A whole genome selection breeding liquid chip for brassica napus and application thereof

Abstract

This invention belongs to the field of genotyping technology and relates to a liquid phase chip for whole-genome selection breeding of Brassica napus, and its application in genotyping and whole-genome selection breeding of Brassica napus. The liquid phase chip includes a Brassica napus 45K site probe mixture and a hybridization capture reagent. The Brassica napus 45K site probe mixture includes background and foreground SNP / InDel site probes. During whole-genome application, this liquid phase chip can more quickly identify suitable matching materials for different traits, helping breeders select target materials more quickly. It offers better site accuracy, higher application efficiency, and better meets the needs of next-generation breeding technologies, improving breeding efficiency and accelerating the breeding process.

Description

Technical Field

[0001] This invention belongs to the field of genotyping technology and relates to a liquid phase chip for whole-genome selection breeding of rapeseed, and the application of the liquid phase chip for genotyping of rapeseed genome and whole-genome selection breeding of rapeseed. Background Technology

[0002] Rapeseed is one of the major oilseed crops, and Brassica napus is the main type of rapeseed. Currently, the key areas for improvement in the breeding of Brassica napus include increasing the yield per unit area of ​​rapeseed, increasing the oil content per unit weight of rapeseed, optimizing quality traits such as glucosinolates, erucic acid, and linolenic acid, and enhancing the stress resistance of rapeseed to improve planting efficiency and expand the planting area.

[0003] Agriculture is currently in a phase of rapid upgrading, and the decline in sequencing costs and the emergence of new genotyping technologies have provided endless possibilities for molecular breeding. However, existing chip products and technologies are mainly based on the needs of rapeseed research, with very few products designed for actual breeding needs. For example, the Bnapus50K and BnaPan50T chips share similar design philosophies; both are developed by selecting loci from resequencing data of a batch of materials and adding some trait-related loci to form product loci, which is insufficient to effectively meet the needs of next-generation breeding.

[0004] In addition, in Brassica napus, the Brassica 60K chip was jointly developed and publicly released by 16 international academic and commercial institutions, integrating a total of 52,157 SNP markers.

[0005] Therefore, a rapeseed gene liquid phase chip that better meets the needs of the next generation of breeding and can provide better technology for breeding is a technical problem that urgently needs to be solved. Summary of the Invention

[0006] The purpose of this invention is to provide a liquid phase chip for whole-genome selection breeding of Brassica napus and its application. Specifically, it combines existing sequencing technologies with GWAS analysis of associated loci, uses whole-genome selection technology to predict field performance of materials, and combines this prediction with years of actual field performance. Through optimization algorithms, it selects 45K SNP / InDel loci suitable for whole-genome selection in my country's main rapeseed producing areas and develops them into chip products. This will promote the iterative upgrading of breeding technology and provide better technology for Brassica napus breeding.

[0007] A liquid-phase microarray for whole-genome selection breeding of Brassica napus includes a Brassica napus 45K site probe mixture and a hybridization capture reagent. The Brassica napus 45K site probe mixture includes background SNP probes and foreground SNP / InDel probes. Information on background SNP / InDel sites is shown in Table 1, and information on foreground SNP / InDel sites is shown in Table 2. The reference genome is Bnapus ZS11.

[0008] A liquid microarray for whole-genome selection breeding of Brassica napus, with background loci obtained using the following method: (1) Initial selection of candidate sites: Based on the resequencing data of 532 parental lines of Brassica napus adapted to the main producing areas such as the Yangtze River and the Yellow River Basin, the quality indicators of resequencing sites were calculated. SNP / InDel polymorphic sites that met the following conditions in all sample populations were selected as initial candidate sites, with a heterozygosity rate ≤0.05, a site deletion frequency ≤0.1, and a MAF ≥0.3. A total of 1,133,900 initial candidate sites were selected. (2) Screening of representative sites: The linkage disequilibrium interval of the rapeseed germplasm resource population was estimated to be 500kb by software. The linkage disequilibrium interval of 500kb and the linkage disequilibrium of each pair of SNPs / InDels ≥0.8 were used as the screening criteria to obtain 44,528 SNPs / InDels that were evenly distributed on the chromosome, which were the background sites.

[0009] A liquid-phase microarray for whole-genome selection breeding of Brassica napus, with foreground loci obtained by the following method: (1) Genome-wide association analysis of important agronomic traits; Based on the resequencing data of 532 rapeseed accessions, the quality index of resequencing sites was calculated, and SNP / InDel polymorphic sites that met the requirements of heterozygosity ≤0.05, site deletion frequency ≤0.1, and MAF ≥0.05 in all sample populations were selected as genotype data. The original genotype data were imputed using software, and then genome-wide association analysis was performed on the agronomic and quality traits of interest. (2) Determination of foreground loci: SNP / InDel loci with P-value <1e-4 in association analysis results were used to determine candidate QTL loci for the trait; SNP / InDel loci associated with candidate QTL loci were screened based on linkage disequilibrium interval of 500kb, linkage disequilibrium ≥0.2 between pairs of SNP / InDel loci, and P-value of SNP / InDel ≤1e-2, and the intervals of QTLs were defined; QTLs with SNP / InDel number ≥10 in the interval were used as QTL intervals for the trait, and the peak SNP / InDel in the QTL interval were used as foreground loci, that is, 100 foreground loci were obtained.

