Trachinotus ovatus DNA fingerprint spectrum and construction method thereof

Abstract

The invention discloses a trachinotus ovatus DNA fingerprint spectrum and a construction method thereof, and the construction method of the trachinotus ovatus DNA fingerprint spectrum comprises the following steps: (1) sample collection and genetic typing; (2) SNP data quality control and filtering; (3) population genetic analysis; (4) screening specific SNP (Single Nucleotide Polymorphism) sites; and (5) constructing a fingerprint spectrum. The trachinotus ovatus DNA fingerprint spectrum constructed by the method has the advantages of high throughput, high resolution, stability, reliability, high practicability, capability of guiding breeding and the like.

Description

Technical Field

[0001] This invention belongs to the field of aquatic genetic breeding and molecular marker technology, specifically relating to a DNA fingerprint of the oval pomfret and its construction method, and particularly to a DNA fingerprint of the oval pomfret (Trachinotus ovatus) constructed based on whole-genome single nucleotide polymorphism (SNP) markers and its construction method. Background Technology

[0002] The oval pomfret (also known as the golden pomfret or yellow pomfret) is an important marine aquaculture fish species in the coastal areas of South my country. It is characterized by its rapid growth, delicious flesh, and strong adaptability, leading to a large-scale aquaculture industry with an annual output exceeding 240,000 tons. However, with the continuous expansion of aquaculture, the industry faces severe challenges such as mixed germplasm resources, decreased genetic diversity due to inbreeding, and the degeneration of desirable traits. Currently, the management of aquaculture populations relies heavily on morphological indicators, lacking accurate and efficient molecular methods for population differentiation and germplasm identification.

[0003] Existing research indicates that the genetic diversity of multiple farmed pomfret populations in my country is low, and the genetic differentiation among different breeding populations is unclear. While traditional morphological analysis methods can provide some distinguishing information, they are easily affected by environmental factors, resulting in insufficient accuracy and stability. Molecular marker technologies, such as SSR (simple sequence repeat) markers, although used to some extent, suffer from low throughput and limited coverage, making it difficult to construct high-resolution, systematic population genetic profiles.

[0004] Therefore, developing a high-throughput, whole-genome molecular marker system and constructing a stable and specific DNA fingerprint of the oval pomfret is of great significance for achieving precise germplasm management of this fish species, protecting genetic resources, guiding scientific breeding, and promoting sustainable industrial development. Summary of the Invention

[0005] The first objective of this invention is to provide a method for constructing a DNA fingerprint of oval pomfret, which is based on whole-genome SNP markers and can efficiently and accurately distinguish different aquaculture populations.

[0006] The present invention also aims to provide a DNA fingerprint of oval pomfret constructed by the above method.

[0007] To achieve the above objectives, the present invention adopts the following technical solution:

[0008] In a first aspect, the present invention provides a method for constructing a DNA fingerprint of oval pomfret, comprising the following steps:

[0009] (1) Sample collection and genotyping: Collect individual samples from multiple representative oval pomfret farming populations, extract genomic DNA, perform whole-genome resequencing or SNP microarray genotyping, and obtain the original SNP dataset;

[0010] (2) SNP data quality control and filtering: The original SNP data is subjected to quality control to obtain a high-quality, low-redundancy set of SNP sites;

[0011] (3) Population genetic analysis: Using the quality-controlled SNP data, principal component analysis (PCA), discriminant analysis and cluster analysis were performed on multiple aquaculture populations to assess the genetic relationships and degree of differentiation among the populations;

[0012] (4) Screening of specific SNP sites: Calculate the genetic differentiation index FST among each population and screen out specific SNP sites with high FST values ​​and population differentiation ability;

[0013] (5) Fingerprint mapping: The specific SNP sites selected in step (4) and their allele frequency distribution information in different populations are integrated to establish a DNA fingerprint database of oval pomfret.

