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PubMed1971

A major genetic locus affecting resistance to infection with murine leukemia viruses. I. Tissue culture studies of naturally occurring viruses.

Previous studies have indicated that all naturally occurring murine leukemia viruses propagate significantly more efficiently on embryo cells of either NIH Swiss or BALB/c mice. Studies of the plaquing efficiency of representative viruses on embryo cells of various inbred and hybrid mice indicate that the pattern of sensitivity of the cells is genetically determined. All of 23 strains tested were found to resemble either NIH Swiss (N-type) or BALB/c (B-type) with respect to plaquing efficiency of these viruses. Virus growth on embryo cells derived from (N-type x B-type)F(1) hybrids indicated dominance of resistance to both types of viruses. Backcross hybrid studies indicated that a single locus is the primary determinant of the host-range patterns observed. This locus has no effect on growth of certain laboratory-passaged leukemia viruses which propagate equally well on embryo cells of all mouse strains, F(1), and backcross hybrids. Though other genetic and nongenetic factors influence viral growth or expression in vitro and in vivo, the genetic locus described appears of major significance in the biology of murine leukemia.

Animals↗

PubMed2005

Analysis of the RELN gene as a genetic risk factor for autism.

Several genome-wide screens have indicated the presence of an autism susceptibility locus within the distal long arm of chromosome 7 (7q). Mapping at 7q22 within this region is the candidate gene reelin (RELN). RELN encodes a signaling protein that plays a pivotal role in the migration of several neuronal cell types and in the development of neural connections. Given these neurodevelopmental functions, recent reports that RELN influences genetic risk for autism are of significant interest. The total data set consists of 218 Caucasian families collected by our group, 85 Caucasian families collected by AGRE, and 68 Caucasian families collected at Tufts University were tested for genetic association of RELN variants to autism. Markers included five single-nucleotide polymorphisms (SNPs) and a repeat in the 5'-untranslated region (5'-UTR). Tests for association in Duke and AGRE families were also performed on four additional SNPs in the genes PSMC2 and ORC5L, which flank RELN. Family-based association analyses (PDT, Geno-PDT, and FBAT) were used to test for association of single-locus markers and multilocus haplotypes with autism. The most significant association identified from this combined data set was for the 5'-UTR repeat (PDT P-value=0.002). These analyses show the potential of RELN as an important contributor to genetic risk in autism.

5' Untranslated Regions↗

PubMed2005

Genetically based resistance to the antiinflammatory effects of methotrexate in the air-pouch model of acute inflammation.

OBJECTIVE: Low-dose methotrexate (MTX), a mainstay in the treatment of rheumatoid arthritis, is effective in only 60-70% of patients, a finding mirrored by poor antiinflammatory efficacy in some animal models, most notably collagen-induced arthritis. To determine whether genetic factors or the model itself is responsible for the poor response to MTX, we directly compared the responses of 4 inbred mouse strains to MTX in the air-pouch model of acute inflammation. METHODS: The exudate leukocyte count and adenosine concentration were determined in inbred mice treated with MTX (0.75 mg/kg intraperitoneally every week for 4 weeks) or vehicle 4 hours after injection of carrageenan into the air pouch using previously described methods. Quantitative trait locus mapping was performed using an in silico, or computer-based, method to identify loci potentially associated with each phenotype. RESULTS: MTX significantly reduced the exudate leukocyte count in C57BL/6J and BALB/cJ mice, but not DBA/1J (the strain used in the collagen-induced arthritis model) or DBA/2J mice. In a parallel manner, MTX increased adenosine concentration in inflammatory exudates of C57BL/6J and BALB/cJ mice, but not DBA/1J or DBA/2J mice. Antiinflammatory and adenosine responses to MTX in DBA/1J x C57BL/6J F(1) and F(2) offspring were most consistent with single genetic loci being responsible for each phenotype. In silico mapping identified partially overlapping loci containing candidate genes involved in both responses. CONCLUSION: Genetic factors contribute to the antiinflammatory efficacy of MTX, and a single locus involved in MTX-induced adenosine up-regulation is likely responsible for the observed resistance to MTX in DBA/1J mice.

Acute Disease↗

PubMed2002

Diffuse large B-cell lymphoma of the stomach: assessment of microsatellite instability, allelic imbalance, and trisomy of chromosomes 3, 12, and 18.

