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  • 1
    Electronic Resource
    Electronic Resource
    Mapping and Genetic Analysis of the Genes for Photoperiod-Sensitive Genic Male Sterility in Rice Using the Original Mutant Nongken 58S (1999)
    Springer
    Crop science 39 (1999), S. 1711-1714 
    Details
    ISSN: 1435-0653
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: 2 populations. Two PSGMS loci, located on chromosomes 7 and 12, respectively, were identified in both crosses. The locus on chromosome 7 was the same as pms1, identified previously in a cross between an indica PSGMS line and an indica cultivar. The one on chromosome 12 was a new locus that we designated as pms3. Both loci had major effects on fertility and acted like a pair of classical duplicated genes in controlling male sterility. Comparison of the present finding with previous results indicated a complex genetic basis of PSGMS. The implications of such genetic complexity in breeding for PSGMS lines are also discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/
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  • 2
    Electronic Resource
    Electronic Resource
    Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique (1999)
    Springer
    Molecular genetics and genomics 261 (1999), S. 439-446 
    Details
    ISSN: 1617-4623
    Keywords: Key words DNA methylation ; Hybrid rice ; Tissue specificity ; Isoschizomers ; PCR amplification
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract DNA methylation is known to play an important role in the regulation of gene expression in eukaryotes. In this study, we assessed the extent and pattern of cytosine methylation in the rice genome, using the technique of methylation-sensitive amplified polymorphism (MSAP), which is a modification of the amplified fragment length polymorphism (AFLP) method that makes use of the differential sensitivity of a pair of isoschizomers to cytosine methylation. The tissues assayed included seedlings and flag leaves of an elite rice hybrid, Shanyou 63, and the parental lines Zhenshan 97 and Minghui 63. In all, 1076 fragments, each representing a recognition site cleaved by either or both of the isoschizomers, were amplified using 16 pairs of selective primers. A total of 195 sites were found to be methylated at cytosines in one or both parents, and the two parents showed approximately the same overall degree of methylation (16.3%), as revealed by the incidence of differential digestion by the isoschizomers. Four classes of patterns were identified in a comparative assay of cytosine methylation in the parents and hybrid; increased methylation was detected in the hybrid compared to the parents at some of the recognition sites, while decreased methylation in the hybrid was detected at other sites. A small proportion of the sites was found to be differentially methylated in seedlings and flag leaves; DNA from young seedlings was methylated to a greater extent than that from flag leaves. Almost all of the methylation patterns detected by MSAP could be confirmed by Southern analysis using the isolated amplified fragments as probes. The results clearly demonstrate that the MSAP technique is highly efficient for large-scale detection of cytosine methylation in the rice genome. We believe that the technique can be adapted for use in other plant species.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004380050986
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  • 3
    Electronic Resource
    Electronic Resource
    Molecular marker heterozygosity and hybrid performance in indica and japonica rice (1996)
    Springer
    Theoretical and applied genetics 93 (1996), S. 1218-1224 
    Details
    ISSN: 1432-2242
    Keywords: Oryza sativa ; Hybrid rice ; Predicting heterosis ; Diallel cross ; Restriction fragment length polymorphism (RFLP) ; Simple sequence repeat (SSR)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract An essential assumption underlying markerbased prediction of hybrid performance is a strong linear correlation between molecular marker heterozygosity and hybrid performance or heterosis. This study was intended to investigate the extent of the correlations between molecular marker heterozygosity and hybrid performance in crosses involving two sets of rice materials, 9 indica and 11 japonica varieties. These materials represent a broad spectrum of the cultivated rice gene pool including landraces, primitive cultivars, historically important cultivars, modern elite cultivars and parents of superior hybrids. Varieties within each set were intermated in all possible nonreciprocal pairs resulting in 36 crosses in the indica set and 55 in the japonica set. The F1s and their parents, 111 entries in total, were examined for performance of seven traits in a replicated field trial. The parents were surveyed for polymorphisms using 96 RFLP and ten SSR markers selected at regular intervals from a published molecular marker linkage map. Molecular marker genotypes of the F1 hybrids were deduced from the parental genotypes. The analysis showed