Cucumber whole genome SNP site combination, liquid phase chip and application of cucumber whole genome SNP site combination and liquid phase chip

Abstract

The invention discloses a cucumber whole genome SNP (Single Nucleotide Polymorphism) site combination, a liquid chip and application of the cucumber whole genome SNP site combination. On the basis of whole genome re-sequencing data and GBS data of cucumbers, a group of SNP locus combinations and liquid phase chips which are uniformly distributed in the whole genome are developed, 17519 SNP loci are selected according to the whole genome re-sequencing data, 7340 SNP loci are selected according to the GBS data, and finally 24859 SNP loci are selected. 24859 SNP loci are uniformly distributed on the whole genome of the cucumber, so that an efficient whole genome genotyping tool is provided for genetic diversity analysis, variety identification, background screening, molecular marker-assisted breeding, gene positioning and whole genome association analysis of the cucumber, and the related research process of the cucumber is promoted. The method has an important application value.

Description

Technical Field

[0001] The invention belongs to the technical field of biomolecular breeding, and particularly relates to a cucumber whole-genome SNP site combination, a liquid phase chip and applications thereof. Background Art

[0002] Cucumber (Cucumis sativus L.) is an important vegetable crop in the Cucurbitaceae family and one of my country's major vegetable varieties. Accelerating the cultivation of superior new cucumber varieties and promoting the sustainable development of the cucumber industry is of great significance. With the completion of cucumber genome sequencing, modern biotechnology and molecular genetic modification techniques have become powerful tools for future molecular design breeding. The design and development of high-density, low-cost molecular marker technology is a prerequisite for molecular design breeding.

[0003] Commonly used molecular markers in cucumber molecular research include SRAP and SCAR. SRAP is a PCR-based molecular marker technology that reveals polymorphisms by amplifying genomic DNA using specific primer combinations. In cucumber research, SRAP markers have been used to study all-female cucumber lines and explore the genetic mechanisms of sex expression in cucumber. SCAR is a marker technology further developed based on SRAP markers. The polymorphic bands of SRAP markers are recovered and sequenced, and new primers are designed to convert them into SCAR markers. This marker can reveal polymorphisms in both parents and the pool, and can obtain amplified fragments of the expected size. Single nucleotide polymorphisms (SNPs) are the most common DNA polymorphism markers in the whole genome. Selecting SNP markers that are evenly distributed throughout the genome can be used for variety identification, QTL positioning, and GWAS analysis. Capture sequencing has strong repeatability and low cost, providing a new method for detecting SNPs in cucumbers.

[0004] Cucumber breeding is relatively underdeveloped compared to the demand for cucumber varieties in production practices. A shift from traditional breeding methods to more efficient whole-genome selection breeding technologies is necessary. Whole-genome SNP profiling is crucial for transitioning this technology from theoretical research to practical application. Therefore, it is crucial to develop a genome-wide representative SNP panel and utilize the latest liquid-phase probe capture sequencing technology based on probe hybridization for high-throughput, low-cost genotyping of cucumber populations. Summary of the Invention

[0005] The purpose of the present invention is to comprehensively analyze cucumber genetic diversity, identify cucumber varieties, screen cucumber backgrounds, etc.

[0006] The present invention first protects a whole-genome SNP site combination in cucumber. The whole-genome SNP site combination in cucumber includes 24,859 SNP sites, of which 3,754 are located on chromosome 1, 3,032 are located on chromosome 2, 5,046 are located on chromosome 3, 3,098 are located on chromosome 4, 3,460 are located on chromosome 5, 3,859 are located on chromosome 6, and 2,610 are located on chromosome 7.

[0007] The locations of the 3754 SNP sites on chromosome 1, the 3032 SNP sites on chromosome 2, the 5046 SNP sites on chromosome 3, the 3098 SNP sites on chromosome 4, the 3460 SNP sites on chromosome 5, the 3859 SNP sites on chromosome 6, and the 2610 SNP sites on chromosome 7 are detailed in the Examples.

[0008] The positions of any of the above-mentioned 24,859 SNP sites on the chromosome are determined based on the sequence alignment of the cucumber Chinese Long genome version V3, that is, the positions of the 24,859 SNP sites on the chromosome are the specific positions on the cucumber Chinese Long genome version V3.

[0009] Any of the above-mentioned cucumber whole-genome SNP site combinations can specifically be composed of any of the above-mentioned 24,859 SNP sites.

[0010] The present invention also protects the use of any of the above-mentioned cucumber genome-wide SNP site combinations, which may be at least one of A2)-A8):

[0011] A2) Analyze the genetic diversity of cucumber germplasm;

[0012] A3) Identification of cucumber germplasm varieties;

[0013] A4) Background for screening cucumber germplasm;

[0014] A5) Conduct molecular marker-assisted breeding on cucumber germplasm;

[0015] A6) Gene mapping in cucumber germplasm;

[0016] A7) Identify the genetic relationships of cucumber germplasm;

[0017] A8) Genome-wide association analysis in cucumber.

[0018] The present invention also protects a cucumber whole genome liquid phase chip, wherein the genotyping objects of the liquid phase chip may include any of the above-mentioned cucumber whole genome SNP site combinations.

[0019] The present invention also protects a cucumber whole genome liquid phase chip, and the detection target of the liquid phase chip can be any of the above-mentioned cucumber whole genome SNP site combinations.

[0020] Any of the above-mentioned cucumber whole-genome liquid phase chips may contain a liquid phase probe set for detecting any of the above-mentioned cucumber whole-genome SNP site combinations.

[0021] Any of the above-mentioned cucumber whole genome liquid phase chips may further contain a hybridization capture reagent.

[0022] Any of the above-mentioned cucumber whole-genome liquid phase chips can be a cucumber 24K or 20K whole-genome liquid phase chip based on targeted capture sequencing.

[0023] The present invention also protects the use of any of the above-mentioned cucumber whole genome liquid phase chips, which can be at least one of A1) to A8):

[0024] A1) detecting the genotype of cucumber based on any of the 24,859 SNP sites described above;

[0025] A2) Analyze the genetic diversity of cucumber germplasm;

[0026] A3) Identification of cucumber germplasm varieties;

[0027] A4) Background for screening cucumber germplasm;

[0028] A5) Conduct molecular marker-assisted breeding on cucumber germplasm;

[0029] A6) Gene mapping in cucumber germplasm;

[0030] A7) Identify the genetic relationships of cucumber germplasm;

[0031] A8) Genome-wide association analysis in cucumber.

[0032] The present invention also protects primers and / or probes for detecting any of the above-mentioned cucumber genome-wide SNP site combinations.

[0033] The present invention also protects the use of primers and / or probes for detecting any of the above-mentioned cucumber genome-wide SNP site combinations, which may be at least one of A1) to A9):

[0034] A1) detecting the genotype of cucumber based on any one of the 24,859 SNP sites described above;

[0035] A2) Analyze the genetic diversity of cucumber germplasm;

[0036] A3) Identification of cucumber germplasm varieties;

[0037] A4) Background for screening cucumber germplasm;

[0038] A5) Conduct molecular marker-assisted breeding on cucumber germplasm;

[0039] A6) Gene mapping in cucumber germplasm;

[0040] A7) Identify the genetic relationships of cucumber germplasm;

[0041] A8) Genome-wide association analysis in cucumber;

[0042] A9) Preparation of cucumber whole genome liquid phase array.

