METHODS AND COMPOSITIONS FOR SELECTING SOYBEAN PLANTS RESISTANT TO SOUTHERN ROOT KNOT NEMATODE
专利汇可以提供METHODS AND COMPOSITIONS FOR SELECTING SOYBEAN PLANTS RESISTANT TO SOUTHERN ROOT KNOT NEMATODE专利检索，专利查询，专利分析的服务。并且，下面是METHODS AND COMPOSITIONS FOR SELECTING SOYBEAN PLANTS RESISTANT TO SOUTHERN ROOT KNOT NEMATODE专利的具体信息内容。
The present invention is in the field of plant breeding and disease resistance. More specifically, the invention includes a method for breeding soybean plants containing quantitative trait loci (QTL) associated with disease resistance to Southern Root Knot Nematode (SRKN), a disease associated with the pathogen Meloidogyne incognita. The invention further relates to the use of genetic markers to identify the QTL for disease resistance to the pathogen Meloidogyne incognita. The invention further includes germplasm and the use of germplasm containing QTL conferring disease resistance for introgression into elite germplasm in a breeding program for resistance to SRKN.
Root-knot nematodes (Meloidogyne spp.) are plant pathogens that infect many hosts and cause extensive damage to crops throughout the world. In the southeastern United States, the Southern Root Knot Nematode (Meloidogyne incognita), herein referred to as SRKN, is a major pest of soybean (Glycine max (L)). Restrictions on the use of nematicides including cancellation of DBCP (1, 2-dibromo3-chloropropane) and EDB (ethylene dibromine) have encouraged development of alternative methods of SRKN control (
Both elite soybean varieties and accession germplasm have been examined for SRKN resistance. Two sources of SRKN resistance are PI 96354 and Palmetto. Phenotypic screening of 2,370 soybean accessions from the USDA Soybean Germplasm Collection (Urbana, IL) identified PI 96354 as the most highly resistant source in the collection (
The present invention provides and includes methods for screening and selecting a soybean plant comprising the SRKN resistance QTL.
The present invention provides
- (1) a method of identifying a soybean plant having SRKN resistance, the method comprising:
- (a)-providing a population of soybean plants,
- (b)-genotyping at least one soybean plant in the population with respect to a soybean genomic nucleic acid marker comprising SEQ ID NO:1,
- (c) selecting from the population at least one soybean plant comprising at least one allele associated with SRKN resistance, wherein the SRKN resistance allele consists of SEQ ID NO:21;
- (2) a method of identifying a soybean plant having SRKN resistance, the method comprising:
- (a)providing a population of soybean plants,
- (b) screening the population with at least one nucleic acid marker assay that detects an SRKN resistance allele of SEQ ID NO:21;
- (c) selecting from the population one or more soybean plants comprising the SRKN resistance allele, wherein the SRKN resistance allele is SRKN resistance allele 1; and
- (3) a method of identifying an SRKN resistance allele in a soybean plant comprising detecting a locus associated with a SNP marker comprising SEQ ID NO:1.
Further disclosed are elite soybean plants identified by the methods above. The elite soybean plant can exhibit a transgenic trait wherein the transgenic trait is selected from the group consisting of herbicide tolerance, increased yield, insect control, fungal disease resistance, virus resistance, nematode resistance, bacterial disease resistance, mycoplasma disease resistance, modified oils production, high oil production, high protein production, germination and seedling growth control, enhanced animal and human nutrition, low raffinose, environmental stress resistance, increased digestibility, improved processing traits, improved flavor, nitrogen fixation, hybrid seed production, and reduced allergenicity. In a further embodiment, the herbicide tolerance conferred is selected from the group consisting of glyphosate, dicamba, glufosinate, sulfonulurea, bromoxynil, 2,4,-Dichlorophenoxyacetic acid, and norflurazon herbicides. The methods provided by this invention can further comprise the step (d) of assaying the selected soybean plant for resistance to a SRKN-inducing pathogen. In certain embodiments of the methods, genotyping is effected in step (b) by an assay which is selected from the group consisting of single base extension (SBE), allele-specific primer extension sequencing (ASPE), DNA sequencing, RNA sequencing, micro-array based analyses, universal PCR, allele specific extension, hybridization, mass spectrometry, ligation, extension-ligation, and Flap-Endonuclease-mediated assays.
Further disclosed is a method of introgressing an allele into a soybean plant comprising: (a) providing a population of soybean plants, (b) screening the population with at least one nucleic acid marker and (c) selecting from the population one or more soybean plants comprising an SRKN resistance allele, wherein the SRKN resistance allele is an allele selected from the group consisting of an SRKN resistance locus where one or more alleles at one or more of their loci is SRKN resistance allele 1.
The soybean or elite soybean plants identified by any of the methods of this invention can further comprise a transgenic trait. The transgenic trait can be selected from the group consisting of herbicide tolerance, increased yield, insect control, fungal disease resistance, virus resistance, nematode resistance, bacterial disease resistance, mycoplasma disease resistance, modified oils production, high oil production, high protein production, germination and seedling growth control, enhanced animal and human nutrition, low raffinose, environmental stress resistance, increased digestibility, improved processing traits, improved flavor, nitrogen fixation, hybrid seed production, and reduced allergenicity. The herbicide tolerance trait can be selected from the group consisting of glyphosate, dicamba, glufosinate, sulfonulurea, bromoxynil, 2,4-Dichlorophenoxyacetic acid, and norflurazon herbicides.
Further disclosed are substantially purified nucleic acid molecules comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1, 5-5, 13-14 and 21and complements thereof. These isolated nucleic acids can be used in practicing the methods of the invention. Isolated nucleic acid molecules for detecting a molecular marker representing a polymorphism in soybean DNA can comprise at least 15 nucleotides that include or are adjacent to the polymorphism, wherein the nucleic acid molecule is at least 90 percent identical to a sequence of the same number of consecutive nucleotides in either strand of DNA that include or are adjacent to the polymorphism, and wherein the molecular marker has the SEQ ID NO:1. The isolated nucleic acid can further comprise a detectable label or provide for incorporation of a detectable label. This detectable label can be selected from the group consisting of an isotope, a fluorophore, an antioxidant, a reductant, a nucleotide, and a hapten. This detectable label can be added to the nucleic acid by a chemical reaction or incorporated by an enzymatic reaction. Isolated nucleic acid molecules provided herein can comprise at least 16, 17, 18, or 20 nucleotides on either strand of the DNA that include or are adjacent to the polymorphism. In other embodiments, the isolated nucleic acid can hybridize to at least one allele of the molecular marker under stringent hybridization conditions.
The soybean plants selected by the methods of the invention may further exhibit increased grain yield in the presence of SRKN as compared to soybean plants lacking SRKN resistance alleles. In these methods, the selected one or more soybean plants may exhibit an increased grain yield of at least 0.5 Bu/A, 1.0 Bu/A or 1.5 Bu/A in the presence of SRKN as compared to plants lacking SRKN resistance alleles.
The accompanying drawings, which are incorporated in and form a part of the specification, illustrate the embodiments of the present invention and together with the description, serve to explain the principles of the invention.
In the drawings:
FIGURE 1 . Listing of SNP markers for the SRKN resistance locus with the resistant and susceptible allele for each marker indicated. For marker NS0102683, there are two resistance alleles, A and G, wherein A is resistant and G is highly resistant.FIGURE 2 . SNP Markers for detecting SRKN resistance. The resistant haplotype for SNP358 is TA and the resistant haplotype for SNP199 is AA. The haplotype from two polymorphisms at each marker can be used in selecting for SRKN resistance.
- SEQ ID NO: 1 is a genomic sequence derived from Glycine max associated with the SRKN resistance locus Rmi.