that, with very few exceptions, correlations in the indica dataset were higher than in that of their japonica counterparts. Among the seven traits analyzed, plant height showed the highest correlation between heterozygosity and hybrid performance and heteorsis in both indica and japonica datasets. Correlations were low to intermediate between hybrid performance and heterozygosity (both general and specific) in yield and yield component traits in both indica and japonica sets, and also low to intermediate between specific heterozygosity and heterosis in the indica set, whereas very little correlation was detected between heterosis and heterozygosity (either general or specific) in the japonica set. In comparison to the results from our previous studies, we concluded that the relationship between molecular marker heterozygosity and heterosis is variable, depending on the genetic materials used in the study, the diversity of rice germplasms and the complexity of the genetic basis of heterosis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00223453
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  • 4
    Electronic Resource
    Electronic Resource
    Genetic basis of low-temperature-sensitive sterility in indica-japonica hybrids of rice as determined by RFLP analysis (1997)
    Springer
    Theoretical and applied genetics 95 (1997), S. 1092-1097 
    Details
    ISSN: 1432-2242
    Keywords: Key words Oryza sativa ; Hybrid sterility ; Ste loci ; Molecular markers ; Hybrid rice breeding
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Low-temperature-sensitive sterility (LTSS) has become one of the major obstacles in indica-japonica hybrid rice breeding. In this study, we determined, using RFLP markers, the genetic basis of LTSS in two populations derived from crosses between indica and japonica parents, the BC1F1 of 3037/02428//3037 and the F2 of 3037/02428. The fertility segregation in the two populations under low-temperature conditions was used as a measurement of the temperature sensitivity of the various genotypes in the populations. A RFLP survey of bulked extremes from the BC1F1 population identified three genomic regions, two on chromosome 1 and one on chromosome 12, that were likely to contain genes for LTSS (or Ste loci). One-way ANOVA and QTL analysis using a total of 19 markers from these three genomic regions resolved three Ste loci in the BC1F1 population and two Ste loci in the F2 population. On the basis of chromosomal location these loci were distinct from those governing wide-compatibility identified in previous studies. Two- and three-way ANOVA showed that these loci acted essentially independent of each other in conditioning LTSS. The main mode of gene action was an interaction between the indica and the japonica alleles within each locus. For each respective locus this resulted in a drastic fertility reduction in the heterozygote state relative to the homozygote state. The results have significant implications in indica-japonica hybrid rice breeding programs.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050667
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  • 5
    Electronic Resource
    Electronic Resource
    The three important traits for cooking and eating quality of rice grains are controlled by a single locus in an elite rice hybrid, Shanyou 63 (1999)
    Springer
    Theoretical and applied genetics 99 (1999), S. 642-648 
    Details
    ISSN: 1432-2242
    Keywords: Key words Rice quality ; Amylose content ; Gel consistency ; Gelatinization temperature ; Genetic analysis ; Molecular marker
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The cooking and eating quality of the rice grain is one of the most serious problems in many rice-producing areas of the world. In this study, we conducted a molecular marker-based genetic analysis of three traits, amylose content (AC), gel consistency (GC) and gelatinization temperature (GT), that are the most important constituents of the cooking and eating quality of rice grains. The materials used in the analysis included F2 seeds, an F2:3 population, and an F9 recombinant inbred-line population from a cross between the parents of ’Shanyou 63’, the most widely grown hybrid in rice production in China. Segregation analyses of these three generations showed that each of the three traits was controlled by a single Mendelian locus. Molecular marker-based QTL (quantitative trait locus) analyses, both by one-way analysis of variance using single marker genotypes and by whole-genome scanning with MAPMAKER/QTL, revealed a single locus that controls the expression of all three traits. This locus coincided with the Wx region on the short arm of chromosome 6, indicating that all three traits were either controlled by the Wx locus or by a genomic region tightly linked to this locus. This finding has provided clues to resolving the molecular bases of GC and GT in future studies. The results also have direct implications for the quality improvement of rice varieties.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220051279
