SNP chip of channa maculata and application

Abstract

The embodiment of the invention discloses an SNP chip of channa maculata and application. The SNP chip comprises a probe combination which is fixedly provided with markers respectively aiming at SNP1-SNP50000. The chip has the advantages of uniform site distribution, high typing accuracy, strong repeatability and higher flexibility, is suitable for mainstream next-generation sequencing platforms such as Illumina and MGI, and has universality. A reliable genotyping technology can be provided for correlation researches such as population genetics analysis, genetic relationship identification, whole genome correlation analysis and genome selection of channa maculata, the breeding efficiency of channa maculata is improved, and the development of the aquatic product breeding industry is promoted.

Description

Technical Field

[0001] The present application relates to the technical field of Channa maculata, and in particular to a SNP chip and application of Channa maculata. Background Art

[0002] Channa maculata belongs to the Channidae family, order Perciformes, and genus Channa. Hybrid snakeheads, the offspring of Channa argus and Channa maculata, exhibit advantages such as rapid growth, strong disease resistance, and a high appetite for artificial formula feeds. Channa maculata has also served as the parental source for new varieties, including "Hangzhou Channa No. 1," "Black-banded Hybrid Channa," and "Male Channa No. 1." However, issues such as inbreeding, germplasm degradation, and frequent disease outbreaks hinder the sustainable and healthy development of snakehead aquaculture. Breeding improved varieties of Channa maculata based on modern molecular breeding techniques is crucial. However, current molecular breeding research for Channa maculata relies on whole-genome resequencing and simplified genome sequencing, lacking stable and efficient breeding microarrays. Summary of the Invention

[0003] This application is based on The 50K SNP breeding chip of the whole genome of snakehead fish designed with targeted capture sequencing technology has the advantages of high throughput, strong flexibility, short cycle and low cost. It can be applied to genetic breeding research such as snakehead fish germplasm resource evaluation, whole genome association analysis, and genome selection, and can meet the needs of breeding of high-quality snakehead fish.

[0004] Based on this, this application discloses at least the following technical solutions:

[0005] In a first aspect, the embodiments disclose a SNP marker combination for genotyping of Channa maculata, comprising:

[0006] In a second aspect, the embodiment discloses a SNP chip, which comprises a probe set immobilized with markers for SNP1 to SNP50000.

[0007] In a third aspect, the embodiments disclose uses of the SNP marker combination described in the first aspect or the SNP chip described in the second aspect.

[0008] In a fourth aspect, an embodiment discloses a method for detecting a biological sample, the method comprising detecting information of markers SNP1 to SNP50000 in the biological sample.

[0009] In a fifth aspect, embodiments disclose a method for constructing a DNA fingerprint database for Channa maculata. The method comprises: extracting genomic DNA from all Channa maculata species used to construct the Channa maculata DNA fingerprint database; and using the SNP chip described in the second aspect to detect markers SNP1 to SNP50000 in the genomic DNA of each Channa maculata species, thereby obtaining genotype data for all Channa maculata species at markers SNP1 to SNP50000, thereby constructing the Channa maculata DNA fingerprint database.

[0010] In a sixth aspect, an embodiment discloses a kit for constructing a DNA fingerprint database of Channa maculata, wherein the kit comprises the SNP chip described in the second aspect and an instruction manual describing the method described in the fifth aspect.

[0011] In the seventh aspect, an embodiment discloses a method for performing population structure analysis on the germplasm resources of the spotted snakehead, comprising: extracting the genomic DNA of all the spotted snakehead species to be subjected to population structure analysis respectively; using the SNP chip described in claim 2 to detect the SNP1 to SNP50000 markers on the genomic DNA of each of the spotted snakeheads, thereby obtaining the genotype data of all the spotted snakeheads at the SNP1 to SNP50000 markers; and performing cluster analysis based on the genotype data to analyze the genetic structure of the spotted snakehead.

[0012] In an eighth aspect, an embodiment discloses a kit for grouping Channa maculata germplasm resources, comprising the SNP chip described in the second aspect and instructions describing the method described in the seventh aspect.