- SEQ ID NO: 2 is a genomic sequence derived from Glycine max associated with the SRKN resistance locus Rmi.
- SEQ ID NO: 3 is a genomic sequence derived from Glycine max associated with the SRKN resistance locus Rmi.
- SEQ ID NO: 4 is a genomic sequence derived from Glycine max associated with the SRKN resistance locus Rmi.
- SEQ ID NO: 5 is a forward PCR primer for amplifying SEQ ID NO: 1.
- SEQ ID NO: 6 is a reverse PCR primer for amplifying SEQ ID NO: 1.
- SEQ ID NO: 7 is a forward PCR primer for amplifying SEQ ID NO: 2.
- SEQ ID NO: 8 is a reverse PCR primer for amplifying SEQ ID NO: 2.
- SEQ ID NO: 9 is a forward PCR primer for amplifying SEQ ID NO: 3.
- SEQ ID NO: 10 is a reverse PCR primer for amplifying SEQ ID NO: 3.
- SEQ ID NO: 11 is a forward PCR primer for amplifying SEQ ID NO: 4.
- SEQ ID NO: 12 is a reverse PCR primer for amplifying SEQ ID NO: 4.
- SEQ ID NO: 13 is a probe for detecting the SRKN resistance locus of SEQ ID NO: 1.
- SEQ ID NO: 14 is a second probe for detecting the SRKN resistance locus of SEQ ID NO: 1.
- SEQ ID NO: 15 is a probe for detecting the SRKN resistance locus of SEQ ID NO: 2.
- SEQ ID NO: 16 is a second probe for detecting the SRKN resistance locus of SEQ ID NO: 2.
- SEQ ID NO: 17 is a probe for detecting the SRKN resistance locus of SEQ ID NO: 3.
- SEQ ID NO: 18 is a second probe for detecting the SRKN resistance locus of SEQ ID NO: 3.
- SEQ ID NO: 19 is a probe for detecting the SRKN resistance locus of SEQ ID NO: 4.
- SEQ ID NO: 20 is a second probe for detecting the SRKN resistance locus of SEQ ID NO: 4.
- SEQ ID NO: 21 is an SRKN resistance allele 1 corresponding to SEQ ID NO: 1.
- SEQ ID NO: 22 is an SRKN resistance allele 2 corresponding to SEQ ID NO: 2.
- SEQ ID NO: 23 is an SRKN resistance allele 3 corresponding to SEQ ID NO: 3.
- SEQ ID NO: 24 is an SRKN resistance allele 4 corresponding to SEQ ID NO: 4.
- SEQ ID NO: 25 is a second SRKN resistance allele motif corresponding to SEQ ID NO: 4.
- SEQ ID NO: 26 is a genomic sequence derived from Glycine max corresponding to the SRKN resistance locus Rmi.
- SEQ ID NO: 27 is a genomic sequence derived from Glycine max corresponding to the SRKN resistance locus on LG-G.
- SEQ ID NO: 28 is a forward PCR primer for amplifying SEQ ID NO: 26.
- SEQ ID NO: 29 is a reverse PCR primer for amplifying SEQ ID NO: 26.
- SEQ ID NO: 30 is a forward PCR primer for amplifying SEQ ID NO: 27.
- SEQ ID NO: 31 is a reverse PCR primer for amplifying SEQ ID NO: 27.
- SEQ ID NO: 32 is a probe for detecting the SRKN resistance locus of SEQ ID NO: 26.
- SEQ ID NO: 33 is a second probe for detecting the SRKN resistance locus of SEQ ID NO: 26.
- SEQ ID NO: 34 is a probe for detecting the SRKN resistance locus of SEQ ID NO: 27.
- SEQ ID NO: 35 is a second probe for detecting the SRKN resistance locus of SEQ ID NO: 27.
- SEQ ID NO: 36 is an SRKN resistance allele 5 corresponding to SEQ ID NO: 26.
- SEQ ID NO: 37 is an SRKN resistance allele 6 corresponding to SEQ ID NO: 27.
- SEQ ID NO: 38 is a hybridization probe for detecting the SRKN resistance locus of SEQ ID NO: 2.
- SEQ ID NO: 39 is a second hybridization probe for detecting the SRKN resistance locus of SEQ ID NO: 2.
- SEQ ID NO: 40 is a hybridization probe for detecting the SRKN resistance locus of SEQ ID NO: 3.
- SEQ ID NO: 41 is a second hybridization probe for detecting the SRKN resistance locus of SEQ ID NO: 3.
- SEQ ID NO: 42 is a forward single base extension probe for detecting the SRKN resistance locus of SEQ ID NO: 2.
- SEQ ID NO: 43 is a reverse single base extension probe for detecting the SRKN resistance locus of SEQ ID NO: 2.
- SEQ ID NO: 44 is a forward single base extension probe for detecting the SRKN resistance locus of SEQ ID NO: 3.
- SEQ ID NO: 45 is a reverse single base extension probe for detecting the SRKN resistance locus of SEQ ID NO: 3.
The definitions and methods provided define the present invention and guide those of ordinary skill in the art in the practice of the present invention. Unless otherwise noted, terms are to be understood according to conventional usage by those of ordinary skill in the relevant art. Definitions of common terms in molecular biology may also be found in
An "allele" refers to an alternative sequence at a particular locus; the length of an allele can be as small as 1 nucleotide base, but is typically larger. Allelic sequence can be denoted as nucleic acid sequence or as amino acid sequence that is encoded by the nucleic acid sequence.
A "locus" is a position on a genomic sequence that is usually found by a point of reference; e.g., a short DNA sequence that is a gene, or part of a gene or intergenic region. The loci of this invention comprise one or more polymorphisms in a population; i.e., alternative alleles present in some individuals.
As used herein, "polymorphism" means the presence of one or more variations of a nucleic acid sequence at one or more loci in a population of one or more individuals. The variation may comprise but is not limited to one or more base changes, the insertion of one or more nucleotides or the deletion of one or more nucleotides. A polymorphism may arise from random processes in nucleic acid replication, through mutagenesis, as a result of mobile genomic elements, from copy number variation and during the process of meiosis, such as unequal crossing over, genome duplication and chromosome breaks and fusions. The variation can be commonly found or may exist at low frequency within a population, the former having greater utility in general plant breeding and the latter may be associated with rare but important phenotypic variation. Useful polymorphisms may include single nucleotide polymorphisms (SNPs), insertions or deletions in DNA sequence (Indels), simple sequence repeats of DNA sequence (SSRs), a restriction fragment length polymorphism, and a tag SNP. A genetic marker, a gene, a DNA-derived sequence, a haplotype, a RNA-derived sequence, a promoter, a 5' untranslated region of a gene, a 3' untranslated region of a gene, microRNA, siRNA, a QTL, a satellite marker, a transgene, mRNA, ds mRNA, a transcriptional profile, and a methylation pattern may comprise polymorphisms. In addition, the presence, absence, or variation in copy number of the preceding may comprise a polymorphism.
As used herein, "marker" means a detectable characteristic that can be used to discriminate between organisms. Examples of such characteristics may include genetic markers, protein composition, protein levels, oil composition, oil levels, carbohydrate composition, carbohydrate levels, fatty acid composition, fatty acid levels, amino acid composition, amino acid levels, biopolymers, pharmaceuticals, starch composition, starch levels, fermentable starch, fermentation yield, fermentation efficiency, energy yield, secondary compounds, metabolites, morphological characteristics, and agronomic characteristics. As used herein, "genetic marker" means polymorphic nucleic acid sequence or nucleic acid feature. A genetic marker may be represented by one or more particular variant sequences, or by a consensus sequence. In another sense, a "genetic marker" is an isolated variant or consensus of such a sequence.
