 14 rice genotypes consisting of seven temperatejaponica rice cultivars, three indica near-isogenic lines, three indica introgression lines, and one breeding line of japonica type adapted to high-altitude areas of the tropics with cold tolerance genes. Fourteen RAPD, 21 ISSR, and 8 AFLP primers could produce 970 loci, with the highest average number of loci (92.5) generated by AFLP. Although polymorphic bands in the genotypes were detected by all marker assays, the AFLP assay discriminated the genotypes effectively with a robust discriminating power (0.99), followed by ISSR (0.76) and RAPD (0.61). While significant polymorphism was detected among the genotypes of japonica and indica through analysis of molecular variance (AMOVA), relatively low polymorphism was detected within the genotypes of japonica rice cultivars. The correlation coefficients of similarity were significant for the three marker systems used, but only the AFLP assay effectively differentiated all tested rice lines. Fingerprinting of backcross-derived resistant progenies using ISSR and AFLP markers easily detected progenies having a maximum rate of recovery for the recurrent parent genome and suggested that our fingerprinting approach adopting the ‘undefined-element-amplifying’ DNA marker system is suitable for incorporating useful alleles from the indica donor genome into the genome of temperate japonica rice cultivars with the least impact of deleterious linkage drag.     

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.     

Relationship between molecular marker heterozygosity and hybrid performance in intra- and inter-subspecific crosses of rice

The objective of this study was to investigate the relationship between molecular marker diversity and heterosis in both intra-and inter-sub-specific hybrids of rice to evaluate the feasibility of predicting hybrid performance using molecular markers. Eleven elite lines were intermated resulting in a diallel set including 10 indica × indica, 15 japonica × japonica and 30 indica × japonica crosses. The F₁ hybrids and parents were evaluated for agronomic performance in a replicated field trial. The parental lines were tested for DNA polymorphisms with 113 restriction fragment length polymorphism (RFLP) probes covering the 12 rice chromosomes. Inter-subspecific crosses showed better performance and higher heterosis than intrasubspecific hybrids. Correlations of marker heterozygosity with hybrid performance and heterosis differed considerably between the two subspecies; they were higher in crosses within japonica subspecies than within indica subspecies. Very little correlation was detected in intersubspecific crosses. It was concluded that relationships between marker heterozygosity and hybrid performance were complex owing to germplasm diversity and the complexity of the genetic basis of heterosis. The implications of the results in predicting hybrid performance using molecular markers are discussed.     

一个新的水稻花粉半不育性位点的定位分析

利用一套以籼稻珍汕97B为背景的粳稻日本晴染色体片段代换系,鉴定发现1个半不育的代换系。全基因组基因型分析表明,该代换系仅含3个粳稻导入片段,而其他遗传背景与珍汕97B相同。在湖北武汉和海南分别种植其衍生的F₂和F₃分离群体,采用单标记分析和区间作图法分析花粉育性和小穗育性的数量性状位点(QTL),结果表明,该代换系的半不育性是第2染色体上的粳稻导入片段引起的,该片段RM262~RM475区间存在1个新的影响花粉育性的QTL,其贡献率为13.9%。研究结果将为进一步精细定位水稻育性QTL以及鉴定相关功能基因提供重要的试验基础。     

Mapping three new interspecific hybrid sterile loci between Oryza sativa and O. glaberrima

Hybrid sterility hinders the transfer of useful traits between Oryza sativa and O. glaberrima. In order to further understand the nature of interspecific hybrid sterility between these two species, a strategy of multi-donors was used to elucidate the range of interspecific hybrid sterility in this study. Fifty-nine accessions of O. glaberrima were used as female parents for hybridization with japonica cultivar Dianjingyou 1, after several backcrossings using Dianjingyou 1 as the recurrent parent and 135 BC₆F₁ sterile plants were selected for genotyping and deducing hybrid sterility QTLs. BC₆F₁ plants containing heterozygous target markers were selected and used to raise BC₇F₁ mapping populations for QTL confirmation and as a result, one locus for gamete elimination on chromosome 1 and two loci for pollen sterility on chromosome 4 and 12, which were distinguished from previous reports, were confirmed and designated as S37(t), S38(t) and S39(t), respectively. These results will be valuable for understanding the range of interspecific hybrid sterility, cloning these genes and improving rice breeding through gene introgression.     