[0010] An application of a 45K liquid phase chip for the whole genome of Brassica napus is proposed for germplasm prediction, population structure analysis, molecular genetic map construction, genome-wide association analysis, marker-assisted selection breeding, whole genome selection breeding, trait-related gene localization, material variety authenticity identification, or germplasm resource improvement.

[0011] The beneficial effects of the liquid phase chip for whole-genome selection breeding of Brassica napus and its application are as follows: (1) The materials used in this invention are based on core materials used in breeding in different ecological zones such as the Yangtze River and the Yellow River in China. That is, the SNP / InDel sites contained in this invention are from 532 resequencing materials. The material types include winter, semi-winter, spring and high oil content materials in my country. Each material has been screened by field phenotypic identification for many years. The selected sites avoid the site loss problem of existing chips (such as Brassica 60K) in terms of applicability to domestic materials, so that the materials can play a greater role in breeding. (2) The present invention uses whole-genome selection model technology to screen and select loci. The selected loci are all trait loci that are of particular interest in actual breeding. They all have specific effect values ​​in whole-genome selection breeding. Specifically, it includes 44,528 loci selected by whole-genome selection technology and 100 prospective loci associated with trait loci of particular interest in actual breeding. This allows the liquid phase chip of the present invention to find suitable combination materials for different traits more quickly during whole-genome use, helping breeders to select target materials more quickly. The loci are more accurate, the application efficiency is higher, and it is more in line with the needs of the next generation of breeding technology. (3) Liquid phase chips have advantages such as flexible site design and low cost of use. The SNP / InDel sites of this invention are developed into products based on liquid phase chips. In use, relying on their price advantage, they will provide breeders with a directly usable tool and provide a method for subsequent material testing, which will greatly improve breeding efficiency and accelerate the breeding process. (4) This liquid phase chip can be used for germplasm prediction, population structure analysis, molecular genetic map construction, genome-wide association analysis, molecular marker-assisted selection breeding, genome-wide selection breeding, trait-related gene localization, material variety authenticity identification or germplasm resource improvement of rapeseed, and has a wide range of application prospects. (5) The chip is a liquid phase chip, which has advantages such as high detection accuracy, more effective information and greater flexibility and diversity compared to solid phase chips. It also effectively reduces detection costs and provides important technical support for the breeding of Brassica napus. Attached Figure Description

[0012] Figure 1 This invention provides the genome-wide distribution of background SNP / InDel loci in Brassica napus.

[0013] Figure 2 This is an annotation of the influence of background SNP / InDel sites on gene function in Brassica napus in this invention.

[0014] Figure 3 This invention provides background SNP / InDel site pairs for Brassica napus. 6 The effect of modification A.

[0015] Figure 4 The AUC curve is the result of five-fold cross-validation of the prediction model in Example 3.

[0016] Figure 5 The prediction results are for the 35 rapeseed germplasms in Example 3.

[0017] Figure 6 In Example 4, A represents the population structure analysis based on principal component analysis (PCA), and B represents the population structure analysis based on phylogenetic tree in Example 4.

[0018] Figure 7 The effect of foreground sites on transcription factor binding sites. Detailed Implementation

[0019] This invention uses 532 accessions of Brassica napus as the basic population and the semi-winter rapeseed Bnapus ZS11 as the reference genome. It extracts core key sites using a comprehensive site screening algorithm and combines important agronomic trait genes and their functional sites to form a 45K liquid phase chip for Brassica napus, "BnaGS 45K".

[0020] The liquid-phase chip for whole-genome selection breeding of rapeseed of the present invention is a product developed based on liquid-phase chip technology. It contains 44,528 loci selected by whole-genome selection technology, distributed on 19 chromosomes, and 100 loci associated with traits of particular interest in actual breeding, such as linolenic acid, linoleic acid, palmitic acid, oleic acid, stearic acid, erucic acid, arachidic acid, protein, docosanoic acid, number of horns, plant height, main inflorescence length, number of horns in the main inflorescence, number of effective branches, branch height, branch angle, and branch height. The use of this liquid-phase chip can help breeders find suitable combination materials for different traits more quickly in breeding, and help breeders select target materials more quickly.

[0021] The 44528+100 loci in this invention are all derived from 532 material data sets owned by our team, including winter, semi-winter, spring, high oil content, strong lodging resistance, cold resistance, drought resistance, and high yield material types in China. Each material has undergone years of field phenotypic screening, enabling it to play a greater role in breeding. The loci were selected using a whole-genome selection model, and each locus has a specific effect value in breeding. The developed 45K whole-genome liquid phase chip for Brassica napus provides a method for subsequent material detection, which is compatible with our team's own whole-genome selection model and can significantly accelerate the breeding process.

