A resistance gene analog useful for targeting disease resistance genes against different pathogens on group 1S chromosomes of barley,wheat and rye

Comparative sequence analysis of the resistance gene analog (RGA) marker locus aACT/CAA (originally found to be tightly linked to the multiallelic barley Mla cluster) from genomes of barley, wheat and rye revealed a high level of relatedness among one another and showed high similarity to a various number of NBS-LRR disease resistance proteins. Using the sequence-specific polymerase chain reaction (PCR), RGA marker aACT/CAA was mapped on group 1S chromosomes of the Triticeae and was associated with disease resistance loci. In barley and rye, the marker showed linkage to orthologous powdery mildew resistance genes Mla1 and Pm17, respectively, while in wheat linkage with a QTL against fusarium head blight (FHB) disease was determined. The use of RGA clones for R gene mapping and their role in the expression of qualitative and quantitative resistance is discussed.     

Identification of the stem rust resistance gene Pg9 and its association with crown rust resistance and endosperm proteins in 'Dumont' oat.

The Canadian oat cultivar 'Dumont' is known to have genes Pc38 and Pc39 for crown rust resistance and genes Pg2 and Pg13 for stem rust resistance. When crossed to a susceptible oat line OT328, 'Dumont' was shown to have an additional dominant gene for crown rust resistance, designated PcX. Tests of segregating progeny indicated that the stem rust resistance gene Pg9 is present and is tightly linked in coupling to PcX. The presence of Pg9 in 'Dumont' was confirmed in crosses involving the cultivar 'Ukraine', which has Pg9 and a crown rust resistance gene tightly linked to it. The association of rust resistance with endosperm proteins in 'Dumont' was investigated. The linkage of gene Pg13 with a 56.6-kDa polypeptide locus (map distance of 10.47 +/- 2.70 cM) was demonstrated using sodium dodecylsulfate - polyacrylamide gel electrophoresis (SDS-PAGE). A 27.9-kDa polypeptide was shown to be associated with the linked PcX/Pg9 loci by SDS-PAGE but appeared to be more reliably separated as an avenin band, designated B4, using acid-PAGE. Another avenin band, designated B2, also was shown to be associated with the PcX/Pg9 loci using acid-PAGE. The loci conditioning the B2 and B4 bands appeared to be tightly linked or allelic and are separated from the linked PcX/Pg9 loci by a map distance of 1.03 +/- 0.36 cM. The association of Pg13 with a 56.6-kDa polypeptide and the tight linkage between PcX/Pg9 and the B2 (in coupling) and B4 (in repulsion) avenin loci offer a useful tool to breeders to detect the presence of these genes in oat breeding.     

Genetic and physical mapping of Lrk10-like receptor kinase sequences in hexaploid oat (Avena sativa L.).

Oat receptor-like kinase gene sequences, homologous to the Lrk10 gene from wheat (Triticum aestivum L.), were mapped in oat (Avena sativa L.). PCR primers designed from the wheat Lrk10 were used to produce ALrk10 from oat. Two DNA sequences, ALrk1A1 and ALrk4A5, were produced from primers designed from coding and noncoding regions of ALrk10. Their use as RFLP probes indicated that the kinase genes mapped to four loci on different hexaploid oat 'Kanota' x 'Ogle' linkage groups (4_12, 5, 6, and 13) and to a fifth locus unlinked to other markers. Three of these linkage groups contain a region homologous to the short arm of chromosome I of wheat and the fourth contains a region homologous to chromosome 3 of wheat. Analysis with several nullisomics of oat indicated that two of the map locations are on satellite chromosomes. RFLP mapping in a 'Dumont' x 'OT328' population indicated that one map location is closely linked to Pg9, a resistance gene to oat stem rust (Puccinia graminis subsp. avenae). Comparative mapping indicates this to be the region of a presumed cluster of crown rust (Puccinia coronata subsp. avenae) and stem rust resistance genes (Pg3, Pg9, Pc44, Pc46, Pc50, Pc68, Pc95, and PcX). The map position of several RGAs located on KO6 and KO3_38 with respect to Lrk10 and storage protein genes are also reported.     

