SNP site combination for constructing coconut SNP fingerprint spectrum and application

Abstract

The embodiment of the invention relates to an SNP site combination for constructing a coconut SNP fingerprint spectrum and application, and belongs to the technical field of molecular biology. The embodiment of the invention aims to solve the technical problem that molecular marker screening is generally carried out on the basis of SSR markers or other experimental means in the past, and the repeatability is poor. The SNP (Single Nucleotide Polymorphism) loci in the embodiment of the invention comprise 260 SNP loci positioned on chromosomes Chr01 to Chr16. The SNP site combination provided by the invention can be used for constructing a coconut SNP fingerprint spectrum and rapidly identifying coconut varieties, brand new identity information exclusive to different coconut varieties is provided, individual authenticity can be effectively distinguished, individual sources can be traced, and the method is suitable for large-scale popularization and application. The method has a good application prospect in the aspects of classification and identification of coconut germplasm resources, molecular assisted breeding and the like.

Description

Technical Field

[0001] The embodiments of the present application relate to the field of molecular biology technology, and in particular to a SNP site combination and application for constructing a coconut SNP fingerprint map. Background Art

[0002] Coconut (Cocos nucifera L.) is an important tropical oil crop, landscape plant and fruit tree, known as the "tree of life". Coconut is widely planted in about 93 countries and regions in the world, with a total global planting area of ​​about 180 million mu, and plays a vital role in the economic life of people in tropical regions. Coconut has a planting history of more than 2,000 years in my country, and is planted in Hainan, Yunnan, Guangdong, Guangxi and other places. Coconut is widely distributed in Asia, Africa, America and Pacific island countries, and there are rich local specialty varieties, including African high species, Hainan high species, Sri Lanka high species, red dwarf, yellow dwarf, brown dwarf, perfume and other varieties. The numerous varieties and complex genetic backgrounds have brought great challenges to the identification of coconut varieties.

[0003] DNA fingerprinting technology is a modern method based on DNA molecular markers that can be used for the classification and identification of germplasm resources. Constructing DNA fingerprints of plant varieties can overcome the limitations of identifying varieties based solely on morphological characteristics, which is very important for the accurate identification of germplasm resources and gene discovery. DNA fingerprinting technology is widely used in the study of variety resource diversity and variety identification, but there are few reports on coconuts. In addition, most of the existing variety identification standards are based on SSR, RAPD, and RFLP markers, and it is rare to construct fingerprints based on SNP molecular markers to achieve coconut variety identification. Summary of the invention

[0004] In view of this, the embodiment of the present application provides a SNP site combination and application for constructing a coconut SNP fingerprint map. 327 coconut samples are taken as research objects, and the fingerprint calculation software GaSnp based on genetic algorithm is used to accurately obtain the SNP site combination with high polymorphism and distinguish all samples. 260 core SNP site information is obtained by calculation, and the unique fingerprint map belonging to each coconut sample is constructed using these SNP site information. The constructed fingerprint map can be used for classification and identification of coconut germplasm resources and breeding, etc., which can effectively overcome the defect that the previous fingerprints are usually based on SSR markers or other experimental means for molecular marker screening, and have poor repeatability.

[0005] In a first aspect, an embodiment of the present application provides a SNP site combination for constructing a coconut SNP fingerprint map, wherein the SNP site combination includes 260 SNP sites located on chromosomes Chr01 to Chr16.

[0006] In some embodiments that may include the above embodiments, the SNP site includes:

[0007] Locus 1 is located on chromosome 1, bp 11,190,781, and the mutation type is T / G;

[0008] Locus 2 is located on chromosome 1 at bp 12235818, and the mutation type is G / A;

[0009] Locus 3 is located on chromosome 1 at bp 17980352, and the mutation type is A / G;

[0010] Locus 4 is located on chromosome 1 at bp 110680094, and the mutation type is A / G;

[0011] Locus 5 is located on chromosome 1 at bp 144832968, and the mutation type is C / G;

[0012] Locus 6 is located on chromosome 1, bp 146014481, and the mutation type is T / A;

[0013] Locus 7 is located on chromosome 1 at bp 146793777, and the mutation type is A / G;

[0014] Locus 8 is located on chromosome 1, bp 154417159, and the mutation type is C / T;

[0015] Locus 9 is located on chromosome 1, bp 157,934,494, and the mutation type is A / G;

[0016] Locus 10 is located on chromosome 1, bp 159488786, and the mutation type is A / G;

[0017] Locus 11 is located on chromosome 1 at bp 1177659160, and the mutation type is A / G;

[0018] Locus 12 is located on chromosome 1, bp 1205295810, and the mutation type is C / T;

[0019] Locus 13 is located on chromosome 1, bp 1209649951, and the mutation type is G / A;

[0020] Locus 14 is located on chromosome 1, bp 1210539345, and the mutation type is T / C;

[0021] Locus 15 is located on chromosome 1, bp 1213678628, and the mutation type is T / C;

[0022] Locus 16 is located on chromosome 2, bp 25,511,596, and the mutation type is A / T;

