Rosa chinensis thorn shape whole genome SNP molecular marker combination and application thereof

Abstract

The invention discloses a Chinese rose spine shape whole genome SNP molecular marker combination and application thereof, 358 Chinese rose re-sequencing materials and spine shape phenotypic data are subjected to whole genome association analysis, 679 significantly related SNP markers are screened out, and a prediction model is constructed. The probe and the chip provided by the invention can efficiently detect the target SNP site in the Chinese rose genome and predict the thorn shape, have the advantages of high efficiency, accuracy, low cost and the like, can obviously shorten the breeding period and reduce the breeding cost, and provide technical support for genetic improvement and new variety cultivation of Chinese roses.

Description

Technical Field

[0001] The present invention relates to the technical field of molecular breeding, and in particular to a whole-genome SNP molecular marker combination for rose prickle shape and an application thereof. Background Art

[0002] Rose prickle shape is a key trait, significantly impacting both ornamental value and conservation. Traditionally, improving prickle shape relies on breeding combined with artificial selection. However, this process is not only time-consuming and labor-intensive, but also requires multiple generations of screening and cultivation, resulting in low efficiency. In horticultural cultivation, prickle shape and density are key characteristics for variety identification, possessing significant ornamental and practical value.

[0003] In recent years, the introduction of molecular marker-assisted breeding technology has provided a new approach to improving the shape of rose prickles. Among them, single nucleotide polymorphisms (SNPs) are widely used due to their high efficiency, accuracy, and low cost. Through SNP markers, researchers can quickly locate gene loci related to prickle shape and achieve precise selection. Specifically, whole-genome selection breeding technology constructs an association model between genotype and prickle shape, and uses training set data to predict the agronomic traits of new materials, thereby significantly shortening the breeding cycle, reducing costs, and accelerating the cultivation process of excellent varieties.

[0004] However, SNP molecular marker technology has not been fully utilized in the current prediction of rose prickle shape. Traditional prediction methods are mainly based on models that combine phenotypic data with genomic information, but their accuracy and efficiency still need to be improved. Against this backdrop, the present invention proposes a set of SNP marker combinations that can accurately predict rose prickle shape. This aims to achieve accurate prediction of prickle shape through molecular marker-assisted breeding technology, improve breeding efficiency, and provide technical support for genetic improvement and the development of new rose varieties.

[0005] Currently, there is a lack of an efficient and accurate genome-wide SNP molecular marker combination for rose prickle shape and its application. Summary of the Invention

[0006] In order to solve the problems of the prior art, the present invention aims to provide a genome-wide SNP molecular marker combination for rose prickle shape and its application.

[0007] In order to achieve the above object, the present invention adopts the following technical solutions:

[0008] In a first aspect, the present application provides a genome-wide SNP molecular marker combination for rose prickle shape.

[0009] In a second aspect, the present application provides a probe for predicting the shape of rose prickles.

[0010] In a third aspect, the present application provides a chip for predicting the shape of rose prickles.

[0011] In a fourth aspect, the present application provides an application of a SNP molecular marker combination, probe or chip in the prediction of rose prickle shape.

[0012] In a fifth aspect, the present application provides a method for predicting rose prickle shape based on a combination of SNP molecular markers.

[0013] In a sixth aspect, the present application provides an application of a SNP site combination, probe, chip or prediction method in rose molecular breeding.

[0014] In a seventh aspect, the present application provides a rose molecular breeding method based on SNP markers.

[0015] In a first aspect, the present application provides a genome-wide SNP molecular marker combination for rose prickle shape, comprising 679 SNP sites distributed on 14 rose chromosomes; the specific information of the SNP sites is represented by a structure of chromosome number_physical position_allele type, and the SNP sites include a dominant allele that is positively and significantly associated with rose prickle shape. The specific site information is shown in Table 1 of the specification.

[0016] Furthermore, the SNP sites were determined by genome-wide association analysis of 358 rose resequencing materials and association screening using multiple software and models.

[0017] In a second aspect, the present application provides a rose prickle shape prediction probe. The screening principles of the probe include: being designed from a combination of SNP sites, being able to specifically bind to the SNP sites, being used to capture target DNA regions, and detecting specific SNP sites. Its sequence information is associated with the SNP site combination, and conforming to various screening principles of probe design, including the absence of InDel markers within 50 bp upstream and downstream of the SNP site, the uniqueness of the 100 bp upstream and downstream sequences throughout the genome, a GC content of 40-60%, and the absence of short segment repeats and N bases.

[0018] In a third aspect, the present application provides a rose prickle shape prediction chip, which comprises probes for detecting the 679 SNP sites. By detecting the genotype of the SNP sites in the genomic DNA of the rose sample to be tested and utilizing a pre-constructed whole-genome selection model, accurate prediction of the rose prickle shape trait is achieved.

[0019] In a fourth aspect, the present application provides an application of a SNP molecular marker combination, probe or chip in the prediction of rose prickle shape, by extracting genomic DNA from rose plants and using the SNP site combination, probe or chip for detection.

[0020] A fifth aspect of the present application provides a method for predicting rose prickle shape based on a combination of SNP molecular markers, comprising the following steps:

[0021] (1) Extracting genomic DNA from the rose plants to be tested;

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

[0023] (3) using probes to perform hybridization capture on the DNA fragments in the library to enrich the DNA fragments containing the target SNP site;

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

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

[0026] (6) The genotype data of the SNP locus combination are input into the whole genome selection model to obtain the prediction results of the prickle shape trait of the rose to be tested.

[0027] Furthermore, Bayes Ridge Regression (BRR) has the highest prediction accuracy among the models, with the overall prediction accuracy being greater than 0.528.

[0028] In a sixth aspect, the present application provides an application of a SNP site combination, probe, chip or prediction method in rose molecular breeding, which is used to predict and screen the prickle shape traits of breeding materials early, accurately and efficiently during the rose breeding process, thereby shortening the breeding cycle, improving selection efficiency, and cultivating new rose varieties with excellent prickle shape traits.

[0029] Furthermore, the whole-genome selection model constructed based on the SNP site combination can predict the shape of rose prickles with a prediction accuracy greater than 0.528.

[0030] In a seventh aspect, the present application provides a rose molecular breeding method based on SNP markers, comprising the following steps: applying a SNP site combination, a prediction probe, or a prediction chip to the breeding process of rose varieties, detecting the genotype in the seed or seedling stage, and predicting its prickle shape trait, thereby screening out plants with an ideal prickle shape, accelerating the cultivation of new rose varieties with fewer or even no prickles, improving the ornamental value and production efficiency of roses, and meeting market demand.