[0022] This invention thoroughly explores the main traits of rapeseed in regions such as Guanzhong and Hanzhong in Shaanxi Province and Xining in Qinghai Province, achieving excellent results. The relevant trait loci play an irreplaceable role in identifying superior genes for subsequent breeding materials, saving breeding time and improving the accuracy of material selection during the breeding process. The whole genome 45K liquid phase chip of this Brassica napus type is named BnaGS 45K liquid phase chip. GS breeding models based on the BnaGS 45K liquid phase chip loci have been developed for the Yangtze River, Huanghuai, and spring rapeseed regions. This will greatly improve breeding efficiency in these regions, effectively shifting the focus from relying on breeder experience to a more targeted selection based on big data analysis, further shortening the breeding cycle.

[0023] Example 1

[0024] This invention relates to a liquid-phase chip for whole-genome selection breeding of Brassica napus, comprising a Brassica napus 45K site probe mixture and a hybridization capture reagent. The Brassica napus 45K site probe mixture includes Brassica napus SNP / InDel background site probes and Brassica napus SNP / InDel foreground site probes; each site has at least two capture probes.

[0025] The hybridization capture reagent was the GenoBaits DNA-seqLibrary Prep kit from Shijiazhuang Borui Biotechnology Co., Ltd., which included individually packaged GenoBaits Block I, GenoBaits Block II, GenoBaits 2×Hyb Buffer, GenoBaits Hyb Buffer Enhancer, GenoBaits 2×BeadsWashBuffer, GenoBaits 10×Wash Buffer I, GenoBaits 10X Wash Buffer II, GenoBaits 10X Wash Buffer III, and GenoBaits 10X Stringent Wash Buffer.

[0026] Locus acquisition process of whole-genome selection breeding liquid phase chip for Brassica napus.

[0027] Based on our team's own 532 rapeseed parent lines and other materials, after three years of field phenotypic identification, we conducted 10X deep resequencing, generating approximately 4TB of sequencing data. Using the Bnapus zs11 genome as a reference genome, we provide the following URL for downloading variation information of the sequencing population data: http: / / ngdc.cncb.ac.cn / gwh / Assembly / 9669 / show . Source: A high-quality Brassica napus genome reveals expansion of transposable elements, subgenomeevolution and disease resistance.

[0028] I. Background Site Screening (1) Initial selection of candidate sites: The selection of chip sites was based on the resequencing data of 532 diverse Brassica napus germplasm resources. The quality indicators of the resequencing sites were calculated, and SNP / InDel polymorphic sites that met the following criteria in all sample populations were selected as initial candidate sites: heterozygosity ≤ 0.05, site deletion frequency ≤ 0.1, and MAF ≥ 0.3. A total of 1,133,900 initial candidate sites were selected.

[0029] (2) Representative locus screening: First, the linkage disequilibrium interval of this rapeseed germplasm resource population was estimated to be 500 kb using PopLDdecay software. Then, using the linkage disequilibrium interval of 500 kb and the linkage disequilibrium of each pair of SNPs / InDels ≥ 0.8 as the screening criteria, SNPs / InDels in the same linkage disequilibrium interval were filtered using the R package bigsnpr. Finally, 44,528 SNPs / InDel loci evenly distributed on the chromosome were obtained and used as background loci for microarray development. The genome-wide distribution of background SNPs / InDel loci of this Brassica napus is shown in Figure 1; the information of the 44,528 background SNPs / InDels is shown in Table 1.

