Whole genome SNP (Single Nucleotide Polymorphism) molecular marker combination for vase life of Chinese rose and application thereof

Abstract

The invention discloses a Chinese rose vase life whole genome SNP molecular marker combination and application thereof, the SNP locus combination comprises 1679 SNP markers significantly associated with Chinese rose vase life, and the SNP markers are uniformly distributed on 14 chromosomes of Chinese rose. The SNP loci are obtained through genome-wide association analysis and screening, a genome-wide selection model constructed by the SNP loci can accurately predict the vase life of the Chinese rose, and the prediction accuracy can reach 0.710 or above. The invention also relates to specific probes designed aiming at the SNP loci and a liquid phase breeding chip containing the probes, which can be used for rapidly and efficiently screening individuals with excellent vase life characters in a Chinese rose seed or seedling stage, so that the breeding period is remarkably shortened, the breeding efficiency is improved, and the breeding cost is reduced. Powerful technical support is provided for molecular breeding and variety improvement of the Chinese roses.

Description

TECHNICAL FIELD

[0001] The present application relates to the technical field of molecular breeding, and particularly relates to a full-genome SNP molecular marker combination for bottle-inserting life of Rosa chinensis and application thereof. BACKGROUND

[0002] As an important ornamental plant, the bottle-inserting life of Rosa chinensis is a core index for determining the ornamental value and economic value, and is of great significance to the development of the Rosa chinensis industry. Traditional breeding methods rely on field phenotype observation, and have problems such as heavy workload, long cycle and low efficiency, and in the breeding process, the genotypes determining the key economic traits such as bottle-inserting life are easily lost due to recombination or mutation, which limits the improvement of directional breeding efficiency.

[0003] In recent years, SNP molecular marker technology is widely used, and full-genome selection breeding technology develops rapidly. Through the construction of a genotype and agronomic trait prediction model, early-stage materials can be efficiently screened, breaking the limitations of traditional breeding which relies too much on field phenotype screening. However, the existing gene prediction model cannot control the complex genetic regulation mechanism behind the bottle-inserting life of Rosa chinensis, and the prediction accuracy is still less than 30%, which cannot meet the urgent needs of the modern Rosa chinensis industry for improvement of the bottle-inserting life and other traits. Traditional breeding methods need to wait until the plant grows to a certain stage to evaluate the traits, which is time-consuming and low in efficiency.

[0004] Therefore, it is urgent to construct a genotype protection technology system and develop a precise and efficient SNP marker combination for predicting the bottle-inserting life of Rosa chinensis and its application. SUMMARY

[0005] In order to solve the problems of the prior art, the purpose of the present application is to provide a full-genome SNP molecular marker combination for bottle-inserting life of Rosa chinensis and application thereof.

[0006] In order to achieve the above-mentioned purpose, the present application adopts the following technical solutions:

[0007] In the first aspect, the present application provides a full-genome SNP molecular marker combination for bottle-inserting life of Rosa chinensis.

[0008] In the second aspect, the present application provides a prediction probe for bottle-inserting life of Rosa chinensis.

[0009] In the third aspect, the present application provides a prediction chip for bottle-inserting life of Rosa chinensis.

[0010] In the fourth aspect, the present application provides an application of the SNP molecular marker combination, the probe or the chip in prediction of bottle-inserting life of Rosa chinensis.

[0011] In the fifth aspect, the present application provides a method for predicting bottle-inserting life of Rosa chinensis based on the SNP molecular marker combination.

[0012] In a sixth aspect, the application provides application of the SNP site combination, the probe, the chip or the prediction method in Rosa molecular breeding.

[0013] In a seventh aspect, the application provides a Rosa molecular breeding method based on SNP markers.

[0014] The first aspect of the application provides a Rosa bottle insertion life whole genome SNP molecular marker combination, the SNP molecular marker combination comprising 1679 SNP sites distributed on 14 chromosomes of Rosa;

[0015] The specific information of the SNP site is represented in the structure of chromosome number_ physical position_ allelic genotype, and the SNP site comprises a dominant allele positively significantly associated with the bottle insertion life of Rosa. The specific site information is shown in Table 1 of the specification.

[0016] Further, the SNP site is determined by whole genome association analysis on 358 Rosa resequencing materials, and is screened by multiple software and model association.

[0017] The second aspect of the application provides a prediction probe for the bottle insertion life of Rosa. The probe is a liquid phase probe, the sequence of which is designed according to the SNP site, and is used for hybridizing with the genomic DNA of Rosa, capturing the DNA fragments in the region where the target SNP site is located, so as to perform subsequent sequencing analysis, determine the genotype of the tested Rosa, and thus predict the bottle insertion life trait.

[0018] The third aspect of the application provides a prediction chip for the bottle insertion life of Rosa. The prediction chip comprises probes for detecting the 1679 SNP sites. By detecting the genotype of these SNP sites in the genomic DNA of the tested Rosa sample, the whole genome selection model is constructed in advance, and the bottle insertion life trait of Rosa is accurately predicted.

[0019] The fourth aspect of the application provides application of the SNP molecular marker combination, the probe or the chip in prediction of the bottle insertion life of Rosa. By extracting the genomic DNA of the Rosa plant, the SNP site combination, the probe or the chip is used for detection.

[0020] The fifth aspect of the application provides a method for predicting the bottle insertion life of Rosa based on the SNP molecular marker combination, comprising the following steps:

[0021] (1) extracting the genomic DNA of the tested Rosa plant;

[0022] (2) constructing a library for the genomic DNA;

[0023] (3) using the probe to hybridize and capture the DNA fragments in the library, and enriching the DNA fragments containing the target SNP site;

[0024] (4) high-throughput sequencing of the captured DNA fragments;

[0025] (5) aligning the sequencing data with the Rosa reference genome to determine the genotype of the SNP site;

[0026] (6) inputting the genotype data of the SNP site into the whole genome selection model to obtain the prediction result of the vase life trait of the Rosa to be tested.

[0027] The sixth aspect of the present application provides an application of the SNP site combination, probe, chip or prediction method in Rosa molecular breeding, which is used for early, accurate and efficient prediction and screening of the vase life trait of the breeding material in the breeding process of Rosa, so as to shorten the breeding cycle, improve the selection efficiency and cultivate new varieties of Rosa with excellent vase life trait.

[0028] Further, the whole genome selection model constructed based on the SNP site combination can predict the vase life of Rosa, and the prediction accuracy is greater than 0.710.

[0029] The seventh aspect of the present application provides a Rosa molecular breeding method based on SNP markers, which comprises the following steps:

[0030] (1) extracting Rosa genomic DNA;

[0031] (2) capturing and enriching the genomic DNA by using the liquid breeding chip;

[0032] (3) high-throughput sequencing of the captured and enriched DNA;

[0033] (4) analyzing the sequencing data to detect the genotype of the 1679 SNP sites.

[0034] Beneficial effects: the present application can realize accurate prediction of the vase life trait of Rosa at the seed or seedling stage by means of the screened SNP marker combination and the corresponding detection technology, without waiting for the plant to mature, so that the breeding cycle is greatly shortened, the breeding efficiency is improved, and the cultivation process of new varieties of Rosa is accelerated.

[0035] Compared with the prior art, the present application has the following advantages:

[0036] (1) the traditional gene prediction model is difficult to effectively control the complex genetic regulation mechanism of the vase life of Rosa, and the prediction accuracy is less than 30%. The present application successfully screens 1679 SNP markers significantly associated with the vase life of Rosa by whole genome association analysis, and constructs a whole genome selection model, the prediction accuracy of which can reach more than 0.710, which significantly improves the prediction accuracy of the vase life of Rosa and provides a more reliable screening basis for breeding work.

[0037] (2) The present application deeply analyzes the distribution characteristics and functional properties of SNP markers related to the vase life of Chinese rose, providing researchers with rich data resources and scientific and detailed theoretical basis, which helps to further explore the mechanism of related genes, and identifies potential target points for subsequent gene editing or genetic improvement, greatly promoting the development of Chinese rose molecular breeding technology, and injecting new vitality and power into the variety improvement and market competitiveness of Chinese rose industry.

[0038] (3) The liquid breeding chip technology developed by the present application can quickly and accurately detect SNP sites significantly associated with key traits such as vase life, with high throughput and high accuracy, effectively reducing costs and improving the efficiency and reliability of breeding material screening, providing strong technical support for the directional breeding and variety improvement of ornamental plants, and having good application prospect and popularization value.

[0039] (4) The SNP marker combination and related technology of the present application can be used to construct a Chinese rose genotype protection technology system, which helps to maintain the excellent characteristics of Chinese rose varieties and prevent the loss or loss of function of genotypes that determine key economic traits such as vase life due to gene recombination or mutation in large-scale breeding practice, providing technical support for the stable inheritance and continuous improvement of Chinese rose varieties. BRIEF DESCRIPTION OF DRAWINGS

[0040] In order to more clearly illustrate the technical solutions in the embodiments of the present application, the drawings needed in the embodiments or prior art description will be briefly introduced. Obviously, the drawings in the following description are only some embodiments of the present application, and other drawings can be obtained by those skilled in the art without creative labor.

[0041] Figure 1 The present application provides an allele frequency graph of vase life of Chinese rose.

[0042] Figure 2 The present application provides a deletion rate graph of vase life of Chinese rose.

[0043] Figure 3 The present application provides a heterozygosity graph of vase life of Chinese rose.

[0044] Figure 4 The present application provides a whole chromosome marker distribution graph of vase life of Chinese rose.

[0045] Figure 5 The present application provides a whole genome selection evaluation result graph of vase life of Chinese rose. DETAILED DESCRIPTION

[0046] With reference to the drawings of the embodiments of the present application, the technical solutions in the embodiments of the present application will be clearly and completely described. Obviously, the described embodiments are only a part of the embodiments of the present application, but not all embodiments of the present application. Based on the embodiments of the present application, all other embodiments obtained by a person of ordinary skill in the art without creative effort are within the scope of protection of the present application.

[0047] In the present application, the term "and / or" describes the association relationship of the associated objects, which means that there can be three kinds of relationships, for example, A and / or B can represent the following three cases: A exists alone, A and B exist together, and B exists alone. Wherein A and B can be singular or plural. The character " / " generally represents an "or" relationship between the associated objects before and after it.

[0048] In the present application, "one or more" means one or more, and "multiple" means two or more. "One or more of the following" or similar expressions refer to any combination of these items, including any combination of single item or multiple items. For example, "one or more of a, b, or c", or "one or more of a, b, and c" can represent a, b, c, a-b (i.e. a and b), a-c, b-c, or a-b-c, wherein a, b, and c can be single or multiple.

[0049] It should be understood that in various embodiments of the present application, the size of the sequence number of the above-mentioned processes does not mean the order of execution, and part or all steps can be executed in parallel or in sequence. The execution order of each process should be determined according to its function and inherent logic, and should not constitute any limitation on the implementation process of the embodiments of the present application.

[0050] The terms used in the embodiments of the present application are only for the purpose of describing specific embodiments, and are not intended to limit the present application. The singular forms "a", "said" and "the" used in the embodiments of the present application and the appended claims are also intended to include the plural forms, unless the context clearly indicates otherwise.

