A SNP locus combination related to rubber tree breeding traits and its application

Abstract

The invention discloses a SNP site combination and application related to rubber tree breeding traits, and belongs to the field of molecular biotechnology. The 298 SNP sites adopted by the present invention are related to the important breeding traits such as bark thickness, cold resistance, stem girth production rate, latex yield and number of latex tubes of rubber tree, and it can be applied to the molecular marker-assisted breeding work of rubber tree, by measuring the genotype of these 298 SNP sites in rubber tree individual DNA, quickly analyzing germplasm resources, determining the dominant allele carried in breeding parent materials, and accelerating breeding process. In addition, 298 SNP sites are relatively few in number, not only reducing the cost of genotype detection, compared with the SNP sites of the whole genome, more suitable for the rough screening of a large number of samples, and more advantageous in the comprehensive trait evaluation of rubber tree breeding than the SNP sites of the whole genome.

Description

Technical Field

[0001] The invention relates to the field of molecular biotechnology, and in particular to a SNP site combination related to rubber tree breeding traits and an application thereof. Background Art

[0002] Molecular markers mainly refer to DNA fragments that can reflect certain differences in the genome between biological individuals or populations. They directly reflect the differences between genomic DNA and are also called DNA markers. Molecular marker analysis methods are all based on DNA polymorphism, such as RFLP, RAPD, AFLP, SSR and SNP markers. Early RFLP, RAPD and AFLP molecular marker technologies often encountered problems such as poor stability, low polymorphism and difficulty in data integration during use, and were not widely used. Since SNP markers have the advantages of high throughput, site specificity, co-dominant inheritance, low false positive rate, sharply reduced development and detection costs, and easy data integration, with the continuous improvement of second-generation sequencing technology, the efficiency of genome sequencing has been greatly improved, and the sequencing cost has also been greatly reduced. SNP markers have become the main marker type for genotype identification, greatly promoting the progress of genetic breeding related research.

[0003] As the most important tropical cash crop, the natural rubber produced by rubber tree is an important strategic resource, which has an irreplaceable role in the fields of military, aerospace, marine engineering and rail transportation. At present, in the breeding process of rubber tree, the traditional phenotypic trait evaluation method is still adopted, which needs to be planted after the seeds are planted, and its trait index is obtained by observing its bark thickness, cold resistance, stem girth production rate and latex yield. The procedure of the traditional breeding method of rubber tree is cumbersome, the young age of rubber tree is long, the breeding cycle is up to 30 years, and the selection method of screening and eliminating according to the early phenotype is extremely inaccurate. With the rapid development of SNP marker technology, different varieties are resequenced, the SNP markers found by resequencing are used, and the whole genome association analysis (Genome wide Association Mapping, GWAS) is used to carry out association analysis on important breeding traits, determine the candidate gene sites related to important breeding traits, and establish a set of efficient and fast, mature and stable, low-cost, high-throughput genotype identification methods, which are the priority directions of genetic breeding researchers. At present, there is no report on establishing a complete set of SNP loci combinations related to rubber tree breeding traits for use in rubber tree molecular breeding. Summary of the invention

[0004] The object of the present invention is to provide a combination of SNP sites related to rubber tree breeding traits and applications thereof, to solve the problems existing in the above-mentioned prior art. The 298 SNP sites adopted in the present invention are related to important breeding traits such as bark thickness, cold tolerance, stem girth production rate, latex yield and number of latex ducts of rubber tree, and can be applied to molecular marker-assisted breeding work of rubber tree.

[0005] To achieve the above object, the present invention provides the following solutions:

[0006] The invention provides a SNP site combination related to a rubber tree breeding trait, comprising 298 SNP sites, each SNP site comprising two alleles of different bases, for detecting allele changes at the site, the physical positions of the 298 SNP sites being determined based on a genome sequence comparison of a rubber tree wild germplasm MT / VB / 25A 57 / 8, the version number of the genome sequence of the rubber tree wild germplasm MT / VB / 25A 57 / 8 being ASM3005281v1, and the variation information of the 298 SNP sites being as follows: the variation information of the SNP sites being represented in the form of chromosome number_physical position_reference genotype / allele type:

[0007] Chr1_15757_G / T;Chr1_731023_C / T;Chr1_2709764_C / T;Chr1_3828026_C / G;Chr1_10086984_T / C;Chr1_13443998_C / A;Chr1_24711557_G / A;Chr1_28410342_G / A;Chr1_31246482_A / G;Chr1_33236009_A / T;Chr1_91047897_G / A;Chr1_94236268_C / T;Chr1_97506370_A / G;Chr1_103644378_T / A;Chr1_105896364_A / C;Chr1_111818657_C / A;Chr1_119761444_G / A;Chr1_119815929_T / A;Chr1_124681987_A / G;Chr2_708272_T / C;Chr2_1091213_A / G;Chr2_1412841_T / G;Chr2_6735215_A / G;Chr2_8387629_A / G;Chr2_8935490_C / T;Chr2_14396160_G / A;Chr2_17221809_G / C;Chr2_23335062_C / T;Chr2_52259102_G / A;Chr2_65921385_C / T;Chr2_71475197_G / T;Chr2_77534372_A / G;Chr2_85191439_T / C;Chr2_102109411_A / C;Chr2_107220134_A / G;Chr2_112911824_G / T;Chr2_116729566_A / G;Chr2_116811799_C / A;Chr2_123601709_T / G;Chr2_124300927_A / G;Chr3_1466320_C / T;Chr3_1960954_T / C;Chr3_4087599_T / A;Chr3_5957222_G / A;Chr3_12089943_G / A;Chr3_12476864_T / C;Chr3_14407329_A / T;Chr3_19609926_G / A;Chr3_25818990_C / T;Chr3_26105771_T / A;Chr3_28011570_A / G;Chr3_55427066_A / G;Chr3_65399028_G / A;Chr3_78061863_G / A;Chr3_83776666_T / G;Chr3_87552482_G / T;Chr3_87849740_G / A;Chr3_89316084_G / A;Chr3_95073582_T / A;Chr3_97394338_A / C;Chr3_97633357_A / G;Chr3_99096014_G / T;Chr3_105554669_T / C;Chr3_108145282_A / C;Chr3_110755926_G / A;Chr3_111315050_G / A;Chr3_113093396_G / T;Chr3_115841960_T / C;Chr4_4836875_T / G;Chr4_5122798_A / G;Chr4_13812464_A / T;Chr4_14259021_T / C;Chr4_20075652_C / A;Chr4_20495918_T / A;Chr4_27655758_T / C;Chr4_28184400_G / A;Chr4_101079315_C / T;Chr4_104972595_C / T;Chr4_109783256_G / A;Chr4_110174839_A / C;Chr4_111315272_A / G;Chr4_115826287_G / T;Chr5_5014612_G / A;Chr5_5023352_C / A;Chr5_5515786_A / T;Chr5_9709308_A / G;Chr5_12766865_T / C;Chr5_15109810_T / A;Chr5_22533448_A / G;Chr5_25929070_A / G;Chr5_65287220_A / G;Chr5_73727319_T / A;Chr5_88048914_G / A;Chr5_99903267_C / G;Chr5_105218154_A / G;Chr5_108901274_A / G;Chr5_110279515_T / C;Chr5_111330503_T / C;Chr5_111547930_C / A;Chr6_810624_T / A;Chr6_3036971_A / G;Chr6_5034063_T / A;Chr6_15910001_C / T;Chr6_24457821_G / A;Chr6_83782657_C / T;Chr6_98816559_G / A;Chr6_98989641_T / A;Chr6_101179647_T / G;Chr6_105804599_G / A;Chr6_106597314_G / A;Chr6_107794933_T / C;Chr7_3136477_A / G;

[0008] Chr7_4403505_C / T;Chr7_6790961_C / G;Chr7_11042954_G / A;Chr7_13203287_T / C;

[0009] Chr7_13586605_T / C;Chr7_19002798_C / A;Chr7_23498422_T / C;Chr7_51574707_G / C;

[0010] Chr7_64866814_T / C;Chr7_86545391_G / C;Chr7_88082006_A / T;Chr7_91885282_T / G;

[0011] Chr7_95451717_G / C;Chr7_101803420_T / C;Chr8_434205_G / T;Chr8_3622765_C / T;

[0012] Chr8_6201463_T / C;Chr8_6777431_G / T;Chr8_16893876_A / T;Chr8_18492509_C / A;

[0013] Chr8_27807713_T / C;Chr8_70878100_C / T;Chr8_87651866_G / T;Chr8_90588981_A / C;