[0014] In the above method for constructing the DNA fingerprint of oval pomfret:

[0015] Preferably, the multiple oval pomfret farming populations mentioned in step (1) include at least seven populations from Zhanjiang Hengxing HX, Zhanjiang Huifu HF, Guangxi Jinggong JG, Hainan Lanliang LL, South China Sea Breeding Base NH, Lingshui Delin DL, and Hainan Chenhai CH.

[0016] Preferably, the quality control of the original SNP data in step (2) includes: removing loci with a genotype deletion rate higher than 5%, removing loci with a minor allele frequency (MAF) lower than 0.2, and using linkage disequilibrium LD analysis to screen for loci independence. The screening parameters are: window 50 kb, step size 5, r 2 Threshold 0.2.

[0017] Preferably, in step (3), R language is used to perform principal component analysis (PCA), discriminant analysis, and cluster analysis on multiple aquaculture groups.

[0018] Preferably, in step (4), the genetic differentiation index FST between each population is calculated, and the top 1% of the FST values ​​are selected as candidates. Based on their distribution on each chromosome, specific SNPs with high FST values ​​and population differentiation ability are screened out.

[0019] Preferably, the number of specific SNP sites screened in step (4) is 270, and these sites are distributed on the 24 chromosomes of the oval pomfret.

[0020] Secondly, the present invention provides a DNA fingerprint map of oval pomfret constructed by the above method. The map contains information on at least 270 specific SNP loci. The information includes the chromosomal location, reference allele, and variant allele of each SNP locus, as well as the allele frequency in at least seven different oval pomfret farming populations, as shown in Table 2 below.

[0021] The DNA fingerprint of oval pomfret constructed in this invention can be applied in the identification of oval pomfret germplasm resources, analysis of population genetic structure, selection of parents, and protection of breed rights. Specifically, it can be applied to identify the population affiliation of oval pomfret individuals of unknown origin, assess the genetic diversity and genetic structure of oval pomfret farming populations, serve as a molecular basis for parent selection and offspring identification in oval pomfret breeding, and serve as a molecular standard for the identification of the authenticity of oval pomfret breeds or strains and the protection of intellectual property rights.

[0022] The present invention has the following beneficial effects:

[0023] (1) High throughput and high resolution: Based on whole-genome SNP markers, it has a large amount of information and can finely characterize the genetic characteristics of different populations at the molecular level. It has strong discrimination ability, with a comprehensive discrimination rate of 71.4% and a discrimination accuracy of >80% for some populations;

[0024] (2) Stable and reliable: The SNP markers used are biallelic genotypes, with good detection repeatability and are not affected by the environment and developmental stage;

[0025] (3) High practicality: The constructed DNA fingerprint can be directly used for germplasm identification, resource assessment and breeding practice, providing the industry with a standardized molecular identification system;

[0026] (4) Guiding breeding: Clear population genetic structure and specific markers can provide scientific guidance for the selection of hybrid parents and avoid inbreeding depression. Attached Figure Description

[0027] Figure 1 This is a two-dimensional scatter plot of principal component analysis (PCA) of the seven cultured populations of oval pomfret in Example 1 of this invention;

[0028] Figure 2 This is a diagram showing the discriminant analysis results of seven cultured populations of oval pomfret in an embodiment of the present invention;

[0029] Figure 3 This is a dendrogram of cluster analysis of seven cultured pomfret populations based on genetic distance in an embodiment of the present invention.

[0030] Figure 4This is a heatmap showing the distribution of 270 specific SNP loci selected in this embodiment of the invention across 24 chromosomes. Detailed Implementation

[0031] The present invention will be further described in detail below with reference to the accompanying drawings and embodiments. It should be understood that the specific embodiments described herein are for illustrative purposes only and are not intended to limit the invention. Unless otherwise specified, the reagents or materials used in the embodiments are all from commercial sources.