[0043] Based on the whole-genome resequencing data and GBS data of cucumber, the present invention developed a set of SNP site combinations with uniform distribution across the whole genome and liquid phase chips. 17,519 SNP sites were selected from the whole-genome resequencing data, 7,340 SNP sites were selected from the GBS data, and ultimately 24,859 SNP sites were selected. The 24,859 SNP sites are evenly distributed across the whole cucumber genome, providing an efficient whole-genome genotyping tool for cucumber genetic diversity analysis, variety identification, background screening, molecular marker-assisted breeding, gene mapping, and genome-wide association studies (GWAS), thus promoting the relevant research progress of cucumber. The present invention has important application value. DETAILED DESCRIPTION

[0044] The present invention will be further described in detail below in conjunction with specific embodiments. The examples provided are only for illustrating the present invention and are not intended to limit the scope of the present invention. The examples provided below can serve as a guide for further improvements by those skilled in the art and are not intended to limit the present invention in any way.

[0045] Unless otherwise specified, the experimental methods in the following examples are conventional methods and were performed according to the techniques or conditions described in the literature in the field or according to the product instructions. The materials and reagents used in the following examples, unless otherwise specified, were all commercially available.

[0046] The quantitative tests in the following examples were all repeated three times, and the results were averaged.

[0047] Example 1: Acquisition of SNP site combinations in cucumber genome, design of liquid phase probes, and development of microarrays

[0048] 1. Obtaining SNP loci combinations across the cucumber genome

[0049] 1. The 115 cucumber whole-genome resequencing data and 1234 GBS data were aligned with the cucumber ChineseLong genome (V3 version) (as the reference genome), and variant detection was performed using bwa and GATK. Markers were filtered according to miss 0.8 and maf 0.01, and 2680597 and 11503 SNP sites were obtained, respectively.

[0050] 2. The SNP sites obtained by screening in step 1 were used to screen the SNP marker combinations according to the screening principles using a perl program script, and finally 17,519 and 7,340 SNP sites were obtained respectively, for a total of 24,859 SNP sites.

[0051] The screening principles are as follows:

[0052] (1) Use bedtools software to extract SNP sites and their upstream and downstream 100bp sequences. SNP sites without simple repeats are retained; SNP sites without indels larger than 5bp are retained; SNP sites with a GC content between 40-60% and no N bases in the sequence are retained;

[0053] (2) The extracted sequences were aligned to the cucumber Chinese Long genome (version V3) using blastn software, retaining only single-copy SNP sites.

[0054] The cucumber genome-wide SNP locus combination consists of the above 24,859 SNP loci. Among the 24,859 SNP loci, 3,754 are located on chromosome 1 of the cucumber genome, 3,032 are located on chromosome 2 of the cucumber genome, 5,046 are located on chromosome 3 of the cucumber genome, 3,098 are located on chromosome 4 of the cucumber genome, 3,460 are located on chromosome 5 of the cucumber genome, 3,859 are located on chromosome 6 of the cucumber genome, and 2,610 are located on chromosome 7 of the cucumber genome.