[0031] Beneficial effects: The probe and chip of the present invention can efficiently detect target SNP sites in the rose genome and predict the shape of the prickles. They have the advantages of high efficiency, accuracy, and low cost. They can significantly shorten the breeding cycle and reduce breeding costs, providing technical support for rose genetic improvement and new variety breeding.

[0032] Compared with the prior art, the present invention has the following advantages:

[0033] (1) Traditional rose breeding methods rely on phenotypic screening, which requires a lot of time and manpower for multiple generations of screening and breeding. The present invention uses SNP marker combinations and probe detection to quickly locate gene loci related to prickle shape, enabling precise selection, significantly shortening the breeding cycle, and improving breeding efficiency.

[0034] (2) The present invention utilizes SNP marker-assisted breeding technology, which reduces field planting and screening processes and reduces research and breeding costs.

[0035] (3) This invention provides important technical support for rose genetic improvement and new variety breeding, promoting the development of the rose industry and providing reference value for the improvement of traits of other horticultural crops. SNP-based probe and chip technology has the advantages of being easy to operate, fast and efficient, and is easy to promote and apply in actual production and research, providing convenient tools and methods for rose breeders.

[0036] (5) The use of SNP molecular marker technology for rose prickle shape prediction for the first time fills a technological gap in this field and provides new ideas for the application of molecular marker-assisted breeding in rose prickle shape improvement. The selected SNP markers and probes have broad applicability and can be used for the detection and evaluation of a variety of rose varieties, showing good application prospects. BRIEF DESCRIPTION OF THE DRAWINGS

[0037] In order to more clearly illustrate the technical solutions in the embodiments of the present application, the following briefly introduces the drawings required for use in the embodiments or descriptions of the prior art. Obviously, the drawings described below are only some embodiments of the present application. For ordinary technicians in this field, other drawings can be obtained based on these drawings without any creative work.

[0038] Figure 1 This is the whole chromosome marker distribution map of rose prickle shape provided by the present invention.

[0039] Figure 2 This is the allele frequency diagram of rose prickle shape provided by the present invention.

[0040] Figure 3 This is a graph showing the missing rate of rose prickles provided by the present invention.

[0041] Figure 4 This is a heterozygosity diagram of rose prickle shape provided by the present invention.

[0042] Figure 5 This is a diagram showing the results of genome-wide selection evaluation of rose prickle shape provided by the present invention. DETAILED DESCRIPTION

[0043] The following will clearly and completely describe the technical solutions in the embodiments of the present invention in conjunction with the accompanying drawings. Obviously, the described embodiments are only part of the embodiments of the present invention, not all of the embodiments. Based on the embodiments of the present invention, all other embodiments obtained by ordinary technicians in this field without making creative efforts are within the scope of protection of the present invention.

[0044] In this application, the term "and / or" describes the relationship between associated objects, indicating that three possible relationships exist. For example, A and / or B can represent: A exists alone, A and B exist simultaneously, and B exists alone. A and B can be singular or plural. The character " / " generally indicates that the associated objects are in an "or" relationship.

[0045] In this application, "-one or more" means one or more, and "more than one" means two or more. "The following - one or more" or similar expressions refer to any combination of these items, including any combination of single items or plural items. For example, "a, b, or c - one or more", or "a, b, and c - one or more" can all mean: a, b, c, ab (i.e., a and b), ac, bc, or abc, where a, b, and c can be single or multiple.

[0046] It should be understood that in the various embodiments of the present application, the size of the serial numbers of the above-mentioned processes does not mean the order of execution. Some or all of the steps can be executed in parallel or sequentially. The execution order of each process should be determined by its function and internal logic, and should not constitute any limitation on the implementation process of the embodiments of the present application.

[0047] The terms used in the embodiments of the present application are for the purpose of describing specific embodiments only and are not intended to limit the present application. The singular forms "a", "an", "the" and "the" used in the embodiments of the present application and the appended claims are also intended to include plural forms unless the context clearly indicates otherwise.

[0048] The weights of the relevant components mentioned in the examples of this application may not only refer to the specific content of each component, but also represent the weight ratio between the components. Therefore, as long as the content of the relevant components is proportionally enlarged or reduced according to the examples of this application, it is within the scope disclosed in the examples of this application. Specifically, the mass described in the examples of this application may be a mass unit known in the chemical industry, such as μg, mg, g, kg, etc.

[0049] In a first aspect of an embodiment of the present application, a genome-wide SNP molecular marker combination for rose prickle shape is provided. The SNP molecular marker combination includes 679 SNP sites distributed on 14 rose chromosomes; the specific information of the SNP sites is represented in the structure of chromosome number_physical position_allele type, and the SNP sites include a dominant allele that is positively and significantly associated with rose prickle shape. The specific site information is shown in Table 1 of the specification.

[0050] The SNP sites were determined through genome-wide association analysis of 358 rose resequencing materials and association screening using multiple software and models.

[0051] A second aspect of an embodiment of the present application provides a rose prickle shape prediction probe. The screening principles of the probe include: being designed from a combination of SNP sites, being able to specifically bind to the SNP site, being used to capture a target DNA region, and detecting a specific SNP site. The sequence information thereof is associated with the SNP site combination, and conforming to various screening principles of probe design, including the absence of indel markers within 50 bp upstream and downstream of the SNP site, having only one copy number in the entire genome for each 100 bp upstream and downstream sequence, a GC content of 40-60%, the absence of short segment repeats within the sequence, and the absence of N bases.

[0052] A third aspect of an embodiment of the present application provides a rose prickle shape prediction chip, which includes probes for detecting the 679 SNP sites. By detecting the genotype of the 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 prickle shape trait is achieved.

[0053] In a fourth aspect, an embodiment of the present application provides an application of a SNP molecular marker combination, probe or chip in the prediction of rose prickle shape, by extracting genomic DNA from rose plants and using the SNP site combination, probe or chip for detection.

[0054] A fifth aspect of the present application provides a method for predicting rose prickle shape based on a combination of SNP molecular markers, comprising the following steps:

[0055] (1) Extracting genomic DNA from the rose plants to be tested;

[0056] (2) constructing a library of the genomic DNA;

[0057] (3) using probes to perform hybridization capture on the DNA fragments in the library to enrich the DNA fragments containing the target SNP site;

[0058] (4) performing high-throughput sequencing on the captured DNA fragments;

[0059] (5) Compare the sequencing data with the rose reference genome to determine the genotype of the SNP site;

[0060] (6) The genotype data of the SNP locus combination are input into the whole genome selection model to obtain the prediction results of the prickle shape trait of the rose to be tested.