[0013] The SNP chip provided in this application contains SNP sites that are unique to the snakehead fish, has a high detection rate, higher genome coverage and lower site deletion rate. The SNP chip can be used as a low-cost, short-cycle, high-quality genotyping tool. The SNP chip is flexible in application and can adjust the target SNP sites by adding or removing probes, and has high application value. The SNP chip has wide adaptability and is suitable for a variety of detection platforms without the need for specific expensive equipment. The 50,000 SNP sites are evenly distributed on the chromosomes, with good detection rates and SNP polymorphisms. The SNP chip genotyping has high accuracy and strong repeatability, and can provide reliable support for genetic analysis of complex traits of the snakehead fish and related breeding work such as germplasm resource evaluation, thereby improving breeding efficiency and promoting the development of the aquatic breeding industry. BRIEF DESCRIPTION OF THE DRAWINGS

[0014] Figure 1 The distribution of 50,000 SNP sites on the Channa maculata genome provided in the embodiment is shown, with a window of 10 Kb.

[0015] Figure 2The minimum allele frequency distribution diagram of 50,000 SNP sites provided in the embodiment ( Figure 2 A) SNP type distribution map Figure 2 B) and statistical diagrams of variants, coding regions, non-coding regions, introns and exons ( Figure 2 C).

[0016] Figure 3 Manhattan scatter plot of the genome-wide association analysis of body weight traits of Channa maculata provided in the example.

[0017] Figure 4 PCA diagram of genetic structure analysis of 67 wild populations provided in the embodiment ( Figure 4 A) Phylogenetic tree diagram ( Figure 4 B) and group structure analysis diagram ( Figure 4 C). DETAILED DESCRIPTION

[0018] In order to make the purpose, technical solutions and advantages of the present application clearer, the present application is further described in detail with reference to the following examples. It should be understood that the specific embodiments described herein are only used to explain the present application and are not intended to limit the present application. The reagents not described separately in detail in the present application are all conventional reagents and can be obtained from commercial channels; the methods not described in detail are all conventional experimental methods and can be learned from the prior art. The terms "SNP" or "SNP marker" or "SNP site" used herein refer to nucleotide sequences present in the genomic sequence of a chromosome. Based on the differences in nucleotide sequences (changes in single nucleotides - A, T, C or G), the polynucleotide sequence changes caused result in the diversity of the chromosome genome, thereby allowing different alleles (e.g., alleles from two different individuals) or different individuals to be distinguished from each other. The changes may occur in the coding region or non-coding region (e.g., promoter region or its vicinity, or intron) of the gene or in the intergenic region. The term "allele" used herein refers to different forms of the same gene present in a given locus on homologous chromosomes.

[0019] The term "linkage disequilibrium" as used herein refers to the non-random association between two or more loci, which may be on the same chromosome or on different chromosomes. Linkage disequilibrium is also known as imbalance at the gamete level or gametic imbalance. From another perspective, linkage disequilibrium is the frequency of alleles or genetic markers in a population that is higher or lower than the haplotype predicted by the random frequency of the alleles. Linkage refers to a limited combination of two or more loci on a chromosome, and linkage disequilibrium is not the same as linkage. The amount of linkage disequilibrium depends on the difference between the observed and expected loci frequencies. For those populations where the frequency of recombined loci or genotypes is equal to the expected one, we call it linkage equilibrium. The degree of linkage disequilibrium depends on many factors, including genetic linkage, selection, and the probability of recombination, genetic drift, assortative mating, and population structure.

[0020] The term "SNP chip" as used herein refers to a biological microchip that can analyze the presence of SNPs contained in sample DNA by arranging and attaching hundreds to hundreds of thousands of biomolecules as probes. The biomolecules, such as DNA, DNA fragments, cDNA, oligonucleotides, RNA, or RNA fragments with known sequences, are fixed at regular intervals on a small solid substrate formed from glass, silicon, nylon, or other organic materials. Depending on the degree of complementarity, hybridization occurs between the nucleic acids contained in the sample and the probes fixed on the surface. By detecting and judging hybridization, information about the substances contained in the sample can be obtained simultaneously.

[0021] SNP marker combinations and SNP chips

[0022] The main types of SNP chips currently available include: on-chip in situ synthesis, which uses modified oligonucleotide monomers to gradually synthesize spatially combined probe sequences in situ to form a SNP chip, thereby directly synthesizing an oligonucleotide probe array on a hard surface. Off-chip synthesis involves using a spotting method to spot pre-synthesized probe sequences onto specific sites to form an SNP chip, thereby forming a DNA probe array fixed to a glass substrate. Microbead method, which involves directly synthesizing DNA probes on coded microbeads, or fixing pre-prepared probe sequences to coded microbeads, and then arbitrarily assembling them to form a microbead chip.