Developing rice lines possessing neutral alleles at sterility loci to improve the width of compatibility

To improve the width of compatibility for overcoming various sterilities in inter‐subspecific hybrid rice, some elite lines combining several sterility‐neutral genes were developed and the effects on mitigating various hybrid sterilities were tested. From Akihikari// IR36/Dular, neutral genes at ga11 and six sterility loci, S5, S7, S8, S9, S15 and S16, were combined and elite lines were obtained in their successive progeny. Four of the lines tested were confirmed to combine the neutral alleles S5‐n, S7‐n, S8‐n, S9‐n, S15‐n and S16‐n at the sterility loci and, among them, two harboured an additional gamete abortion‐neutral allele, ga11‐n. F₁s, which used the lines and various testers as parents, mitigated the spikelet sterilities by six sterility loci and gamete abortion by a gametophyte gene, ga11. These lines could be selectively used as parents or donors to increase the width of compatibility of rice varieties for improving fertility in inter‐subspecific hybrid rice breeding.     

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

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

Assessment of genetic diversity within and among Basmati and non-Basmati rice varieties using AFLP,ISSR and SSR markers

Molecular markers provide novel tools to differentiate between the various grades of Basmati rice, maintain fair-trade practices and to determine its relationship with other rice groups in Oryza sativa. We have evaluated the genetic diversity and patterns of relationships among the 18 rice genotypes representative of the traditional Basmati, cross-bred Basmati and non-Basmati (indica and japonica) rice varieties using AFLP, ISSR and SSR markers. All the three marker systems generated higher levels of polymorphism and could distinguish between all the 18 rice cultivars. The minimum number of assay-units per system needed to distinguish between all the cultivars was one for AFLP, two for ISSR and five for SSR. A total of 171 (110 polymorphic), 240 (188 polymorphic) and 160 (159 polymorphic) bands were detected using five primer combinations of AFLP, 25 UBC ISSR primers and 30 well distributed, mapped SSR markers, respectively. The salient features of AFLP, ISSR and SSR marker data analyzed using clustering algorithms, principal component analysis, Mantel test and AMOVA analysis are as given below: (i) the two traditional Basmati rice varieties were genetically distinct from indica and japonica rice varieties and invariably formed a separate cluster, (ii) the six Basmati varieties developed from various indica × Basmati rice crosses and backcrosses were grouped variably depending upon the marker system employed; CSR30 and Super being more closer to traditional Basmati followed by HKR228, Kasturi, Pusa Basmati 1 and Sabarmati, (iii) AFLP, ISSR and SSR marker data-sets showed moderate levels of positive correlation (Mantel test, r = 0.42–0.50), and (iv) the partitioning of the variance among and within rice groups (traditional Basmati, cross-bred Basmati, indica and japonica) using AMOVA showed greater variation among than within groups using SSR data-set, while reverse was true for both ISSR and AFLP data-sets. The study emphasizes the need for using a combination of different marker systems for a comprehensive genetic analysis of Basmati rice germplasm. The high-level polymorphism generated by SSR, ISSR and AFLP assays described in this study shall provide novel markers to differentiate between traditional Basmati rice supplies from cheaper cross-bred Basmati and long-grain non-Basmati varieties at commercial level.The first two authors have equal contribution     

Complexity of indica-japonica varietal differentiation in Bangladesh rice landraces revealed by microsatellite markers

To understand the genetic diversity and indica-japonica differentiation in Bangladesh rice varieties, a total of 151 accessions of rice varieties mostly Bangladesh traditional varieties including Aus, Boro, broadcast Aman, transplant Aman and Rayada varietal groups were genotyped using 47 rice nuclear SSRs. As a result, three distinct groups were detected by cluster analysis, corresponding to indica, Aus and japonica rice. Among deepwater rice varieties analyzed some having particular morphological features that mainly corresponded to the japonica varietal group. Some small seeded and aromatic varieties from Bangladesh also corresponded to the japonica varietal group. This research for the first time establishes that the japonica varietal group is a prominent component of traditional varieties in Bangladesh, particularly in deepwater areas.     

