CN112501317B - SNP (Single nucleotide polymorphism) markers applicable to Cryptocaryon irritans resistant breeding of large yellow croakers - Google Patents
SNP (Single nucleotide polymorphism) markers applicable to Cryptocaryon irritans resistant breeding of large yellow croakers Download PDFInfo
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Abstract
A group of SNP markers which can be applied to the breeding of Cryptocaryon irritans-resistant large yellow croakers relates to the field of molecular assisted selective breeding. Discloses its physical location on the large yellow croaker genome (BioProject: PRJNA 505758). Based on the whole genome association analysis, a group of (670) SNP molecular marker sets which can ensure that the model prediction accuracy reaches the best are found through the whole genome selection model optimization, and the cryptocaryon irritans resistant offspring cultivated by utilizing the group of SNP markers shows good insect resistance in the virus attack verification. The molecular marker related to cryptocaryon irritans resistance of the large yellow croaker can be quickly applied to the breeding industry, high-resistance offspring can be cultivated within a short time, economic loss of the cryptocaryon irritans to the large yellow croaker breeding industry is reduced, and the molecular marker has wide application prospect and commercial value.
Description
Technical Field
The invention relates to the field of molecular assisted selective breeding, in particular to the field of insect-resistant breeding of large yellow croakers by utilizing a group of SNP molecular markers associated with cryptocaryon irritans resistance of the large yellow croakers.
Background
The large yellow croaker (Pseudosciaenae) belongs to Perciformes, scienidae (Scienidae) and Pseudosciaena crocea (Larimichthys) and is distributed in the southwest sea area of the Pacific, is an important marine culture economic fish species in China, is also a marine culture variety with the highest annual yield, and brings huge economic benefits to southeast coastal areas such as Fujian and the like. In recent years, due to the rapid development of the large yellow croaker breeding industry, the improvement of breeding density, a large amount of residual baits and other factors, the water environment of coastal gulf is deteriorated, and a plurality of diseases are brought along with the deterioration. Among all diseases, especially ichthyophthiriasis is the most dangerous, and the pathogenic microorganism causing ichthyophthiriasis belongs to a unicellular marine ciliate, cryptocaryon irritans (Cryptocaryon irritans). Cryptocaryon irritans parasitize on the body surface, gill, eyes and the like of the fish, so that dyspnea can be caused, and a large amount of death of a host can be caused; the shedding of the trophozoite can cause skin damage, cause secondary infection of bacteria, fungi and the like, and also cause mass death of the host. The ichthyophthiriasis causes huge economic loss to the large yellow croaker breeding industry, and the loss is billions of yuan per year according to statistics. Until now, no prevention and treatment measures can be effectively, economically and environmentally applied to the breeding industry, and the promotion of the cryptocaryon irritans resistance of the large yellow croakers through genetic breeding has great application prospect, so that the economic loss of the cryptocaryon irritans to the large yellow croakers breeding industry can be fundamentally reduced.
Genetic breeding has a long development history, and with the development of modern biotechnology, breeding technology is also undergoing deep revolution and continuous innovation, and high genetic gain can be obtained within several generations. With the discovery and widespread use of single nucleotide polymorphism markers (SNPs), breeding technologies have revolutionized the development of molecular assisted selection breeding (MAS), and with the leap forward of the ability of computers to process large data, genome-wide selection technologies (GS) have been developed that can use SNP markers covering the entire genome to breed. The molecular information is utilized for auxiliary breeding, the molecular information is widely applied to the field of disease-resistant genetic breeding of plants and livestock, but the molecular information is rarely used successfully in disease-resistant breeding of aquatic animals. The SNP marker set provided by the invention has extremely important commercial value in the Cryptocaryon irritans-resistant breeding industry of large yellow croakers, and the application process can be popularized in a large-scale demonstration manner.
Disclosure of Invention
The invention aims to provide a group of SNP markers which can be applied to the Cryptocaryon irritans resistance breeding of large yellow croakers, and the SNP markers are applied to the Cryptocaryon irritans resistance breeding industry of large yellow croakers.