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  • 6
    Electronic Resource
    Electronic Resource
    Mapping and genetic analysis of two fertility restorer loci in the wild-abortive cytoplasmic male sterility system of rice (Oryza sativa L.) (1997)
    Springer
    Euphytica 98 (1997), S. 183-187 
    Details
    ISSN: 1573-5060
    Keywords: fertility restoration ; hybrid rice ; linkage analysis ; Oryza sativa ; RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Hybrid varieties developed by making use of the wild abortive cytoplasmic male sterility system account for 90% of hybrid rice produced. Previous inheritance studies have established that the fertility restoration in this system is controlled by two major loci, but the chromosomal locations of the fertility restorer (Rf) loci have yet to be resolved. In this study we determined the genomic locations of the two Rf loci by their linkage to molecular markers. The Rf gene containing regions were identified by surveying two bulks, made of 30 highly fertile and 46 highly sterile plants from a large F2 population of the cross between Zhenshan 97A and Minghui 63, with RFLP markers covering the entire rice genome. The survey identified two likely Rf gene containing regions, located on chromosomes 1 and 10 respectively. This was confirmed by ANOVA using a large random sample from the same F2 population and also with a genome-wide QTL analysis of a test-cross population. The results also showed that both loci have major effects of almost complete dominance on fertility restoration and the effect of the locus on chromosome 10 is larger than the one on chromosome 1. The two loci acted as a pair of classical duplicate genes; a single dominant allele at one of the two loci would suffice to restore the fertility to normal or nearly normal. Closely linked markers identified in this study may be used for marker assisted selection in hybrid rice breeding programs.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003165116059
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  • 7
    Electronic Resource
    Electronic Resource
    An analysis of hybrid sterility in rice using a diallel cross of 21 parents involving indica, japonica and wide compatibility varieties (1996)
    Springer
    Euphytica 90 (1996), S. 275-280 
    Details
    ISSN: 1573-5060
    Keywords: Oryza sativa ; inter-varietal cross ; spikelet fertility ; genetic basis ; rice
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary There is much interest in the inter-varietal fertility of Asian cultivated rice. In this study, we analyzed the fertility of hybrids in a diallel set of 210 crosses involving 21 parents representing a broad range of the cultivated rice germplasm including landraces, primitive cultivars, modern elite cultivars and parents of hybrid rice. The materials were also carefully selected with respect to indica-japonica classification including typical indica/japonica, more or less intermediate and wide compatibility varieties. The level of hybrid fertility varied widely among the crosses from almost completely sterile to fully fertile. In general, hybrid fertility of intra-subspecific crosses, i.e., indica by indica (I×I) and japonica by japonica (J×J), is much higher than inter-subspecific crosses (I×J or J×I). The fertility varied widely in hybrids involving wide compatibility varieties and also in inter-subspecific crosses not involving wide compatibility varieties. An analysis of variance showed that both the main effects of indica and japonica parents and the interaction between the parents are highly significant in determining hybrid fertility. We speculate that, in addition to wide compatibility, the overall genetic difference between the indica and japonica parents, that may involve a series of minor mutations, play an important role in determining the hybrid fertility. There are also genes of sizable effect that influence fertility in hybrids resulting from specific combinations of the parents.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00027476
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  • 8
    Electronic Resource
    Electronic Resource
    Copia-like retrotransposons in rice: sequence heterogeneity, species distribution and chromosomal locations (1997)
    Springer
    Plant molecular biology 33 (1997), S. 1051-1058 
    Details
    ISSN: 1573-5028