[0061] In some embodiments, Bayes Ridge Regression (BRR) has the highest prediction accuracy among the models, with an overall prediction accuracy greater than 0.528.

[0062] In a sixth aspect, the present application provides an application of a SNP site combination, probe, chip or prediction method in rose molecular breeding, which is used to predict and screen the prickle shape traits of breeding materials early, accurately and efficiently during the rose breeding process, thereby shortening the breeding cycle, improving selection efficiency, and cultivating new rose varieties with excellent prickle shape traits.

[0063] In some embodiments, a genome-wide selection model constructed based on a combination of SNP sites can predict the prickle shape of roses with a prediction accuracy greater than 0.528.

[0064] In a seventh aspect, the present application provides a rose molecular breeding method based on SNP markers, comprising the following steps: applying a SNP site combination, a prediction probe, or a prediction chip to the breeding process of rose varieties, detecting the genotype in the seed or seedling stage, and predicting its prickle shape trait, thereby screening out plants with an ideal prickle shape, accelerating the cultivation of new rose varieties with fewer or even no prickles, improving the ornamental value and production efficiency of roses, and meeting market demand.

[0065] Example 1

[0066] The present invention provides a genome-wide SNP molecular marker combination for rose prickle shape, comprising 679 SNP loci distributed on 14 rose chromosomes; the specific information of the SNP loci is represented using a structure of chromosome number_physical position_allele type; the SNP loci contain dominant alleles that are positively and significantly associated with rose prickle shape, and the specific locus information is shown in Table 1.

