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  • 1
    Electronic Resource
    Electronic Resource
    Detection and genotyping of SNPs tightly linked to two disease resistance loci, Rsv1 and Rsv3, of soybean (2004)
    Oxford, UK : Blackwell Publishing Ltd
    Plant breeding 123 (2004), S. 0 
    Details
    ISSN: 1439-0523
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Allele-specific polymerase chain reaction (AS-PCR) for assaying single nucleotide polymorphisms (SNPs) would be more widely used with increased availability of AS primers sufficient to distinguish between SNP alleles. AS-PCR could be a means unambiguously to detect the presence or absence of PCR products. Examples are given here of the detection and genotyping of SNPs in the genomic DNA fragments tightly linked to two soybean mosaic virus resistance genes, Rsv1 and Rsv3, with a modified AS-PCR procedure in soybean. The modified AS-PCR that introduces an additional base mismatch closest to the 3′-end of the AS primers and uses publicly available microsatellite markers as positive controls directly determined SNP alleles from primary PCR of genomic DNAs. It was demonstrated that a set of AS primers designed from two adjacent SNP loci could simultaneously detect the two SNP loci. Using the modified procedure, many SNP loci in eight soybean parental lines and F2 individuals of three mapping populations could be genotyped. The modified AS-PCR procedure could greatly facilitate small-to-medium scale marker-assisted selection programmes for agronomically important genes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1439-0523.2004.00981.x
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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
    Evolution of resistance to scald, powdery mildew, and net blotch in barley composite cross II populations (1983)
    Springer
    Theoretical and applied genetics 66 (1983), S. 279-283 
    Details
    ISSN: 1432-2242
    Keywords: Disease resistance ; Genetic variability ; Plant breeding
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Progenies of barley plants taken at random from generations F8, F13, F23, and F45 of Composite Cross II were tested for reaction to three barley pathogens, Helminthosporium teres, Erysiphe graminis, and Rhynchosporium secalis (four races). The frequency of families resistant to each of the three pathogens (excepting one race of R. secalis) increased from early to later generations. Many families carrying combinations of multiple resistance not observed among the parents were found in the later generations; one-half of the parents were susceptible to all three diseases but only 4% of the families in generation F45 were of this phenotype. The frequency of multiply resistant families also increased sharply over generations. Among the parents the greatest concentration of resistant reactions observed was triple resistance: 14% were triply resistant; none were quadruply resistant; nor were any resistant to all three pathogens. In generation F43 36% of the families were triply resistant, 32% were quadruply resistant and 6% were resistant in five of the six disease reactions. The value of later generations of Composite Cross II for breeding against pathogens thus appears to have been increased by recombination and natural selection. Significant positive correlations were found for resistance to races 40, 61, and 74 of R. secalis whereas correlations between resistance to R. secalis, E. graminis, and H. teres were generally nonsignificant. Use of these multiply resistant genotypes in breeding is thus unlikely to be hindered by negative associations between resistance to the three diseases.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00251159
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  • 4
    Electronic Resource
    Electronic Resource
    Analysis of the barley and rice genomes by comparative RFLP linkage mapping (1996)
    Springer
    Theoretical and applied genetics 92 (1996), S. 541-551 
    Details
    ISSN: 1432-2242
    Keywords: Synteny ; Orthologous evolution ; Genetic maps ; Triticeae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Comparative genetic mapping of rice and barley, both major crop species with extensive genetic resources, offers the possibility of uniting two well-established and characterized genetic systems. In the present study, we screened 229 molecular markers and utilized 110 polymorphic orthologous loci to construct comparative maps of the rice and barley genomes. While extensive chromosomal rearrangements, including inversions and intrachromosomal translocations, differentiate the rice and barley genomes, several syntenous chromosomes are evident. Indeed, several chromosomes and chromosome arms appear to share nearly identical gene content and gene order. Seventeen regions of conserved