[0030] Table 1. Location information of background SNPs / InDel sites in the reference genome Bnapus ZS11 of Brassica napus. 56290,79178,278207,290968,300823,304435,307016,319269,334464,334483,335627,335795,336555,337604,346091,348970,358880,369042,407956,421186,425080,441428,450680,462406,511061,547404,592674,594123,606646,610764,615070,639178,654005,691684,699832,701130,702056,702626,726416,768443,808492,834957,837655,839647,840006,840117,858266,859412,860927,861541,867296,869070,871930,872093,872106,879567,886527,888388,901760,954430,959755,960670,963143,963434,963668,966334,966756,977760,984836,985454,985808,990972,993777,1006084,1049147,1049227,1049398,1076697,1086595,1086713,1088571,1089197,1090658,1093562,1095308,1101471,1114029,1114611,1121246,1124020,1133246,1143496,1147523,1151675,1164572,1180766,1182988,1183065,1183756,1186028,1186881,1188821,1203935,1204056,1204448,1206224,1206351,1207207,1207600,1208005,1208458,1209722,1212919,1219693,1222862,1223956,1224037,1226037,1226402,1226800,1227303,1229758,1244124,1253665,1253755,1254502,1254545,1254860,1255604,1259815,1264292,1273253,1274246,1274709,1276398,1282818,1284996,1287384,1293840,1295731,1299226,1301868,1307683,1318191,1322286,1323967,1323982,1341268,1342646,1345386,1348125,1348662,1349943,1351465,1351557,1353165,1353186,1356948,1359463,1366206,1369729,1371036,1371312,1380708,1392381,1392721,1393059,1393297,1396924,1398103,1398402,1411947,1426846,1427998,1435586,1436105,1437759,1442759,1443871,1444002,1452029,1460148,1462492,1479933,1480165,1480583,1480876,1481072,1481928,1482949,1487333,1491319,1493438,1494905,1495756,1497530,1497739,1497756,1497941,1500162,1500312,1501030,1504061,1507944,1508517,1508554,1510091,1512041,1514437,1517234,1518923,1519820,1519906,1520128,1520232,1520233,1520430,1523363,1523584,1524080,1525367,1525528,1525641,1529728,1536561,1537011,1538294,1539721,1550679,1551123,1551949,1554603,1556895,1557416,1559837,1560042,1560103,1561942,1561961,1571383,1571479,1592312,1606186,1609906,1610116,1611661,1616432,1618349,1621528,1622383,1622440,1622452,1622551,1623169,1623421,1624770,1629088,1629406,1634544,1635358,1635685,1635843,1635990,1636718,1637449,1638331,1638606,1639854,1639926,1640415,1640770,1641364,1643871,1654620,1661417,1668258,1674259,1680750,1684031,1687552,1687925,1688595,1688902,1691535,1693140,1695473,1696041,1715371,1715671,1715686,1716920,1717188,1717287,1717290,1717659,1717704,1717759,1721372,1723010,1728278,1741834,1748200,1757245,1760739,1762028,1764461,1790807,1795555,1795827,1825620,1826704,1826883,1832244,1833996,1834308,1837513,1853689,1864164,1875379,1876766,1876779, 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10793818,10795861,10796651,10797244,10797742,10798317,10800325,10800463,10800557,10803910,10834041,10834434,10834566,10843394,10843701,10846048,10849819,10850169,10850276,10855316,10855482,10862460,10862674,10862682,10872594,10874907,10878312,10905685,10906776,10914110,10917182,10940037,10945719,10945916,10947843,10947865,10948818,10949186,10949732,10971284,10979564,10980712,10991102,11041747,11072649,11301975,11306745,11307693,11322408,11324608,11341373,11341463,11365454,11373600,11373807,11374314,11429840,11434841,11484980,11493554,11499398,11500376,11502429,11505015,11505741,11508192,11508848,11537036,11546573,11566447,11566521,11580607,11581996,11582012,11584537,11598304,11600745,11603559,11605609,11607071,11618353,11618612,11619606,11652549,11655121,11659770,11660896,11661845,11688514,11691060,11750215,11760645,11764710,11765083,11766064,11769971,11770249,11778752,11779540,11792174,11796157,11809271,11824845,11914156,11921011,11923134,11927438,11938915,11942566,11945836,11946006,11953131,11955407,11956514,11957112,11957432,11982062,12060147,12096752,12106516,12115315,12149775,12157299,12157766,12161492,12161679,12193524,12425215,12427143,12437490,12513812,12514758,12515988,12519136,12521112,12521339,12547178,12549034,12553691,12556575,12561328,12562158,12562525,12605682,12608041,12610446,12617994,12620114,12620606,12621750,12624204,12636840,12640852,12653959,12658289,12667317,12667860,12669665,12678394,12689028,12709707,12779022,12961010,12981569,13012873,13016627,13114598,13143743,13145678,13146232,13158148,13162567,13168306,13249136,13251860,13262734,13319305,13326258,13384037,13396647,13406856,13497585,13497851,13536426,13544511,13548145,13572797,13573433,13877442,14019974,14104672,14175894,14210829,14357064,14400432,14555799,14814574,14825629,14836210,14844745,14856317,14947131,15759016,17229989,21247272,21273201,21441009,21441764,21721330,21723440,21741184,21757881,21765975,21768037,21810677,21831783,21961300,21965107,21965587,21973960,21974753,21983394,21984145,22041417,22061703,22062603,22075938,22111039,22202967,22224653,22250608,22260361,22263222,22309846,22339537,22345148,22352077,22414038,22425650,22426379,22426493,22447921,22453125,22454372,22454440,22464029,22465046,22465304,22473806,22474716,22474863,22476204,22614377,22641907,22645120,22659664,22671767,22711191,22721721,22731120,22752427,22830284,22865567,22866173,22912195,22912349,22966084,23025273,23026199,23143230,23238873,23252703,23385555, 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Locus information on chromosome A02 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Locus information on chromosome A03 119863,126899,127196,129580,129811,136404,138720,140755,141282,149967,151257,151596,156066,156195,175961,192336,212149,215419,269598,269810,269874,288398,288528,306278,312995,321996,336220,336468,338857,355688,360176,363186,363250,365175,365529,367215,375446,386414,390903,393902,396298,396751,396850,411458,412686,413296,413370,413917,415196,415734,415747,417389,425107,428165,437410,445334,450514,451109,452511,452654,452707,453724,453823,454344,462459,462823,462956,465846,467763,473765,475450,475772,475805,476953,478505,479024,489427,491440,491873,492629,493644,493681,493795,496817,498693,499595,500519,500574,501121,506054,516085,516304,518655,528980,537927,540666,544645,544877,549167,570589,594098,598606,605382,605790,605978,607823,611619,611701,611741,612455,630905,640012,640516,645978,647043,653381,653986,662356,670765,672461,673038,673232,673528,676705,677194,680653,697945,699294,702423,702468,702839,709780,710263,711395,711473,711545,711620,722215,722462,722806,723879,724676,725916,740277,744800,745867,746150,746160,746973,748626,749835,751202,751232,751745,751941,752280,754936,754962,756659,758631,781022,782349,782379,782982,784196,786609,789561,793173,793229,814822,819502,821069,821112,821513,827322,832556,834284,840631,840778,840829,841228,845672,846403,850122,851165,860991,863126,865851,866214,866448,867140,867147,889487,890311,891822,892640,939115,939528,939741,943625,1038732,1044044,1046783,1047696,1048017,1063317,1097237,1137531,1189506,1190310,1193776,1204868,1205943,1208752,1219293,1228243,1235835,1262116,1291703,1301653,1303705,1305702,1321987,1346400,1369710,1371163,1371641,1374817,1375578,1378383,1401838,1407702,1408471,1410114,1414228,1416344,1421310,1422491,1427929,1428182,1460548,1465582,1469160,1477707,1483501,1485095,1487817,1518416,1518865,1530161,1571103,1572089,1572866,1573272,1584972,1592407,1593332,1593413,1593800,1594282,1601622,1602654,1603121,1606928,1607053,1607134,1616852,1620010,1620528,1621168,1626187,1626455,1626741,1639389,1640388,1642549,1642630,1646776,1646830,1647292,1651725,1657884,1658590,1659369,1661678,1670263,1671486,1674307,1954941,1955204,1987895,1993318,1993517,1993550,1993773,1994002,1994217,1994830,1996164,1998708,2001702,2002540,2004707,2005115,2007057,2008551,2010456,2013313,2019016,2019215,2019426,2021681,2024261,2024865,2024905,2025049,2025720,2026883,2027834,2031851,2032064,2032382,2032505,2032702,2033958,2034342,2034595,2035286,2035328,2035481,2035559,2035916,2036881,2036967, 