[0014] Chr8_98580941_G / A;Chr8_99079868_A / G;Chr8_100597325_C / G;Chr9_1813979_C / G;

[0015] Chr9_5709469_C / A;Chr9_7401382_C / A;Chr9_7664635_A / C;Chr9_14855094_T / C;

[0016] Chr9_17665225_T / C;Chr9_18653960_C / T;Chr9_20264134_A / T;Chr9_20707073_A / G;

[0017] Chr9_24502054_A / C;Chr9_24854055_A / C;Chr9_34308910_C / T;Chr9_34873585_T / C;

[0018] Chr9_75435371_C / T;Chr9_77610735_G / A;Chr9_86585759_T / A;Chr9_88315788_A / G;

[0019] Chr9_91502195_G / A;Chr9_95436365_T / A;Chr9_97867065_G / A;Chr10_1470878_A / T;

[0020] Chr10_5824840_G / C;Chr10_8136996_A / T;Chr10_10507992_G / A;Chr10_15719936_T / A;

[0021] Chr10_27591981_C / A;Chr10_87585142_C / G;Chr10_90419402_C / A;Chr10_90421003_G / A;

[0022] Chr10_94722518_G / A;Chr10_96108456_C / T;Chr10_98147463_C / G;Chr11_678127_C / T;

[0023] Chr11_736365_A / G;Chr11_1115977_C / G;Chr11_7196081_G / A;Chr11_10848831_G / C;

[0024] Chr11_14918947_T / C;Chr11_18839922_C / G;Chr11_22924094_C / T;Chr11_52683514_T / G;

[0025] Chr11_72064153_A / G;Chr11_73664189_C / T;Chr11_74555756_A / G;Chr11_75121758_C / T;

[0026] Chr11_82668555_T / G;Chr11_91501311_T / G;Chr11_93188716_T / G;Chr11_95071313_C / T;

[0027] Chr11_96208291_C / T;Chr11_98880506_C / T;Chr12_684080_C / A;Chr12_2931612_T / C;

[0028] Chr12_6899137_T / A;Chr12_7707046_A / G;Chr12_12156787_A / T;Chr12_13341210_T / A;

[0029] Chr12_16307269_C / T;Chr12_16328314_A / G;Chr12_22494251_T / C;Chr12_23601414_G / C;

[0030] Chr12_26680799_C / G;Chr12_26973865_C / A;Chr12_32544120_A / T;Chr12_35993093_T / C;

[0031] Chr12_37011239_C / A;Chr12_38908419_A / C;Chr12_40517500_A / G;Chr12_45207311_T / C;

[0032] Chr12_45440599_T / C;Chr12_69549182_A / G;Chr12_79376136_C / G;Chr13_4356832_G / T;

[0033] Chr13_8875751_T / C;Chr13_13255560_G / T;Chr13_13918244_A / G;Chr13_15886975_T / A;

[0034] Chr13_16924693_A / G;Chr13_25851280_T / C;Chr13_31683642_A / G;Chr13_48641671_C / G;

[0035] Chr13_69350364_G / A;Chr13_69392735_G / A;Chr13_70291223_T / A;Chr13_77454106_G / A;

[0036] Chr13_77704508_T / A;Chr13_78200581_G / A;Chr13_83025236_G / A;Chr13_83094380_T / G;

[0037] Chr13_86155184_C / T;Chr13_89160461_G / A;Chr13_89846004_T / G;Chr14_3754938_G / A;

[0038] Chr14_4002023_A / G;Chr14_5279683_T / G;Chr14_5988595_C / T;Chr14_16631275_G / T;Chr14_16668074_C / T;Chr14_23975735_C / T;Chr14_24930605_T / A;Chr14_29279540_C / T;Chr14_68126151_A / G;Chr14_68309126_G / A;Chr14_69200024_A / G;Chr14_74583350_A / C;Chr14_81298104_C / A;Chr14_83285431_C / G;Chr14_89010870_G / A;Chr14_91155262_G / T;Chr15_2986762_C / G;Chr15_3196798_C / A;Chr15_8687335_G / A;Chr15_23754687_A / G;Chr15_35180027_A / G;Chr15_40670852_C / T;Chr15_47894762_G / T;Chr15_52881987_T / A;Chr15_53642786_G / T;Chr15_54447431_T / C;Chr15_63208884_C / T;Chr15_66357157_G / T;Chr15_70990505_A / G;Chr15_73033483_T / C;Chr16_8093869_T / C;Chr16_8130467_G / A;Chr16_9976916_G / A;Chr16_41093450_C / A;Chr16_41892017_T / C;Chr16_43339238_A / C;Chr16_47328276_T / C;Chr16_50459414_T / C;Chr16_55859604_A / G;Chr16_61536320_A / G;Chr16_64893652_A / C;Chr16_69033394_C / T;Chr16_70631013_C / A;Chr17_4332955_G / C;Chr17_5300940_C / T;Chr17_11344297_A / G;Chr17_14450909_C / T;Chr17_24540321_G / A;Chr17_25427335_G / A;Chr17_39194976_G / A;Chr17_47016224_A / G;Chr17_51749822_A / G;Chr17_55881919_C / T;Chr17_58004068_A / G; Chr18_2465717_T / A; Chr18_7859243_A / G; Chr18_28775131_C / T; Chr18_29989533_G / A; Chr18_35440358_C / T; Chr18_4119 0847_A / G; Chr18_42439396_C / A; Chr18_42574751_A / C; Chr18_45891002 _C / T; Chr18_46892894_C / T; Chr18_50817494_G / C; Chr18_51611167_T / C;

[0039] The breeding traits include bark thickness, cold tolerance, stem girth production rate, latex yield and latex duct number;

[0040] The 52 SNP loci associated with bark thickness and their dominant alleles are as follows:

[0041] Chr1_731023_T; Chr1_10086984_T; Chr1_28410342_A; Chr1_91047897_G; Chr1_103644378_A; Chr1_119761444_A; Chr2_708272_T; Chr2_107220134_G; Chr2_116811799_A; Chr3_12476864_C; Chr3_28011570_A; Chr3_65399028_G; Chr3_89316084_G; Chr3_97394338_A; Chr3_110755926_G; Chr4_5122798_A; Chr4_104972595_T; Chr4_115826287_T; Chr5_5023352_C; Chr5_12766865_C; Chr5_108901274_A; Chr6_810624_T; Chr6_101179647_T; Chr7_11042954_A; Chr7_91885282_T; Chr8_6777431_G; Chr8_87651866_G; Chr9_5709469_C; Chr9_14855094_T; Chr9_20707073_A; Chr9_3487 3585_T; Chr9_97867065_G; Chr10_1470878_A; Chr10_87585142_C; Chr11_14918947_T; Chr11_73664189_C; Chr11_93188716_T; Chr12_2931612 _C; Chr12_22494251_T; Chr13_70291223_T; Chr13_83025236_G; Chr14_89010870_G; Chr15_66357157_G; Chr15_73033483_T; Chr16_8093869_T ;Chr16_41892017_T; Chr16_50459414_T; Chr16_64893652_A; Chr17_11344297_G; Chr17_47016224_A; Chr17_55881919_C; Chr18_45891002_T;

[0042] The 39 SNP loci associated with cold tolerance and their dominant alleles are as follows:

[0043] Chr1_15757_G; Chr2_8387629_A; Chr2_112911824_T; Chr2_123601709_T; Chr3_1466320_T; Chr 3_105554669_C; Chr3_111315050_A; Chr4_111315272_G; Chr5_5515786_A; Chr6_98816559_A; C hr7_4403505_C; Chr8_18492509_C; Chr8_27807713_T; Chr8_100597325_C; Chr9_7664635_C; Ch r9_17665225_T; Chr9_24854055_A; Chr9_34308910_T; Chr10_15719936_T; Chr10_94722518_A; Chr11_18839922_C; Chr11_75121758_T; Chr11_96208291_C; Chr12_7707046_G; Chr12_1630726 9_C; Chr12_26973865_A; Chr12_40517500_A; Chr13_16924693_G; Chr13_31683642_A; Chr13_86 155184_T; Chr14_5988595_C; Chr14_16668074_C; Chr14_24930605_A; Chr14_81298104_A; Chr1 6_41093450_A; Chr17_24540321_A; Chr18_2465717_A; Chr18_29989533_A; Chr18_46892894_T;

[0044] The 61 SNP loci and their dominant alleles associated with stem girth production rate are as follows:

[0045] Chr1_2709764_C;Chr1_94236268_C;Chr1_111818657_C;Chr2_6735215_A;Chr2_17221809_C; Chr2_116729566_A; Chr3_5957222_A; Chr3_19609926_A;Chr3_25818990_T; Chr3_87849740_A; Chr3_95073582_A; Chr3_115841960_T;Chr4_14259021_C; Chr4_28184400_G; Chr5_15109810_A; Chr5_25929070_G;Chr5_105218154_G;Chr5_111547930_A;Chr6_106597314_A;Chr7_13203287_C;Chr7_95451717_G;Chr9_1813979_C;Chr9_7401382_C;Chr9_20264134_T;Chr9_75435371_T;Chr9_88315788_A;Chr10_8136996_A;Chr10_90421003_G;Chr10_96108456_T;Chr11_736365_G;Chr11_10848831_C;Chr11_91501311_G;Chr12_16328314_G;Chr12_26680799_G;Chr12_35993093_T;Chr12_45207311_C;Chr12_69549182_G;Chr12_79376136_G;Chr13_4356832_G;Chr13_15886975_T;Chr13_25851280_C;Chr13_48641671_C;Chr13_77704508_A;Chr13_89160461_A;Chr14_3754938_G;Chr14_16631275_G;Chr14_29279540_T;Chr14_68309126_G;Chr14_91155262_T;Chr15_3196798_A;Chr15_47894762_T;Chr15_53642786_G;Chr15_63208884_T;Chr16_43339238_A;Chr16_61536320_G;Chr17_5300940_T;Chr17_14450909_T;Chr17_51749822_A;Chr18_28775131_T;Chr18_41190847_A;Chr18_51611167_T;

[0046] The 82 SNP loci associated with latex production and their dominant alleles are as follows:

[0047] Chr1_731023_T;Chr1_13443998_A;Chr1_24711557_A;Chr1_31246482_A;Chr1_105896364_C; Chr1_124681987_A; Chr2_1412841_T; Chr2_23335062_C;Chr2_52259102_G; Chr2_65921385_C; Chr2_71475197_G; Chr2_85191439_T;Chr2_124300927_A; Chr3_4087599_T; Chr3_14407329_A; Chr3_26105771_T;Chr3_55427066_A; Chr3_78061863_G;Chr3_87552482_G; Chr3_99096014_G;Chr3_108145282_A; Chr4_4836875_T; Chr4_20495918_T; Chr4_101079315_C;Chr4_110174839_A; Chr5_9709308_A; Chr5_22533448_A; Chr5_65287220_A;Chr5_73727319_T; Chr5_88048914_G; Chr5_110279515_T; Chr6_3036971_A;Chr6_15910001_C; Chr6_24457821_A; Chr6_83782657_C; Chr6_98989641_T;Chr6_107794933_T; Chr7_6790961_C; Chr7_13586605_C; Chr7_23498422_T;Chr7_86545391_G;Chr8_3622765_C;Chr8_16893876_A;Chr8_70878100_T;Chr8_90588981_A;Chr8_98580941_G;Chr9_24502054_A;Chr9_77610735_G;Chr9_86585759_T;Chr9_95436365_A;Chr10_10507992_G;Chr10_98147463_C;Chr11_1115977_C;Chr11_7196081_G;Chr11_22924094_T;Chr11_72064153_A;Chr11_98880506_C;Chr12_684080_C;Chr12_12156787_T;Chr12_37011239_C;Chr13_8875751_C; Chr13_13918244_G; Chr13_69392735_G; Chr13_77454106_G; Chr13_83094380_T; Chr13_89 846004_T; Chr14_5279683_T; Chr14_23975735_C; Chr14_68126151_G; Chr14_74583350_A; Chr15_8687335_G; Chr15_23754687_A; Chr15_40670852_C; Chr15_52881987_T; Chr16_8130467_A; Chr16_55859604_A; Chr16_69 033394_C; Chr17_25427335_G; Chr17_39194976_A; Chr17_58004068_A; Chr18_7859243_A; Chr18_42574751_A;

[0048] The 65 SNP loci associated with the number of milk ducts and their dominant alleles are as follows:

[0049] Chr1_3828026_G;Chr1_33236009_T;Chr1_97506370_A;Chr1_119815929_T;Chr2_1091213_A;Chr2_8935490_T;Chr2_14396160_G;Chr2_77534372_A;Chr2_102109411_A;Chr3_1960954_T; Chr3_12089943_A; Chr3_83776666_G; Chr3_97633357_G;Chr3_113093396_G; Chr4_13812464_A; Chr4_20075652_A; Chr4_27655758_T;Chr4_109783256_A; Chr5_5014612_G; Chr5_99903267_G; Chr5_111330503_T;Chr6_5034063_T;Chr6_105804599_A;Chr7_3136477_G;Chr7_19002798_A;Chr7_51574707_G;Chr7_64866814_T;Chr7_88082006_A;Chr7_101803420_C;Chr8_434205_T;Chr8_6201463_T;Chr8_99079868_G;Chr9_18653960_C;Chr9_91502195_G;Chr10_5824840_C;Chr10_27591981_A;Chr10_90419402_A;Chr11_678127_C;Chr11_52683514_T;Chr11_74555756_A;Chr11_82668555_T;Chr11_95071313_T;Chr12_6899137_T;Chr12_13341210_A;Chr12_23601414_G;Chr12_32544120_A;Chr12_38908419_C;Chr12_45440599_C;Chr13_13255560_G;Chr13_69350364_G;Chr13_78200581_G;Chr14_4002023_A;Chr14_69200024_G;Chr14_83285431_G;Chr15_2986762_G;Chr15_35180027_A;Chr15_54447431_T;Chr15_70990505_G;Chr16_9976916_A;Chr16_47328276_T;Chr16_70631013_A; Chr17_4332955_G; Chr18_35440358_C; Chr18_42439396_A; Chr18_50817494_C. ;

[0050] The present invention also provides an application of the SNP site combination in molecular assisted breeding of rubber trees, wherein the molecular assisted breeding is based on the breeding traits of rubber trees, and the breeding traits of rubber trees include bark thickness, cold resistance, stem girth production rate, latex yield and latex duct number.

[0051] The present invention also provides a probe for detecting the SNP site combination.

[0052] The present invention also provides the use of the probe in molecular assisted breeding of rubber trees, wherein the molecular assisted breeding is based on the breeding traits of rubber trees, and the breeding traits of rubber trees include bark thickness, cold resistance, stem girth production rate, latex yield and latex duct number.

[0053] The present invention also provides the use of the probe in preparing a liquid-phase gene chip for detecting the SNP site combination.

[0054] The present invention also provides the use of the probe in genetic typing of breeding traits of rubber tree germplasm resources, wherein the breeding traits include bark thickness, cold resistance, stem girth production rate, latex yield and latex duct number.

[0055] The present invention also provides a liquid-phase gene chip for detecting the SNP site combination, wherein the liquid-phase gene chip contains a set of nucleotide probes for detecting the SNP site combination.

[0056] The present invention also provides the application of the liquid-phase gene chip in the molecular-assisted breeding of rubber trees. The molecular-assisted breeding is based on the breeding traits of rubber trees for breeding. The breeding traits of rubber trees include bark thickness, cold resistance, stem girth production rate, latex yield and the number of latex ducts.

[0057] The present invention also provides the application of the liquid-phase gene chip in genetic typing of breeding traits of rubber tree germplasm resources, wherein the breeding traits include bark thickness, cold resistance, stem girth production rate, latex yield and latex duct number.

[0058] The present invention discloses the following technical effects:

[0059] The 298 SNP sites adopted by the present invention are related to the important breeding traits such as bark thickness, cold tolerance, stem girth production rate, latex yield and number of latex tubes of rubber tree, and it can be applied to the molecular marker-assisted breeding work of rubber tree, by measuring the genotype of these 298 SNP sites in rubber tree individual DNA, fast analysis of germplasm resources, determining the dominant allele carried in the breeding parent material, and accelerating the breeding process. In addition, 298 SNP sites are relatively few in number, not only reducing the cost of genotype detection, compared with the SNP sites of the whole genome, more suitable for the rough screening of a large number of samples, and more advantageous in the comprehensive trait assessment of rubber tree breeding than the SNP sites of the whole genome. BRIEF DESCRIPTION OF THE DRAWINGS

[0060] In order to more clearly illustrate the embodiments of the present invention or the technical solutions in the prior art, the drawings required for use in the embodiments will be briefly introduced below. Obviously, the drawings described below are only some embodiments of the present invention. For ordinary technicians in this field, other drawings can be obtained based on these drawings without paying creative work.

