CN111041110A - Molecular marker related to intramuscular fat content traits of pigs and application thereof - Google Patents
Molecular marker related to intramuscular fat content traits of pigs and application thereof Download PDFInfo
- Publication number
- CN111041110A CN111041110A CN202010047313.8A CN202010047313A CN111041110A CN 111041110 A CN111041110 A CN 111041110A CN 202010047313 A CN202010047313 A CN 202010047313A CN 111041110 A CN111041110 A CN 111041110A
- Authority
- CN
- China
- Prior art keywords
- pig
- type
- chromosome
- fat content
- intramuscular fat
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Pending
Links
- 238000007918 intramuscular administration Methods 0.000 title claims abstract description 82
- 241000282887 Suidae Species 0.000 title claims abstract description 34
- 239000003147 molecular marker Substances 0.000 title claims abstract description 27
- 210000000349 chromosome Anatomy 0.000 claims abstract description 48
- 108090000623 proteins and genes Proteins 0.000 claims abstract description 30
- 239000003550 marker Substances 0.000 claims abstract description 21
- 230000008859 change Effects 0.000 claims abstract description 13
- 238000001514 detection method Methods 0.000 claims abstract description 8
- 238000000034 method Methods 0.000 claims description 22
- 230000002068 genetic effect Effects 0.000 claims description 21
- 239000002773 nucleotide Substances 0.000 claims description 16
- 125000003729 nucleotide group Chemical group 0.000 claims description 16
- 238000004364 calculation method Methods 0.000 claims description 14
- 238000009395 breeding Methods 0.000 claims description 8
- 230000001488 breeding effect Effects 0.000 claims description 8
- 239000000523 sample Substances 0.000 claims description 8
- 238000003307 slaughter Methods 0.000 claims description 5
- 238000002474 experimental method Methods 0.000 claims description 3
- 238000009394 selective breeding Methods 0.000 claims 1
- 108020004414 DNA Proteins 0.000 abstract description 6
- 101150091468 IGSF8 gene Proteins 0.000 abstract description 3
- 101100396614 Homo sapiens IGSF8 gene Proteins 0.000 abstract description 2
- 101150108458 usf1 gene Proteins 0.000 abstract description 2
- 241000282898 Sus scrofa Species 0.000 description 61
- 235000015277 pork Nutrition 0.000 description 9
- 238000004458 analytical method Methods 0.000 description 6
- 150000007523 nucleic acids Chemical class 0.000 description 6
- 235000013372 meat Nutrition 0.000 description 4
- 210000003205 muscle Anatomy 0.000 description 4
- 108020004707 nucleic acids Proteins 0.000 description 4
- 102000039446 nucleic acids Human genes 0.000 description 4
- 238000012216 screening Methods 0.000 description 4
- 238000011161 development Methods 0.000 description 3
- 238000010586 diagram Methods 0.000 description 3
- 230000006872 improvement Effects 0.000 description 3
- 230000035772 mutation Effects 0.000 description 3
- 108700028369 Alleles Proteins 0.000 description 2
- 108091028043 Nucleic acid sequence Proteins 0.000 description 2
- 239000000796 flavoring agent Substances 0.000 description 2
- 235000019634 flavors Nutrition 0.000 description 2
- 230000004322 lipid homeostasis Effects 0.000 description 2
- 238000004519 manufacturing process Methods 0.000 description 2
- 238000012986 modification Methods 0.000 description 2
- 230000004048 modification Effects 0.000 description 2
- 238000011160 research Methods 0.000 description 2
- 238000010187 selection method Methods 0.000 description 2
- 102100024942 Calsequestrin-1 Human genes 0.000 description 1
- 101000761381 Homo sapiens Calsequestrin-1 Proteins 0.000 description 1
- 101000573300 Homo sapiens NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial Proteins 0.000 description 1
- 101000671637 Homo sapiens Upstream stimulatory factor 1 Proteins 0.000 description 1
- 102100036489 Immunoglobulin superfamily member 8 Human genes 0.000 description 1
- 102100026360 NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial Human genes 0.000 description 1
- 238000012408 PCR amplification Methods 0.000 description 1
- 102100040105 Upstream stimulatory factor 1 Human genes 0.000 description 1
- 230000009286 beneficial effect Effects 0.000 description 1
- 238000003766 bioinformatics method Methods 0.000 description 1
- 238000010219 correlation analysis Methods 0.000 description 1
- 230000003247 decreasing effect Effects 0.000 description 1
- 238000013461 design Methods 0.000 description 1
- 238000003745 diagnosis Methods 0.000 description 1
- 230000037149 energy metabolism Effects 0.000 description 1
- 238000005516 engineering process Methods 0.000 description 1
- 239000012634 fragment Substances 0.000 description 1
- 238000003205 genotyping method Methods 0.000 description 1
- 210000003701 histiocyte Anatomy 0.000 description 1
- 238000000338 in vitro Methods 0.000 description 1
- 235000020997 lean meat Nutrition 0.000 description 1
- 230000007774 longterm Effects 0.000 description 1
- 238000005259 measurement Methods 0.000 description 1
- 238000005065 mining Methods 0.000 description 1
- 239000003068 molecular probe Substances 0.000 description 1
- 238000002205 phenol-chloroform extraction Methods 0.000 description 1
- 230000008569 process Effects 0.000 description 1
- 230000001105 regulatory effect Effects 0.000 description 1