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Locus information on chromosome A04 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Locus information on chromosome A05 38849,44925,94198,99449,100647,100899,101133,101979,119195,138558,141990,148113,150685,151912,152698,259122,270027,296475,297848,297867,299362,302720,303583,308778,309616,309758,310181,310285,312644,312908,312952,316635,317150,317729,343659,346677,347772,349779,350704,350784,350985,351066,351156,351177,353059,365483,365587,365702,366082,368656,369654,370422,371585,373676,374788,374924,377937,380018,380166,380354,381022,381884,384001,389917,401950,440232,440636,442029,450754,450802,464393,466071,467137,467353,467662,468380,475316,475452,493418,526466,529308,529693,536252,537896,540668,541259,541985,543368,550135,553779,566324,566507,566777,569308,661333,667743,667776,668692,669909,670296,671929,673990,674190,674567,678573,678776,680300,681042,681287,681834,682195,682372,682624,686674,686885,687537,694862,694914,696910,697180,698415,699852,700303,702366,703585,703790,704928,712840,719978,725526,729900,779943,787103,795018,856930,867519,868732,877413,902164,903123,907144,907378,916423,917194,941083,941182,942311,942475,942815,942816,942870,942984,943161,943691,946058,947912,948019,950535,950715,951710,954104,956423,957423,967549,967565,967989,968458,968533,968743,969955,995192,996344,1001157,1006943,1007527,1008726,1010112,1010839,1022731,1055398,1062956,1065397,1065576,1068565,1069264,1071480,1074587,1075255,1075574,1075872,1076187,1076502,1076746,1077431,1081708,1082135,1082245,1082694,1083236,1083480,1083591,1083624,1094701,1096305,1099435,1099632,1102218,1102538,1106177,1110977,1124717,1125851,1126875,1127496,1132575,1165891,1176688,1178596,1178777,1192983,1194967,1196134,1200347,1200407,1201115,1202462,1211848,1228942,1230022,1235983,1235992,1237680,1256289,1261954,1262714,1264842,1270063,1270108,1271199,1419582,1469806,1477718,1477754,1479946,1480439,1480499,1488660,1497124,1500158,1501632,1504704,1505434,1506820,1507619,1508045,1511830,1514762,1517671,1517807,1540400,1541254,1554671,1555602,1556304,1557053,1566780,1592116,1596067,1596207,1598337,1598425,1599127,1599491,1604503,1608915,1608918,1609020,1609083,1609306,1609962,1611037,1611503,1611913,1612106,1612338,1612408,1613143,1613351,1613451,1621223,1623803,1624078,1625951,1626180,1626396,1630463,1632669,1632742,1635056,1638945,1640704,1644211,1644566,1644618,1644706,1650012,1650036,1652760,1653262,1685642,1685752,1686015,1686104,1688111,1694690,1694902,1697969,1697999,1698056,1698227,1699069,1699881,1701050,1702485,1704123,1711205,1714379,1714603,1717854,1751975,1765533,1766514, 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28600484; Locus information on chromosome A06 27004,72647,94555,104593,125413,146899,148505,151639,160862,187520,189780,190339,192078,192121,192305,209977,218879,218996,223129,228914,229597,233373,251693,258500,265601,265963,267127,267516,268757,269918,271129,271336,271374,271443,271457,271671,271820,272002,272219,272640,272834,272851,273651,277977,282187,296227,343221,362634,365425,366672,375130,380361,405752,407788,430277,432801,433645,434549,434897,434985,435371,435727,435844,437174,437216,437370,437545,437561,440535,441126,441196,444097,444325,448846,448867,449070,449372,449825,450055,456478,457786,458269,458311,460496,464925,465751,492390,495610,496617,496760,497016,497758,504969,505276,509065,509170,509416,509510,509577,511118,511291,512566,513219,513399,515417,517175,519880,528358,529895,532444,532720,544347,551742,653294,653509,671016,671948,672192,672201,672651,672894,672928,674914,674986,675965,676505,676786,676909,676955,679050,679384,680281,680329,682299,682371,684186,686212,687178,688193,689183,689961,691461,693703,695880,717157,745794,747177,747208,779554,780599,785328,790997,791615,792140,792270,795212,797503,800550,800841,800949,803485,803719,804283,804715,805404,806308,806804,806870,806885,806970,807095,807723,807957,810568,810638,811512,811650,812136,813130,817447,817665,818479,820468,820615,820740,821296,821329,821453,825298,825388,825962,827935,829185,832084,832855,834181,841740,844574,852574,852586,854982,856854,859985,860761,873368,880129,891213,892593,896259,900669,901422,907082,908468,915696,925168,925335,939952,950550,953354,953540,956417,956837,957007,957128,957637,960814,968123,977317,1004944,1005345,1006001,1017802,1017818,1018183,1019802,1020206,1020210,1020694,1020799,1020841,1020953,1022141,1022184,1022898,1035088,1054896,1055170,1056408,1056698,1057022,1057197,1070761,1072429,1078127,1081286,1081721,1101107,1101226,1104193,1106813,1120201,1121215,1121449,1128011,1128143,1128183,1128677,1128967,1129477,1129732,1129755,1130202,1130498,1130505,1131876,1132108,1136353,1149989,1150530,1150629,1153388,1153876,1156218,1156609,1159090,1166146,1174605,1177016,1181240,1186140,1186280,1234061,1234130,1235442,1235770,1241013,1247761,1248720,1249967,1252133,1252916,1253197,1253296,1253830,1253845,1253972,1254166,1254779,1254980,1255004,1255079,1255984,1256044,1256297,1256645,1258352,1258886,1260389,1261275,1261724,1261734,1262369,1266132,1266590,1266671,1268501,1269173,1269235,1269519,1269884,1272771,1285488,1300213,1300551,1300637,1301215,1301416,1301733, 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27990130,28006244,28009972,28009989,28019132,28019388,28023530,28024428,28024510,28026456,28026786,28035913,28037529,28038982,28039284,28044331,28047559,28048448,28052824,28055369,28055595,28055604,28059311,28060438,28060558,28061818,28063631,28067985,28069891,28070549,28074902,28076435,28077906,28080107,28088507,28109925,28111816,28113325,28116900,28117240,28117748,28118988,28120987,28121507,28124184,28124742,28127955,28128047,28128306,28128345,28128480,28133590,28141312,28143631,28203696,28249425,28252920,28257121,28284946,28284952,28289208,28548158,28657054,28665794,28690162,28740567,28819573,28926493,29000227,29245698,29246124,29246581,29252096,29252965,29264419,29277146,29281971,29288398,29295295,29298211,29327527,29334681,29339365,29354405,29381666,29383784,29421446,29422130,29429802,29434456,29440446,29445417,29469408,29505195,29539130,29593853; Locus information on chromosome A07 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Locus information on chromosome A08 