[0023] In one aspect, the embodiments provide a SNP marker combination for genotyping Channa maculata. The SNP marker combination comprises SNP1 to SNP50000 SNP markers. The SNP1 to SNP50000 markers are sequentially represented in Table 1, for example, arranged sequentially from chromosome 1 to chromosome 21. After the SNP sites on each chromosome are arranged, the SNP sites are then arranged in the next chromosome. The reference genome of Channa maculata is GenBank: GCA_020496755.1; assembly number: ASM2049675v1.

[0024] The GenBank accession number of chromosome 1 is CM035599.1. 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[0115] The GenBank number of chromosome 2 is CM035600.1. The SNPs are: 32918, 37384, 51395, 63253, 78072, 92398, 104905, 113404, 122663, 129457, 150243, 167235, 182674, 190973, 203769, 215505, 225446, 239231, 256061, 259298, 279678, 292251, 294915, 316173, 336736, 346626, 353943, 367250, 385791, 391068, 409243, 4135 60,427667,435729,451655,463102,482386,496811,541920,551925,564482,579156,586844,599816,609388,623462,633750,652262,658094,674 236,690282,692053,703901,717287,726390,738775,758340,762066,779882,787146,797942,813099,825083,838580,845296,854712,874594,88 2561,893830,901611,916636,930369,943134,952774,969340,972247,994840,1005454,1010994,1021586,1036167,1049449,1058730,1076817,1 086605,1097185,1105597,1117256,1133856,1140375,1150591,1167137,1180218,1182986,1203009,1214482,1220338,1233902,1252365,125631 7,1274697,1278818,1295700,1302577,1316639,1333202,1339264,1354895,1367367,1377382,1386735,1404692,1410103,1419440,1430187,144 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[0206] The GenBank number of chromosome 3 is CM035601.1. The SNPs are: 8905, 14237, 32345, 44913, 54689, 61461, 76959, 88764, 94918, 105678, 126439, 139374, 150755, 154208, 166957, 180113, 192211, 205025, 217361, 227392, 242730, 250028, 273813, 285985, 295285, 312334, 326078, 334368, 351690, 369876, 376637, 394949 ,402324,419846,429217,436655,454331,459354,472818,492062,523180,535317,544948,559880,563042,580777,586084,603958,610164,6226 07,642311,647617,665873,672283,680445,707951,715629,727023,747425,757512,770651,807752,816301,821643,833188,845398,860240,870 417,884149,897492,903219,916995,925239,938488,957427,969878,976025,984752,1006381,1014420,1032449,1051073,1068629,1077953,10 89875,1110329,1123861,1142067,1156667,1163991,1180227,1187529,1200133,1215705,1218950,1235720,1247704,1256021,1272995,1282553 ,1296237,1302830,1317283,1328375,1345055,1353326,1367814,1390710,1403991,1461272,1474187,1479881,1487932,1507617,1519280,154 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[0297] The GenBank number of chromosome 4 is CM035602.1. The SNPs are: 6943, 16763, 24778, 43651, 50764, 62043, 116879, 118260, 135483, 141559, 158734, 172746, 176429, 195583, 202738, 220294, 235872, 254979, 269249, 290732, 293173, 310284, 322278, 334035, 347927, 359444, 364487, 380515, 394067, 399975, 410969, 4243 30,436906,453758,456685,474153,480628,495539,507603,524638,532055,549378,554685,571802,576848,593156,601378,618754,630443,637 926,653763,660686,678607,683299,695667,720664,729681,738849,753930,762756,784284,794416,798356,817358,823265,833142,856306,87 7552,883769,894803,906268,920464,935078,942765,960035,968091,974749,987442,1002553,1014777,1026888,1037707,1052927,1059082,1 073199,1087858,1093775,1104512,1123711,1129811,1143352,1157921,1169511,1172229,1189739,1194745,1214561,1222433,1239470,124324 9,1257762,1264910,1276918,1290582,1300032,1321794,1332624,1343395,1348603,1363808,1372194,1385092,1401612,1415160,1427393,143 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[0388] The GenBank number of chromosome 5 is CM035603.1. The SNPs are: 41411, 63843, 131841, 140756, 152870, 166240, 177796, 191736, 218255, 222488, 245307, 255484, 264568, 278906, 291834, 295211, 305753, 345254, 354714, 367673, 376785, 404921, 420595, 423903, 450502, 474427, 488732, 499055, 513656, 537871, 543025 ,561581,567489,574687,595237,600388,609339,631250,636343,646355,664899,671382,683503,702271,707436,714949,733392,744428,7565 81,761439,777287,794313,806673,816418,830598,836481,852521,865233,868514,883682,900903,905803,916658,929464,941803,955137,964 711,972908,993262,1000842,1008196,1019190,1032484,1049128,1063218,1071009,1082702,1095976,1104168,1120114,1133654,1145101,11 50299,1164823,1172468,1184380,1197035,1212831,1222241,1232495,1242742,1260594,1272112,1280211,1294581,1305755,1311462,1328331 ,1343969,1357192,1366454,1371220,1389960,1400285,1413764,1419050,1439862,1443534,1462991,1468397,1479799,1495908,1502887,151 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[0479] The GenBank number of chromosome 6 is CM035604.1. The SNP sites are: 119051, 194297, 226801, 253558, 257942, 269486, 289694, 300255, 312489, 317118, 336536, 341091, 370459, 375827, 414528, 548040, 559527, 560926, 567205, 578613, 585677, 597883, 620022, 626647, 634162, 656093, 685027, 694843, 708170, 723397, 726 657,760612,771837,789857,814311,839896,874125,889748,890824,912381,923419,926218,938407,955085,963207,976363,989777,997567,1 008847,1026975,1040047,1051286,1057331,1070199,1087388,1097811,1102136,1119466,1126391,1205872,1225577,1239972,1243900,126050 0,1274077,1285232,1289448,1308842,1321797,1324345,1338259,1349837,1369097,1371411,1384728,1401593,1415987,1419038,1431833,14 65626,1514573,1530992,1535180,1548864,1563621,1576253,1580740,1596210,1631871,1648501,1659507,1670285,1685306,1693103,1707114 ,1714351,1722617,1743006,1744594,1778141,1783987,1795857,1810145,1817226,1836264,1847656,1854551,1871620,1878584,1885800,190 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28603539,28620867,28636348,28641840,28658390,28663351,28679301,28685817,28697991,28715007,28724783,28741771,28752914,28763629,28769938,28783932,28800209,28812946,28819415,28834726,28842814,28858802,28862639,28969989,28985152,