[0032] Example 1: Sample Collection and Genotyping

[0033] (1) Sample collection and genotyping:

[0034] Sample source: A total of 211 healthy individuals were collected from seven major oval pomfret farming companies / bases along the coast of South China (see Table 1 for details);

[0035] Table 1 Sample Information Table

[0036]

[0037] DNA extraction and sequencing: Fin rays or muscle tissue were taken from each fish, and genomic DNA was extracted using the conventional phenol-chloroform method or a commercial kit. After passing quality inspection, whole genome resequencing (average depth ≥10×) was performed. Sequence alignment and SNP calling were performed using standard procedures such as BWA and GATK to obtain SNP data in the original VCF format.

[0038] (2) SNP data quality control and screening:

[0039] The raw SNP data underwent rigorous quality control using PLINK software (v1.9). The commands and results are as follows:

[0040] Remove sites with a genotype deletion rate >5%: plink --vcf snpfilter2.vcf --geno 0.05 --autosome-num 24 --make-bed --out snpfilter41, leaving 745,387 variant sites.

[0041] Remove sites with minor allele frequency (MAF) < 0.2: plink --bfile snpfilter41 --maf0.2 --make-bed --out snpfilter42, leaving 294,857 variant sites.

[0042] Linkage disequilibrium (LD) pruning: plink --bfile snpfilter42 --indep-pairwise 505 0.2 --make-bed --out snpfilter43. After removing highly linked sites, 127,683 independent SNP sites remain for subsequent analysis.

[0043] (3) Population genetic analysis: Using 127,683 SNPs after quality control, PCA, discriminant analysis and cluster analysis were performed using tools such as R (results are shown in the figure). Figure 1-3 (As shown in the figure); the analysis showed that there was obvious genetic differentiation among the seven populations. Among them, the NH, CH and LL populations were genetically closely related, while the morphological genetic differences between the HX and DL populations, and the JG and LL populations were significant.

[0044] (4) FST calculation and specific SNP screening: The genetic differentiation index (FST) between each two populations was calculated using VCFtools or similar software; the top 1% of loci with the highest FST values ​​were selected as candidates, and their distribution on each chromosome was considered (e.g., Figure 4 As shown in the figure, 270 specific SNP loci with high population discrimination ability were finally screened out. These loci are distributed on 24 chromosomes of the oval pomfret.

[0045] (5) Fingerprint mapping: The specific SNP sites selected in step (4) and their allele frequency distribution information in different populations are integrated to establish a DNA fingerprint database of oval pomfret. The list of these sites is shown below.

[0046] The following columns are, in order: chromosome number, locus information, reference allele, variant allele, each allele and its frequency.

[0047] 19670862CTC:0.611374T:0.388626;

[0048] 112051350TCT:0.732227C:0.267773;

[0049] 112075536TAT:0.63981A:0.36019;

[0050] 112684524TAT:0.514218A:0.485782;

[0051] 113840039GAG:0.611374A:0.388626;

[0052] 115683096TAT:0.675355A:0.324645;

[0053] 116490308TGT:0.556872G:0.443128;

[0054] 118614750TAT:0.57109A:0.42891;

[0055] 122462376AGA:0.798578G:0.201422;

[0056] 123601232CTC:0.7891T:0.2109;

[0057] 124257380CTC:0.561611T:0.438389;

[0058] 125226664CTC:0.613744T:0.386256;

[0059] 132820161CAC:0.722749A:0.277251;

[0060] 134145115GAG:0.554502A:0.445498;

[0061] 134735671GCG:0.518957C:0.481043;

[0062] 137794412GCG:0.545024C:0.454976;

[0063] 139060755GAG:0.668246A:0.331754;

[0064] 139071098GTG:0.760664T:0.239336;

[0065] 139104899AGA:0.736967G:0.263033;

[0066] 139455579GAG:0.729858A:0.270142;

[0067] 2171182CTC:0.507109T:0.492891;

[0068] 2415756CTC:0.770142T:0.229858;