[0023] Site 17 is located at 242777399bp on chromosome 2, and the variation type is T / C; Site 18 is located at 2104373536bp on chromosome 2, and the variation type is C / T; Site 19 is located at 2134120172bp on chromosome 2, and the variation type is T / C; Site 20 is located at 2139741917bp on chromosome 2, and the variation type is T / C; Site 21 is located at 2140969969bp on chromosome 2, and the variation type is A / G; Site 22 is located at 2141004076bp on chromosome 2, and the variation type is A / G; Site 23 is located at 2134120172bp on chromosome 2, and the variation type is T / C; Site 24 is located at 2139741917bp on chromosome 2, and the variation type is A / G. The 24th site is located at 2155951920bp on chromosome 2, and the variation type is C / G; the 25th site is located at 2168814238bp on chromosome 2, and the variation type is G / A; the 26th site is located at 2171030095bp on chromosome 2, and the variation type is T / A; the 27th site is located at 2173296480bp on chromosome 2, and the variation type is A / G; the 28th site is located at 2175131148bp on chromosome 2, and the variation type is C / G; the 29th site is located at 2168814238bp on chromosome 2, and the variation type is G / A; the 2171030095bp on chromosome 2, and the variation type is T / A; the 22nd site is located at 2173296480bp on chromosome 2, and the variation type is A / G; the 23rd site is located at 2175131148bp on chromosome 2, and the variation type is C / G; the 24th site is located at 2175131148bp on chromosome 2, and the variation type is C / G; the 25th site is located at 2168814238bp on chromosome 2, and the variation type is G / A; the 26th site is located at 2171030095bp on chromosome 2, and the variation type is T / A; the 27th site is located at 2173296480bp on chromosome 2, and the variation type is A / G. The mutation type is T / C at 2175229826bp; the mutation type is A / C at site 30, which is located at 2177772806bp on chromosome 2; the mutation type is G / A at site 31, which is located at 2184028384bp on chromosome 2; the mutation type is T / C at site 32, which is located at 2184558347bp on chromosome 2; the mutation type is T / A at site 33, which is located at 2185183473bp on chromosome 2; the mutation type is C / T at site 34, which is located at 2186374217bp on chromosome 2; the mutation type is C / T at site 35, which is located at 370779 on chromosome 3. The 49bp site is located on chromosome 3, and the variation type is C / A; the 36th site is located on chromosome 3, 39467662bp, and the variation type is A / G; the 37th site is located on chromosome 3, 323482912bp, and the variation type is G / A; the 38th site is located on chromosome 3, 333226223bp, and the variation type is G / A; the 39th site is located on chromosome 3, 333957544bp, and the variation type is A / G; the 40th site is located on chromosome 3, 334035592bp, and the variation type is A / G; the 41st site is located on chromosome 3, 344675912bp, and the variation type is C / T;Site 42 is located at 349598945bp on chromosome 3, with a variation type of A / G; Site 43 is located at 349967597bp on chromosome 3, with a variation type of A / G; Site 44 is located at 350712941bp on chromosome 3, with a variation type of G / T; Site 45 is located at 355447906bp on chromosome 3, with a variation type of A / G; Site 46 is located at 356509055bp on chromosome 3, with a variation type of C / T; Site 47 is located at 357193563bp on chromosome 3, with a variation type of T / C; Site 48 is located at 36301 The 49th site is located at 364932466bp on chromosome 3, and the variation type is G / A; the 50th site is located at 368304699bp on chromosome 3, and the variation type is C / T; the 51st site is located at 3160699507bp on chromosome 3, and the variation type is G / A; the 52nd site is located at 3161671764bp on chromosome 3, and the variation type is G / A; the 53rd site is located at 3168627960bp on chromosome 3, and the variation type is T / C; the 54th site is located at 3170406066bp on chromosome 3, and the variation type is C / T; Site 55 is located at 3171148457bp on chromosome 3, with a variation type of T / C; Site 56 is located at 3171572870bp on chromosome 3, with a variation type of T / A; Site 57 is located at 3173329295bp on chromosome 3, with a variation type of T / C; Site 58 is located at 3181396863bp on chromosome 3, with a variation type of C / T; Site 59 is located at 3185748145bp on chromosome 3, with a variation type of T / A; Site 60 is located at 43488085bp on chromosome 4, with a variation type of A / G; Site 61 is located at 4947070bp on chromosome 4, with a variation type of The 62nd site is located at 420370567bp on chromosome 4, and the variation type is T / C; the 63rd site is located at 422158504bp on chromosome 4, and the variation type is G / A; the 64th site is located at 493029245bp on chromosome 4, and the variation type is A / G; the 65th site is located at 4133737637bp on chromosome 4, and the variation type is T / A; the 66th site is located at 4136800305bp on chromosome 4, and the variation type is T / C; the 67th site is located at 4140123972bp on chromosome 4, and the variation type is A / C;Site 68 is located on chromosome 4, 4142148415bp, with a variation type of T / G; Site 69 is located on chromosome 4, 4150103302bp, with a variation type of T / C; Site 70 is located on chromosome 4, 4150752420bp, with a variation type of A / G; Site 71 is located on chromosome 4, 4151876715bp, with a variation type of G / A; Site 72 is located on chromosome 4, 4153027020bp, with a variation type of G / A; Site 73 is located on chromosome 4, 4154635908bp, with a variation type of C / T; Site 74 is located on chromosome 4, 4157572576bp, with a variation type of G / T; Site 75 is located on chromosome 41 The 76th site is located at 4163952706bp on chromosome 4, and the variation type is T / C; the 77th site is located at 4164312912bp on chromosome 4, and the variation type is G / A; the 78th site is located at 4167462144bp on chromosome 4, and the variation type is T / C; the 79th site is located at 4174584167bp on chromosome 4, and the variation type is T / C; the 80th site is located at 4175575716bp on chromosome 4, and the variation type is T / A; the 81st site is located at 4179391103bp on chromosome 4, and the variation type is A / G; the 82nd site is located at 5101002bp on chromosome 5, and the variation type is C / A;

[0024] Locus 83 is located on chromosome 5, bp 54050477, and the mutation type is T / C;

[0025] Locus 84 is located on chromosome 5, bp 56210415, and the mutation type is C / T;

[0026] Locus 85 is located on chromosome 5, bp 57353166, and the mutation type is T / C;

[0027] Locus 86 is located on chromosome 5, bp 57907806, and the mutation type is T / G;

[0028] Site 87 is located at 58122046bp on chromosome 5, and the variation type is C / T; Site 88 is located at 512139653bp on chromosome 5, and the variation type is A / G; Site 89 is located at 512139824bp on chromosome 5, and the variation type is T / C; Site 90 is located at 513420754bp on chromosome 5, and the variation type is T / C; Site 91 is located at 516715793bp on chromosome 5, and the variation type is C / T; Site 92 is located at 521548705bp on chromosome 5, and the variation type is A / G; Site 93 is located at 512139824bp on chromosome 5, and the variation type is T / C; The mutation type is T / C at site 94, which is located at 524040590bp on chromosome 5, and the mutation type is T / C; the mutation type is T / C at site 95, which is located at 527470277bp on chromosome 5, and the mutation type is T / C; the mutation type is A / C at site 96, which is located at 530565269bp on chromosome 5; the mutation type is A / C at site 97, which is located at 531991099bp on chromosome 5, and the mutation type is A / T; the mutation type is G / T at site 98, which is located at 535018979bp on chromosome 5; the mutation type is G / T at site 99, which is located at 536993723bp on chromosome 5. , the variation type is G / T; the 100th site is located on chromosome 5, 537746327bp, and the variation type is G / A; the 101st site is located on chromosome 5, 543138430bp, and the variation type is T / C; the 102nd site is located on chromosome 5, 543944445bp, and the variation type is C / T; the 103rd site is located on chromosome 5, 550429114bp, and the variation type is T / C; the 104th site is located on chromosome 5, 561180240bp, and the variation type is A / G; the 105th site is located on chromosome 5, 565131503bp, and the variation type is G / A; Site 106, located at 570663061bp on chromosome 5, with a variation type of A / T; Site 107, located at 5144968891bp on chromosome 5, with a variation type of C / T; Site 108, located at 5144969368bp on chromosome 5, with a variation type of T / A; Site 109, located at 5155396989bp on chromosome 5, with a variation type of A / C; Site 110, located at 5161684131bp on chromosome 5, with a variation type of C / A; Site 111, located at 5161685301bp on chromosome 5, with a variation type of T / C;Site 112 is located at 5164032398bp on chromosome 5, with a variation type of A / T; Site 113 is located at 5164856997bp on chromosome 5, with a variation type of A / G; Site 114 is located at 6778804bp on chromosome 6, with a variation type of T / C; Site 115 is located at 62344276bp on chromosome 6, with a variation type of G / A; Site 116 is located at 63607324bp on chromosome 6, with a variation type of G / A; Site 117 is located at 69812751bp on chromosome 6, with a variation type of C / G; Site 118 is located at 6778804bp on chromosome 6, with a variation type of T / C; The mutation type is C / T at position 615808467 of chromosome 6; the mutation type is G / A at position 119 at position 617634309 of chromosome 6; the mutation type is A / T at position 120 at position 622461159 of chromosome 6; the mutation type is G / A at position 121 at position 626460149 of chromosome 6; the mutation type is G / A at position 122 at position 627819611 of chromosome 6; the mutation type is T / C at position 123 at position 636016335 of chromosome 6; the mutation type is G / T at position 124 at position 614249 The 125th site is located on chromosome 6, 6142498639bp, and the variation type is G / T; the 126th site is located on chromosome 6, 6143663591bp, and the variation type is A / G; the 127th site is located on chromosome 6, 6145585715bp, and the variation type is A / C; the 128th site is located on chromosome 6, 6149622668bp, and the variation type is G / A; the 129th site is located on chromosome 6, 6157761880bp, and the variation type is C / G; the 130th site is located on chromosome 6, 6170724270 bp, the variation type is C / G; the 131st site is located on chromosome 6, 6170763361bp, the variation type is A / G; the 132nd site is located on chromosome 7, 71710306bp, the variation type is T / C; the 133rd site is located on chromosome 7, 73264083bp, the variation type is C / G; the 134th site is located on chromosome 7, 77548057bp, the variation type is A / C; the 135th site is located on chromosome 7, 77750449bp, the variation type is T / A; the 136th site is located on chromosome 7, 712649262bp, the variation type is T / A;Site 137 is located at 712909310bp on chromosome 7, with a variation type of A / G; Site 138 is located at 712989315bp on chromosome 7, with a variation type of C / G; Site 139 is located at 713199095bp on chromosome 7, with a variation type of T / C; Site 140 is located at 714493374bp on chromosome 7, with a variation type of C / G ; Site 141, located at 718532969bp on chromosome 7, with a variation type of C / G; Site 142, located at 723461275bp on chromosome 7, with a variation type of C / T; Site 143, located at 729251772bp on chromosome 7, with a variation type of C / T; Site 144, located at 737148816bp on chromosome 7, with a variation type of C / T ; Site 145, located at 747094940bp on chromosome 7, with a variation type of T / C; Site 146, located at 751336679bp on chromosome 7, with a variation type of C / A; Site 147, located at 7162732167bp on chromosome 7, with a variation type of A / G; Site 148, located at 81371158bp on chromosome 8, with a variation type of A / G; Site 149, located at 86789650bp on chromosome 8, with a variation type of G / A; Site 150, located at 88437771bp on chromosome 8, with a variation type of T / C; Site 151, located at 814588094bp on chromosome 8, with a variation type of G / A; Site 152, located at 815736361bp on chromosome 8, with a variation type of A / G;