[0570] The GenBank number of chromosome 7 is CM035605.1. The SNP sites are: 56503, 62976, 75359, 87902, 99970, 110491, 124166, 135235, 141484, 163155, 171593, 185606, 195254, 210108, 212272, 233847, 238243, 252214, 269135, 271030, 286917, 299675, 315817, 319940, 337934, 350370, 360427, 364889, 385720, 388247, 405625, 41 3033,421937,443997,453452,465767,478971,489909,491806,508692,518147,532624,548917,560420,565875,581560,592058,619589,625777, 640373,651484,666321,671286,690657,694546,710397,725088,731467,749047,759801,761607,775980,792779,804983,818069,830893,837061 ,849302,859051,868733,880787,900904,906687,918975,933032,940075,952085,968147,979923,994273,999672,1009132,1024715,1036220,1 047974,1064958,1071359,1081759,1091291,1110281,1115173,1125515,1141903,1158858,1166393,1171124,1193317,1194408,1207690,122116 3,1235785,1247164,1264301,1275543,1279305,1289887,1304373,1312794,1331656,1346212,1349420,1360982,1379928,1387087,1396370,141 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[0571] The GenBank number of chromosome 8 is CM035606.1. The SNP sites are: 43483, 54882, 58822, 77130, 86193, 100940, 107946, 118922, 137762, 142004, 159979, 171848, 181078, 198885, 201552, 210792, 225741, 235027, 251253, 268564, 276856, 290760, 297714, 315965, 323812, 329274, 345355, 355642, 368322, 377028, 389689, 39 8871,413785,423085,442333,455764,460006,475359,488004,501505,511279,516875,527443,541850,560163,573175,578657,589051,606596, 613901,624241,635685,647480,658298,670967,683041,701236,712748,717537,734087,745918,755399,762359,774754,788459,802846,819053 ,831119,840263,850575,864322,873890,886926,894411,906653,919171,936177,944106,953651,970370,981353,990051,1006223,1014827,10 23773,1038592,1053621,1055380,1076041,1078870,1096445,1102996,1123145,1133115,1146362,1157352,1170414,1173683,1192388,1207365 ,1225148,1231566,1251172,1253381,1283361,1293817,1299834,1319432,1334600,1341282,1352111,1368129,1371407,1390900,1398974,140 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[0662] The GenBank number of chromosome 9 is CM035607.1. The SNPs are: 80937, 99592, 108530, 121220, 131535, 198539, 201445, 221838, 230589, 242077, 255641, 261647, 275108, 315075, 318261, 332671, 345764, 360905, 366808, 379561, 396037, 400836, 415380, 425824, 435741, 445956, 488787, 525323, 535033, 547600, 557654 ,563081,575980,587948,605024,619680,627507,638208,644881,658349,676068,685951,697399,711862,718693,735274,744567,757154,7666 71,775566,786055,798347,813358,830024,840132,844691,860223,877405,887360,892601,903079,936192,946365,957424,966009,973260,984 984,996448,1013474,1026755,1041707,1045285,1055297,1074119,1088466,1096652,1108744,1112792,1132779,1137439,1158193,1169345,1 182148,1193671,1204076,1206945,1218093,1238154,1241352,1253513,1274911,1297814,1309158,1320858,1326044,1338334,1357414,136747 5,1372555,1382039,1403086,1405269,1426066,1432573,1445751,1461012,1466695,1481838,1495183,1506562,1515019,1522145,1542087,154 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[0663] The GenBank number of chromosome 10 is CM035608.1. The SNP sites are: 14085, 26336, 45867, 53796, 60971, 81500, 89325, 101822, 112956, 130535, 143083, 152813, 174877, 185124, 191535, 206343, 218044, 231180, 234706, 252665, 265808, 275348, 288241, 293981, 309407, 327692, 337667, 350317, 362867, 366228, 385491, 39 1964,409690,413716,431297,433435,451356,462555,470029,485951,494615,504146,525966,534530,545855,558163,562670,580187,591084, 