[0069] 25352447ACA:0.514218C:0.485782;

[0070] 26988394AGA:0.646919G:0.353081;

[0071] 29226386CGC:0.661137G:0.338863;

[0072] 29227550CTC:0.606635T:0.393365;

[0073] 29951640TAT:0.751185A:0.248815;

[0074] 212060542TAT:0.770142A:0.229858;

[0075] 214748357AGA:0.56872G:0.43128;

[0076] 214752785AGA:0.556872G:0.443128;

[0077] 217843212CTC:0.663507T:0.336493;

[0078] 218553957CTC:0.7109T:0.2891;

[0079] 220814355TCT:0.504739C:0.495261;

[0080] 221050786AGA:0.582938G:0.417062;

[0081] 223261977CAC:0.632701A:0.367299;

[0082] 223271761CGC:0.613744G:0.386256;

[0083] 223272767TCT:0.511848C:0.488152;

[0084] 231984319GTG:0.765403T:0.234597;

[0085] 233732183CTC:0.661137T:0.338863;

[0086] 235421679GTG:0.763033T:0.236967;

[0087] 33241081GAG:0.507109A:0.492891;

[0088] 34007906GAG:0.670616A:0.329384;

[0089] 36896208TGT:0.708531G:0.291469;

[0090] 36962383TCT:0.542654C:0.457346;

[0091] 37985245ATA:0.748815T:0.251185;

[0092] 310119694ACA:0.770142C:0.229858;

[0093] 319548238AGA:0.739336G:0.260664;

[0094] 325078659GAG:0.727488A:0.272512;

[0095] 327885968GAG:0.708531A:0.291469;

[0096] 330250115AGA:0.777251G:0.222749;

[0097] 335017373CTC:0.78673T:0.21327;

[0098] 43004966AGA:0.561611G:0.438389;

[0099] 43107148TAT:0.718009A:0.281991;

[0100] 43303699TGT:0.718009G:0.281991;

[0101] 43795954CTC:0.732227T:0.267773;

[0102] 48720847AGA:0.523697G:0.476303;

[0103] 49204607TCT:0.580569C:0.419431;

[0104] 49503100GCG:0.620853C:0.379147;

[0105] 49745119CGC:0.696682G:0.303318;

[0106] 410284810AGA:0.758294G:0.241706;

[0107] 414690047CAC:0.741706A:0.258294;

[0108] 414733008ACA:0.684834C:0.315166;

[0109] 414798807CTC:0.646919T:0.353081;

[0110] 417646482CTC:0.720379T:0.279621;

[0111] 419114126GAG:0.720379A:0.279621;

[0112] 426312523GTG:0.611374T:0.388626;

[0113] 427043138ATA:0.680095T:0.319905;

[0114] 427711343TCT:0.654028C:0.345972;

[0115] 429001962AGA:0.646919G:0.353081;

[0116] 430189771CTC:0.632701T:0.367299;

[0117] 433024982CAC:0.646919A:0.353081;

[0118] 435137111TGT:0.753555G:0.246445;

[0119] 51451544TGT:0.781991G:0.218009;

[0120] 53338584ATA:0.64455T:0.35545;

[0121] 55711328ACA:0.672986C:0.327014;

[0122] 56385664GAG:0.748815A:0.251185;

[0123] 56784031TCT:0.767773C:0.232227;

[0124] 57740278GAG:0.64218A:0.35782;

[0125] 59274119GAG:0.630332A:0.369668;

[0126] 510607390GAG:0.767773A:0.232227;

[0127] 515391598TAT:0.751185A:0.248815;

[0128] 517312548CAC:0.578199A:0.421801;

[0129] 62977335TCT:0.751185C:0.248815;

[0130] 62984649TCT:0.753555C:0.246445;

[0131] 68016523TAT:0.701422A:0.298578;

[0132] 610874553ACA:0.632701C:0.367299;

[0133] 610966220CAC:0.668246A:0.331754;