Several types of genetic aberrations including microsatellite instability (MSI), allelic imbalance (AI), and chromosomal trisomies have been reported in low-grade (LG) mucosa-associated lymphoid tissue (MALT)-type gastric lymphomas. Presence of such genetic alterations could be a discriminator between de novo large cell lymphoma and high-grade (HG) MALT-type lymphoma. We investigated 17 primary gastric large B-cell lymphomas with and without features of MALT-type lymphoma for MSI, AI, and presence of trisomy of chromosomes 3, 12, and 18. We studied resection specimens from 17 primary gastric extranodal diffuse large B-cell lymphomas. Cases classified as HG MALT-type lymphoma, based on either the presence of LG MALT-type lymphoma component in the background (L/H MALT) or large cell lymphoepithelial lesions (HG MALT), and diffuse large B-cell lymphoma (DLBCL-NOS) when no features of MALT were present. MSI was analyzed using fluorescently labeled polymerase chain reaction primers (D3S11, D6S262, D3S1261, D3S1262, D3S1265). Paired tumor and normal DNA samples were amplified, and PCR products were analyzed on a DNA sequencer (ABI PRISM 373XL) with GeneScan (Applied Biosystems, Foster City, CA). MSI was defined as a gain of a novel-length allele compared with the corresponding normal tissue. AI was assessed at locus 3q27 (D3S1262 and D3S1265). The cases were analyzed for the presence of trisomy of chromosomes 3, 12, and 18 using interphase fluorescence in situ hybridization. MSI was detected in 4 out of 15 (27%) cases from which DNA was amplifiable with all primers and all MALT-type lymphomas. In two cases (13%), MSI was present at two loci sufficient to be classified as high-frequency MSI (MSI-H); this was seen exclusively in HG MALT lymphomas (P = 0.04). In the remaining two cases, MSI was detected at a single locus (low-frequency MSI). Allelic imbalance at the locus D3S1262 was detected in 4 out of 17 (24%) cases. It occurred more commonly in stage IE lymphomas when compared with higher stages (P = 0.03), regardless of lymphoma subtype. Trisomy 12 was detected in 3 out of 17 cases (18%) exclusively in stage IE lymphomas (P = 0.08). MSI was uncommon and was found exclusively in MALT-type lymphomas. MSI-H was even less common but occurred in HG MALT lymphomas only. Allelic imbalance at 3q27 (D3S1262) and trisomy 12 were found more commonly in low-stage disease. The latter two findings are in concordance with the recent suggestion that the published variation in gain of chromosomal material in high-grade gastric lymphomas may be related to stage rather than to the subtype of lymphoma. Because of the relatively low frequency of MSI in the high-grade B-cell lymphomas of the stomach, this feature cannot be used to reliably discriminate between the histologic types of extranodal diffuse large B-cell lymphoma.

Allelic Imbalance↗

PubMed2005

Linear allele-specific long-range amplification: a novel method of long-range molecular haplotyping.

Haplotypes have been repeatedly shown to be more powerful than collections of single-locus markers in gene-mapping studies. Various haplotyping methods including statistical estimation are employed but molecular haplotyping, the acquisition of information directly on physical DNA sequences, has been in demand for its accuracy and independence from family pedigrees. We investigated the allelic specificity of long-range PCR, which was successful for long-range haplotyping in recent reports, and found problems of initial mispriming and crossover amplification significantly confounded its application. Based on these observations, we designed a novel method based on linear amplification of a hemizygous DNA segment with a single phosphorothioate-modified oligonucleotide. Our results revealed, with a single nucleotide polymorphism as the discriminative marker, downstream haplotypes of 14-15 kb DNA segment could be confidently scored. With two rounds of the method and five single nucleotide polymorphisms, molecular haplotypes of 29.3 kb spanning the HCR and CDSN genes, two genes associated with the susceptibility of psoriasis, of 11 members, belonging to a CEPH family, were revealed. Clear Mendelian segregation of 35 highly heterozygous SNPs confirmed the accuracy of the method. Problems of low specificity associated with long-range PCR were not observed. The simplicity, along with long-sequence accessibility and feasibility of a single nucleotide difference as the discriminative marker indicated our method holds promise for future gene-mapping studies.

Adenomatous Polyposis Coli↗

PubMed1983

Mutations at more than one locus may be involved in cystic fibrosis--evidence based on first-cousin data and direct counting of cases.