[0061] Figure 1 The figure is a distribution map of 298 SNP sites related to rubber tree breeding traits on chromosomes of the present invention;

[0062] Figure 2 The minimum allele frequency distribution diagram of 298 SNP sites related to rubber tree breeding traits of the present invention;

[0063] Figure 3 The heterozygosity frequency distribution diagram of 298 SNP sites related to rubber tree breeding traits of the present invention;

[0064] Figure 4 This is a correlation analysis diagram of the comprehensive breeding index and the number of dominant alleles related to breeding traits in Example 3 of the present invention;

[0065] Figure 5 This is a graph of the genotyping results of the rubber tree material in Example 4 of the present invention, wherein each row represents a SNP genotype, each column represents a material, and black, gray, light gray and white represent non-dominant alleles, heterozygous genes, dominant alleles and deletions, respectively. DETAILED DESCRIPTION

[0066] Various exemplary embodiments of the present invention will now be described in detail. This detailed description should not be considered as limiting the present invention, but should be understood as a more detailed description of certain aspects, features, and embodiments of the present invention.

[0067] It should be understood that the terms described in the present invention are only for describing a particular embodiment and are not intended to limit the present invention. In addition, for the numerical range in the present invention, it should be understood that each intermediate value between the upper and lower limits of the scope is also specifically disclosed. The intermediate value in any stated value or stated range, and each smaller range between any other stated value or intermediate value in the described range is also included in the present invention. The upper and lower limits of these smaller ranges can be independently included or excluded in the scope.

[0068] Unless otherwise indicated, all technical and scientific terms used herein have the same meanings as those generally understood by those skilled in the art. Although the present invention describes only preferred methods and materials, any methods and materials similar or equivalent to those described herein may also be used in the implementation or testing of the present invention. All documents mentioned in this specification are incorporated by reference to disclose and describe the methods and / or materials associated with the documents. In the event of a conflict with any incorporated document, the content of this specification shall prevail.

[0069] It will be apparent to those skilled in the art that various modifications and variations may be made to the specific embodiments of the present invention description without departing from the scope or spirit of the present invention. Other embodiments derived from the present invention description will be apparent to those skilled in the art. The present invention description and examples are exemplary only.

[0070] The words “include,” “including,” “have,” “contain,” etc. used in this document are open-ended terms, meaning including but not limited to.

[0071] Example 1

[0072] A combination of SNP sites related to rubber tree breeding traits includes 298 SNP sites, each SNP site contains two alleles of different bases, and is used to detect allele changes at the site; the physical positions of the above 298 SNP sites are determined based on the genome sequence alignment of rubber tree wild germplasm MT / VB / 25A 57 / 8; the version number of the genome sequence of rubber tree wild germplasm MT / VB / 25A 57 / 8 is ASM3005281v1, and the website for obtaining the genome sequence of rubber tree wild germplasm MT / VB / 25A 57 / 8 is: https: / / ftp.ncbi.nlm.nih.gov / genomes / all / GCA / 030 / 052 / 815 / GCA_030052815.1_ASM3005281v1 / ; the variation information of the above 298 SNP sites is as follows, which is expressed in the form of chromosome number_physical position_reference genotype / allele type:

[0073] Chr1_15757_G / T;Chr1_731023_C / T;Chr1_2709764_C / T;Chr1_3828026_C / G;Chr1_10086984_T / C;Chr1_13443998_C / A;Chr1_24711557_G / A;Chr1_28410342_G / A;Chr1_31246482_A / G;Chr1_33236009_A / T;Chr1_91047897_G / A;Chr1_94236268_C / T;Chr1_97506370_A / G;Chr1_103644378_T / A;Chr1_105896364_A / C;Chr1_111818657_C / A;Chr1_119761444_G / A;Chr1_119815929_T / A;Chr1_124681987_A / G;Chr2_708272_T / C;Chr2_1091213_A / G;Chr2_1412841_T / G;Chr2_6735215_A / G;Chr2_8387629_A / G;Chr2_8935490_C / T;Chr2_14396160_G / A;Chr2_17221809_G / C;Chr2_23335062_C / T;Chr2_52259102_G / A;Chr2_65921385_C / T;Chr2_71475197_G / T;Chr2_77534372_A / G;Chr2_85191439_T / C;Chr2_102109411_A / C;Chr2_107220134_A / G;Chr2_112911824_G / T;Chr2_116729566_A / G;Chr2_116811799_C / A;Chr2_123601709_T / G;Chr2_124300927_A / G;Chr3_1466320_C / T;Chr3_1960954_T / C;Chr3_4087599_T / A;Chr3_5957222_G / A;Chr3_12089943_G / A;Chr3_12476864_T / C;Chr3_14407329_A / T;Chr3_19609926_G / A;Chr3_25818990_C / T;Chr3_26105771_T / A;Chr3_28011570_A / G;Chr3_55427066_A / G;Chr3_65399028_G / A;Chr3_78061863_G / A;Chr3_83776666_T / G;Chr3_87552482_G / T;Chr3_87849740_G / A;Chr3_89316084_G / A;Chr3_95073582_T / A;Chr3_97394338_A / C;Chr3_97633357_A / G;Chr3_99096014_G / T;Chr3_105554669_T / C;Chr3_108145282_A / C;Chr3_110755926_G / A;Chr3_111315050_G / A;Chr3_113093396_G / T;Chr3_115841960_T / C;Chr4_4836875_T / G;Chr4_5122798_A / G;Chr4_13812464_A / T;Chr4_14259021_T / C;Chr4_20075652_C / A;Chr4_20495918_T / A;Chr4_27655758_T / C;Chr4_28184400_G / A;Chr4_101079315_C / T;Chr4_104972595_C / T;Chr4_109783256_G / A;Chr4_110174839_A / C;Chr4_111315272_A / G;Chr4_115826287_G / T;Chr5_5014612_G / A;Chr5_5023352_C / A;Chr5_5515786_A / T;Chr5_9709308_A / G;Chr5_12766865_T / C;Chr5_15109810_T / A;Chr5_22533448_A / G;Chr5_25929070_A / G;Chr5_65287220_A / G;Chr5_73727319_T / A;Chr5_88048914_G / A;Chr5_99903267_C / G;Chr5_105218154_A / G;Chr5_108901274_A / G;Chr5_110279515_T / C;Chr5_111330503_T / C;Chr5_111547930_C / A;Chr6_810624_T / A;

[0074] Chr6_3036971_A / G;Chr6_5034063_T / A;Chr6_15910001_C / T;Chr6_24457821_G / A;

[0075] Chr6_83782657_C / T;Chr6_98816559_G / A;Chr6_98989641_T / A;Chr6_101179647_T / G;

[0076] Chr6_105804599_G / A;Chr6_106597314_G / A;Chr6_107794933_T / C;Chr7_3136477_A / G;

[0077] Chr7_4403505_C / T;Chr7_6790961_C / G;Chr7_11042954_G / A;Chr7_13203287_T / C;

[0078] Chr7_13586605_T / C;Chr7_19002798_C / A;Chr7_23498422_T / C;Chr7_51574707_G / C;

[0079] Chr7_64866814_T / C;Chr7_86545391_G / C;Chr7_88082006_A / T;Chr7_91885282_T / G;

[0080] Chr7_95451717_G / C;Chr7_101803420_T / C;Chr8_434205_G / T;Chr8_3622765_C / T;

[0081] Chr8_6201463_T / C;Chr8_6777431_G / T;Chr8_16893876_A / T;Chr8_18492509_C / A;

[0082] Chr8_27807713_T / C;Chr8_70878100_C / T;Chr8_87651866_G / T;Chr8_90588981_A / C;

[0083] Chr8_98580941_G / A;Chr8_99079868_A / G;Chr8_100597325_C / G;Chr9_1813979_C / G;

[0084] Chr9_5709469_C / A;Chr9_7401382_C / A;Chr9_7664635_A / C;Chr9_14855094_T / C;

[0085] Chr9_17665225_T / C;Chr9_18653960_C / T;Chr9_20264134_A / T;Chr9_20707073_A / G;

[0086] Chr9_24502054_A / C;Chr9_24854055_A / C;Chr9_34308910_C / T;Chr9_34873585_T / C;

[0087] Chr9_75435371_C / T;Chr9_77610735_G / A;Chr9_86585759_T / A;Chr9_88315788_A / G;

[0088] Chr9_91502195_G / A;Chr9_95436365_T / A;Chr9_97867065_G / A;Chr10_1470878_A / T;