[0029] Locus 153 is located on chromosome 8 at bp 825810325, and the variant type is G / C;

[0030] Locus 154 is located on chromosome 8, bp 826325818, and the mutation type is T / G;

[0031] Locus 155 is located on chromosome 8, bp 837475933, and the mutation type is T / C;

[0032] Site 156 is located at 874738903bp on chromosome 8, and the variant type is A / G; Site 157 is located at 8138002896bp on chromosome 8, and the variant type is C / T; Site 158 is located at 8142021696bp on chromosome 8, and the variant type is C / A; Site 159 is located at 8145208971bp on chromosome 8, and the variant type is C / T ; Site 160, located at 8146286654bp on chromosome 8, with a variation type of A / G; Site 161, located at 8150404881bp on chromosome 8, with a variation type of T / A; Site 162, located at 8151594514bp on chromosome 8, with a variation type of T / C; Site 163, located at 91438383bp on chromosome 9, with a variation type of C / T;

[0033] Locus 164 is located on chromosome 9, 911449710bp, and the mutation type is T / C;

[0034] Locus 165 is located on chromosome 9, bp 913479358, and the variant type is G / C;

[0035] Locus 166 is located on chromosome 9, bp 913489579, and the mutation type is C / G;

[0036] The 167th site is located on chromosome 9, 941147490bp, and the variation type is A / C; the 168th site is located on chromosome 9, 9141925303bp, and the variation type is T / C; the 169th site is located on chromosome 9, 9142775138bp, and the variation type is T / C; the 170th site is located on chromosome 9, 9147110013bp, and the variation type is C / T; the 171st site is located on chromosome 9, 9147846861bp, and the variation type is G / A; the 172nd site is located on chromosome 9, 9151353465bp, and the variation type is C / T; the 173rd site is located on chromosome 9, 9151353465bp, and the variation type is C / T; The 174th site is located on chromosome 9, 9153698062bp, and the variation type is T / C; the 175th site is located on chromosome 9, 9154824375bp, and the variation type is C / G; the 176th site is located on chromosome 9, 9155548198bp, and the variation type is A / G; the 177th site is located on chromosome 9, 9155548252bp, and the variation type is G / A; the 178th site is located on chromosome 9, 9155576669bp, and the variation type is C / G; the 179th site is located on chromosome 9, 9155576669bp, and the variation type is C / G. The 180th site is located at 102302094bp on chromosome 10, and the variation type is G / C; the 181st site is located at 1017416902bp on chromosome 10, and the variation type is A / T; the 182nd site is located at 10121954875bp on chromosome 10, and the variation type is G / A; the 183rd site is located at 10130315170bp on chromosome 10, and the variation type is A / T; the 184th site is located at 10132041600bp on chromosome 10, and the variation type is G / T; the 185th site is located at 1017416902bp on chromosome 10, and the variation type is A / T; The 186th site is located at 10142022816bp on chromosome 10, and the variation type is C / T; the 187th site is located at 10143214786bp on chromosome 10, and the variation type is G / A; the 188th site is located at 10143714885bp on chromosome 10, and the variation type is A / G; the 189th site is located at 10144007893bp on chromosome 10, and the variation type is C / T; the 190th site is located at 1155339362bp on chromosome 11, and the variation type is G / A;Site 191 is located at 1190715627bp on chromosome 11, and the variation type is A / G; Site 192 is located at 1194597680bp on chromosome 11, and the variation type is T / G; Site 193 is located at 1194839888bp on chromosome 11, and the variation type is A / T; Site 194 is located at 1195818114bp on chromosome 11, and the variation type is T / C; Site 195 is located at 11105015249bp on chromosome 11, and the variation type is G / A; Site 196 is located at 11118023633bp on chromosome 11, and the variation type is C / A; The 197th site is located at 11128125475bp on chromosome 11, and the variation type is A / G; the 198th site is located at 11133467339bp on chromosome 11, and the variation type is G / A; the 199th site is located at 11138493485bp on chromosome 11, and the variation type is C / T; the 200th site is located at 123684982bp on chromosome 12, and the variation type is G / A; the 201st site is located at 125995960bp on chromosome 12, and the variation type is G / A; the 202nd site is located at 126835408bp on chromosome 12, and the variation type is T / C; Site 3 is located at 1213550741bp on chromosome 12, with a variation type of T / C; Site 204 is located at 1213899205bp on chromosome 12, with a variation type of A / C; Site 205 is located at 1214447869bp on chromosome 12, with a variation type of G / A; Site 206 is located at 12107960617bp on chromosome 12, with a variation type of T / G; Site 207 is located at 12119478235bp on chromosome 12, with a variation type of T / C; Site 208 is located at 12120018613bp on chromosome 12, with a variation type of C / T; Site 209 is located at 1214447869bp on chromosome 12, with a variation type of G / A; Site 210 is located at 1214447869bp on chromosome 12, with a variation type of T / G; Site 211 is located at 1214447869bp on chromosome 12, with a variation type of Site 9 is located at 12124086849bp on chromosome 12, and the variation type is G / T; Site 210 is located at 12124453241bp on chromosome 12, and the variation type is G / A; Site 211 is located at 12128376164bp on chromosome 12, and the variation type is T / G; Site 212 is located at 12128559402bp on chromosome 12, and the variation type is G / A; Site 213 is located at 12128953055bp on chromosome 12, and the variation type is C / T; Site 214 is located at 12130582077bp on chromosome 12, and the variation type is A / G;The 215th site is located on chromosome 12, 12132475469bp, and the variation type is A / G; the 216th site is located on chromosome 12, 12134372645bp, and the variation type is A / C; the 217th site is located on chromosome 12, 12138491493bp, and the variation type is C / T; the 218th site is located on chromosome 12, 12140124081bp, and the variation type is C / G; the 219th site is located on chromosome 12, 12140239381bp, and the variation type is G / T; the 220th site is located on chromosome 13, 1327030687bp, and the variation type is A / G; Site 221, located at 1334684042bp on chromosome 13, with a variation type of C / T; Site 222, located at 1345894210bp on chromosome 13, with a variation type of C / T; Site 223, located at 1353577453bp on chromosome 13, with a variation type of A / G; Site 224, located at 1353812335bp on chromosome 13, with a variation type of A / G; Site 225, located at 1360489824bp on chromosome 13, with a variation type of T / G; Site 226, located at 1367836217bp on chromosome 13, with a variation type of C / T; Site 227, located at 1373891012bp on chromosome 13, with a variation type of T / C; Site 228, located at 1376533867bp on chromosome 13, with a variation type of A / G; Site 229, located at 1383098051bp on chromosome 13, with a variation type of T / C; Site 230, located at 1388748630bp on chromosome 13, with a variation type of G / A; Site 231, located at 1389057411bp on chromosome 13, with a variation type of C / T; Site 232, located at 1390232542bp on chromosome 13, with a variation type of A / G; Site 233, located at 1390395203bp on chromosome 13, with a variation type of A / G; Site 234, located at 1465570441bp on chromosome 14, with a variation type of G / A; Site 235, located at 1469425337bp on chromosome 14, with a variation type of A / G; Site 236, located at 1475905772bp on chromosome 14, with a variation type of G / A; Site 237, located at 1478843002bp on chromosome 14, with a variation type of T / C; Site 238, located at 1481865290bp on chromosome 14, with a variation type of C / T;Site 239 is located at 1481945414bp on chromosome 14, and the variation type is A / T; Site 240 is located at 1484299928bp on chromosome 14, and the variation type is C / T; Site 241 is located at 1485726361bp on chromosome 14, and the variation type is G / A; Site 242 is located at 1488144162bp on chromosome 14, and the variation type is G / A;