Cystic fibrosis was present in 35 of 5,265 first cousins of index cases with the disease. The gene frequency was estimated to be .0281 +/- .00544, using an improved method that allows for the influence of cousin sibship size upon the estimate. This figure is higher than that obtained by direct counting of cases in Victoria, Australia, from 1955-1979 (.0198 +/- .000127), raising the possibility that multiple gene loci may be involved in this disease. Further analysis showed that the number of affected first cousins fitted very well with an expected number based on a model involving two gene loci, each responsible for half the cases of cystic fibrosis. Agreement with expectations based on a single locus was not good. An alternate explanation of gross underascertainment of cases is dismissed because the index sibships were shown to fit very closely a truncate binomial distribution. The gene frequencies at the putative two loci would then each be .0140 and heterozygote frequencies one in 36. One in 18 people would be heterozygous at either one or the other of the loci.

Adult↗

PubMed2006

Impact of small fitness costs on pest adaptation to crop varieties with multiple toxins: a heuristic model.

A deterministic two-locus model was used to examine how small fitness costs to individuals carrying resistance alleles could impact the risk of panmictic insect pest populations adapting to crop varieties that produced two distinct toxins. Parameters examined were (1) level of toxicity of each toxin, (2) initial frequencies of alleles for adaptation to the toxins, (3) percentage of population feeding on nontoxic plants, and (4) level of fitness cost associated with adaptation to each of the two toxins. Resistance to each toxin was assumed to be biochemically independent, controlled by a resistance coding allele at a single locus, and inherited as a partially recessive trait in the field. When plants are extremely toxic to the pest, effective refuge size is 10%, and there is a fitness cost to resistance alleles only when in homozygous form (5%), the pest population is never predicted to adapt to either toxin as long as the initial frequencies of the resistance alleles are below 0.05. Even if the initial frequency of the allele for adapting to one toxin is 0.95 when a two-toxin cultivar completely replaces a one-toxin cultivar, the model predicts that a low equilibrium allelic frequency will develop for both resistance alleles, as long as the frequency of the allele for adapting to the second toxin is initially 0.001 or less. If cultivars with one and two toxins are planted, the model predicts that resistance will develop. Nonrandom mating and stochastic variation within subpopulations also could lead to evolution of resistance.

Adaptation, Physiological↗

PubMed1997

Rapid induction of B-cell lymphomas in mice carrying a human IgH/c-mycYAC.

Activation of the c-myc proto-oncogene by one of the immunoglobulin (Ig) loci after chromosomal translocation is a consistent feature of Burkitt's lymphoma. Different subtypes of this tumor vary in the molecular architecture of the translocation region. In most cases there are no known regulatory elements of the Ig locus neighboring the oncogene and this considerably obscures the mechanism of its deregulation. In order to assess possible oncogene activation signals, we produced an experimental translocation region by insertion of a c-myc gene about 50 kb from the IgH intron enhancer in a yeast artificial chromosome (YAC) containing a 220 kb region of the human Ig heavy chain (IgH) locus. Single copy integration of this YAC into the genome of mouse embryonic stem (ES) cells was achieved by spheroplast fusion. Chimeric mice derived from these ES cells developed monoclonal B-cell lymphomas expressing surface IgM by 8-16 weeks of age. The IgH/c-myc translocus showed different V(h)DJ(H) rearrangement in almost all tumors without any alterations of the distance between c-myc and the IgH intron enhancer. This mouse model can be used for the in vivo analysis of c-myc deregulation and the tumor formation capacity of the IgH locus in aberrant rearrangements.

Animals↗

PubMed1978

Group selection on a quantitative character.

We derive a model of group and individual selection on a quantitative character that is similar to the single-locus "metapopulation" models of group selection. Two alternative methods for the colonization of new or vacant habitats are examined and their effects are contrasted. In one model, all populations contribute migrants to a common pool, the "migrant pool," from which colonists are drawn at random to fill vacant sites. In the migrant pool there is complete mixing of individuals from different populations. This model of colonization is the one used in all previous models of group selection. In the other model, the "propagule pool" model, each propagule is made up of individuals derived from a single population and there is no mixing of colonists from different populations during propagule formation. The analysis shows that much more between-population genetic variance can be maintained with the propagule pool model than with the migrant pool model. Consequently, group selection can be much more effective in natural populations than is commonly supposed.

Journal Article↗

PubMed1985

Insertion of the bacterial gpt gene into the germ line of mice by retroviral infection.