[0067] Table 1

[0068] Chr1A_4367663_T / C,Chr1A_23239172_T / C,Chr1A_25735463_G / A,Chr1A_30298170_C / T,Chr1A_30732831_T / C,Chr1A_30732845_A / G,Chr1A_30732851_T / G,Chr1A_32653039_G / T,Chr1A_33850809_G / A,Chr1A_49858588_T / A,Chr1A_49859643_G / T,Chr1A_49860539_A / G,Chr1A_49860569_A / G,Chr1A_49860731_A / C,C hr1A_49860757_G / A,Chr1A_49860763_T / G,Chr1A_49860798_A / G,Chr1A_49860883_C / T,Chr1A_49860907_T / C,Chr1A_49860953_A / G,Chr1A_49860964_A / G,Chr1A_49862220_A / G,Chr1A_49864433_T / C,Chr1A_50901111_G / T,Chr1A_50901120_G / C,Chr1A_50901128_A / G,Chr1A_50901129_A / G,Chr1A_54884666_T / G,Chr1A_54884672_G / T,Chr1A_56786426_T / A,Chr1A_56786468_A / G,Chr1A_57555708_T / C,Chr1A_68616021_C / T,C hr1A_68616044_G / A,Chr1A_68616061_A / G,Chr1B_414272_G / T,Chr1B_414331_C / A,Chr1B_414540_G / T,Chr1B_414562_C / T,Chr1B_414584_C / G,Chr1B_414757_C / T,Chr1B_414818_G / A,Chr1B_428916_G / A,Chr1B_429189_G / A,Chr1B_429366_C / T,Chr1B_429371_G / T,Chr1B_429608_C / A,Chr1B_430188_C / T,Chr1B_430595_C / T,Chr1B_430795_A / C,Chr1B_431177_C / T,Chr1B_431307_C / T,Chr1B_5776338_A / T,Chr1B_8939946_G / T,Chr1B_8939959_C / T,Chr1B_8940069_G / A,Chr1B_9788434_A / G,Chr1B_12276036_C / T,Chr1B_26796928_A / T,Ch r1B_26796945_A / G,Chr1B_46238204_A / G,Chr2A_3163629_C / T,Chr2A_3163641_C / T,Chr2A_3243443_T / A,C hr2A_3335818_G / T,Chr2A_5984947_G / A,Chr2A_18535656_A / T,Chr2A_18535663_A / G,Chr2A_29737162_T / G,Chr2A_38285858_G / T,Chr2A_39542942_G / T,Chr2A_39721215_C / A,Chr2A_46866232_G / A,Chr2A_46885872_G / A,Chr2A_47387948_G / A,Chr2A_47387949_G / T,Chr2A_47929208_G / A,Chr2A_51055666_A / G,Chr2A_59721342_G / A,Chr2A_71426739_G / A,Chr2A_78098472_T / C,Chr2A_78185585_T / G,Chr2A_78185618_T / C,Chr2A_78185626_T / A,Chr2A_78185627_A / T,Chr2A_78490228_A / G,Chr2A_78640040_T / G,Chr2A_78750415_C / T,Chr2A_78934221_A / G,Chr2B_3711719_A / G,Chr2B_4776517_C / T,Chr2B_4776526_G / A,Chr2B_5627331_G / A,Chr2B_5627341_C / T,Chr2B_7595902_C / T,Chr2B_35231045_T / A,Chr2B_35363288_T / C,Chr2B_35363383_C / T,Chr2B_35363401_T / C,Chr2B_35363404_G / A,Chr2B_35363409_A / G,Chr2B_35363415_G / A,Chr2B_35967389_A / C,Chr2B_35967392_A / C,Chr2B_35967561_C / A,Chr2B_35967860_G / A,Chr2B_38451034_T / C,Chr2B_39277424_A / T,Chr2B_39277432_C / G,Chr2B_39401772_C / T,Chr2B_39420075_G / A,Chr2B_41548025_G / C,Chr2B_44108220_G / A,Chr2B_44108246_C / T,Chr2B_44160728_T / C,Chr2B_44799912_T / C,Chr2B_45452303_A / C,Chr2B_47820923_C / T,Chr2B_50886573_G / A,Chr2B_68110495_C / T,Chr2B_69567687_G / C,Chr2B_69567730_A / G,Chr2B_69829787_T / C,Chr2B_70498902_C / T,Chr2B_74626430_A / T,Chr2B_74662338_A / G,Chr2B_74670633_G / A,Chr2B_75059699_T / C,Chr2B_75060411_T / G,Chr2B_75060470_G / T,Chr2B_75122403_T / C,Chr2B_75122416_C / T,Chr2B_75131828_T / C,Chr2B_75131971_T / C,Chr2B_75132017_G / A,Chr2B_75132244_C / T,Chr2B_75132286_C / T,Chr2B_75233231_G / A,Chr2B_75233336_T / C,Chr2B_75233412_C / G,Chr2B_75233843_G / A,Chr3A_8459221_C / T,Chr3A_31476002_C / T,Chr3A_31476088_G / A,Chr3A_31476093_G / A,Chr3A_31476098_G / A,Chr3A_38856348_A / C,Chr3A_45967724_C / T,Chr3A_45967725_A / G,Chr3A_49183625_C / T,Chr3B_43466754_A / G,Chr3B_47320867_T / A,Chr4A_1839563_G / A,Chr4A_7391953_A / C,Chr4A_10470240_T / C,Chr4A_10470303_C / T,Chr4A_10471246_A / G,Chr4A_15005513_A / G,Chr4A_16185344_A / T,Chr4A_24508189_C / T,Chr4A_28055981_A / G,Chr4A_28141183_C / G,Chr4A_37484980_T / G,Chr4A_37767259_C / T,Chr4A_42558904_T / C,Chr4A_42558905_C / T,Chr4A_42572488_G / A,Chr4A_43193259_G / C,Chr4A_43651746_C / G,Chr4A_43674699_T / G,Chr4A_43674725_T / G,Chr4A_43674752_C / T,Chr4A_44102106_G / A,Chr4A_44164852_G / A,Chr4A_44417060_A / T,Chr4A_44818012_T / C,Chr4A_45423516_A / C,Chr4A_50510102_T / C,Chr4A_61094092_A / T,Chr4A_61270789_C / A,Chr4A_61393755_G / A,Chr4A_62654926_G / T,Chr4A_62654932_G / A,Chr4A_62654992_T / A,Chr4A_66447935_C / T,Chr4B_16799368_G / A,Chr4B_16819495_G / A,Chr4B_16963214_C / T,Chr4B_28084396_T / C,Chr4B_29828139_A / G,Chr4B_33206219_A / T,Chr4B_33206224_T / A,Chr4B_33206458_T / A,Chr4B_33206751_A / T,Chr4B_33206775_A / C,Chr4B_33206783_A / G,Chr4B_33221865_A / C,Chr4B_33221891_T / C,Chr4B_33221892_G / A,Chr4B_33221902_G / C,Chr4B_33222038_C / T,Chr4B_50196366_A / C,Chr4B_52967821_T / C,Chr4B_52986590_C / A,Chr4B_54919304_G / A,Chr4B_55245522_G / C,Chr4B_55266983_A / C,Chr4B_55662292_C / T,Chr5A_623755_A / G,Chr5A_7814973_C / T,Chr5A_10573348_T / C,Chr5A_12856769_C / G,Chr5A_12856836_A / T,Chr5A_26498719_C / T,Chr5A_26498735_A / G,Chr5A_26843655_G / A,Chr5A_50244117_T / A,Chr5A_50244121_C / A,Chr5A_50562402_G / A,Chr5A_57378931_G / T,Chr5A_57558528_A / G,Chr5A_58846257_G / A,Chr5A_58846791_A / G,Chr5A_58846956_C / T,Chr5A_59390619_C / A,Chr5A_59390623_G / T,Chr5A_61056072_C / T,C hr5A_61056088_C / G,Chr5A_61233461_G / A,Chr5A_61233511_C / G,Chr5A_61233526_A / G,Chr5A_62489376_G / A,Chr5A_63473824_C / T,Chr5A_63478729_A / G,Chr5A_63478876_C / T,Chr5A_63478886_T / A,Chr5A_63479011_G / T,Chr5A_63479116_G / A,Chr5A_63479370_C / T,Chr5A_63479376_C / T,Chr5A_63480005_A / T,Chr5A_63480234_C / T,Chr5A_63480319_A / T,Chr5A_63480325_C / T,Chr5A_63838004_A / C,Chr5A_63838033_T / A,Chr5A_63838137_T / A,Chr5A_63839323_G / T,Chr5A_65367445_G / T,Chr5A_65722500_C / G,Chr5A_66949941_C / T,Chr5A_67351580_G / A,Chr5A_67351591_C / A,Chr5A_68157006_C / A,Chr5A_68157007_G / A,Chr5A_68157337_G / A,Chr5A_68739305_G / A,Chr5A_68750315_C / G,Chr5A_68811454_C / T,Chr5A_68852901_A / G,Chr5A_69974628_G / C,Chr5A_69974632_A / C,Chr5A_69974634_A / G,Chr5A_69976981_C / T,Chr5A_69977017_C / T,Chr5A_69977019_A / T,Chr5A_69977033_A / T,Chr5A_72161010_A / T,Chr5A_72161130_G / A,Chr5A_72253089_A / T,Chr5A_72254108_G / A,Chr5A_72254207_C / T,Chr5A_72254272_G / A,Chr5A_72255692_C / A,Chr5A_72255927_C / T,Chr5A_72256223_G / T,Chr5A_72256411_C / A,Chr5A_72256473_T / G,Chr5A_72481448_G / A,Chr5A_72707224_C / T,Chr5A_73595329_T / C,Chr5A_80529538_A / G,Chr5A_81243708_G / A,Chr5A_81243712_C / A,Chr5A_83238431_C / T,Chr5A_83250041_G / A,Chr5A_83253082_C / T,Chr5A_83296689_A / G,Chr5A_83296693_G / A,Chr5A_83296749_A / G,Chr5A_83301508_G / A,Chr5A_83301655_C / T,Chr5A_83319594_T / C,Chr5A_83324618_C / A,Chr5A_83324619_C / A,Chr5A_83349276_G / T,Chr5A_83462319_T / A,Chr5A_83462475_C / T,Chr5A_83510934_C / T,Chr5A_83539847_G / C,Chr5A_83539892_A / G,Chr5A_83540159_A / G,Chr5A_83540177_G / C,Chr5A_83540193_C / T,Chr5A_83540329_G / A,Chr5A_83540355_T / C,Chr5A_83543333_C / T,Chr5A_83543480_A / G,C hr5A_83547793_T / G,Chr5A_83578393_A / G,Chr5A_83581533_G / T,Chr5A_83581930_G / T,Chr5A_83582488_T / C,Chr5A_83601580_G / A,Chr5A_83601605_T / G,Chr5A_83603630_T / C,Chr5A_83614541_G / A,Chr5A_83614559_T / A,Chr5A_83614561_T / A,Chr5A_83614562_C / G,Chr5A_83614798_T / C,Chr5A_83615119_G / A,Chr5A_83615197_G / A,Chr5A_83615215_G / T,Chr5A_83615734_C / T,Chr5A_83615878_A / G,Chr5A_83615912_C / T,C hr5A_83616994_G / A,Chr5A_83617025_A / C,Chr5A_83617254_G / A,Chr5A_83617271_C / T,Chr5A_83617292_T / C,Chr5A_83619865_C / T,Chr5A_83619882_A / G,Chr5A_83620690_T / G,Chr5A_83624626_A / T,Chr5A_83637390_A / C,Chr5A_83637391_C / T,Chr5A_83637480_T / C,Chr5A_83637542_C / T,Chr5A_83637545_G / A,Chr5A_83637612_T / G,Chr5A_83672438_A / T,Chr5A_83678376_A / C,Chr5A_83690507_T / A,Chr5A_83743340_G / C,Chr5A_83743460_C / T,Chr5A_83745142_C / T,Chr5A_83746622_C / T,Chr5A_83746718_A / T,Chr5A_83749361_T / G,Chr5A_83749409_T / C,Chr5A_83749419_C / T,Chr5A_83753582_A / G,Chr5A_87366034_C / T,Chr5B_18005099_A / C,Chr5B_18005103_T / C,Chr5B_25687860_A / G,Chr5B_25687882_T / G,Chr5B_25763573_C / A,Chr5B_25763574_G / C,Chr5B_25763641_C / T,Chr5B_25763643_A / G,Chr5B_25763698_G / T,Chr5B_26599287_C / T,Chr5B_26599351_T / C,Chr5B_28494392_T / G,Chr5B_32766392_T / C,Chr5B_32775324_T / C,Chr5B_41555318_C / T,Chr5B_42707783_C / A,Chr5B_42707802_A / G,Chr5B_42707867_A / T,Chr5B_4 7040483_T / C,Chr5B_47040508_G / T,Chr5B_47040573_G / T,Chr5B_47040590_C / T,Chr5B_47040626_C / T,Chr5B_47040890_G / A,Chr5B_47447539 _A / G,Chr5B_47759393_G / A,Chr5B_47930506_G / T,Chr5B_47930528_T / C,Chr5B_47930529_G / A,Chr5B_47930530_G / A,Chr5B_47950660_T / C,Chr5B_47952943_C / A,Chr5B_47953025_G / A,Chr5B_47953039_G / A,Chr5B_53080141_G / A,Chr5B_54955864_A / T,Chr5B_55603413_C / T,Chr5B_5677 8648_C / T,Chr5B_57087813_C / T,Chr5B_57087817_G / A,Chr5B_58562435_T / C,Chr5B_60646147_T / C,Chr5B_60782618_G / A,Chr5B_60782642_G / A,Chr5B_60782655_C / A,Chr5B_60922583_C / T,Chr5B_61112850_G / T,Chr5B_61112877_T / A,Chr5B_61117922_T / C,Chr5B_61117941_G / T,Chr5B_ 61117943_G / A,Chr5B_61118554_C / G,Chr5B_61136422_G / C,Chr5B_61159851_T / C,Chr5B_61159920_G / C,Chr5B_61159933_G / A,Chr5B_6156981 1_A / T,Chr5B_61640904_C / A,Chr5B_62070919_T / A,Chr5B_63643056_G / T,Chr5B_64862734_C / T,Chr5B_65005714_A / G,Chr5B_69002625_C / A,Ch r5B_70125782_G / C,Chr5B_70190479_C / T,Chr5B_70190601_T / A,Chr5B_70190678_C / G,Chr5B_70190691_G / A,Chr5B_70190832_G / A,Chr5B_70190947_G / A,Chr5B_70190954_G / A,Chr5B_70201981_T / A,Chr5B_70210888_C / T,Chr5B_70231472_T / C,Chr5B_70520657_T / C,Chr5B_70718782_T / A,Chr5B_70755943_T / C,Chr5B_71424573_A / T,Chr5B_71430127_C / T,Chr5B_71430199_C / T,Chr5B_71503053_T / C,Chr5B_71507936_C / A,Chr5B_71508029_G / A,Chr5B_71508047_C / T,Chr5B_71508063_G / A,Chr5B_71613758_A / T,Chr5B_71613765_G / A,Ch r5B_71639515_C / T,Chr5B_71639578_T / C,Chr5B_73108912_G / A,Chr5B_73489958_C / A,Chr5B_76918579_T / G,Chr5B_79396147_T / A,Chr5B_79919968_A / G,Chr5B_80073341_T / C,Chr5B_80073382_C / T,Chr5B_80073580_T / C,Chr5B_80074249_A / G,Chr5B_80174810_C / T,Chr5B_80174811_C / T,Chr5B_80555373_G / A,Chr6A_6318303_T / C,Chr6A_7413204_G / A,Chr6A_18628018_G / C,Chr6A_46697909_T / C,Chr6A_46697914_C / T,Chr6A_46697940_A / G,Chr6A_50404350_G / A,Chr6A_50404352_A / G,Chr6A_50749253_C / T,Chr6A_50797099_G / A,Ch r6A_50846881_G / A,Chr6A_52538968_G / A,Chr6A_52952489_C / T,Chr6A_53763280_C / A,Chr6A_59967437_G / A,Chr6A_59967663_A / T,Chr6A_59967930_A / G,Chr6A_59967951_C / G,Chr6A_59967953_A / G,Chr6A_59967955_C / T,Chr6A_64803429_T / G,Chr6A_64803437_A / T,Chr6A_64803441_A / C,Chr6A_64803533_T / A,Chr6A_64803539_G / T,Chr6A_64803549_T / C,Chr6A_64803551_C / T,Chr6A_64803620_C / A,Chr6A_64803630_A / G,Chr6A_64803647_C / G,Chr6A_64803666_G / T,Chr6A_64809973_T / C,Chr6A_64810315_A / G,Chr6A_64810353_A / T,Chr6A_64810366_C / T,Chr6A_64810374_C / T,Chr6A_64810377_G / T,Chr6A_64810393_C / A,Chr6A_64810395_A / G,Chr6A_64810420_G / A,Chr6A_64810427_G / A,Chr6A_64810571_T / C,Chr6A_64820628_G / A,Chr6A_64820770_G / A,Chr6A_64820818_G / T,Chr6A_64824773_A / G,Chr6A_64847787_T / G,Chr6A_65321649_A / G,Chr6A_65598744_G / T,Chr6A_66581130_T / C,Chr6A_67479129_A / G,Chr6B_1362802_A / G,Chr6B_1362808_A / T,Chr6B_1857547_A / T,Chr6B_1857561_G / A,Chr6B_10417927_C / T,Chr6B_10417949_A / G,Chr6B_10417977_A / T,Chr6B_12078409_A / G,Chr6B_12290634_T / G,Chr6B_12932358_C / T,Chr6B_12932434_A / G,Chr6B_12932460_G / C,Chr6B_15352523_A / G,Chr6B_15914902_C / A,Chr6B_17070959_T / C,Chr6B_18456798_C / T,Chr6B_18457044_C / G,Chr6B_18457059_A / G,Chr6B_18457190_T / C,Chr6B_18463454_G / A,Chr6B_21941095_T / C,Chr6B_23580233_T / G,Chr6B_23580238_C / T,Chr6B_23580273_G / A,Chr6B_23580278_A / G,Chr6B_33382958_A / G,C hr6B_34467649_G / A,Chr6B_34467653_G / A,Chr6B_34467661_C / T,Chr6B_34467666_T / G,Chr6B_34467674_T / C,Chr6B_34467692_T / C,Chr6B_34467698_A / C,Chr6B_34467701_C / T,Chr6B_34467718_T / A,Chr6B_34467732_A / G,Chr6B_53206943_A / G,Chr6B_53206949_C / T,Chr6B_53709080_G / A,Chr6B_61100670_T / C,Chr6B_61895036_A / C,Chr6B_62051202_G / A,Chr7A_4351051_A / G,Chr7A_4354687_C / T,Chr7A_4354742_T / C,Chr7A_4354748_T / A,Chr7A_4355167_T / C,Chr7A_4355174_A / C,Chr7A_4355212_T / C,Chr7A_4355274_A / G,Chr7A_4355283_G / A,Chr7A_4355361_C / A,Chr7A_4363146_C / T,Chr7A_4365155_G / A,Chr7A_4365491_A / G,Chr7A_4365530_A / C,Chr7A_4365571_T / C,Chr7A_4365586_T / C,Chr7A_4365616_T / G,Chr7A_4365683_G / A,Chr7A_4365711_G / A,Chr7A_4365805_A / G,Chr7A_4365914_C / G,Chr7A_4365920_C / A,Chr7A_4365928_C / A,Chr7A_4365951_C / T,Chr7A_4366164_G / A,Chr7A_4366203_A / G,Chr7A_4367108_G / T,Chr7A_4367204_G / A,Chr7A_4379895_C / T,Chr7A_4379936_T / A,Chr7A_4380506_A / T,Chr7A_4380507_T / A,Chr7A_5232689_C / G,Chr7A_5245328_G / A,Chr7A_5249589_C / T,Chr7A_8833896_C / T,Chr7A_27126989_C / T,Chr7A_30856722_C / T,Chr7A_32759829_T / C,Chr7A_32872852_G / A,Chr7A_37527840_T / C,Chr7A_3779 1197_T / C,Chr7A_38320214_T / A,Chr7A_48222328_T / C,Chr7A_48282624_A / G,Chr7A_49875797_G / A,Chr7A_49929484_G / A,Chr7A_49929490_T / G,Chr7A_49956383_A / G,Chr7A_49956388_T / C,Chr7A_50361199_T / A,Chr7A_50363709_G / A,Chr7A_50364527_C / T,Chr7A_50951312_G / A,Chr7A_5160780 7_C / T,Chr7A_51723951_T / G,Chr7A_51725491_T / A,Chr7A_51758577_C / T,Chr7A_51758587_A / T,Chr7A_51760087_A / C,Chr7A_51760121_G / T,Chr7A_55227288_T / A,Chr7A_55227364_A / G,Chr7A_55227388_G / A,Chr7A_55227406_T / C,Chr7A_55227552_T / A,Chr7A_55229280_G / C,Chr7A_55229307_A / G,Chr7A_56591496_A / G,Chr7A_56774868_G / A,Chr7A_57127064_C / A,Chr7A_57327682_G / A,Chr7A_57329734_C / T,Chr7A_57329998_C / T,Chr7A_57331575_G / A,Chr7A_57537711_A / T,Chr7A_57753488_G / C,Chr7A_57760229_T / G,Chr7A_57904521_C / T,Chr7A_59025813_A / G,Chr7A_60373679_T / C,Chr7A_63068870_C / A,Chr7A_63343889_T / C,Chr7A_63381234_A / C,Chr7A_63381243_T / C,Chr7A_63468190_G / A,Chr7A_63472028_T / C,Chr7A_63472085_T / C,Chr7A_63472754_T / C,Chr7A_63474048_C / T,Chr7B_2139165_A / G,Chr7B_3693083_T / C,Chr7B_25910464_G / T,Chr7B_37904818_G / C,Chr7B_37904821_G / C,Chr7B_37904822_A / T,Chr7B_40288243_A / G,Chr7B_40914118_A / G,Chr7B_40914132_G / T,Chr7B_40914134_G / A,Chr7B_40997542_A / C,Chr7B_41199557_T / A,Chr7B_41883949_T / C,Chr7B_41883970_C / T,Chr7B_41883971_C / T,Chr7B_41884014_C / T,Chr7B_41884044_C / A,Chr7B_41884048_G / A,Chr7B_41884055_T / A,Chr7B_41884107_C / T,C hr7B_41884109_A / G,Chr7B_41884118_T / C,Chr7B_41884750_C / T,Chr7B_41885617_G / A,Chr7B_41885702_T / G,Chr7B_41885720_G / A,Chr7B_41885762_T / C,Chr7B_41885874_A / G,Chr7B_42607114_T / C,Chr7B_42607122_C / T,Chr7B_42607157_A / C,Chr7B_42631484_C / T,Chr7B_42631506_G / T,Chr7B_44121825_C / T,Chr7B_44168497_G / T,Chr7B_44168506_G / T,Chr7B_45518173_G / A,Chr7B_49152174_C / T,Chr7B_49152219_C / T,Chr7B_49411717_G / A,

