US20030180761A1 - Map-based genome mining method for identifying regulatory loci controlling the level of gene transcripts and products - Google Patents

Map-based genome mining method for identifying regulatory loci controlling the level of gene transcripts and products Download PDF

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US20030180761A1
US20030180761A1 US10/333,150 US33315003A US2003180761A1 US 20030180761 A1 US20030180761 A1 US 20030180761A1 US 33315003 A US33315003 A US 33315003A US 2003180761 A1 US2003180761 A1 US 2003180761A1
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genes
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regulatory
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Yves Castonguay
Louise O'Donoughue
Serge Laberge
Antonio Monroy
Louis Vezina
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DNA LandMarks Inc
Agriculture and Agri-Food Canada
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6897—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids involving reporter genes operably linked to promoters
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection

Definitions

  • the present invention relates to a method for the identification of regulatory loci that control gene expression within any organism. More specifically, the present invention relates to the use of mRNA transcripts, and variation in transcript levels for the identification of quantitative trait loci pertaining to a desired trait within an organism.
  • Combination of techniques such as differential display of mRNA species, subtractive or normalized libraries and gene array can be used to single out regulatory genes, however these techniques are not specific to the analysis of the expression of a single gene and are time consuming. Moreover, with these techniques the transcripts of the regulatory genes of interest must be present in samples used to generate the libraries in order for the transcripts to be identified. The task can be overwhelming when multiple regulatory genes, with unsynchronised expression are involved.
  • a quantitative trait locus is a region of the genome that codes for one or more proteins and that explains a significant proportion of the variability of a given phenotype that may be controlled by multiple genes.
  • QTL quantitative trait locus
  • one or more genetic markers have been used to identify a desired QTL.
  • most QTL studies of plant species have looked at gross morphological or agronomic phenotypes (e.g. yield, disease and stress resistance, time to flowering etc.). For instance, in WO 2000/18963 soybean plants comprising QTL associated with enhanced yields, and methods for selecting and breeding those plants is disclosed.
  • This method involved the use of a specific marker nucleic acid capable of hybridizing to a second nucleic acid molecule that maps to specific region of Glycine soja and that is associated with enhanced yield.
  • a QTL associated with brown stem rot (BSR) resistance in a soybean plant was identified.
  • the QTL associated with BSR resistance may be used for plant selection using marker assisted selection.
  • WO 99/31964 discloses the use of a marker nucleic acid that is genetically linked to a set of 63 specified loci for plant selection.
  • the identified polymorphisms may be used in DNA fingerprinting and for mapping genes or QTLs associated with pest or disease resistance.
  • Dumas et al. disclose the use of mRNA as a phenotypic marker to map QTL associated with stress gene expression in rat.
  • the present invention is directed to the identification of genomic regions involved in the genetic regulation of the expression of one or more genes of interest associated with a desired trait.
  • loci for regulatory genes associated with the differential accumulation of transcripts or gene products are identified.
  • the present invention relates to the use of mRNA transcripts, and variation in transcript levels for the identification of quantitative trait loci pertaining to a desired trait within an organism. More specifically, the present invention relates to a method for the identification of loci for regulatory genes that control gene expression for a given trait within any organism. Finally, the present invention relates to a method for the identification of genes and gene sequences that regulate expression of genes and regulatory cascades controlling expressional traits within the organism.
  • a method for identifying one or more regions within a genome of an organism of interest that mediate the expression of one or more genes of interest comprising:
  • RNA extracting RNA from each of the segregated progeny and quantifying the level of gene expression of one or more genes of interest, the one or more genes of interest associated with the response to an environmental stimulus, or the process of interest;
  • QTL quantitative trait loci
  • the present invention also includes the method as defined as above, wherein after the step of crossing (step iii)), and prior to the step of extracting RNA, the segregated progeny are subjected to a desired environmental stimulus or are characterized as being at a specific developmental stage.
  • the method of the present invention as described above may be used for the identification of one or more QTLs corresponding to a transcription factor or any factor controlling the expression of the one or more genes of interest.
  • this invention pertains to the method as described above wherein after the step of determining (step vi)), one or more genes located at the one or more QTL are isolated and characterized.
  • the present invention is also directed to the method as described above wherein in the step of determining (step vi)), a marker is identified at the QTL.
  • the marker may be used for:
  • marker-assisted selection map-based cloning, hybrid certification, fingerprinting, genotyping, as an allele specific marker, or a combination thererof.
  • the present invention also embraces a method (B) for identifying a regulatory gene that mediates the expression of a gene of interest comprising:
  • step iv) sequencing the one or more regulatory genes isolated in step iv).
  • This invention also includes a method of mediating the response of an organism of interest to an environmental stimulus comprising, transforming the organism of interest with a regulatory gene identified using the method (B) as described above.