Four QTLs determine crown rust (Puccinia coronata f. sp. lolii) resistance in a perennial ryegrass (Lolium perenne) population

Crown rust resistance is an important selection criterion in ryegrass breeding. The disease, caused by the biotrophic fungus Puccinia coronata, causes yield losses and reduced quality. In this study, we used linkage mapping and QTL analysis to unravel the genomic organization of crown rust resistance in a Lolium perenne population. The progeny of a pair cross between a susceptible and a resistant plant were analysed for crown rust resistance. A linkage map, consisting of 227 loci (AFLP, SSR, RFLP and STS) and spanning 744 cM, was generated using the two-way pseudo-testcross approach from 252 individuals. QTL analysis revealed four genomic regions involved in crown rust resistance. Two QTLs were located on LG1 (LpPc4 and LpPc2) and two on LG2 (LpPc3 and LpPc1). They explain 12.5, 24.9, 5.5 and 2.6% of phenotypic variance, respectively. An STS marker, showing homology to R genes, maps in the proximity of LpPc2. Further research is, however, necessary to check the presence of functional R genes in this region. Synteny at the QTL level between homologous groups of chromosomes within the Gramineae was observed. LG1 and LG2 show homology with group A and B chromosomes of oat on which crown rust-resistance genes have been identified, and with the group 1 chromosomes of the Triticeae, on which leaf rust-resistance genes have been mapped. These results are of major importance for understanding the molecular background of crown rust resistance in ryegrasses. The identified markers linked to crown rust resistance have the potential for use in marker-assisted breeding.     

Chromosomal mapping of tRNA genes from Dictyostelium discoideum

Summary Different wild-type isolates of Dictyostelium discoideum exhibit extensive polymorphism in the length of restriction fragments carrying tRNA genes. These size differences were used to study the organisation of two tRNA gene families which encode a tRNA^Val(GUU) and a tRNA^Val(GUA) gene. The method used involved a combination of classitics. The tRNA genes were mapped to specific linkage groups (chromosomes) by correlating the presence of polymorphic DNA bands that hybridized with the tRNA gene probes with the presence of genetic markers for those linkage groups. These analyses established that both of the tRNA gene families are dispersed among sites on several of the chromosomes. Information of nine tRNA^Val(GUU) genes from the wild-type isolate NC4 was obtained: three map to linkage group I (C, E, F,), two map to linkage group II (D, I), one maps to linkage group IV (G), one, which corresponds to the cloned gene, maps to either linkage group III or VI (B), and two map to one of linkage groups III, VI or VIII (A, H). Six tRNA^Val(GUA) genes from the NC4 isolate were mapped; one to linkage group I (D), two to linkage group III, VI or VII (B, C) and three to linkage group VII or III (A, E, F).     

Mapping Three Classical Isozyme Loci in Tetrahymena: Meiotic Linkage of Esta to the Chxa Linkage Group

We demonstrate a reliable method for mapping conventional loci and obtaining meiotic linkage data for the ciliated protozoan Tetrahymena thermophila. By coupling nullisomic deletion mapping with meiotic linkage mapping, loci known to be located on a particular chromosome or chromosome arm can be tested for recombination. This approach has been used to map three isozyme loci, EstA (Esterase A), EstB (Esterase B), and AcpA (Acid Phosphatase A), with respect to the ChxA locus (cycloheximide resistance) and 11 RAPDs (randomly amplified polymorphic DNAs). To assign isozyme loci to chromosomes, clones of inbred strains C3 or C2 were crossed to inbred strain B nullisomics. EstA, EstB and AcpA were mapped to chromosomes 1R, 3L and 3R, respectively. To test EstA and AcpA for linkage to known RAPD loci on their respective chromosomes, a panel of Round II (genomic exclusion) segregants from a B/C3 heterozygote was used. Using the MAPMAKER program, EstA was assigned to the ChxA linkage group on chromosome 1R, and a detailed map was constructed that includes 10 RAPDs. AcpA (on 3R), while unlinked to all the RAPDs assigned to chromosome 3 by nullisomic mapping, does show linkage to a RAPD not yet assignable to chromosomes by nullisomic mapping.     

