CN114736985A - Tomato whole genome chip and application thereof - Google Patents
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Abstract
The invention discloses a tomato whole genome chip and application thereof, finds and screens genotyping objects which can be used for chip design, and comprises 1377 SNP sites and 80 Indel sites positioned on a tomato reference genome SL2.50, and utilizes a liquid phase chip to realize tomato genotyping by a targeted capture sequencing technology; experimental results show that the chip designed by the invention can be used for tomato genetic diversity analysis, variety identification, genetic relationship identification, whole genome association analysis and genome selective breeding.
Description
Technical Field
The invention belongs to the technical field of whole genome gene chips, and particularly relates to a tomato whole genome chip and application thereof.
Background
Molecular Marker Technology (Molecular Marker Technology) is an important tool in Molecular breeding. Traditional molecular markers, such as Restriction Fragment Length Polymorphism (RFLP) and Simple Sequence Repeat (SSR), play important roles in the field of genetic breeding. However, there are some limitations, such as small distribution number of genome, complicated operation process and low throughput, which can not meet the requirement of large-scale commercial breeding application. Single Nucleotide Polymorphism (SNP) refers to a variation of a Single Nucleotide in a genome, including a transition, transversion, insertion or deletion of a Single base pair. As a genetic marker distributed more widely in a genome, SNP has the characteristics of high density, high genetic stability, easy automation analysis and the like, and is developed into a common molecular marker in the research of animal genetic variation.
At present, in the gene chip technology for SNP locus typing, the traditional solid phase chip carries out typing through a fluorescent color development signal of a marker based on complementary hybridization of a probe and a DNA sequence. The liquid phase chip is based on a re-sequencing technology, carries out specificity capture on each target site, carries out high-depth re-sequencing and has the advantages of high detection accuracy and high flux. The liquid phase chip generally comprises a Biotin (Biotin) label designed for each site to be detected according to the DNA complementary principle and a probe covering target SNP, the probes are hybridized with a genome target region in a liquid state to form a double chain, the adsorption effect of streptavidin-coated magnetic beads and molecules with Biotin can be utilized, and the second-generation sequencing is carried out after elution, amplification and library establishment, so that the genotype states of the target site and the surrounding SNP are finally reduced. The liquid phase chip has mature application in the aspects of species evolution analysis, germplasm resource evaluation and DNA fingerprint identification, molecular genetic map construction, gene/QTL positioning and gene cloning, molecular marker assisted selection, whole genome selection and the like (Xuyunbi, Yang quan, Zheng Honghuan, and the like; targeted sequencing genotype detection (GBTS) technology and application thereof; Chinese agricultural science, 2020, 53 (15): 29833004).
At present, in animal breeding, a cattle 90K chip, a sheep Illumina 50K chip, a goat Illumina 50K chip, a pig high-density chip, chicken 600K, a corn 40K liquid chip and a 1K liquid chip, a rice 40K liquid chip and the like are widely used for large-scale commercial breeding, and specific applications comprise germplasm resource genetic diversity analysis, genetic and evolutionary analysis, genetic relationship identification, whole genome association analysis and genome selection.
However, the conventional solid-phase gene chip, for example, bovine 90K solid-phase chip, has the following problems in the detection process and application: firstly, the number of typing sites is large; secondly, the cattle 90K solid-phase chip can only carry out typing on SNP sites contained on the chip, the SNP sites around the sites can not be typed, once the solid-phase chip is designed, the sites which can be detected are fixed, the increase and the deletion can not be carried out, and the flexibility is poor; finally, solid phase chip typing costs are high.
Disclosure of Invention
The invention aims to provide a tomato whole genome chip and application thereof.
In order to achieve the purpose, the invention provides the following technical scheme: the tomato whole genome chip has gene typing target comprising 1377 SNP sites and 80 Indel sites in the reference tomato genome SL 2.50.
1377 SNP sites (specifically consisting of 1004 newly-found SNP sites and 373 known SNP sites) positioned on a tomato reference genome SL2.50 can provide SNP molecular marker combinations for positioning, genetic diversity analysis, whole genome association analysis, genome selection, variety identification, genetic relationship identification, germplasm resource improvement and protection of various tomato variety trait related genes at home and abroad;
the genotyping object of the chip comprises 80 Indel sites, including 25 markers of 48 Indel markers of NY/T2471-2013 tomato variety identification technical specification Indel molecular marker method and 55 newly-found Indel markers; the chip provides result analysis of partial Indel markers in national standard, and is used for positioning of related genes of tomato variety traits, genetic diversity analysis, whole genome association analysis, genome selection, variety identification, genetic relationship identification, germplasm resource improvement and protected Indel molecular marker combination;
8 SNP sites (related NCBI accession numbers are respectively NC-004005.1, NC-002692.1, NC-001367.1 and MT 018320) positioned on genomes of Tomato Yellow Leaf Curl Virus (TYLCV), Tomato Mosaic Virus (TMV), tobacco mosaic virus (ToMV) and tomato brown wrinkle fruit virus (ToBRFV), so that the chip can diagnose diseases of tomato virus diseases simultaneously.