[0069] The SNP sites were determined through genome-wide association analysis of 358 rose resequencing materials and association screening using multiple software and models.

[0070] Example 2

[0071] The present invention provides a rose prickle shape prediction probe. The screening principles of the probe include: being designed from a combination of SNP sites, being able to specifically bind to the SNP sites, being used to capture a target DNA region, and realizing the detection of a specific SNP site. The sequence information of the probe is associated with the SNP site combination, and conforming to various screening principles of probe design, including the absence of Indel markers within 50 bp upstream and downstream of the SNP site, having only one copy number in the entire genome of the 100 bp upstream and downstream sequences, a GC content of 40-60%, and the absence of short segment repeats and N bases in the sequence.

[0072] Example 3

[0073] The present invention discloses a rose prickle shape prediction chip, which includes probes for detecting 679 SNP sites. By detecting the genotypes of the SNP sites in the genomic DNA of the rose sample to be tested and utilizing a pre-constructed whole-genome selection model, the chip can accurately predict the rose prickle shape trait.

[0074] Example 4

[0075] The invention discloses an application of a SNP molecular marker combination, a probe or a chip in the prediction of rose prickle shape, which involves extracting genomic DNA from rose plants and performing detection using the SNP site combination, the probe or the chip.

[0076] Example 5

[0077] A method for predicting rose prickle shape based on a combination of SNP molecular markers of the present invention comprises the following steps:

[0078] (1) Extracting genomic DNA from the rose plants to be tested;

[0079] (2) constructing a library of the genomic DNA;

[0080] (3) using probes to perform hybridization capture on the DNA fragments in the library to enrich the DNA fragments containing the target SNP site;

[0081] (4) performing high-throughput sequencing on the captured DNA fragments;

[0082] (5) Compare the sequencing data with the rose reference genome to determine the genotype of the SNP site;

[0083] (6) The genotype data of the SNP loci were input into the whole genome selection model to obtain the prediction results of the rose prickle shape trait. Bayes Ridge Regression (BRR) had the highest prediction accuracy among the models, with an overall prediction accuracy greater than 0.528.

[0084] Example 6

[0085] The application of a SNP site combination, probe, chip or prediction method of the present invention in rose molecular breeding is used to perform early, accurate and efficient prediction and screening of the prickle shape trait of breeding materials during the rose breeding process, thereby shortening the breeding cycle, improving selection efficiency, and cultivating new rose varieties with excellent prickle shape traits.

[0086] The whole-genome selection model constructed based on SNP site combination can predict the shape of rose prickles with a prediction accuracy greater than 0.528.

[0087] Example 7

[0088] The present invention provides a rose molecular breeding method based on SNP markers, comprising the following steps: applying a SNP site combination, a prediction probe, or a prediction chip to the selection and breeding process of rose varieties; detecting the genotype at the seed or seedling stage; predicting the prickle shape trait; thereby screening plants with an ideal prickle shape; accelerating the cultivation of new rose varieties with fewer or even no prickles; improving the ornamental value and production efficiency of roses; and meeting market demand.

[0089] Example 8

[0090] Analyze the whole genome resequencing data of 358 roses to conduct genome-wide association analysis of prickle shape, including the following process:

[0091] (1) Genomic DNA from 358 rose tissues was extracted using the magnetic bead method, and a whole-genome resequencing library was constructed. DNA fragments that met the sequencing requirements were screened by magnetic beads, and after qbit quantification, sequencing was performed using BGI DNBSEQ-T7.

[0092] (2) The fq.gz format second-generation sequencing data obtained in step (1) were aligned to the modern rose 'Samantha' genome v2 genome using bwa software. https: / / figshare.com / articles / dataset / _i_R_hybrida_i_Samantha_genome_v2_ / 28738781?file=53454104. SNP variation data were analyzed using GATK software, and 115,219,112 high-quality SNP sites were finally identified.

[0093] (3) The SNP sites screened out in step (2) were retained, and the SNP sites with allele frequencies greater than 0.01 and missing rates less than 0.2 were retained to obtain 35,335,433 high-quality SNP sites. Figure 2 The allele frequency diagram of the rose prickles provided by the present invention reflects the enrichment degree of the target allele during the breeding process. Figure 3 This is a missing rate graph of the number of rose prickles provided by the present invention.

[0094] (4) Collection of agronomic traits of prickle shape. 1 represents oblique straight (large and straight thorns), 2 represents straight thorns (small and straight thorns), and 3 represents curved thorns. Three replicates were collected, and the mean and BLUP values ​​were calculated. A total of five data sets were used for GWAS association analysis.

[0095] (5) Six models were used to correlate prickle shape with agronomic traits using four software programs: emmax, gemma, rmvp (FARMCPU model, GLM model, MLM model), and tassel (GLM model). The p-value threshold was set at 1E-4, and 268,779 SNP markers were consistently associated. After deduplication of association results from different software models, 134,868 SNP loci were obtained.

[0096] (6) Probe evaluation was performed on the SNPs screened in step (5). Screening principles: no InDel markers within 50 bp upstream and downstream of the SNP site; only one copy of the 100 bp upstream and downstream sequence in the entire genome; GC content of 40-60%; no short segment repeats within the sequence; no N bases within the sequence. Finally, 5710 SNP sites remained.

[0097] (7) The SNP sites selected in step (6) were sorted according to the number of software and model associations and the association results, and the 679 SNP markers with the largest number of software associations and significant association values ​​were selected. Figure 1 As shown, Figure 1 This is the whole chromosome marker distribution map of rose prickle shape provided by the present invention.

[0098] (8) The SNP sites selected in step (7) were evaluated for prediction accuracy using 13 genome-wide 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, using the genotypes and agronomic traits of prickle shape of 348 materials. The results showed that Ridge had the lowest prediction accuracy, while Bayes RidgeRegression (BRR) had the highest prediction accuracy. The overall prediction accuracy was greater than 0.528, indicating good prediction accuracy. Figure 5 As shown, Figure 5 This is a diagram showing the results of genome-wide selection evaluation of rose prickle shape provided by the present invention.

[0099] (9) The SNP sites screened in step (7) are synthesized into probe sequences for capture sequencing.

[0100] Example 9

[0101] Method for detecting rose using the liquid phase probe corresponding to 679 SNPs described in Example 8

[0102] Genomic DNA extraction: Rose leaves were collected, stored with ice packs and promptly transported back to the laboratory, and the total DNA of the roses was extracted using the magnetic bead method.

[0103] Genomic DNA library construction: Genomic DNA fragmentation (200-300bp), DNA fragment end repair, connection adapter Pre-PCR amplification library

[0104] Probe hybridization with the target region: Use the prepared SNP probe to hybridize with the Pre-PCR library, and the streptomycin-modified probe to capture the complementary DNA library. After enriching the target DNA library, the other library DNA is eluted. That is, the captured Pre-PCR library is purified by magnetic beads, amplified and enriched to the DNA concentration required for high-throughput sequencing, and then high-throughput sequencing is performed.