[0134] 613548476AGA:0.64218G:0.35782;

[0135] 618862407GTG:0.779621T:0.220379;

[0136] 619213930AGA:0.675355G:0.324645;

[0137] 619415876ACA:0.630332C:0.369668;

[0138] 621045504CTC:0.706161T:0.293839;

[0139] 623494258GAG:0.7109A:0.2891;

[0140] 71336489TCT:0.526066C:0.473934;

[0141] 72512748CTC:0.71564T:0.28436;

[0142] 76385664TCT:0.71327C:0.28673;

[0143] 712051350GAG:0.516588A:0.483412;

[0144] 712193621GAG:0.651659A:0.348341;

[0145] 712389974TAT:0.7891A:0.2109;

[0146] 712831511ATA:0.767773T:0.232227;

[0147] 722076295CTC:0.670616T:0.329384;

[0148] 722243344AGA:0.663507G:0.336493;

[0149] 723168080GTG:0.722749T:0.277251;

[0150] 724095724CGC:0.592417G:0.407583;

[0151] 724778318ATA:0.755924T:0.244076;

[0152] 726520846ATA:0.772512T:0.227488;

[0153] 726540747CGC:0.753555G:0.246445;

[0154] 81931639TCT:0.699052C:0.300948;

[0155] 83162728ACA:0.708531C:0.291469;

[0156] 84545290CAC:0.620853A:0.379147;

[0157] 85343265TCT:0.592417C:0.407583;

[0158] 87503371TAT:0.563981A:0.436019;

[0159] 88207242ACA:0.7891C:0.2109;

[0160] 88253175ATA:0.654028T:0.345972;

[0161] 89214974GAG:0.526066A:0.473934;

[0162] 810743516GCG:0.663507C:0.336493;

[0163] 811875555TCT:0.535545C:0.464455;

[0164] 812242711AGA:0.620853G:0.379147;

[0165] 812619843CTC:0.753555T:0.246445;

[0166] 813227482GCG:0.552133C:0.447867;

[0167] 816458215TCT:0.734597C:0.265403;

[0168] 816888437CAC:0.732227A:0.267773;

[0169] 817636030AGA:0.734597G:0.265403;

[0170] 820625304ATA:0.732227T:0.267773;

[0171] 824084305CAC:0.696682A:0.303318;

[0172] 828043871ACA:0.611374C:0.388626;

[0173] 9789603GAG:0.675355A:0.324645;

[0174] 9789748TCT:0.528436C:0.471564;

[0175] 91517251GAG:0.718009A:0.281991;

[0176] 92283832CTC:0.635071T:0.364929;

[0177] 92999489GAG:0.521327A:0.478673;

[0178] 94078272TCT:0.677725C:0.322275;

[0179] 94339308TGT:0.632701G:0.367299;

[0180] 913821847AGA:0.779621G:0.220379;

[0181] 914093556TCT:0.575829C:0.424171;

[0182] 917147355GAG:0.630332A:0.369668;

[0183] 917561676GAG:0.632701A:0.367299;

[0184] 917641966TAT:0.696682A:0.303318;

[0185] 925013878CTC:0.718009T:0.281991;

[0186] 926879284CTC:0.547393T:0.452607;

[0187] 926914799AGA:0.7109G:0.2891;

[0188] 927009825CAC:0.637441A:0.362559;

[0189] 928478239TCT:0.675355C:0.324645;

[0190] 102019607AGA:0.635071G:0.364929;

[0191] 103647006AGA:0.537915G:0.462085;

[0192] 105817713TCT:0.651659C:0.348341;

[0193] 109580638GAG:0.526066A:0.473934;

[0194] 1010878156ATA:0.736967T:0.263033;

[0195] 1010921934CAC:0.575829A:0.424171;

[0196] 1010960002CAC:0.64455A:0.35545;

[0197] 1015385855GAG:0.739336A:0.260664;