[0037] Locus 243 is located on chromosome 14, bp 1489143409, and the variant type is G / A;

[0038] Locus 244 is located on chromosome 15, bp 153,183,570, and the mutation type is C / T;

[0039] Locus 245 is located at 154250994bp on chromosome 15, and the variant type is G / A;

[0040] Locus 246 is located at 157960137bp on chromosome 15, and the variant type is A / G;

[0041] Locus 247 is located on chromosome 15, bp 1512731347, and the variant type is A / G;

[0042] Locus 248 is located on chromosome 15, bp 1515374666, and the mutation type is C / T;

[0043] Locus 249 is located on chromosome 15, bp 1520140486, and the mutation type is T / G;

[0044] Locus 250 is located at 1526989810bp on chromosome 15, and the mutation type is A / T;

[0045] Locus 251 is located on chromosome 15, bp 1585734438, and the mutation type is C / T;

[0046] Locus 252 is located at 1632401183bp on chromosome 16, and the variant type is G / A;

[0047] Locus 253 is located at 1649669601bp on chromosome 16, and the mutation type is T / C;

[0048] Locus 254 is located on chromosome 16, bp 1656467304, and the variant type is A / G;

[0049] Locus 255 is located at 1662417000bp on chromosome 16, and the mutation type is G / T;

[0050] Locus 256 is located at 1665186178bp on chromosome 16, and the variant type is A / G;

[0051] Locus 257 is located on chromosome 16, bp 1667185586, and the variant type is A / G;

[0052] Locus 258 is located on chromosome 16, bp 1668159645, and the mutation type is T / C;

[0053] Locus 259 is located at 1670703024bp on chromosome 16, and the mutation type is G / A;

[0054] Site 260 is located on bp 1674142244 of chromosome 16, and the mutation type is T / G.

[0055] The second aspect of the embodiment of the present application also provides a coconut DNA fingerprint map, which is constructed using the above-mentioned SNP site combination.

[0056] The third aspect of the embodiments of the present application also provides the application of the above-mentioned SNP site combination in constructing a coconut DNA fingerprint.

[0057] The fourth aspect of the embodiments of the present application also provides the application of the above-mentioned SNP site combination in the classification and identification of coconut germplasm resources.

[0058] The fifth aspect of the embodiment of the present application also provides a method for identifying coconut germplasm using the above-mentioned SNP locus combination, comprising the following steps:

[0059] (1) Extracting DNA from coconut samples;

[0060] (2) Sequencing the genome of individual species of coconut sample DNA;

[0061] (3) Genotyping was performed based on the sequencing results compared with the dwarf coconut reference genome (URL: http: / / arecaceae-gdb.com / # / download, genome name: cocos_nucifera_dwarf.genome.fa) to identify the SNP loci information of each variety;

[0062] (4) Based on the genotype combination of the known fingerprint SNP loci, the similarity between the sample to be tested and the known fingerprint sample is determined, thereby evaluating the variety and source information of the coconut.

[0063] In some embodiments, which may include the above embodiments, the coconut sample is fresh coconut leaves.

[0064] Compared with the prior art, the embodiments of the present application have the following beneficial effects:

[0065] (1) The SNP loci combination obtained in this application based on coconut resequencing is evenly distributed in the chromosome and has high polymorphism, which can be used to construct coconut SNP fingerprint maps and rapid identification of coconut varieties.

[0066] (2) This application provides brand new identity information unique to 327 coconut germplasms, which can effectively identify the authenticity of individuals and trace their sources.

[0067] (3) The present application utilizes a combination of SNP loci to effectively construct a coconut SNP fingerprint map and establish a genotype ID card for coconut. It only requires the corresponding genome sequence detection of the sample to be tested and comparison with the fingerprint map library to identify the source classification of the sample to be tested, determine the closeness of the relationship between varieties, and measure the genetic distance between varieties. The coconut SNP fingerprint map obtained in the present application has a high accuracy rate for coconut variety identification. BRIEF DESCRIPTION OF THE DRAWINGS

[0068] In order to more clearly illustrate the embodiments of the present application or the technical solutions in the prior art, the drawings required for use in the embodiments or the description of the prior art will be briefly introduced below. Obviously, the drawings described below are some embodiments of the present application. For ordinary technicians in this field, other drawings can be obtained based on these drawings without paying any creative work.

[0069] Figure 1 a is the evolutionary tree constructed using the original 7,650,000 SNPs. Figure 1 b is an evolutionary tree constructed using 260 fingerprint SNP loci, where blue represents tall coconut groups and purple represents dwarf coconut groups. The population structure and clustering results are basically consistent. DETAILED DESCRIPTION

[0070] In order to make the purpose, technical solution and advantages of the embodiments of the present application clearer, the technical solution in the embodiments of the present application will be clearly and completely described below in conjunction with the drawings in the embodiments of the present application. Obviously, the described embodiments are part of the embodiments of the present application, not all of the embodiments. Based on the embodiments in the present application, all other embodiments obtained by ordinary technicians in this field without creative work are within the scope of protection of this application.

[0071] Unless otherwise specified, the experimental methods used in the examples of this application are all conventional methods.

[0072] In the following examples, unless otherwise specified, all raw materials can be obtained by commercial purchase or conventional methods.