619792,632201,634478,651859,660046,672223,683005,701003,704014,723181,735963,737951,760262,767803,779903,787934,802553,811282 ,824876,839811,852691,865320,877056,886827,901243,913100,917456,928956,941192,951770,964805,979377,987352,1006293,1013539,10 21881,1041306,1052663,1059444,1075292,1086467,1111011,1118392,1136344,1154644,1165452,1179924,1185506,1208547,1229141,1235403 ,1246845,1259864,1266123,1281954,1289837,1303669,1321299,1333548,1343043,1352164,1366972,1374954,1383092,1403640,1406950,142 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[0754] The GenBank number of chromosome 11 is CM035609.1. The SNP sites are: 25339, 49750, 63364, 80497, 88963, 96523, 115937, 125459, 140439, 148018, 159199, 173548, 182701, 188636, 212206, 226945, 244356, 250769, 261976, 274162, 289480, 303426, 317914, 337430, 343183, 361087, 372674, 379287, 393509, 408446, 413922, 42 3455,441240,446580,466131,468750,485588,503181,507339,525283,534260,548163,552364,564834,579187,595506,604453,619634,627940, 637253,644700,663092,676139,689240,696716,706724,723247,730070,742611,757106,769732,776021,787784,797387,818831,829162,831965 ,853609,856390,876899,879150,890013,906675,917199,925803,948158,958642,966272,982432,994760,997497,1017212,1021879,1047054,1 076263,1083421,1104941,1129196,1146895,1158099,1170234,1174749,1188793,1199308,1207667,1220663,1237534,1244145,1263508,127182 0,1280958,1299432,1308442,1313307,1323216,1346167,1349408,1365248,1376081,1389350,1403276,1413821,1421626,1436017,1447091,145 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[0755] The GenBank number of chromosome 12 is CM035610.1. The SNPs are: 11237, 27664, 46819, 56491, 68802, 77096, 93044, 121025, 139661, 146146, 161293, 170753, 185127, 190644, 199667, 223831, 244687, 254992, 266428, 272794, 284016, 294107, 314197, 327100, 333475, 350585, 353667, 370303, 379476, 390335, 405463, 421 433,422199,435662,445042,462477,468782,482174,495697,506872,522749,537262,539084,559065,562754,583731,588481,600435,613537,6 23451,632986,647460,657451,676427,689054,692144,712190,715064,735401,739784,752494,771084,776531,795583,802621,818148,820857, 834302,845797,862031,869439,887884,895683,902171,922772,931264,945336,952022,974318,989956,999169,1018435,1027838,1040687,10 45296,1056494,1075151,1086751,1100099,1107899,1112651,1145704,1152228,1160306,1179056,1188556,1200725,1212985,1221227,1236337 ,1246450,1263979,1273306,1287776,1306096,1327992,1337743,1346610,1369742,1387975,1396535,1419501,1432503,1443989,1456769,146 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[0846] The GenBank number of chromosome 13 is CM035611.1. The SNPs are: 34462, 41841, 49363, 67595, 79742, 93407, 94870, 114965, 128761, 131100, 143956, 152724, 165086, 183876, 197949, 205584, 217111, 225239, 243073, 253324, 257821, 280333, 283163, 296854, 324042, 330764, 349707, 361509, 365191, 380505, 387854, 400 022,419753,442152,445348,468207,478935,486661,500101,505268,526774,529924,545031,561292,571845,594398,600057,611550,621225,64 1888,652846,661048,672827,680513,700917,702817,723454,733621,743672,749564,771420,782756,788792,806244,813679,823780,838870,8 54524,860094,870965,899042,907866,914863,934180,943908,957177,971663,977905,986263,1002249,1017400,1021247,1033595,1044871,1 065229,1075767,1085058,1111643,1118792,1135280,1137787,1157876,1169883,1178274,1187748,1200762,1207024,1222697,1239742,124558 