  • this invention realtes a method of mediating development of the organism of interest comprising, transforming the organism of interest with a regulatory gene identified using the method (B) as described above.
  • the present invention also embraces a method (C) for identifying a regulatory sequence that mediates the expression of a gene of interest comprising:
  • step iv) sequencing the regulatory sequence of the one or more regulatory genes isolated in step iv).
  • This invention pertains to a method of mediating the response of an organism of interest to an environmental stimulus comprising, transforming the organism of interest with a regulatory sequence fused to a gene of interest, the regulatory sequence being identified using the method (C) as described above.
  • this invention includes a method of mediating development of the organism of interest comprising, transforming the organism of interest with a regulatory sequence fused to a gene of interest, the regulatory sequence being identified using the method (C) as described above.
  • the present method allows the identification of genes that share common regulatory loci or that are under the same regulation. This may have important implications for many claimed applications, for example, but not limited to marker-assisted selection, phenotyping, pathway mapping cascade analysis, gene regulation interaction, gene flux analysis etc.
  • Genomic regions associated with the level of expression of genes can be identified using QTL mapping analysis. This approach, using gene expression level as a quantitative trait permits identifying gene expression control mechanisms by narrowing the search for such regulatory genes and regulatory sequences to specific genomic regions.
  • the significant QTLs identified herein, and the unexpected high level of variance that they explain indicate the potential of using QTL analysis of gene expression to locate important regulatory factors responsible for stress-induced gene expression. Comparative QTL analysis of multiple genes induced by the same external stimulus further permits the elucidation of complex pathways regulating gene expression and to regroup genes that share regulatory factors.
  • the technique of the present invention is applicable to genes of interest whose expression is regulated by any factors using a population segregating for levels of expression of such genes. It will allow for the identification of genomic regions. Once identified, these genomic regions can be used to characterize a given genotype without environmental or developmental interferences inherent to techniques based on gene expression.
  • the technique of the present invention may also identify one or more QTLs that are commonly related to the phenotypic trait being analysed and the expression of genes of important adaptative value for that given trait. Regulatory genes and regulatory sequences found within these loci are likely to be of important value for the improvement of the polygenic trait.
  • the technique of the present invention is applicable to any host organism, however, there are several organisms, for example, but not limited to, unicellular organisms or plants that offer unique advantages over other eukaryotic systems with regard to the application of the technique of the present invention.
  • FIG. 1 shows a linkage map of diploid alfalfa. Loci are listed on the right, and recombination distances (cM) are listed on the left of each linkage group. Bars on the right of linkage groups indicate the approximate position of loci.
  • Cold-regulated (msaCI) genes are double framed and genes with homology to genes with regulatory function are framed. Genes that are members of multigene families are numerically distinguished, for example C3358.1 and C3358.3.
  • FIG. 2 Position and statistical significance (LOD scores) of QTLs for LT 50 and cold regulated msaCI gene expression.
  • msaCI genes are double framed and genes with homology to genes with regulatory function are framed.
  • the graph for LOD scores of expression in crown is shown at the top and the graph for LOD scores of expression in leaves is shown at the bottom.
  • LT 50 QTLs apply to whole plants and are independent of tissue type. Genes that are members of multigene families are numerically distinguished for example C3358.1 and C3358.3.
  • FIG. 3 shows one example of a dot blot analysis of the expression of a gene of interest, in this case the msaCIA gene, in segregating F 2 progeny of diploid alfalfa.
  • a gene of interest in this case the msaCIA gene
  • Each dot corresponds to a unique genotype except for the last column where a control is dotted in triplicate.
  • Level of transcripts are quantified by densitometry and used as a quantitative trait for QTL analysis. Optical density value is indicated for each genotype and the control.
  • the present invention relates to a method for the identification o L regulatory loci that control gene expression within any organism. More specifically, the present invention relates to the use of mRNA transcripts, and variation in transcript levels for the identification of quantitative trait loci pertaining to a desired trait within an organism.
  • a quantitative trait locus is a region of the genome that explains a significant proportion of the variability of a given phenotype controlled by multiple genes, for example, but not limited to, traits associated with increased yield, freezing tolerance, drought tolerance and the like. Within these regions are located one or more genes coding for factors that have a significant effect on the phenotype of the organism.
  • a linkage map constructed using any type of marker such as morphological, isozyme or DNA based markers may be used to locate each gene of interest to a given location on the map.
  • the expression of a single gene of interest is considered as a quantitative trait.
  • a major quantitative trait locus should be located close to the location of the structural gene.
  • the variance of the expression of the gene of interest is highly, and significantly explained by QTLs located elsewhere in the genome (see FIG. 1).
  • genomic regions located at a distance from the gene of interest are controlling, or regulating the expression of the gene of interest. These genomic regions may be identified using the linkage map and the regulatory genes that encode factors that control the expression of the gene of interest are then identified using techniques as known to one of skill in the art.