Preferably, the chip is a liquid phase chip.
The invention provides an application of a tomato whole genome chip, including the application in tomato breeding.
Preferably, the method comprises the application in tomato genome selection, tomato trait related gene localization, tomato genetic diversity analysis, tomato backcross transformation, tomato whole genome association analysis, tomato variety identification, tomato genetic relationship identification or tomato germplasm resource improvement and protection.
Preferably, the detection method of the molecular marker adopted in the tomato breeding is a typing method based on SNP sites and Indel sites of a liquid phase chip. For example, targeted capture sequencing techniques.
The molecular marker is associated with the main economic traits of tomato, wherein the economic traits relate to fruit color, fruit hardness, single fruit weight, crack resistance, fruit setting rate, internode length, first ear flower number and node position, leaf color, length, growth vigor and plant type.
Preferably, 59 molecular marker sites related to disease resistance in the 1377 SNP sites and the 80 Indel sites comprise: sl2.50ch01_ 1124825; sl2.50ch01_ 1125796; sl2.50ch01_ 1677737; sl2.50ch01_ 2078506; sl2.50ch01_ 3973295; sl2.50ch01_ 3974505; sl2.50ch02_ 34285108; sl2.50ch02_ 34285162; sl2.50ch03_ 64540483; sl2.50ch04 — 1813305; sl2.50ch04 — 1813331; sl2.50ch04 — 39555167; sl2.50ch05_ 6381569; sl2.50ch05_ 6404126; sl2.50ch06_ 2161990; sl2.50ch06_ 2162280; sl2.50ch06_ 2163925; sl2.50ch06_ 2354841; sl2.50ch06_ 34370002; sl2.50ch06_ 34370158; sl2.50ch06_ 34389411; sl2.50ch06_ 34389561; sl2.50ch06_ 35009157; sl2.50ch06_ 35009202; sl2.50ch06_ 35009232; sl2.50ch06_ 35009237; sl2.50ch06_ 35009245; sl2.50ch06_ 35009250; sl2.50ch06_ 35009260; sl2.50ch06_ 35009272; sl2.50ch06_ 35950028; sl2.50ch06_ 37186202; sl2.50ch07_ 63597481; sl2.50ch08_ 61642121; sl2.50ch09_ 56697; sl2.50ch09_ 57025; sl2.50ch09_ 4943007; sl2.50ch09_ 5090186; sl2.50ch09_ 13621583; sl2.50ch09_ 13621676; sl2.50ch09_ 13621682; sl2.50ch09_ 13621846; sl2.50ch09_ 71434430; sl2.50ch09_ 71436208; sl2.50ch09_ 72029144; sl2.50ch09_ 72029219; sl2.50ch09_ 72032340; sl2.50ch09_ 72032691; sl2.50ch11_ 9317442; sl2.50ch11_ 54264376; sl2.50ch11_ 54531455; sl2.50ch11_ 54531515; sl2.50ch11_ 54897353; sl2.50ch11_ 54913693; sl2.50ch11_ 55071011; sl2.50ch11_ 55299325; sl2.50ch12_ 2941301; sl2.50ch12_ 3809589; sl2.50ch12_ 4543132.
Preferably, 32 molecular marker sites related to color in the 1377 SNP sites and the 80 Indel sites comprise: sl2.50ch01_ 78745063; sl2.50ch01_ 78747579; sl2.50ch01_ 78747639; sl2.50ch01_ 78747668; sl2.50ch01_ 78747838; sl2.50ch01_ 78911282; sl2.50ch01_ 82203699; sl2.50ch01_ 82205102; sl2.50ch01_ 82207046; sl2.50ch02_ 45196896; sl2.50ch03_ 52152865; sl2.50ch03_ 52152879; sl2.50ch03_ 52152905; sl2.50ch03_ 52153104; sl2.50ch03_ 52153202; sl2.50ch03_ 52153309; sl2.50ch03_ 52153473; sl2.50ch03_ 52153858; sl2.50ch03_ 52154291; sl2.50ch03_ 52154481; sl2.50ch03_ 52154565; sl2.50ch03_ 52154574; sl2.50ch03_ 52154673; sl2.50ch03_ 52154825; sl2.50ch03_ 52155769; sl2.50ch03_ 52180873; sl2.50ch03_ 52182577; sl2.50ch03_ 52386476; sl2.50ch03_ 52406077; sl2.50ch03_ 65751759; sl2.50ch05_ 8998720; sl2.50ch05_ 9313748.