Mouse substrains genetically transmitting the exogenous Moloney murine leukemia virus (Mo-MuLV) at a single locus have been derived previously by infection of preimplantation embryos. Here we explore the potential of retroviral vectors for transferring nonviral genes into the germ line of mice. Preimplantation mouse embryos were cocultivated with a cell line that produces a recombinant retrovirus whose genome carries the Escherichia coli gene gpt. We show that the vector sequence was inserted into the genome of the embryo and into the germ line at a frequency similar to that for the Mo-MuLV-helper sequence. A new mouse strain, Mgpt-1, was developed that is homozygous for a single MSVgpt proviral genome. The proviral sequences were highly methylated and not expressed in tissues of Mgpt-1 mice. When cells derived from transgeneic animals were treated with 5-azacytidine, the proviral sequences were not methylated and were transcriptionally activated. These results indicate that nonviral genes that are under the control of the viral long terminal repeat are inactivated when transferred into the germ line of animals.

Animals↗

PubMed1995

Spatial analysis of nuclear and mitochondrial RFLP genotypes in populations of the chestnut blight fungus, Cryphonectria parasitica.

Spatial structure of both nuclear and mitochondrial RFLPs were studied in several populations of the chestnut blight fungus, Cryphonectria parasitica, using a variety of spatial autocorrelation tests designed to detect nonrandom patterns. Fungal individuals were sampled from cankers on infected chestnut trees, and the location of each tree was mapped. Single-locus nuclear RFLPs, nuclear fingerprints, and mitochondrial DNA haplotypes were determined for each individual. Individuals with the same DNA fingerprint genotypes occurred closer together than would be expected at random in four of the five plots, while mitochondrial DNA haplotypes were aggregated in all five plots. Genetic distances between individuals, expressed as one minus the proportion of shared restriction fragment size classes for fingerprints and mitochondrial haplotypes, were significantly correlated with Euclidean distances between individuals in four of the five populations, but these correlations were very weak (r < 0.18). The same DNA fingerprint and single-copy nuclear RFLP alleles occurred on the same trees or immediately neighbouring trees more often than would be expected at random. Most of the aggregation for all three genetic markers occurred among individuals within the same cluster of chestnut stems or on neighbouring trees. Lack of spatial autocorrelation in one population was probably due to sampling on a larger scale that was too coarse to detect any patterns. Significant aggregation of genotypes in C. parasitica is most likely caused by some degree of restricted dispersal within populations. The implications of restricted dispersal are discussed in relation to the breeding system and isolation by distance in populations of C. parasitica.

Cell Nucleus↗

PubMed2000

Correcting for ascertainment bias of relative-risk estimates obtained using affected-sib-pair linkage data.

Locus-specific sibling relative risk is often estimated using affected-sib-pair lod score analysis of affected sibships and may be used to decide whether to continue or discontinue the search for additional susceptibility genes. We showed that relative-risk estimates obtained using affected-sib-pair data are asymptotically unbiased when each pair is given a weight inversely proportional to the sibship ascertainment probability. Here we show by simulation that the extent of the bias of relative risks estimated using the incorrect ascertainment weights is small for dominant models, but large for single-locus recessive models and some two-locus heterogeneity models. Since in practice the ascertainment scheme is often unknown, we investigate methods for jointly estimating ascertainment and relative risks from affected-sibship data. Given a sufficient sample size, a reasonable estimate of relative risk may always be obtained using only affected pairs from sibships with two affected and no unaffected siblings. This estimate, which has a large variance, may then be used in a three-stage procedure (which we call the alpha method) to estimate consistently both the ascertainment probabilities and the relative risks with greater precision. We additionally propose correction factors to eliminate small-sample bias of relative risks and investigate the bias due to error in the estimate of disease locus location.

Bias↗

PubMed2004

spa typing method for discriminating among Staphylococcus aureus isolates: implications for use of a single marker to detect genetic micro- and macrovariation.

Strain typing of microbial pathogens has two major aims: (i). to index genetic microvariation for use in outbreak investigations and (ii). to index genetic macrovariation for use in phylogenetic and population-based analyses. Until now, there has been no clear indication that one genetic marker can efficiently be used for both purposes. Previously, we had shown that DNA sequence analysis of the protein A gene variable repeat region (spa typing) provides a rapid and accurate method to discriminate Staphylococcus aureus outbreak isolates from those deemed epidemiologically unrelated. Here, using the hypothesis that the genetic macrovariation within a low-level recombinogenic species would accurately be characterized by a single-locus marker, we tested whether spa typing could congruently index the extensive genetic variation detected by a whole-genome DNA microarray in a collection of 36 isolates, which was recovered from 10 countries on four continents over a period of four decades, that is representative of the breadth of diversity within S. aureus. Using spa and coa typing, pulsed-field gel electrophoresis (PFGE), and microarray and multilocus enzyme electrophoresis (MLEE) data in molecular epidemiologic and evolutionary analyses, we determined that S. aureus likely has a primarily clonal population structure and that spa typing can singly index genetic variation with 88% direct concordance with the microarray and can correctly assign isolates to phylogenetic lineages. spa typing performed better than MLEE, PFGE, and coa typing in discriminatory power and in the degree of agreement with the microarray at various phylogenetic depths. This study showed that genetic analysis of the repeat region of protein A comprehensively characterizes both micro- and macrovariation in the primarily clonal population structure of S. aureus.