- 238000007894 restriction fragment length polymorphism technique Methods 0.000 description 1
- 239000004065 semiconductor Substances 0.000 description 1
- 238000012163 sequencing technique Methods 0.000 description 1
- 238000007619 statistical method Methods 0.000 description 1
- 238000012360 testing method Methods 0.000 description 1
- 210000001519 tissue Anatomy 0.000 description 1
- 238000012800 visualization Methods 0.000 description 1
Images
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/124—Animal traits, i.e. production traits, including athletic performance or the like
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
Landscapes
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Analytical Chemistry (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Organic Chemistry (AREA)
- Physics & Mathematics (AREA)
- Biotechnology (AREA)
- Zoology (AREA)
- Molecular Biology (AREA)
- Genetics & Genomics (AREA)
- Wood Science & Technology (AREA)
- General Health & Medical Sciences (AREA)
- Biophysics (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Theoretical Computer Science (AREA)
- Immunology (AREA)
- Microbiology (AREA)
- Medical Informatics (AREA)
- Evolutionary Biology (AREA)
- Bioinformatics & Computational Biology (AREA)
- Biochemistry (AREA)
- General Engineering & Computer Science (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Abstract
The invention relates to the technical field of molecular markers, in particular to a molecular marker related to the intramuscular fat content of pigs and application thereof, and specifically relates to two molecular markers which are respectively positioned in a USF1 gene and an IGSF8 gene and are related to the intramuscular fat content of pigs, two selection signal regions which are positioned on a No. 4 chromosome and are related to the traits and application thereof. Carrying out gene typing on DNA data of pigs to obtain SNP typing data; based on FSTAnd an XPEHH selective signal detection method, wherein two sections of selective signal areas which are positioned on a No. 4 pig chromosome and are related to the intramuscular fat content character are identified by constructing a gradient change population pair, two molecular markers related to the character are screened, and the marker-assisted selection can be carried out aiming at the intramuscular fat content character of the pig by utilizing the markers.
Description
[ technical field ] A method for producing a semiconductor device
The invention relates to the technical field of pig molecular marker screening, in particular to a molecular marker related to the intramuscular fat content of pigs and application thereof.
[ background of the invention ]
Pork quality traits are important economic traits and always are the key points of attention of breeding workers. The intramuscular fat content is an important meat quality character, largely determines the taste, flavor and quality of pork, and has important economic value (Zhang et al.2019). In the process of long-term pursuit of lean-type pig breeding, the lean meat percentage of the pig is greatly improved through selection of the backfat thickness character, but the taste, flavor and quality of pork in commercial pig varieties are reduced to different degrees. How to improve the pork quality and produce high-quality and delicious pork with high intramuscular fat content is the demand of the current market and is also an important target of breeding work. However, meat quality traits require post-slaughter measurements, fall into the category of traits that are difficult to measure, with greater difficulty in genetic improvement (Ma et al.2018). The main ideas in the present stage are as follows: the pork quality traits such as intramuscular fat content and the like are genetically improved by a marker-assisted selection method or a genome selection method, but the molecular markers related to the intramuscular fat content traits of pigs are still quite limited at present.
The invention utilizes FSTAccording to the detection method of the selection signals between the two populations of Weir et al.1984 and XPEHH (Sabtebi et al.2007), aiming at the intramuscular fat content character of the big white pig, 3 phenotype gradient change population pairs are constructed, the specific selection signal association site of the intramuscular fat content character is accurately positioned, the potential character specific selection signal candidate area is determined, and two important SNP markers positioned on the No. 4 chromosome and two gene fragments are accurately positioned and closely related to the intramuscular fat content character by combining biological information analysis means such as database mining and the like. At present, the results are not reported, so that the marker has potential important value for genetic improvement of pork quality traits.
[ summary of the invention ]
In view of the above, there is a need to provide a molecular marker related to the intramuscular fat content of pigs and an application thereof, wherein the molecular marker can be applied to screening pigs with high/low intramuscular fat content, and provides a new molecular marker basis for the selection and improvement of the intramuscular fat content of pigs.