[0105] Hybridization conditions: The streptavidin-labeled probe was hybridized with the target library at 50°C for 16 hours. The biotin-labeled magnetic beads were combined with the streptavidin-labeled probe at room temperature for 30 minutes to enrich the target library. The non-target region library was rinsed with wash buffer and eluted with nuclease-free water.

[0106] High-throughput sequencing: The library obtained after capture and amplification in step (4) was subjected to high-throughput sequencing using the MGI DNBSEQ-T7 sequencing platform to obtain the sequencing results of the genomic DNA, and the obtained data was subjected to basic cleaning processing.

[0107] Evaluation of liquid phase probe capture efficiency: The cleaned sequencing data were aligned to the modern rose 'Samantha' genome v2 reference sequence using bwa software to evaluate its capture efficiency.

[0108] Test Example 1

[0109] Evaluation of liquid probe capture efficiency for 12 rose varieties

[0110] Experimental Materials

[0111] Twelve rose leaves were selected, refrigerated, and promptly transported to the laboratory. Total DNA from each individual plant was extracted using the CTAB method. The sample numbers are shown in Table 2.

[0112] Table 2

[0113] serial number variety serial number variety Test1 Phuket Test2 Green Apple Test3 Xiushan Red Test4 Golden Age Test5 Smurfs Test6 pink fan Test7 Ruby Star Test8 rainbow Test9 After the powder Test10 Perfume Woman Test11 Titanic Test12 Charlotte

[0114] Capture efficiency evaluation

[0115] Based on the evaluation results of 12 rose materials, the coverage depth detection rate of 12 rose varieties was measured. The detection rate of 679 SNPs ranged from 97.62% to 98.81%, and the coverage depth was 391.08-531.36X. The overall capture efficiency was good and can be used for subsequent SNP detection and whole genome selection evaluation of other samples. The detection rate statistics of capture sequencing samples G17 are shown in Table 3:

[0116] The experiment selected 12 representative samples, including Buji, Xiushanhong, and Smurf, as research subjects. Each sample underwent multiple, comprehensive rounds of testing using advanced gene sequencing or similar high-precision detection technologies. During the testing process, strict control was exercised over temperature, humidity, and other environmental conditions to ensure optimal instrument performance and data accuracy and reliability. After testing, professional data processing software was used to statistically analyze the raw data and calculate the coverage depth and detection rate for each sample.

[0117] Table 3 presents the test results of 12 samples. The table header contains three columns: "Sample_ID" (sample name), "Coverage Depth", and "Detection Rate (%)", which are used to identify the sample, record the numerical value of the sample detection coverage, and reflect the proportion of target substances detected. From the data in the table, it can be seen that the coverage depth of sample "Titanic" is the highest, reaching 510.36, which means that the sample was covered the deepest during the detection process; "Pink Fan" has the lowest coverage depth, which is 348.08. In terms of detection rate, "Blue Smurf" has the highest detection rate of 98.78%, while "Xiushanhong" has a relatively low detection rate of 97.12%. These data can provide important reference for subsequent sample characteristic research and detection method optimization.

[0118] Table 3

[0119] Sample_ID Coverage Depth Detection rate (%) Phuket 426.52 98.27 Xiushan Red 446.64 97.12 Smurfs 383.08 98.78 Ruby Star 489.58 98.46 After the powder 447.16 98.37 Titanic 510.36 97.93 Green Apple 458.16 98.37 Golden Age 437.1 98.83 pink fan 348.08 97.37 rainbow 457.56 98.74 Perfume Woman 491.58 98.33 Charlotte 489.62 98.19

[0120] The basic principles, main features and advantages of the present invention are shown and described above. It should be understood by those skilled in the art that the present invention is not limited to the above embodiments. The above embodiments and descriptions are merely illustrative of the principles of the present invention. Various changes and improvements may be made to the present invention without departing from the spirit and scope of the present invention. The scope of protection claimed in the present invention is defined by the appended claims, the description and their equivalents.

Claims

1. A genome-wide SNP molecular marker combination for rose prickle shape, characterized by: The SNP molecular marker combination includes 679 SNP sites distributed on the 14 chromosomes of roses; the specific information of the SNP sites is represented by the structure of chromosome number_physical position_allele type, and the SNP sites contain dominant alleles that are positively and significantly associated with the shape of rose prickles. The specific site information is shown in Table 1 of the specification.

2. The genome-wide SNP molecular marker combination for rose prickle shape 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 through multiple software and model associations.

3. A rose prickle-shaped prediction probe, characterized by: The screening principles of the probe include: being designed from the SNP site combination of claim 1, being able to specifically bind to the SNP site, being used to capture the target DNA region, and realizing the detection of a specific SNP site, and its sequence information being associated with the SNP site combination, and complying with various screening principles of probe design, including the absence of InDel markers within 50 bp upstream and downstream of the SNP site, the uniqueness of the 100 bp upstream and downstream sequences throughout the genome, the GC content being 40-60%, and the absence of short segment repeat sequences and N bases.

4. A chip for predicting rose prickle shapes, characterized by: The prediction chip includes probes for detecting the 679 SNP sites. By detecting the genotype of the 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 prickle shape traits is 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 rose prickle shape, 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 rose prickle shape 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) The genotype data of the SNP site combination described in claim 1 is input into the genome-wide selection model described in claim 4 to obtain the prediction result of the prickle shape trait of the rose to be tested.

7. The method for predicting rose prickle shape using a combination of SNP molecular markers according to claim 6, wherein: Among the models, Bayes Ridge Regression (BRR) has the highest prediction accuracy, with an overall prediction accuracy greater than 0.

528.

8. 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 prediction and screening of the prickle shape traits of breeding materials during the rose breeding process, thereby shortening the breeding cycle, improving selection efficiency, and cultivating new rose varieties with excellent prickle shape traits.

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

528.

10. A rose molecular breeding method based on SNP markers, characterized in that The method comprises the following steps: applying the SNP site combination of claim 1, the prediction probe of claim 3 or the prediction chip of claim 4 to the breeding process of rose varieties, detecting the genotype at the seed or seedling stage, predicting the prickle shape trait, thereby screening out plants with an ideal prickle shape, accelerating the breeding of new rose varieties with fewer or even no prickles, improving the ornamental value and production efficiency of roses, and meeting market demand.

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