[0055] The locations of the 3754 SNPs on chromosome 1 (chr1) are as follows: 11401, 23472, 26256, 38448, 44532, 50568, 60303, 76114, 86628, 91785, 100609, 103159, 113059, 116644, 118655, 118757, 126887, 138236, 140229, 142953, 142990, 143192, 143207, 143762, 148978, 155782, 161018, 180422, 197749, 202598, 213598, 218371, 22428 8,226196,233904,240852,242427,254471,258498,263743,273315,281187,283708,292735,293318,303318,303768,312032,314032,328925,3368 00,348945,349999,363540,367453,367564,377929,380154,396983,403728,407440,410367,413126,422011,422018,434894,434933,445753,456 676,472094,485679,485703,495714,505023,510440,521356,524034,532143,541809,541858,553027,561915,570119,585860,590337,612037,61 5583,621582,631655,642655,647245,649151,649716,650177,664410,678215,682221,694854,704546,708277,714166,715866,733189,733228,7 36504,743271,755545,768652,777190,777242,781120,792322,807290,815218,815557,815786,815879,821562,839289,848095,854768,854914, 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[0056] The locations of the 3032 SNPs on chromosome 2 (i.e., chr2) are as follows: 137235, 140543, 141943, 154700, 166714, 172946, 189940, 193757, 193927, 202419, 216045, 228903, 234991, 239336, 240880, 242480, 253715, 260936, 261054, 275879, 280578, 284761, 296004, 302738, 310259, 324930, 330048, 341048, 343048, 343986, 357227, 362277 57303,357615,368262,370856,384351,397817,405424,414759,423490,431670,441087,441108,443308,451971,466960,469896,482046,501549 ,502043,503279,518271,520113,522961,532488,541488,543688,549966,550493,552548,562949,573888,583150,597310,603450,613329,61957 5,623770,639309,639350,639456,646843,646946,659590,667723,673513,687394,691034,695588,695774,700701,718842,718923,735317,741 869,745054,745274,747274,747774,756310,763331,778742,780845,805966,812876,812923,815358,820828,831790,844349,851431,869637,87 8843,885019,893529,901344,907534,910225,921210,948592,952313,968744,979449,981209,999461,1003997,1010723,1011804,1023925,103 9251,1044431,1052431,1052731,1058530,1058836,1060272,1072648,1088313,1088635,1091480,1107739,1119146,1124589,1139592,1139627,1141894,1152980,1153380,1157166,1165860,1178661,1189135,1193355,1203384,1203505,1203637,1215103,1215159,1215319,1224956,1237776,1247897,1251155,1255479,1262410,1267632,1271382,1281304,1294815,1297566,1309813,1309851,1311451,1317279,1327894,1334853,1335152,1340057,1367648,1372037,1381837,1382037,1386063,1390385,1390399,1400418,1411247,1420846,1439118,1441083,1442663,1451365,1468518,1477190,1483645,1490599,1500121,1500256,1500321,1518951,1520990,1521134,1534057,1539512,1541808,1552827,1561638,1561792,1562026,1570861,1584280,1595711,1600411,1600911,1607055,1610989,1619010,1619147,1623084,1633536,1648890,1655524,1664376,1671671,1686601,1693314,1700814,1701314,1704458,1713480,1720884,1729799,1732195,1743648,1757058,1766572,1767521,1770879,1784303,1795254,1804294,1811303,1828892,1833404,1835376,1848569,1857452,1861020,1868555,1872769,1887052,1887112,1895219,1900785,1911785,1911985,1914896,1925936,1936471,1943854,1954422,1963674,1972675,1981746,1993526,2001207,2012207,2012407,2016839,2016934,2017006,2017108,2018628,2024161,2025593,2025710,2027735,2027788,2032199,2048443,2051879,2057781,2061878,2062001,2076098,2086257,2090058,2106329,2112624,2112824,2126581,2139488,2148037,2148065,2151486,2154102,2154665,2157650,2160298,2173885,2183234,2193659,2208873,2218315,2223318,2230325,2230413,2247077,2256533,2266289,2279444,2279748,2282182,2299344,2307337,2311726,2321781,2330781,2330881,2333103,2340167,2359975,2363009,2378426,2387123,2399176,2400267,2418570,2421855,2430960,2431360,2432149,2445479,2450218,2460019,2471075,2487897,2492261,2531861,2539861,2539945,2574255,2618808,2619408,2620899,2623048,2632048,2634003,2640603,2659198,2660514,2670015,2675542,2680861,2690351,2699907,2711925,2720230,2732352,2742352,2745377,2752407,2763352,2775436,2784897,2785878,2793357,2794051,2794525,2801071,2802029,2811818,2814831,2821925,2832925,2834394,2842132,2851370,2852420,2861640,2869015,2870098,2870101,2874547,2884076,2905440,2914450,2926305,2936126,2944423,2944844,2951644,3015063,3027384,3038305,3040197,3045271,3055171,3056603,3072706,3080158,3095262,3106380,3119184,3124986,3132688,3132821,3142686,3151030,3166293,3170134,3170227,3174051,3181737,3186249,3199477,3199798,3218906,3224954,3236394,3245735,3250294,3268878,3278335,3286549,3286949,3300744,3319369,3324220,3336425,3345472,3350060,3351194,3369191,3379217,3381180,3391107,3391153,3407093,3412733,3425825,3429602,3437679,3440234,3455083,3457632,3460166,3475857,3480476,3483125,3489471,3497415,3500568,3517421,3522087,3536805,3541043,3546951,3551481,3559650,3562151,3577665,3582623,3595180,3597910,3597965,3606806,3614917,3623688,3638203,3640614,3650573,3651569,3651703,3651834,3665281,3672071,3688945,3696042,3702183,3713301,3724201,3724501,3726971,3734590,3747110,3749413,3759140,3760030,3771784,3775597,3788504,3793596,3800130,3811008,3824251,3824951,3833819,3835173,3840745,3857778,3860293,3862987,3868152,3868192,3879461,3879795,3882562,3891689,3892980,3909846,3918234,3918911,3927058,3932529,3945114,3953179,3962429,3978930,3983391,3997432,4000842,4001097,4015018,4020427,4030164,4033164,4033264,4049448,4057450,4060371,4075811,4086419,4090950,4103399,4118585,4120191,4133191,4134091,4135464,4141328,4161225,4173029,4186086,4194840,4197429,4199227,4200060,4201086,4213838,4213858,4214423,4221008,4234008,4234708,4235756,4237499,4237502,4248221,4264643,4272022,4286097,4287848,4296813,4308900,4318901,4325417,4328825,4334825,4335425,4339661,4340694,4367151,4371494,4371559,4373160,4380269,4405653,4418102,4431773,4440607,4459766,4462840,4488382,4504257,4512396,4520185,4520280,4524903,4530262,4541345,4541545,4541765,4551549,4565136,4584649,4605424,4605893,4627153,4634213,4647106,4655606,4655615,4668886,4684913,4694302,4694360,4695170,4712113,4728345,4738777,4740028,4748401,4752427,4755827,4756527,4765183,4771512,4786456,4792711,4798861,4807111,4816249,4823358,4836021,4841174,4856723,4857223,4878782,4879038,4882393,4898126,4900881,4905851,4916648,4923761,4930808,4949307,4950410,4954360,4960031,4973112,4973122,4973950,4984609,4984652,4984712,4996753,5008107,5017943,5026769,5032123,5037353,5041053,5046583,5053877,5067474,5074025,5085025,5085225,5100348,5106247,5113230,5129099,5129183,5135057,5140202,5151876,5161376,5179240,5181653,5185653,5193072,5202956,5211003,5223553,5235067,5238142,5249397,5254729,5268094,5270018,5283098,5286197,5286497,5297462,5303053,5312380,5323525,5341360,5350771,5364503,5386831,5388304,5389404,5408817,5410180,5425104,5434899,5445987,5457044,5469477,5472006,5481878,5488878,5490878,5532696,5544852,5559646,5564225,5564308,5569846,5570032,5589032,5591332,5592190,5602392,5617755,5620348,5637572,5641298,5659461,5664835,5675473,5682320,5689498,5697184,5701912,5719009,5729322,5738193,5742767,5744844,5749951,5768580,5773149,5778055,5788768,5789182,5790452,5802312,5802452,5802778,5815457,5835653,5842469,5862371,5873014,5888678,5898090,5901532,5905482,5912215,5912286,592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34,20508159,20508201,20509985,20510389,20520609,20533734,20547789,20559328,20565578,20575692,20579932,20580245,20583945,20585245,20595308,20601083,20601211,20601284,20610196,20626732,20632191,20632963,20645238,20659131,20662350,20670651,20672772,20673630,20673685,20675141,20688364,20691241,20708719,20713588,20721975,20731949,20734941,20735006,20744487,20749716,20752698,20757747,20760560,20776498,20780303,20791303,20792103,20796542,20802243,20814337,20820109,20838139,20847150,20847309,20847387,20852656,20863321,20868091,20871669,20878443,20889092,20897952,20903957,20910997,20911085,20911185,20922067,20933007,20941806,20954731,20962777,20962910,20963416,20978303,20980679,20994336,21002144,21002312,21011312,21011512,21017943,21022581,21039413,21046973,21050444,21112093,21112393,21117630,21122474,21132921,21143623,21157621,21163966,21175190,21181699,21192083,21208940,21208987,21215047,21224656,21233633,21240082,21240159,21252213,21258012,21264714,21273268,21283988,21284221,21296688,21301204,21312865,21316973,21323963,21324296,21340296,21340496,21341360,21366473,21372225,21374963,21388116,21390052,21403510,21426080,21430191,21440419,21441419,21445931,21452754,21453807,21468101,21473510,21480072,21496074,21506052,21519470,21520059,21524111,21530114,21542114,21542214,21546890,21550525,21558468,21558736,21565369,21565750,21578211,21588119,21589101,21589635,21589675,21600885,21612876,21625929,21636403,21642603,21643003,21646266,21652008,21673817,21685140,21685157,21685319,21694370,21699182,21706134,21714722,21725477,21725503,21738168,21740389,21743389,21759299,21759445,21763862,21777995,21778155,21780508,21794133,21806820,21813826,21822336,21834887,21843738,21853880,21858438,21861562,21873907,21880270,21895456,21908251,21911697,21921093,21939385,21940153,21943992,21944592,21950656,21957603,21960750,21976305,21983574,21996434,22009332,22011838,22015741,22025313,22033127,22043329,22044664,22045164,22059208,22059346,22062482,22071127,22073035,22073083,22080842,22092391,22103980,22111573,22121555,22138907,22144605,22145105,22149215,22156353,22168636,22175418,22181353,22190339,22204076,22211044,22224996,22230281,22234990,22241435,22250294,22260517,22277512,22280165,22295071,22308380,22315071,22324898,22331249,22347342,22347425,22347464,22350509,22351009,22359689,22363112,22373512,22380101,22399505,22404373,22410343,22424389,22431345,22445844,22450149,22451149,22466004,22466276,22466347,22474219,22480250,22494796,22505600,22510776,22527740,22529845,22531557,22532387,22542523,22551323,22551923,22556864,22569145,22572798,22572956,22580485,22580752,22592251,22604421,22614283,22629909,22629935,22647650,22652176,22662675,22662953,22674718,22688027,22691104,22706025,22718254,22722486,22722918,22732895,22749697,22753927,22760056,22760129,22774687,22778189,22788125,22794048,22809620,22827356,22827590,22838211,22841686,22853436,22860336,22860836,22863718,22875236,22882441,22892253,22925951,22939397,22943060,22959175,22959187,22960201,22960269,22961269,22972621,22980913,22991667,23009327,23013723,23013765,23028062,23039463,23045951,23047401,23053091,23061727,23062127,23069359,23074189,23077206,23080839,23091660,23104748,23115535,23122994,23147936,23151746,23162146,23162746,23167274,23174989,23186823,23195130,23209268,23209307,23209505,23209508,23216950,23222255,23230946,23240012,23250442,23253568,23262919,23263619,23269466,23274306,23287274,23291032,23300564,23304730,23314461,23322773,23334662,23348151,23354468,23361167,23361761,23363761,23373462,23373524,23376754,23381292,23395518,23395644,23419122,23428923,23430719,23430866,23458243,23465554,23478680,23491353,23505377,23514613,23520084,23535379,23537793,23540313,23558026,23562591,23570313,23571363,23580467,23588347,23599823,23600228,23602095,23625843,23633646,23647400,23658909,23661302,23670402,23670802,23676351,23682919,23698734,23708973,23710330,23725089,23734928,23742015,23754001,23767869,23773665,23786185,23790528,23809878,23812444,23829737,23830022,23847262,23852121,23870072,23875925,23876325,23883907,23892608,23892665,23892765,23904843,23911357,23922039,23945944,23957006,23960024,23974467,23983897,23983909,24008980,24010561,24020752,24030288,24048868,24059965,24060103,24060592,24060648,24073789,24083908,24084337,24084837,24095148,24095279,24106047,24113288,24127059,24130261,24142230,24151247,24157150,24168065,24171772,24184039,24191507,24191542,24191807,24207886,24214361,24223388,24223754,24232727,24249345,24257413,24261758,24272819,24277125,24281819,24295993,24296193,24297347,24302254,24326079,24333963,24346517,24348997,24355390,24371041,24381459,24391172,24391202,24407734,24410107,24410125,24410307,24422098,24438760,24446871,24455942,24462803,24470343,24481029,24483250,24491608,24508308,24510334,24510417,24511834,24524457,24533781,24534013,24543978,24548373,24552037,24568712,24574541,24597131,24602126,24611199,24612199,24612994,24620522,24620687,24623164,24623174,24623285,24630304,24649171,24655099,24664113,24676701,24682122,24693851,24706984,24711684,24713384,24717778,24728972,24731112,24742439,24751470,24764549,24775679,24785205,24794714,24802052。,