In order to achieve the purpose, the technical scheme adopted by the invention is as follows:
a molecular genetic marker associated with intramuscular fat content in pigs, said molecular genetic marker comprising at least one of:
marking one: 89398587 th nucleotide located on No. 4 pig chromosome, wherein the base of the site is G or A, and the 51 st base of the corresponding nucleotide sequence table SEQ ID NO. 1; (rs55617884)
Marking II: is located on 90378144 th nucleotide of No. 4 pig chromosome, the base of the site is T or C, and the corresponding nucleotide sequence table SEQ ID NO.2 is the 51 st base. (rs80782100)
Further, when the 89398587 th base of the pig chromosome 4 is a homozygote of G, it is a GG type; when the 89398587 th base of the No. 4 pig chromosome is a homozygote of A, the chromosome is of an AA type; the 89398587 th base of the pig No. 4 chromosome is a hybrid of G and A, and is GA type; when the 90378144 th base of the No. 4 pig chromosome is a homozygote of C, the chromosome is CC type; the 90378144 th base of the pig No. 4 chromosome is TT type when being homozygote of T; and when the 90378144 th base of the pig No. 4 chromosome is a hybrid of C and T, the pig chromosome is of a TC type.
Further, the intramuscular fat content of the AA type gene pig is higher than that of the GA type and GG type; the intramuscular fat content of the pig with the TC type gene is higher than that of the pig with the TT type gene and the pig with the CC type gene.
A primer for amplifying the molecular genetic marker or a probe for identifying the molecular genetic marker.
A kit containing the primer or probe.
The invention also comprises the application of the molecular genetic marker in breeding of the high or low intramuscular fat content pig breed or strain.
The invention also comprises a method for breeding or assisting in selecting pigs with high/low intramuscular fat content by utilizing the molecular marker, which comprises the following steps: extracting total DNA of a target pig, detecting 89398587 th nucleotide of No. 4 chromosome of the pig, and judging the genotype of the pig to be GG type, GA type or AA type; detecting 90378144 th nucleotide of the pig, and judging the genotype of the pig to be CC type, TC type or TT type; pigs of different genotypes were selected for demand.
The invention discloses a method for obtaining a molecular genetic marker related to intramuscular fat content of pigs, which is characterized by comprising the following steps: the intramuscular fat content of the pigs is measured in a slaughtering experiment, and 3 phenotype gradient change population pairs are constructed; detection method F using inter-population selection signalSTXPEHH respectively detects the selection signal characteristics of the population pairs with three pairs of extreme phenotype gradient changes; calculating the SNP site selection signal gradient change index of the significant selection signal sites in the 3 groups of gradient pairs; expressed as index 1, index 2; the 1 st index is the difference between the calculated statistic of the highest difference gradient pair and the calculated statistic of the medium difference gradient pair, and the 2 nd index is the difference between the calculated statistic of the normal difference gradient pair and the calculated statistic of the medium difference gradient pairThe magnitude gradient of the current statistic is increased progressively, namely, the site with the 1 st index as a positive value and the 2 nd index as a negative value of the gradient change index of the selected site is calculated and defined as the target trait associated site, so that the method has the selection potential. Based on FSTThe method detects 4 SNP molecular marker sites which meet the conditions on SSC 4; respectively calculating XPEHH statistics in 3 groups of extreme phenotype difference gradient pairs, respectively carrying out rank ordering on positive and negative statistics obtained by calculation in the 3 groups of extreme phenotype difference pairs, wherein the value of the statistic positioned at the first 1% is defined as a significant site of a selection signal, jointly detecting 14 SNP molecular marker sites which are positioned on SSC4 and meet the conditions on the basis of an XPEHH method, defining a region of about 100kb of the SNP molecular site associated with the target traits as a candidate region of the selection signal of the target traits, and combining the regions with coincidence to obtain a specific selection signal region associated with the intramuscular fat content traits.
The invention has the following beneficial effects:
the position of the gene related to the content of the intramuscular fat of the pig is judged by the screened molecular marker through a new modeling method, and then the gene locus related to the content of the intramuscular fat of the pig is found through further fine positioning, and the locus can be applied to the genotype of the gene related to the intramuscular fat of the pig or the correlation analysis related to the intramuscular fat of the pig, so that a new molecular marker resource is provided for the molecular marker-assisted selection of the intramuscular fat of the pig. The invention can detect the genotype of the pig by adopting a gene chip technology in vitro, and can be used for carrying out molecular marker assisted selection on the intramuscular fat of the pig for the non-diagnosis purpose.
[ description of the drawings ]
FIG. 1: the intramuscular fat content gradient change population is used for carrying out linkage disequilibrium level degree and attenuation trend graph on the whole genome of each subgroup. Wherein, the left graph is a whole genome linkage disequilibrium level degree and attenuation trend graph of each subgroup with high intramuscular fat content; the right graph is a graph of the whole genome linkage disequilibrium level degree of each subgroup with low intramuscular fat content and the attenuation trend thereof; high _1(High _2, High _3) and Low _1(Low _2, Low _3) in the diagram represent two sub-populations of the 1(2,3) th population pair.