86594,116319,286841,449977,469443,476370,489127,489189,490818,511159,524539,694210,695708,696000,696052,697310,699135,699561,715514,723086,724364,725014,739999,758940,758964,759199,767865,780572,790095,793481,823900,824708,825990,826086,827226,827764,830142,832540,833443,833686,839865,839942,862516,864806,943252,979876,979895,980032,980211,980634,981492,981833,988613,990220,990516,990919,991711,993651,993766,1104275,1110666,1121899,1123745,1144817,1145262,1167032,1167355,1170800,1184310,1184507,1186913,1188070,1188387,1193933,1218123,1223536,1231146,1240972,1255390,1265433,1270419,1282165,1295907,1300272,1300812,1489899,1514988,1524419,1524725,1528315,1529661,1576606,1581742,1624266,1626086,1628213,1854133,1865816,2017649,2272734,2293640,2329968,2330200,2331162,2338066,2339676,2349495,2363725,2366697,2367123,2367380,2376742,2391005,2392784,2395424,2395616,2399336,2401031,2499479,2515939,2520791,2525880,2535667,2537215,2556139,2562880,2572311,2643418,2644143,2690370,2696419,2698380,2700818,2751926,2774446,2780171,2793371,2803084,2817211,2900646,2994927,3002084,3002855,3056536,3062048,3089454,3092770,3096869,3101441,3162051,3168648,3185636,3200262,3205808,3227677,3231348,3239510,3246581,3252221,3252388,3262816,3271729,3272214,3288320,3302093,3303721,3316701,3317473,3317775,3356471,3362094,3488148,3488204,3569935,3600799,3637181,3673556,3674814,3677379,3681686,3691483,3863171,3933826,3959027,3959350,3963698,3968506,3973597,4103776,4106625,4130825,4136547,4182034,4192816,4275366,4291546,4312284,4486854,4507219,4514492,4562469,4654964,4671032,4671399,4671571,4734596,4738164,4779897,5095835,5122745,5133316,5493880,5549564,5571995,5584062,5637503,5710693,5880930,5939615,6008997,6009173,6046227,6067472,6083229,6085348,6115291,6202685,6278846,6300511,6321388,6471470,6473170,6516582,6561423,7060189,7314418,7343694,7412838,7502163,7584748,7754831,7763670,7764475,7795625,7850858,7852342,7870031,7875717,8012601,8269312,8433730,8500857,8522691,8603719,8637711,8645886,8769555,8799239,8801665,8845357,8965385,9053538,9086490,9112355,9136861,9148337,9187685,9189910,9194194,9213280,9237823,9341461,9347546,9358704,9359247,9388046,9496537,9538231,9543631,9564184,9574333,9675145,9783182,9785172,9816451,9829840,9850536,9857728,9858163,9861127,9890664,9892704,9898834,9901296,9901686,9902467,9914226,9967711,9987211,9987512,9988749,10029224,10029225,10032302,10032428,10529660,10625755,10637923,10669489,10736698,10778202,10840789,10873625,10877730,10886318,10896748,10982104, 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22555457,22560718,22560811,22561699,22562532,22562930,22565462,22565927,22571148,22573424,22575391,22590359,22598678,22599170,22647209,22691068,22796562,22931583,23022611,23025726,23027856,23028553,23030402,23076242,23088375,23102934,23103427,23107917,23110245,23125010,23208457; Locus information on chromosome A09 4995,1510978,1642332,1740302,1741804,2219509,2269129,2535851,2611306,2851990,2877880,2939767,2987828,3220350,3224750,3249573,3320851,3352795,3429142,3471916,3526839,3854668,4949291,6172706,6195450,6252020,6314641,6314951,6388590,6392378,6636488,6672126,6729075,6729107,6734572,6861428,7209065,7209133,7340284,7455677,7456514,7457574,7457581,7498812,7591511,7623816,7721739,7741365,7759288,7767955,7901817,7909942,7935521,8062802,8062953,8063702,8065485,8067463,8069162,8070931,8089164,8090026,8091742,8091823,8093808,8098191,8106336,8512042,8514287,8515140,8520483,8521680,8575711,8626157,8628012,8630460,8630861,8689188,8691068,8714725,8725874,8726701,8918119,9172661,9675721,9777355,9778063,9782681,9783190,9794206,9821229,9823572,9827273,9846204,9880882,9886040,9900047,9905993,9934866,9934926,9936126,9936179,9939411,9939665,9979082,9982990,9998693,10003665,10020998,10022641,10023921,10023974,10034313,10036716,10040861,10040924,10048777,10068463,10069451,10071430,10094373,10098318,10114038,10114686,10114817,10136136,10136448,10286781,10359806,10368992,10373036,10373993,10374017,10374113,10376895,10379570,10379906,10380078,10383342,10385046,10385689,10385947,10391556,10392824,10395520,10395758,10396129,10411070,10414475,10417088,10417415,10421129,10463751,10472201,10479063,10485849,10489531,10490105,10500738,10501123,10509384,10515031,10526692,10528924,10529388,10690373,10710079,10745436,10748576,10859638,10860436,10870429,10881355,10890356,10890570,10941822,11024416,11025703,11025995,11031964,11038965,11039315,11065164,11074820,11084345,11187566,11197159,11221523,11225334,11232404,11253627,11253751,11342797,11365415,11403809,11405595,11406484,11409149,11474715,11481784,11482669,11520733,11556261,11556587,11569307,11584846,11702932,11743007,11780829,11814934,11815256,11815990,11833646,11879258,11893949,11894406,11923187,11924236,11924321,11992156,11998459,12012718,12019962,12022116,12030014,12054049,12086555,12095714,12100874,12105699,12106462,12107733,12109138,12110442,12110505,12119565,12122500,12122519,12134952,12140241,12159821,12189619,12196892,12200787,12221628,12221640,12230685,12238104,12238837,12245638,12248378,12250286,12250448,12259344,12275171,12289424,12307851,12368711,12443877,12446006,12448726,12448752,12465805,12487983,12507056,12517831,12518963,12525570,12528554,12547830,12553917,12666617,12835956,12853455,12904452,12920303,12924810,12961266,12985280,13008331,13341204,13534432,13534755,13536910,13549188,13560838, 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Locus information on chromosome A10 68238,87880,97401,98902,127699,134883,145983,148050,148525,149038,152187,163083,163646,164056,177298,179907,180008,189329,194781,208931,223493,224709,226272,226453,226912,231217,231422,233645,245860,246226,267086,276657,298431,331711,355415,366263,372389,372775,373077,373943,373970,393025,396155,397124,398951,399311,409464,410254,411901,413936,417427,434401,437366,440232,441533,443830,451970,463612,464996,486262,488649,496075,498090,517785,518799,525662,544970,549758,554164,565799,567977,568286,568558,568727,569346,643801,671826,678549,689910,691899,720581,741483,743156,743599,743887,744718,745995,746833,747325,748269,748607,748848,748935,749264,749407,759688,760624,761344,762331,762595,767088,768278,769405,769943,771365,772603,772615,772766,773070,773103,778658,779844,780163,781869,782532,784108,785335,785838,789081,795028,795759,805698,808188,810684,811539,813000,813520,816977,817033,819238,819592,829337,830449,830611,830751,831285,831534,831818,831918,832117,832468,832630,832873,834053,834136,834233,834887,835074,835463,836179,836721,840130,851404,851906,852378,852542,854032,854141,854336,854424,854514,861667,864072,869841,870669,870706,872609,873414,888440,888807,889292,893418,894981,895068,896400,899338,899577,899700,899706,899846,899900,899959,900123,900149,900693,915602,922563,928514,931336,931730,934013,934123,934225,934436,934984,936521,937277,937547,938225,938234,938634,938645,940325,941553,952994,967582,967638,969949,970169,970243,970565,971971,976456,981074,981250,981986,982090,982147,982623,982626,983010,985764,985875,985931,986223,988322,988334,1001016,1002794,1017951,1023715,1024846,1025121,1025151,1025315,1026781,1027576,1028305,1028626,1029017,1029386,1029906,1030137,1030262,1031766,1032155,1032445,1032468,1032527,1032656,1032998,1033067,1033080,1033253,1033327,1033414,1033535,1033579,1034696,1036050,1043801,1044763,1044781,1044855,1046507,1046990,1049487,1051534,1051629,1144713,1144896,1145308,1145369,1147753,1147849,1149185,1149540,1149954,1150630,1150852,1155779,1156479,1156567,1157661,1158267,1159215,1159822,1163155,1172606,1207300,1209390,1210015,1211352,1214414,1214489,1218696,1218726,1223600,1224177,1224579,1226821,1240408,1240535,1241208,1243602,1243713,1243833,1244170,1250681,1250767,1250966,1251379,1252072,1252356,1255399,1257630,1258210,1261070,1274956,1372164,1423418,1426412,1442493,1449076,1463849,1484456,1484663,1511379,1515611,1517308,1517657,1526243,1535960,1537784,1544222,1544625,1544637,1545976, 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Claims