Mapping of the bovine blood group systems J,N', R', and Z show evidence for oligo-genetic inheritance

Genes determining the bovine erythrocyte antigens were mapped by linkage analysis. In total 9591 genotypes of 20 grandsire families with 1074 sires from a grand-daughter design were elucidated for the genes determining the erythrocyte antigens EAA, EAB, EAC, EAF, EAJ, EAL, EAM, EAN', EAR', EAS, EAT', and EAZ according to standard paternity testing procedures in the blood typing laboratories. Linkage analyses were performed with 248 microsatellite markers, eight SSCP markers and four polymorphic proteins and enzymes covering the 29 autosomes and the pseudoautosomal region of the sex chromosomes. The number of informative meioses for the blood group systems ranged from 76 to 947. Blood group systems EAM and EAT' were non-informative. Most of the erythrocyte antigen loci showed significant linkage to a single chromosome and were mapped unequivocally. The genes determining erythrocyte antigen EAA, EAB, EAC, EAL, and EAS were mapped to chromosomes 15, 12, 18, 3, and 21, respectively. Lod-score values ranged from 11.43 to 107.83. Moreover, the EAF system could be mapped to chromosome 17. However, the EAN' system previously known as part of the EAF system could be mapped to chromosome 5. In addition, the blood group systems EAJ, the new EAN', EAR', and EAZ, showed significant linkage to microsatellite markers on various chromosomes and also to other blood groups. The appearance of a single blood group system might be therefore either dependent on the existence of other blood group systems or because of an interaction between different loci on various chromosomes as is known in humans and in pigs.     

Genetic dissection of pathotype-specific resistance to ascochyta blight disease in chickpea (<Emphasis Type="Italic">Cicer arietinum</Emphasis> L.) using microsatellite markers

Ascochyta blight is an economically important disease of chickpea caused by the fungus Ascochyta rabiei. The fungus shows considerable variation for pathogenicity in nature. However, studies on the genetics of pathotype-specific resistance are not available for this plant-pathosystem. The chickpea landrace ILC 3279 has resistance to pathotype I and II of the pathogen. In order to understand the inheritance of pathotype-specific resistance in this crop, both Mendelian and quantitative trait loci analyses were performed using a set of intraspecific, recombinant inbred lines derived from a cross between the susceptible accession ILC 1272 and the resistant ILC 3279, and microsatellite markers. We identified and mapped a major locus (ar1, mapped on linkage group 2), which confers resistance to pathotype I, and two independent recessive major loci (ar2a, mapped on linkage group 2 and ar2b, mapped on linkage group 4), with complementary gene action conferring resistance to pathotype II. Out of two pathotype II-specific resistance loci, one (ar2a) linked very closely with the pathotype I-specific resistance locus, indicating a clustering of resistance genes in that region of the chickpea genome.     

Genetic markers linked to neuronal ceroid lipofuscinosis in English setter dogs

The neuronal ceroid lipofuscinoses (NCL) are a group of fatal autosomal recessive neurodegenerative diseases occurring in human and some domesticated animal species. A canine form of the disease (CNCL) has been extensively studied in a Norwegian colony of inbred English setters since 1960. A resource family developed for genetic mapping and comprising 170 individuals was typed for 103 genetic markers. Linkage analysis showed three genetic markers to be linked to the disease locus with the closest marker at a distance of about 3 c m . Two other loci were linked with these markers making a linkage group of five genetic markers. The linkage group spanned a distance of 54 c m . Two genes for human forms of the disease, CLN2 and CLN3 , have been identified and mapped to human chromosome 11p15 and 16p12, respectively. The present study did not indicate any linkage between CNCL and the canine CLN3 homologue or to homologues of markers for genes that map close to human CLN2 .     

Characterization of genetic loci conferring adult plant resistance to leaf rust and stripe rust in spring wheat.