In order to achieve the purpose of the invention, 670 SNP marker information for breeding large yellow croaker against cryptocaryon irritans is shown in Table 1, and the detailed steps are obtained as follows:
1) Performing large-scale cryptocaryon irritans challenge experiment on large yellow croakers, selecting death samples and survival samples in the challenge experiment, performing genome DNA extraction (phenol chloroform method), and detecting the quality of the extracted DNA by using agarose gel electrophoresis;
2) Performing simplified genome sequencing on the sample, parting by using software GATK or stacks2, performing quality control filtration on an original parting result by using software such as plink, beagle, haploview and the like, filling missing genotypes and the like to obtain a final parting result;
3) Using a second classification phenotype record, combining genotype results, performing whole genome association analysis (GWAS) by using an R language gaston package, and ranking all markers according to significance from large to small (P value from small to large);
4) And (3) judging the optimal marker combination by using a full genome model (GS) in combination with 5-fold cross validation, wherein the specific steps are that according to the ranking, the number of 10 SNPs is taken as an interval, the markers arranged in the front are gradually increased, and the prediction accuracy of the GS model under each marker density is calculated. The combination of the corresponding markers when the prediction accuracy is the highest, i.e. the best marker set.
TABLE 1
Note: (1) the specific meaning of English header, CHR (chromosome) stands for chromosome number; SNP stands for single nucleotide polymorphism marker number; BP represents the physical location of the SNP marker on the chromosome; a1 represents the first allele of the SNP marker; a2 represents a second allele of the SNP marker; p represents the significance of the SNP marker in the genome-wide association analysis; OR represents the ratio of the gene frequency of the allele A1 in the surviving individuals to the gene frequency in the dead individuals in the binary traits.
(2) Chromosome 25 is not a true stain, but rather binds contigs and scaffolds fragments that have not been assembled in 24 chromosomes.
The 670 SNP markers have relevance to the cryptocaryon irritans resistance phenotype traits of the large yellow croakers.
And calculating a polygenic risk score (prs) of the candidate parent according to the SNP marker information, and selecting smaller prs from the candidate parent at a certain selection strength according to the score to breed, wherein the offspring has higher cryptocaryon irritans resistance.
The 670 SNP markers are applied to the Cryptocaryon irritans-resistant breeding industry of large yellow croakers, and the application comprises the following steps:
1) Extracting the genome DNA of the candidate parent, and detecting the extraction quality of the DNA by using agarose gel electrophoresis;
in step 1), the candidate parent genome DNA extraction can adopt any DNA extraction method such as phenol chloroform method, kit and the like.
2) Genotyping 670 SNP markers;
in step 2), genotyping the 670 SNP markers may take any form of sequencing technique, including one of simplified genome sequencing, whole genome re-sequencing, gene chips, multiplex PCR, etc.
3) Calculating prs of candidate parents by using open source software PRSice-2 software according to the SNP marker typing result of the step 2) (at least ensuring that more than 300 molecular markers in 670 molecular markers are successfully typed), and combining 670 SNP marker information;
4) Selecting individuals with the prs values of the candidate parents ranked in front (the prs values are ranked from small to large) as parent fishes according to certain selection strength;
5) Breeding the parent fish selected in the step 4), wherein offspring is an individual with high resistance to cryptocaryon irritans, and performing cryptocaryon irritans counteracting verification on the high-resistance offspring.
The 670 molecular marker information provided by the invention can be quickly applied to the cryptocaryon irritans-resistant breeding industry of large yellow croakers, and considerable genetic gain can be obtained for one generation. By means of the provided marking information and the application process, the invention at least has the following advantages and beneficial effects:
1) The invention firstly utilizes the whole genome association analysis to obtain a group of SNP markers related to the Cryptocaryon irritans phenotypic traits of the large yellow croakers.
2) 670 marker information provided by the invention can be quickly applied to selecting candidate parents with potential cryptocaryon irritans strong resistance.
3) The method for breeding the new cryptocaryon irritans-resistant line of the large yellow croaker is an efficient and convenient selective breeding method, can quickly increase genetic gain within one generation, also provides a reference case for disease-resistant breeding of other aquatic animals, and accelerates the commercialization process of the disease-resistant breeding.
Drawings
Figure 1 is a manhattan plot of the GWAS results in step 3) of example 1 according to the present invention.