Preferably, 105 molecular marker sites related to the background of gooseberry tomato LA2093 in the 1377 SNP sites and the 80 Indel sites comprise: sl2.50ch01_ 40124913; sl2.50ch01_ 53317722; sl2.50ch01_ 72488048; sl2.50ch01_ 77558637; sl2.50ch01_ 98247086; sl2.50ch02_ 29935554; sl2.50ch02_ 44944551; sl2.50ch04 — 978312; sl2.50ch04 — 4834961; sl2.50ch04 — 9633653; sl2.50ch04 — 53335117; sl2.50ch05_ 44420698; sl2.50ch05_ 54497816; sl2.50ch06_ 15767679; sl2.50ch06_ 37444105; sl2.50ch08_ 1381293; sl2.50ch08 — 23948349; sl2.50ch08_ 28887544; sl2.50ch08_ 44832241; sl2.50ch08_ 45610138; sl2.50ch08_ 49276668; sl2.50ch08_ 57714845; sl2.50ch08_ 58664027; sl2.50ch08_ 60599653; sl2.50ch08_ 61583858; sl2.50ch08_ 62573296; sl2.50ch08_ 63731190; sl2.50ch08_ 64621335; sl2.50ch08_ 65360761; sl2.50ch09_ 1468885; sl2.50ch09_ 5365363; sl2.50ch09_ 15147765; sl2.50ch09_ 37706150; sl2.50ch09_ 42531761; sl2.50ch10_ 10257147; sl2.50ch11_ 500493; sl2.50ch11_ 2795604; sl2.50ch11_ 4360855; sl2.50ch11_ 7764094; sl2.50ch11_ 8090264; sl2.50ch11_ 8297787; sl2.50ch11_ 8705537; sl2.50ch11_ 8764030; sl2.50ch11_ 8885924; sl2.50ch11_ 8990978; sl2.50ch11_ 9273987; sl2.50ch11_ 9679304; sl2.50ch11_ 9825111; sl2.50ch11_ 51503295; sl2.50ch11_ 55107953; sl2.50ch01_ 21006695; sl2.50ch01_ 97390074; sl2.50ch08_ 21514991; sl2.50ch08_ 21935647; sl2.50ch08_ 30124360; sl2.50ch08_ 33554881; sl2.50ch08_ 33572491; sl2.50ch08_ 38712700; sl2.50ch08_ 50888332; sl2.50ch08_ 51018195; sl2.50ch08 — 54478887; sl2.50ch08_ 56039111; sl2.50ch08_ 57456680; sl2.50ch08 — 58242820; sl2.50ch08_ 58416149; sl2.50ch08_ 60629674; sl2.50ch08_ 61189832; sl2.50ch08_ 62230910; sl2.50ch08_ 64423423; sl2.50ch08_ 65229257; sl2.50ch09_ 12741885; sl2.50ch09_ 15742079; sl2.50ch09_ 17741716; sl2.50ch09_ 29293428; sl2.50ch09_ 39342186; sl2.50ch09_ 43433842; sl2.50ch09_ 48527593; sl2.50ch11_ 10108015; sl2.50ch11_ 10261139; sl2.50ch11_ 11892235; sl2.50ch11_ 11964698; sl2.50ch11_ 12358446; sl2.50ch11_ 12437087; sl2.50ch11_ 12527879; sl2.50ch11_ 13305592; sl2.50ch11_ 13816619; sl2.50ch11_ 16722717; sl2.50ch11_ 16910740; sl2.50ch11_ 1803553; sl2.50ch11_ 21561965; sl2.50ch11_ 21720369; sl2.50ch11_ 37251169; sl2.50ch11_ 37453090; sl2.50ch11_ 46447098; sl2.50ch11_ 4797112; sl2.50ch11_ 49374653; sl2.50ch11_ 50510190; sl2.50ch11_ 51447653; sl2.50ch11_ 54433869; sl2.50ch11_ 55446914; sl2.50ch11_ 8705656; sl2.50ch11_ 8830219; sl2.50ch12_ 41942023; sl2.50ch12_ 42437286; sl2.50ch12_ 60945631.