[0089] Chr10_5824840_G / C;Chr10_8136996_A / T;Chr10_10507992_G / A;Chr10_15719936_T / A;

[0090] Chr10_27591981_C / A;Chr10_87585142_C / G;Chr10_90419402_C / A;Chr10_90421003_G / A;

[0091] Chr10_94722518_G / A;Chr10_96108456_C / T;Chr10_98147463_C / G;Chr11_678127_C / T;

[0092] Chr11_736365_A / G;Chr11_1115977_C / G;Chr11_7196081_G / A;Chr11_10848831_G / C;

[0093] Chr11_14918947_T / C;Chr11_18839922_C / G;Chr11_22924094_C / T;Chr11_52683514_T / G;

[0094] Chr11_72064153_A / G;Chr11_73664189_C / T;Chr11_74555756_A / G;Chr11_75121758_C / T;

[0095] Chr11_82668555_T / G;Chr11_91501311_T / G;Chr11_93188716_T / G;Chr11_95071313_C / T;

[0096] Chr11_96208291_C / T;Chr11_98880506_C / T;Chr12_684080_C / A;Chr12_2931612_T / C;

[0097] Chr12_6899137_T / A;Chr12_7707046_A / G;Chr12_12156787_A / T;Chr12_13341210_T / A;

[0098] Chr12_16307269_C / T;Chr12_16328314_A / G;Chr12_22494251_T / C;Chr12_23601414_G / C;

[0099] Chr12_26680799_C / G;Chr12_26973865_C / A;Chr12_32544120_A / T;Chr12_35993093_T / C;

[0100] Chr12_37011239_C / A;Chr12_38908419_A / C;Chr12_40517500_A / G;Chr12_45207311_T / C;

[0101] Chr12_45440599_T / C;Chr12_69549182_A / G;Chr12_79376136_C / G;Chr13_4356832_G / T;

[0102] Chr13_8875751_T / C;Chr13_13255560_G / T;Chr13_13918244_A / G;Chr13_15886975_T / A;

[0103] Chr13_16924693_A / G;Chr13_25851280_T / C;Chr13_31683642_A / G;Chr13_48641671_C / G;

[0104] Chr13_69350364_G / A;Chr13_69392735_G / A;Chr13_70291223_T / A;Chr13_77454106_G / A;Chr13_77704508_T / A;Chr13_78200581_G / A;Chr13_83025236_G / A;Chr13_83094380_T / G;Chr13_86155184_C / T;Chr13_89160461_G / A;Chr13_89846004_T / G;Chr14_3754938_G / A;Chr14_4002023_A / G;Chr14_5279683_T / G;Chr14_5988595_C / T;Chr14_16631275_G / T;Chr14_16668074_C / T;Chr14_23975735_C / T;Chr14_24930605_T / A;Chr14_29279540_C / T;Chr14_68126151_A / G;Chr14_68309126_G / A;Chr14_69200024_A / G;Chr14_74583350_A / C;Chr14_81298104_C / A;Chr14_83285431_C / G;Chr14_89010870_G / A;Chr14_91155262_G / T;Chr15_2986762_C / G;Chr15_3196798_C / A;Chr15_8687335_G / A;Chr15_23754687_A / G;Chr15_35180027_A / G;Chr15_40670852_C / T;Chr15_47894762_G / T;Chr15_52881987_T / A;Chr15_53642786_G / T;Chr15_54447431_T / C;Chr15_63208884_C / T;Chr15_66357157_G / T;Chr15_70990505_A / G;Chr15_73033483_T / C;Chr16_8093869_T / C;Chr16_8130467_G / A;Chr16_9976916_G / A;Chr16_41093450_C / A;Chr16_41892017_T / C;Chr16_43339238_A / C;Chr16_47328276_T / C;Chr16_50459414_T / C;Chr16_55859604_A / G;Chr16_61536320_A / G;Chr16_64893652_A / C;Chr16_69033394_C / T; Chr16_70631013_C / A; Chr17_4332955_G / C; Chr17_5300940_C / T; Chr17_11344297_A / G; Chr17_14450909_C / T; Chr17 _24540321_G / A; Chr17_25427335_G / A; Chr17_39194976_G / A; Chr17_47016224_A / G; Chr17_51749822_A / G; Chr17_55881919_C / T; Chr17_580 04068_A / G; Chr18_2465717_T / A; Chr18_7859243_A / G; Chr18_28775131_C / T; Chr18_29989533_G / A; Chr18_35440358_C / T; Chr18_41190847_ A / G; Chr18_42439396_C / A; Chr18_42574751_A / C; Chr18_45891002_C / T; Chr18_46892894_C / T; Chr18_50817494_G / C; Chr18_51611167_T / C. ;

[0105] In this embodiment, the above 298 SNP marker site combinations related to rubber tree breeding traits are derived from whole genome resequencing information and related GWAS sites of 142 rubber tree germplasm materials, and the method for obtaining the same comprises the following steps:

[0106] 1. Obtaining SNP marker loci for the whole genome of rubber trees

[0107] Young leaves of rubber trees were taken and high-quality genomic DNA of rubber trees was extracted using the CTAB method. The DNA was used for genome resequencing, and the amount of high-quality clean data obtained by sequencing was 4089Gb, with an average of 29Gb per sample and a sequencing depth of about 20×. The sequencing data was aligned to the rubber tree reference genome (version number ASM3005281v1) using BWA software, and high-quality SNPs were obtained using GATK software. Marker sites with genotype loss less than 10% and minimum allele frequency greater than 5% were filtered out.

[0108] 2. Perform genome-wide association analysis on the obtained rubber tree SNP marker loci and phenotypic traits of rubber trees

[0109] 1) Sample collection and acquisition

[0110] 142 core rubber tree germplasm resources were planted in the National Rubber Tree Germplasm Resource Nursery in Danzhou City, Hainan Province from 2006 to 2007, with 5 trees planted for each germplasm and normal field management.

[0111] 2) Phenotypic detection

[0112] Five breeding traits of 142 rubber tree germplasms were tested, including bark thickness, cold tolerance, stem girth production rate, latex yield and number of latex tubes, and the average values ​​of five replicates were measured as phenotypic input files for genome-wide association analysis and construction of genomic selection breeding models. The detection methods of the five breeding traits are as follows:

[0113] Bark thickness: In 2015, the bark thickness of rubber trees was measured 1.5 m above the ground with a ruler, with an accuracy of 0.1 cm.

[0114] Cold resistance: The cold damage level is divided into 5 levels, namely 0, 1, 2, 3, and 4; the average value of 5 repetitions is taken as the phenotypic value of cold resistance.

[0115] Stem girth production rate: In 2009, 2010, 2012, 2013 and 2014, the stem girth of rubber trees was measured at 1.5 m above the ground with a tape measure, with a measurement accuracy of 0.1 cm. The stem girth growth rate was calculated using linear regression: y = b1x i +b0, b1 is the slope, x i is the stem girth length in the i-th year, b0 is the stem girth length at planting, and the slope b1 is used to represent the stem girth growth rate.

[0116] Latex production: Latex production was measured for three consecutive years from 2017 to 2019. The annual average latex production per knife was calculated based on the total production as the phenotypic data of latex production.

[0117] Number of laticiferous ducts: The number of laticiferous ducts was measured for 3 consecutive years from 2017 to 2019; the average value of 5 replicates was used as the phenotypic value of the number of laticiferous ducts.

[0118] 3) Screening for dominant alleles associated with each phenotypic trait and obtaining the association between the phenotypic trait and the dominant allele

[0119] The obtained SNP marker sites were subjected to genome-wide association analysis with the measured phenotypic information to obtain the SNP markers associated with each of the five traits. Different QTLs were divided according to the linkage disequilibrium decay distance. The most significant SNP marker sites were screened for each QTL. The effect value and dominant allele type were obtained in combination with each phenotypic trait. A total of 299 dominant alleles were obtained for the five phenotypic traits. The association results are as follows (all SNP marker names are expressed in the form of chromosome number_physical position):

[0120] The corresponding relationship between the 52 SNP marker alleles related to bark thickness and the bark thickness phenotype is shown in Table 1:

[0121] Table 1 Correspondence between the alleles of 52 SNP markers related to bark thickness and the bark thickness phenotype

[0122]

[0123]

[0124] The corresponding relationship between the 39 SNP marker alleles related to cold tolerance and the cold tolerance phenotype is shown in Table 2:

[0125] Table 2 Correspondence between the alleles of 39 SNP markers related to cold tolerance and the cold tolerance phenotype

[0126]

[0127] Note: The higher the average value, the stronger the cold resistance.