Leaf (brown) and stripe (yellow) rusts, caused by Puccinia triticina and Puccinia striiformis, respectively, are fungal diseases of wheat (Triticum aestivum) that cause significant yield losses annually in many wheat-growing regions of the world. The objectives of our study were to characterize genetic loci associated with resistance to leaf and stripe rusts using molecular markers in a population derived from a cross between the rust-susceptible cultivar 'Avocet S' and the resistant cultivar 'Pavon76'. Using bulked segregant analysis and partial linkage mapping with AFLPs, SSRs and RFLPs, we identified 6 independent loci that contributed to slow rusting or adult plant resistance (APR) to the 2 rust diseases. Using marker information available from existing linkage maps, we have identified additional markers associated with resistance to these 2 diseases and established several linkage groups in the 'Avocet S' x 'Pavon76' population. The putative loci identified on chromosomes 1BL, 4BL, and 6AL influenced resistance to both stripe and leaf rust. The loci on chromosomes 3BS and 6BL had significant effects only on stripe rust, whereas another locus, characterized by AFLP markers, had minor effects on leaf rust only. Data derived from Interval mapping indicated that the loci identified explained 53% of the total phenotypic variation (R2) for stripe rust and 57% for leaf rust averaged across 3 sets of field data. A single chromosome recombinant line population segregating for chromosome 1B was used to map Lr46/Yr29 as a single Mendelian locus. Characterization of slow-rusting genes for leaf and stripe rust in improved wheat germplasm would enable wheat breeders to combine these additional loci with known slow-rusting loci to generate wheat cultivars with higher levels of slow-rusting resistance.     

Genetic mapping of two genes conferring resistance to powdery mildew in common bean (Phaseolus vulgaris L.)

Powdery mildew (PM) is a serious disease in many legume species, including the common bean (Phaseolus vulgaris L.). This study investigated the genetic control behind resistance reaction to PM in the bean genotype, Cornell 49242. The results revealed evidence supporting a qualitative mode of inheritance for resistance and the involvement of two independent genes in the resistance reaction. The location of these resistance genes was investigated in a linkage genetic map developed for the XC RIL population. Contingency tests revealed significant associations for 28 loci out of a total of 329 mapped loci. Fifteen were isolated or formed groups with less than two loci. The thirteen remaining loci were located at three regions in linkage groups Pv04, Pv09, and Pv11. The involvement of Pv09 was discarded due to the observed segregation in the subpopulation obtained from the Xana genotype for the loci located in this region. In contrast, the two subpopulations obtained from the Xana genotype for the BM161 locus, linked to the Co-3/9 anthracnose resistance gene (Pv04), and from the Xana genotype for the SCAReoli locus, linked to the Co-2 anthracnose resistance gene (Pv11), exhibited monogenic segregations, suggesting that both regions were involved in the genetic control of resistance. A genetic dissection was carried out to verify the involvement of both regions in the reaction to PM. Two resistant recombinant lines were selected, according to their genotypes, for the block of loci included in the Co-2 and Co-3/9 regions, and they were crossed with the susceptible parent, Xana. Linkage analysis in the respective F₂ populations supported the hypothesis that a dominant gene (Pm1) was located in the linkage group Pv11 and another gene (Pm2) was located in the linkage group Pv04. This is the first report showing the localization of resistance genes against powdery mildew in Phaseolus vulgaris and the results offer the opportunity to increase the efficiency of breeding programs by means of marker-assisted selection.     

Restriction fragment length polymorphisms linked to genes for resistance to crown rust (Puccinia coronata) in near-isogenic lines of hexaploid oat (Avena sativa).

Crown rust, perhaps the most important fungal disease of oat, is caused by Puccinia coronata. An examination of near-isogenic lines (NILs) of hexaploid oat (Avena sativa) was conducted to identify markers linked to genes for resistance to crown rust. These lines were created such that a unique resistance gene is present in each of the two recurrent parent backgrounds. The six NILs of the current study, X434-II, X466-I, and Y345 (recurrent parent C237-89) and D486, D494, and D526 (recurrent parent Lang), thus provide a pair of lines to study each of three resistance genes. Restriction fragment length polymorphisms and resistance loci were mapped using BC1F2 populations. Three markers were found linked to a locus for resistance to crown rust race 203, the closest at 1.9 cM in line D494 and 3.8 cM in line X466-I. In lines D526 and Y345 a marker was placed 1.0 and 1.9 cM, respectively, from the locus conferring resistance to crown rust race 345, and in D486 and X434-II a marker mapped at 8.0 and 10.2 cM from the locus for resistance to rust race 264B.     