[0051] The weight of the related components mentioned in the specification of the embodiments of the present application can not only refer to the specific content of each component, but also represent the weight ratio between each component. Therefore, as long as the content of the related components in the specification of the embodiments of the present application is enlarged or reduced in proportion, it is within the scope disclosed in the specification of the embodiments of the present application. Specifically, the mass mentioned in the specification of the embodiments of the present application can be μg, mg, g, kg and other mass units commonly known in the chemical field.

[0052] The first aspect of the embodiment of the present application provides a full-genome SNP molecular marker combination for Rosa chinensis cutting life, wherein the SNP molecular marker combination comprises 1679 SNP loci distributed on 14 chromosomes of Rosa chinensis;

[0053] The specific information of the SNP loci is represented in the form of chromosome number_ physical position_ allelic genotype, and the SNP loci comprise a dominant allele positively significantly associated with the cutting life of Rosa chinensis, and the specific locus information is shown in Table 1.

[0054] In some embodiments, the SNP loci are determined by full-genome association analysis on 358 resequencing materials of Rosa chinensis, and are screened by multiple software and model associations.

[0055] The second aspect of the embodiment of the present application provides a prediction probe for the cutting life of Rosa chinensis, wherein the probe is a liquid-phase probe, the sequence of the probe is designed according to the SNP loci, and the probe is used for hybridizing with the genomic DNA of Rosa chinensis, capturing the DNA fragments in the region where the target SNP loci are located, so as to perform subsequent sequencing analysis, determine the genotype of the to-be-tested Rosa chinensis, and thus predict the cutting life trait of the to-be-tested Rosa chinensis.

[0056] The third aspect of the embodiment of the present application provides a prediction chip for the cutting life of Rosa chinensis, wherein the prediction chip comprises probes for detecting the 1679 SNP loci, and the genotype of the SNP loci in the genomic DNA of the to-be-tested Rosa chinensis sample is detected, and a full-genome selection model is constructed in advance, so as to realize accurate prediction of the cutting life trait of Rosa chinensis.

[0057] The fourth aspect of the embodiment of the present application provides an application of the SNP molecular marker combination, the probe or the chip in the prediction of the cutting life of Rosa chinensis, wherein the genomic DNA of the Rosa chinensis plant is extracted, and the SNP loci combination, the probe or the chip is used for detection.

[0058] The fifth aspect of the embodiment of the present application provides a method for predicting the cutting life of Rosa chinensis based on the SNP molecular marker combination, and the method comprises the following steps:

[0059] (1) extracting the genomic DNA of the to-be-tested Rosa chinensis plant;

[0060] (2) constructing a library for the genomic DNA;

[0061] (3) using the probe to hybridize and capture the DNA fragments in the library, and enriching the DNA fragments containing the target SNP loci;

[0062] (4) performing high-throughput sequencing on the captured DNA fragments;

[0063] (5) comparing and analyzing the sequencing data with the Rosa chinensis reference genome to determine the genotype of the SNP loci.

[0064] (6) inputting the genotype data of the SNP sites into a whole genome selection model to obtain a prediction result of the bottle insertion life trait of the to-be-tested Rosa chinensis, and in some embodiments, the whole genome selection model constructed based on the SNP site combination can be used to predict the bottle insertion life of the Rosa chinensis, and the prediction accuracy is greater than 0.710; the model is realized by integrating 13 types of algorithms, including: machine learning models: LightGBM, Random Forest, SVR; penalty regression models: Lasso, Ridge, rrBLUP; Bayesian models: BRR, BL, BayesC / B / B / A; hybrid models: RKHS, GBLUP. Among them, Bayes Ridge Regression (BRR) is the optimal model.

[0065] The sixth aspect of the embodiments of the present application provides an application of a SNP site combination, a probe, a chip or a prediction method in Rosa chinensis molecular breeding, which is used for early, accurate and efficient prediction and screening of the bottle insertion life trait of breeding materials in the breeding process of Rosa chinensis, so as to shorten the breeding cycle, improve the selection efficiency, and cultivate new varieties of Rosa chinensis with excellent bottle insertion life trait.

[0066] In some embodiments, the whole genome selection model constructed based on the SNP site combination can be used to predict the bottle insertion life of the Rosa chinensis, and the prediction accuracy is greater than 0.710.

[0067] The seventh aspect of the embodiments of the present application provides a Rosa chinensis molecular breeding method based on SNP markers, which comprises the following steps:

[0068] (1) extracting genomic DNA of Rosa chinensis;

[0069] (2) capturing and enriching the genomic DNA by using the liquid breeding chip described above;

[0070] (3) performing high-throughput sequencing on the DNA after capture and enrichment;

[0071] (4) analyzing the sequencing data to detect the genotype of the 1679 SNP sites.

[0072] Embodiment 1

[0073] The SNP molecular marker combination for the bottle insertion life of Rosa chinensis in the present application comprises 1679 SNP sites distributed on 14 chromosomes of Rosa chinensis;

[0074] The specific information of the SNP sites is represented in the structural form of chromosome number_ physical position_ allelic genotype, and the SNP sites contain dominant alleles positively significantly associated with the bottle insertion life of Rosa chinensis, and the specific site information is shown in Table 1.