[0128] The corresponding relationship between the 61 SNP marker alleles related to stem girth production rate and the stem girth production rate phenotype is shown in Table 3:

[0129] Table 3 Correspondence between the alleles of 61 SNP markers related to stem girth production rate and the phenotypes of stem girth production rate

[0130]

[0131]

[0132] The corresponding relationship between the 82 SNP marker alleles related to latex yield and the latex yield phenotype is shown in Table 4:

[0133] Table 4 Correspondence between the alleles of 82 SNP markers related to latex yield and the phenotype of latex yield

[0134]

[0135]

[0136]

[0137] The corresponding relationship between the 65 SNP marker alleles related to the number of laticifers and the phenotype of the number of laticifers is shown in Table 5:

[0138] Table 5 Correspondence between the alleles of 65 SNP markers related to the number of laticifers and the phenotype of the number of laticifers

[0139]

[0140]

[0141] 4) Acquisition of 298 dominant alleles

[0142] The obtained 299 dominant alleles are deduplicated to obtain the dominant alleles of 298 SNP marker sites, that is, the 298 SNP site combinations related to the rubber tree breeding traits of the present invention.

[0143] 5) Analyze the distribution of 298 SNP sites on chromosomes. The results are shown in Figure 1 ; The distribution of the minor allele frequency of 298 SNP loci was statistically analyzed, with a variation range of 0.05 to 0.49 and an average value of 0.27 (see Figure 2 ); The heterozygosity distribution of 298 SNP sites was statistically analyzed, with a variation range of 0.01 to 0.96 and an average value of 0.34 (see Figure 3 ).

[0144] Example 2

[0145] Based on the 298 SNP sites related to rubber tree breeding traits obtained in Example 1, probes for detecting the 298 SNP marker sites were designed, probe combinations were obtained, and liquid gene chips for detecting the 298 SNP marker sites were prepared.

[0146] Example 3

[0147] A total of 299 dominant alleles related to bark thickness, cold tolerance, stem girth production rate, latex yield and latex duct number obtained in Example 1 were verified, and the verification operation method is as follows:

[0148] 1, choose a total of 223 parts of rubber tree germplasm resources from China, Indonesia, Malaysia, Sri Lanka, Brazil and Vietnam as test material (table 6), measure the bark thickness, cold tolerance, stem girth production rate, latex yield and the latex duct quantity phenotype of these 223 parts of rubber trees by the method described in Example 1;

[0149] Table 6 Statistics on the sources of 223 rubber tree germplasm resources

[0150]

[0151] 2. Establish a comprehensive breeding index based on these 5 breeding traits. The economic weights of latex yield, number of latex tubes, bark thickness, cold resistance and stem girth production rate are set to 0.3, 0.2, 0.2, 0.2 and 0.1 respectively. The comprehensive breeding index is calculated by using the value after trait normalization, and the comprehensive breeding index=0.3×latex yield+0.2×number of latex tubes+0.2×bark thickness+0.2×cold resistance+0.1×stem girth production rate. The influence of the dimension between the trait phenotypic values ​​is removed by normalization. Since latex yield is the most direct and important target trait in rubber tree breeding, latex yield is given a higher economic weight; The other 4 traits can be given different weights according to the importance of breeding, and the other 4 breeding traits, number of latex tubes, bark thickness, cold resistance and stem girth production rate weights are set to 0.2, 0.2, 0.2 and 0.1 respectively in the present embodiment.

[0152] 3. The genotypes of 298 SNP marker loci related to five breeding traits, including bark thickness, cold resistance, stem girth production rate, latex yield and latex duct number, were determined in 223 rubber tree germplasm materials.

[0153] 4. The aggregation of 298 dominant alleles related to five breeding traits, namely bark thickness, cold tolerance, stem girth production rate, latex yield and number of latex tubes, in 223 rubber tree germplasm materials was analyzed. The results are shown in Figure 4 The results show that the more 298 dominant alleles related to the five breeding traits that are aggregated in an individual, the higher the value of its comprehensive breeding index. Therefore, the dominant alleles of the corresponding phenotypic traits obtained in Example 1 can be used to evaluate the comprehensive breeding index of rubber trees. The more 298 dominant alleles related to the five agronomic traits are aggregated, the better the performance of the target individual in the comprehensive breeding traits.

[0154] Example 4

[0155] A method for molecular assisted breeding of rubber trees comprises the following steps:

[0156] 1. The liquid-phase gene chip described in Example 2 was used to perform functional gene detection on germplasm resources and breeding materials to clarify the allele type of the 298 SNP sites related to rubber tree breeding traits;

[0157] 2. Gene identification was performed on the rubber tree germplasm resource material obtained in Example 3 using the dominant allele described in Example 1 to determine the dominant alleles of breeding traits carried in the germplasm material, wherein each row represents a SNP genotype, each column represents a material, and black, gray, light gray and white represent non-dominant alleles, heterozygous genes, dominant alleles and deletions, respectively (see Figure 5 ).

[0158] 3. Screen materials with a large number of complementary dominant alleles and use them as parents for hybridization in order to obtain ideal offspring individuals containing more dominant alleles, thereby achieving molecular marker-assisted selection breeding.

[0159] The embodiments described above are only descriptions of the preferred modes of the present invention, and are not intended to limit the scope of the present invention. Without departing from the design spirit of the present invention, various modifications and improvements made to the technical solutions of the present invention by ordinary technicians in this field should all fall within the protection scope determined by the claims of the present invention.