Genetic heterogeneity in neuronal ceroid lipofuscinosis (NCL): Evidence that the late-infantile subtype (Jansky-Bielschowsky disease; CLN2) is not an allelic form of the juvenile or infantile subtypes

The neuronal ceroid lipofuscinoses (NCLs) are a group of inherited neurodegenerative disorders characterized by the accumulation of autofluorescent lipopigment in neurons and other cell types. Inheritance is autosomal recessive. Three main childhood subtypes are recognized: infantile (Haltia-Santavuori disease; MIM 256743), late infantile (Jansky-Bielschowsky disease; MIM 204500), and juvenile (Spielmeyer-Sjögren-Vogt, or Batten, disease; MIM 204200). The gene loci for the juvenile (CLN3) and infantile (CLN1) types have been mapped to human chromosomes 16p and 1p, respectively, by linkage analysis. Linkage analysis of 25 families segregating for late-infantile NCL has excluded these regions as the site of this disease locus (CLN2). The three childhood subtypes of NCL therefore arise from mutations at distinct loci.     

A Third Locus for Autosomal Dominant Cerebellar Ataxia Type 1 Maps to Chromosome 14q24.3-qter: Evidence for the Existence of a Fourth Locus

The autosomal dominant cerebellar ataxias (ADCA) type I are a group of neurological disorders that are clinically and genetically heterogeneous. Two genes implicated in the disease, SCA1 (spinal cerebellar ataxia 1) and SCA2, are already localized. We have mapped a third locus to chromosome 14q24.3-qter, by linkage analysis in a non-SCA1/non-SCA2 family and have confirmed its existence in a second such family. We suggest designating this new locus “SCA3.” Combined analysis of the two families restricted the SCA3 locus to a 15-cM interval between markers D14S67 and D14S81. The gene for Machado-Joseph disease (MJD), a clinically different form of ADCA type I, has been recently assigned to chromosome 14q24.3-q32. Although the SCA3 locus is within the MJD region, linkage analyses cannot yet demonstrate whether they result from mutations of the same gene. Linkage to all three loci (SCA1, SCA2, and SCA3) was excluded in another family, which indicates the existence of a fourth ADCA type I locus.     

Molecular Mapping of Wheat: Major Genes and Rearrangements in Homoeologous Groups 4, 5, and 7

A molecular-marker linkage map of hexaploid wheat (Triticum aestivum L. em. Thell) provides a framework for integration with the classical genetic map and a record of the chromosomal rearrangements involved in the evolution of this crop species. We have constructed restriction fragment length polymorphism (RFLP) maps of the A-, B-, and D-genome chromosomes of homoeologous groups 4, 5, and 7 of wheat using 114 F(7) lines from a synthetic X cultivated wheat cross and clones from 10 DNA libraries. Chromosomal breakpoints for known ancestral reciprocal translocations involving these chromosomes and for a known pericentric inversion on chromosome 4A were localized by linkage and aneuploid analysis. Known genes mapped include the major vernalization genes Vrn1 and Vrn3 on chromosome arms 5AL and 5DL, the red-coleoptile gene Rc1 on 7AS, and presumptively the leaf-rust (Puccinia recondita f.sp. tritici) resistance gene Lr34 on 7DS and the kernel-hardness gene Ha on 5DS. RFLP markers previously obtained for powdery-mildew (Blumeria graminis f.sp. tritici) resistance genes Pm2 and Pm1 were localized on chromosome arms 5DS and 7AL.     

Genetic mapping of Bt-toxin binding proteins in a Cry1A-toxin resistant strain of diamondback moth Plutella xylostella