3,1263136,1266874,1285158,1292577,1301908,1313569,1324834,1342652,1357032,1362076,1379947,1383371,1403076,1407162,1423349,143 3572,1441913,1465864,1480207,1494539,1501624,1516055,1527093,1537078,1547512,1561568,1573931,1583437,1597370,1612548,1625787,1638565,1646594,1650882,1670270,1681511,1697163,1703170,1726452,1734823,1751475,1763501,1772714,1785846,1794543,1813897,1821768,1835965,1848785,1856884,1865370,1880887,1891273,1908004,1920170,1937699,1945639,1957857,1989854,1992069,2012001,2022252,2028926,2042896,2060161,2063320,2079596,2094833,2099442,2109231,2128213,2132563,2143872,2157940,2166944,2181966,2190852,2206822,2223596,2230859,2239836,2253630,2269497,2282476,2294052,2302917,2309956,2329553,2341531,2351999,2363732,2373377,2377909,2399920,2408153,2417091,2431046,2444448,2451382,2466979,2478521,2485387,2503014,2516406,2519562,2536705,2571617,2581382,2588194,2605744,2614761,2630010,2645514,2653168,2669296,2671687,2688707,2698844,2705913,2722878,2739590,2750329,2758933,2772015,2782331,2796089,2805244,2819387,2825380,2840124,2853930,2861309,2873013,2883992,2911549,2936791,2948903,2954799,2967119,2978872,2987109,2997903,3018779,3024327,3041577,3048028,3067317,3072576,3085160,3098791,3107686,3117689,3130512,3146290,3154256,3168288,3183273,3186255,3206619,3213857,3221904,3233334,3246149,3264664,3276422,3283060,3292256,3307302,3322774,3336098,3346463,3358539,3361546,3373537,3390473,3402229,3416439,3428416,3432878,3443015,3462924,3471199,3480947,3490177,3512206,3523998,3531519,3540318,3549946,3569599,3574879,3583866,3602214,3611633,3625498,3638962,3648201,3659921,3673810,3684133,3690064,3700341,3720017,3734494,3745987,3748426,3764242,3776684,3783017,3803191,3806190,3816810,3833182,3848688,3855425,3868443,3883432,3897043,3906276,3915266,3931407,3935910,3953661,3959013,3980004,3989296,3997809,4006506,4021330,4035094,4044691,4052759,4064771,4085603,4095290,4102490,4115472,4131143,4139804,4155691,4161214,4172655,4183251,4196025,4214050,4216517,4229739,4241647,4253884,4263120,4279144,4285826,4299477,4313770,4343003,4352989,4357870,4373300,4381454,4394348,4413388,4423804,4426561,4438173,4459824,4465387,4481207,4488707,4500727,4512865,4522556,4540053,4548963,4565818,4575263,4586105,4591223,4606908,4618046,4633653,4641916,4657608,4661535,4679345,4694315,4706351,4713024,4718799,4732980,4742001,4758964,4769335,4777474,4792802,4803142,4816824,4831986,4841827,4849880,4862964,4881739,4890311,4897162,4913694,4925806,4929808,4943253,4963003,4975646,4980684,4990953,5008676,5018345,5034235,5045587,5052947,5068954,5080004,5085705,5098976,5109349,5121716,5129973,5149558,5157213,5174348,5178206,5196170,5209122,5215588,5224076,5239489,5246100,5257118,5273944,5291136,5293828,5313610,5316655,5328538,5344518,5360709,5365189,5385648,5395601,5403310,5417326,5422964,5439229,5454988,5457236,5468626,5485937,5497758,5508273,5525340,5528320,5539250,5551669,5568066,5584656,5593339,5607660,5616606,5621963,5640471,5646923,5655902,5677243,5682084,5701639,5710390,5719457,5730741,5740240,5749170,5764956,5780385,5784613,5796895,5807928,5820874,5837695,5850263,5859389,5872625,5887230,5891573,5905158,5916897,5931982,5937331,5954933,5967242,5972373,5985215,6003277,6013082,6024101,6035738,6043420,6055511,6071259,6084599,6095319,6101599,6120119,6132388,6138640,6152845,6164994,6170434,6182581,6198282,6211282,6218493,6237333,6249639,6259334,6267406,6276083,6296868,6304809,6321502,6333693,6344445,6355636,6365517,6373200,6386380,6404075,6407814,...