The invention has the following beneficial effects:
according to the invention, key functional sites and variety specific sites of the tomato are mined from large-scale sequencing data, 1377 SNP sites and 80 Indel sites (namely about 1.5K) which can be used for chip design are discovered and screened, 1004 newly discovered SNP sites and 55 Indel markers are found, and genotyping can be realized by utilizing the designed chip, so that the chip has high application value in multiple fields in tomato breeding.
The tomato liquid chip related by the invention can not only carry out typing on the target site, but also accurately type the SNP in a certain range around the target site based on the targeted capture sequencing technology, thereby obtaining more SNP typing information than the marker site; compared with the traditional solid phase chip, the flexibility is higher, and the labeling sites can be added at any time according to the application requirements; meanwhile, the liquid phase chip is based on a second-generation sequencing platform, so that the typing cost is low, and a technical means is provided for large-scale typing.
Drawings
FIG. 1 is a diagram showing the uniform distribution of SNP markers of the present invention on different chromosomes.
FIG. 2 is a table of SNP sites and genomic positions of the present invention.
FIG. 3 is a diagram of the positions of SNP sites and genome according to the present invention.
FIG. 4 is a reference genomic information table according to the present invention.
Detailed Description
The technical solutions in the embodiments of the present invention will be clearly and completely described below with reference to the drawings in the embodiments of the present invention, and it is obvious that the described embodiments are only a part of the embodiments of the present invention, and not all of the embodiments. All other embodiments, which can be derived by a person skilled in the art from the embodiments given herein without making any creative effort, shall fall within the protection scope of the present invention.
The present invention will be described in further detail with reference to the accompanying fig. 1-4 and examples, which are provided for illustration only and are not intended to limit the scope of the present invention.
Design and preparation of tomato 1.5K liquid phase chip
According to the invention, 325 parts of re-sequencing data of breeding materials are utilized, SNP analysis is firstly carried out, 65304324 SNP sites are obtained after the site is filtered for subsequent screening.
The target SNP sites screened by the invention comprise the following types: related SNPs of tomato functional genes, related SNPs of currant tomato background, related SNPs of tomato yield, plant morphology, fruit traits, flowering habit, tomato quality and the like, and SNP sites on Tomato Yellow Leaf Curl Virus (TYLCV), Tomato Mosaic Virus (TMV), tobacco mosaic virus (ToMV) and tomato brown wrinkle fruit virus (ToBRFV) genomes. The specific screening process for these classes of sites is as follows:
1. the 903 SNP markers in the background marker were screened over the full gene re-sequencing data range to retain a minimum allele frequency greater than 0.3 (maf >0.3Na <0.2Ho < 0.1), with the remainder: 161,589SNPs, standard screen for up to 3 SNPs 100bp upstream and downstream, the remainder: 59,639snps, blast removed repeats (HSP identity and coverage greater than two at 90 positions) remainder: 25,075snps, randomly selecting one snp every 193kb, the rest: 3,002snps as candidate sites.
2. Determination of important functional sites: for functional genes related to important economic traits such as tomato yield, plant morphology, fruit traits, flowering habit, tomato quality, disease resistance and the like, which are reported in the literature, at least one candidate SNP site is screened on each exon of the genes, or SNP sites related to tomato yield, color and quality, which are obtained by genome-wide association analysis and reported in the literature, are used as candidate sites.
Number of markers at quality-related sites 63;
the number of markers of the national standard Indel is 45;
number of markers for color-related sites 38;
marker number of functional gene-associated sites 42;
number of markers 59 for disease resistance-associated sites;
a currant tomato background-related marker number 103;
number of markers 192 relevant to GWAS analysis;
number of markers at yield-related sites 14;
number of markers for background markers 903.
3. According to Tomato Yellow Leaf Curl Virus (TYLCV), Tomato Mosaic Virus (TMV), tobacco mosaic virus (ToMV) and tomato brown wrinkle fruit virus (ToBRFV) genomes (related NCBI accession numbers are NC-004005.1, NC-002692.1, NC-001367.1 and MT018320 respectively, 8 sites are selected as candidate sites by performing blast by taking nt/nr library as a target database.
4. SNP site and genomic POSITION (POSITION).
5. According to the positions and the sequences at two sides of the 3,002SNP sites and the positions and the sequences at two sides of the 78 Indel sites, primers are designed and probe synthesis is carried out by adopting a targeted capture sequencing technology by Shijiazhuang Boruidi biotechnology limited, so that the tomato 1.5K liquid phase chip is obtained.