FIG. 2: schematic distribution diagram of specific selection signal sites of intramuscular fat content characters of pigs. Wherein the upper diagram is represented by FSTThe intramuscular fat content character disclosed by the method is specific in the distribution of the selection signal sites; the lower graph shows the distribution of specific selection signal sites for intramuscular fat content traits revealed by the XPEHH method; description of reference numerals: visualization of specific selection signals of intramuscular fat content characters. The black dots represent trait-specific selection signals. The squares (dots, triangles) points represent the selection signals identified in the 1 st (2,3) population pair, where the XPEHH method has a selection indicator, L represents a subpopulation with low intramuscular fat content, and H represents a subpopulation with high intramuscular fat content.
[ detailed description ] embodiments
In order to make the aforementioned objects, features and advantages of the present invention comprehensible, embodiments accompanied with figures are described in detail below. In the following description, numerous specific details are set forth in order to provide a thorough understanding of the present invention. This invention may, however, be embodied in many different forms and should not be construed as limited to the embodiments set forth herein, but rather should be construed as broadly as the present invention is capable of modification in various respects, all without departing from the spirit and scope of the present invention.
Example 1:
genotyping and detection
Under the same production condition, 233 pigs are fed by the same feed formula until the weight of slaughter, slaughter experiments are carried out, intramuscular fat content phenotype data are obtained, and 3 phenotype gradient change population pairs are constructed according to the phenotype data.
(1) Genomic DNA of individual ear tissues of 233 big white pigs was extracted using a standard phenol-chloroform method, and entire pig groups were genotyped using Illumina pig SNP 60k chip (Illumina, San Diego, Calif., USA) to obtain SNP typing data.
(2) By performing on genotype dataQuality control by eliminating minimum allele frequency<11624 SNPs at 0.05, 42 markers deleted by HW test (p)<＝10-6) The final dataset consisted of 37061 SNPs on 18 chromosomes.
(3) And calculating the minimum allele frequency of the meat quality of each subgroup of the subgroup divided by the intramuscular fat content, and analyzing the whole genome linkage disequilibrium level of all subgroups and the attenuation rule thereof.
Example 2:
detecting intramuscular fat content characters of the white pigs by using a specific selection signal:
to detect trait-specific selection signals, in this study, we first constructed three pairs of population pairs with gradient phenotype, with a difference in the number of samples between adjacent pairs of gradients of 40. Aiming at the content of intramuscular fat, the following steps are specific:
(1) carrying out rank ordering on the statistical intramuscular fat content phenotype values of the 233 big white pigs;
(2) selecting 105 individuals with the highest intramuscular fat content and 105 individuals with the lowest intramuscular fat content to form a common difference gradient pair according to the sorting result, and recording the common difference gradient pair as a first population pair;
(3) on the basis of the common difference gradient pair, selecting 75 individuals with higher intramuscular fat content from 105 individuals with high intramuscular fat content, selecting 75 individuals with lower intramuscular fat content from 105 individuals with low intramuscular fat content, creating a medium difference gradient pair, and recording the medium difference gradient pair as a second population pair;
(4) selecting 35 individuals with higher intramuscular fat content from 75 individuals with higher intramuscular fat content and 35 individuals with lower intramuscular fat content from 75 individuals with lower intramuscular fat content on the basis of the moderate difference gradient pair, creating a maximum difference gradient pair, and recording the maximum difference gradient pair as a third population pair;
(5) the results of linkage disequilibrium analysis of each subgroup show that the artificially-made phenotype gradient difference population has no significant influence on the genome structural features of each population (FIG. 1: as shown in the figure, the decay rates of LD curve decay trends in all sub-populations are similar, which indicates that the influence of population division does not negatively influence the detection of the trait-specific selection signal).
(6) Detection method F using inter-population selection signalSTAnd XPEHH detects the selection signal characteristics of three pairs of population pairs with extreme phenotypic gradient changes respectively.
First, F obtained by calculationSTThe statistics are rank ordered, with the statistics at the top 1% of each gradient pair value defined as the selected signal significant sites. Calculating the gradient change indexes of the SNP site selection signals of the significant selection signal sites in the 3 groups of gradient pairs, and expressing the indexes as the 1 st index and the 2 nd index. The 1 st index is the highest difference gradient pair calculation statistic-medium difference gradient pair calculation statistic, the 2 nd index is the common difference gradient pair calculation statistic-medium difference gradient pair calculation statistic, the gradient increasing of the statistic size is presented, namely, the site with the 1 st index being a positive value and the 2 nd index being a negative value of the gradient change index of the calculation selection site is defined as the target character association site, and the method has the selection potential. Based onFSTThe method detects 4 SNP molecular marker sites which meet the conditions on SSC4 (Table 1).
Next, XPEHH statistics were calculated separately in 3 sets of extreme phenotypic difference gradient pairs. And (3) respectively carrying out rank ordering on positive and negative statistics obtained by calculation in 3 groups of extreme phenotype difference pairs, wherein the value of the statistic positioned at the top 1% is defined as a significant site of the selection signal. On the basis of the above significant selection signal sites, sites presenting a gradient with increasing magnitude of the positive value of the statistic (or decreasing magnitude of the negative value) in 3 groups of gradient pairs are defined as target trait associated sites, and have selection potential. 14 SNP molecular marker sites on SSC4 that meet the above conditions were co-detected based on XPEHH method (Table 2).