[0057] The locations of the 5046 SNPs on chromosome 3 (i.e., chr3) are as follows: 8192, 11690, 11722, 137422, 266522, 269222, 272255, 288965, 296950, 306185, 313484, 319689, 324286, 333619, 341243, 355041, 362696, 366715, 369715, 376240, 383766, 387020, 387159, 391902, 393816, 393862, 393870, 398629, 403774, 410514, 420904, 42993 5,442478,442531,443163,454251,459541,466919,470966,480829,498359,500437,512870,528733,530162,531525,535726,545332,559250,567 162,573585,580896,581696,584224,594245,600532,604553,615309,627670,632492,642366,657492,662599,681599,682123,682523,698144,70 2051,710973,723948,725913,732110,756236,765796,766116,775579,781579,782579,789736,790855,800486,813319,820766,837100,842515, 859765,861784,881884,883284,886512,890617,890812,890861,890918,902695,919612,928429,930887,937570,939352,939441,940020,955224 ,962907,973223,981556,982556,983556,991702,996551,1003334,1013211,1014150,1027464,1037079,1048370,1052534,1063422,1082241,108 2351,1082651,1083401,1084051,1097142,1102490,1125615,1130335,1149338,1155283,1168570,1171873,1182873,1184873,1185764,1199329,1200433,1212142,1227130,1233561,1245299,1255162,1264020,1274273,1281972,1282972,1285072,1297224,1304879,1314427,1331091,1340361,1348964,1374999,1382169,1383265,1385265,1396165,1399790,1401507,1401837,1404427,1408339,1413429,1414289,1427983,1439025,1445904,1455226,1467595,1483895,1489495,1495957,1501302,1549635,1550016,1564218,1582402,1590860,1608997,1610522,1629670,1631433,1632346,1642442,1651831,1667091,1672711,1689188,1690988,1691788,1706421,1715426,1728972,1736543,1745398,1756017,1765458,1772860,1780642,1791242,1792642,1799238,1799315,1799333,1799367,1801008,1808587,1810547,1820932,1836831,1842717,1857075,1865099,1872053,1880846,1891132,1891932,1892932,1908067,1917822,1929175,1934999,1936189,1936261,1945515,1949061,1957034,1958235,1963806,1972854,1972890,1991566,1992366,1992966,2008743,2014665,2024631,2039067,2044185,2056392,2070440,2086462,2092484,2093484,2107348,2112545,2112548,2128443,2134280,2148138,2156088,2166934,2178317,2183465,2192492,2193492,2196404,2196628,2204470,2210933,2220556,2238275,2238486,2245429,2252851,2265670,2266574,2292974,2293574,2297047,2302302,2317747,2328059,2329109,2337557,2344335,2365446,2368907,2377636,2383739,2392923,2393923,2395033,2395071,2419550,2424632,2446258,2457139,2463081,2474292,2492894,2493894,2493994,2503115,2511000,2511052,2511078,2539081,2541090,2550133,2560208,2576846,2594306,2594406,2600948,2613162,2615813,2620367,2631737,2645420,2650893,2662883,2677107,2683867,2691977,2693823,2700118,2710721,2724743,2732416,2740043,2753737,2764310,2777520,2780197,2798612,2800066,2800116,2816266,2821646,2830565,2841639,2856155,2863702,2873827,2880026,2899259,2906455,2906473,2907523,2917434,2919433,2925833,2944975,2951671,2971923,2981191,2983459,2996360,3006460,3006660,3006804,3015318,3025616,3036170,3040233,3050213,3068887,3079537,3084342,3103456,3107456,3107656,3132932,3144890,3156705,3166019,3169788,3179472,3185174,3185231,3185736,3189174,3190712,3202855,3203140,3211154,3221064,3232114,3245804,3250235,3263980,3271139,3275585,3281497,3282304,3294231,3294500,3300324,3311294,3321770,3322170,3324996,3339217,3343818,3354455,3358615,3358885,3364402,3368646,3373559,3381197,3396991,3400108,3418638,3421036,3422136,3423236,3439081,3442730,3468217,3477768,3483517,3485062,3492733,3499914,3512316,3523116,3523716,3527755,3534282,3545582,3559759,3561935,3565032,3566886,3569016,3572073,3589375,3590139,3600820,3623420,3626620,3649470,3655832,3661472,3677971,3684168,3695767,3709431,3709436,3712936,3723936,3724223,3732083,3748115,3755180,3760163,3772626,3781582,3794820,3808741,3811346,3821093,3824093,3832593,3838524,3844256,3851540,3866236,3875620,3881405,3892554,3905481,3910850,3923429,3924529,3933829,3939748,3942430,3955913,3967528,3972105,3985706,3999580,4008247,4012906,4024906,4028335,4031453,4040220,4040272,4045275,4053500,4053521,4068611,4075295,4080929,4081021,4095801,4100364,4102468,4113517,4125717,4141989,4153489,4155808,4168557,4175690,4175929,4176258,4182522,4182608,4186161,4191528,4214896,4221675,4225675,4231852,4249588,4258112,4266229,4276022,4279928,4280312,4290534,4296280,4303748,4316925,4325825,4329376,4330088,4332454,4338357,4338359,4344168,4352932,4364805,4370933,4380733,4386615,4388061,4393625,4406439,4407043,4408182,4414616,4426616,4428839,4434711,4448974,4454330,4461298,4476275,4482875,4489336,4489579,4494003,4509282,4513111,4527063,4527706,4530731,4551639,4567286,4579358,4581222,4582086,4582367,4583367,4593620,4606433,4613321,4626384,4630436,4642528,4650169,4664219,4671648,4671791,4671815,4672013,4675533,4684133,4688279,4698888,4721355,4730755,4732420,4741196,4752175,4774988,4782689,4791406,4801270,4803270,4831070,4837885,4842959,4843018,4848024,4853403,4862424,4870389,4888441,4899608,4899793,4903393,4915295,4926053,4932721,4949099,4963804,4976591,5002643,5004243,5013293,5021240,5033240,5035170,5040782,5054768,5064497,5069852,5074782,5074878,5085669,5091550,5095031,5104431,5106269,5116524,5116777,5129309,5130236,5133236,5142343,5157613,5164399,5172829,5199203,5209134,5211364,5211431,5224748,5234380,5244155,5251249,5251353,5262146,5273968,5284361,5293459,5307525,5310131,5312831,5321413,5339940,5339942,5352006,5354900,5361983,5377001,5399631,5405737,5412780,5426913,5428275,5428307,5436644,5442884,5451233,5452233,5466056,5468921,5471500,5483574,5484503,5493265,5493335,5502029,5512973,5527834,5530973,5546501,5552301,5556521,5568501,5577716,5581866,5582063,5602659,5613459,5614323,5620832,5637892,5642589,5653278,5661023,5671484,5687950,5698493,5699445,5707070,5712432,5713432,5724412,5728737,5739195,5742604,5757401,5760092,5761092,5771333,5774974,5781298,5791923,5802966,5814666,5814801,5825007,5834576,5836337,5836425,5839355,5842945,5848540,5849803,5852997,5861372,5873957,5888181,5891563,5891869,5903105,5909970,5910597,5914897,5927349,5929611,5930142,5933952,5934505,5941686,5953752,5958225,5967221,5971186,5981317,5989373,5991170,6015270,6018379,6025066,603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[0058] The locations of the 3098 SNPs on chromosome 4 (i.e., chr4) are as follows: 26300, 33830, 43100, 51899, 64666, 74128, 89734, 90509, 105240, 117602, 121326, 124729, 134327, 147789, 152104, 160517, 170007, 180607, 181007, 181836, 198109, 208693, 210763, 237470, 249963, 254896, 261464, 263767, 271827, 276986, 280986, 281 086,287914,299187,312668,318357,323967,342686,343085,359185,360067,362968,375611,377306,385673,391877,408196,409279,411180,41 1315,412944,421889,433748,446779,452505,468849,470047,481048,481914,492014,492314,496656,502894,510146,524746,530341,544343,5 53528,565098,568113,577162,584564,592464,592564,595390,603203,610158,623474,636083,645330,653862,665176,666687,671111,687656, 692003,693003,693203,706497,712446,730095,735988,745883,746046,748891,751600,768550,770536,781565,783358,792594,793594,806448 ,810797,827335,839433,845012,853112,854162,866018,876851,879907,880306,893706,894306,895359,910996,929877,939722,944622,97337 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5989010,25990872,26003823,26019459,26022729,26032374,26036575,26037775,26045310,26056981,26063010,26066540,26073473,26081495,26082973,26096860,26101667,26115053,26120681,26131747,26138255,26144570,26160505,26175696,26181578,26190120,26198345,26203026,26215062,26220674,26220678,26220860,26230502,26230942,26244703,26251154,26264814,26270061,26289220,26294569,26296158,26302820,26313787,26324760,26339003,26339189,26346495,26350787,26351800,26356262,26364382,26376278,26380299,26398979,26402039,26418624,26421135,26436431,26441603,26457100,26468500,26469406,26471705,26484211,26498501,26502632,26516049,26529555,26548490,26550921,26564085,26568485,26572485,26574669,26581423。,