[0075] Table 1

[0076] Chr1A_4813520_A / G, Chr1A_4813537_T / C, Chr1A_30834011_C / T, Chr1A_32221286_C / T, Chr1A_32223961_G / A, Chr1A_33011346_C / T, Chr1A_44091992_A / C, Chr1A_44092015_T / C, Chr1A_44092019_T / G, Chr1A_44092068_C / T, Chr1A_45921074_G / A, Chr1A_46150241_C / T, Chr1A_46225710_C / T, Chr1A_53233599_G / A, Chr1A_57148115_A / T, Chr1A_57177061_T / C, Chr1A_57177067_A / T, Chr1A_57198742_C / G, Chr1A_57420833_T / C, Chr1A_57555262_C / T, Chr1A_57555276_T / A, Chr1A_57556169_A / T, Chr1A_57629705_G / T, Chr1A_66409844_G / A, Chr1B_2660966_T / A, Chr1B_4958719_G / C, Chr1B_4958724_A / C, Chr1B_5726434_T / C, Chr1B_10905523_G / A, Chr1B_30541369_G / T, Chr1B_42202981_C / T, Chr1B_42480174_T / C, Chr1B_42775273_C / T, Chr1B_42832224_A / G, Chr1B_42875461_C / G, Chr1B_42875469_C / T, Chr1B_42948251_A / G, Chr1B_42948257_T / C, Chr1B_42948335_T / C, Chr1B_42948342_A / G, Chr1B_42948362_A / G, Chr1B_42948374_T / A, Chr1B_42948391_G / A, Chr1B_42948417_C / A, Chr1B_42948418_G / A, Chr1B_42948427_T / C, Chr1B_42948444_C / G, Chr1B_42987522_A / G, Chr1B_43030552_C / A, Chr1B_43208938_G / A, Chr1B_43365653_A / G, Chr1B_43365662_C / G, Chr1B_43365688_C / T,Chr1B_43366627_T / C, Chr1B_43367112_T / G, Chr1B_43367220_C / T, Chr1B_43367247_T / A, Chr1B_43367250_G / A, Chr1B_43367268_G / A, Chr1B_43367343_G / A, Chr1B_43486476_G / A, Chr1B_43486987_G / A, Chr1B_43721968_T / A, Chr1B_43724534_C / T, Chr1B_43726160_A / C, Chr1B_44043034_C / G, Chr1B_44074222_G / C, Chr1B_44074231_T / A, Chr1B_44528425_C / G, Chr1B_44685299_G / C, Chr1B_44685301_A / G, Chr1B_44692217_A / T, Chr1B_44700845_T / A, Chr1B_44700861_T / A, Chr1B_44775277_C / T, Chr1B_45134170_G / C, Chr1B_45134197_C / T, Chr1B_45134246_C / T, Chr1B_45134271_G / A, Chr1B_45207975_T / G, Chr1B_45207977_T / C, Chr1B_45208096_A / C, Chr1B_45648144_C / T, Chr1B_45674023_C / T, Chr1B_45925789_C / T, Chr1B_45925829_T / C, Chr1B_45925862_C / A, Chr1B_45927058_A / G, Chr1B_45927108_G / A, Chr1B_45927134_C / T, Chr1B_46884773_T / C, Chr1B_54544249_C / T, Chr2A_1339133_C / T, Chr2A_17004165_A / G, Chr2A_17331036_C / T, Chr2A_18807941_T / C, Chr2A_18807986_G / A, Chr2A_21855809_A / G, Chr2A_21938533_G / A, Chr2A_21947911_T / C, Chr2A_21956572_G / T, Chr2A_21956591_C / T, Chr2A_21956594_G / A, Chr2A_22073008_C / T, Chr2A_22073019_T / C,Chr2A_22073020_G / A, Chr2A_22084527_T / A, Chr2A_22093230_C / A, Chr2A_22177699_G / T, Chr2A_22432517_T / G, Chr2A_22441656_C / T, Chr2A_22441666_A / G, Chr2A_22441667_G / A, Chr2A_22441704_C / T, Chr2A_22441738_T / G, Chr2A_22441740_C / T, Chr2A_22441789_C / T, Chr2A_22453037_A / C, Chr2A_22453045_G / A, Chr2A_22453110_G / T, Chr2A_22453127_C / T, Chr2A_22453129_C / T, Chr2A_22454646_C / T, Chr2A_22455438_A / T, Chr2A_22455550_G / A, Chr2A_22552814_G / A, Chr2A_22582070_A / T, Chr2A_22587117_G / T, Chr2A_22587138_G / A, Chr2A_22590683_C / T, Chr2A_22590979_A / T, Chr2A_22590992_C / G, Chr2A_22610998_C / T, Chr2A_22623945_G / A, Chr2A_22623953_C / T, Chr2A_22626330_A / G, Chr2A_22629251_C / A, Chr2A_22654482_A / C, Chr2A_22655657_A / T, Chr2A_22655814_C / A, Chr2A_22655821_T / G, Chr2A_22655951_A / T, Chr2A_22656440_T / C, Chr2A_22664493_C / T, Chr2A_22665978_T / C, Chr2A_22666455_T / A, Chr2A_22666472_G / A, Chr2A_22666488_T / C, Chr2A_22666721_T / A, Chr2A_22666999_G / A, Chr2A_22667134_C / T, Chr2A_22694982_G / A, Chr2A_22695005_A / G, Chr2A_22696019_G / A, Chr2A_22696051_C / G, Chr2A_22696052_C / T, Chr2A_22696055_C / T,Chr2A_22696119_G / A, Chr2A_22696140_G / A, Chr2A_22696164_C / T, Chr2A_22712562_G / T, Chr2A_23060073_A / C, Chr2A_23301722_G / A, Chr2A_23316902_G / A, Chr2A_23331772_C / G, Chr2A_23477308_C / T, Chr2A_23478448_C / G, Chr2A_23478468_T / G, Chr2A_23478482_C / A, Chr2A_23479059_A / C, Chr2A_23515383_C / T, Chr2A_23515399_C / A, Chr2A_23515461_G / A, Chr2A_23515476_G / A, Chr2A_23515574_G / A, Chr2A_23515623_T / C, Chr2A_23523624_C / T, Chr2A_23524024_A / T, Chr2A_23527692_G / A, Chr2A_23527744_C / T, Chr2A_23562795_C / T, Chr2A_23562839_A / C, Chr2A_23644776_C / T, Chr2A_23933055_G / T, Chr2A_23933504_T / C, Chr2A_23933577_G / A, Chr2A_23933662_A / C, Chr2A_23993161_A / C, Chr2A_23993416_C / A, Chr2A_24212909_T / C, Chr2A_24212921_A / G, Chr2A_24220945_C / T, Chr2A_24492172_A / G, Chr2A_24493845_A / T, Chr2A_24535170_C / A, Chr2A_24550319_C / T, Chr2A_24550329_G / A, Chr2A_24550426_G / A, Chr2A_24550475_C / T, Chr2A_24550486_G / T, Chr2A_24550641_A / G, Chr2A_24551070_T / A, Chr2A_24570327_T / C, Chr2A_24570354_A / T, Chr2A_24570454_T / C, Chr2A_24570463_C / A, Chr2A_24588798_T / C, Chr2A_24628953_G / C, Chr2A_24628959_A / C,Chr2A_24777641_C / T, Chr2A_24777666_C / T, Chr2A_24777687_C / A, Chr2A_24822275_G / A, Chr2A_24822551_C / A, Chr2A_24829231_C / T, Chr2A_24829236_A / T, Chr2A_24851454_G / A, Chr2A_24858454_A / G, Chr2A_25007959_A / G, Chr2A_25471472_T / G, Chr2A_52830239_A / G, Chr2A_62335175_G / A, Chr2A_62335202_A / G, Chr2A_64361234_A / G, Chr2A_64361252_C / T, Chr2A_64827402_T / C, Chr2A_64872171_C / T, Chr2A_64873313_G / A, Chr2A_64901593_A / T, Chr2A_65295690_G / A, Chr2A_65295735_T / C, Chr2A_65307954_C / T, Chr2A_65307957_T / C, Chr2A_65376433_T / C, Chr2A_65381789_G / A, Chr2A_65381812_A / G, Chr2A_65381816_A / G, Chr2A_65381846_A / G, Chr2A_65381847_C / T, Chr2A_65381881_T / C, Chr2A_65577570_C / T, Chr2A_65577693_C / T, Chr2A_65577730_C / T, Chr2A_65577776_C / A, Chr2A_65577910_A / C, Chr2A_65578070_G / A, Chr2A_65578083_A / G, Chr2A_65578092_T / C, Chr2A_65578093_G / T, Chr2A_65578095_A / G, Chr2A_65585159_A / T, Chr2A_65623669_C / T, Chr2A_65635989_C / T, Chr2A_65692989_G / A, Chr2A_65819814_A / G, Chr2A_65819816_A / G, Chr2A_65843931_A / G, Chr2A_65843933_A / G, Chr2A_65843949_C / T, Chr2A_65844044_A / T, Chr2A_65844052_T / C,Chr2A_65844163_T / G, Chr2A_65844242_T / C, Chr2A_65844588_C / G, Chr2A_65844682_T / C, Chr2A_65844736_T / C, Chr2A_65844743_T / C, Chr2A_65844745_A / G, Chr2A_65844818_T / C, Chr2A_65845203_T / C, Chr2A_65845244_G / A, Chr2A_65845255_A / G, Chr2A_65845287_C / A, Chr2A_65845327_T / C, Chr2A_65845383_G / C, Chr2A_65845392_T / C, Chr2A_65845406_A / G, Chr2A_65845419_T / C, Chr2A_65845429_T / C, Chr2A_65845548_A / G, Chr2A_65845602_A / G, Chr2A_65845614_A / C, Chr2A_65845687_A / G, Chr2A_65845713_T / C, Chr2A_65845725_C / A, Chr2A_65845752_A / C, Chr2A_65845830_A / C, Chr2A_65866330_G / A, Chr2A_65904955_A / T, Chr2A_65908880_T / A, Chr2A_65909057_G / A, Chr2A_65909212_T / C, Chr2A_65909417_A / G, Chr2A_65909469_C / G, Chr2A_65909565_G / T, Chr2A_65909581_T / C, Chr2A_65909607_C / T, Chr2A_65909632_G / A, Chr2A_65909654_A / T, Chr2A_65909758_G / A, Chr2A_65909773_C / T, Chr2A_65909978_T / C, Chr2A_65910010_G / A, Chr2A_65910024_G / A, Chr2A_65910026_A / C, Chr2A_65910050_G / A, Chr2A_65910066_C / T, Chr2A_65910292_G / A, Chr2A_65910479_C / T, Chr2A_65910506_G / A, Chr2A_65910557_G / A, Chr2A_65910608_T / C, Chr2A_65910816_C / T,Chr2A_65963135_C / T, Chr2A_65963285_T / C, Chr2A_65963286_G / A, Chr2A_65974835_T / C, Chr2A_65974880_G / A, Chr2A_65996929_G / A, Chr2A_66006615_T / A, Chr2A_66026413_C / A, Chr2A_66026578_C / G, Chr2A_66122909_A / T, Chr2A_66123702_C / G, Chr2A_66123705_A / G, Chr2A_66123750_C / T, Chr2A_66123763_T / G, Chr2A_66123780_G / T, Chr2A_66123791_G / A, Chr2A_66124689_T / C, Chr2A_66124690_A / C, Chr2A_66124705_G / A, Chr2A_66125591_C / G, Chr2A_66126087_C / T, Chr2A_66126254_T / C, Chr2A_66126288_G / A, Chr2A_66126296_T / C, Chr2A_66126578_A / G, Chr2A_66126752_T / C, Chr2A_66129581_T / A, Chr2A_66129843_C / T, Chr2A_66129856_T / C, Chr2A_66129884_T / A, Chr2A_66129896_G / A, Chr2A_66130710_G / A, Chr2A_66130715_G / A, Chr2A_66133012_T / A, Chr2A_66133039_C / T, Chr2A_66133130_A / G, Chr2A_66133134_C / T, Chr2A_66133452_C / T, Chr2A_66133498_G / C, Chr2A_66133761_A / G, Chr2A_66133794_G / C, Chr2A_66133898_C / T, Chr2A_66138080_C / T, Chr2A_66141241_G / T, Chr2A_66141258_A / G, Chr2A_66141272_T / C, Chr2A_66141886_G / C, Chr2A_66142612_T / C, Chr2A_66142614_G / T, Chr2A_66142620_A / G, Chr2A_66142635_T / G, Chr2A_66196635_C / T,Chr2A_66242970_A / G, Chr2A_66242978_A / T, Chr2A_66243501_G / T, Chr2A_66243504_A / T, Chr2A_66243507_A / T, Chr2A_66243509_A / T, Chr2A_66243514_T / A, Chr2A_66263649_A / G, Chr2A_66263663_A / G, Chr2A_66268212_A / T, Chr2A_66278252_A / G, Chr2A_66278255_G / A, Chr2A_66298536_C / G, Chr2A_66306593_C / T, Chr2A_66306739_C / T, Chr2A_66306756_C / T, Chr2A_66306898_T / C, Chr2A_66311385_G / C, Chr2A_66354597_C / T, Chr2A_66354602_T / C, Chr2A_66359511_A / G, Chr2A_66359646_G / A, Chr2A_66359776_A / T, Chr2A_66362348_A / T, Chr2A_66362473_G / C, Chr2A_66362540_G / A, Chr2A_66362628_C / T, Chr2A_66362756_A / G, Chr2A_66362764_G / A, Chr2A_66362856_A / T, Chr2A_66362860_G / T, Chr2A_66362942_C / A, Chr2A_66362949_G / A, Chr2A_66363127_T / A, Chr2A_66363331_C / T, Chr2A_66368855_A / G, Chr2A_66368902_G / A, Chr2A_66368942_A / T, Chr2A_66371670_G / A, Chr2A_66373395_C / G, Chr2A_66373585_C / G, Chr2A_66373652_A / G, Chr2A_66374053_A / C, Chr2A_66393805_G / A, Chr2A_66401846_G / A, Chr2A_66416677_A / C, Chr2A_66464776_G / A, Chr2A_66495373_C / T, Chr2A_66495377_A / C, Chr2A_66495491_A / G, Chr2A_66495523_C / T, Chr2A_66497552_C / T,Chr2A_66497589_G / A, Chr2A_66497856_T / C, Chr2A_66497892_A / G, Chr2A_66497912_G / T, Chr2A_66497969_A / G, Chr2A_66497978_G / A, Chr2A_66498018_A / G, Chr2A_66498019_C / T, Chr2A_66498058_C / T, Chr2A_66498060_T / C, Chr2A_66498084_T / G, Chr2A_66498087_G / T, Chr2A_66498092_C / T, Chr2A_66498097_G / A, Chr2A_66498150_G / A, Chr2A_66498157_G / A, Chr2A_66498275_G / C, Chr2A_66498335_A / G, Chr2A_66498336_T / C, Chr2A_66501362_C / T, Chr2A_66501420_A / T, Chr2A_66501725_G / T, Chr2A_66501726_C / G, Chr2A_66502551_T / C, Chr2A_66502565_C / T, Chr2A_66502609_A / T, Chr2A_66502623_G / A, Chr2A_66502638_G / A, Chr2A_66502659_G / A, Chr2A_66502696_C / T, Chr2A_66502702_T / A, Chr2A_66502711_C / T, Chr2A_66502716_G / A, Chr2A_66502726_G / A, Chr2A_66502746_A / G, Chr2A_66502760_G / C, Chr2A_66502770_G / A, Chr2A_66502798_G / A, Chr2A_66502907_G / A, Chr2A_66502924_C / T, Chr2A_66503012_A / T, Chr2A_66503067_A / C, Chr2A_66503115_C / T, Chr2A_66503183_C / T, Chr2A_66503186_T / G, Chr2A_66503190_C / T, Chr2A_66503202_C / G, Chr2A_66503242_C / T, Chr2A_66503305_G / A, Chr2A_66503313_T / A, Chr2A_66503328_C / T, Chr2A_66503717_G / A,Chr2A_66503812_C / T, Chr2A_66503823_T / G, Chr2A_66504233_T / G, Chr2A_66504263_C / A, Chr2A_66504264_C / A, Chr2A_66504284_G / C, Chr2A_66506552_T / C, Chr2A_66506616_G / T, Chr2A_66521691_G / A, Chr2A_66521695_A / G, Chr2A_66521980_A / T, Chr2A_66558963_A / G, Chr2A_66560711_T / A, Chr2A_66560715_C / T, Chr2A_66560734_A / T, Chr2A_66582309_C / G, Chr2A_66582513_T / C, Chr2A_66582517_C / A, Chr2A_66583153_G / T, Chr2A_66583836_A / T, Chr2A_66602095_A / C, Chr2A_66622961_G / A, Chr2A_66632566_A / T, Chr2A_66649978_C / G, Chr2A_66688977_A / G, Chr2A_66688993_G / C, Chr2A_66689020_T / G, Chr2A_66699411_C / T, Chr2A_66699851_A / G, Chr2A_66701157_C / T, Chr2A_66701174_T / C, Chr2A_66701229_T / C, Chr2A_66701961_G / A, Chr2A_66702950_C / T, Chr2A_66703015_C / T, Chr2A_66703024_G / A, Chr2A_66729693_C / A, Chr2A_66770831_T / A, Chr2A_66774364_A / G, Chr2A_66774377_C / T, Chr2A_66785604_C / T, Chr2A_66789031_C / T, Chr2A_66789048_G / A, Chr2A_66789350_C / T, Chr2A_66789363_A / T, Chr2A_66789521_T / G, Chr2A_66789530_C / G, Chr2A_66789562_A / T, Chr2A_66810490_T / G, Chr2A_66810510_T / C, Chr2A_66810535_A / T, Chr2A_66817549_T / A,Chr2A_66817590_T / C, Chr2A_66825137_G / T, Chr2A_66833318_C / T, Chr2A_66884959_T / C, Chr2A_66884961_C / T, Chr2A_66926783_C / T, Chr2A_66930195_A / G, Chr2A_66936223_G / A, Chr2A_66937543_A / T, Chr2A_66937568_A / G, Chr2A_66939070_C / A, Chr2A_66939102_G / A, Chr2A_66952798_A / G, Chr2A_66952806_C / T, Chr2A_66952821_G / T, Chr2A_66952826_G / A, Chr2A_66960201_C / G, Chr2A_66964733_T / C, Chr2A_66965218_C / A, Chr2A_66965303_C / T, Chr2A_66965322_T / C, Chr2A_66965330_A / G, Chr2A_66967124_G / T, Chr2A_66967127_G / A, Chr2A_66973746_C / T, Chr2A_66974406_A / G, Chr2A_66974437_C / A, Chr2A_66974441_C / T, Chr2A_66974710_A / C, Chr2A_66974713_A / C, Chr2A_66974718_G / A, Chr2A_66974732_C / T, Chr2A_66974844_T / A, Chr2A_66974891_G / A, Chr2A_66974896_T / C, Chr2A_66974911_T / C, Chr2A_66974986_G / C, Chr2A_66975010_T / G, Chr2A_66975014_A / T, Chr2A_66975033_T / C, Chr2A_66975095_T / C, Chr2A_66975118_A / C, Chr2A_66975166_G / A, Chr2A_66987096_G / A, Chr2A_66987106_G / T, Chr2A_66987121_G / C, Chr2A_66987576_G / T, Chr2A_66987591_G / T, Chr2A_66987992_C / G, Chr2A_66988016_G / T, Chr2A_66988032_G / A, Chr2A_66988057_G / A,Chr2A_66988127_A / G, Chr2A_66988135_G / A, Chr2A_66989214_G / A, Chr2A_67033879_C / A, Chr2A_67033892_G / T, Chr2A_67053281_T / G, Chr2A_67101163_G / A, Chr2A_67101357_G / A, Chr2A_67101429_C / T, Chr2A_67147341_G / T, Chr2A_67246253_T / C, Chr2A_67261854_T / C, Chr2A_67261900_C / A, Chr2A_67273093_T / C, Chr2A_67273121_A / G, Chr2A_67323380_C / T, Chr2A_67324506_T / G, Chr2A_67324523_A / T, Chr2A_67342360_G / T, Chr2A_67357986_A / T, Chr2A_67357987_C / T, Chr2A_67357988_A / T, Chr2A_67360984_C / T, Chr2A_67437965_A / G, Chr2A_67437998_G / A, Chr2A_67441982_C / G, Chr2A_67442022_G / A, Chr2A_67442127_C / T, Chr2A_67442131_T / C, Chr2A_67442149_T / C, Chr2A_67442155_C / T, Chr2A_67449306_G / A, Chr2A_67449308_G / A, Chr2A_67449310_A / G, Chr2A_67449312_C / T, Chr2A_67449318_A / G, Chr2A_67449319_C / T, Chr2A_67449346_G / A, Chr2A_67484933_G / A, Chr2A_67484957_A / C, Chr2A_67499327_A / G, Chr2A_67499361_A / G, Chr2A_67499468_T / C, Chr2A_67499549_C / T, Chr2A_67499574_C / T, Chr2A_67499593_A / T, Chr2A_67499644_C / T, Chr2A_67499758_C / A, Chr2A_67499770_T / C, Chr2A_67499778_C / T, Chr2A_67499794_T / C, Chr2A_67499856_G / A,Chr2A_67500321_A / G, Chr2A_67500323_C / T, Chr2A_67505622_G / A, Chr2A_67689893_G / A, Chr2A_67689932_G / A, Chr2A_67689933_T / A, Chr2A_67690031_A / G, Chr2A_67690212_T / C, Chr2A_67690612_C / A, Chr2A_67690638_T / C, Chr2A_67690646_A / T, Chr2A_67690881_C / G, Chr2A_67690901_T / G, Chr2A_67690906_G / T, Chr2A_67700440_A / G, Chr2A_67700451_G / A, Chr2A_67700548_C / G, Chr2A_67700700_G / A, Chr2A_67700702_A / G, Chr2A_67700730_T / A, Chr2A_67700735_C / A, Chr2A_67700767_C / T, Chr2A_67700857_C / G, Chr2A_67700916_A / C, Chr2A_67700924_G / C, Chr2A_67700955_T / C, Chr2A_67700968_G / A, Chr2A_67700994_A / G, Chr2A_67701045_T / A, Chr2A_67701061_C / A, Chr2A_67701106_G / A, Chr2A_67701108_C / A, Chr2A_67701331_A / G, Chr2A_67701377_G / A, Chr2A_67701380_A / G, Chr2A_67701962_G / A, Chr2A_67702115_T / A, Chr2A_67702121_G / A, Chr2A_67702148_A / G, Chr2A_67702157_G / A, Chr2A_67702698_T / C, Chr2A_67702950_C / A, Chr2A_67703004_T / C, Chr2A_67703023_C / G, Chr2A_67703195_T / C, Chr2A_67703438_C / A, Chr2A_67703511_T / G, Chr2A_67703542_T / A, Chr2A_67707255_T / C, Chr2A_67710270_C / A, Chr2A_67710281_A / G, Chr2A_67710285_A / G,Chr2A_67723848_T / A, Chr2A_67922243_G / A, Chr2A_67936108_C / T, Chr2A_67945744_G / A, Chr2A_67947210_T / C, Chr2A_67948880_T / C, Chr2A_67948890_G / A, Chr2A_67948938_T / C, Chr2A_67949103_A / C, Chr2A_67949115_C / T, Chr2A_67949119_T / C, Chr2A_67960580_T / G, Chr2A_67960729_G / A, Chr2A_67960736_G / C, Chr2A_67960821_G / A, Chr2A_67960842_C / T, Chr2A_67960867_G / A, Chr2A_67960884_C / T, Chr2A_67961046_C / A, Chr2A_67961087_A / G, Chr2A_67961127_C / T, Chr2A_67961168_A / G, Chr2A_67961178_T / G, Chr2A_67961186_G / A, Chr2A_67961250_T / C, Chr2A_67961259_T / G, Chr2A_67961286_T / G, Chr2A_67964127_T / C, Chr2A_67964130_C / T, Chr2A_67964139_C / T, Chr2A_67964146_T / C, Chr2A_67964152_A / G, Chr2A_67964160_G / A, Chr2A_67964169_G / A, Chr2A_67964193_A / T, Chr2A_68205323_C / T, Chr2A_68207319_G / T, Chr2A_69490501_A / C, Chr2A_69490642_T / C, Chr2A_69490643_G / A, Chr2A_77462850_C / A, Chr2A_79148333_C / A, Chr2A_79410445_A / G, Chr2A_79410495_A / T, Chr2A_79410499_A / G, Chr2A_79410506_G / A, Chr2A_79479988_A / G, Chr2A_79480042_C / T, Chr2A_79480059_A / G, Chr2A_79488008_A / G, Chr2A_83203595_T / C, Chr2A_83290598_G / T,Chr2A_83313086_A / G, Chr2A_83369579_A / T, Chr2A_83369643_A / C, Chr2A_83385112_A / T, Chr2A_83385158_G / A, Chr2A_83385907_C / T, Chr2A_83387330_C / G, Chr2A_83736086_A / C, Chr2A_83757921_C / A, Chr2A_83757995_T / C, Chr2A_83980746_A / G, Chr2A_83980751_G / C, Chr2A_83980843_T / C, Chr2A_83989866_G / T, Chr2A_83989946_T / A, Chr2A_83989947_C / A, Chr2A_83990186_C / T, Chr2A_83990383_T / C, Chr2A_83990417_C / T, Chr2A_83990499_G / A, Chr2A_83990597_C / T, Chr2A_83991729_A / C, Chr2A_83991773_C / A, Chr2A_83992201_G / A, Chr2A_83994252_G / A, Chr2A_84191328_G / A, Chr2A_84191583_G / A, Chr2A_84245898_T / C, Chr2A_84254780_G / A, Chr2A_84254783_G / T, Chr2A_84305167_T / C, Chr2A_84335744_G / A, Chr2A_84386573_T / C, Chr2A_84386597_C / T, Chr2A_84539162_A / G, Chr2A_84698188_A / C, Chr2A_84825533_G / A, Chr2A_84865221_A / T, Chr2A_85043605_A / T, Chr2A_85131482_A / G, Chr2A_85243407_A / G, Chr2A_85403859_G / A, Chr2A_85471810_T / A, Chr2A_85553081_A / G, Chr2A_85553127_C / T, Chr2A_85553144_T / G, Chr2A_85553151_A / G, Chr2A_85660308_C / T, Chr2A_85660311_T / A, Chr2A_85660325_T / C, Chr2A_85691341_C / A, Chr2A_85694911_A / T,Chr2A_85699914_T / C, Chr2A_85699923_A / G, Chr2A_85699924_T / C, Chr2A_85700106_C / T, Chr2A_85700288_A / G, Chr2A_85701866_A / G, Chr2A_85705706_C / T, Chr2A_85718365_C / A, Chr2A_85718407_T / A, Chr2A_85740874_G / T, Chr2A_85744889_C / T, Chr2A_85744928_A / T, Chr2A_85770759_T / G, Chr2A_85775450_T / G, Chr2A_85775466_G / C, Chr2A_85800086_G / A, Chr2A_85800869_T / C, Chr2A_85800907_A / T, Chr2A_85806406_G / A, Chr2A_85806412_C / T, Chr2A_85806420_A / G, Chr2A_85806491_C / G, Chr2A_85806550_C / A, Chr2A_85806748_A / G, Chr2A_85806753_T / C, Chr2A_85806818_C / T, Chr2A_85807058_T / A, Chr2A_85829383_C / T, Chr2A_85840528_C / T, Chr2A_85848277_A / G, Chr2A_85863418_G / A, Chr2A_85863473_A / C, Chr2A_85867415_T / C, Chr2A_85949066_C / A, Chr2A_85949131_A / C, Chr2A_86017599_C / A, Chr2A_86027521_G / A, Chr2A_86027522_A / T, Chr2A_86028594_A / G, Chr2A_86046909_T / G, Chr2A_86127102_T / A, Chr2A_86127382_T / G, Chr2A_86127390_C / T, Chr2A_86131831_T / A, Chr2A_86135853_T / C, Chr2A_86135942_T / A, Chr2A_86136158_T / C, Chr2A_86137410_C / T, Chr2A_86147446_G / A, Chr2A_86147512_C / T, Chr2A_86156419_A / G, Chr2A_86165443_A / T,Chr2A_86208695_C / T, Chr2A_86208696_C / A, Chr2A_86208707_T / C, Chr2A_86217601_T / C, Chr2A_86217664_A / T, Chr2A_86254514_A / T, Chr2A_86255255_C / T, Chr2A_86255465_G / A, Chr2A_86256150_A / G, Chr2A_86256216_C / T, Chr2A_86258949_G / A, Chr2A_86259040_C / A, Chr2A_86283248_A / T, Chr2A_86492440_A / G, Chr2A_86492450_G / C, Chr2A_86493641_G / A, Chr2B_7595902_C / T, Chr2B_9243020_C / T, Chr2B_18136856_G / A, Chr2B_18136867_T / G, Chr2B_20286964_T / A, Chr2B_22286959_C / G, Chr2B_32531061_C / T, Chr2B_33176780_A / G, Chr2B_44539083_G / T, Chr2B_54579465_C / T, Chr2B_54579615_C / T, Chr2B_62283365_G / C, Chr2B_62283417_G / C, Chr2B_62286782_A / G, Chr2B_62286883_G / A, Chr2B_62293045_A / T, Chr2B_62293106_T / A, Chr2B_62293155_A / G, Chr2B_62293393_G / T, Chr2B_62293413_C / T, Chr2B_62293422_A / C, Chr2B_62293519_G / A, Chr2B_62293551_C / G, Chr2B_62293573_C / T, Chr2B_62293615_A / G, Chr2B_62293625_A / T, Chr2B_62293636_A / T, Chr2B_62293960_G / A, Chr2B_62326898_T / A, Chr2B_62331447_C / A, Chr2B_62331450_T / G, Chr2B_62362932_C / T, Chr2B_62363194_A / G, Chr2B_62363225_T / C, Chr2B_62363244_A / G, Chr2B_62363294_A / G,Chr2B_62363516_C / G, Chr2B_62581017_A / C, Chr2B_62946525_A / G, Chr2B_62946538_A / G, Chr2B_62946680_T / C, Chr2B_62950390_C / T, Chr2B_63021796_A / T, Chr2B_63021846_A / G, Chr2B_63021857_A / G, Chr2B_63107436_T / C, Chr2B_63108604_C / T, Chr2B_63145010_A / G, Chr2B_63442552_T / A, Chr2B_63631946_A / G, Chr2B_63631949_T / C, Chr2B_63631956_T / A, Chr2B_63716424_C / T, Chr2B_63716461_G / A, Chr2B_63792073_G / T, Chr2B_63863924_C / G, Chr2B_63863937_G / A, Chr2B_63892181_G / T, Chr2B_63924256_T / A, Chr2B_63934513_A / C, Chr2B_63934637_A / C, Chr2B_63954064_C / T, Chr2B_63954106_C / A, Chr2B_63954110_A / G, Chr2B_63995236_A / T, Chr2B_63995329_T / A, Chr2B_63995359_T / A, Chr2B_63996613_A / G, Chr2B_63996615_A / G, Chr2B_63998775_T / C, Chr2B_63998922_A / T, Chr2B_63998955_G / A, Chr2B_63998997_C / A, Chr2B_63999000_T / G, Chr2B_64023718_C / G, Chr2B_64023779_T / C, Chr2B_64023788_G / T, Chr2B_64026019_A / C, Chr2B_64030459_C / T, Chr2B_64149988_T / C, Chr2B_64150009_C / A, Chr2B_64150056_C / G, Chr2B_64150074_C / G, Chr2B_64150125_T / C, Chr2B_64205480_A / T, Chr2B_64337440_T / A, Chr2B_64375514_A / T, Chr2B_64375830_C / A,Chr2B_64375928_G / A, Chr2B_64376043_C / T, Chr2B_64376058_C / T, Chr2B_64376479_G / A, Chr2B_64376680_C / T, Chr2B_64376687_G / A, Chr2B_64376820_C / T, Chr2B_64379986_G / A, Chr2B_64380016_A / G, Chr2B_64380205_C / T, Chr2B_64380241_G / A, Chr2B_64380269_G / A, Chr2B_64380326_A / G, Chr2B_64380365_G / A, Chr2B_64380400_G / T, Chr2B_64380402_C / T, Chr2B_64380430_G / A, Chr2B_64380552_G / T, Chr2B_64380653_G / A, Chr2B_64380675_G / A, Chr2B_64380707_G / A, Chr2B_64380758_C / A, Chr2B_64381082_G / A, Chr2B_64381103_G / T, Chr2B_64381313_C / T, Chr2B_64381316_C / T, Chr2B_64381340_C / A, Chr2B_64526752_C / T, Chr2B_64526761_C / A, Chr2B_64527445_T / C, Chr2B_64527451_C / T, Chr2B_64638498_A / G, Chr2B_64638501_A / C, Chr2B_64644739_A / G, Chr2B_64647653_G / A, Chr2B_64649464_C / T, Chr2B_64649482_T / G, Chr2B_64649608_G / A, Chr2B_65197985_G / A, Chr2B_65469937_T / C, Chr2B_69134895_G / A, Chr2B_75122406_A / C, Chr2B_75344354_C / T, Chr2B_77402954_G / C, Chr2B_80328564_C / T, Chr2B_80828780_G / A, Chr2B_80936137_T / C, Chr2B_81232003_G / A, Chr2B_81232126_G / A, Chr2B_81239815_T / G, Chr2B_81334785_G / T, Chr2B_81338734_C / T,Chr2B_81345224_A / T, Chr2B_81409154_T / A, Chr2B_81419561_C / A, Chr2B_81421826_C / A, Chr2B_81422412_T / G, Chr2B_81424855_A / C, Chr2B_81424934_G / A, Chr2B_81425784_A / C, Chr2B_81425802_C / A, Chr2B_81425980_C / T, Chr2B_81426028_T / C, Chr2B_82015647_C / T, Chr2B_82057366_G / T, Chr2B_82081664_T / C, Chr2B_82292899_G / T, Chr2B_82366417_A / G, Chr2B_82785817_T / C, Chr2B_82787315_T / G, Chr2B_83066965_C / T, Chr2B_83077507_A / T, Chr2B_83572866_A / G, Chr2B_84131203_G / C, Chr3A_21707094_C / G, Chr3A_21707097_C / G, Chr3A_21707102_A / G, Chr3A_21707103_C / A, Chr3A_21707130_A / T, Chr3A_21707136_A / T, Chr3A_21707140_C / A, Chr3A_21707146_C / G, Chr3A_21707149_T / G, Chr3A_21707154_A / G, Chr3A_21707266_T / A, Chr3A_21707271_A / G, Chr3A_31296192_C / A, Chr3A_31499680_A / G, Chr4A_14607459_C / G, Chr4A_14607467_T / C, Chr4A_14607482_A / C, Chr4A_14607486_A / T, Chr4A_14607505_T / A, Chr4A_33515569_A / G, Chr4A_34421064_C / G, Chr4A_35186034_G / A, Chr4A_49671519_T / A, Chr4A_49671522_T / C, Chr4A_49671532_G / A, Chr4A_66109263_T / G, Chr4B_3113532_T / G, Chr4B_4419403_C / T, Chr4B_4864511_T / C, Chr4B_5266843_A / T,Chr4B_55445501_C / T, Chr5A_15051750_C / T, Chr5A_19254188_A / T, Chr5A_20192685_G / A, Chr5A_20258846_T / C, Chr5A_20259257_C / T, Chr5A_20269559_C / T, Chr5A_20269584_G / A, Chr5A_20269611_T / C, Chr5A_20281598_T / A, Chr5A_20281641_G / A, Chr5A_20299478_A / T, Chr5A_20299572_T / G, Chr5A_20299670_C / A, Chr5A_20299826_G / A, Chr5A_20300898_C / T, Chr5A_20406145_C / T, Chr5A_20536458_C / G, Chr5A_20536465_A / G, Chr5A_20536473_T / A, Chr5A_20536476_G / A, Chr5A_20536613_A / G, Chr5A_20536621_A / G, Chr5A_20537276_G / C, Chr5A_20537415_C / T, Chr5A_20596792_A / G, Chr5A_20972159_G / A, Chr5A_20973194_C / T, Chr5A_20973202_C / T, Chr5A_20974614_G / T, Chr5A_20974676_A / C, Chr5A_20974688_C / G, Chr5A_20974920_C / G, Chr5A_20974928_G / A, Chr5A_20974965_G / T, Chr5A_20975001_T / C, Chr5A_20975003_T / A, Chr5A_20975005_T / A, Chr5A_20976997_C / T, Chr5A_20977885_C / T, Chr5A_20978375_C / A, Chr5A_20978471_C / T, Chr5A_20978605_A / G, Chr5A_20978613_G / A, Chr5A_20990425_A / G, Chr5A_20990482_A / G, Chr5A_20990524_A / G, Chr5A_20990532_T / C, Chr5A_20990533_G / A, Chr5A_20990534_G / A, Chr5A_20990549_G / T, Chr5A_20990550_C / G,Chr5A_21010593_G / T, Chr5A_21094373_C / T, Chr5A_21094508_T / C, Chr5A_21094533_G / A, Chr5A_21094536_G / A, Chr5A_21108096_T / C, Chr5A_21108854_T / A, Chr5A_21117534_C / T, Chr5A_21117544_C / T, Chr5A_21203896_C / T, Chr5A_21489052_G / T, Chr5A_21580701_G / A, Chr5A_21596255_G / T, Chr5A_21596268_C / T, Chr5A_23435054_G / A, Chr5A_31014330_A / G, Chr5A_33357516_C / A, Chr5A_74251316_A / C, Chr5A_76214067_A / G, Chr5A_76245190_T / G, Chr5A_76245374_C / T, Chr5A_76245387_C / T, Chr5A_76245685_T / C, Chr5A_76745283_C / T, Chr5A_77133652_C / T, Chr5A_77146950_C / A, Chr5A_77147047_C / G, Chr5A_77148493_G / A, Chr5A_77186753_C / T, Chr5A_77186833_T / C, Chr5A_77186838_G / A, Chr5A_77186844_T / G, Chr5A_77361976_G / C, Chr5A_77655957_T / C, Chr5A_78394334_T / C, Chr5A_78394366_T / C, Chr5A_78394434_C / T, Chr5A_78394436_C / T, Chr5A_78636949_G / T, Chr5A_78713534_T / A, Chr5A_78815771_T / C, Chr5A_78961378_C / G, Chr5A_78961922_C / A, Chr5A_78961974_G / A, Chr5A_78961995_A / C, Chr5A_78962013_G / A, Chr5A_78962330_G / A, Chr5A_78971043_T / C, Chr5A_78971198_T / C, Chr5A_78971603_C / G, Chr5A_78971698_C / T, Chr5A_78971782_A / G,Chr5A_78972176_T / G, Chr5A_78972191_T / C, Chr5A_79044862_A / G, Chr5A_79044866_A / T, Chr5A_79045234_T / A, Chr5A_79045332_T / C, Chr5A_79045361_C / T, Chr5A_79045375_G / A, Chr5A_79123820_C / T, Chr5A_79248545_A / T, Chr5A_79518435_C / T, Chr5A_79528046_G / A, Chr5A_79535916_T / C, Chr5A_79571650_A / G, Chr5A_79982959_G / C, Chr5A_80126010_C / A, Chr5A_80435914_T / A, Chr5A_80681797_A / G, Chr5A_80681812_C / A, Chr5A_80681973_A / G, Chr5A_80684818_T / C, Chr5A_80684918_A / T, Chr5A_80745900_C / T, Chr5A_80756378_T / C, Chr5A_80797881_T / C, Chr5A_80808060_T / C, Chr5A_80857985_C / T, Chr5A_80857989_C / T, Chr5A_81217913_A / C, Chr5A_81217981_C / G, Chr5A_81217993_G / A, Chr5A_81218028_G / T, Chr5A_81218170_T / G, Chr5A_81218251_C / T, Chr5A_81354626_C / G, Chr5A_81473741_A / T, Chr5A_81509566_C / T, Chr5A_81509823_G / A, Chr5A_81509921_G / A, Chr5A_81548430_G / A, Chr5A_81556151_G / A, Chr5A_81744071_G / A, Chr5A_81747479_C / A, Chr5A_81747810_A / T, Chr5A_81747826_A / G, Chr5A_81747954_A / T, Chr5A_81747956_A / T, Chr5A_81747970_G / T, Chr5A_81751391_G / T, Chr5A_81751397_C / T, Chr5A_81755082_G / A, Chr5A_81759038_T / C,Chr5A_81769987_G / A, Chr5A_82560459_C / A, Chr5A_85058524_T / C, Chr5A_85077996_G / C, Chr5A_85129188_C / T, Chr5A_85598728_C / T, Chr5A_85794633_C / T, Chr5A_85952857_A / C, Chr5A_89540375_T / C, Chr5A_89540395_T / C, Chr5A_89540400_T / C, Chr5A_89540405_C / T, Chr5A_89589057_A / T, Chr5B_17867240_T / C, Chr5B_17867243_C / T, Chr5B_17867529_A / G, Chr5B_17867538_A / G, Chr5B_17867561_A / G, Chr5B_17867667_A / T, Chr5B_18018518_C / G, Chr5B_18018816_A / G, Chr5B_18020799_C / T, Chr5B_18045745_A / G, Chr5B_18645807_C / T, Chr5B_18826608_C / T, Chr5B_19282333_C / A, Chr5B_19695844_T / C, Chr5B_19695863_C / T, Chr5B_19766656_G / A, Chr5B_19766662_G / A, Chr5B_19816401_A / G, Chr5B_19817064_T / G, Chr5B_19861189_C / T, Chr5B_20116060_C / T, Chr5B_20116203_G / A, Chr5B_20144084_C / T, Chr5B_20153910_A / T, Chr5B_20153921_T / C, Chr5B_20154026_A / G, Chr5B_20154290_C / T, Chr5B_20206639_G / A, Chr5B_30339803_G / A, Chr5B_30339816_G / A, Chr5B_30584791_C / T, Chr5B_31928686_C / G, Chr5B_31928694_A / G, Chr5B_53855683_C / T, Chr5B_53855703_T / C, Chr5B_53941504_G / A, Chr5B_53941671_T / G, Chr5B_54900291_G / A, Chr5B_54900322_G / A,Chr5B_55108475_C / G, Chr5B_55109194_T / G, Chr5B_55109306_C / T, Chr5B_55247890_A / G, Chr5B_66916889_T / G, Chr5B_69002627_T / C, Chr5B_74045937_C / T, Chr5B_74048129_T / A, Chr5B_74048132_G / A, Chr5B_74306748_C / T, Chr5B_74321711_T / A, Chr5B_74472049_C / T, Chr5B_74472090_C / T, Chr5B_74605105_T / A, Chr5B_74605126_A / G, Chr5B_74606787_A / G, Chr5B_74607238_G / T, Chr5B_77228700_T / C, Chr5B_77415560_G / A, Chr5B_77680797_T / C, Chr5B_82461255_C / T, Chr5B_84451021_C / T, Chr5B_85330711_C / A, Chr6A_5693656_C / T, Chr6A_7509618_G / A, Chr6A_7516325_C / T, Chr6A_7520207_C / A, Chr6A_7571723_C / A, Chr6A_7824382_C / T, Chr6A_7874843_G / A, Chr6A_7906316_A / C, Chr6A_7994431_T / A, Chr6A_10514367_G / A, Chr6A_23803122_T / C, Chr6A_28190185_A / G, Chr6A_32719714_A / G, Chr6A_33374167_A / G, Chr6A_33803758_A / G, Chr6A_33848006_C / A, Chr6A_34084402_A / C, Chr6A_34472908_A / C, Chr6A_34472996_G / A, Chr6A_34615635_C / G, Chr6A_35105127_G / A, Chr6A_35105130_A / G, Chr6A_35105205_T / C, Chr6A_35105259_A / C, Chr6A_35723439_T / A, Chr6A_35723459_T / G, Chr6A_35725765_T / C, Chr6A_35727054_T / C, Chr6A_35727102_T / C, Chr6A_36986743_T / C,Chr6A_48292184_T / A, Chr6A_56895284_C / T, Chr6A_57749037_G / C, Chr6A_57749067_G / C, Chr6A_57749074_T / C, Chr6A_57749092_C / A, Chr6A_57749097_G / T, Chr6A_62603318_C / T, Chr6A_62746712_G / A, Chr6A_62755651_T / C, Chr6A_62837380_G / A, Chr6A_62892985_T / C, Chr6A_62952420_C / T, Chr6A_63082146_C / T, Chr6A_63494745_G / A, Chr6A_63509435_T / C, Chr6A_63539500_T / C, Chr6A_63556309_T / C, Chr6A_63556454_T / C, Chr6A_63556703_C / T, Chr6A_63558115_G / A, Chr6A_63558143_C / T, Chr6A_63559908_A / G, Chr6A_63559925_C / T, Chr6A_63568626_G / T, Chr6A_63619535_C / A, Chr6A_63694789_A / G, Chr6A_63708116_C / T, Chr6A_63708122_A / G, Chr6A_63708247_C / T, Chr6A_63708896_C / T, Chr6A_63708925_T / A, Chr6A_63709873_G / A, Chr6A_63711550_T / C, Chr6A_63711552_G / A, Chr6A_63711572_G / A, Chr6A_63711577_A / G, Chr6A_63729769_T / C, Chr6A_63749702_C / A, Chr6A_63955194_G / A, Chr6A_63968507_T / C, Chr6A_64014158_A / C, Chr6A_64014377_C / T, Chr6A_64014384_A / T, Chr6A_64018144_T / C, Chr6A_64065654_T / G, Chr6A_64089052_C / A, Chr6A_64089065_A / T, Chr6A_64089081_G / C, Chr6A_64129753_T / G, Chr6A_64129778_G / A, Chr6A_64129788_C / T,Chr6A_64146599_C / T, Chr6A_64147204_T / G, Chr6A_64147222_G / A, Chr6A_64147432_G / A, Chr6A_64147454_C / T, Chr6A_64147496_T / C, Chr6A_64147568_G / A, Chr6A_64147579_T / G, Chr6A_64147587_C / T, Chr6A_64148745_G / T, Chr6A_64160084_A / T, Chr6A_64160149_C / T, Chr6A_64161185_T / A, Chr6A_64162430_A / G, Chr6A_64162511_G / T, Chr6A_64179945_A / G, Chr6A_64180112_T / C, Chr6A_64180117_C / T, Chr6A_64201129_C / T, Chr6A_64201358_G / A, Chr6A_64201367_C / T, Chr6A_64201381_C / T, Chr6A_64202146_G / A, Chr6A_64209425_G / A, Chr6A_64209471_T / C, Chr6A_64267134_A / T, Chr6A_64290145_G / A, Chr6A_64290217_C / T, Chr6A_64290248_C / T, Chr6A_64290579_C / T, Chr6A_64312740_G / A, Chr6A_64315382_A / C, Chr6A_64315386_T / C, Chr6A_64315496_C / T, Chr6A_64315628_C / G, Chr6A_64315775_G / A, Chr6A_64315782_T / C, Chr6A_64315844_C / T, Chr6A_64316410_G / A, Chr6A_64323599_T / C, Chr6A_64325861_A / G, Chr6A_64325943_G / A, Chr6A_64362054_C / T, Chr6A_64364558_C / T, Chr6A_64462109_G / A, Chr6A_64474018_A / G, Chr6A_65189489_T / A, Chr6A_65282097_G / A, Chr6A_65460066_G / C, Chr6A_66169829_C / T, Chr6A_66217634_G / A, Chr6A_66490103_T / G,Chr6A_66490142_G / A, Chr6A_67147650_C / T, Chr6A_67220087_T / G, Chr6A_67311017_C / T, Chr6A_68456880_A / G, Chr6B_4325212_G / T, Chr6B_4847775_C / A, Chr6B_6609426_G / T, Chr6B_6771187_A / T, Chr6B_11487741_T / C, Chr6B_11975072_C / G, Chr6B_12318905_C / T, Chr6B_12946938_C / T, Chr6B_12949566_C / T, Chr6B_12949597_T / C, Chr6B_13883766_A / T, Chr6B_14242589_A / C, Chr6B_14528883_A / G, Chr6B_14770825_A / G, Chr6B_18361661_C / A, Chr6B_18911444_C / A, Chr6B_19526750_G / C, Chr6B_19911569_A / G, Chr6B_20266043_G / T, Chr6B_23739373_C / A, Chr6B_25662011_A / C, Chr6B_25985348_G / T, Chr6B_25989154_A / G, Chr6B_26050033_T / C, Chr6B_26543473_C / T, Chr6B_26570395_A / T, Chr6B_26571017_A / C, Chr6B_31663576_A / G, Chr6B_31721317_C / T, Chr6B_32169890_A / G, Chr6B_32169910_G / T, Chr6B_32171826_C / A, Chr6B_32173240_T / C, Chr6B_32214694_G / A, Chr6B_32214858_C / T, Chr6B_32232106_T / C, Chr6B_32232799_C / T, Chr6B_32233972_A / C, Chr6B_32254175_C / G, Chr6B_32442378_A / G, Chr6B_32442388_C / T, Chr6B_32442398_A / G, Chr6B_32564949_A / G, Chr6B_32609563_C / T, Chr6B_32843726_C / G, Chr6B_33137971_C / G, Chr6B_33137973_C / T,Chr6B_33196441_A / G, Chr6B_33196614_T / C, Chr6B_33196674_T / C, Chr6B_33214263_T / C, Chr6B_33214319_G / T, Chr6B_33384504_A / C, Chr6B_33523882_A / G, Chr6B_33524341_G / A, Chr6B_33573770_G / A, Chr6B_33573780_C / T, Chr6B_33573800_T / A, Chr6B_33573806_T / C, Chr6B_33573853_T / C, Chr6B_33573912_T / C, Chr6B_33573978_A / G, Chr6B_33573991_T / C, Chr6B_33573995_A / G, Chr6B_33574285_T / C, Chr6B_33575584_A / G, Chr6B_33575647_G / A, Chr6B_33575746_T / C, Chr6B_33576775_A / G, Chr6B_33576791_T / A, Chr6B_34018441_G / A, Chr6B_34018945_T / G, Chr6B_34100199_T / G, Chr6B_34359886_A / T, Chr6B_34398836_T / G, Chr6B_34403318_A / T, Chr6B_34409269_A / C, Chr6B_34409296_C / A, Chr6B_34409299_T / G, Chr6B_34448255_G / A, Chr6B_34487985_G / A, Chr6B_34487995_T / C, Chr6B_34487996_T / G, Chr6B_34488004_T / G, Chr6B_34488005_G / C, Chr6B_34488179_A / G, Chr6B_34557817_C / A, Chr6B_34666117_C / T, Chr6B_34666690_T / C, Chr6B_35008381_T / C, Chr6B_35010204_T / A, Chr6B_35010206_A / G, Chr6B_35010207_A / G, Chr6B_35115243_T / C, Chr6B_35123606_T / C, Chr6B_35237047_T / C, Chr6B_35306212_C / G, Chr6B_49616231_A / G, Chr6B_56736395_C / T,Chr6B_58825298_A / G, Chr6B_58977821_C / T, Chr6B_58977822_C / T, Chr6B_59590903_C / T, Chr6B_59952552_G / A, Chr6B_60118099_C / G, Chr6B_60118101_T / A, Chr6B_60118112_T / C, Chr6B_60124531_A / G, Chr6B_60169214_T / G, Chr6B_60384887_G / C, Chr6B_61487225_T / C, Chr7A_4010260_G / A, Chr7A_6787129_C / T, Chr7A_6787131_A / G, Chr7A_6877736_G / C, Chr7A_6932258_G / A, Chr7A_6932262_C / T, Chr7A_7099517_G / A, Chr7A_7099574_G / A, Chr7A_7347235_C / T, Chr7A_7347280_C / T, Chr7A_7347281_T / C, Chr7A_11805037_A / T, Chr7A_11806349_G / A, Chr7A_20401198_T / C, Chr7A_20401216_A / T, Chr7A_24669884_C / T, Chr7A_24835244_C / T, Chr7A_24842488_T / G, Chr7A_24846097_T / G, Chr7A_29939357_A / G, Chr7A_30352532_A / C, Chr7A_30741443_A / G, Chr7A_30741452_A / T, Chr7A_30741489_T / C, Chr7A_30741506_T / G, Chr7A_30741952_G / A, Chr7A_30742119_C / T, Chr7A_30804617_G / C, Chr7A_30880032_G / C, Chr7A_30881362_C / T, Chr7A_30888667_G / A, Chr7A_30888672_G / A, Chr7A_30891398_C / A, Chr7A_30891401_T / C, Chr7A_30891523_C / T, Chr7A_30892530_T / C, Chr7A_30892636_G / A, Chr7A_30893081_A / C, Chr7A_30893248_C / T, Chr7A_30893264_G / A, Chr7A_30894905_G / A,Chr7A_30895345_T / A, Chr7A_30895352_A / T, Chr7A_30895364_G / T, Chr7A_30895396_A / G, Chr7A_30895413_G / A, Chr7A_30895477_A / G, Chr7A_30895626_C / T, Chr7A_30898570_G / T, Chr7A_30900735_C / T, Chr7A_30900980_A / G, Chr7A_30901058_A / T, Chr7A_30903866_G / A, Chr7A_30904344_G / A, Chr7A_30914244_G / A, Chr7A_30925635_C / T, Chr7A_30925640_C / T, Chr7A_30925659_A / T, Chr7A_30932762_A / T, Chr7A_30940974_A / G, Chr7A_31143985_G / A, Chr7A_31144853_C / T, Chr7A_31145673_C / T, Chr7A_31145768_T / C, Chr7A_31146593_C / T, Chr7A_31147976_G / A, Chr7A_31147977_T / C, Chr7A_31148501_A / G, Chr7A_31160834_A / T, Chr7A_31161521_C / T, Chr7A_31161548_C / A, Chr7A_31161554_G / A, Chr7A_31170545_C / A, Chr7A_31170932_T / A, Chr7A_31171449_C / T, Chr7A_31220612_T / A, Chr7A_31220624_A / G, Chr7A_31234283_G / A, Chr7A_31384339_T / A, Chr7A_31420434_A / G, Chr7A_31420833_T / C, Chr7A_31421014_G / A, Chr7A_31421016_T / C, Chr7A_31465333_T / C, Chr7A_31465343_C / T, Chr7A_31465350_G / A, Chr7A_31465491_C / T, Chr7A_31465992_C / T, Chr7A_31465993_C / T, Chr7A_31465995_G / A, Chr7A_31466001_A / T, Chr7A_31466421_G / T, Chr7A_31479815_C / T,Chr7A_31479831_C / T, Chr7A_31479840_T / C, Chr7A_31479897_C / T, Chr7A_31479928_A / G, Chr7A_31479984_C / A, Chr7A_31482728_A / C, Chr7A_31485022_A / G, Chr7A_31485027_A / G, Chr7A_31485052_A / T, Chr7A_31485151_A / T, Chr7A_31488313_C / G, Chr7A_31516628_G / A, Chr7A_31518809_G / A, Chr7A_31519031_C / T, Chr7A_31519114_A / T, Chr7A_31520548_C / A, Chr7A_31521077_C / T, Chr7A_31521099_T / A, Chr7A_31521277_C / T, Chr7A_31521340_C / T, Chr7A_31521506_G / A, Chr7A_31521595_G / A, Chr7A_31521758_C / T, Chr7A_31521870_C / T, Chr7A_31521894_C / T, Chr7A_31524952_T / C, Chr7A_31532475_G / T, Chr7A_31537394_C / T, Chr7A_31556841_A / G, Chr7A_31876085_G / C, Chr7A_31877224_T / C, Chr7A_31877301_T / A, Chr7A_31877424_C / T, Chr7A_31877728_G / A, Chr7A_31900559_G / A, Chr7A_31901028_T / A, Chr7A_32547445_T / C, Chr7A_34436369_A / G, Chr7A_35368267_C / T, Chr7A_35768998_G / A, Chr7A_43490348_C / G, Chr7A_47206152_G / A, Chr7A_47315753_C / T, Chr7A_48836095_C / T, Chr7A_56946307_G / T, Chr7A_59075352_T / C, Chr7A_67604192_C / T, Chr7A_67604193_A / G, Chr7B_177532_A / G, Chr7B_1916898_C / G, Chr7B_3230059_G / T, Chr7B_3230074_A / G,Chr7B_3990844_T / C, Chr7B_6603491_G / T, Chr7B_7284354_G / A, Chr7B_26453266_G / A, Chr7B_26453325_A / G, Chr7B_26453379_T / C, Chr7B_26453397_C / T, Chr7B_26453399_G / A, Chr7B_26474514_G / A, Chr7B_31622066_C / T, Chr7B_31623393_T / C, Chr7B_46513292_T / G,