  • gene of interest it is meant one or more known genes that may be used as a quantitative trait that is being characterized using the method of the present invention, and may include upstream and down stream regulatory regions, introns, and exons.
  • a gene of interest is typically, but not always, expressed under conditions used to determine the effect of regulatory genes on the expression, or suppression, of the gene of interest.
  • the level of expression of the gene of interest may be determined using any methods known in the art, for example, Northern analysis, RNase protection, array analysis, PCR and the like.
  • the gene of interest or the level of its transcripts is a quantitative trait that is used for further identification of one or more QTLs associated with the expression of the gene of interest.
  • One or more genes of interest may be used within the method of the present invention for the analysis of a response to an environmental stimulus or other process of interest as defined herein.
  • By increasing the number of genes of interest used within the analysis it is possible to identify one or more QTLs that are responsible for the regulation of several genes of interest associated with the response to the environmental stimulus or other process of interest within the plant, possibly highlighting the importance of the QTLs. Such an approach is disclosed below and in the Examples.
  • regulatory gene it is meant a gene whose product directly or indirectly effects the expression of a gene of interest, and includes the coding region, upstream (5′) and downstream (3′) non-coding and regulatory regions, and introns.
  • a regulatory gene is differentially expressed, in response to a stimulus, for example but not limited to, an environmental stimulus such as heat shock or temperature stress.
  • An example of a regulatory gene includes, but is not limited to, a gene that encodes a transcriptional factor, or a gene that encodes another protein factor that in some manner regulates the expression of another gene.
  • the product encoded by a regulatory gene may directly effect the expression of a gene of interest, for example which is not intended to be limiting in any manner, by binding regulatory regions upstream (5′) or downstream (3′) of the coding region of the gene of interest, or within introns, as is known in the art, and enhancing or silencing the expression of the gene of interest.
  • a regulatory gene may also encode a product that effects either the stability of the transcript of the gene of interest, the rate or stability of translation or the transcript synthesized from the gene of interest, or both post transcriptional and post translational events pertaining to the expression of the gene of interest.
  • a regulatory gene may effect the differential expression of a gene of interest indirectly, by mediating the expression of one or more secondary genes, whose products may then interact with the expression of the gene of interest. It is also contemplated that one or more regulatory genes may act synergistically to mediate the differential expression of a gene of interest.
  • the method of the present invention allows for the identification of genes that share common regulatory loci or that are under the same regulation. This may have important implications for many applications, for example, but not limited to marker assisted selection, phenotyping, pathway mapping cascade analysis, gene regulation interaction, gene flux analysis, or the identification of regulatory genes having significant effects on polygenic traits
  • the organism of interest may be a plant, plant organ, tissue or cell
  • the environmental stimulus may be, for example but not limited to, biotic stimuli including infestation by a virus, bacteria, fungi, insect, nematode or other herbivore, or an abiotic stimuli, for example but not limited to, a stress associated with chilling, freezing, water, drought, osmotic, heat, salt, oxidative, or pollutant.
  • An environmental stimulus may also include the effects of mineral nutrition, light, and endogenous or exogenous chemicals on organism of interest or an organ, tissue or cell thereof.
  • process of interest it is meant any process that produces a measurable effect within an organism of interest or an organ, tissue, or cell thereof, for example, which is not to be considered limiting in any manner, a plant.
  • a process of interest may include but is not limited to, developmental, chemical or environmental control of gene expression during, in the non-limiting case of a plant, embryogenesis, flower, seed, root or leaf development, organogenesis, or circadian, ultradian and other internal rhythms.
  • Other processes of interest may include but are not limited to, harvestable yield, photosynthate translocation, sink and source, leaf area index, root shoot ratio, nutritive value of harvested material, plant morphology, rate of cell cycle, rate of cell differentiation, cell size, plant life cycle, senescence, maturation, dormancy, germination, or genomic rearrangements, for example, due to transposon activation.
  • analogous or other unique processes may be characterized using the methods described herein, within any organism of interest.
  • an organism of interest it is meant any organism within which one or more QTLs are to be identified and characterized, for example but not limited to a plant (algae, bryophytes, ferns, angiosperm, or gymnosperm), an animal, a unicellular organism, bacteria, phytoplankton, yeast, fungi, and also includes cell or tissue cultures of these organisms.
  • a plant algae, bryophytes, ferns, angiosperm, or gymnosperm
  • an animal a unicellular organism, bacteria, phytoplankton, yeast, fungi, and also includes cell or tissue cultures of these organisms.
  • the method of the present invention may be used to identify the level of transcripts of a gene that maps to a specific location in the genome and to determine whether the accumulation of the encoded transcript, or protein, is regulated by genes located at loci elsewhere in the genome.