[0059] The locations of the 3460 SNPs on chromosome 5 (i.e., chr5) are as follows: 14364,19758,25770,37007,45916,58595,58941,62096,62769,73305,83700,98511,98596,100980,114238,119994,120413,126435,139420,141116,152257,154018,164086,168890,178392,179166,180900,199344,201658,212251,223317,231035 50546,265154,279087,283182,293468,303691,311935,325676,331918,340918,343758,346929,359484,359495,366283,373036,383165,391105, 400213,404122,409964,410303,412103,420818,430417,441117,441417,441645,452785,473605,481699,491611,491981,504705,505373,505451 ,519140,529835,535572,541572,549068,550016,562053,573349,578947,584219,590253,602127,614092,624972,636028,642983,661463,66336 7,671816,689272,708200,715926,723100,733368,743056,743156,748695,752605,780720,782917,795836,802453,813990,827296,833016,8430 16,844016,849069,851531,855163,863562,863702,873952,883795,914560,927068,939467,945140,951836,968573,977466,980654,994651,100 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[0060] The locations of the 3859 SNPs on chromosome 6 (i.e., chr6) are as follows: 5928, 5976, 20439, 32893, 49352, 50893, 50921, 67326, 78070, 78128, 87768, 91603, 106003, 106603, 108724, 119225, 120091, 125187, 130439, 149427, 178202, 188150, 189135, 192595, 206595, 206695, 218629, 219867, 224041, 231491, 244149 72232,286330,286346,294964,306664,306768,307659,307717,309021,316914,326021,329120,330608,343344,343529,352819,369422,373363 ,387058,397793,404858,406858,418477,423601,433487,438901,443309,450021,450045,469014,473818,488807,494205,502637,507737,51835 4,528349,531744,541104,550204,554960,568517,578830,581222,591938,595402,605138,608172,617373,621196,621778,633459,642261,650 334,652764,656607,661874,663745,672400,680496,696285,702837,708954,718018,725211,733381,745362,746679,747913,748122,751772,75 1921,765682,777677,784953,793225,793744,805139,809116,817240,817418,817476,820694,830427,847232,852285,866629,879285,881642,8 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8453,29198462,29204278,29208701,29212229,29222641,29238206,29240399,29258731,29261894,29270894,29271094,29278112,29281233,29290761,29300210,29313556,29313608,29322511,29338439,29339389,29348972,29350490,29351679,29367696,29375510,29385102,29391024,29394771,29399023,29399254,29407929,29410563,29410707,29425803,29433559,29438702,29441308,29442668,29453072,29462546,29472281,29481069,29495973,29497129,29501348,29511348,29511548,29513698,29525198,29531782,29531948,29535316,29536116,29540048,29550930,29555911,29557388,29558313,29558426,29562351,29573480,29575389,29576379,29580502,29590153,29609039,29609156,29610186,29611392,29612392,29625183,29635994,29648709,29659515,29662273,29662293,29662401,29662427,29679132,29683768,29683860,29696629,29700516,29711516,29712716,29715680,29724938,29735111,29735568,29741079,29755704,29764540,29770473,29788315,29790256,29797682,29800706,29804544,29810132,29826010,29830165,29842547,29852894,29865169,29872122,29880435,29892323,29904073,29919821,29920725,29930725,29931003,29939576,29949634,29950154,29967933,29978952,29980647,29990991,29998513,30002541,30017187,30020951,30030853,30037589,30040049,30049824,30059359,30065389,30075500,30080828,30097369,30101885,30102007,30116122,30131122,30131522,30131870,30140711,30155398,30155622,30155945,30164234,30173779,30188996,30189259,30189269,30197010,30197128,30205936,30207597,30212317,30223551,30228829,30237651,30247434,30255648,30260491,30272158,30273553,30273704,30273780,30273889,30288698,30290172,30290778,30290790,30290976,30295251,30296995,30314446,30322317,30322548,30337786,30338107,30343189,30356109,30365340,30371501,30375114,30375221,30384922,30390799,30407208,30410331,30424231,30427186,30437019,30441544,30455611,30469562,30478593,30485575,30489955,30491427,30491527,30505617,30513406,30513892,30528844,30538333,30547005,30549953,30567657,30577100,30580303,30591703,30592303,30594275,30595641,30597810,30602828,30615303,30620767,30631480,30641897,30657739,30668287,30668595,30675517,30685098,30692098,30693098,30699687,30701447,30714183,30728254,30733053,30742085,30755772,30765911,30770428,30785367,30790760,30792905,30793905,30802448,30810556,30822611,30833435,30848685,30855973,30857594,30867819,30873873,30889897,30898188,30902064,30904871,30937731,30938747,30942335,30948802,30956252,30956275,30962205,30978996,30980046,30980087,30984435,30990388,31005370,31011716,31023954,31037948,31045407,31054071,31066881,31078803。,