[0077] The SNP sites are determined by whole genome association analysis on 358 Rosa resequencing materials, and are screened by multiple software and model association.

[0078] Embodiment 2

[0079] The probe for predicting the vase life of Rosa rea is a liquid phase probe, the sequence of which is designed according to the SNP site, and is used for hybridizing with the genomic DNA of Rosa, capturing the DNA fragments in the region where the target SNP site is located, so as to perform subsequent sequencing analysis, determine the genotype of the tested Rosa, and predict the vase life trait thereof.

[0080] Embodiment 3

[0081] The prediction chip for predicting the vase life of Rosa rea comprises probes for detecting the 1679 SNP sites, and by detecting the genotypes of these SNP sites in the genomic DNA of the tested Rosa sample, the whole genome selection model is constructed in advance, and the vase life trait of Rosa is accurately predicted.

[0082] Embodiment 4

[0083] The application of the SNP molecular marker combination, probe or chip in the prediction of the vase life of Rosa rea is that the genomic DNA of the Rosa plant is extracted, and the SNP site combination, probe or chip is used for detection.

[0084] Embodiment 5

[0085] The method for predicting the vase life of Rosa rea based on the SNP molecular marker combination comprises the following steps:

[0086] (1) extracting the genomic DNA of the tested Rosa plant;

[0087] (2) constructing a library for the genomic DNA;

[0088] (3) using probes to hybridize capture DNA fragments in the library, enriching DNA fragments containing target SNP sites;

[0089] (4) high-throughput sequencing of the captured DNA fragments;

[0090] (5) comparing and analyzing the sequencing data with the Rosa reference genome to determine the genotype of the SNP site;

[0091] (6) inputting the genotype data of the SNP site into a whole genome selection model to obtain the prediction result of the bottle insertion life trait of the Rosa to be tested.

[0092] Example 6

[0093] The application of the SNP site combination, probe, chip or prediction method of the application in Rosa molecular breeding is used for early, accurate and efficient prediction and screening of the bottle insertion life trait of breeding materials in the breeding process of Rosa, so as to shorten the breeding cycle, improve the selection efficiency and cultivate new varieties of Rosa with excellent bottle insertion life trait.

[0094] The whole genome selection model constructed based on the SNP site combination can predict the bottle insertion life of Rosa, and the prediction accuracy is greater than 0.710.

[0095] Example 7

[0096] The Rosa molecular breeding method based on SNP markers of the application comprises the following steps:

[0097] (1) extracting Rosa genomic DNA;

[0098] (2) using the liquid breeding chip to capture and enrich the genomic DNA;

[0099] (3) high-throughput sequencing of the captured and enriched DNA;

[0100] (4) analyzing the sequencing data to detect the genotype of the 1679 SNP sites.

[0101] Example 8

[0102] The bottle insertion life whole genome association analysis of 358 Rosa whole genome resequencing data comprises the following processes:

[0103] (1) using the magnetic bead method to extract the genomic DNA of 358 Rosa leaf tissues, constructing a whole genome resequencing library, screening the DNA fragments meeting the sequencing requirements by magnetic beads, quantifying by qbit, and using Huada DNBSEQ-T7 for sequencing;

[0104] (2) The fq.gz format of the sequencing data obtained in step (1) is aligned with the R. hybrida 'Samantha' genome (v2) using bwa software

[0105] (https: / / figshare.com / articles / dataset / _i_R_hybrida_i_Samantha_genome_v2_ / 28738781?file=53454104) genome. The SNP variation data is analyzed using GATK software, and finally 115219112 high-quality SNP sites are determined,

[0106] (3) The SNP sites screened in step (2) are filtered to retain SNP sites with allele frequency greater than 0.01 and deletion rate less than 0.2. After filtering, 35335433 high-quality SNP sites are retained, and the population allele frequency ( Figure 1 ), deletion rate ( Figure 2 ) and heterozygosity ( Figure 3 ) distribution meet the requirements of subsequent association analysis.