(II) process for detecting tomato DNA sample by using tomato 1.5K liquid chip
Extracting tomato genome DNA: samples were taken from tomato seedlings, and DNA was extracted using a CTAB method or a magnetic bead adsorption method using a genome extraction kit (Tiangen Biotech Co., Ltd., Beijing).
And (3) detecting the quality of the DNA sample: agarose gel electrophoresis with the mass fraction of 1-1.5% is used for detection, and a gel imaging system (GelDocXRSystem, American Bio-Rad company) is used for judging the electrophoresis result so as to ensure the integrity of the genome; the concentration of the genomic DNA is measured with a micro-UV spectrophotometer (Q5000, Quawell, USA) or a similar nucleic acid protein analyzer, and the concentration of the DNA is adjusted to a working concentration of 10-50 ng/. mu.L.
Detecting a tomato liquid chip: the procedure was followed according to the standard protocol for tomato 1.5K liquid chip detection (http:// www.molbreeding.com/index. php/Technology/genoBaits. html).
And (3) data analysis: the raw data obtained were subjected to quality control using fastp software (CHENS, ZHOUY, CHENY, equivalent. fastp: and-fast in-one FASTQ preprocessors, 2018, 34 (17): i884-i90), after which sequencing data were mapped onto tomato reference genome SL2.50 using BWA software (LIH. aligning sequence reads, clone sequences and analysis constraints with BWA-MEM. arXprint arXiv: 13033997, 2013.) and detected using GATK software (VAN DER AUWERA G A, CARNEIRO M O, HARTL C, equivalent. from fast data high-compatibility algorithms: genes analysis algorithms, 19. 7. SNP, 11.0.1. 3. SNP of gene expression).
(III) application of tomato 1.5K liquid chip in whole genome correlation analysis
(IV) application of tomato 1.5K liquid chip in variety identification
(V) advantages of tomato 1.5K liquid chip
(1) Compared with the traditional solid phase chip, the invention can detect more SNP sites (4-10K) compared with the solid phase chip with the same number of probes. And the design is flexible, and interested marker sites can be added at any time in the later period.
(2) Compared with whole genome re-sequencing, the method has obvious price advantage, and can be used for carrying out large-scale typing on tomato materials, thereby promoting the breeding work of tomatoes.
(3) The invention contains a large number of tomato functional gene related sites, screens the sites which are obviously related to the functional genes related to important economic traits such as tomato yield, plant morphology, fruit character, flowering habit, tomato quality, disease resistance and the like in the prior research, and increases the accuracy of basic research of the chip.
(4) The sample for designing the chip is derived from the re-sequencing data of breeding materials, namely has medium-high frequency SNP sites specific to more cultivars, is more suitable for the research of tomato breeding, and is favorable for the development of breeding work and the research and utilization of tomato germplasm resources.
Although embodiments of the present invention have been shown and described, it will be appreciated by those skilled in the art that changes, modifications, substitutions and alterations can be made in these embodiments without departing from the principles and spirit of the invention, the scope of which is defined in the appended claims and their equivalents.
Claims (8)
1. The tomato whole genome chip is characterized in that the genotyping objects of the chip comprise 1377 SNP sites and 80 Indel sites which are positioned on a tomato reference genome SL 2.50; these SNP sites and Indel sites include, at the molecular marker sites of the reference genome:
SL2.50ch01_1124825；SL2.50ch01_1125796；SL2.50ch01_1677737；SL2.50ch01_2078506；SL2.50ch01_3973295；SL2.50ch01_3974505；SL2.50ch02_34285108；SL2.50ch02_34285162；SL2.50ch03_64540483；SL2.50ch04_1813305；SL2.50ch04_1813331；SL2.50ch04_39555167；SL2.50ch05_6381569；SL2.50ch05_6404126；SL2.50ch06_2161990；SL2.50ch06_2162280；SL2.50ch06_2163925；SL2.50ch06_2354841；SL2.50ch06_34370002；SL2.50ch06_34370158；SL2.50ch06_34389411；SL2.50ch06_34389561；SL2.50ch06_35009157；SL2.50ch06_35009202；SL2.50ch06_35009232；SL2.50ch06_35009237；SL2.50ch06_35009245；SL2.50ch06_35009250；SL2.50ch06_35009260；SL2.50ch06_35009272；SL2.50ch06_35950028；SL2.50ch06_37186202；SL2.50ch07_63597481；SL2.50ch08_61642121；SL2.50ch09_56697；SL2.50ch09_57025；SL2.50ch09_4943007；SL2.50ch09_5090186；SL2.50ch09_13621583；SL2.50ch09_13621676；SL2.50ch09_13621682；SL2.50ch09_13621846；SL2.50ch09_71434430；SL2.50ch09_71436208；SL2.50ch09_72029144；SL2.50ch09_72029219；SL2.50ch09_72032340；SL2.50ch09_72032691；SL2.50ch11_9317442；SL2.50ch11_54264376；SL2.50ch11_54531455；SL2.50ch11_54531515；SL2.50ch11_54897353；SL2.50ch11_54913693；SL2.50ch11_55071011；SL2.50ch11_55299325；SL2.50ch12_2941301；SL2.50ch12_3809589；SL2.50ch12_4543132；
SL2.50ch01_78745063；SL2.50ch01_78747579；SL2.50ch01_78747639；SL2.50ch01_78747668；SL2.50ch01_78747838；SL2.50ch01_78911282；SL2.50ch01_82203699；SL2.50ch01_82205102；SL2.50ch01_82207046；SL2.50ch02_45196896；SL2.50ch03_52152865；SL2.50ch03_52152879；SL2.50ch03_52152905；SL2.50ch03_52153104；SL2.50ch03_52153202；SL2.50ch03_52153309；SL2.50ch03_52153473；SL2.50ch03_52153858；SL2.50ch03_52154291；SL2.50ch03_52154481；SL2.50ch03_52154565；SL2.50ch03_52154574；SL2.50ch03_52154673；SL2.50ch03_52154825；SL2.50ch03_52155769；SL2.50ch03_52180873；SL2.50ch03_52182577；SL2.50ch03_52386476；SL2.50ch03_52406077；SL2.50ch03_65751759；SL2.50ch05_8998720；SL2.50ch05_9313748；
SL2.50ch01_40124913；SL2.50ch01_53317722；SL2.50ch01_72488048；SL2.50ch01_77558637；SL2.50ch01_98247086；SL2.50ch02_29935554；SL2.50ch02_44944551；SL2.50ch04_978312；SL2.50ch04_4834961；SL2.50ch04_9633653；SL2.50ch04_53335117；SL2.50ch05_44420698；SL2.50ch05_54497816；SL2.50ch06_15767679；SL2.50ch06_37444105；SL2.50ch08_1381293；SL2.50ch08_23948349；SL2.50ch08_28887544；SL2.50ch08_44832241；SL2.50ch08_45610138；SL2.50ch08_49276668；SL2.50ch08_57714845；SL2.50ch08_58664027；SL2.50ch08_60599653；SL2.50ch08_61583858；SL2.50ch08_62573296；SL2.50ch08_63731190；SL2.50ch08_64621335；SL2.50ch08_65360761；SL2.50ch09_1468885；SL2.50ch09_5365363；SL2.50ch09_15147765；SL2.50ch09_37706150；SL2.50ch09_42531761；SL2.50ch10_10257147；SL2.50ch11_500493；SL2.50ch11_2795604；SL2.50ch11_4360855；SL2.50ch11_7764094；SL2.50ch11_8090264；SL2.50ch11_8297787；SL2.50ch11_8705537；SL2.50ch11_8764030；SL2.50ch11_8885924；SL2.50ch11_8990978；SL2.50ch11_9273987；SL2.50ch11_9679304；SL2.50ch11_9825111；SL2.50ch11_51503295；SL2.50ch11_55107953；SL2.50ch01_21006695；SL2.50ch01_97390074；SL2.50ch08_21514991；SL2.50ch08_21935647；SL2.50ch08_30124360；SL2.50ch08_33554881；SL2.50ch08_33572491；SL2.50ch08_38712700；SL2.50ch08_50888332；SL2.50ch08_51018195；SL2.50ch08_54478887；SL2.50ch08_56039111；SL2.50ch08_57456680；SL2.50ch08_58242820；SL2.50ch08_58416149；SL2.50ch08_60629674；SL2.50ch08_61189832；SL2.50ch08_62230910；SL2.50ch08_64423423；SL2.50ch08_65229257；SL2.50ch09_12741885；SL2.50ch09_15742079；SL2.50ch09_17741716；SL2.50ch09_29293428；SL2.50ch09_39342186；SL2.50ch09_43433842；SL2.50ch09_48527593；SL2.50ch11_10108015；SL2.50ch11_10261139；SL2.50ch11_11892235；SL2.50ch11_11964698；SL2.50ch11_12358446；SL2.50ch11_12437087；SL2.50ch11_12527879；SL2.50ch11_13305592；SL2.50ch11_13816619；SL2.50ch11_16722717；SL2.50ch11_16910740；SL2.50ch11_1803553；SL2.50ch11_21561965；SL2.50ch11_21720369；SL2.50ch11_37251169；SL2.50ch11_37453090；SL2.50ch11_46447098；SL2.50ch11_4797112；SL2.50ch11_49374653；SL2.50ch11_50510190；SL2.50ch11_51447653；SL2.50ch11_54433869；SL2.50ch11_55446914；SL2.50ch11_8705656；SL2.50ch11_8830219；SL2.50ch12_41942023；SL2.50ch12_42437286；SL2.50ch12_60945631。
2. the tomato whole genome chip according to claim 1, wherein the chip is a liquid phase chip.