[0061] The locations of the 2610 SNPs on chromosome 7 (i.e., chr7) are as follows: 74618, 82493, 91102, 95802, 125538, 165825, 174482, 186156, 191103, 198003, 205480, 215129, 218362, 224982, 246626, 258928, 264521, 272592, 291592, 298792, 299056, 299100, 302024, 310554, 319626, 322824, 324068, 331442, 343416, 357201, 361196, 36522 0,372360,372517,373501,384259,392756,402052,403002,403142,419627,425808,428105,437014,442913,455085,464891,471917,484365,4957 34,503233,503344,515430,523973,543281,546617,546661,553114,553380,553507,568926,573041,585664,597808,599595,600212,600612,603 612,604012,613042,621310,645042,650636,669760,676330,685826,693457,701643,703643,704843,713817,729083,733434,741680,744541,7 45300,753034,767715,768190,774117,789572,797302,800909,808204,809887,810697,820368,829994,830006,847307,851258,869048,879888, 885049,891139,900096,912806,930106,930406,937267,943040,949807,955357,968500,973319,989161,992572,1001931,1004036,1014861,102 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917,22279233,22288972,22296143,22300489,22312571,22312607,22324643,22324683,22336939,22339891,22340046,22349647,22357367,22359141,22360987,22363987,22372842,22381332,22395924,22404946,22411288,22423819,22433891,22440283,22450807;

[0062] It should be noted that the position of the above-mentioned SNP site on the chromosome represents the specific position on the cucumber Chinese Long genome (V3 version).

[0063] 2. Design of liquid phase probe and development of chip

[0064] 1. Design and synthesize the nucleotide sequence of liquid phase probes based on the 24,859 SNP sites screened in step 1 for subsequent capture sequencing.

[0065] Specifically, according to the location information of the SNP site, a genomic sequence with a length of 100-110 bp before and after is used as a probe for the SNP site for test synthesis, and two probe sequences are designed for each SNP site.

[0066] 2. The liquid phase probes containing the above 24,859 SNP sites were developed according to the conventional design principles of liquid phase chips to obtain a cucumber 24K whole-genome liquid phase chip based on targeted capture sequencing.

[0067] Example 2: Establishment of a method for detecting the genotype of cucumbers based on 24,859 SNP sites using the liquid phase probe prepared in Example 1

[0068] The inventors of this application used the liquid-phase probe prepared in Example 1 to establish a method for detecting the genotype of the cucumber based on 24,859 SNP loci. Some of the steps were carried out with reference to the literature (Shu Diao, et al. Development of 51K liquid-phased probe array for loblolly and slash pines and its application to GWAS of slash pine breeding population. Industrial Crops and Products. Volume 216, 15 September 2024, 118777). The specific steps are as follows:

[0069] 1. Extraction of cucumber genomic DNA

[0070] The cucumber leaves to be tested were collected, stored with ice packs and promptly transported back to the laboratory, and the genomic DNA of the cucumber was extracted using the magnetic bead method.

[0071] 2. Genomic DNA library construction

[0072] The cucumber genomic DNA extracted in step 1 was sequentially subjected to genomic DNA fragmentation, end repair, and ligation with second-generation sequencing adapters to construct a whole-genomic DNA library.

[0073] 3. Preparation of Blocked Whole-Genome DNA Library

[0074] The repetitive regions in the whole genomic DNA library constructed in step 2 were blocked using Blocker (prepared using genomic DNA of more than 50 mg cucumber) to obtain a blocked whole genomic DNA library.

[0075] 4. Probe hybridization capture

[0076] The cucumber 24K whole genome liquid phase chip based on targeted capture sequencing prepared in Example 1 was hybridized with the closed whole genome DNA library prepared in step 3 to capture the target region DNA library.

[0077] 5. Sequencing library

[0078] The target region DNA library obtained in step 4 was purified using magnetic beads, and after passing the quality inspection, a sequencing library was obtained.

[0079] 6. High-throughput sequencing

[0080] The sequencing library obtained in step 5 was subjected to high-throughput sequencing using the MGI DNBSEQ-T7 sequencing platform to obtain sequencing data and perform basic data filtering (i.e., cleaning processing) on ​​the sequencing data to obtain cleaned sequencing data.

[0081] 7. Obtain genotype data of the cucumber to be tested based on 24,859 SNP sites

[0082] The cleaned sequencing data obtained in step 6 were aligned to the Chinese Long cucumber genome (V3 version) using bwa software, and the genotype data of the cucumber to be tested based on 24,859 SNP sites were obtained using GATK software. Based on the genotype data of the cucumber to be tested based on 24,859 SNP sites, the genotype of the cucumber to be tested based on 24,859 SNP sites can be obtained.

[0083] Example 3: Evaluation of the capture efficiency of the liquid probe prepared in Example 1

[0084] 1. The genotypes of 12 cucumber samples based on 24,859 SNP sites were detected according to the method of Example 2.

[0085] 2. Based on the genotype data of 24,859 SNP sites in 12 cucumber samples, the detection rate and coverage depth of SNP sites were determined, and then the capture efficiency of SNP sites was analyzed.

[0086] The test results are shown in Table 1. In terms of detection rate, the proportion of SNP sites captured by the samples ranged from 97.27% to 97.71%. In terms of coverage depth, the sample sequencing depth ranged from 65.18% to 88.56%. This indicates that the liquid-phase probe prepared in Example 1 captured a large number of SNP sites with a high capture rate, and has important application value in genetic diversity analysis, gene mapping, and molecular-assisted breeding of cucumber germplasm resources.

