Aegilops convex whole genome SNP site combination, probe, chip and application thereof

Abstract

The invention discloses an aegilops variabilis whole genome SNP site combination, a probe, a chip and application of the aegilops variabilis whole genome SNP site combination, the probe and the chip. The aegilops variabilis whole genome SNP site combination is composed of 10K SNP sites composed of 4K Dv subgenome SNP sites and 6K Nv subgenome SNP sites. According to the method, the genome information of the aegilops tauschii can be detected in a high-quality, high-efficiency and high-throughput manner, so that an efficient detection technical means is provided for molecular breeding application of the excellent genes of the aegilops tauschii and the chromosome segments of the excellent genes, and an efficient detection tool is provided for exploration and breeding utilization of the excellent genes.

Description

Technical Field

[0001] This invention relates to the field of wheat genetic breeding technology, specifically to a genome-wide SNP locus combination, probe, chip, and its application in Aegilops convexus. Background Technology

[0002] Aegilops ventricosa (2n=4X=28, genome DvDvNvNv) is an allotetraploid closely related species in the Triticum tribe. As early as the 1980s, international wheat breeders introduced the superior chromosome fragment 2NvS of Aegilops ventricosa into common wheat, creating the internationally renowned VPM1 wheat material. Using VPM1, many disease-resistant wheat varieties such as Jagger and Renan have been bred internationally. However, due to the lack of genomic information, it is difficult to conduct high-throughput detection of exogenous chromosome fragments of Aegilops ventricosa internationally.

[0003] Aegilops convexis is an important genetic resource for global wheat genetic improvement. Current technologies can only perform cytological chromosome observation through FISH or GISH techniques to macroscopically detect larger Aegilops convexis chromosome fragments that have infiltrated into ordinary wheat, which is inefficient and lacks precision. Summary of the Invention

[0004] The purpose of this invention is to provide a combination of SNP sites, probes, chips, and their applications for the whole genome of *Aegilops convexus*, in order to solve the problems of low efficiency and low accuracy in existing technologies that can only macroscopically detect larger *Aegilops convexus* chromosome fragments infiltrated into common wheat.

[0005] To achieve the above objectives, the present invention provides the following technical solution: The present invention provides a genome-wide SNP locus combination of Aegilops convexus, wherein the genome-wide SNP locus combination of Aegilops convexus consists of 10K SNP loci composed of 4K Dv subgenome SNP loci and 6K Nv subgenome SNP loci, and the physical location information of the 10K SNP loci is shown in Table 1. The physical locations of the 10K SNP sites were obtained based on the Dv and Nv subgenomes, both of which were derived from Aegilops ventricosa RM271 (DvDvNvNv genome). The genome sequence URL is: JBrowse Chr1D:208714945..313064586. They are numbered according to their physical location in the reference genome and their genotype, and according to the reference genome Chromosome (chromosome / linked chromosome). The chromosomes are arranged in ascending order of their positions (lock groups). Chr1D represents the chromosome of the Dv subgenome, and Chr1N represents the chromosome of the Nv subgenome. The table includes the genomic chromosome, physical location, and locus genotype. A, T, G, and C are abbreviations for deoxyribonucleotides, representing adenine deoxynucleotide (dAMP), thymine deoxynucleotide (dTMP), guanine deoxynucleotide (dGMP), and cytosine deoxynucleotide (dCMP), respectively. Table 1

[0006] On the other hand, the present invention also provides an application of a probe combination for detecting the SNP site combination of the whole genome of Aegilops convexus in the rapid detection of Aegilops convexus genome fragments and / or in breeding, which can perform whole genome detection on offspring containing the Aegilops convexus genome and can accurately detect and identify specific sites from Aegilops convexus RM271.

[0007] Finally, the present invention also provides an application of a chip for detecting the SNP site combination of the whole genome of Aegilops convexus in the rapid detection of Aegilops convexus genome fragments and / or in breeding, the chip comprising the probe combination described above.

[0008] Based on the above technical solution, the embodiments of the present invention can produce at least the following technical effects: (1) This invention utilizes the genome of Aegilops RM271 and, by comparing it with the known published genomes of common wheat (AABBDD) and diploid jointed goatgrass (DD), develops specific SNP molecular probes for the Dv and Nv subgenomes and develops a 10K SNP chip.

[0009] (2) The present invention can detect the genome information of Aegilops convexus with high quality, high efficiency and high throughput. This provides an efficient detection method for the molecular breeding application of superior genes and chromosome fragments of Aegilops convexus, and provides an efficient detection tool for the discovery and breeding utilization of superior genes. Attached Figure Description

[0010] To more clearly illustrate the technical solutions in this invention or the prior art, the drawings used in the description of the embodiments or the prior art will be briefly introduced below. Obviously, the drawings described below are only some embodiments of this invention. For those skilled in the art, other drawings can be obtained based on the structures shown in these drawings without creative effort.

[0011] Figure 1 This is the distribution of SNP probes in the Dv subgenome of *Aegilops spp.* according to an embodiment of the present invention; Figure 2 This is the distribution of SNP probes in the Nv subgenome of *Aegilops convexus* according to an embodiment of the present invention; Figure 3This is the result of SNP chip detection of tetraploid durum wheat LM (AABB genome) according to an embodiment of the present invention; Figure 4 This is the result of SNP chip detection of hexaploid common wheat CM104 (AABBDD genome) in an embodiment of the present invention; Figure 5 The results of the SNP chip in this embodiment of the invention for detecting LM and RM271 and their descendants are as follows; Figure 6 This is the first detection result of the SNP chip on the progeny of RM271 (DvDvNvNv genome) in an embodiment of the present invention; Figure 7 This is the second result of the SNP chip detection of the RM271 (DvDvNvNv genome) progeny in this embodiment of the invention. Detailed Implementation

[0012] Various exemplary embodiments of the present invention will now be described in detail. This detailed description should not be considered as a limitation of the present invention, but rather as a more detailed description of certain aspects, features, and embodiments of the present invention.