Antigens, Bacterial↗

PubMed1986

HL-A and disease.

Of more than 500 diseases or syndromes studied for HL-A markers, more than 40 are known to be associated with an allele of class I, II, or III. Seven are linked to the HL-A region: six are recessive (idiopathic hemochromatosis, C2, C4A, and C4B deficiencies, congenital and late-onset deficiencies) and one is dominant (spinocerebellar ataxia). In addition, insulin-dependent diabetes mellitus is also linked to HL-A with more than one single locus. HL-A typing is of practical interest for diagnosis of ankylosing spondylitis by B27 antigen determination and for prevention of idiopathic hemochromatosis by genotyping of siblings of the index case. Prenatal diagnosis of 21-OH deficiency by genotyping fetal cells permits genetic counseling. Indeed, the discovery of the relationship between HL-A and disease can be considered a new approach to medical genetics. Extensive use of HL-A technology will probably allow better prediction of risk and may elucidate the mechanisms of certain diseases. For the first time the study of one single immunogenetic system may have a significant effect on public health through the possibility of wide-scale prevention.

Alleles↗

PubMed1998

Genetic structure of five susceptibility gene regions for coronary artery disease: disequilibria within and among regions.

We analyzed two-locus disequilibria for 16 polymorphic loci of seven susceptibility genes for coronary artery disease located in five chromosomal regions distributed across four chromosomes. Included were the genes coding for apolipoprotein B (ApoB, chromosome 2, four marker loci), lipoprotein lipase (LPL, chromosome 8, three marker loci), apolipoproteins AI, CIII AIV (ApoAI-CIII-AIV, chromosome 11, three marker loci), apolipoprotein E (ApoE, chromosome 19, two marker loci), and the low density lipoprotein receptor (LDLR, chromosome 19, four marker loci). Our sample included 540 unrelated individuals from the Rochester, Minn. population. There were no statistically significant deviations of single-locus genotypes from Hardy-Weinberg equilibrium. The strongest associations within genes were for composite diallelic disequilibria; 17/19 were significant (13 at Pr <0.001, 1 at Pr <0.01, 3 at Pr <0.05). These observations suggest marker alleles within genes have a shared evolutionary history reflected by disequilibria that have not been dissipated by recombination. Disequilibrium was not generally concordant with the physical orderings of markers. Only two significant higher-order disequilibria were observed although 12 triallelic disequilibria were at maximum possible values. We observed 19 statistically significant disequilibria (Pr <0.05; 4 composite diallelic, 13 triallelic, and 2 quadriallelic) between 101 pairs of marker loci, where each locus in a pair was from a different unlinked region. These unexpected results are most likely explained by recent historical factors, including worldwide population expansion and amalgamation with continuous admixture, that influence the genetic structure (organization of alleles and non-alleles into genotypes) of a population. We conclude that disequilibria between loci from unlinked regions may be more extensive than is commonly assumed. Our findings also suggest that it is, on average, at least 15 times more likely to not detect significant disequilibrium among unlinked loci when it is really present than to make a false positive inference. Disequilibria between functional loci within or between regions will impact estimates of genetic variance associated with particular functional mutations within a susceptibility gene region.

Apolipoproteins↗

PubMed1988

Estimation of allele frequencies at isoloci.

In some polyploid animals and plants, pairs of duplicated loci occur that share alleles encoding proteins with identical electrophoretic mobilities. Except in cases where these "isoloci" are known to be inherited tetrasomically, individual genotypes cannot be determined unambiguously, and there is no direct way to assign observed variation to a particular locus of the pair. For a pair of diallelic isoloci, nine genotypes are possible but only five phenotypes can be identified, corresponding to individuals with 0-4 doses of the variant allele. A maximum likelihood (ML) approach is used here to identify the set of allele frequencies (p, q) at the individual gene loci with the highest probability of producing the observed phenotypic distribution. A likelihood ratio test is used to generate the asymmetrical confidence intervals around ML estimates. Simulations indicate that the standard error of p is typically about twice the binomial sampling error associated with single locus allele frequency estimates. ML estimates can be used in standard indices of genetic diversity and differentiation and in goodness-of-fit tests of genetic hypotheses. The noncentral chi 2 distribution is used to evaluate the power of a test of apparent heterozygote deficiency that results from attributing all variation to one locus when both loci are polymorphic.