    Keywords: genetic diversity ; indica ; japonica ; mapping ; reverse transcriptase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Degenerated oligonucleotide primers were used to amplify, clone, and analyze sequence heterogeneity and chromo-somal distribution of 23 PCR fragments corresponding to the reverse transcriptase domain of copia-like retrotrans-posons in rice. Of the 23 fragments 22 could be aligned by their deduced amino acid sequences and were divided into 6 groups according to the phylogenetic and Southern blot analyses. Amino acid sequence differences among the 22 aligned fragments ranged from 1 to 64%. Southern blot analysis of 10 rice accessions including indica, japonica and common wild rice, using these 23 fragments as probes, showed that copia-like retrotransposons were present in moderate to high copy numbers in all the rice genome although the exact copy number cannot be determined. The major difference revealed by southern analysis is a differentiation between the four indica varieties as one group and the four japonica varieties and the two wild rice accessions as another group. Polymorphisms were also detected among the indica and japonica varieties by major bands and repeatable minor bands. Five hybridization bands were mapped to chromosomes 3, 4, 8, and 9, respectively. All the five bands were inherited in a dominant Mendelian fashion and were not allelic with each other, indicating that the same element did not reside on the same location in different rice accessions. No transcript of the copia-like reverse transcriptase was detected on northern blot. The results suggest that the sequence heterogeneity and distributional variability of retrotransposons may be one of contributory factors causing genetic diversity in rice.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1005715118851
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  • 9
    Electronic Resource
    Electronic Resource
    Molecular divergence and hybrid performance in rice (1995)
    Springer
    Molecular breeding 1 (1995), S. 133-142 
    Details
    ISSN: 1572-9788
    Keywords: genetic distance ; heterosis ; Oryza sativa ; restriction fragment length polymorphism (RFLP) ; simple sequence repeat (SSR)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract This study was undertaken to determine the relationship between genetic distance of the parents based on molecular markers and F1 performance in a set of diallel crosses involving eight commonly used parental lines in hybrid rice production. The F1s and their parents were measured for five traits including heading date, plant height, straw weight, grain yield and biomass. The parental lines were assayed for DNA polymorphisms using two classes of markers: 140 probes for restriction fragment length polymorphisms (RFLPs) and 12 simple sequence repeats (SSRs), resulting in a total of 105 polymorphic markers well spaced along the 12 rice chromosomes. SSRs detected more polymorphism than RFLPs among the eight lines. A cluster analysis based on marker genotypes separated these eight lines into three groups which agree essentially with the available pedigree information. Correlations were mostly low between general heterozygosity based on all the markers and F1 performance and heterosis. In contrast, very high correlations were detected between midparent heterosis and specific heterozygosity based on the markers that detected significant effects for all the five traits; these correlations may have practical utility in predicting heterosis. The analyses also suggest the existence of two likely heterotic groups in the rice germplasm represented by these eight lines.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01249698
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  • 10
    Electronic Resource
    Electronic Resource
    Relationships of differential gene expression in leaves with heterosis and heterozygosity in a rice diallel cross (1998)
    Springer
    Molecular breeding 4 (1998), S. 129-136 
    Details
    ISSN: 1572-9788
    Keywords: differential display ; gene expression ; hybrid vigor ; molecular marker heterozygosity ; Oryza sativa L.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Using differential display analysis, we assessed the patterns of differential gene expression in hybrids relative to their parents in a diallel cross involving 8 elite rice lines. The analysis revealed several patterns of differential expression including: (1) bands present in one parent and F1 but absent in the other parent, (2) bands observed in both parents but not in the F1, (3) bands occurring in only one parent but not in the F1 or the other parent, and, (4) bands detected only in the F1 but in neither of the parents. Relationships between differential gene expression and heterosis and marker heterozygosity were evaluated using data for RFLPs, SSRs and a number of agronomic characters. The analysis showed that there was very little correlation between patterns of differential expression and the F1 means for all six agronomic traits. Differentially expressed fragments that occurred only in one parent but not in the other parent or in F1 in each of the respective crosses were positively correlated with heterosis and heterozygosity. And conversely, fragments that were detected in F1s but in neither of the respective parents were negatively correlated with heterosis and heterozygosity. The remaining patterns of differential expression were not correlated with heterosis or heterozygosity. The relationships between the patterns of differential expression and heterosis observed in this study were not consistent with expectations based on dominance or overdominance hypotheses.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1009685820649
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