1. A liquid phase chip for whole-genome selection breeding of Brassica napus, characterized in that, The invention includes a 45K site probe mixture from Brassica napus and a hybridization capture reagent. The 45K site probe mixture from Brassica napus includes SNP / InDel background site probes and SNP / InDel foreground site probes from Brassica napus. The locations of the SNP / InDel background sites of Brassica napus on the reference genome Bnapus ZS11 are shown in the table below: The information on the SNP / InDel foreground sites of Brassica napus is shown in the table below: 。 2. The liquid phase chip for whole genome selection breeding of Brassica napus as described in claim 1, characterized in that, Background sites were obtained using the following method: (1) Initial selection of candidate sites: Based on the resequencing data of 532 parental lines of Brassica napus, the quality indicators of resequencing sites were calculated, and SNP / InDel polymorphic sites that met the following conditions in all sample populations were selected as initial candidate sites, with a heterozygosity rate ≤0.05, a site deletion frequency ≤0.1, and a MAF ≥0.

3. A total of 1,133,900 initial candidate sites were selected. (2) Screening of representative sites: The linkage disequilibrium interval of the rapeseed germplasm resource population was estimated to be 500kb by software. The linkage disequilibrium interval of 500kb and the linkage disequilibrium of each pair of SNPs / InDels ≥0.8 were used as the screening criteria to obtain 44,528 SNPs / InDels that were evenly distributed on the chromosome, which were the background sites.