Genetic analysis of a novel dominant rice dwarf mutant 986083D

This study was to determine the agronomic and genetic characteristics of a novel rice dominant dwarf mutant 986083D (japonica) and its potential in breeding. 986083D derived from the anther culture of an autotetraploid indica/japonica hybrid and its progeny segregated into normal and dwarf plants. Homozygous and heterozygous 986083D plants looked similar phenotypically, showing shortened stature, erect leaves, more tillers and poor fertility. The segregation ratio of dwarf to normal plants fit the expected 3:1 by χ²-test in 77 out of 88 tested lines. Crosses between homozygous 986083D and eight other rice varieties had uniform semi-dwarf F₁ plants. The F₁ plants from crosses between heterozygous 986083D and five other varieties had normal and semi-dwarf plants close to the expected ratio of 1:1. The reduction of plant height in F₁ plants ranged from 40.0 to 53.5% in a subtropical environment and from 37.5 to 48.2% in a temperate environment. 986083D showed moderate sensitivity to exogenously applied GA₃ in terms of elongation of shoots and induction of α-amylase activity in the endosperm. Linkage analysis showed that the dominant dwarf gene (designated as Dx) in 986083D was not allelic to D53. Dx was roughly mapped to the short arm of chromosome 8. All results showed that 986083D was a novel mutant controlled by single dominant gene, providing a valuable material in rice breeding. Ruizhen Qin, Yang Qiu contributed equally to this work.     

Two linked genes on rice chromosome 2 for F1 pollen sterility in a hybrid between Oryza sativa and O. glumaepatula

Hybrid incompatibility plays an important role in establishment of post-zygotic reproductive isolation. To unveil genetic basis of hybrid incompatibilities between diverged species of genus Oryza AA genome species, we conducted genetic dissection of hybrid sterility loci, S22(t), which had been identified in backcross progeny derived from Oryza sativa ssp. japonica (recurrent parent) and South American wild rice O. glumaepatula near the end of the short arm of chromosome 2. The S22(t) region was found to be composed of two loci, designated S22A and S22B, that independently induce F₁ pollen sterility. Pollen grains containing either of the sterile alleles (S22A-glum^s or S22B-glum^s) were sterile if produced on a heterozygous plant. No transmission of the S22A-glum^s allele via pollen was observed, whereas a low frequency of transmission of S22B-glum^s was observed. Cytological analysis showed that the sterile pollen grains caused by S22A could reach the bicellular or tricellular stage, and the nearly-sterile pollen grains caused by S22B could reach the tricellular stage. Our genetic analysis showed repulsion linkage effect is possible to induce strong reproductive barrier by high pollen sterility based on recombination value and transmission ratio of hybrid sterility gene to the progeny was influenced by frequency of competitors on fertilization.     

A simple method to control the seed purity of japonica hybrid rice varieties using PCR-based markers

Cytoplasmic male sterility (CMS) by the cms‐bo cytoplasm and its restoration by the nuclear restorer gene, Rf‐1, are used for seed production of japonica hybrid rice varieties. To produce pure hybrid seeds, a prerequisite is to properly manage the seed purity of parental lines, especially CMS lines. In this study, three dominant polymerase chain reaction (PCR)‐based markers (M1, M2 and M3) were developed to detect mutual contamination in seed batches of CMS lines, maintainer lines, restorer lines and hybrids. M1 detected the mitochondrial sequence that was present in the cytoplasm of common japonica varieties and absent in the cms‐bo cytoplasm. M2 and M3 detected the chromosomal sequence related to the Rf‐1 allele in restorer lines and the rf‐1 allele in common japonica varieties, respectively. By the strategic use of these markers, japonica hybrids and their parental lines could be efficiently distinguished from each other. Furthermore, sensitivity tests for the three markers with a series of crude DNA samples prepared from polished grains demonstrated that these markers could detect one contaminating grain among 500 or 1000 grains. Therefore, the bulk PCR analyses with the markers developed here probably make it possible to control the seed purity of japonica hybrids properly by selecting appropriate seed batches of their parental lines quickly and efficiently.     

Identification of a locus for asynchronous heading in rice, <Emphasis Type="Italic">Oryza sativa</Emphasis> L.

We have identified a locus for asynchronous heading in rice. The length of heading period in a plant was measured as the indicator of asynchronous heading in 98 backcross inbred lines (BILs). These lines were derived using a single-seed descent method from a backcross of (japonica Nipponbare/indica Kasalath)/Nipponbare, and we used this mapping population in quantitative trait locus (QTL) analysis. We located a single QTL related to asynchronous heading (qah7) in the region of R2401–C39 on chromosome 7, and its contribution to the total variation was 0.14 (r²), with the positive effect due to the Kasalath allele. A near isogenic line (NILah7) that carries a Kasalath chromosomal segment corresponding to qah7 in the Nipponbare genetic background was selected and analyzed to identify a locus for asynchronous heading. The length of heading period in NILah7 was significantly longer (P < 0.001) than that in Nipponbare.