[0198] 1019836288ACA:0.654028C:0.345972;

[0199] 1020673676GAG:0.654028A:0.345972;

[0200] 1021923422CTC:0.646919T:0.353081;

[0201] 117755004GAG:0.507109A:0.492891;

[0202] 118301224CTC:0.727488T:0.272512;

[0203] 1111983530CTC:0.684834T:0.315166;

[0204] 1113932784ATA:0.552133T:0.447867;

[0205] 1114928776TCT:0.632701C:0.367299;

[0206] 1115064745TGT:0.755924G:0.244076;

[0207] 1115296343ACA:0.699052C:0.300948;

[0208] 1119873476GAG:0.665877A:0.334123;

[0209] 1127122219ACA:0.514218C:0.485782;

[0210] 12694705TGT:0.528436G:0.471564;

[0211] 12738069CTC:0.540284T:0.459716;

[0212] 121918845TCT:0.71564C:0.28436;

[0213] 126666770GAG:0.630332A:0.369668;

[0214] 1212970631TAT:0.765403A:0.234597;

[0215] 1214496372AGA:0.658768G:0.341232;

[0216] 1218456580TCT:0.720379C:0.279621;

[0217] 1223178368ACA:0.727488C:0.272512;

[0218] 1224351814ATA:0.708531T:0.291469;

[0219] 1225440746TGT:0.675355G:0.324645;

[0220] 1226390293AGA:0.542654G:0.457346;

[0221] 133649141TCT:0.774882C:0.225118;

[0222] 138993900TCT:0.781991C:0.218009;

[0223] 1313171625GAG:0.734597A:0.265403;

[0224] 1314149166GAG:0.635071A:0.364929;

[0225] 1320656024TCT:0.627962C:0.372038;

[0226] 1322790071TGT:0.528436G:0.471564;

[0227] 1324443473CTC:0.552133T:0.447867;

[0228] 14221352CAC:0.50237A:0.49763;

[0229] 145648199TCT:0.504739C:0.495261;

[0230] 145999906CTC:0.540284T:0.459716;

[0231] 146466340ACA:0.518957C:0.481043;

[0232] 147114588CTC:0.71327T:0.28673;

[0233] 147463626ATA:0.549763T:0.450237;

[0234] 147892576ATA:0.57109T:0.42891;

[0235] 1412831511ACA:0.777251C:0.222749;

[0236] 1418177501AGA:0.656398G:0.343602;

[0237] 1420695003TCT:0.680095C:0.319905;

[0238] 158128838CAC:0.625592A:0.374408;

[0239] 158702995CTC:0.658768T:0.341232;

[0240] 1515284776CTC:0.601896T:0.398104;

[0241] 1519557555AGA:0.706161G:0.293839;

[0242] 1521657168CAC:0.706161A:0.293839;

[0243] 1522876890GAG:0.504739A:0.495261;

[0244] 1523043355GTG:0.533175T:0.466825;

[0245] 1610865399AGA:0.566351G:0.433649;

[0246] 1611570318ATA:0.763033T:0.236967;

[0247] 1611608306AGA:0.796209G:0.203791;

[0248] 1615018150GTG:0.613744T:0.386256;

[0249] 1615363580GCG:0.542654C:0.457346;

[0250] 1615955888TCT:0.696682C:0.303318;

[0251] 1619097104GTG:0.677725T:0.322275;

[0252] 1619395259ACA:0.78673C:0.21327;

[0253] 17142180CAC:0.791469A:0.208531;

[0254] 171823899CGC:0.535545G:0.464455;

[0255] 174408588CTC:0.658768T:0.341232;

[0256] 174896062AGA:0.559242G:0.440758;

[0257] 179019765GCG:0.556872C:0.443128;

[0258] 18359363CTC:0.668246T:0.331754;

[0259] 185868315TGT:0.63981G:0.36019;

[0260] 189059640ACA:0.630332C:0.369668;