3. The liquid phase chip for whole genome selection breeding of Brassica napus as described in claim 1, characterized in that, Foreground sites were obtained using the following method: (1) Genome-wide association analysis of important agronomic traits; Based on the resequencing data of 532 rapeseed accessions, the quality index of resequencing sites was calculated, and SNP / InDel polymorphic sites that met the requirements of heterozygosity ≤0.05, site deletion frequency ≤0.1, and MAF ≥0.05 in all sample populations were selected as genotype data. The original genotype data were imputed using software, and then genome-wide association analysis was performed on the agronomic and quality traits of interest. (2) Determination of foreground sites; Candidate QTL sites for traits were identified using SNP sites with P-values ​​< 1e-4 from association analysis results; SNP / InDel sites associated with candidate QTL sites were screened and QTL intervals were defined using linkage disequilibrium intervals of 500 kb, pairwise SNP / InDel linkage disequilibrium ≥ 0.2, and SNP / InDel P-values ​​≤ 1e-2. The QTLs with ≥10 SNP / InDel counts within the interval were taken as the QTL intervals for the trait, and the peak SNP / InDel counts within the QTL intervals were taken as foreground loci, thus obtaining 100 foreground loci.

4. An application of a liquid phase chip for whole-genome selection breeding of Brassica napus, characterized in that, Used for germplasm prediction, population structure analysis, molecular genetic map construction, genome-wide association analysis, marker-assisted selection breeding, genome-wide selection breeding, trait-related gene localization, material variety authenticity identification, or germplasm resource improvement of Brassica napus.

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