organization were detected, spanning 287 cM (24%) and 321 cM (31%) of the rice and barley genomes, respectively. The results also indicate that most (72%) of the single-copy sequences in barley are also single copy in rice, suggesting that the large barley genome arose by unequal crossing over and amplification of repetitive DNA sequences and not by the duplication of single-copy sequences. Combining these results with those previously reported for comparative analyses of rice and wheat identified nine putatively syntenous chromosomes among barley, wheat and rice. The high degree of gene-order conservation as detected by comparative mapping has astonishing implications for interpreting genetic information among species and for elucidating chromosome evolution and speciation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00224556
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  • 5
    Electronic Resource
    Electronic Resource
    Rpg1, a soybean gene effective against races of bacterial blight, maps to a cluster of previously identified disease resistance genes (1998)
    Springer
    Theoretical and applied genetics 96 (1998), S. 1013-1021 
    Details
    ISSN: 1432-2242
    Keywords: Key words Nucleotide binding site ; Leucine-rich repeats ; RFLP mapping ; Recombinant-inbred lines
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Alleles, or tightly linked genes, at the soybean (Glycine max L. Merr.) Rpg1 locus confer resistance to races of Pseudomonas syringae pv. glycinea that express the avirulence genes avrB or avrRpm1. In this study we demonstrate that Rpg1 maps to a cluster of previously identified resistance genes, including those effective against fungal, viral and nematode pathogens. Rpg1 is in molecular linkage group (MLG) F, flanked by the markers K644 and B212. The RFLP markers R45, php2265 and php2385 cosegregated with Rpg1, as did the marker nbs61, which encodes a protein related to previously isolated resistance genes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220050833
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  • 6
    Electronic Resource
    Electronic Resource
    A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome (1993)
    Springer
    Theoretical and applied genetics 86 (1993), S. 705-712 
    Details
    ISSN: 1432-2242
    Keywords: RFLP ; Mapping ; Barley ; Genome ; Centromeres
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A map of the barley genome consisting of 295 loci was constructed. These loci include 152 cDNA restriction fragment length polymorphism (RFLP), 114 genomic DNA RFLP, 14 random amplified polymorphic DNA (RAPD), five isozyme, two morphological, one disease resistance and seven specific amplicon polymorphism (SAP) markers. The RFLP-identified loci include 63 that were detected using cloned known function genes as probes. The map covers 1,250 centiMorgans (cM) with a 4.2 cM average distance between markers. The genetic lengths of the chromosomes range from 124 to 223 cM and are in approximate agreement with their physical lengths. The centromeres were localized to within a few markers on all of the barley chromosomes except chromosome 5. Telomeric regions were mapped for the short (plus) arms of chromosomes 1, 2 and 3 and the long (minus) arm of chromosomes 7.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222660
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  • 7
    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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  • 8
    Electronic Resource
    Electronic Resource
    Worldwide pattern of multilocus structure in barley determined by discrete log-linear multivariate analyses (1990)
    Springer
    Theoretical and applied genetics 80 (1990), S. 121-128 
    Details
    ISSN: 1432-2242
    Keywords: Barley ; Log-linear multivariate analyses ; Multilocus associations ; Enzyme loci
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Data from the electrophoretic assay for seven enzyme loci of 1,032 accessions of cultivated barley, Hordeum vulgare L., from the USDA world barley collection were analyzed for multilocus structure using discrete log-linear multivariate techniques. Three major steps were involved in the analysis: (i) identification and elimination of terms that have inconsequential effects in multilocus association; (ii) construction of a log-linear model that best describes the complete multilocus structure of the genetic system; and (iii) evaluation of each of the association terms included in the model. The results of analyses of two subsets of loci show that the multilocus genetic system of cultivated barley, including loci located on different chromosomes, is organized into hierarchically structured complexes of loci. Multilocus structure differs in various geographical regions of the world. The structure of barleys from Southwest Asia, the putative center of origin for cultivated barley, is intermediate for both subsets of loci. Differences increased progressively across the Eurasian-African landmasses in each direction with increasing distance from Southwest Asia, with the consequence that the barleys from West Europe, East Asia, and Ethiopia are maximally different from those of Southwest Asia and Middle South Asia.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00224025