As used herein, "marker assay" means a method for detecting a polymorphism at a particular locus using a particular method, e.g. measurement of at least one phenotype (such as seed color, flower color, or other visually detectable trait), restriction fragment length polymorphism (RFLP), single base extension, electrophoresis, sequence alignment, allelic specific oligonucleotide hybridization (ASO), random amplified polymorphic DNA (RAPD), microarray-based technologies, and nucleic acid sequencing technologies, etc.
As used herein, "typing" refers to any method whereby the specific allelic form of a given soybean genomic polymorphism is determined. For example, a single nucleotide polymorphism (SNP) is typed by determining which nucleotide is present (i.e. an A, G, T, or C). Insertion/deletions (Indels) are determined by determining if the Indel is present. Indels can be typed by a variety of assays including, but not limited to, marker assays.
As used herein, the phrase "adjacent", when used to describe a nucleic acid molecule that hybridizes to DNA containing a polymorphism, refers to a nucleic acid that hybridizes to DNA sequences that directly abut the polymorphic nucleotide base position. For example, a nucleic acid molecule that can be used in a single base extension assay is "adjacent" to the polymorphism.
As used herein, "interrogation position" refers to a physical position on a solid support that can be queried to obtain genotyping data for one or more predetermined genomic polymorphisms.
As used herein, "consensus sequence" refers to a constructed DNA sequence which identifies SNP and Indel polymorphisms in alleles at a locus. Consensus sequence can be based on either strand of DNA at the locus and states the nucleotide base of either one of each SNP in the locus and the nucleotide bases of all Indels in the locus. Thus, although a consensus sequence may not be a copy of an actual DNA sequence, a consensus sequence is useful for precisely designing primers and probes for actual polymorphisms in the locus.
As used herein, the term "single nucleotide polymorphism," also referred to by the abbreviation "SNP," means a polymorphism at a single site wherein said polymorphism constitutes a single base pair change, an insertion of one or more base pairs, or a deletion of one or more base pairs.
As used herein, the term "haplotype" means a chromosomal region within a haplotype window defined by at least one polymorphic molecular marker. The unique marker fingerprint combinations in each haplotype window define individual haplotypes for that window. Further, changes in a haplotype, brought about by recombination for example, may result in the modification of a haplotype so that it comprises only a portion of the original (parental) haplotype operably linked to the trait, for example, via physical linkage to a gene, QTL, or transgene. Any such change in a haplotype would be included in our definition of what constitutes a haplotype so long as the functional integrity of that genomic region is unchanged or improved.
As used herein, the term "haplotype window" means a chromosomal region that is established by statistical analyses known to those of skill in the art and is in linkage disequilibrium. Thus, identity by state between two inbred individuals (or two gametes) at one or more molecular marker loci located within this region is taken as evidence of identity-by-descent of the entire region. Each haplotype window includes at least one polymorphic molecular marker. Haplotype windows can be mapped along each chromosome in the genome. Haplotype windows are not fixed per se and, given the ever-increasing density of molecular markers, this invention anticipates the number and size of haplotype windows to evolve, with the number of windows increasing and their respective sizes decreasing, thus resulting in an ever-increasing degree confidence in ascertaining identity by descent based on the identity by state at the marker loci.
As used herein, "genotype" means the genetic component of the phenotype and it can be indirectly characterized using markers or directly characterized by nucleic acid sequencing. Suitable markers include a phenotypic character, a metabolic profile, a genetic marker, or some other type of marker. A genotype may constitute an allele for at least one genetic marker locus or a haplotype for at least one haplotype window. In some embodiments, a genotype may represent a single locus and in others it may represent a genome-wide set of loci. In another embodiment, the genotype can reflect the sequence of a portion of a chromosome, an entire chromosome, a portion of the genome, and the entire genome.
As used herein, "phenotype" means the detectable characteristics of a cell or organism which can be influenced by gene expression.
As used herein, "linkage" refers to relative frequency at which types of gametes are produced in a cross. For example, if locus A has genes "A" or "a" and locus B has genes "B" or "b" and a cross between parent I with AABB and parent B with aabb will produce four possible gametes where the genes are segregated into AB, Ab, aB and ab. The null expectation is that there will be independent equal segregation into each of the four possible genotypes, i.e. with no linkage ¼ of the gametes will of each genotype. Segregation of gametes into a genotypes differing from ¼ are attributed to linkage.
As used herein, "linkage disequilibrium" is defined in the context of the relative frequency of gamete types in a population of many individuals in a single generation. If the frequency of allele A is p, a is p', B is q and b is q', then the expected frequency (with no linkage disequilibrium) of genotype AB is pq, Ab is pq', aB is p'q and ab is p'q'. Any deviation from the expected frequency is called linkage disequilibrium. Two loci are said to be "genetically linked" when they are in linkage disequilibrium.
As used herein, "quantitative trait locus (QTL)" means a locus that controls to some degree numerically representable traits that are usually continuously distributed.
As used herein, "resistance allele" means the nucleic acid sequence that includes the polymorphic allele associated with resistance to SRKN.
As used herein, the term "soybean" means Glycine max and includes all plant varieties that can be bred with soybean, including wild soybean species.
As used herein, the term "comprising" means "including but not limited to".
As used herein, the term "elite line" means any line that has resulted from breeding and selection for superior agronomic performance. Non-limiting examples of elite soybean varieties that are commercially available to farmers or soybean breeders include AG00802, A0868, AG0902, A1923, AG2403, A2824, A3704, A4324, A5404, AG5903 and AG6202 (Asgrow Seeds, Des Moines, Iowa, USA); BPR0144RR, BPR 4077NRR and BPR 4390NRR (Bio Plant Research, Camp Point, Illinois, USA); DKB17-51 and DKB37-51 (DeKalb Genetics, DeKalb, Illinois, USA); and DP 4546 RR, and DP 7870 RR (Delta & Pine Land Company, Lubbock, Texas, USA); JG 03R501, JG 32R606C ADD and JG 55R503C (JGL Inc., Greencastle, Indiana, USA); NKS13-K2 (NK Division of Syngenta Seeds, Golden Valley, Minnesota, USA); 90M01, 91M30, 92M33, 93M11, 94M30, 95M30 and 97B52 (Pioneer Hi-Bred International, Johnston, Iowa, USA); SG4771NRR and SG5161NRR/STS (Soygenetics, LLC, Lafayette, Indiana, USA); S00-K5, S11-L2, S28-Y2, S43-B1, S53-A1, S76-L9 and S78-G6 (Syngenta Seeds, Henderson, Kentucky, USA). An elite plant is a representative plant from an elite variety.
The present invention provides SNP DNA markers useful for screening for the SRKN resistance QTL, located on Linkage Group O and Linkage Group G (
The present invention also provides a soybean plant comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 21-25, 36-37 and complements thereof. The present invention also provides a soybean plant comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-4, 25, and 26 fragments thereof, and complements of both. The present invention also provides a soybean plant comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 5-20 and 27-34, fragments thereof, and complements of both. In one aspect, the soybean plant comprises 2, 3, or 4 nucleic acid sequences selected from the group consisting of SEQ ID NOs: 21-25 and 36-37 and complements thereof. In another aspect, the soybean plant comprises 2, 3, or 4 nucleic acid sequences selected from the group consisting of SEQ ID NOs: 1-4, 26 and 27, fragments thereof, and complements of both. In a further aspect, the soybean plant comprises 2, 3, or 4 nucleic acid sequences selected from the group consisting of SEQ ID NOs: 5-20 and 27-34, fragments thereof, and complements of both.
As used herein, SRKN refers to any SRKN variant or isolate. A soybean plant of the present invention can be resistant to one or more nematodes capable of causing or inducing SRKN. In one aspect, the present invention provides plants resistant to SRKN as well as methods and compositions for screening soybean plants for resistance or susceptibility to SRKN, caused by the genus Meloidogyne. In a preferred aspect, the present invention provides methods and compositions for screening soybean plants for resistance or susceptibility to Meloidogyne incognita.