Claims

1. An application of a SNP locus combination associated with rubber tree breeding traits in rubber tree molecular assisted breeding, characterized in that, The SNP site combination consists of 298 SNP sites, each SNP site contains two alleles of different bases, which are used to detect the allele changes of the site. The physical positions of the 298 SNP sites are determined based on the genome sequence comparison of the rubber tree wild germplasm MT / VB / 25A 57 / 8, and the version number of the genome sequence of the rubber tree wild germplasm MT / VB / 25A 57 / 8 is ASM3005281v1. The variation information of the 298 SNP sites is as follows: The variation information of the SNP sites is represented in the form of chromosome number_physical position_reference genotype / allele type: Chr1_15757_G / T; Chr1_731023_C / T; Chr1_2709764_C / T; Chr1_3828026_C / G;Chr1_10086984_T / C; Chr1_13443998_C / A; Chr1_24711557_G / A; Chr1_28410342_G / A;Chr1_31246482_A / G; Chr1_33236009_A / T; Chr1_91047897_G / A; Chr1_94236268_C / T;Chr1_97506370_A / G; Chr1_103644378_T / A; Chr1_105896364_A / C; Chr1_111818657_C / A; Chr1_119761444_G / A; Chr1_119815929_T / A; Chr1_124681987_A / G; Chr2_708272_T / C; Chr2_1091213_A / G; Chr2_1412841_T / G; Chr2_6735215_A / G; Chr2_8387629_A / G;Chr2_8935490_C / T; Chr2_14396160_G / A; Chr2_17221809_G / C; Chr2_23335062_C / T;Chr2_52259102_G / A; Chr2_65921385_C / T; Chr2_71475197_G / T; Chr2_77534372_A / G;Chr2_85191439_T / C; Chr2_102109411_A / C; Chr2_107220134_A / G; Chr2_112911824_G / T; Chr2_116729566_A / G; Chr2_116811799_C / A; Chr2_123601709_T / G; Chr2_124300927_A / G; Chr3_1466320_C / T; Chr3_1960954_T / C; Chr3_4087599_T / A; Chr3_5957222_G / A; Chr3_12089943_G / A; Chr3_12476864_T / C; Chr3_14407329_A / T; Chr3_19609926_G / A; Chr3_25818990_C / T; Chr3_26105771_T / A; Chr3_28011570_A / G; Chr3_55427066_A / G; Chr3_65399028_G / A;Chr3_78061863_G / A; Chr3_83776666_T / G; Chr3_87552482_G / T; Chr3_87849740_G / A; Chr3_89316084_G / A; Chr3_95073582_T / A; Chr3_97394338_A / C; Chr3_97633357_A / G; Chr3_99096014_G / T; Chr3_105554669_T / C; Chr3_108145282_A / C; Chr3_110755926_G / A; Chr3_111315050_G / A; Chr3_113093396_G / T;Chr3_115841960_T / C; Chr4_4836875_T / G; Chr4_5122798_A / G; Chr4_13812464_A / T;Chr4_14259021_T / C; Chr4_20075652_C / A; Chr4_20495918_T / A; Chr4_27655758_T / C;Chr4_28184400_G / A; Chr4_101079315_C / T; Chr4_104972595_C / T; Chr4_109783256_G / A; Chr4_110174839_A / C; Chr4_111315272_A / G; Chr4_115826287_G / T; Chr5_5014612_G / A; Chr5_5023352_C / A; Chr5_5515786_A / T; Chr5_9709308_A / G; Chr5_12766865_T / C;Chr5_15109810_T / A; Chr5_22533448_A / G; Chr5_25929070_A / G; Chr5_65287220_A / G;Chr5_73727319_T / A; Chr5_88048914_G / A; Chr5_99903267_C / G; Chr5_105218154_A / G;Chr5_108901274_A / G; Chr5_110279515_T / C; Chr5_111330503_T / C; Chr5_111547930_C / A; Chr6_810624_T / A; Chr6_3036971_A / G; Chr6_5034063_T / A; Chr6_15910001_C / T;Chr6_24457821_G / A; Chr6_83782657_C / T;Chr6_98816559_G / A; Chr6_98989641_T / A;Chr6_101179647_T / G; Chr6_105804599_G / A; Chr6_106597314_G / A; Chr6_107794933_T / C; Chr7_3136477_A / G; Chr7_4403505_C / T; Chr7_6790961_C / G; Chr7_11042954_G / A;Chr7_13203287_T / C; Chr7_13586605_T / C; Chr7_19002798_C / A; Chr7_23498422_T / C;Chr7_51574707_G / C; Chr7_64866814_T / C; Chr7_86545391_G / C; Chr7_88082006_A / T;Chr7_91885282_T / G; Chr7_95451717_G / C; Chr7_101803420_T / C; Chr8_434205_G / T;Chr8_3622765_C / T; Chr8_6201463_T / C; Chr8_6777431_G / T; Chr8_16893876_A / T;Chr8_18492509_C / A; Chr8_27807713_T / C; Chr8_70878100_C / T; Chr8_87651866_G / T;Chr8_90588981_A / C; Chr8_98580941_G / A; Chr8_99079868_A / G; Chr8_100597325_C / G;Chr9_1813979_C / G; Chr9_5709469_C / A; Chr9_7401382_C / A; Chr9_7664635_A / C; Chr9_14855094_T / C; Chr9_17665225_T / C; Chr9_18653960_C / T; Chr9_20264134_A / T; Chr9_20707073_A / G; Chr9_24502054_A / C; Chr9_24854055_A / C; Chr9_34308910_C / T; Chr9_34873585_T / C; Chr9_75435371_C / T; Chr9_77610735_G / A; Chr9_86585759_T / A; Chr9_88315788_A / G; Chr9_91502195_G / A; Chr9_95436365_T / A;Chr9_97867065_G / A; Chr10_1470878_A / T; Chr10_5824840_G / C; Chr10_8136996_A / T; Chr10_10507992_G / A; Chr10_15719936_T / A; Chr10_27591981_C / A; Chr10_87585142_C / G; Chr10_90419402_C / A;Chr10_90421003_G / A; Chr10_94722518_G / A; Chr10_96108456_C / T; Chr10_98147463_C / G; Chr11_678127_C / T; Chr11_736365_A / G; Chr11_1115977_C / G; Chr11_7196081_G / A;Chr11_10848831_G / C; Chr11_14918947_T / C; Chr11_18839922_C / G; Chr11_22924094_C / T; Chr11_52683514_T / G; Chr11_72064153_A / G; Chr11_73664189_C / T; Chr11_74555756_A / G; Chr11_75121758_C / T; Chr11_82668555_T / G; Chr11_91501311_T / G;Chr11_93188716_T / G; Chr11_95071313_C / T; Chr11_96208291_C / T; Chr11_98880506_C / T; Chr12_684080_C / A; Chr12_2931612_T / C; Chr12_6899137_T / A; Chr12_7707046_A / G;Chr12_12156787_A / T; Chr12_13341210_T / A; Chr12_16307269_C / T; Chr12_16328314_A / G; Chr12_22494251_T / C; Chr12_23601414_G / C; Chr12_26680799_C / G; Chr12_26973865_C / A; Chr12_32544120_A / T; Chr12_35993093_T / C; Chr12_37011239_C / A;Chr12_38908419_A / C; Chr12_40517500_A / G; Chr12_45207311_T / C; Chr12_45440599_T / C;Chr12_69549182_A / G; Chr12_79376136_C / G; Chr13_4356832_G / T; Chr13_8875751_T / C; Chr13_13255560_G / T; Chr13_13918244_A / G; Chr13_15886975_T / A; Chr13_16924693_A / G; Chr13_25851280_T / C; Chr13_31683642_A / G; Chr13_48641671_C / G;Chr13_69350364_G / A; Chr13_69392735_G / A; Chr13_70291223_T / A; Chr13_77454106_G / A; Chr13_77704508_T / A; Chr13_78200581_G / A; Chr13_83025236_G / A; Chr13_83094380_T / G; Chr13_86155184_C / T; Chr13_89160461_G / A; Chr13_89846004_T / G;Chr14_3754938_G / A; Chr14_4002023_A / G; Chr14_5279683_T / G; Chr14_5988595_C / T;Chr14_16631275_G / T; Chr14_16668074_C / T; Chr14_23975735_C / T; Chr14_24930605_T / A; Chr14_29279540_C / T; Chr14_68126151_A / G; Chr14_68309126_G / A; Chr14_69200024_A / G; Chr14_74583350_A / C; Chr14_81298104_C / A; Chr14_83285431_C / G;Chr14_89010870_G / A; Chr14_91155262_G / T; Chr15_2986762_C / G; Chr15_3196798_C / A;Chr15_8687335_G / A; Chr15_23754687_A / G; Chr15_35180027_A / G; Chr15_40670852_C / T; Chr15_47894762_G / T; Chr15_52881987_T / A; Chr15_53642786_G / T; Chr15_54447431_T / C; Chr15_63208884_C / T;Chr15_66357157_G / T; Chr15_70990505_A / G;Chr15_73033483_T / C; Chr16_8093869_T / C; Chr16_8130467_G / A; Chr16_9976916_G / A;Chr16_41093450_C / A; Chr16_41892017_T / C; Chr16_43339238_A / C; Chr16_47328276_T / C; Chr16_50459414_T / C; Chr16_55859604_A / G; Chr16_61536320_A / G; Chr16_64893652_A / C; Chr16_69033394_C / T; Chr16_70631013_C / A; Chr17_4332955_G / C;Chr17_5300940_C / T; Chr17_11344297_A / G; Chr17_14450909_C / T; Chr17_24540321_G / A; Chr17_25427335_G / A; Chr17_39194976_G / A; Chr17_47016224_A / G; Chr17_51749822_A / G; Chr17_55881919_C / T; Chr17_58004068_A / G; Chr18_2465717_T / A;Chr18_7859243_A / G; Chr18_28775131_C / T; Chr18_29989533_G / A; Chr18_35440358_C / T; Chr18_41190847_A / G; Chr18_42439396_C / A; Chr18_42574751_A / C; Chr18_45891002_C / T; Chr18_46892894_C / T; Chr18_50817494_G / C; Chr18_51611167_T / C;; The 52 SNP loci associated with bark thickness and their dominant alleles are as follows: Chr1_731023_T; Chr1_10086984_T; Chr1_28410342_A; Chr1_91047897_G; Chr1_103644378_A; Chr1_119761444_A; Chr2_708272_T; Chr2_107220134_G; Chr2_116811799_A; Chr3_12476864_C; Chr3_28011570_A; Chr3_65399028_G; Chr3_89316084_G; Chr3_97394338_A; Chr3_110755926_G; Chr4_5122798_A; Chr4_104972595_T; Chr4_115826287_T; Chr5_5023352_C; Chr5_12766865_C; Chr5_108901274_A; Chr6_810624_T; Chr6_101179647_T; Chr7_11042954_A; Chr7_91885282_T; Chr8_6777431_G; Chr8_87651866_G; Chr9_5709469_C; Chr9_14855094_T; Chr9_20707073_A; Chr9_34873585_T; Chr9_97867065_G; Chr10_1470878_A; Chr10_87585142_C; Chr11_14918947_T; Chr11_73664189_C; Chr11_93188716_T; Chr12_2931612_C; Chr12_22494251_T; Chr13_70291223_T; Chr13_83025236_G; Chr14_89010870_G; Chr15_66357157_G; Chr15_73033483_T; Chr16_8093869_T; Chr16_41892017_T; Chr16_50459414_T; Chr16_64893652_A; Chr17_11344297_G; Chr17_47016224_A; Chr17_55881919_C; Chr18_45891002_T; The 39 SNP loci associated with cold tolerance and their dominant alleles are as follows: Chr1_15757_G; Chr2_8387629_A; Chr2_112911824_T; Chr2_123601709_T; Chr3_1466320_T; Chr3_105554669_C; Chr3_111315050_A; Chr4_111315272_G; Chr5_5515786_A; Chr6_98816559_A; Chr7_4403505_C; Chr8_18492509_C; Chr8_27807713_T; Chr8_100597325_C; Chr9_7664635_C; Chr9_17665225_T; Chr9_24854055_A; Chr9_34308910_T; Chr10_15719936_T; Chr10_94722518_A; Chr11_18839922_C; Chr11_75121758_T; Chr11_96208291_C; Chr12_7707046_G; Chr12_16307269_C; Chr12_26973865_A; Chr12_40517500_A; Chr13_16924693_G; Chr13_31683642_A; Chr13_86155184_T; Chr14_5988595_C; Chr14_16668074_C; Chr14_24930605_A; Chr14_81298104_A; Chr16_41093450_A; Chr17_24540321_A; Chr18_2465717_A; Chr18_29989533_A; Chr18_46892894_T; The 61 SNP loci and their dominant alleles associated with stem girth production rate are as follows: Chr1_2709764_C; Chr1_94236268_C; Chr1_111818657_C; Chr2_6735215_A; Chr2_17221809_C; Chr2_116729566_A; Chr3_5957222_A; Chr3_19609926_A; Chr3_25818990_T; Chr3_87849740_A; Chr3_95073582_A; Chr3_115841960_T; Chr4_14259021_C; Chr4_28184400_G; Chr5_15109810_A; Chr5_25929070_G; Chr5_105218154_G; Chr5_111547930_A; Chr6_106597314_A; Chr7_13203287_C; Chr7_95451717_G; Chr9_1813979_C; Chr9_7401382_C; Chr9_20264134_T; Chr9_75435371_T; Chr9_88315788_A;Chr10_8136996_A; Chr10_90421003_G; Chr10_96108456_T; Chr11_736365_G; Chr11_10848831_C; Chr11_91501311_G; Chr12_16328314_G; Chr12_26680799_G; Chr12_35993093_T; Chr12_45207311_C; Chr12_69549182_G; Chr12_79376136_G; Chr13_4356832_G; Chr13_15886975_T; Chr13_25851280_C; Chr13_48641671_C; Chr13_77704508_A; Chr13_89160461_A; Chr14_3754938_G; Chr14_16631275_G; Chr14_29279540_T; Chr14_68309126_G; Chr14_91155262_T; Chr15_3196798_A; Chr15_47894762_T; Chr15_53642786_G; Chr15_63208884_T; Chr16_43339238_A; Chr16_61536320_G; Chr17_5300940_T; Chr17_14450909_T;Chr17_51749822_A; Chr18_28775131_T; Chr18_41190847_A; Chr18_51611167_T;; The 82 SNP loci associated with latex production and their dominant alleles are as follows: Chr1_731023_T; Chr1_13443998_A; Chr1_24711557_A; Chr1_31246482_A; Chr1_105896364_C; Chr1_124681987_A; Chr2_1412841_T; Chr2_23335062_C; Chr2_52259102_G; Chr2_65921385_C; Chr2_71475197_G; Chr2_85191439_T; Chr2_124300927_A; Chr3_4087599_T; Chr3_14407329_A; Chr3_26105771_T; Chr3_55427066_A; Chr3_78061863_G; Chr3_87552482_G; Chr3_99096014_G; Chr3_108145282_A; Chr4_4836875_T; Chr4_20495918_T; Chr4_101079315_C; Chr4_110174839_A; Chr5_9709308_A; Chr5_22533448_A; Chr5_65287220_A; Chr5_73727319_T; Chr5_88048914_G; Chr5_110279515_T; Chr6_3036971_A; Chr6_15910001_C; Chr6_24457821_A; Chr6_83782657_C; Chr6_98989641_T; Chr6_107794933_T; Chr7_6790961_C; Chr7_13586605_C; Chr7_23498422_T; Chr7_86545391_G; Chr8_3622765_C; Chr8_16893876_A; Chr8_70878100_T; Chr8_90588981_A; Chr8_98580941_G; Chr9_24502054_A; Chr9_77610735_G; Chr9_86585759_T; Chr9_95436365_A; Chr10_10507992_G; Chr10_98147463_C; Chr11_1115977_C; Chr11_7196081_G; Chr11_22924094_T; Chr11_72064153_A; Chr11_98880506_C; Chr12_684080_C;Chr12_12156787_T; Chr12_37011239_C; Chr13_8875751_C; Chr13_13918244_G; Chr13_69392735_G; Chr13_77454106_G; Chr13_83094380_T; Chr13_89846004_T; Chr14_5279683_T; Chr14_23975735_C; Chr14_68126151_G; Chr14_74583350_A; Chr15_8687335_G; Chr15_23754687_A; Chr15_40670852_C; Chr15_52881987_T; Chr16_8130467_A; Chr16_55859604_A; Chr16_69033394_C; Chr17_25427335_G; Chr17_39194976_A; Chr17_58004068_A; Chr18_7859243_A; Chr18_42574751_A;; The 65 SNP loci associated with the number of milk ducts and their dominant alleles are as follows: Chr1_3828026_G; Chr1_33236009_T; Chr1_97506370_A; Chr1_119815929_T; Chr2_1091213_A; Chr2_8935490_T; Chr2_14396160_G; Chr2_77534372_A; Chr2_102109411_A; Chr3_1960954_T; Chr3_12089943_A; Chr3_83776666_G; Chr3_97633357_G; Chr3_113093396_G; Chr4_13812464_A; Chr4_20075652_A; Chr4_27655758_T; Chr4_109783256_A; Chr5_5014612_G; Chr5_99903267_G; Chr5_111330503_T; Chr6_5034063_T; Chr6_105804599_A; Chr7_3136477_G; Chr7_19002798_A; Chr7_51574707_G; Chr7_64866814_T; Chr7_88082006_A; Chr7_101803420_C; Chr8_434205_T; Chr8_6201463_T;Chr8_99079868_G; Chr9_18653960_C; Chr9_91502195_G; Chr10_5824840_C; Chr10_27591981_A; Chr10_90419402_A; Chr11_678127_C; Chr11_52683514_T; Chr11_74555756_A; Chr11_82668555_T; Chr11_95071313_T; Chr12_6899137_T; Chr12_13341210_A; Chr12_23601414_G; Chr12_32544120_A; Chr12_38908419_C; Chr12_45440599_C; Chr13_13255560_G; Chr13_69350364_G; Chr13_78200581_G; Chr14_4002023_A; Chr14_69200024_G; Chr14_83285431_G; Chr15_2986762_G; Chr15_35180027_A; Chr15_54447431_T; Chr15_70990505_G;Chr16_9976916_A; Chr16_47328276_T; Chr16_70631013_A; Chr17_4332955_G; Chr18_35440358_C; Chr18_42439396_A; Chr18_50817494_C;; The molecular assisted breeding is carried out based on the breeding traits of rubber trees, and the breeding traits of rubber trees are bark thickness, cold resistance, stem girth production rate, latex yield and latex duct number.