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  • 9
    Electronic Resource
    Electronic Resource
    Use of RFLP markers to search for alleles in a maize population for improvement of an elite hybrid (1992)
    Springer
    Theoretical and applied genetics 83 (1992), S. 903-911 
    Details
    ISSN: 1432-2242
    Keywords: Zea mays L. ; RFLPs ; Quantitative traits ; Favorable alleles ; Epistasis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Molecular markers can be used to detect alleles in donor genetic material for improvement of existing cultivars or hybrids. DNA restriction fragment length polymorphisms (RFLPs) were used as markers to search for favorable alleles at quantitative trait loci in the maize (Zea mays L.) population BS11(FR)C7 which were not in the hybrid ‘FRB73 x FRMo17.’ Thirty-four RFLP markers were used to determine RFLP ‘fingerprints’ for 220 [BS11(FR)C7 x FRMo17] F2 individuals; multiple morphs (bands) were observed at most markers. Statistical associations between RFLPs and trait expression in F2 x FRB73 progeny were found for grain yield, stalk and root lodging, plant and ear height, maturity, and seven grain yield component traits. Associations were found using linear contrasts among RFLP marker classes to estimate trait effects. Estimated effects for grain yield ranged from 213 to 538 kg ha-1, 3.0–7.5% of the experimental mean, respectively. RFLP markers with greatest probability of association with grain yield were NPI234 (short arm of chromosome 1) and UMC16 (long arm of chromosome 3). Digenic epistasis appeared to be important in grain yield expression, as indicated by a 12% increase in the proportion of genotypic variation accounted for when significant di-marker interactions were added to a linear model, including all markers individually associated with grain yield. The majority of interactions associated with grain yield involved markers NPI234 and UMC21 (long arm of chromosome 6). Many RFLP markers were associated with multiple traits. At some markers, the same bands were associated with favorable effects for stalk lodging, grain yield, and yield components. RFLP bands unique to BS11(FR)C7 showed associations favorable over those from FRMo17 for at least one marker in all but one trait. The results of this study will be useful in future RFLP marker-assisted selection programs aimed at developing lines for improved performance in combination with FRB73.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00226714
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  • 10
    Electronic Resource
    Electronic Resource
    Ribosomal DNA polymorphisms and the Oriental-Occidental genetic differentiation in cultivated barley (1992)
    Springer
    Theoretical and applied genetics 84 (1992), S. 682-687 
    Details
    ISSN: 1432-2242
    Keywords: rDNA polymorphism ; Hordeum vulgaressp. vulgare ; Geographical differentiation ; Evolution ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A total of 289 accessions of cultivated barley were assayed for ribosomal DNA (rDNA) polymorphisms. These accessions comprised four independent samples: (1) 79 entries from China, (2) 59 accessions from Ethiopia, (3) 59 entries from Tibet and (4) 92 entries representing 36 barley growing countries of the world (referred to as “world sample”). In all, 17 rDNA phenotypes (genotypes) were observed, which were composed 10 alleles at two rDNA loci, Rrn1 and Rrn2. The world sample contained the largest number of phenotypes and alleles and also demonstrated the highest level of diversity. Ribosomal DNA phenotypes 104, 112 and 107, 112 occurred at high frequencies worldwide. Allele 112 was the predominant allele of Rrn1 in all four samples, and 104 and 107 were the two major alleles of Rrn2 worldwide. The distributions of rDNA genotypes and alleles demonstrated a clear differentiation of two distinct barley groups: an Oriental group represented by the samples from China and Tibet, which is characterized by allele 107 at the Rrn2 locus (rDNA phenotype 107, 112); and an Occidental group, represented by Ethiopian and world samples, which is comprised mostly of allele 104 at the Rrn2 locus (rDNA phenotype 104, 112). The results also raised new questions concerning the phylogeny and evolution of cultivated barley.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00224168
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