FIG. 2 is a graph showing the results of determining the optimal SNP set in step 4) in example 1 according to the present invention. In fig. 2, the abscissa indicates the number of markers sorted by the significance P value, the ordinate in the upper graph in the figure represents the degree of model fitting (Goodness of Fit), and the ordinate in the lower graph indicates the model prediction accuracy (prediction). The results show that the prediction accuracy of the 5-fold cross validation of the model reaches the highest under the first 670 marks.
Fig. 3 is a graph of the experimental results of the toxicity-counteracting verification of the new insect-resistant strain of large yellow croaker bred in example 2 according to the present invention. The results show that the new insect-resistant strain has statistically significantly higher insect resistance than the two control groups.
Detailed Description
The following examples will further illustrate the present invention with reference to the accompanying drawings.
Example 1 determination of 670 SNP sets provided by the invention
1) Large-scale large yellow croaker cryptocaryon irritans challenge experiments were performed in month 6, and the specifications of the experimental fish were 6 months old (body weight: 6.80 ± 2.52g, body length: 7.8 +/-1.1 cm), and 240 death samples and 240 survival samples of the challenge experiment are selected for genome DNA extraction (phenol chloroform method).
2) Performing simplified genome sequencing on the sample, using a ddRAD library building strategy, using bwa and samtools to perform genome comparison on large yellow croakers of original reads; genotyping using stacks 2; quality control is carried out on the original typing result by using plink, wherein the quality control parameters are that the minimum allele frequency is more than 0.05, the detection rate of single SNP locus is more than 0.9, and the detection rate of all SNP loci of a single individual is more than 0.9; filling up the deleted genotypes by using beagle software; tag SNPs (SNPs which can represent certain genomic regions) are searched by using haploview software, so that the correlation among SNP sites is reduced, and the multiple collinearity of a subsequent GS model is reduced. Finally, 12385 SNP markers with high quality are obtained.
3) Using the two-classification phenotype records, in combination with the genotype results, the R language gaston package was used to perform genome wide association analysis (GWAS), and all markers were ranked from large to small in significance (P values from small to large), fig. 1 is a manhattan plot display of the GWAS results.
4) Establishing a full genome model (GS) by using an R language BGLR package, judging the optimal marker combination by combining 5-fold cross validation, and specifically comprising the steps of gradually increasing the markers arranged in the front by taking 10 SNP (single nucleotide polymorphism) quantities as intervals according to the ranking, and calculating the prediction accuracy of the GS model under each marker density. As can be seen from FIG. 2, the marker combinations corresponding to the highest prediction accuracy are the first 670 SNP markers ranked in P value, and these markers are the 670 SNP marker combinations provided by the invention.
Example 2 application of the provided SNP marker information to pest-resistant breeding of large yellow croakers
1) And selecting about 500 tail and 2-year-old robust large yellow croakers as candidate parent groups in the net cage culture area of all Australia in Fujiangningde Sandu in 12 months in the second year, shearing fin lines of the candidate parent groups, and driving electronic marks into the fin lines. Extracting the genome DNA of the candidate parent, and adopting a phenol chloroform method.
2) Candidate parents were pooled and genotyped by ddRAD, the same procedure as described in step 2) of example 1. The genotype file with the 670 molecular markers was generated using plink software.
3) According to the candidate parent SNP marker typing result of the step 2), combining the 670 SNP marker information, calculating prs of the candidate parent by using open source software PRSice-2 software, wherein the calculation codes under a Linux system are as follows:
the train base document is 670 marker information provided by the invention, and has 6 columns, wherein each column respectively represents a chromosome number, an SNP number, a physical position of the SNP, a P value obtained by an allele 1, an allele 2 and a GWAS result and an OR value specific to a binary trait. target is the prefix of the candidate parent genotype file, and needs to contain three files in the plink software format, target. After the program is run, a file with a suffix name of prs is generated, and the file contains the estimated prs value of the candidate parent.
4) And sorting the prs values of the candidate parents from small to large, selecting 47 individuals with the front rows from 491 successfully typed candidate parents as the parents of the resistant offspring, and thus selecting the parents with the strength of about 0.1. The female-male ratio of 47 selected parents is about 2: 1.