  • QTL quantitative trait loci
  • genes found within these QTLs could encode for members of multigene families under different transcriptional controls (for example, harbouring important cis-regulating sequences which in turn influence the regulation of transcription or act on upstream or downstream sequences required for enhanced translation or mRNA stability), transcription factors (including enhancer and repressors), signal transduction pathway proteins (for example, protein kinases, protein phosphatases, 14-3-3 proteins etc.), external signals receptors, proteins involved in the regulation of secondary messenger levels (Ca 2 +, IP 3 , cAMP, etc.), nucleases involved in the degradation of transcripts, proteases and proteases inhibitors, novel transcription regulating factors.
  • transcription factors including enhancer and repressors
  • signal transduction pathway proteins for example, protein kinases, protein phosphatases, 14-3-3 proteins etc.
  • external signals receptors proteins involved in the regulation of secondary messenger levels (Ca 2 +, IP 3 , cAMP, etc.)
  • nucleases involved in the degradation of transcripts proteases and protea
  • An example of the approach used for identifying regulatory genes that control, mediate, or influence, the expression of one or more genes of interest involves:
  • Population types can include, but are not restricted to, F1 (from heterozygous parents), F2, or F3 families, Recombinant Inbred lines, Doubled Haploids, Backcross lines, Testcross lines, and gymnosperm segregating megagametophytes;
  • RNA may be obtained from flower, primordia, leaf, stem or root tissues, or cells;
  • DNA based markers such as, RFLP (Restriction Fragment Length Polymorphism), AFLP (Amplified Fragment Length Polymorphism), RAPD (Random Amplified Polymorphic DNA), microsatellites, IMP (Inter
  • a relationship may be determined using any method known to one of skill in the art, for example, but not limited to, single point ANOVAs, simple regression, Interval mapping, Composite interval mapping.
  • Such an analysis may be performed using MAPMAKER/QTL, MQTL, QTL Cartographer, or other similar software. The statistical significance and percent of variance for each QTL are also calculated.
  • the method as described herein provides an effective method for the exhaustive identification of many, if not all, the regulatory factors (genes) involved in the control of the expression of a gene of interest, and provides an estimate of the relative contribution of each factors to the observed variability of expression of the gene of interest, as well as identifying the regulatory gene's genomic location and associated markers which can be used in traditional plant breeding.
  • “master switch” regulatory genes affecting the expression of many genes for example within a cascade, can be identified when multiple genes induced by a given environmental stimulus or that are related to a given process are analysed simultaneously.
  • each of these loci and linked markers may be used either directly as markers, for example, but not limited to breeding and screening purposes, including plant breeding, or further characterized to determine the gene or genes involved with the expression of the gene of interest, using map-based cloning methods as would be known to one of skill in the art. For example one or more known regulatory genes can be mapped to determine if the genetic location of these genes coincide with the QTLs controlling mRNA expression of the gene of interest.
  • Confirmation that such a coinciding regulatory gene is effecting the expression of one or more genes of interest can be obtained using standard techniques in the art, for example, but not limited to, genetic transformation, gene complementation or gene knock-out techniques, or overexpression.
  • the genetic linkage map can also be used to isolate the regulatory gene, including any novel regulatory genes, via map-based cloning approaches that are known within the art whereby the markers positioned at the QTL are used to walk to the gene of interest using contigs of large insert genomic clones.
  • Positional cloning is one such a method that may be used to isolate one or more regulatory genes as described in Martin et. al. (Martin, G. B., Brommonschenkel, S.
  • the present invention is directed to identifying regions within the genome of a plant that are involved in mediating the expression of one or more genes of interest in response to an environmental stimulus, or a process associated with differential gene expression within a process of interest.
  • the present invention is also directed to characterizing the identified QTL to identify the one or more regulatory genes and regulatory sequences at these loci.
  • the method of the present invention may also be used to identify loci corresponding to factors (encoded by regulatory genes) associated with the control or mediation of expression of a gene of interest in an organism of interest.
  • This method can be used for the identification of regulatory genes that control and modulate the level of mRNA transcripts of one or more genes of interest, whether or not this variation is found in nature or induced by gene mutation, gene disruption, or gene insertion, for example, but not limited to, genes of interest that are regulated by factors involved in:
  • biotic stresses for example but not limited to virus, bacteria, fungi, insects, or nematodes;
  • abiotic stresses including but not limited to chilling, freezing, water, drought, osmotic, heat, salt, oxidative, pollutants;
  • embryogenesis for example, but not limited to tissue, or organ development, which in the case of a plant may include seed development, organogenesis, floral development;
  • chemical inducers including natural growth regulators, for example, in the case of a plant being the organism of interest, auxins, gibberellins, ABA, cytokinins, ethylene, and their analogs, synthetic hormones, herbicides, salicylic acid, jasmonic acid;
  • nutritive value of biomass for example but not limited to, harvested material and associated effects on the levels of quality factors such as cofactors, vitamins, proteins, antioxidants, highly digestible fibers;
  • morphology for example, but not limited, in plants, to the effect of regulatory genes on flower color (e.g. genes involved in anthocyanins synthesis), plant height (e.g genes involved in gibberellins synthesis), internode length, leaf insertion;
  • rate of cell cycle for example but not limited to cyclins
  • rate of cell differentiation for example but not limited to homeodomain proteins
  • cell size for example but not limited to, in plants, to genes involved in auxin synthesis, auxin receptors, auxin-induced genes;
  • organism life cycle for example through the effect of regulatory genes on senescence, maturation, dormancy, germination;
  • genomic rearrangements for example, transposon activation
  • markers located in these QTL may also be used in applied breeding.