Table 1: intramuscular fat content F of pig chromosome 4 target regionSTStatistics
| Chromosome | Position (bp) | Common differential gradient pair | Intermediate differential gradient pair | Maximum difference gradient pair |
| 4 | 89339474 | 4.479927e-02 | 5.703801e-02 | 1.500577e-01 |
| 4 | 89381548 | 3.306270e-02 | 6.583257e-02 | 1.042938e-01 |
| 4 | 89449590 | 3.330626e-02 | 7.143678e-02 | 1.775239e-01 |
| 4 | 89669667 | 3.321305e-02 | 6.301678e-02 | 1.269859e-01 |
Table 2: intramuscular fat content XPEHH statistic of target region of pig chromosome 4
(7) And defining a region of 100kb left and right of the SNP molecular site related to the target character as a target character selection signal candidate region, and combining overlapped regions to obtain two regions of 89239474bp-89769667bp and 89982606bp-90446408bp positioned on SSC4 as specific selection signal regions related to the intramuscular fat content character.
Based on the two trait-specific selection signal candidate regions in step (7), genes located within the above candidate regions were detected using the BioMart program based on the "database gene 95" and "porcine gene (Sscrofa 11.1)" databases. Through the idea of gene ortholog homology comparison, a MGI database is utilized to further screen functional candidate genes influencing muscle traits in a mouse phenotype database, and part of genes with function reports are shown in Table 3. The reliability that the 89239474bp-89769667bp and 89982606bp-90446408bp regions on SSC4 identified in the research are intramuscular fat content character specific selection signal candidate regions is proved to a great extent by genes with clear functions found in the character specific selection signal regions.
TABLE 35 functional candidate genes related to intramuscular fat content of pig chromosome 4 target region
For example, two important functional candidate genes related to energy metabolism and lipid homeostasis, namely NDUFS2 and USF1, are enriched in the 89239474bp-89769667bp region of chromosome 4; two important functional candidate genes related to muscle development, namely CASQ1 and IGSF8, are enriched in the 89982606bp-90446408bp region of chromosome 4. The analysis of the SNPs in the two regions respectively shows that two variations (rs55617884 (89398587 th base) and rs80782100 (90378144 th base)) are respectively located in the USF1 gene and the IGSF8 gene, and the two SNPs are also selection signal sites specific to intramuscular fat content traits, so that the sites can be inferred to influence the functions of the genes, thereby influencing the lipid homeostasis and muscle development functions of the genes and further influencing the meat quality traits of pigs.
In the embodiment, the method for evaluating the pork quality character specific selection region by using the gradient change index of the selected SNP locus is mainly used, and the regions of 89239474bp-89769667bp and 89982606bp-90446408bp on SSC4 are screened out to be the pork quality character specific selection region. Through bioinformatics analysis, candidate genes with the function of regulating muscle development are enriched, and the reliability of the research result is proved; meanwhile, two functional candidate sites closely related to the intramuscular fat content of the pigs are disclosed.
Carrying out statistical analysis on the content of fat in the histiocytes, and when the 89398587 th base of the No. 4 pig chromosome is a homozygote of A, the chromosome is of an AA type; the 89398587 th base of the pig No. 4 chromosome is a hybrid of G and A, and is GA type; when the 90378144 th base of the No. 4 pig chromosome is a homozygote of C, the chromosome is CC type; TT type when 90378144 th base of pig 4 th chromosome is homozygote of T; and when the 90378144 th base of the pig No. 4 chromosome is a hybrid of C and T, the pig chromosome is of a TC type. The results of the intramuscular fat content analysis of the samples are given in tables 4 and 5:
table 4: analysis result of 89398587 th nucleotide genotype and intramuscular fat content of pig chromosome 4
| Genotype(s) | Pig number (head) | Genotype frequency | Intramuscular fat content (%) |
| AA type | 64 | 0.27 | 2.26±0.55 |
| GA type | 130 | 0.56 | 2.21±0.52 |
| GG type | 39 | 0.17 | 2.19±0.54 |
It can be seen that the intramuscular fat content of the AA type pig is higher than that of the GA type pig and that of the GG type pig.
Table 5: analysis result of 90378144 th nucleotide genotype and intramuscular fat content of pig chromosome 4
| Genotype(s) | Pig number (head) | Genotype frequency | Intramuscular fat content (%) |
| TT type | 21 | 0.09 | 2.14±0.54 |
| TC type | 118 | 0.51 | 2.28±0.52 |
| CC type | 94 | 0.40 | 2.17±0.54 |
The intramuscular fat content of TC type pigs is higher than that of CC type pigs and that of TT type pigs.