The present invention further provides that the selected plant is from the group consisting of members of the genus Glycine, more specifically from the group consisting of Glycine arenaria, Glycine argyrea, Glycine canescens, Glycine clandestine, Glycine curvata, Glycine cyrtoloba, Glycine falcate, Glycine latifolia, Glycine latrobeana, Glycine max, Glycine microphylla, Glycine pescadrensis, Glycine pindanica, Glycine rubiginosa, Glycine soja, Glycine sp., Glycine stenophita, Glycine tabacina and Glycine tomentella
Plants of the present invention can be a soybean plant that is very resistant, resistant, substantially resistant, mid-resistant, comparatively resistant, partially resistant, mid-susceptible, or susceptible.
In a preferred aspect, the present invention provides a soybean plant to be assayed for resistance or susceptibility to SRKN by any method to determine whether a soybean plant is very resistant, resistant, substantially resistant, mid-resistant, comparatively resistant, partially resistant, mid-susceptible, or susceptible.
In one aspect, the present invention provides methods and compositions for screening soybean plants for resistance, immunity, or susceptibility to SRKN, caused by the species Meloidogyne incognita. In a preferred aspect, the present invention provides methods and compositions for screening soybean plants for resistance, immunity, or susceptibility to Meloidogyne incognita. Soybean plants are phenotyped and scored for resistance, immunity, or susceptibility to SRKN based upon number of galls or egg masses (
The SRKN resistance QTL of the present invention may be introduced into an elite Glycine max line. An "elite line" is any line that has resulted from breeding and selection for superior agronomic performance.
The SRKN resistance QTL of the present invention may also be introduced into an elite Glycine max transgenic plant that contains one or more genes for herbicide tolerance, increased yield, insect control, fungal disease resistance, virus resistance, nematode resistance, bacterial disease resistance, mycoplasma disease resistance, modified oils production, high oil production, high protein production, germination and seedling growth control, enhanced animal and human nutrition, low raffinose, environmental stress resistant, increased digestibility, industrial enzymes, pharmaceutical proteins, peptides and small molecules, improved processing traits, improved flavor, nitrogen fixation, hybrid seed production, reduced allergenicity, biopolymers, and biofuels among others. These agronomic traits can be provided by the methods of plant biotechnology as transgenes in Glycine max.
A disease resistant QTL allele or alleles can be introduced from any plant that contains that allele (donor) to any recipient soybean plant. In one aspect, the recipient soybean plant can contain additional SRKN resistant loci. In another aspect, the recipient soybean plant can contain a transgene. In another aspect, while maintaining the introduced QTL, the genetic contribution of the plant providing the disease resistant QTL can be reduced by back-crossing or other suitable approaches. In one aspect, the nuclear genetic material derived from the donor material in the soybean plant can be less than or about 50%, less than or about 25%, less than or about 13%, less than or about 5%, 3%, 2% or 1%, but that genetic material contains the SRKN resistant locus or loci of interest.
It is further understood that a soybean plant of the present invention may exhibit the characteristics of any relative maturity group. In an aspect, the maturity group is selected from the group consisting of 000, 00, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10.
An allele of a QTL can comprise multiple genes or other genetic factors even within a contiguous genomic region or linkage group, such as a haplotype. As used herein, an allele of a resistance locus can therefore encompass more than one gene or other genetic factor where each individual gene or genetic component is also capable of exhibiting allelic variation and where each gene or genetic factor is also capable of eliciting a phenotypic effect on the quantitative trait in question. In an aspect of the present invention the allele of a QTL comprises one or more genes or other genetic factors that are also capable of exhibiting allelic variation. The use of the term "an allele of a QTL" is thus not intended to exclude a QTL that comprises more than one gene or other genetic factor. Specifically, an "allele of a QTL" in the present in the invention can denote a haplotype within a haplotype window wherein a phenotype can be pest resistance. A haplotype window is a contiguous genomic region that can be defined, and tracked, with a set of one or more polymorphic markers wherein the polymorphisms indicate identity by descent. A haplotype within that window can be defined by the unique fingerprint of alleles at each marker. As used herein, an allele is one of several alternative forms of a gene occupying a given locus on a chromosome. When all the alleles present at a given locus on a chromosome are the same, that plant is homozygous at that locus. If the alleles present at a given locus on a chromosome differ, that plant is heterozygous at that locus. Plants of the present invention may be homozygous or heterozygous at any particular SRKN resistance locus or for a particular polymorphic marker.
The present invention also provides for parts of the plants of the present invention. Plant parts, without limitation, include seed, endosperm, ovule and pollen. In a particularly preferred aspect of the present invention, the plant part is a seed.
The present invention also provides a container of soybean in which greater than 50%, 60%, 70%, 80%, 90%, 95%, or 99% of the seeds comprising the SRKN resistant loci where one or more alleles at the loci are selected from the group consisting of SRKN resistant allele 1, SRKN resistance allele 2, SRKN resistance allele 3, or SRKN resistance allele 4.
The container of soybean seeds can contain any number, weight, or volume of seeds. For example, a container can contain at lest, or greater than, about 10, 25, 50, 100, 200, 300, 400, 500, 600, 700, 80, 90, 1000, 1500, 2000, 2500, 3000, 3500, 4000 or more seeds. In another aspect, a container can contain about, or greater than about, 1 gram, 5 grams, 10 grams, 15 grams, 20 grams, 25 grams, 50 grams, 100 grams, 250 grams, 500 grams, or 1000 grams of seeds. Alternatively, the container can contain at least, or greater than, about 0 ounces, 1 ounce, 5 ounces, 10 ounces, 1 pound, 2 pounds, 3 pounds, 4 pounds, 5 pounds, 10 pounds, 15 pounds, 20 pounds, 25 pounds, or 50 pounds or more seeds.
Containers of soybean seeds can be any container available in the art. For example, a container can be a box, a bag, a can, a packet, a pouch, a tape roll, a pail, or a tube.
In another aspect, the seeds contained in the containers of soybean seeds can be treated or untreated soybean seeds. In one aspect, the seeds can be treated to improve germination, for example, by priming the seeds, or by disinfection to protect against seed-born pathogens. In another aspect, seeds can be coated with any available coating to improve, for example, plantability, seed emergence, and protection against seed-born pathogens. Seed coating can be any form of seed coating including, but not limited to, pelleting, film coating, and encrustments.
Plants or parts thereof of the present invention may be grown in culture and regenerated. Methods for the regeneration of Glycine max plants from various tissue types and methods for the tissue culture of Glycine max are known in the art (See, for example,
The disease resistant effect of the QTL can vary based on the individual genotype and on the environmental conditions in which the disease resistance effect is measured. It is within the skill of those in the art of plant breeding and without undue experimentation to use the methods described herein to select from a population of plants or from a collection of parental genotypes those that when containing a disease locus result in enhanced disease resistance relative to the genotype.
The present invention includes a method of introgressing an allele into a soybean plant comprising (A) crossing at least one first soybean plant comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 21 through 25, 36 and 37 with at least one second soybean plant in order to form a population, (B) screening the population with one or more nucleic acid markers to determine if one or more soybean plants from the population contains the nucleic acid sequence, and (C) selecting from the population one or more soybean plants comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 21 through 25, 36, and 37.
The present invention includes a method of introgressing an allele into a soybean plant comprising: (A) crossing at least one SRKN resistant soybean plant with at least one SRKN sensitive plant in order to form a population; (B) screening said population with one or more nucleic acid markers to determine if one or more soybean plants from said population contains the SRKN resistance locus on LG-O or LG-G.