5) Breeding the selected parents to obtain offspring, namely the individuals with high resistance to cryptocaryon irritans, namely the insect-resistant lines, breeding the rest candidate parents in the same way, using the offspring as a control group 1, and using the commercial offspring cultured in the same period as a control group 2.
6) In 6 th of the third year, cryptocaryon irritans infection experiments are performed on the insect-resistant line, the control group 1 and the control group 2, survival analysis is performed by using the R language survivval bag, and the result shows that the insect-resistant line has statistically significant high insect resistance compared with the two control groups, and the result is shown in figure 3. Through the toxicity attacking and verifying experiment results, the effectiveness of 670 SNP markers provided by the invention is further illustrated, and the usability and operability of the cryptocaryon irritans resistance of large yellow croakers are rapidly improved in a short period.
The invention discloses the physical position of the gene on the large yellow croaker genome (BioProject: PRJNA 505758) for the first time. The invention is based on the whole genome association analysis, and a group of (670) SNP molecular marker sets which can lead the model prediction accuracy to reach the best are found through the whole genome selection model optimization, and the cryptocaryon irritans resistant offspring cultured by utilizing the group of SNP markers shows good insect resistance in the virus attack verification. The molecular marker related to cryptocaryon irritans resistance of large yellow croakers, provided by the invention, can be quickly applied to the breeding industry, high-resistance offspring can be cultivated within a short time, economic loss of cryptocaryon irritans to the large yellow croaker breeding industry is reduced, and the molecular marker has wide application prospect and commercial value.
Claims (5)
1. A group of SNP markers which can be applied to breeding of large yellow croaker against cryptocaryon irritans, 670 SNP marker information for breeding of large yellow croaker against cryptocaryon irritans are shown in Table 1; the 670 SNP markers have relevance to the cryptocaryon irritans resistance phenotype traits of the large yellow croakers;
the 670 SNP markers are used for breeding the large yellow croaker against the cryptocaryon irritans, and comprise the following steps:
1) Extracting the genome DNA of the candidate parent, and detecting the extraction quality of the DNA by using agarose gel electrophoresis;
2) Genotyping 670 SNP markers;
3) Calculating prs of candidate parents by using open source software PRSice-2 according to the SNP marker typing result of the step 2) and combining 670 SNP marker information;
4) Selecting individuals with the prs values of the candidate parents ranked in front as parent fishes according to certain selection strength;
5) Breeding the parent fish selected in the step 4), wherein the offspring is an individual with high resistance to cryptocaryon irritans, and performing cryptocaryon irritans challenge verification on the high-resistance offspring.
2. The set of SNP markers for breeding Cryptocaryon irritans resistance in large yellow croaker according to claim 1, wherein 670 SNP markers are applied in the Cryptocaryon irritans resistance breeding industry in large yellow croaker.
3. The set of SNP markers for breeding large yellow croaker to stimulate Cryptocaryon irritans according to claim 1, wherein in the step 1), the extraction of the genome DNA of the candidate parent adopts phenol chloroform method and any DNA extraction method of a kit.
4. The set of SNP markers applicable to breeding of Cryptocaryon irritans-resistant large yellow croakers as claimed in claim 1, wherein in step 2), genotyping of 670 SNP markers takes any form of sequencing technology, and the sequencing technology comprises one of simplified genome sequencing, whole genome re-sequencing, gene chip, and multiplex PCR.
5. The set of SNP markers for breeding Cryptocaryon irritans resistance of large yellow croaker according to claim 1, wherein at least 300 of the 670 markers are successfully typed in step 3).
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| CN108424958A (en) * | 2018-06-08 | 2018-08-21 | 集美大学 | A kind of relevant SNP marker of Larimichthys crocea genetic sex and its primer and application |
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| CN107814833A (en) * | 2017-10-11 | 2018-03-20 | 福建农林大学 | Stimulate cryptonucleus insect recombinant protein vaccine and preparation method and application |
| CN108424958A (en) * | 2018-06-08 | 2018-08-21 | 集美大学 | A kind of relevant SNP marker of Larimichthys crocea genetic sex and its primer and application |
| CN108991236A (en) * | 2018-07-10 | 2018-12-14 | 中国水产科学研究院黄海水产研究所 | Feed for improving disease resistance of large yellow croakers and preparation method thereof |
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