[0073] Example 1- Acquisition of SNP site combinations and construction of coconut variety fingerprints

[0074] All SNP sites were developed based on the resequencing data, and the original SNP sites were filtered and screened to remove SNP sites with a deletion number greater than 1% and homozygous genotypes 0 / 0 and 1 / 1 less than 2. The correlation between each SNP site was calculated, and the correlation R between two adjacent SNP sites was retained. 2 SNP sites with a score >0.95 were used as candidate sites for subsequent genetic algorithms.

[0075] Using GaSnp software, the genotype format was converted and the SNP sites were randomly combined to calculate a set of filtered SNP site combinations that distinguish all varieties. Finally, 260 core SNP sites were selected to construct the coconut variety fingerprint. The name, chromosome, location, variation type and allele frequency of each SNP site are shown in Table 1, and the fingerprints of each variety are shown in Table 2.

[0076] The present application uses the SNP sites obtained in Table 1 to identify the 327 coconut materials in Table 2 and obtains the corresponding fingerprint sequences of each variety. It can be seen from the table that the fingerprint sequences of each variety are different, indicating that the 327 materials can be effectively distinguished to achieve accurate identification of different coconut varieties.

[0077] Table 1 Combinations of SNP loci used to construct coconut SNP fingerprints

[0078]

[0079]

[0080]

[0081]

[0082]

[0083]

[0084] Table 2 Coconut varieties and their fingerprint sequences

[0085]

[0086]

[0087]

[0088]

[0089]

[0090]

[0091]

[0092]

[0093]

[0094]

[0095]

[0096]

[0097]

[0098]

[0099]

[0100]

[0101]

[0102]

[0103]

[0104]

[0105]

[0106]

[0107]

[0108]

[0109] In the fingerprint coding table of different coconut samples in Table 2, "0" in the fingerprint code refers to genotype 0 / 0; it means that the site in a certain sample of the coconut sample is homozygous, that is, it is consistent with the site in the reference genome; "2" in the fingerprint code refers to genotype 0 / 1, which means that the site in the sample is heterozygous, that is, it is partially consistent with the site in the reference genome; "1" in the fingerprint code refers to genotype 1 / 1; it means that the site in the sample is variant, that is, it is completely different from the site in the reference genome.

[0110] Example 2 - Identification of Coconut Germplasm

[0111] The method for identifying coconut germplasm using the above SNP locus combination comprises the following steps:

[0112] (1) Fresh coconut leaves were used as coconut samples, and the CTAB method was used to extract DNA from coconut samples:

[0113] ① Take about 2g of fresh leaves, put them in a pre-cooled mortar, add about 0.08g of PVP, quickly grind them into powder in liquid nitrogen, transfer them into a pre-cooled 50mL centrifuge tube, add 20mL of pre-heated 2% CTAB lysis buffer, slowly invert upside down to mix thoroughly, and then place in a 65℃ water bath for 90min. In the water bath, invert and mix once every 15min;

[0114] ②Take out the centrifuge tube and cool it to room temperature, add an equal volume of chloroform / isoamyl alcohol (24:1) and mix well. After balancing, let it stand for 10 minutes, put it in a centrifuge, and centrifuge it at 12000r / min for 10 minutes. Aspirate the supernatant and transfer it to a new 50mL centrifuge tube, repeat the previous step; aspirate the supernatant and transfer it to a new 50mL centrifuge tube, add pre-cooled anhydrous ethanol, pick out the floating DNA, and finally collect the DNA into a 1.5mL centrifuge tube, wash it with 75% anhydrous ethanol, air-dry the DNA precipitate, add TE buffer, add RNaseA (20mg / mL) after dissolution, and place it in a 37℃ water bath for 30min, take it out and store it at 4℃ for later use;

[0115] (2) High-throughput sequencing was used to detect SNP sites in coconut sample DNA:

[0116] ① Using the PCR amplification primer pair combination for amplifying the SNP site combination, PCR amplification and electrophoresis detection were performed on the coconut sample DNA; PCR amplification system (2μl DNA, 1μl primer, 17μl mix solution) was prepared in a PCR plate, and the PCR amplification program was set; 2% agarose gel was prepared, and 4μl PCR amplification product was taken for electrophoresis detection; ② The PCR product containing the target band was sent to a sequencing company for sequencing to obtain the corresponding sequence information;

[0117] (3) The sequencing sequences were aligned with the reference genome, and genotyping was performed using GATK software to identify the SNP sites. The coconut varieties and source information were identified based on the variation information of the SNP sites and the similarity between them and the 327 germplasm libraries.

[0118] Example 3 - Verification of the accuracy of the coconut SNP fingerprint

[0119] This application analyzes the genetic diversity and genetic relationship between coconut varieties with high repetition and similarity, and finds that the cluster analysis using molecular markers is completely consistent with the traditional classification, indicating that the coconut fingerprint obtained can be effectively used for the classification and identification of coconut germplasm resources, including:

[0120] (1) The genetic variation and structure of the obtained coconut population were evaluated by using the above-mentioned SNP loci combination of the present application, and it was found that the obtained coconut sample population had rich genetic variation;

[0121] (2) The genetic diversity and kinship analysis of the coconut variety resources obtained showed that the clustering results were consistent with the traditional morphological classification results, and the genetic similarity coefficient was high;

[0122] (3) The evolutionary tree constructed using the coconut SNP site combination of the present application is the same as the evolutionary tree constructed using other sites, indicating that the 327 coconut SNP fingerprint sites obtained are sufficient to restore the population structure of the coconut population. The fingerprint map can effectively identify different coconut samples with high accuracy. Figure 1 shown.

[0123] Finally, it should be noted that the above embodiments are only used to illustrate the technical solutions of the present application, rather than to limit it. Although the present application has been described in detail with reference to the aforementioned embodiments, those skilled in the art should understand that they can still modify the technical solutions described in the aforementioned embodiments, or replace some or all of the technical features therein with equivalents. However, these modifications or replacements do not cause the essence of the corresponding technical solutions to deviate from the scope of the technical solutions of the embodiments of the present application.

Claims

1. A SNP site combination for constructing a coconut SNP fingerprint, characterized in that: The SNP site combination includes 260 SNP sites located on chromosomes Chr01 to Chr16.