  • identified polymorphisms associated with one or more identified genetic markers located at a locus may be used: for genome-based diagnostic and selection techniques:
  • genomic DNA sequence surrounding a gene-coding or non-coding DNA sequence for example, but not limited to a promoter or a regulatory sequence
  • regulatory loci associated with the expression of a gene of interest at the whole organism, organ, tissue or cell specific level, in response to an environmental stimulus, or a phenotype associated with differential gene expression associated with a process of interest may also be identified.
  • candidate regulatory genes that modulate the expression of mRNA such as (also see Table 2 Example 2):
  • Mitogen-activated protein kinases (MMK4, MMK3, MMK2, MMK1);
  • Protein phosphatases (type 2A and 2C);
  • Ca 2+ -binding proteins for example Calmodulin
  • [0127] may be evaluated to determine if they map to regions of the genome (QTL) that explain a large proportion of the expression of cold-regulated genes in a plant, for example but not limited to, alfalfa ( Medicago falcata L.).
  • the method as described herein may be used to complement high throughput genome analysis studies based on DNA chips and grid arrays, or any other system capable of measuring gene expression. Using segregating populations, it is possible to locate QTLs regulating the transcripts level of genes which expressions is related to phenotypes of interest (e.g stress and disease resistance, biochemical production, morphological variations etc.). Mapping of candidate genes from EST collections establishes potential co-location to important QTLs and allows for the identification of allelic polymorphism and the development of allele-specific markers. The identification of these QTLs, and the associated regulatory genes, may be used for genome-based diagnostic and selection techniques for assessment of gene expression potential under given developmental or environmental conditions and the coordination of gene expression in a developmental, tissue, or environmental manner.
  • phenotypes of interest e.g stress and disease resistance, biochemical production, morphological variations etc.
  • Mapping of candidate genes from EST collections establishes potential co-location to important QTLs and allows for the identification of allelic polymorphism and
  • Genomic regions associated with the level of expression of genes can be identified using QTL mapping analysis. This approach, using gene expression level as a quantitative trait permits identifying gene expression control mechanisms by narrowing the search for such regulatory genes to specific genomic regions. DNA sequences responsible for variation in gene expression are also likely to be found within these regions.
  • the gene identification method described herein will become easier and more rapid with the availability of whole genome sequences and the routine integration of increasingly large number of ESTs onto high density maps or by taking advantage of the extensive collinearity of blocks of genes along chromosomes of related species in comparative genetic mapping.
  • the technique of the present invention will be applicable to genes which expression is regulated by any factors using a population segregating for levels of expression of such genes. It will allow for the identification of genomic regions that can be used to characterize a given genotype without environmental or developmental interferences inherent to techniques based on gene expression.
  • probes are obtained from known regulatory genes, for example, but not limited to the regulatory genes listed above, and in Table 2 of Example 2, and these regulatory genes, or their expression products are mapped on a linkage map. These probes may include nucleotide fragments or full-length genes for the detection of DNA or RNA, or antibodies for the detection of the expression products of a regulatory gene.
  • unknown regulatory genes located at one or more QTLs may also be identified using methods as known to one of skill in the art, for example, but not limited to, positional cloning and mapping portions of the sequenced DNA to determine if the cloned DNA co-locates (maps) with the one or more identified QTLs.
  • the location of the candidate regulatory genes at one or more QTLs is confirmed, for example by mapping upstream or downstream regions from each putative regulatory gene on the linkage map. In this manner, only regulatory genes that are characterized by having 5′ or 3′ regions that co-locate with the same QTLs are used for further characterization.
  • Regulatory genes that are located within one or more QTLs that are associated with the expression of one or more genes of interest may then be isolated and characterized, and their expression modulated within a transgenic plant, for example but not limited to alfalfa, in order to assess their effect on expression of the gene of interest, and if desired, their effect on the response of the organism of interest to an environmental stress.
  • Such analysis may include, but is not limited to, complementation or gene knockout, and gene activation, studies involving transformation of the organism of interest with a sense or antisense construct of the regulatory gene or enhancer sequences, respectively.