[0013] It should be understood that the terminology used in this invention is merely for describing particular embodiments and is not intended to limit the invention. Furthermore, with respect to numerical ranges in this invention, it should be understood that each intermediate value between the upper and lower limits of the range is also specifically disclosed. Every smaller range between any stated value or intermediate value within a stated range, and any other stated value or intermediate value within said range, is also included in this invention. The upper and lower limits of these smaller ranges may be independently included or excluded from the range.

[0014] Unless otherwise stated, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. While only preferred methods and materials have been described herein, any methods and materials similar or equivalent to those described herein may be used in the implementation or testing of this invention. All references to this specification are incorporated by way of citation to disclose and describe methods and / or materials associated with those references. In the event of any conflict with any incorporated reference, the content of this specification shall prevail.

[0015] Various modifications and variations can be made to the specific embodiments described in this specification without departing from the scope or spirit of the invention, as will be apparent to those skilled in the art. Other embodiments derived from this specification will also be apparent to those skilled in the art. This specification and embodiments are merely exemplary.

[0016] The terms “include,” “including,” “have,” “contain,” etc., used in this article are all open-ended terms, meaning that they include but are not limited to.

[0017] Example 1 Using the genome of *Aegilops convexus* RM271 and comparing it with the known published genomes of common wheat (AABBDD) and diploid *Alternaria alternata* (DD), specific SNP molecular probes for the Dv and Nv subgenomes were developed. A 10K SNP chip was developed, containing 10,000 probe sequences, including 4K for the Dv subgenome and 6K for the Nv subgenome, totaling 10K. These 10K probes are evenly distributed across the 28 chromosomes of *Aegilops convexus*. Figure 1 and Figure 2 As shown.

[0018] Specifically, the development of the SNP molecular probes is based on the Aegilops RM271 genome (DvDvNvNv) and all existing common wheat genomes (AABBDD) and diploid jointed goatgrass genome (DD). By comparing the DNA sequence of each chromosome in the whole genome, the unique single nucleotide polymorphisms (SNPs) between the Dv and Nv subgenomes and other genomes are identified. Then, based on the single nucleotide polymorphisms, SNP molecular probes for the Aegilops RM271 genome (DvDvNvNv) are developed.

[0019] A 10K SNP probe chip was developed to perform whole-genome sequencing and validation on offspring containing the Aegilops convexus genome. This accurately detected and identified specific loci from Aegilops convexus RM271, such as... Figures 3 to 7 As shown.

[0020] Specifically, using conventional breeding techniques and greenhouse generation techniques, common wheat (AABBDD) was used as the female parent and Aegilops RM271 (DvDvNvNv) as the male parent for hybridization. Then, common wheat was used as the recurrent parent for backcrossing. Chromosomal fragments of the Dv and Nv subgenomes of RM271 were introduced into the genetic background of common wheat to construct the BC2F2 population. A developed 10K chip was used to perform whole-genome scanning of the BC2F2 population lines to validate the chip.

[0021] LM represents tetraploid durum wheat (AABB genome), and CM104 represents hexaploid common wheat (AABBDD genome). Validation results show that this chip can detect chromosome introgression and the size of introgressed fragments in RM271 (DvDvNvNv) and its derived progeny with high quality and efficiency.

[0022] Example 2 This embodiment is a supplement to the specific implementation method of Embodiment 1. In this embodiment, common wheat Chuanmai 42 was first used as the female parent and Aegilops RM271 (DvDvNvNv) was used as the male parent for hybridization.

[0023] In this embodiment, the BC2F2 breeding population was created by backcrossing using Chuanmai 42 as a recurrent parent. This population contains Dv and Nv subgenome fragments that can be detected efficiently and with high quality by the chip in this patent, which greatly improves the efficiency of wheat genetic improvement using Aegilops spp. (DvDvNvNv).

[0024] In this embodiment, new wheat breeding materials with different chromosomal segments from the Dv and Nv subgenomes have been created.

[0025] The above description is only a preferred embodiment of the present invention. It should be noted that those skilled in the art can make several modifications and improvements without departing from the inventive concept of the present invention, and these all fall within the protection scope of the present invention.

Claims

1. A genome-wide SNP locus combination of *Aegilops spp.*, characterized in that, The whole genome SNP locus combination of Aegilops convexus consists of 10K SNP loci, which are composed of 4K Dv subgenome SNP loci and 6K Nv subgenome SNP loci. The physical location information of the 10K SNP loci is shown in Table 1. Table 1. 10K SNP sites 。 2. The application of a probe array for detecting the SNP site combination of the whole genome of *Aegilops convexus* as described in claim 1 in the rapid detection of *Aegilops convexus* genome fragments and / or in breeding, characterized in that, It can perform whole-genome sequencing on offspring containing the Aegilops spp. genome, and can accurately detect and identify specific loci from Aegilops spp. RM271.

3. The application of a chip for detecting the SNP locus combinations of the entire genome of *Aegilops convexus* as described in claim 1 in the rapid detection of *Aegilops convexus* genome fragments and / or breeding, characterized in that, The chip comprises the probe assembly as described in claim 2.

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