Example 3:
according to the gene results obtained by screening, the molecular genetic marker related to the porcine intramuscular fat is shown to be located at the 89398587 th nucleic acid site of the No. 4 chromosome of the pig, wherein the position is an A > G mutation and corresponds to the 51 st nucleic acid site (rs55617884 gene) of the nucleic acid sequence table SEQ ID NO. 1; or 90378144 th nucleic acid site of chromosome 4, wherein the position is a T > C mutation and corresponds to the 51 st nucleic acid site (rs55617884 gene) of the nucleic acid sequence table SEQ ID NO. 1.
Example 4:
the skilled person can easily design primers for amplifying the molecular marker or probes for identifying the molecular marker according to the present invention, and then use the primers or probes for detecting the molecular marker, for example, the molecular marker is obtained by PCR amplification, and the corresponding sequence is obtained by clone sequencing, or the Bsm-RFLP polymorphism is used for detection. Thus, the invention also includes primers for amplifying the molecular genetic marker or probes for identifying the molecular genetic marker, and kits containing the primers or probes.
Example 5:
the molecular genetic marker can be applied to assist pig breeding or auxiliary breeding work, and the specific method comprises the following steps: extracting total DNA of a target pig, detecting 89398587 th nucleotide of No. 4 chromosome of the pig, and judging the genotype of the pig to be GG type, GA type or AA type; detecting 90378144 th nucleotide of the pig, and judging the genotype of the pig to be CC type, TC type or TT type; pigs of different genotypes were selected for demand.
In conclusion, the method can simply, efficiently and accurately obtain the molecular genetic marker related to the intramuscular fat of the pig, and a primer for amplifying the molecular marker and a probe for identifying the molecular marker can be designed according to the mutation; the pigs with intramuscular fat content meeting the requirements are quickly screened out, and the accuracy and efficiency of screening molecular markers can be effectively improved.
The above examples are merely illustrative of several embodiments of the present invention, and the description thereof is more specific and detailed, but not to be construed as limiting the scope of the invention. It should be noted that, for a person skilled in the art, several variations and modifications can be made without departing from the inventive concept, which falls within the scope of the present invention. Therefore, the protection scope of the present invention should be subject to the appended claims.
Sequence listing
<110> Guangxi Yangxiang GmbH
University of agriculture in china
<120> molecular marker related to intramuscular fat content traits of pigs and application thereof
<160>2
<170>SIPOSequenceListing 1.0
<210>1
<211>101
<212>DNA
<213> pig (Sus scrofa)
<220>
<221>misc_feature
<222>(15)..(15)
<223>n is g or a
<220>
<221>misc_feature
<222>(51)..(51)
<223>n is a, c, g, t or u
<400>1
agaagggaac caataggatg ggggtgtggc acgggatggt gaggcagcta nagctgcctt 60
gacccaaagc tctaggctct ccctttctgg atgtttctac t 101
<210>2
<211>101
<212>DNA
<213> pig (Sus scrofa)
<220>
<221>misc_feature
<222>(15)..(15)
<223>n is t or c
<220>
<221>misc_feature
<222>(51)..(51)
<223>n is a, c, g, t or u
<400>2
tttaaaaact cccagatgat tcagggtgca gacagggtgg gaaccaactg ngtctaagat 60
cgctagctca tcagagctat caggtaatgg ggggccaggc t 101
Claims (8)
1. A molecular genetic marker associated with intramuscular fat content in pigs, wherein said molecular genetic marker comprises at least one of the following markers:
marking one: 89398587 th nucleotide located on No. 4 pig chromosome, wherein the base of the site is G or A, and the 51 st base of the corresponding nucleotide sequence table SEQ ID NO. 1;
marking II: is located on 90378144 th nucleotide of No. 4 pig chromosome, the base of the site is T or C, and the corresponding nucleotide sequence table SEQ ID NO.2 is the 51 st base.
2. The molecular genetic marker related to the content of intramuscular fat of pigs as claimed in claim 1, wherein when the 89398587 th base of the No. 4 chromosome of the pig is a homozygote of G, the chromosome is GG type; when the 89398587 th base of the No. 4 pig chromosome is a homozygote of A, the chromosome is of an AA type; the 89398587 th base of the pig No. 4 chromosome is a hybrid of G and A, and is GA type; when the 90378144 th base of the No. 4 pig chromosome is a homozygote of C, the chromosome is CC type; the 90378144 th base of the pig No. 4 chromosome is TT type when being homozygote of T; and when the 90378144 th base of the pig No. 4 chromosome is a hybrid of C and T, the pig chromosome is of a TC type.
3. The molecular genetic marker related to the intramuscular fat content of the pig as claimed in claim 2, wherein the pig with the AA type gene has the intramuscular fat content higher than that of the GA type and the GG type; the intramuscular fat content of the pig with the TC type gene is higher than that of the pig with the TT type gene and the pig with the CC type gene.