  • An organism of interest that lacks or exhibits a weak response to an environmental stimulus, or a process of interest, is transformed with a sense construct of the regulatory gene, while an organism of interest that exhibits a strong response, or scores positively for process of interest, is transformed with an antisense construct of the regulatory gene, or disrupted by insertion of a foreign DNA such as T-DNA into the coding region of the gene, or activated by insertion of an enhancer sequence 5′ or 3′ of the gene of interest.
  • Expression of one or more genes of interest, and the regulatory gene may then be monitored to determine the effect of the sense, antisense, knockout, or enhancer insertion regulatory gene on the organisms response to an environmental stimulus, or on process of interest.
  • the effect of the sense, antisense, knockout, or enhancer insertion constructs on a physiological response to an environmental stress may also be determined.
  • a regulatory gene located at a specific QTL, or groups of QTLs may also be used as a marker for the one or more QTLs within breeding programs.
  • this invention also pertains to a method for identifying a regulatory gene that mediates the expression of a gene of interest comprising:
  • the present invention is also directed to mediating a response of an organism of interest to an environmental stress, or characterizing the in vivo effect of an identified and isolated regulatory gene, by introducing the regulatory gene into the organism of interest and, optionally, determining the effect of the regulatory gene on the expression of one or more genes of interest, or its effect on the response of an organism of interest to an environmental stimulus.
  • msaCI cold-regulated genes
  • LT 50 phenotypes
  • QTL quantitative trait loci
  • An F 1 population is constructed by intercrossing diploid parents exhibiting contrasting cold tolerance ( M. falcata ⁇ M. sativa ).
  • the F 1 line is produced by a cross-pollination between a cold sensitive M. sativa genotype from the cultivated alfalfa at the diploid level group (Bingham, E. T. and T. J. McCoy. 1979. Crop Sci. 19: 97-100) as the female parent with one hardy diploid genotype from M. falcata cv. Anik (Pankiw, P. and Siemens, B. 1976. Can. J. Plant Sci. 56: 203-205) as the male parent. Flowers are emasculated and hand pollinated. One randomly selected genotype of the F 1 is selfed by hand pollination and the F 2 progeny from this cross is used to produce a linkage map and QTL analysis.
  • Plants are cold acclimated two weeks in a growth chamber at 2° C., with an 8 h photoperiod and an irradiance of approximately 125 ⁇ mol m ⁇ 2 s ⁇ 1 photosynthetic photon flux density.
  • RNA is quantitated by UV absorption at 260 nm (Fourney, R. M., J. Miyakoshi, R. S. Day III, and M. C. Paterson. 1988. Focus 10:1).
  • RNA For each parental genotype and each genotype of the segregating population, five ⁇ g of total RNA are vacuum-transfered to a nylon membrane (Hybond N + , Amersham Pharmacia Biotech, Oakville, ON) using a Bio-DotTM apparatus (Bio-Rad, Mississauga, ON) and immobilized by cross-linking under UV light for 3 minutes. Membranes are hybridized overnight at 68° C. in 2 ⁇ SSC, 0.25% (W/V) low-fat powder milk, 1% SDS with [ 32 P]dCTP-labeled probe prepared from purified inserts of cold-regulated genes according to standard protocoles (Sambrook, J., Maniatis, T. and Fritsch. 1989.
  • a genetic linkage map is constructed based on AFLP and RFLP.
  • DNA is extracted from 1-2 g of fresh leaf tissue from 4-6 week-old clonal propagules.
  • the method for extraction is essentially as described by Doyle and Doyle (Doyle, J. J., and Doyle, J. L. 1990. Isolation of plant DNA from fresh tissue. FOCUS 12, 13-15), except that the leaf tissue is ground without liquid nitrogen at room temperature.
  • DNA purified from 169 F 2 genotypes is separately digested with restriction enzymes DraI and EcoRV. Each digested DNA sample (6 ⁇ g per genotype is separated on horizontal gels (0.9% agarose, 1 XTAE), and the separated fragments transferred to nylon membranes (Hybond N + , Amersham Pharmacia Biotech, Oakville, ON) by capillary blotting. Ten duplicate copies of membranes are made for simultaneous segregation analyses with multiple probes. Membranes are hybridized overnight at 65° C. with probes labelled with [ 32 P]-dCTP.
  • DNA probes consist of randomly selected cDNAs and cDNAs selected according to their homology to regulatory genes both obtained from Medicago sativa cDNA libraries, and the 7 msaCI cDNAs described above.
  • cDNA inserts are first specifically amplified by PCR and labelled by random hexamer labelling using the T7 QuickPrimeTM Kit (Amersham Pharmacia Biotech, Oakville, ON). Prehybridization, hybridization, and probe labeling are performed according to standard protocols (Sambrook, J., Maniatis, T. and Fritsch. 1989. Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Col Spring Harbor, N.Y.).