The present invention includes isolated nucleic acid molecules. Such molecules include those nucleic acid molecules capable of detecting a polymorphism genetically or physically linked to a SRKN locus. Such molecules can be referred to as markers Additional markers can be obtained that are linked to SRKN resistance locus by available techniques. In one aspect, the nucleic acid molecule is capable of detecting the presence or absence of a marker located less than 30, 25, 20, 15, 10, 5, 2, or 1 centimorgans from the SRKN resistance locus. In another aspect, a marker exhibits a LOD score of 2 or greater, 3 or greater, or 4 or greater with SRKN measuring using Qgene Version 2.23 (1996) and default parameters. In another aspect, the nucleic acid molecule is capable of detecting a marker in a locus selected from the group SRKN resistance locus Rmi. In another aspect, the nucleic acid molecule is capable of detecting a marker in the SRKN resistance QTL. In a further aspect, a nucleic acid molecule is selected from the group consisting of SEQ ID NOs: 1 through 4, 26 and 27, fragments thereof, complements thereof, and nucleic acid molecules capable of specifically hybridizing to one or more of these nucleic acid molecules.
In a preferred aspect, a nucleic acid molecule of the present invention includes those that will specifically hybridize to one or more of the nucleic acid molecules set forth in SEQ ID NO: 1 through SEQ ID NO: 45 or complements thereof or fragments of either under moderately stringent conditions, for example at about 2.0x SSC and about 65°C. In a particularly preferred aspect, a nucleic acid of the present invention will specifically hybridize to one or more of the nucleic acid molecules set forth in SEQ ID NO: 1 through SEQ ID NO: 45 or complements or fragments of either under high stringency conditions. In one aspect of the present invention, a preferred marker nucleic acid molecule of the present invention has the nucleic acid sequence set forth in SEQ ID NO: 1 through SEQ ID NO: 45 or complements thereof or fragments of either. In another aspect of the present invention, a preferred marker nucleic acid molecule of the present invention shares between 80% and 100% or 90% and 100% sequence identity with the nucleic acid sequence set forth in SEQ ID NO: 1 through SEQ ID NO: 45 or complement thereof or fragments of either. In a further aspect of the present invention, a preferred marker nucleic acid molecule of the present invention shares between 95% and 100% sequence identity with the sequence set forth in SEQ ID NO: 1 through SEQ ID NO: 45 or complement thereof or fragments of either. In a more preferred aspect of the present invention, a preferred marker nucleic acid molecule of the present invention shares between 98% and 100% sequence identity with the nucleic acid sequence set forth in SEQ ID NO: 1 through SEQ ID NO: 45 or complement thereof or fragments of either.
Nucleic acid molecules or fragments thereof are capable of specifically hybridizing to other nucleic acid molecules under certain circumstances. As used herein, two nucleic acid molecules are capable of specifically hybridizing to one another if the two molecules are capable of fonning an anti-parallel, double-stranded nucleic acid structure. A nucleic acid molecule is the "complement" of another nucleic acid molecule if they exhibit complete complementarity. As used herein, molecules are exhibit "complete complementarity" when every nucleotide of one of the molecules is complementary to a nucleotide of the other. Two molecules are "minimally complementary" if they can hybridize to one another with sufficient stability to permit them to remain annealed to one another under at least conventional "low-stringency" conditions. Similarly, the molecules are "complementary" if they can hybridize to one another with sufficient stability to permit them to remain annealed to one another under conventional "high-stringency" conditions. Conventional stringency conditions are described by
As used herein, a substantially homologous sequence is a nucleic acid sequence that will specifically hybridize to the complement of the nucleic acid sequence to which it is being compared under high stringency conditions. The nucleic-acid probes and primers of the present invention can hybridize under stringent conditions to a target DNA sequence. The term "stringent hybridization conditions" is defined as conditions under which a probe or primer hybridizes specifically with a target sequence(s) and not with non-target sequences, as can be determined empirically. The term "stringent conditions" is functionally defined with regard to the hybridization of a nucleic-acid probe to a target nucleic acid (i.e., to a particular nucleic-acid sequence of interest) by the specific hybridization procedure discussed in Sambrook et al., 1989, at 9.52-9.55. See also, Sambrook et al., 1989 at 9.47-9.52, 9.56-9.58;
It is contemplated that lower stringency hybridization conditions such as lower hybridization and/or washing temperatures can be used to identify related sequences having a lower degree of sequence similarity if specificity of binding of the probe or primer to target sequence(s) is preserved. Accordingly, the nucleotide sequences of the present invention can be used for their ability to selectively form duplex molecules with complementary stretches of DNA, RNA, or cDNA fragments.
A fragment of a nucleic acid molecule can be any sized fragment and illustrative fragments include fragments of nucleic acid sequences set forth in SEQ ID NO: 1 to SEQ ID NO: 45 and complements thereof. In one aspect, a fragment can be between 15 and 25, 15 and 30, 15 and 40, 15 and 50, 15 and 100, 20 and 25, 20 and 30, 20 and 40, 20 and 50, 20 and 100, 25 and 30, 25 and 40, 25 and 50, 25 and 100, 30 and 40, 30 and 50, and 30 and 100. In another aspect, the fragment can be greater than 10, 15, 20, 25, 30, 35, 40, 50, 100, or 250 nucleotides.
Genetic markers of the present invention include "dominant" or "codominant" markers. "Codominant markers" reveal the presence of two or more alleles (two per diploid individual). "Dominant markers" reveal the presence of only a single allele. The presence of the dominant marker phenotype (e.g., a band of DNA) is an indication that one allele is present in either the homozygous or heterozygous condition. The absence of the dominant marker phenotype (e.g., absence of a DNA band) is merely evidence that "some other" undefined allele is present. In the case of populations where individuals are predominantly homozygous and loci are predominantly dimorphic, dominant and codominant markers can be equally valuable. As populations become more heterozygous and multiallelic, codominant markers often become more informative of the genotype than dominant markers.
Markers, such as single sequence repeat markers (SSR), AFLP markers, RFLP markers, RAPD markers, phenotypic markers, SNPs, isozyme markers, microarray transcription profiles that are genetically linked to or correlated with alleles of a QTL of the present invention can be utilized (Walton, 1993; Burow et al. 1988). Methods to identify such markers are known in the art.
The detection of polymorphic sites in a sample of DNA, RNA, or cDNA may be facilitated through the use of nucleic acid amplification methods. Such methods specifically increase the concentration of polynucleotides that span the polymorphic site, or include that site and sequences located either distal or proximal to it. Such amplified molecules can be readily detected by gel electrophoresis, fluorescence detection methods, or other means.
A method of achieving such amplification employs the polymerase chain reaction (PCR) (
In a preferred method for detecting polymorphisms, SNPs and Indels can be detected by methods disclosed in
A useful assay is available from AB Biosystems as the Taqman® assay which employs four synthetic oligonucleotides in a single reaction that concurrently amplifies the soybean genomic DNA, discriminates between the alleles present, and directly provides a signal for discrimination and detection. Two of the four oligonucleotides serve as PCR primers and generate a PCR product encompassing the polymorphism to be detected. Two others are allele-specific fluorescence-resonance-energy-transfer (FRET) probes. In the assay, two FRET probes bearing different fluorescent reporter dyes are used, where a unique dye is incorporated into an oligonucleotide that can anneal with high specificity to only one of the two alleles. Useful reporter dyes include, but are not limited to, 6-carboxy-4,7,2',7'-tetrachlorofluorecein (TET), 2'-chloro-7'-phenyl-1,4-dichloro-6-carboxyfluorescein (VIC) and 6-carboxyfluorescein phosphoramidite (FAM). A useful quencher is 6-carboxy-N,N,N',N'-tetramethylrhodamine (TAMRA). Additionally, the 3'end of each FRET probe is chemically blocked so that it can not act as a PCR primer. Also present is a third fluorophore used as a passive reference, e.g., rhodamine X (ROX) to aid in later normalization of the relevant fluorescence values (correcting for volumetric errors in reaction assembly). During each cycle of the PCR, the FRET probes anneal in an allele-specific manner to the template DNA molecules. Annealed (but not non-annealed) FRET probes are degraded by TAQ DNA polymerase as the enzyme encounters the 5' end of the annealed probe, thus releasing the fluorophore from proximity to its quencher, wherein the fluorescence of each of the two fluorescers, as well as that of the passive reference, is determined fluorometrically. The normalized intensity of fluorescence for each of the two dyes will be proportional to the amounts of each allele initially present in the sample, and thus the genotype of the sample can be inferred.