Claims

1. A SNP marker combination for Channa maculata, comprising markers SNP1 to SNP50000.

2. SNP chip, including probe combinations fixed with markers for SNP1 to SNP50000 respectively.

3. The method for preparing the SNP chip according to claim 2, wherein the chip is made by in-situ photolithography synthesis, photoresist parallel synthesis, microfluidic channel on-chip synthesis, light-guided in-situ synthesis, soft lithography in-situ synthesis, inkjet synthesis, molecular stamp on-chip synthesis, maskless chip synthesis, BeadArray method or suspension chip method.

4. Use of the SNP marker combination according to claim 1 or the SNP chip according to claim 2.

5. The use according to claim 4, wherein the use is selected from at least one of the following (a) to (n): (a) Identification of germplasm resources of Channa maculata; (b) Identify the relationship of Channa maculata; (c) SNP typing of Channa maculata; (d) identifying or characterizing species of Channa macroura; (e) Molecular breeding of Channa maculata; (f) constructing a DNA fingerprint database of Channa maculata; (g) testing the purity of Channa maculata species; (h) Genetic analysis of Channa maculata germplasm resources; (i) Selection of Channa maculata genome; (j) Gene localization and cloning of Channa maculata; (k) Identification of functional genes in Channa maculata; (l) Construction of genetic map of Channa maculata; (m) Genetic evolution and analysis; (n) Genome-wide association analysis.

6. A method for detecting a biological sample, the method comprising detecting information of SNP1 to SNP50000 markers in the biological sample.

7. A method for constructing a DNA fingerprint database of Channa maculata, comprising: The genomic DNA of all Channa maculata species used to construct the Channa maculata DNA fingerprint database were extracted respectively; The SNP chip of claim 2 is used to detect the SNP1 to SNP50000 markers of the genomic DNA of each Channa maculata species, thereby obtaining the genotype data of all Channa maculata species at the SNP1 to SNP50000 markers, thus forming a Channa maculata DNA fingerprint database.

8. A kit for constructing a DNA fingerprint database of Channa maculata, comprising the SNP chip of claim 2 and an instruction manual recording the method of claim 7.

9. A method for analyzing the population structure of Channa maculata germplasm resources, comprising: The genomic DNA of all species of Channa maculata to be analyzed for population structure were extracted respectively; Using the SNP chip of claim 2 to detect the SNP1 to SNP50000 markers on the genomic DNA of each Channa maculata, thereby obtaining the genotype data of all the Channa maculata at the SNP1 to SNP50000 markers; Based on the genotype data, cluster analysis was performed to analyze the genetic structure of the Channa maculata.

10. A kit for grouping Channa maculata germplasm resources, comprising the SNP chip of claim 2 and an instruction manual recording the method of claim 9.

Images