Alleles↗

PubMed2003

Single nucleotide polymorphisms in genes associated with isoniazid resistance in Mycobacterium tuberculosis.

Isoniazid (INH) is a central component of drug regimens used worldwide to treat tuberculosis. Previous studies have identified resistance-associated mutations in katG, inhA, kasA, ndh, and the oxyR-ahpC intergenic region. DNA microarray-based experiments have shown that INH induces several genes in Mycobacterium tuberculosis that encode proteins physiologically relevant to the drug's mode of action. To gain further insight into the molecular genetic basis of INH resistance, 20 genes implicated in INH resistance were sequenced for INH resistance-associated mutations. Thirty-eight INH-monoresistant clinical isolates and 86 INH-susceptible isolates of M. tuberculosis were obtained from the Texas Department of Health and the Houston Tuberculosis Initiative. Epidemiologic independence was established for all isolates by IS6110 restriction fragment length polymorphism analysis. Susceptible isolates were matched with resistant isolates by molecular genetic group and IS6110 profiles. Spoligotyping was done with isolates with five or fewer IS6110 copies. A major genetic group was established on the basis of the polymorphisms in katG codon 463 and gyrA codon 95. MICs were determined by the E-test. Semiquantitative catalase assays were performed with isolates with mutations in the katG gene. When the 20 genes were sequenced, it was found that 17 (44.7%) INH-resistant isolates had a single-locus, resistance-associated mutation in the katG, mabA, or Rv1772 gene. Seventeen (44.7%) INH-resistant isolates had resistance-associated mutations in two or more genes, and 76% of all INH-resistant isolates had a mutation in the katG gene. Mutations were also identified in the fadE24, Rv1592c, Rv1772, Rv0340, and iniBAC genes, recently shown by DNA-based microarray experiments to be upregulated in response to INH. In general, the MICs were higher for isolates with mutations in katG and the isolates had reduced catalase activities. The results show that a variety of single nucleotide polymorphisms in multiple genes are found exclusively in INH-resistant clinical isolates. These genes either are involved in mycolic acid biosynthesis or are overexpressed as a response to the buildup or cellular toxicity of INH.

Bacterial Proteins↗

PubMed2002

The mapping of QTLS for chlorophyll content and responsiveness to gibberellic (GA3) and abscisic (ABA) acids in rye.

Genetic maps containing molecular markers are useful tools for the identification of genes underlying quantitative traits (QTLs). Three traits important for plant physiology, i.e. chlorophyll content, sensitivity to GA and sensitivity to ABA, were evaluated for 99 F2 families of the DS2 x RXL10 rye mapping population. The observed variation in the chlorophyll content in rye leaves was shown to be under the genetic control of four independent QTLs. They were located on the following chromosome arms: 1RL (QChc-1R.1), 3RS (QChc-3R.1), 4RL (QChc-4R.1) and 5RL (QChc-5R.1) The marker-assisted selection of recombinants comprising positively-acting alleles at these loci may significantly increase the chlorophyll content in rye leaves, which should result in a higher efficiency of photosynthesis. A decreasing of plant height in rye is one of the major aims of breeders selecting for lodging resistance. The polymorphism of genes controlling sensitivity to gibberellic acid may be the basis for a potential selection strategy. Three QTLs underlying the sensitivity of rye seedlings to GA were located on chromosomes 5RL (QGar-5R.1), 1RL (QGar-1R.1) and on 7RL (QGar-7R.1). The dwarfing allele of a Dw1 locus present in line RXL10 was mapped in the same position as the QGar-5R.1 gene. Sensitivity to ABA plays an important role in imposing dormancy in rye grain. Three QTLs affecting sensitivity to ABA were found. They were mapped on chromosomes 1RS (QAbr-1R.1), 2R in the centromeric region (QAbr-2R.1) and on 5RL (QAbr-5R.1). QAbr-5R.1, Dw1 and QGar-5R.1 are located in the same position on the distal part of the 5RL chromosome arm, which suggests that they belong to a single locus for a major regulatory gene controlling the development of rye plants.

Abscisic Acid↗