For the purpose of QTL mapping, the markers included should be diagnostic of origin in order for inferences to be made about subsequent populations. SNP markers are ideal for mapping because the likelihood that a particular SNP allele is derived from independent origins in the extant populations of a particular species is very low. As such, SNP markers are useful for tracking and assisting introgression of QTLs, particularly in the case of haplotypes which are closely linked alleles inherited as a unit.
The genetic linkage of additional marker molecules can be established by a gene mapping model such as, without limitation, the flanking marker model reported by Lander et al. (
A maximum likelihood estimate (MLE) for the presence of a marker is calculated, together with an MLE assuming no QTL effect, to avoid false positives. A log10 of an odds ratio (LOD) is then calculated as: LOD = log10 (MLE for the presence of a QTL/MLE given no linked QTL). The LOD score essentially indicates how much more likely the data are to have arisen assuming the presence of a QTL versus in its absence. The LOD threshold value for avoiding a false positive with a given confidence, say 95%, depends on the number of markers and the length of the genome. Graphs indicating LOD thresholds are set forth in Lander et al. (1989), and further described by
Additional models can be used. Many modifications and alternative approaches to interval mapping have been reported, including the use of non-parametric methods (
Selection of appropriate mapping populations is important to map construction. The choice of an appropriate mapping population depends on the type of marker systems employed (
An F2 population is the first generation of selfing. Usually a single F1 plant is selfed to generate a population segregating for all the genes in Mendelian (1:2:1) fashion. Maximum genetic information is obtained from a completely classified F2 population using a codominant marker system (
Recombinant inbred lines (RIL) (genetically related lines; usually >F5, developed from continuously selfing F2 lines towards homozygosity) can be used as a mapping population. Information obtained from dominant markers can be maximized by using RIL because all loci are homozygous or nearly so. Under conditions of tight linkage (i.e., about <10% recombination), dominant and co-dominant markers evaluated in RIL populations provide more information per individual than either marker type in backcross populations (
Backcross populations (e.g., generated from a cross between a successful variety (recurrent parent) and another variety (donor parent) carrying a trait not present in the former) can be utilized as a mapping population. A series of backcrosses to the recurrent parent can be made to recover most of its desirable traits. Thus a population is created consisting of individuals nearly like the recurrent parent but each individual carries varying amounts or mosaic of genomic regions from the donor parent. Backcross populations can be useful for mapping dominant markers if all loci in the recurrent parent are homozygous and the donor and recurrent parent have contrasting polymorphic marker alleles (Reiter et al. 1992). Information obtained from backcross populations using either codominant or dominant markers is less than that obtained from F2 populations because one, rather than two, recombinant gametes are sampled per plant. Backcross populations, however, are more informative (at low marker saturation) when compared to RILs as the distance between linked loci increases in RIL populations (i.e. about .15% recombination). Increased recombination can be beneficial for resolution of tight linkages, but may be undesirable in the construction of maps with low marker saturation.
Near-isogenic lines (NIL) created by many backcrosses to produce an array of individuals that are nearly identical in genetic composition except for the trait or genomic region under interrogation can be used as a mapping population. In mapping with NILs, only a portion of the polymorphic loci are expected to map to a selected region.
Bulk segregant analysis (BSA) is a method developed for the rapid identification of linkage between markers and traits of interest (
Plants of the present invention can be part of or generated from a breeding program. The choice of breeding method depends on the mode of plant reproduction, the heritability of the trait(s) being improved, and the type of cultivar used commercially (e.g., F1 hybrid cultivar, pureline cultivar, etc). A cultivar is a race or variety of a plant species that has been created or selected intentionally and maintained through cultivation.
Selected, non-limiting approaches for breeding the plants of the present invention are set forth below. A breeding program can be enhanced using marker assisted selection (MAS) on the progeny of any cross. It is understood that nucleic acid markers of the present invention can be used in a MAS (breeding) program. It is further understood that any commercial and non-commercial cultivars can be utilized in a breeding program. Factors such as, for example, emergence vigor, vegetative vigor, stress tolerance, disease resistance, branching, flowering, seed set, seed size, seed density, standability, and threshability etc. will generally dictate the choice.
For highly heritable traits, a choice of superior individual plants evaluated at a single location will be effective, whereas for traits with low heritability, selection should be based on mean values obtained from replicated evaluations of families of related plants. Popular selection methods commonly include pedigree selection, modified pedigree selection, mass selection, and recurrent selection. In a preferred aspect, a backcross or recurrent breeding program is undertaken.
Breeding lines can be tested and compared to appropriate standards in environments representative of the commercial target area(s) for two or more generations. The best lines are candidates for new commercial cultivars; those still deficient in traits may be used as parents to produce new populations for further selection.
Pedigree breeding and recurrent selection breeding methods can be used to develop cultivars from breeding populations. Breeding programs combine desirable traits from two or more cultivars or various broad-based sources into breeding pools from which cultivars are developed by selfing and selection of desired phenotypes. New cultivars can be evaluated to determine which have commercial potential.
Backcross breeding has been used to transfer genes for a simply inherited, highly heritable trait into a desirable homozygous cultivar or inbred line, which is the recurrent parent. The source of the trait to be transferred is called the donor parent. After the initial cross, individuals possessing the phenotype of the donor parent are selected and repeatedly crossed (backcrossed) to the recurrent parent. The resulting plant is expected to have most attributes of the recurrent parent (e.g., cultivar) and, in addition, the desirable trait transferred from the donor parent.
The single-seed descent procedure in the strict sense refers to planting a segregating population, harvesting a sample of one seed per plant, and using the one-seed sample to plant the next generation. When the population has been advanced from the F2 to the desired level of inbreeding, the plants from which lines are derived will each trace to different F2 individuals. The number of plants in a population declines each generation due to failure of some seeds to germinate or some plants to produce at least one seed. As a result, not all of the F2 plants originally sampled in the population will be represented by a progeny when generation advance is completed.
Descriptions of other breeding methods that are commonly used for different traits and crops can be found in one of several reference books (
As used herein, a "nucleic acid molecule", be it a naturally occurring molecule or otherwise may be "substantially purified", if desired, referring to a molecule separated from substantially all other molecules normally associated with it in its native state. More preferably a substantially purified molecule is the predominant species present in a preparation. A substantially purified molecule may be greater than 60% free, preferably 75% free, more preferably 90% free, and most preferably 95% free from the other molecules (exclusive of solvent) present in the natural mixture. The term "substantially purified" is not intended to encompass molecules present in their native state.
The agents of the present invention will preferably be "biologically active" with respect to either a structural attribute, such as the capacity of a nucleic acid to hybridize to another nucleic acid molecule, or the ability of a protein to be bound by an antibody (or to compete with another molecule for such binding). Alternatively, such an attribute may be catalytic, and thus involve the capacity of the agent to mediate a chemical reaction or response.