[0087] Table 1

[0088] Cucumber samples to be tested Coverage Depth Detection rate (%) Cucumber sample 1 65.42 97.58 Cucumber sample 2 to be tested 69.94 97.56 Cucumber sample 3 to be tested 65.18 97.64 Cucumber sample 4 to be tested 71.43 97.58 Cucumber sample 5 to be tested 69.86 97.71 Cucumber sample 6 70.26 97.27 Cucumber sample 7 69.43 97.60 Cucumber sample 8 83.27 97.57 Cucumber sample 9 88.56 97.40 Cucumber sample 10 67.36 97.63 Cucumber sample 11 66.85 97.56 Cucumber sample 12 65.18 97.69

[0089] The present invention has been described in detail above. For those skilled in the art, without departing from the purpose and scope of the present invention, and without the need to carry out unnecessary experimental conditions, the present invention can be implemented in a wide range under equivalent parameters, concentrations and conditions. Although the present invention provides specific embodiments, it should be understood that further improvements can be made to the present invention. In short, according to the principles of the present invention, this application is intended to include any changes, uses or improvements to the present invention, including changes that depart from the disclosed scope in this application and are made using conventional techniques known in the art.

Claims

1. The cucumber genome-wide SNP locus combination includes 24,859 SNP loci; among them, The locations of the 3754 SNP sites on chromosome 1 are as follows: 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586448,30589651,30598154,30598816,30607436,30610552,30638103,30649787,30664880,30677686,30686054,30687110,30690118,30700033,30704176,30714436,30721174,30723579,30734854,30745389,30752398,30752698,30763994,30768180,30773930,30789890,30790899,30801671,30807398,30811098,30812578,30822220,30839777,30845079,30857198,30860232,30872767,30891183,30906864,30908268,30911368,30919446,30922360,30923436,30937283,30943660,30953869,30967624,30970495,30981755,30998176,31008448,31017260,31019736,31019772,31019830,31024230,31029938,31039943,31119913,31144013,31149750,31158508,31160112,31166653,31173065,31175467,31185358,31220158,31292458,31304125,31310957,31320957,31326947,31338726,31342844,31343682,31352676,31360182,31377432,31384389,31392617,31392730,31403376,31421976,31473609,31487140,31487373,31497129,31508032,31516910,31526739,31532296,31537865,31546289,31551513,31560451,31565547,31565578,31574803,31575853,31585692,31591441,31595713,31597713,31609746,31609895,31610637,31628199,31632532,31642726,31651106,31669862,31669875,31675244,31688058,31693457,31698457,31707080,31711428,31727305,31739852,31740928,31758124,31764020,31773626,31775626,31784012,31791166,31791430,31792994,31800094,31806970,31815547,31824356,31845661,31848286,31855948,31861501,31870413,31876413,31882695,31891206,31900787,31901106,31911205,31922696,31936975,31946525,31959421,31969835,31978879,31984123,31984295,31999397,32001856,32009429,32016378,32021845,32023272,32023716,32031196,32042733,32053015,32065675,32074187,32085187,32086821,32091343,32103966,32104092,32113521,32113623,32113673,32121944,32132345,32140806,32152140,32167563,32176798,32180910,32185910,32204310,32204626,32209860,32229358,32232620,32234716,32248351,32258309,32262652,32273683,32280532,32286532,32297309,32298352,32305136,32314732,32324078,32330214,32331264,32341343,32350259,32359492,32361782,32383738,32387418,32399291,32409065,32410639,32423004,32431829,32432284,32457154,32460885,32478284,32487984,32488141,32499836,32508724,32508862,32509418,32516040,32520655,32532655,32536869,32578260,32580567,32588667,32595825,32601397,32613141,32624145,32631478,32633204,32647686,32652645,32652693,32662189,32687705,32690455,32706626,32710696,32719079,32728514,32735414,32739772,32740295,32746635,32753308,32760958,32775061,32782796,32790796,32794491； The locations of the 3032 SNP sites on chromosome 2 are as follows: 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The locations of the 5046 SNP sites on chromosome 3 are as follows: 8192,11690,11722,137422,266522,269222,272255,288965,296950,306185,313484,319689,324286,333619,341243,355041,362696,366715,369715,376240,383766,387020,387159,391902,393816,393862,393870,398629,403774,410514,420904,429935,442478,442531,443163,454251,459541,466919,470966,480829,498359,500437,512870,528733,530162,531525,535726,545332,559250,567162,573585,580896,581696,584224,594245,600532,604553,615309,627670,632492,642366,657492,662599,681599,682123,682523,698144,702051,710973,723948,725913,732110,756236,765796,766116,775579,781579,782579,789736,790855,800486,813319,820766,837100,842515,859765,861784,881884,883284,886512,890617,890812,890861,890918,902695,919612,928429,930887,937570,939352,939441,940020,955224,962907,973223,981556,982556,983556,991702,996551,1003334,1013211,1014150,1027464,1037079,1048370,1052534,1063422,1082241,1082351,1082651,1083401,1084051,1097142,1102490,1125615,1130335,1149338,1155283,1168570,1171873,1182873,1184873,1185764,1199329,1200433,1212142,1227130,1233561,1245299,1255162,1264020,1274273,1281972,1282972,1285072,1297224,1304879,1314427,1331091,1340361,1348964,1374999,1382169,1383265,1385265,1396165,1399790,1401507,1401837,1404427,1408339,1413429,1414289,1427983,1439025,1445904,1455226,1467595,1483895,1489495,1495957,1501302,1549635,1550016,1564218,1582402,1590860,1608997,1610522,1629670,1631433,1632346,1642442,1651831,1667091,1672711,1689188,1690988,1691788,1706421,1715426,1728972,1736543,1745398,1756017,1765458,1772860,1780642,1791242,1792642,1799238,1799315,1799333,1799367,1801008,1808587,1810547,1820932,1836831,1842717,1857075,1865099,1872053,1880846,1891132,1891932,1892932,1908067,1917822,1929175,1934999,1936189,1936261,1945515,1949061,1957034,1958235,1963806,1972854,1972890,1991566,1992366,1992966,2008743,2014665,2024631,2039067,2044185,2056392,2070440,2086462,2092484,2093484,2107348,2112545,2112548,2128443,2134280,2148138,2156088,2166934,2178317,2183465,2192492,2193492,2196404,2196628,2204470,2210933,2220556,2238275,2238486,2245429,2252851,2265670,2266574,2292974,2293574,2297047,2302302,2317747,2328059,2329109,2337557,2344335,2365446,2368907,2377636,2383739,2392923,2393923,2395033,2395071,2419550,2424632,2446258,2457139,2463081,2474292,2492894,2493894,2493994,2503115,2511000,2511052,2511078,2539081,2541090,2550133,2560208,2576846,2594306,2594406,2600948,2613162,2615813,2620367,2631737,2645420,2650893,2662883,2677107,2683867,2691977,2693823,2700118,2710721,2724743,2732416,2740043,2753737,2764310,2777520,2780197,2798612,2800066,2800116,2816266,2821646,2830565,2841639,2856155,2863702,2873827,2880026,2899259,2906455,2906473,2907523,2917434,2919433,2925833,2944975,2951671,2971923,2981191,2983459,2996360,3006460,3006660,3006804,3015318,3025616,3036170,3040233,3050213,3068887,3079537,3084342,3103456,3107456,3107656,3132932,3144890,3156705,3166019,3169788,3179472,3185174,3185231,3185736,3189174,3190712,3202855,3203140,3211154,3221064,3232114,3245804,3250235,3263980,3271139,3275585,3281497,3282304,3294231,3294500,3300324,3311294,3321770,3322170,3324996,3339217,3343818,3354455,3358615,3358885,3364402,3368646,3373559,3381197,3396991,3400108,3418638,3421036,3422136,3423236,3439081,3442730,3468217,3477768,3483517,3485062,3492733,3499914,3512316,3523116,3523716,3527755,3534282,3545582,3559759,3561935,3565032,3566886,3569016,3572073,3589375,3590139,3600820,3623420,3626620,3649470,3655832,3661472,3677971,3684168,3695767,3709431,3709436,3712936,3723936,3724223,3732083,3748115,3755180,3760163,3772626,3781582,3794820,3808741,3811346,3821093,3824093,3832593,3838524,3844256,3851540,3866236,3875620,3881405,3892554,3905481,3910850,3923429,3924529,3933829,3939748,3942430,3955913,3967528,3972105,3985706,3999580,4008247,4012906,4024906,4028335,4031453,4040220,4040272,4045275,4053500,4053521,4068611,4075295,4080929,4081021,4095801,4100364,4102468,4113517,4125717,4141989,4153489,4155808,4168557,4175690,4175929,4176258,4182522,4182608,4186161,4191528,4214896,4221675,4225675,4231852,4249588,4258112,4266229,4276022,4279928,4280312,4290534,4296280,4303748,4316925,4325825,4329376,4330088,4332454,4338357,4338359,4344168,4352932,4364805,4370933,4380733,4386615,4388061,4393625,4406439,4407043,4408182,4414616,4426616,4428839,4434711,4448974,4454330,4461298,4476275,4482875,4489336,4489579,4494003,4509282,4513111,4527063,4527706,4530731,4551639,4567286,4579358,4581222,4582086,4582367,4583367,4593620,4606433,4613321,4626384,4630436,4642528,4650169,4664219,4671648,4671791,4671815,4672013,4675533,4684133,4688279,4698888,4721355,4730755,4732420,4741196,4752175,4774988,4782689,4791406,4801270,4803270,4831070,4837885,4842959,4843018,4848024,4853403,4862424,4870389,4888441,4899608,4899793,4903393,4915295,4926053,4932721,4949099,4963804,4976591,5002643,5004243,5013293,5021240,5033240,5035170,5040782,5054768,5064497,5069852,5074782,5074878,5085669,5091550,5095031,5104431,5106269,5116524,5116777,5129309,5130236,5133236,5142343,5157613,5164399,5172829,5199203,5209134,5211364,5211431,5224748,5234380,5244155,5251249,5251353,52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The locations of the 3098 SNP sites on chromosome 4 are as follows: 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22514,25324034,25325772,25339270,25342196,25342239,25344198,25352141,25367494,25370780,25388718,25395219,25402697,25413114,25426447,25426647,25429154,25430882,25433713,25434430,25442033,25458170,25463035,25465016,25465082,25465139,25471470,25482418,25493411,25526175,25534015,25544282,25550875,25567279,25571270,25571549,25586315,25591582,25603875,25616003,25623097,25631488,25634606,25634706,25642717,25642738,25654190,25666611,25668053,25679329,25680805,25695444,25696846,25705579,25710333,25720841,25730367,25735517,25735917,25743752,25755927,25763395,25781224,25786978,25795019,25801707,25803635,25804286,25804382,25816531,25821873,25829454,25830645,25835908,25836108,25844737,25851096,25860134,25872547,25889658,25894810,25907159,25926078,25926335,25926385,25931477,25936554,25936954,25949010,25956441,25960996,25970430,25973386,25988528,25989010,25990872,26003823,26019459,26022729,26032374,26036575,26037775,26045310,26056981,26063010,26066540,26073473,26081495,26082973,26096860,26101667,26115053,26120681,26131747,26138255,26144570,26160505,26175696,26181578,26190120,26198345,26203026,26215062,26220674,26220678,26220860,26230502,26230942,26244703,26251154,26264814,26270061,26289220,26294569,26296158,26302820,26313787,26324760,26339003,26339189,26346495,26350787,26351800,26356262,26364382,26376278,26380299,26398979,26402039,26418624,26421135,26436431,26441603,26457100,26468500,26469406,26471705,26484211,26498501,26502632,26516049,26529555,26548490,26550921,26564085,26568485,26572485,26574669,26581423； The locations of the 3460 SNP sites on chromosome 5 are as follows: 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The locations of the 3859 SNP sites on chromosome 6 are as follows: 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The locations of the 2610 SNP sites on chromosome 7 are as follows: 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The positions of the 24,859 SNP sites on the chromosomes are all determined based on the sequence alignment of the cucumber Chinese Long genome version V3, that is, the positions of the 24,859 SNP sites on the chromosomes are all specific positions on the cucumber Chinese Long genome version V3.