[0261] 1810818990GTG:0.616114T:0.383886;

[0262] 1813205608TCT:0.78673C:0.21327;

[0263] 1813606422AGA:0.511848G:0.488152;

[0264] 1814305983CTC:0.5T:0.5;

[0265] 1814969120TAT:0.760664A:0.239336;

[0266] 1816024649GTG:0.665877T:0.334123;

[0267] 1816942470ATA:0.507109T:0.492891;

[0268] 194979350CTC:0.601896T:0.398104;

[0269] 198637542GAG:0.566351A:0.433649;

[0270] 199339531CAC:0.57109A:0.42891;

[0271] 1911057525TCT:0.680095C:0.319905;

[0272] 1911114596TCT:0.575829C:0.424171;

[0273] 1911570645GTG:0.760664T:0.239336;

[0274] 1912667273CTC:0.78436T:0.21564;

[0275] 1913926779TAT:0.535545A:0.464455;

[0276] 1915962030TAT:0.637441A:0.362559;

[0277] 1915965961CTC:0.57109T:0.42891;

[0278] 201912848GAG:0.637441A:0.362559;

[0279] 201921600AGA:0.63981G:0.36019;

[0280] 201925571ACA:0.63981C:0.36019;

[0281] 203000908ATA:0.613744T:0.386256;

[0282] 204226462CTC:0.632701T:0.367299;

[0283] 204665076ATA:0.71564T:0.28436;

[0284] 206145867TAT:0.772512A:0.227488;

[0285] 209826551TCT:0.509479C:0.490521;

[0286] 2011519079TAT:0.741706A:0.258294;

[0287] 2016835634GAG:0.722749A:0.277251;

[0288] 2017900822GTG:0.611374T:0.388626;

[0289] 213335965CTC:0.696682T:0.303318;

[0290] 214319323CTC:0.78673T:0.21327;

[0291] 214516479CTC:0.755924T:0.244076;

[0292] 218902040AGA:0.661137G:0.338863;

[0293] 219361370AGA:0.798578G:0.201422;

[0294] 2113659120AGA:0.521327G:0.478673;

[0295] 2115316198TCT:0.646919C:0.353081;

[0296] 2115971204CTC:0.672986T:0.327014;

[0297] 2115992633TCT:0.736967C:0.263033;

[0298] 2116572497ATA:0.523697T:0.476303;

[0299] 2118232370TAT:0.632701A:0.367299;

[0300] 22837917CTC:0.535545T:0.464455;

[0301] 22843577CTC:0.7109T:0.2891;

[0302] 22845220CTC:0.542654T:0.457346;

[0303] 22851382GAG:0.526066A:0.473934;

[0304] 224640919CTC:0.727488T:0.272512;

[0305] 227582664CTC:0.675355T:0.324645;

[0306] 227596087CTC:0.793839T:0.206161;

[0307] 2213758860AGA:0.680095G:0.319905;

[0308] 2218315709TCT:0.530806C:0.469194;

[0309] 231856898AGA:0.751185G:0.248815;

[0310] 233004966GAG:0.746445A:0.253555;

[0311] 234798746TCT:0.78673C:0.21327;

[0312] 235740044TGT:0.618483G:0.381517;

[0313] 239156082GAG:0.751185A:0.248815;

[0314] 241164599GTG:0.656398T:0.343602;

[0315] 2414902176CTC:0.753555T:0.246445;

[0316] 2416773637TCT:0.684834C:0.315166.

[0317] The DNA fingerprinting of oval pomfret constructed in this invention can distinguish between different populations and can also be used for the following purposes, such as: Germplasm identification: For an oval pomfret sample of unknown origin, targeted sequencing or genotyping is performed on 270 loci in the fingerprinting, and its allele frequency spectrum is compared with seven reference populations in a database. Through discriminant analysis or similarity calculation, it can be determined which aquaculture population it most likely belongs to. Genetic diversity assessment: Parameters such as observed heterozygosity (Ho) and expected heterozygosity (He) of a sample from a certain aquaculture population are calculated at the above 270 loci or all quality control loci to quantitatively assess its genetic diversity level. Breeding assistance: In hybridization breeding, populations with large differences in fingerprinting can be selected as parents to obtain greater hybrid vigor. It can also be used to identify the authenticity of hybrid offspring.