[0107] (4) Collection of vase life agronomic traits. Select healthy, disease-free, and similar development flower branches, and insert the flower branches to a depth of 10-15 cm in a standardized environment. The water change frequency is set to every 2-3 days. Vase life refers to the duration from the beginning of the flower branch insertion into water to the appearance of obvious signs of decay (such as severe discoloration, wilting, and shedding of petals, and drying of stamens), and the loss of ornamental value, with the unit being days. Collect 3 replicate vase life data, calculate the average and BLUP value, and a total of 5 data are used for GWAS association analysis.

[0108] (5) Use emmax, gemma, rmvp (FARMCPU model, GLM model, MLM model), and tassel (GLM model) to associate the vase life agronomic traits with 268779 SNP markers at a p-value threshold of 1E-4. After removing the duplicate results of different software models, 134868 SNP sites are obtained.

[0109] (6) Probe evaluation of the SNP screened in step (5). Screening principle: no InDel marker within 50bp upstream and downstream of the SNP site; each 100bp sequence has only one copy number in the whole genome; GC content is 40-60%; no short repetitive sequence in the sequence; no N base in the sequence, finally remaining 5710 SNP sites.

[0110] (7) The SNP sites screened in step (6) are sorted according to the number of associated software and models and the association results, and the software associated with a large number of and significant association values are screened out, 1679 SNP markers with the largest number of software associations are screened out, and finally 1679 SNP markers are screened out (see Table 1 for specific information), and the chromosome distribution characteristics are as shown in Figure 4 As shown in Figure 4 As shown in Figure 4 The full-chromosome marker distribution map of the rose bottle insertion life provided by the present application.

[0111] (8) The SNP sites screened in step (7) are used in 13 whole genome selection models, including LightGBM (lgb), Random Forest (RF), SVR (svr), Lasso Regression (Lasso), Ridge Regression (Ridge), rrBLUP (rrblup), Reproducing Kernel Hilbert Space (RKHS), Bayes Ridge Regression (BRR), BayesianLasso (BL), BayesC, BayesB, BayesA and GBLUP, and the genotypes and bottle insertion life agronomic traits of 348 materials are used to evaluate the prediction accuracy of bottle insertion life. The results show that the prediction accuracy of Ridge is the lowest, the prediction accuracy of Bayes Ridge Regression (BRR) is the highest, and the overall prediction accuracy is greater than 0.710, and the prediction accuracy is good. As shown in Figure 5 As shown in Figure 5 The whole genome selection evaluation result diagram of the rose bottle insertion life provided by the present application.

[0112] (9) The SNP sites screened in step (7) are synthesized into probe sequences for capture sequencing. The prediction accuracy of each model is as shown in Figure 5 Among them, the Bayes Ridge Regression (BRR) model has the highest prediction accuracy, and the overall accuracy is greater than 0.710.

[0113] Example 9

[0114] The method for detecting roses by using the 1679 SNPs in Example 8

[0115] (1) Genomic DNA extraction: Collect rose leaves, store them with ice packs and timely transport them back to the laboratory, and use magnetic bead method to extract total DNA of roses.

[0116] (2) Genomic DNA library construction: genomic DNA fragmentation (200-300 bp), DNA fragment end repair connection adapter Pre-PCR amplification library.

[0117] (3) Probe hybridization with target region: using prepared SNP probes to hybridize with Pre-PCR library, streptomycin-modified probes to capture complementary DNA library, and then elute other library DNA after enrichment of target DNA library, i.e. Pre-PCR library after capture. Hybridization conditions: streptomycin-labeled probes hybridize with target library at 50°C for 16h, biotin-labeled magnetic beads bind with streptomycin-labeled probes at room temperature for 30min to enrich target library, and then wash buffer is used to wash non-target region library, and finally nuclease-free water is used for elution.

[0118] (4) After magnetic bead purification, the DNA concentration required for high-throughput sequencing is amplified and enriched, and then high-throughput sequencing is performed.

[0119] (5) High-throughput sequencing: the library obtained after capture and amplification in step (4) is subjected to high-throughput sequencing using DNBSEQ-T7 sequencing platform of Huada Zhi Zao, and the sequencing results of genomic DNA are obtained, and the obtained data are subjected to basic cleaning treatment.

[0120] (6) Liquid-phase probe capture rate evaluation: the cleaned sequencing data are aligned to the Rosa hybrida 'Samantha' reference sequence using bwa software, and the capture efficiency is evaluated.

[0121] Test Example 1

[0122] Evaluation of liquid-phase probe capture efficiency for 12 Rosa varieties

[0123] Experimental materials: 12 Rosa leaf samples (covering 11 varieties, including 2 independent individuals of Circus) were selected, and the specific information is shown in Table 2. The samples were immediately frozen with liquid nitrogen after collection, and stored at -80°C for standby. CTAB method was used to extract genomic DNA of each single plant, and agarose gel electrophoresis and Nanodrop detection showed that the OD260 / 280 was between 1.8-2.0, and the concentration was ≥50 ng / μL, meeting the library construction requirements.

[0124] Table 2

[0125] Number Rose variety Number Rose variety Test 1 Morris Test 2 Coffee Dream Test 3 Golden Fortune Test 4 Black Baccara Test 5 Circus Test 6 Circus Test 7 Rhapsody in Green Test 8 Chantal Test 9 Orange Bower Test 10 Ingrid Bergman Test 11 Ave's Rose Test 12 Lovers' Meeting

[0126] Experimental method

[0127] (1) Library construction

[0128] DNA was fragmented to 200-300 bp using Covaris M220 ultrasonic disrupter;

[0129] KAPA HyperPrep library construction kit was used for end repair, adapter addition and pre-amplification.

[0130] (2) Target region capture

[0131] Liquid probes (NimbleGen SeqCap EZ system) designed for 1679 SNP sites of Example 8 were used;

[0132] 95℃ denaturation for 5 min, 65℃ hybridization for 16 h, and target fragments were enriched by streptavidin magnetic beads.

[0133] (3) High-throughput sequencing

[0134] Huada DNBSEQ-T7 platform, PE150 sequencing mode;

[0135] Average data volume: 1.5 Gb / sample (range: 1.2-1.8 Gb).

[0136] (4) Data analysis

[0137] Coverage depth: average depth of target SNP region calculated by SAMtools;

[0138] Call rate: the proportion of successfully typed SNPs to the total number of markers (threshold: depth ≥ 30X, base quality Q ≥ 30).

[0139] 3. Capture efficiency evaluation results

[0140] Results analysis:

[0141] Ultra-high coverage depth: the average depth of all samples was > 390X (range: 393.67-530.84X), far exceeding the minimum detection threshold (30X); the highest depth sample was Rose of Aves (530.84X), and the lowest was Morris (393.67X). Stable high call rate: the call rate ranged from 97.62% to 98.81% (mean 98.24% ± 0.39%); the difference between different individuals of the same variety was small (e.g., Circus individual 1: 98.81% vs. individual 2: 97.66%). Key conclusion: The capture efficiency of 1679 SNP markers was stable between 97.62% and 98.81%, and the coverage depth was higher than 390X, proving that the liquid probe design can accurately cover the genomic variation of various varieties of Chinese rose and meet the requirements of whole-genome selection breeding for genotyping accuracy.

[0142] Table 3

[0143]

[0144] The verification confirms that the probe system maintains high capture efficiency (> 97.5%) for rose varieties with large genetic background differences; provides technical support for the prediction method of Example 5 and molecular breeding of Example 6; is significantly superior to traditional solid-phase chips (average detection rate < 95%), and is suitable for large-scale breeding screening.

[0145] The above shows and describes the basic principles, main features and advantages of the present application. Those skilled in the art should understand that the present application is not limited to the above examples, and the above examples and descriptions in the specification are only to illustrate the principles of the present application. Without departing from the spirit and scope of the present application, various changes and improvements can be made to the present application, and the scope of protection of the present application is defined by the appended claims, the specification and their equivalents.

Claims

1. A genome-wide SNP molecular marker combination for vase life of rose, characterized by: The SNP molecular marker combination includes 1679 SNP sites distributed on 14 chromosomes of rose; The specific information of the SNP site is represented by the structure of chromosome number_physical position_allele type. The SNP site contains a dominant allele that is significantly positively associated with the vase life of roses. The specific site information is shown in Table 1 of the specification.

2. The genome-wide SNP molecular marker combination for vase life of rose according to claim 1, characterized in that: The SNP sites were determined by performing genome-wide association analysis on 358 rose resequencing materials and screening with multiple software and model associations.

3. A probe for predicting the vase life of Chinese roses, characterized by: The probe is a liquid phase probe, the sequence of which is designed according to the SNP site, and is used to hybridize with the rose genomic DNA to capture the DNA fragments in the region where the target SNP site is located, so as to perform subsequent sequencing analysis to determine the genotype of the rose to be tested, thereby predicting its vase life traits.

4. A chip for predicting the vase life of roses, characterized by: The prediction chip contains probes for detecting the 1,679 SNP sites. By detecting the genotypes of these SNP sites in the genomic DNA of the rose sample to be tested and using a pre-constructed whole-genome selection model, accurate prediction of the rose vase life traits can be achieved.

5. Use of the SNP molecular marker combination according to claim 1, the probe according to claim 3, or the chip according to claim 4 in predicting the vase life of roses, characterized in that: The genomic DNA of the rose plant is extracted and detected using the SNP site combination, probe or chip.

6. A method for predicting the vase life of roses based on the SNP molecular marker combination according to claim 1, characterized in that The steps include: (1) Extracting genomic DNA from the rose plants to be tested; (2) constructing a library of the genomic DNA; (3) using the probe described in claim 3 to perform hybridization capture on the DNA fragments in the library to enrich the DNA fragments containing the target SNP site; (4) performing high-throughput sequencing on the captured DNA fragments; (5) comparing the sequenced data with the rose reference genome to determine the genotype of the SNP site; (6) Inputting the genotype data of the SNP site into the genome-wide selection model described in claim 4 to obtain the prediction results of the vase life trait of the rose to be tested.

7. Use of the SNP locus combination, probe, chip or prediction method according to claim 1 in rose molecular breeding, characterized in that: It is used to make early, accurate and efficient predictions and screenings of the vase-life traits of breeding materials during the rose breeding process, thereby shortening the breeding cycle, improving selection efficiency and cultivating new rose varieties with excellent vase-life traits.

8. Use of the SNP locus combination, probe, chip or prediction method according to claim 1 in rose molecular breeding, characterized in that: The whole genome selection model constructed based on the SNP site combination can predict the vase life of roses with a prediction accuracy greater than 0.

710.

9. A rose molecular breeding method based on SNP markers, characterized in that The steps include: (1) Extracting rose genomic DNA; (2) using the above-mentioned liquid-phase breeding chip to capture and enrich genomic DNA; (3) high-throughput sequencing of the captured and enriched DNA; (4) Analyze the sequencing data and detect the genotypes of the 1679 SNP sites.

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