2. The method for detecting the application of a probe of the SNP site combination as claimed in claim 1 in rubber tree molecular assisted breeding, characterized in that: The molecular assisted breeding is carried out based on the breeding traits of rubber trees, and the breeding traits of rubber trees are bark thickness, cold resistance, stem girth production rate, latex yield and latex duct number.

3. The application of the probe for detecting the SNP site combination as claimed in claim 1 in the breeding trait genotyping of rubber tree germplasm resources, characterized in that, The breeding traits are bark thickness, cold tolerance, stem girth production rate, latex yield and latex duct number.

4. for detecting the application of the liquid phase gene chip of the SNP site combination as claimed in claim 1 in rubber tree molecular assisted breeding, it is characterized in that, The liquid-phase gene chip contains a set of nucleotide probes for detecting the SNP site combination as claimed in claim 1; The molecular assisted breeding is carried out based on the breeding traits of rubber trees, and the breeding traits of rubber trees are bark thickness, cold resistance, stem girth production rate, latex yield and latex duct number.

5. The liquid phase gene chip used to detect the SNP site combination as described in claim 1 is used to carry out the application in the breeding trait genotyping of rubber tree germplasm resources, characterized in that, The breeding traits include bark thickness, cold tolerance, stem girth production rate, latex yield and latex duct number.

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