2. The cucumber genome-wide SNP locus combination according to claim 1, characterized in that: The cucumber whole genome SNP site combination consists of the 24,859 SNP sites described in claim 1.

3. The use of the cucumber genome-wide SNP locus combination according to claim 1 or 2, which is at least one of A2) to A8): A2) Analyze the genetic diversity of cucumber germplasm; A3) Identification of cucumber germplasm varieties; A4) Background for screening cucumber germplasm; A5) Conduct molecular marker-assisted breeding on cucumber germplasm; A6) Gene mapping in cucumber germplasm; A7) Identify the genetic relationships of cucumber germplasm; A8) Genome-wide association analysis in cucumber.

4. A cucumber whole genome liquid phase chip, characterized by: The genotyping objects of the liquid phase chip include the cucumber whole genome SNP site combination described in claim 1 or 2.

5. A cucumber whole genome liquid phase chip, characterized by: The detection target of the liquid phase chip is the cucumber whole genome SNP site combination described in claim 1 or 2.

6. The cucumber whole genome liquid phase chip according to claim 4 or 5, characterized in that: The cucumber whole genome liquid phase chip contains a liquid phase probe set for detecting the cucumber whole genome SNP site combination described in claim 1 or 2.

7. The cucumber whole genome liquid phase chip according to any one of claims 4 to 6, characterized in that: The cucumber whole genome liquid phase chip is a cucumber 24K or 20K whole genome liquid phase chip based on targeted capture sequencing.

8. Use of the cucumber whole genome liquid phase array according to any one of claims 4 to 7, wherein at least one of A1) to A8) is: A1) detecting the genotype of cucumber based on the 24859 SNP sites described in claim 1 or 2; A2) Analyze the genetic diversity of cucumber germplasm; A3) Identification of cucumber germplasm varieties; A4) Background for screening cucumber germplasm; A5) Conduct molecular marker-assisted breeding on cucumber germplasm; A6) Gene mapping in cucumber germplasm; A7) Identify the genetic relationships of cucumber germplasm; A8) Genome-wide association analysis in cucumber.

9. Primers and / or probes for detecting the cucumber genome-wide SNP site combination as claimed in claim 1 or 2.

10. Use of primers and / or probes for detecting the cucumber genome-wide SNP site combination as claimed in claim 1 or 2, which is at least one of A1) to A9): A1) detecting the genotype of cucumber based on the 24859 SNP sites described in claim 1 or 2; A2) Analyze the genetic diversity of cucumber germplasm; A3) Identification of cucumber germplasm varieties; A4) Background for screening cucumber germplasm; A5) Conduct molecular marker-assisted breeding on cucumber germplasm; A6) Gene mapping in cucumber germplasm; A7) Identify the genetic relationships of cucumber germplasm; A8) Genome-wide association analysis in cucumber; A9) Preparation of cucumber whole genome liquid phase array.