2. The SNP site combination for constructing a coconut SNP fingerprint according to claim 1, wherein the SNP site comprises: Locus 1 is located on chromosome 1, bp 11,190,781, and the mutation type is T / G; Locus 2 is located on chromosome 1 at bp 12235818, and the mutation type is G / A; Locus 3 is located on chromosome 1 at bp 17980352, and the mutation type is A / G; Locus 4 is located on chromosome 1 at bp 110680094, and the mutation type is A / G; Locus 5 is located on chromosome 1 at bp 144832968, and the mutation type is C / G; Locus 6 is located on chromosome 1, bp 146014481, and the mutation type is T / A; Locus 7 is located on chromosome 1 at bp 146793777, and the mutation type is A / G; Locus 8 is located on chromosome 1, bp 154417159, and the mutation type is C / T; Locus 9 is located on chromosome 1, bp 157,934,494, and the mutation type is A / G; Locus 10 is located on chromosome 1, bp 159488786, and the mutation type is A / G; Locus 11 is located on chromosome 1 at bp 1177659160, and the mutation type is A / G; Locus 12 is located on chromosome 1, bp 1205295810, and the mutation type is C / T; Locus 13 is located on chromosome 1, bp 1209649951, and the mutation type is G / A; Locus 14 is located on chromosome 1, bp 1210539345, and the mutation type is T / C; Locus 15 is located on chromosome 1, bp 1213678628, and the mutation type is T / C; Locus 16 is located on chromosome 2, bp 25,511,596, and the mutation type is A / T; Locus 17 is located at bp 242777399 on chromosome 2, and the mutation type is T / C; Locus 18 is located on chromosome 2, bp 2104373536, and the mutation type is C / T; Locus 19 is located at 2134120172bp on chromosome 2, and the mutation type is T / C; Locus 20 is located at bp 2139741917 on chromosome 2, and the mutation type is T / C; Locus 21 is located at bp 2140969969 on chromosome 2, and the mutation type is A / G; Locus 22 is located at bp 2141004076 on chromosome 2, and the mutation type is A / G; Locus 23 is located at bp 2144312732 on chromosome 2, and the mutation type is C / G; Locus 24 is located on chromosome 2, bp 2155951920, and the mutation type is C / T; Locus 25 is located at bp 2168814238 on chromosome 2, and the mutation type is G / A; Locus 26 is located on chromosome 2, bp 2171030095, and the mutation type is T / A; Locus 27 is located on chromosome 2, bp 2173296480, and the variant type is A / G; Locus 28 is located on chromosome 2, bp 2175131148, and the mutation type is C / G; Locus 29 is located at bp 2175229826 on chromosome 2, and the mutation type is T / C; Locus 30 is located on chromosome 2, bp 2177772806, and the variant type is A / C; Locus 31 is located on chromosome 2, bp 2184028384, and the variant type is G / A; Locus 32 is located at bp 2184558347 on chromosome 2, and the mutation type is T / C; Locus 33 is located at 2185183473bp on chromosome 2, and the mutation type is T / A; Locus 34 is located on chromosome 2, bp 2186374217, and the mutation type is C / T; Locus 35 is located at bp 37077949 on chromosome 3, and the mutation type is C / A; Locus 36 is located at bp 39467662 on chromosome 3, and the mutation type is A / G; Locus 37 is located at bp 323482912 on chromosome 3, and the mutation type is G / A; Locus 38 is located at bp 333226223 on chromosome 3, and the mutation type is G / A; Locus 39 is located at bp 333957544 on chromosome 3, and the variant type is A / G; Locus 40 is located at bp 334035592 on chromosome 3, and the variant type is A / G; Locus 41 is located at bp 344675912 on chromosome 3, and the mutation type is C / T; Locus 42 is located at bp 349598945 on chromosome 3, and the variant type is A / G; Locus 43 is located at bp 349967597 on chromosome 3, and the variant type is A / G; Locus 44 is located at 350712941bp on chromosome 3, and the mutation type is G / T; Locus 45 is located at bp 355447906 on chromosome 3, and the variant type is A / G; Locus 46 is located at bp 356509055 on chromosome 3, and the mutation type is C / T; Locus 47 is located at bp 357193563 on chromosome 3, and the mutation type is T / C; Locus 48 is located at bp 363014229 on chromosome 3, and the variant type is G / A; Locus 49 is located at bp 364932466 on chromosome 3, and the variant type is G / A; Locus 50 is located on chromosome 3, bp 368304699, and the mutation type is C / T; Locus 51 is located on chromosome 3, bp 3160699507, and the variant type is G / A; Locus 52 is located on chromosome 3, bp 3161671764, and the variant type is G / A; Locus 53 is located on chromosome 3, bp 3168627960, and the mutation type is T / C; Locus 54 is located on chromosome 3, bp 3170406066, and the mutation type is C / T; Locus 55 is located on chromosome 3, bp 3171148457, and the mutation type is T / C; Locus 56 is located on chromosome 3, bp 3171572870, and the mutation type is T / A; Locus 57 is located on chromosome 3, bp 3173329295, and the mutation type is T / C; Locus 58 is located on chromosome 3, bp 3181396863, and the mutation type is C / T; Locus 59 is located on chromosome 3, bp 3185748145, and the mutation type is T / A; Locus 60 is located at 43488085bp on chromosome 4, and the mutation type is A / G; Locus 61 is located at 49185469bp on chromosome 4, and the mutation type is T / C; Locus 62 is located at 420370567bp on chromosome 4, and the mutation type is T / C; Locus 63 is located at 422158504bp on chromosome 4, and the variant type is G / A; Locus 64 is located at 493029245bp on chromosome 4, and the variant type is A / G; Locus 65 is located on chromosome 4, bp 4133737637, and the mutation type is T / A; Locus 66 is located on chromosome 4, bp 4136800305, and the mutation type is T / C; Locus 67 is located on chromosome 4, bp 4140123972, and the variant type is A / C; Locus 68 is located at 4142148415bp on chromosome 4, and the mutation type is T / G; Locus 69 is located on chromosome 4, bp 4150103302, and the mutation type is T / C; Locus 70 is located on chromosome 4, bp 4150752420, and the variant type is A / G; Locus 71 is located on chromosome 4 at bp 4151876715, and the variant type is G / A; Locus 72 is located on chromosome 4, bp 4153027020, and the variant type is G / A; Locus 73 is located on chromosome 4, bp 4154635908, and the mutation type is C / T; Locus 74 is located on chromosome 4, bp 4157572576, and the mutation type is G / T; Locus 75 is located at 4162608762bp on chromosome 4, and the variation type is G / C; Locus 76 is located on chromosome 4, bp 4163952706, and the mutation type is T / C; Locus 77 is located at 4164312912bp on chromosome 4, and the variant type is G / A; Locus 78 is located at 4167462144bp on chromosome 4, and the mutation type is T / C; Locus 79 is located on chromosome 4, bp 4174584167, and the mutation type is T / C; Locus 80 is located at 4175575716bp on chromosome 4, and the mutation type is T / A; Locus 81 is located at 4179391103bp on chromosome 4, and the variant type is A / G; Locus 82 is located on chromosome 5, bp 5101002, and the mutation type is C / A; Locus 83 is located on chromosome 5, bp 54050477, and the mutation type is T / C; Locus 84 is located on chromosome 5, bp 56210415, and the mutation type is C / T; Locus 85 is located on chromosome 5, bp 57353166, and the mutation type is T / C; Locus 86 is located on chromosome 5, bp 57907806, and the mutation type is T / G; Locus 87 is located on chromosome 5, bp 58122046, and the mutation type is C / T; Locus 88 is located on chromosome 5, bp 512139653, and the variant type is A / G; Locus 89 is located on chromosome 5, bp 512139824, and the mutation type is T / C; Locus 90 is located on chromosome 5, bp 513420754, and the mutation type is T / C; Locus 91 is located at 516715793bp on chromosome 5, and the mutation type is C / T; Locus 92 is located