The agents of the present invention may also be recombinant. As used herein, the term recombinant means any agent (e.g. DNA, peptide etc.), that is, or results, however indirect, from human manipulation of a nucleic acid molecule.
The agents of the present invention may be labeled with reagents that facilitate detection of the agent (e.g. fluorescent labels (
Having now generally described the invention, the same will be more readily understood through reference to the following examples which are provided by way of illustration, and are not intended to be limiting of the present invention, unless specified.
SNP markers for the SRKN resistance QTL Rmi were identified by screening nucleic acid sequence flanking the Rmi locus in linkage group (LG) O in SRKN resistant and susceptible soybean lines.
Soybean plants were phenotyped and scored according to the number of galls or egg masses present on the plant roots (Table 1). The greater the number of galls or egg masses, the more susceptible a plant is. The average gall index was then calculated and plants were assigned a SRKN rating of resistant, moderately resistant, moderately susceptible, or susceptible (Table 2).
In order to test the utility and predictability of the SRKN resistance markers of the present invention, 16 publicly available soybean lines with reported resistance and susceptibility reactions to SRKN were genotyped (Table 3). The haplotypes of the known resistant and susceptible varieties were found to be consistent using the SNP markers NS0094902, NS0097935, NS0135583, and NS0102683. The four SNP markers were found to be predictive of SRKN resistance in publicly available soybean germplasm.
Table 4 provides further validation of the four SNP markers. Fourteen public entries with reported SRKN resistance responses were genotyped. In addition, Palmetto was used as the SRKN resistant control and a SRKN susceptible line was used as a negative control. By using the four SNP markers, the haplotypes of twelve of the varieties were found to be consistent with that of the resistant control. One variety, G93-9223, had a different allelic state at only one of the markers, NS0102683. Two varieties, Musen and LS97-1610, had genotypes corresponding to the susceptible type. SRKN reaction was based on reported reaction rather than phenotyping in this example. However, the SNP markers were predictive of the SRKN reaction of the majority of lines and have utility in predicting soybean SRKN reactions.
Five public entries with reported SRKN susceptibility were genotyped (Table 5) with Palmetto as the SRKN resistant control and a susceptible line as the negative control. The haplotypes of the five entries were found to be consistent with that of the susceptible control.
Four SNP markers, NS0094902, NS0097935, NS0135583, and NS0102683, were found to be predictive of the SRKN QTL (Rmi) in public soybean varieties.
The SRKN resistance SNP markers were validated using Monsanto proprietary lines with known resistance and susceptibility reactions to SRKN disease. Eight MR/R varieties (Table 6) and 17 susceptible varieties (Table 7) were used. Disease ratings are based on average gall index scores as previously described in Table 2. In this example, phenotyping was conducted, and SRKN classification was based on either greenhouse testing or greenhouse testing with field testing.
Eight Monsanto proprietary varieties were phenotyped. Based on gall index ratings, these lines were classified as resistant/moderately resistant. Leaf tissue was genotyped. The haplotype of the eight varieties were found to be consistent with that of the resistant control Palmetto (Table 6).
Seventeen Monsanto proprietary varieties were phenotyped and rated as susceptible based on gall index ratings. Leaf tissue was genotyped, and the haplotype of the 17 varieties was found to be consistent with that of the susceptible type control (Table 7).
The four SNP markers were found to be useful for detecting the SRKN resistance QTL (Rmi) in Monsanto proprietary lines.
Two sources for SRKN resistance are Palmetto and PI96354. The SNP markers of the present invention can be used to distinguish between Palmetto and PI 96354 as the source of the SRKN resistance QTL (Rmi) (Table 8). The information provided by the markers can be useful in pedigree analyses.
SNP markers linked to SRKN resistance QTL on LG-O and LG-G were developed through the use of bacterial artificial chromosome (BAC) ends and SSR-containing genomic DNA clones. Three SNPs were identified in Satt358 source-sequences located near the major SRKN resistance QTL on LG-O. Three SNPs were identified in Satt199 source- sequences located near the minor SRKN resistance QTL on LG-G.
SNP genotype analysis was performed with 94 F2 plants from the cross of P196354 x Bossier. DNA was extracted from individual parental genotypes and individual field- grown F2 plants. F2:3 lines were evaluated in the greenhouse for SRKN galling.
A direct hybridization (DH) assay was developed and optimized using SNP358 from Satt358 source sequence on LG-O. Allele-specific oligonucleotide probes corresponding to each of PI 96354 and Bossier sequence variants were designed so that the two polymorphic bases at the 83 and 91 base position were included in the probe. The ASO358-TA probe was specific for the PI 96354 haploype and the ASO358-AG probe was specific for the Bossier haplotype. For the minor SRKN resistance QTL on LG-G, a DH assay was developed with SNP199 from the Satt199 source sequence of LG-G. The ASO199-AA probe was specific for the PI 96354 haplotype and the ASO199-TG probe was specific for the Bossier haplotype. The effectiveness of SNP358 and SNP199 were compared with their respective SSR markers, Satt358 and Satt199 by assaying 12 SRKN resistant and 12 SRKN susceptible soybean lines. Genotyping was conducted by a multiplex assay in which reaction specific microspheres fluoresce at different frequencies. Table 9 provides the results of the assays. Eleven of the 12 SRKN resistant lines carrying a 200- bp allele at Satt358 have approximately a 10 x higher positive signal for the ASO358-TA probe specific to the PI 96354 allele (resistant) than the ASO358-AG probe specific to the Bossier allele (susceptible). All SRKN susceptible lines carrying the 192-bp allele at Satt358 had a positive signal for the Bossier-specific ASO358-AG probe. Susceptible soybean line FC 33243 has a unique haplotype (AA) at SNP358. Therefore, SNP358 has three SNP haplotypes TA, AG, and AA in 24 soybean lines.
Oligonucleotides can also be used to detect or type the polymorphisms associated with SRKN resistance disclosed herein by hybridization-based SNP detection methods. Oligonucleotides capable of hybridizing to isolated nucleic acid sequences which include the polymorphism are provided. It is within the skill of the art to design assays with experimentally determined stringency to discriminate between the allelic states of the polymorphisms presented herein. Exemplary assays include Southern blots, Northern blots, microarrays, in situ hybridization, and other methods of polymorphism detection based on hybridization. Exemplary oligonucleotides for use in hybridization-based SNP detection are provided in Table 10. These oligonucleotides can be detectably labeled with radioactive labels, fluorophores, or other chemiluminescent means to facilitate detection of hybridization to samples of genomic or amplified nucleic acids derived from one or more soybean plants using methods known in the art.
Oligonucleotides can also be used to detect or type the polymorphisms associated with SRKN resistance disclosed herein by single base extension (SBE)-based SNP detection methods. Exemplary oligonucleotides for use in SBE-based SNP detection are provided in Table 11. SBE methods are based on extension of a nucleotide primer that is hybridized to sequences adjacent to a polymorphism to incorporate a detectable nucleotide residue upon extension of the primer. It is also anticipated that the SBE method can use three synthetic oligonucleotides. Two of the oligonucleotides serve as PCR primers and are complementary to the sequence of the locus which flanks a region containing the polymorphism to be assayed. Exemplary PCR primers that can be used to type polymorphisms disclosed in this invention are provided in
Having illustrated and described the principles of the present invention, it should be apparent to persons skilled in the art that the invention can be modified in arrangement and detail without departing from such principles. We claim all modifications that are within the spirit and scope of the appended claims.