[0318] Therefore, this invention successfully constructed the first high-resolution DNA fingerprint of oval pomfret based on genome-wide SNPs. This fingerprint is highly systematic and accurate, providing an indispensable molecular tool for germplasm resource management, breeding, and industrial standardization of oval pomfret.

[0319] The above embodiments are only used to illustrate the present invention, and the scope of protection of the present invention is not limited to the above embodiments. Those skilled in the art can achieve the purpose of the present invention based on the above disclosure. Any improvements and modifications made based on the concept of the present invention fall within the scope of protection of the present invention, the specific scope of protection being as described in the claims.

Claims

1. A method for constructing a DNA fingerprint of oval pomfret, characterized in that, Includes the following steps: (1) Sample collection and genotyping: Collect individual samples from multiple representative oval pomfret farming populations, extract genomic DNA, perform whole-genome resequencing or SNP microarray genotyping, and obtain the original SNP dataset; (2) SNP data quality control and filtering: The original SNP data is subjected to quality control to obtain a high-quality, low-redundancy set of SNP sites; (3) Population genetic analysis: Using the quality-controlled SNP data, principal component analysis (PCA), discriminant analysis and cluster analysis were performed on multiple aquaculture populations to assess the genetic relationships and degree of differentiation among the populations; (4) Screening of specific SNP sites: Calculate the genetic differentiation index FST among each population and screen out specific SNP sites with high FST values ​​and population differentiation ability; (5) Fingerprint mapping: The specific SNP sites selected in step (4) and their allele frequency distribution information in different populations are integrated to establish a DNA fingerprint database of oval pomfret.

2. The method for constructing a DNA fingerprint of oval pomfret according to claim 1, characterized in that, The multiple pomfret farming populations mentioned in step (1) include at least seven populations from Zhanjiang Hengxing HX, Zhanjiang Huifu HF, Guangxi Jinggong JG, Hainan Lanliang LL, South China Sea Breeding Base NH, Lingshui Delin DL, and Hainan Chenhai CH.

3. The method for constructing a DNA fingerprint of oval pomfret according to claim 1, characterized in that, Step (2) involves quality control of the raw SNP data, including removing loci with a genotype deletion rate higher than 5%, removing loci with a minor allele frequency (MAF) lower than 0.2, and using linkage disequilibrium LD analysis to screen for loci independence. The screening parameters are: window size 50kb, step size 5, r 2 Threshold 0.

2.

4. The method for constructing a DNA fingerprint of oval pomfret according to claim 1, characterized in that, In step (3), R language is used to perform principal component analysis (PCA), discriminant analysis, and cluster analysis on multiple aquaculture populations.

5. The method for constructing a DNA fingerprint of oval pomfret according to claim 1, characterized in that, In step (4), the genetic differentiation index FST between each population is calculated. The top 1% of FST values ​​are selected as candidates, and their distribution on each chromosome is combined to screen out specific SNPs with high FST values ​​and population differentiation capabilities.

6. The method for constructing a DNA fingerprint of oval pomfret according to claim 1, characterized in that, The number of specific SNP sites screened in step (4) is 270, which are distributed on the 24 chromosomes of the oval pomfret.

7. A DNA fingerprint of the oval pomfret constructed using the method of any one of claims 1-6, characterized in that, The map contains information on at least 270 specific SNP loci, including the chromosomal location, reference allele, and variant allele of each SNP locus, as well as the allele frequencies in at least seven different farmed pomfret populations, as shown in Table 2 of the specification.

Images