at 521548705bp on chromosome 5, and the variant type is A / G; Locus 93 is located at 522923012bp on chromosome 5, and the mutation type is T / C; Locus 94 is located on chromosome 5, bp 524040590, and the mutation type is T / C; Locus 95 is located at 527470277bp on chromosome 5, and the mutation type is T / C; Locus 96 is located on chromosome 5, bp 530,565,269, and the variant type is A / C; Locus 97 is located on chromosome 5, bp 531991099, and the mutation type is A / T; Locus 98 is located on chromosome 5, bp 535018979, and the mutation type is G / T; Locus 99 is located at 536993723bp on chromosome 5, and the mutation type is G / T; Locus 100 is located at 537746327bp on chromosome 5, and the variation type is G / A; Locus 101 is located on chromosome 5, bp 543138430, and the mutation type is T / C; Locus 102 is located on chromosome 5, bp 543944445, and the mutation type is C / T; Locus 103 is located at 550429114bp on chromosome 5, and the mutation type is T / C; Locus 104 is located on chromosome 5, bp 561180240, and the variant type is A / G; Locus 105 is located at 565131503bp on chromosome 5, and the variant type is G / A; Locus 106 is located on chromosome 5, bp 570663061, and the mutation type is A / T; Locus 107 is located on chromosome 5, bp 5144968891, and the mutation type is C / T; Locus 108 is located on chromosome 5, bp 5144969368, and the mutation type is T / A; Locus 109 is located on chromosome 5, bp 5155396989, and the variant type is A / C; Locus 110 is located on chromosome 5, bp 5161684131, and the variant type is C / A; Locus 111 is located on chromosome 5, bp 5161685301, and the mutation type is T / C; Locus 112 is located on chromosome 5, bp 5164032398, and the mutation type is A / T; Locus 113 is located on chromosome 5, bp 5164856997, and the variant type is A / G; Locus 114 is located on chromosome 6, bp 6778804, and the mutation type is T / C; Locus 115 is located on chromosome 6, bp 62344276, and the variant type is G / A; Locus 116 is located on chromosome 6, bp 63,607,324, and the variant type is G / A; Locus 117 is located on chromosome 6, bp 69812751, and the mutation type is C / G; Locus 118 is located on chromosome 6, bp 615808467, and the mutation type is C / T; Locus 119 is located on chromosome 6, bp 617634309, and the variant type is G / A; Locus 120 is located on chromosome 6, bp 622461159, and the mutation type is A / T; Locus 121 is located on chromosome 6, bp 626460149, and the variant type is G / A; Locus 122 is located on chromosome 6, bp 627819611, and the mutation type is T / C; Locus 123 is located on chromosome 6, bp 636016335, and the mutation type is G / T; Locus 124 is located on chromosome 6, bp 6142497880, and the variant type is C / A; Locus 125 is located on chromosome 6, bp 6142498639, and the mutation type is G / T; Locus 126 is located on chromosome 6, bp 6143663591, and the variant type is A / G; Locus 127 is located on chromosome 6, bp 6145585715, and the variant type is A / C; Locus 128 is located on chromosome 6, bp 6149622668, and the variant type is G / A; Locus 129 is located on chromosome 6, bp 6157761880, and the variant type is C / G; Locus 130 is located on chromosome 6, bp 6170724270, and the variation type is C / G; Locus 131 is located on chromosome 6, bp 6170763361, and the variant type is A / G; Locus 132 is located on chromosome 7, bp 71710306, and the mutation type is T / C; Locus 133 is located on chromosome 7, bp 73,264,083, and the mutation type is C / G; Locus 134 is located on chromosome 7, bp 77,548,057, and the variant type is A / C; Locus 135 is located on chromosome 7, bp 77750449, and the mutation type is T / A; Locus 136 is located at 712649262bp on chromosome 7, and the mutation type is T / A; Locus 137 is located on chromosome 7, bp 712909310, and the variant type is A / G; Locus 138 is located on chromosome 7 at bp 712989315, and the mutation type is C / G; Locus 139 is located on chromosome 7, bp 713199095, and the mutation type is T / C; Locus 140 is located on chromosome 7, bp 714493374, and the mutation type is C / G; Locus 141 is located on chromosome 7, bp 718532969, and the variant type is C / G; Locus 142 is located on chromosome 7, bp 723461275, and the mutation type is C / T; Locus 143 is located on chromosome 7, bp 729251772, and the mutation type is C / T; Locus 144 is located on chromosome 7, bp 737148816, and the mutation type is C / T; Locus 145 is located on chromosome 7, bp 747094940, and the mutation type is T / C; Locus 146 is located on chromosome 7, bp 751,336,679, and the variant type is C / A; Locus 147 is located on chromosome 7, bp 7162732167, and the variant type is A / G; Locus 148 is located on chromosome 8, bp 81371158, and the variant type is A / G; Locus 149 is located on chromosome 8, bp 86789650, and the variant type is G / A; Locus 150 is located on chromosome 8, bp 88437771, and the mutation type is T / C; Locus 151 is located on chromosome 8, bp 814588094, and the variant type is G / A; Locus 152 is located on chromosome 8, bp 815736361, and the variant type is A / G; Locus 153 is located on chromosome 8 at bp 825810325, and the variant type is G / C; Locus 154 is located on chromosome 8, bp 826325818, and the mutation type is T / G; Locus 155 is located on chromosome 8, bp 837475933, and the mutation type is T / C; Locus 156 is located on chromosome 8, bp 874738903, and the variant type is A / G; Locus 157 is located on chromosome 8, bp 8138002896, and the mutation type is C / T; Locus 158 is located on chromosome 8, bp 8142021696, and the variant type is C / A; Locus 159 is located on chromosome 8, bp 8145208971, and the mutation type is C / T; Locus 160 is located on chromosome 8, bp 8146286654, and the variant type is A / G; Locus 161 is located on chromosome 8, bp 8150404881, and the mutation type is T / A; Locus 162 is located on chromosome 8, bp 8151594514, and the mutation type is T / C; Locus 163 is located on chromosome 9, bp 91438383, and the mutation type is C / T; Locus 164 is located on chromosome 9, 911449710bp, and the mutation type is T / C; Locus 165 is located on chromosome 9, bp 913479358, and the variant type is G / C; Locus 166 is located on chromosome 9, bp 913489579, and the mutation type is C / G; Locus 167 is located on chromosome 9, bp 941147490, and the variant type is A / C; Locus 168 is located on chromosome 9, 9141925303bp, and the mutation type is T / C; Locus 169 is located on chromosome 9, bp 9142775138, and the mutation type is T / C; Locus 170 is located on chromosome 9, 9147110013bp, and the mutation type is C / T; Locus 171 is located on chromosome 9, bp 9147846861, and the variant type is G / A; Locus 172 is located on chromosome 9, 9151353465bp, and the mutation type is C / T; Locus 173 is located on chromosome 9, bp 9153453729, and the mutation type is T / C; Locus 174 is located on chromosome 9, bp 9153698062, and the mutation type is T / A; Locus 175 is located on chromosome 9, bp 9154824375, and the variant type is C / G; Locus 176 is located on chromosome 9, bp 9155548198, and the variant type is A / G; Locus 177 is located on chromosome 9, bp 9155548252, and the variant type is G / A; Locus 178 is located on chromosome 9, bp 9155576669, and the variant type is C / G; Locus 179 is located on chromosome 10, bp 102302094, and the variant type is G / C; Locus 180 is located at 109432633bp on chromosome 10, and the mutation type is T / C; Locus 181 is located on chromosome 10, bp 1017416902, and the mutation type is A / T; Locus 182 is located on chromosome 10, bp 10121954875, and the variant type is G / A; Locus 183 is located on chromosome 10, bp 10130315170, and the mutation type is A / T; Locus 184 is located on chromosome 10, 10132041600bp, and the