All publications and published patent documents cited in this specification are incorporated herein by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
- <110> Narvel, James Concibido, Vergel Cerny, Liesa Tamulonis, John P Hancock, Floyd Dougherty, Richard Boerma, Henry Roger Ha, Bo-Keun
- <120> Methods and Compositions for Selecting Soybean Plants Resistant to Southern Root Knot Nematode
- <130> 46-21(53775)
- <140>
<141>
- <150>
US 61/055519 <151> 2008-05-23
- <150>
US 60/9638736 <151> 2007-08-07
- <160> 45
- <210> 1
<211> 532
<212> DNA
<213> Glycine max
- <400> 1
- <210> 2
<211> 703
<212> DNA
<213> Glycine max
- <220>
<221> unsure
<222> (693)..(693)
<223> n = a,t,c, or g
- <220>
<221> unsure
<222> (1)..(703)
<223> unsure at all n locations
- <400> 2
- <210> 3
<211> 792
<212> DNA
<213> Glycine max
- <400> 3
- <210> 4
<211> 835
<212> DNA
<213> Glycine max
- <220>
<221> unsure
<222> (692)..(692)
<223> n = a,t,c, or g
- <220>
<221> unsure
<222> (1)..(835)
<223> unsure at all n locations
- <400> 4
- <210> 5
<211> 21
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic primer
- <400> 5
tcctccccct ttttgttgtt g 21
- <210> 6
<211> 22
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic primer
- <400> 6
tgcaagcttt ggttgaattg tt 22
- <210> 7
<211> 28
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic primer
- <400> 7
aaattaatta ggacatttcg ttttgtca 28
- <210> 8
<211> 29
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic primer
- <400> 8
ctagtttttt aattttttct tgtggcatt 29
- <210> 9
<211> 27
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic primer
- <400> 9
aaaacagtgt gtataatccc aacaaca 27
- <210> 10
<211> 20
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic primer
- <400> 10
ggaaggcagt gcaagcaact 20
- <210> 11
<211> 28
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic primer
- <400> 11
cattgcgtca ctctaacata tgtattca 28
- <210> 12
<211> 28
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic primer
- <400> 12
tgtaattcat cattgacatg tttaggaa 28
- <210> 13
<211> 15
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 13
tttatcacca tgccc 15
- <210> 14
<211> 19
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 14
ttgttgttgt ttatttatc 19
- <210> 15
<211> 18
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 15
caagagaaaa gtcaatct 18
- <210> 16
<211> 18
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 16
caagagaaaa gtgaatct 18
- <210> 17
<211> 15
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 17
tacacggttc atcta 15
- <210> 18
<211> 19
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 18
tgtacataca cagttcatc 19
- <210> 19
<211> 18
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 19
caaagaaacg tagataag 18
- <210> 20
<211> 16
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 20
aaacgtggat aagaaa 16
- <210> 21
<211> 34
<212> DNA
<213> Artificial Sequence
- <220>
<223> artificial sequence
- <400> 21
tgttgttgtt gtttatcacc atgcccctca aaca 34
- <210> 22
<211> 35
<212> DNA
<213> Artificial Sequence
- <220>
<223> artificial sequence
- <400> 22
gtcacaagag aaaagtgaat cttaatgtat gtaat 35
- <210> 23
<211> 35
<212> DNA
<213> Artificial Sequence
- <220>
<223> artificial sequence
- <400> 23
acattattag atgaaccgtg tatgtacata cattc 35
- <210> 24
<211> 35
<212> DNA
<213> Artificial Sequence
- <220>
<223> artificial sequence
- <400> 24
ttcaacaaag aaacgtggat aagaaatgtt tccta 35
- <210> 25
<211> 35
<212> DNA
<213> Artificial Sequence
- <220>
<223> artificial sequence
- <400> 25
ttcaacaaag aaacgtagat aagaaatgtt tccta 35
- <210> 26
<211> 439
<212> DNA
<213> Glycine max
- <400> 26
- <210> 27
<211> 378
<212> DNA
<213> Glycine max
- <400> 27
- <210> 28
<211> 23
<212> DNA
<213> Artificial Sequence
- <220>
<223> artificial sequence
- <400> 28
gaattttatt ttgaacgcct ttc 23
- <210> 29
<211> 23
<212> DNA
<213> Artificial Sequence
- <220>
<223> artificial sequence
- <400> 29
gcagagtgcg gagtaattaa act 23
- <210> 30
<211> 24
<212> DNA
<213> Artificial Sequence
- <220>
<223> artificial sequence
- <400> 30
aaataggcaa aacaccgtat gaaa 24
- <210> 31
<211> 21
<212> DNA
<213> Artificial Sequence
- <220>
<223> artificial sequence
- <400> 31
gggcaaaact taacaggcaa g 21
- <210> 32
<211> 23
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 32
agcgcatagc taagaattaa agg 23
- <210> 33
<211> 23
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 33
agcgcacagc taagtattaa agg 23
- <210> 34
<211> 20
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 34
taatattaga ctgtaaacgt 20
- <210> 35
<211> 19
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 35
tattattagg ctgtaaacg 19
- <210> 36
<211> 35
<212> DNA
<213> Artificial Sequence
- <220>
<223> artificial sequence
- <400> 36
gctatccttt aattcttagc tatgcgcttt atgta 35
- <210> 37
<211> 33
<212> DNA
<213> Artificial Sequence
- <220>
<223> artificial sequence
- <400> 37
ttattattat taatattaga ctgtaaacgt ttt 33
- <210> 38
<211> 16
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 38
aaaagtgaat cttaat 16
- <210> 39
<211> 16
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 39
aaaagtcaat cttaat 16
- <210> 40
<211> 16
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 40
atgaaccgtg tatgta 16
- <210> 41
<211> 16
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 41
atgaactgtg tatgta 16
- <210> 42
<211> 17
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 42
tgtcacaaga gaaaagt 17
- <210> 43
<211> 17
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 43
attacataca ttaagat 17
- <210> 44
<211> 17
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 44
cacattatta gatgaac 17
- <210> 45
<211> 17
<212> DNA
<213> Artificial Sequence
- <220>
<223> Other information: Description of artificial sequence: synthetic probe
- <400> 45
gaatgtatgt acataca 17
| 标题 | 发布/更新时间 | 阅读量 |
|---|---|---|
| 一次性收集松材线虫分离装置 | 2020-05-08 | 614 |
| 产胞外果聚糖的解淀粉芽孢杆菌及其应用 | 2020-05-08 | 799 |
| 来自植物的杀昆虫蛋白及其使用方法 | 2020-05-08 | 615 |
| 半年生马尾松苗嫩梢表皮划伤法人工接种松材线虫的方法及其应用 | 2020-05-08 | 737 |
| 毕赤酵母的高效生产及其在促进植物和动物健康中的用途 | 2020-05-11 | 474 |
| 一种防治水稻根结线虫的生防菌株AW2017及其应用 | 2020-05-08 | 256 |
| 一种乙酰氨基葡萄糖产量提高的重组谷氨酸棒杆菌及其应用 | 2020-05-08 | 830 |
| 杀有害生物活性噻吩衍生物 | 2020-05-11 | 777 |
| 一种番茄抗线虫抗黄化曲叶病毒品种的选育方法 | 2020-05-08 | 270 |
| 在稻中防治稻害虫的方法 | 2020-05-08 | 74 |
高效检索全球专利专利汇是专利免费检索,专利查询,专利分析-国家发明专利查询检索分析平台，是提供专利分析，专利查询，专利检索等数据服务功能的知识产权数据服务商。
我们的产品包含105个国家的1.26亿组数据，免费查、免费专利分析。
专利汇分析报告产品可以对行业情报数据进行梳理分析，涉及维度包括行业专利基本状况分析、地域分析、技术分析、发明人分析、申请人分析、专利权人分析、失效分析、核心专利分析、法律分析、研发重点分析、企业专利处境分析、技术处境分析、专利寿命分析、企业定位分析、引证分析等超过60个分析角度，系统通过AI智能系统对图表进行解读，只需1分钟，一键生成行业专利分析报告。