3. The tomato whole genome chip of claim 2, wherein the chip is used in tomato breeding.
4. The tomato whole genome chip of claim 2, which is used for tomato genome selection, tomato trait related gene mapping, tomato genetic diversity analysis, tomato backcross transformation, tomato whole genome association analysis, tomato variety identification, tomato genetic relationship identification or tomato germplasm resource improvement and protection.
5. The application of the tomato whole genome chip as claimed in claim 3, wherein the molecular marker detection method adopted in tomato breeding is a typing method based on SNP sites and Indel sites of a liquid phase chip.
6. The tomato whole genome chip as claimed in claim 5, wherein 59 molecular marker loci related to disease resistance among 1377 SNP loci and 80 Indel loci comprise: sl2.50ch01_ 1124825; sl2.50ch01_ 1125796; sl2.50ch01_ 1677737; sl2.50ch01_ 2078506; sl2.50ch01_ 3973295; sl2.50ch01_ 3974505; sl2.50ch02_ 34285108; sl2.50ch02_ 34285162; sl2.50ch03_ 64540483; sl2.50ch04 — 1813305; sl2.50ch04 — 1813331; sl2.50ch04 — 39555167; sl2.50ch05_ 6381569; sl2.50ch05_ 6404126; sl2.50ch06_ 2161990; sl2.50ch06_ 2162280; sl2.50ch06_ 2163925; sl2.50ch06_ 2354841; sl2.50ch06_ 34370002; sl2.50ch06_ 34370158; sl2.50ch06_ 34389411; sl2.50ch06_ 34389561; sl2.50ch06_ 35009157; sl2.50ch06_ 35009202; sl2.50ch06_ 35009232; sl2.50ch06_ 35009237; sl2.50ch06_ 35009245; sl2.50ch06_ 35009250; sl2.50ch06_ 35009260; sl2.50ch06_ 35009272; sl2.50ch06_ 35950028; sl2.50ch06_ 37186202; sl2.50ch07_ 63597481; sl2.50ch08_ 61642121; sl2.50ch09_ 56697; sl2.50ch09_ 57025; sl2.50ch09_ 4943007; sl2.50ch09_ 5090186; sl2.50ch09_ 13621583; sl2.50ch09_ 13621676; sl2.50ch09_ 13621682; sl2.50ch09_ 13621846; sl2.50ch09_ 71434430; sl2.50ch09_ 71436208; sl2.50ch09_ 72029144; sl2.50ch09_ 72029219; sl2.50ch09_ 72032340; sl2.50ch09_ 72032691; sl2.50ch11_ 9317442; sl2.50ch11_ 54264376; sl2.50ch11_ 54531455; sl2.50ch11_ 54531515; sl2.50ch11_ 54897353; sl2.50ch11_ 54913693; sl2.50ch11_ 55071011; sl2.50ch11_ 55299325; sl2.50ch12_ 2941301; sl2.50ch12_ 3809589; sl2.50ch12_ 4543132.
7. The tomato whole genome chip application of claim 5, wherein 32 molecular marker loci related to color in 1377 SNP loci and 80 Indel loci comprise: sl2.50ch01_ 78745063; sl2.50ch01_ 78747579; sl2.50ch01_ 78747639; sl2.50ch01_ 78747668; sl2.50ch01_ 78747838; sl2.50ch01_ 78911282; sl2.50ch01_ 82203699; sl2.50ch01_ 82205102; sl2.50ch01_ 82207046; sl2.50ch02_ 45196896; sl2.50ch03_ 52152865; sl2.50ch03_ 52152879; sl2.50ch03_ 52152905; sl2.50ch03_ 52153104; sl2.50ch03_ 52153202; sl2.50ch03_ 52153309; sl2.50ch03_ 52153473; sl2.50ch03_ 52153858; sl2.50ch03_ 52154291; sl2.50ch03_ 52154481; sl2.50ch03_ 52154565; sl2.50ch03_ 52154574; sl2.50ch03_ 52154673; sl2.50ch03_ 52154825; sl2.50ch03_ 52155769; sl2.50ch03_ 52180873; sl2.50ch03_ 52182577; sl2.50ch03_ 52386476; sl2.50ch03_ 52406077; sl2.50ch03_ 65751759; sl2.50ch05_ 8998720; sl2.50ch05_ 9313748.