mutation type is G / T; Locus 185 is located on chromosome 10, bp 10137888718, and the mutation type is C / T; Locus 186 is located on chromosome 10, bp 10142022816, and the variant type is A / G; Locus 187 is located on chromosome 10, bp 10143214786, and the variant type is G / A; Locus 188 is located on chromosome 10, bp 10143714885, and the variant type is A / G; Locus 189 is located on chromosome 10, bp 10144007893, and the mutation type is C / T; Locus 190 is located on chromosome 11, 1155,339,362 bp, and the mutation type is G / A; Locus 191 is located on chromosome 11, 1190715627bp, and the variant type is A / G; Locus 192 is located on chromosome 11, 1194,597,680 bp, and the mutation type is T / G; Locus 193 is located on chromosome 11, 1194,839,888 bp, and the mutation type is A / T; Locus 194 is located on chromosome 11, 1195,818,114 bp, and the mutation type is T / C; Locus 195 is located at 11105015249bp on chromosome 11, and the variant type is G / A; Locus 196 is located at 11118023633bp on chromosome 11, and the variant type is C / A; Locus 197 is located at 11128125475bp on chromosome 11, and the variant type is A / G; Locus 198 is located on chromosome 11, 1133467339 bp, and the variant type is G / A; Locus 199 is located on chromosome 11, 1138493485 bp, and the mutation type is C / T; Locus 200 is located at 123684982bp on chromosome 12, and the mutation type is G / A; Locus 201 is located at 125995960bp on chromosome 12, and the mutation type is G / A; Locus 202 is located on chromosome 12, bp 126835408, and the mutation type is T / C; Locus 203 is located on chromosome 12, bp 1213550741, and the mutation type is T / C; Locus 204 is located on chromosome 12, bp 1213899205, and the variant type is A / C; Locus 205 is located on chromosome 12, bp 1214447869, and the variant type is G / A; Locus 206 is located on chromosome 12, 12107960617bp, and the mutation type is T / G; Locus 207 is located on chromosome 12, bp 12119478235, and the mutation type is T / C; Locus 208 is located on chromosome 12, 12120018613bp, and the mutation type is C / T; Locus 209 is located on chromosome 12, 12124086849bp, and the mutation type is G / T; Locus 210 is located on chromosome 12, bp 12124453241, and the variant type is G / A; Locus 211 is located on chromosome 12, 12128376164bp, and the mutation type is T / G; Locus 212 is located at 12128559402bp on chromosome 12, and the mutation type is G / A; Locus 213 is located on chromosome 12, 12128953055bp, and the mutation type is C / T; Locus 214 is located on chromosome 12, bp 12130582077, and the variant type is A / G; Locus 215 is located on chromosome 12, 12132475469bp, and the variant type is A / G; Locus 216 is located on chromosome 12, bp 12134372645, and the variant type is A / C; Locus 217 is located on chromosome 12, 12138491493 bp, and the mutation type is C / T; Locus 218 is located on chromosome 12, 12140124081bp, and the mutation type is C / G; Locus 219 is located on chromosome 12, 12140239381bp, and the mutation type is G / T; Locus 220 is located on chromosome 13, bp 1327030687, and the variant type is A / G; Locus 221 is located on chromosome 13, bp 1,334,684,042, and the mutation type is C / T; Locus 222 is located on chromosome 13, bp 1,345,894,210, and the mutation type is C / T; Locus 223 is located on chromosome 13, bp 1353577453, and the variant type is A / G; Locus 224 is located on chromosome 13, bp 1353812335, and the variant type is A / G; Locus 225 is located on chromosome 13, bp 1360489824, and the mutation type is T / G; Site 226 is located at 1367836217bp on chromosome 13, and the mutation type is C / T; Site 227 is located at 1373891012bp on chromosome 13, and the mutation type is T / C; Locus 228 is located on chromosome 13, bp 1376533867, and the variant type is A / G; Locus 229 is located on chromosome 13, bp 1383098051, and the mutation type is T / C; Locus 230 is located on chromosome 13, bp 1388748630, and the variant type is G / A; Locus 231 is located on chromosome 13, 1389057411bp, and the mutation type is C / T; Locus 232 is located on chromosome 13, bp 1390232542, and the variant type is A / G; Locus 233 is located on chromosome 13, 1390395203bp, and the variant type is A / G; Locus 234 is located on chromosome 14, bp 1465570441, and the variant type is G / A; Locus 235 is located on chromosome 14, bp 1469425337, and the variant type is A / G; Locus 236 is located at 1475905772bp on chromosome 14, and the variant type is G / A; Locus 237 is located at 1478843002bp on chromosome 14, and the mutation type is T / C; Locus 238 is located on chromosome 14, bp 1481865290, and the mutation type is C / T; Locus 239 is located on chromosome 14, bp 1481945414, and the mutation type is A / T; Locus 240 is located at 1484299928bp on chromosome 14, and the mutation type is C / T; Locus 241 is located on chromosome 14, bp 1485726361, and the variant type is G / A; Locus 242 is located at 1488144162bp on chromosome 14, and the variant type is G / A; Locus 243 is located on chromosome 14, bp 1489143409, and the variant type is G / A; Locus 244 is located on chromosome 15, bp 153,183,570, and the mutation type is C / T; Locus 245 is located at 154250994bp on chromosome 15, and the variant type is G / A; Locus 246 is located at 157960137bp on chromosome 15, and the variant type is A / G; Locus 247 is located on chromosome 15, bp 1512731347, and the variant type is A / G; Locus 248 is located on chromosome 15, bp 1515374666, and the mutation type is C / T; Locus 249 is located on chromosome 15, bp 1520140486, and the mutation type is T / G; Locus 250 is located at 1526989810bp on chromosome 15, and the mutation type is A / T; Locus 251 is located on chromosome 15, bp 1585734438, and the mutation type is C / T; Locus 252 is located at 1632401183bp on chromosome 16, and the variant type is G / A; Locus 253 is located at 1649669601bp on chromosome 16, and the mutation type is T / C; Locus 254 is located on chromosome 16, bp 1656467304, and the variant type is A / G; Locus 255 is located at 1662417000bp on chromosome 16, and the mutation type is G / T; Locus 256 is located at 1665186178bp on chromosome 16, and the variant type is A / G; Locus 257 is located on chromosome 16, bp 1667185586, and the variant type is A / G; Locus 258 is located at 1668159645bp on chromosome 16, and the mutation type is T / C; Locus 259 is located on chromosome 16, bp 1670703024, and the variant type is G / A; Site 260 is located on bp 1674142244 of chromosome 16, and the mutation type is T / G.

3. A coconut DNA fingerprint, characterized in that: The method is constructed by combining the SNP sites described in claim 1 or 2.

4. Application of the SNP locus combination described in claim 1 or 2 in constructing a coconut DNA fingerprint.

5. Application of the SNP locus combination according to claim 1 or 2 in the classification and identification of coconut germplasm resources.

6. A method for identifying coconut germplasm using the SNP locus combination according to claim 1 or 2, characterized in that: The steps include: (1) Extracting DNA from coconut samples; (2) Sequencing the genome of individual species of coconut sample DNA; (3) Genotyping was performed based on the sequencing results compared with the dwarf coconut reference genome to identify the SNP loci information of each variety; (4) Based on the genotype combination of the known fingerprint SNP loci, the similarity between the sample to be tested and the known fingerprint sample is determined, thereby evaluating the variety and source information of the coconut.

7. The method according to claim 6, characterized in that The coconut samples are fresh coconut leaves.

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