A major mechanism of resistance to Bacillus thuringiensis (Bt) toxins in Lepidoptera is a reduction of toxin binding to sites in the midgut membrane. Genetic studies of three different species have shown that mutations in a candidate Bt receptor, a 12-cadherin-domain protein, confer Cry1A toxin resistance. Despite a similar resistance profile in a fourth lepidopteran species, Plutella xylostella, we have previously shown that the cadherin orthologue maps to a different linkage group (LG8) than Cry1Ac resistance (LG22). Here we tested the hypothesis that mutations in other genes encoding candidate Bt-binding targets could be responsible for Bt resistance, by mapping eight aminopeptidases, an alkaline phosphatase (ALP), an intestinal mucin, and a P252 glycoprotein with respect to the 29 AFLP marked linkage groups in a P. xylostella cross segregating for Cry1Ac resistance. A homologue of the Caenorhabditis elegans Bt resistance gene bre-2 was also mapped. None of the genes analysed were on the same chromosome containing the Cry1Ac resistance locus, eliminating them as candidate resistance genes in the parental resistant strain SC1. Although this finding excludes cis-acting mutations in these genes as causing resistance in this strain, one or more of the expressed proteins may still bind Cry1Ac toxin, and post-translational modifications could affect this binding and thereby exert a trans-acting effect on resistance.     

Comparative mapping of homoeologous group 1 regions and genes for resistance to obligate biotrophs in Avena, Hordeum, and Zea mays.

The colinearity of markers linked with resistance loci on linkage group A of diploid oat, on the homoeologous groups in hexaploid oat, on barley chromosome 1H, and on homoeologous maize chromosomes was determined. Thirty-two DNA probes from homoeologous group 1 chromosomes of the Gramineae were tested. Most of the heterologous probes detected polymorphisms that mapped to linkage group A of diploid oat, two linkage groups of hexaploid oat, barley chromosome 1H, and maize chromosomes 3, 6, and 8. Many of these DNA markers appeared to have conserved linkage relationships with resistance and prolamin loci in Avena, Hordeum, and Zea mays. These resistance loci included the Pca crown rust resistance cluster in diploid oat, the R203 crown rust resistance locus in hexaploid oat, the Mla powdery mildew resistance cluster in barley, and the rp3, wsm1, wsm2, mdm1, ht2, and htn1 resistance loci in maize. Prolamin encoding loci included Avn in diploid oat and Hor1 and Hor2 in barley. A high degree of colinearity was revealed among the common RFLP markers on the small chromosome fragments among these homoeologous groups. Key words : disease resistance, colinearity, Gramineae, cereals.     

Molecular mapping of Rxp conditioning reaction to bacterial pustule in soybean.

The Rxp locus in soybean [Glycine max (L.) Merr.] that conditions reaction to bacterial pustule was mapped by simple sequence repeat (SSR) marker analysis. A population of 116 F4-derived lines from a cross between the resistant parent Young and the susceptible parent PI 416937 was used for mapping. The Rxp locus was mapped 3.9 cM from Satt372 and 12.4 cM from Satt014 on linkage group D2. Linkage associations were confirmed by identifying a close association between the SSR genotype at each locus identified as flanking Rxp and the bacterial pustule reaction of individual lines derived from a population different from the one used for mapping. A molecular pedigree analysis showed that bacterial pustule-resistant cultivars inherited the resistance gene rxp from the ancestral cultivar CNS based on their consistent genotypic pattern at flanking marker loci. Based on the results of the study, marker-assisted selection for rxp would be very effective.     

Mapping muscle protein genes by in situ hybridization using biotin-labeled probes.

The genes coding for the myosin heavy chain isoforms (unc-54, myo-1, myo-2 and myo-3) and the actins (act-1,2,3 and act-4) have been mapped on the embryonic metaphase chromosomes of Caenorhabditis elegans by in situ hybridization. The genes were cloned in a cosmid vector and the entire cosmid was nick translated to incorporate biotin-labeled dUTP. This produced a probe DNA complementary to a 35-45 kb length of chromosomal DNA. The hybridization signal from the cosmid probe, detected by immunofluorescence, could be easily seen by eye. The clear signals and the specific hybridization of the cosmid probes provided a faster means of mapping these single copy genes than small probes cloned in plasmid or lambda vectors. The myosin heavy chain genes are not clustered. Only unc-54 and myo-1 mapped to the same chromosome; the unc-54 locus is at the extreme right end of linkage group I and myo-1 mapped 40-50% from the left end of linkage group I. Myo-2 mapped to the X, 52-75% from the left end. The myo-3 gene mapped to the middle of linkage group V near the cluster of three actin genes (act-1,2,3). The fourth actin gene, act-4 mapped to 20-35% from the left end of X.