8. The tomato whole genome chip application as claimed in claim 5, wherein 105 molecular marker loci related to the background of the chestnut tomato LA2093 in 1377 SNP loci and 80 Indel loci comprise: sl2.50ch01_ 40124913; sl2.50ch01_ 53317722; sl2.50ch01_ 72488048; sl2.50ch01_ 77558637; sl2.50ch01_ 98247086; sl2.50ch02_ 29935554; sl2.50ch02_ 44944551; sl2.50ch04 — 978312; sl2.50ch04 — 4834961; sl2.50ch04 — 9633653; sl2.50ch04 — 53335117; sl2.50ch05_ 44420698; sl2.50ch05_ 54497816; sl2.50ch06_ 15767679; sl2.50ch06_ 37444105; sl2.50ch08_ 1381293; sl2.50ch08_ 23948349; sl2.50ch08_ 28887544; sl2.50ch08_ 44832241; sl2.50ch08_ 45610138; sl2.50ch08_ 49276668; sl2.50ch08_ 57714845; sl2.50ch08_ 58664027; sl2.50ch08_ 60599653; sl2.50ch08_ 61583858; sl2.50ch08 — 62573296; sl2.50ch08_ 63731190; sl2.50ch08_ 64621335; sl2.50ch08_ 65360761; sl2.50ch09_ 1468885; sl2.50ch09_ 5365363; sl2.50ch09_ 15147765; sl2.50ch09_ 37706150; sl2.50ch09_ 42531761; sl2.50ch10_ 10257147; sl2.50ch11_ 500493; sl2.50ch11_ 2795604; sl2.50ch11_ 4360855; sl2.50ch11_ 7764094; sl2.50ch11_ 8090264; sl2.50ch11_ 8297787; sl2.50ch11_ 8705537; sl2.50ch11_ 8764030; sl2.50ch11_ 8885924; sl2.50ch11_ 8990978; sl2.50ch11_ 9273987; sl2.50ch11_ 9679304; sl2.50ch11_ 9825111; sl2.50ch11_ 51503295; sl2.50ch11_ 55107953; sl2.50ch01_ 21006695; sl2.50ch01_ 97390074; sl2.50ch08_ 21514991; sl2.50ch08_ 21935647; sl2.50ch08_ 30124360; sl2.50ch08_ 33554881; sl2.50ch08_ 33572491; sl2.50ch08_ 38712700; sl2.50ch08 — 50888332; sl2.50ch08_ 51018195; sl2.50ch08_ 54478887; sl2.50ch08_ 56039111; sl2.50ch08_ 57456680; sl2.50ch08_ 58242820; sl2.50ch08_ 58416149; sl2.50ch08_ 60629674; sl2.50ch08_ 61189832; sl2.50ch08_ 62230910; sl2.50ch08 — 64423423; sl2.50ch08_ 65229257; sl2.50ch09_ 12741885; sl2.50ch09_ 15742079; sl2.50ch09_ 17741716; sl2.50ch09_ 29293428; sl2.50ch09_ 39342186; sl2.50ch09_ 43433842; sl2.50ch09_ 48527593; sl2.50ch11_ 10108015; sl2.50ch11_ 10261139; sl2.50ch11_ 11892235; sl2.50ch11_ 11964698; sl2.50ch11_ 12358446; sl2.50ch11_ 12437087; sl2.50ch11_ 12527879; sl2.50ch11_ 13305592; sl2.50ch11_ 13816619; sl2.50ch11_ 16722717; sl2.50ch11_ 16910740; sl2.50ch11_ 1803553; sl2.50ch11_ 21561965; sl2.50ch11_ 21720369; sl2.50ch11_ 37251169; sl2.50ch11_ 37453090; sl2.50ch11_ 46447098; sl2.50ch11_ 4797112; sl2.50ch11_ 49374653; sl2.50ch11_ 50510190; sl2.50ch11_ 51447653; sl2.50ch11_ 54433869; sl2.50ch11_ 55446914; sl2.50ch11_ 8705656; sl2.50ch11_ 8830219; sl2.50ch12_ 41942023; sl2.50ch12_ 42437286; sl2.50ch12_ 60945631.
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