4. A primer for amplifying a molecular genetic marker according to claims 1-3 or a probe for identifying a molecular genetic marker according to claim 1.
5. A kit comprising the primer or probe of claim 4.
6. Use of a molecular genetic marker as defined in claims 1-3 for the selective breeding of a breed or line with high or low intramuscular fat content in pigs.
7. A method for breeding or assisting in selecting pigs with high/low intramuscular fat by using the molecular marker of claims 1-3, which is characterized by comprising the following steps: extracting total DNA of a target pig individual, detecting 89398587 th nucleotide of No. 4 chromosome of the pig, and judging the genotype of the pig to be GG type, GA type or AA type; detecting 90378144 th nucleotide of the pig, and judging the genotype of the pig to be CC type, TC type or TT type; pigs of different genotypes were selected for demand.
8. Obtaining and pig muscleA method for molecular genetic marking associated with internal fat content, said method comprising: the intramuscular fat content of the pigs is measured in a slaughtering experiment, and 3 phenotype gradient change population pairs are constructed; detection method F using inter-population selection signalSTXPEHH respectively detects the selection signal characteristics of the population pairs with three pairs of extreme phenotype gradient changes; calculating the SNP site selection signal gradient change index of the significant selection signal sites in the 3 groups of gradient pairs; expressed as index 1, index 2; the 1 st index is the difference between the calculation statistic of the highest difference gradient pair and the calculation statistic of the medium difference gradient pair, the 2 nd index is the difference between the calculation statistic of the common difference gradient pair and the calculation statistic of the medium difference gradient pair, and the gradient increasing of the statistic magnitude is presented, namely, the site with the 1 st index being a positive value and the 2 nd index being a negative value of the gradient change index of the calculation selection site is defined as the target character association site, and the method has the selection potential. Based on FSTThe method detects 4 SNP molecular marker sites which meet the conditions on SSC 4; respectively calculating XPEHH statistics in 3 groups of extreme phenotype difference gradient pairs, respectively carrying out rank ordering on positive and negative statistics obtained by calculation in the 3 groups of extreme phenotype difference pairs, wherein the value of the statistic positioned at the first 1% is defined as a significant site of a selection signal, jointly detecting 14 SNP molecular marker sites which are positioned on SSC4 and meet the conditions on the basis of an XPEHH method, defining a region of about 100kb of the SNP molecular site associated with the target traits as a candidate region of the selection signal of the target traits, and combining the regions with coincidence to obtain a specific selection signal region associated with the intramuscular fat content traits.
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN202010047313.8A CN111041110A (en) | 2020-01-16 | 2020-01-16 | Molecular marker related to intramuscular fat content traits of pigs and application thereof |
Applications Claiming Priority (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN202010047313.8A CN111041110A (en) | 2020-01-16 | 2020-01-16 | Molecular marker related to intramuscular fat content traits of pigs and application thereof |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| CN111041110A true CN111041110A (en) | 2020-04-21 |
Family
ID=70244705
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CN202010047313.8A Pending CN111041110A (en) | 2020-01-16 | 2020-01-16 | Molecular marker related to intramuscular fat content traits of pigs and application thereof |
Country Status (1)
| Country | Link |
|---|---|
| CN (1) | CN111041110A (en) |
Cited By (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN111363833A (en) * | 2020-04-24 | 2020-07-03 | 佛山科学技术学院 | SNP molecular marker related to pork conductivity character and application thereof |
| CN112176072A (en) * | 2020-09-29 | 2021-01-05 | 吉林省农业科学院 | Reagent, primer, kit and application for detecting intramuscular fat content of beef cattle |
| CN112980970A (en) * | 2021-04-20 | 2021-06-18 | 黑龙江省农业科学院畜牧研究所 | PABPN1 molecular marker breeding method for improving intramuscular fat content of pigs and application thereof |
| CN113913536A (en) * | 2021-11-30 | 2022-01-11 | 湖北省农业科学院畜牧兽医研究所 | Genetic marker for intramuscular fat content character by using variation of first exon of pig EEPD1 gene and application |
Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN108315433A (en) * | 2018-03-06 | 2018-07-24 | 华南农业大学 | It is a kind of influence Duroc boar intramuscular fat content molecular labeling and application |
| CN109680078A (en) * | 2019-02-22 | 2019-04-26 | 华中农业大学 | Utilize the method for SNP site selection signal change of gradient Index Assessment economic characters candidate gene |
-
2020
- 2020-01-16 CN CN202010047313.8A patent/CN111041110A/en active Pending
Patent Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN108315433A (en) * | 2018-03-06 | 2018-07-24 | 华南农业大学 | It is a kind of influence Duroc boar intramuscular fat content molecular labeling and application |