  • F 2 DNAs are digested with EcoRI and MseI restriction enzymes, ligated to Eco- and Mse-specific primer adapters, then amplified by pre-selective Eco and Mse PCR primers (Vos. P., Hogers, R., Bleeker, M., Reijans, M., van der Lee, T., Homes, M., Frijters, A., Pot, J., Pelerman, I., Kuiper, M, and Zabeau, M. 1995, Nucleic Acids Res. 23, 4407-4414).
  • Pre-selective amplicons are diluted 20-fold to be used as material for selective amplification.
  • the Eco primer is labelled with IRD dyes, which permit the detection of amplicons by the infrared laser of a LI-COR automated sequencer (LI-COR, Inc. Lincoln, Nebr., USA).
  • Selective amplification is carried out according to the “touch down” protocol described by Vos et al. (1995, Nucleic Acids Res. 23, 4407-4414). After selective amplification, amplicons were separated on 25 cm gels composed of 7% Long Ranger acrylamide, 7 M urea, and 0.6 ⁇ TBE, using a LI-COR automated DNA sequencer model 4000L.
  • the genetic map of the diploid cross is constructed using the segregation data from 112 RFLP and 117 AFLP segregating markers. Co-segregation analyses are performed using MAPMAKER/EXP v 3.0 software (Lander, E. S., Green, P., Albertson, J., Barlow, A., Daly, M. J., Lincoln, S. E., and Newburg, L 1987. Genomics 1, 174-181) to determine the linkage group assignment of each marker and the location of each molecular marker within each linkage group. Individual linkage groups are obtained using two-point analysis with a minimum LOD score of 15 and maximum recombination level of 30%. Multiple point analysis with an LOD threshold of 2.0 is then used to order the loci within the linkage groups. The resulting map (FIG. 1) covers approximately 1400 cM and has an average marker interval of approximately 8 cM. Fifteen markers remained unlinked.
  • QTLs involved in msaCI gene expression are identified with MAPMAKER/QTL v 1.1.(Lander, E. S., and Boststein, D. 1989, Genetics 121, 185-199).
  • the linkage map is scanned for the presence of QTLs in specific regions of the genome using the expression of each gene as a quantitative trait.
  • the action of each QTL in relation to each other and the percent of the variance of msaCI gene expression explained by each QTL is determined.
  • An LOD threshold of 2.0 is used for the identification of QTL.
  • QTLs related to the variability of msaCI gene transcript levels observed among genotypes are found for all 7 msaCI genes, and for the LT 50 phenotype (Table 1). Genes that play an important regulatory role in the expression of msaCI genes are found within these QTLs.
  • the number of QTLs associated with expression of msaCI genes varied from 1 (msaCIF) up to 5 (msaCIC). In most cases their LODs were highly significant.
  • the phenotypic variation explained by these QTLs varied from 10 to 60%. In most cases the increase in expression and frost tolerance, respectively, was due to the allele from the cold tolerant M. falcata parent.
  • QTLs relating to freezing tolerance are identified. Two of these QTLs are located in linkage group E in a genomic region associated also with the expression of msaCIB and msaCID.
  • QTLs for the expression of msaCI genes are found associated with the position of the corresponding structural gene for msaCIA (see linkage group D, FIG. 2) msaCID (see linkage group E, FIG. 2) and msaCIG (linkage group F, FIG. 2).
  • msaCID the RFLP locus coincides with expression QTLs for three genes; the msaCID gene itself, msaCIA and msaCIB (see Linkage Group E, FIG. 2). This suggests that either msaCID is a regulatory gene or a regulatory gene is located in its vicinity.
  • a series of ESTs showing homology to genes with known regulatory functions are isolated from a ⁇ gt10 cDNA library prepared from mRNA isolated from crowns of tetraploid alfalfa ( M. sativa L. cv. Apica; R. Michaud, C. Richard, C. Willemot and H. Gasser 1983. Can. J. Plant Sci. 63: 547-549):
  • Protein phosphatases (type 2A and 2C)
  • Probes for specific regulatory genes listed in table 2 are prepared by PCR amplification, purified on Sephacryl S-200 MicroSpin Columns (Amersham Pharmacia Biotech, Oakville, ON) and stored at ⁇ 20° C. These probes are used for Southern hybridization to restricted DNA from F 2 diploid genotypes of the progeny of the cross described in Example 1. Purified probes are radiolabeled to high specific activity by random hexamer labelling and hybridized to DNA blots according to standard protocols for RFLPs as described in Example 1 (Sambrook, J., Maniatis, T. and Fritsch. 1989. Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Col Spring Harbor, N.Y.).
  • EST sequences are also used to design primers for the amplification of the identified loci as STS (Sequence Tagged Sites) from DNA of the individuals of the segregating population.