| CN109680078A (en) * | 2019-02-22 | 2019-04-26 | 华中农业大学 | Utilize the method for SNP site selection signal change of gradient Index Assessment economic characters candidate gene |
Non-Patent Citations (2)
| Title |
|---|
| WU ABGC: ""rs55617884"", 《UCSC》 * |
| WU ABGC: ""rs80782100"", 《UCSC》 * |
Cited By (8)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN111363833A (en) * | 2020-04-24 | 2020-07-03 | 佛山科学技术学院 | SNP molecular marker related to pork conductivity character and application thereof |
| CN111363833B (en) * | 2020-04-24 | 2023-10-31 | 佛山科学技术学院 | SNP molecular marker related to pork conductivity and application thereof |
| CN112176072A (en) * | 2020-09-29 | 2021-01-05 | 吉林省农业科学院 | Reagent, primer, kit and application for detecting intramuscular fat content of beef cattle |
| CN112176072B (en) * | 2020-09-29 | 2022-07-01 | 吉林省农业科学院 | Reagent, primer, kit and application for detecting intramuscular fat content of beef cattle |
| CN112980970A (en) * | 2021-04-20 | 2021-06-18 | 黑龙江省农业科学院畜牧研究所 | PABPN1 molecular marker breeding method for improving intramuscular fat content of pigs and application thereof |
| CN112980970B (en) * | 2021-04-20 | 2021-12-07 | 黑龙江省农业科学院畜牧研究所 | PABPN1 molecular marker breeding method for improving intramuscular fat content of pigs and application thereof |
| CN113913536A (en) * | 2021-11-30 | 2022-01-11 | 湖北省农业科学院畜牧兽医研究所 | Genetic marker for intramuscular fat content character by using variation of first exon of pig EEPD1 gene and application |
| CN113913536B (en) * | 2021-11-30 | 2022-08-16 | 湖北省农业科学院畜牧兽医研究所 | Genetic marker for intramuscular fat content character by using variation of first exon of pig EEPD1 gene and application |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| CN111041110A (en) | Molecular marker related to intramuscular fat content traits of pigs and application thereof | |
| CN112322753B (en) | SNP molecular marker related to intramuscular fat of pork and application thereof | |
| CN110218798B (en) | SNP molecular marker located on pig chromosome 7 and related to eye muscle area and eye muscle thickness and application | |
| CN108103208A (en) | A kind of SNP marker for influencing sheep Fecundity Trait and its application | |
| CN110894542A (en) | Primer for identifying types of GS5 gene and GLW7 gene of rice and application of primer | |
| WO2023201950A1 (en) | Snp molecular marker combination for beijing black pig genotyping, chip, and preparation method therefor and use thereof | |
| CN111235282B (en) | SNP molecular marker related to total number of porcine papillae and application and acquisition method thereof | |
| CN104911273B (en) | A kind of chicken FABP1 gene molecule genetic marker related to the excellent production traits of chicken and its application | |
| CN111455066B (en) | Genetic molecular marker related to pork quality conductivity character | |
| CN112575096A (en) | SNP molecular marker related to total papilla number of large white pigs and acquisition method thereof | |
| CN115820879B (en) | Molecular marker related to intramuscular fat traits of pigs in pig AOPEP gene and application thereof | |
| CN116286804A (en) | SNP molecular marker related to pig correction of backfat thickness of 115 kg body weight and application | |
| CN106947826B (en) | Method for detecting single nucleotide polymorphism of cattle SERPINA3 gene and application thereof | |
| CN115927667A (en) | Molecular marker and primer related to pig intramuscular fat character and application of molecular marker and primer | |
| CN116083598A (en) | SNP molecular marker related to intramuscular fat traits of pigs and application thereof | |
| CN114250309A (en) | Molecular marker influencing diameter property of cashmere fiber of Xinjiang nan cashmere goat and specific primer pair and application thereof | |
| CN108588242B (en) | SNP locus of crassostrea gigas AHR gene | |
| CN113322333A (en) | CNV molecular marker combination related to Guangxi hemp chicken body size and slaughter traits based on whole genome sequencing screening and application | |
| CN112779339A (en) | SNP molecular marker related to total papilla number of large white pigs as well as acquisition and application thereof | |
| CN111154889A (en) | SNP molecular marker related to pig body weight and application and acquisition method thereof | |
| CN110468220A (en) | One kind SNP marker relevant to chicken green-egg-shelled blackening and its application | |
| CN115820875B (en) | Molecular marker for evaluating area of porcine eye muscle and screening method and application thereof | |
| CN116162714B (en) | Haplotype molecular marker related to intramuscular fat traits of pigs in SYK gene and application | |
| CN112391482B (en) | SNP molecular marker related to pork conductivity and application thereof | |
| CN116042849B (en) | Genetic marker for assessing pig feed intake and screening method and application thereof |
Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| PB01 | Publication | ||
| PB01 | Publication | ||
| SE01 | Entry into force of request for substantive examination | ||
| SE01 | Entry into force of request for substantive examination | ||
| RJ01 | Rejection of invention patent application after publication |
Application publication date: 20200421 |
|
| RJ01 | Rejection of invention patent application after publication |