  • STS Sequence Tagged Sites
  • the PCR products are restricted with various enzymes to detect polymorphism. If no polymorphism is detected the PCR products obtained from the two parents are individually sequenced and SNPs (Single Nucleotide Polymorphims) are searched.
  • Example 1 The candidate regulatory genes described above are mapped as RFLPs within the F 2 progeny as described in Example 1 in order to assess whether they are localized within QTLs associated with variation in cold-induced expression of msaCI genes as identified in Example 1.
  • C2186(SCOF-1 homolog) is mapping to a region containing a QTL for LT 50 (linkage group C, FIG. 2).
  • COR msaCI
  • kinases appears to be a homologue of the ASK1 serine/threonine kinase 1 from Arabidopsis (Munnik, T. and H. J. G. Meijer. 2001. FEBS Letters 498: 172-178). Confirmation of the roles of such candidate regulatory genes may be obtained using methodologies outlined below.
  • ESTs of candidate regulatory genes that map to one or more QTLs associated with variation of the expression of msaCI genes are isolated from a genomic library constructed in EMBL3 phage (Sambrook, J., Maniatis, T. and Fritsch. 1989. Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.), using DNA from the two parents identified above. Each candidate regulatory gene is sequenced in its entirety including upstream and downstream regions of the coding region using the dideoxynucleotide chain termination method (Sambrook, J., Maniatis, T. and Fritsch. 1989. Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.).
  • Comparisons between allelic forms from each parent is also made to identify mutations responsible for the QTL. Confirmation of the localization of candidate regulatory genes is carried out by mapping upstream or downstream regions of each regulatory gene on the linkage map generated above. Only regulatory genes that are characterized by having 5′ or 3′ regions co-mapping with the same one or more QTLs are used for further characterization in complementation or gene knockout studies.
  • Alfalfa transformation is performed using Agrobacterium tumefaciens as previously described by Desgagair et al. (Desgagair R., S. Laberge, G. Allard, H. Khoudi, Y. Castonguay, J. Lapointe, R. Michaud and L. -P. Vézina. 1994. Plant Cell Tissue Organ Cult 42: 129-140). Two approaches are taken; 1) Constitutive expression of the candidate gene using a gene fusion to a constitutive promoter, for example, but not to be limited 35S; and inducible expression.
  • the coding region of the candidate gene is fused in frame to a full-length 35S promoter and the resulting construct is cloned into the binary expression vector pGA482.
  • Full length candidate regulatory genes i.e. candidate regulatory genes that, with surrounding 5′ and 3′ regions, map to one or more QTLs identified above
  • Constructs for both constitutive and inducible expression in the sense orientation are used to transform plants that lacks the allele at the QTL corresponding to expression of the trait of interest (for example, but not to be limited to msaCI gene expression), and the antisense orientation constructs are used to transform plants that harbor the allele at the QTL.
  • the transgenics are then grown and subject to cold acclimation conditions, as needed to determine the effect of the introduced sense or antisense gene on both expression of one or more msaCI genes and the LT 50 , thereby validating the candidate gene as the regulatory factor controlling mRNA expression of the msaCI genes at the QTL.

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US20060241869A1 (en) * 2003-08-05 2006-10-26 Rosetta Inpharmatics Llc Computer systems and methods for inferring causality from cellullar constituent abundance data
US7653491B2 (en) 2002-05-20 2010-01-26 Merck & Co., Inc. Computer systems and methods for subdividing a complex disease into component diseases
US7729864B2 (en) 2003-05-30 2010-06-01 Merck Sharp & Dohme Corp. Computer systems and methods for identifying surrogate markers
US8843356B2 (en) 2002-12-27 2014-09-23 Merck Sharp & Dohme Corp. Computer systems and methods for associating genes with traits using cross species data
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US7653491B2 (en) 2002-05-20 2010-01-26 Merck & Co., Inc. Computer systems and methods for subdividing a complex disease into component diseases
US8843356B2 (en) 2002-12-27 2014-09-23 Merck Sharp & Dohme Corp. Computer systems and methods for associating genes with traits using cross species data
US7729864B2 (en) 2003-05-30 2010-06-01 Merck Sharp & Dohme Corp. Computer systems and methods for identifying surrogate markers
US20060241869A1 (en) * 2003-08-05 2006-10-26 Rosetta Inpharmatics Llc Computer systems and methods for inferring causality from cellullar constituent abundance data
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WO2005107412A3 (en) * 2004-04-30 2006-06-29 Rosetta Inpharmatics Llc Systems and methods for reconstruction gene networks in segregating populations
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CN115216559A (zh) * 2022-09-20 2022-10-21 中国农业科学院北京畜牧兽医研究所 紫花苜蓿叶面积相关的snp分子标记组合及应用
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