CN114107523B - Snp molecular marker associated with growth traits of litopenaeus vannamei, detection primer and application of detection primer - Google Patents
Snp molecular marker associated with growth traits of litopenaeus vannamei, detection primer and application of detection primer Download PDFInfo
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- 241000238553 Litopenaeus vannamei Species 0.000 title claims abstract description 45
- 238000001514 detection method Methods 0.000 title claims abstract description 31
- 239000003147 molecular marker Substances 0.000 title claims abstract description 29
- 238000009395 breeding Methods 0.000 claims abstract description 20
- 230000001488 breeding effect Effects 0.000 claims abstract description 18
- 238000000034 method Methods 0.000 claims abstract description 10
- 238000012163 sequencing technique Methods 0.000 claims description 7
- 230000037396 body weight Effects 0.000 claims description 2
- 230000004584 weight gain Effects 0.000 claims 2
- 235000019786 weight gain Nutrition 0.000 claims 2
- 241000238557 Decapoda Species 0.000 abstract description 9
- 230000009286 beneficial effect Effects 0.000 abstract description 2
- 238000012216 screening Methods 0.000 abstract description 2
- 238000004904 shortening Methods 0.000 abstract description 2
- 230000035772 mutation Effects 0.000 description 9
- 101150011377 TRMT10A gene Proteins 0.000 description 7
- 108090000623 proteins and genes Proteins 0.000 description 6
- 101000645364 Homo sapiens tRNA methyltransferase 10 homolog A Proteins 0.000 description 5
- 150000001413 amino acids Chemical group 0.000 description 5
- 235000001014 amino acid Nutrition 0.000 description 4
- 229940024606 amino acid Drugs 0.000 description 4
- 241001465754 Metazoa Species 0.000 description 3
- AYFVYJQAPQTCCC-UHFFFAOYSA-N Threonine Natural products CC(O)C(N)C(O)=O AYFVYJQAPQTCCC-UHFFFAOYSA-N 0.000 description 3
- 239000004473 Threonine Substances 0.000 description 3
- 239000002299 complementary DNA Substances 0.000 description 3
- 238000010586 diagram Methods 0.000 description 3
- 230000004879 molecular function Effects 0.000 description 3
- WHUUTDBJXJRKMK-UHFFFAOYSA-N Glutamic acid Natural products OC(=O)C(N)CCC(O)=O WHUUTDBJXJRKMK-UHFFFAOYSA-N 0.000 description 2
- DCXYFEDJOCDNAF-REOHCLBHSA-N L-asparagine Chemical compound OC(=O)[C@@H](N)CC(N)=O DCXYFEDJOCDNAF-REOHCLBHSA-N 0.000 description 2
- MEFKEPWMEQBLKI-AIRLBKTGSA-N S-adenosyl-L-methioninate Chemical compound O[C@@H]1[C@H](O)[C@@H](C[S+](CC[C@H](N)C([O-])=O)C)O[C@H]1N1C2=NC=NC(N)=C2N=C1 MEFKEPWMEQBLKI-AIRLBKTGSA-N 0.000 description 2
- 238000005259 measurement Methods 0.000 description 2
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- 125000003729 nucleotide group Chemical group 0.000 description 2
- 238000012360 testing method Methods 0.000 description 2
- DCXYFEDJOCDNAF-UHFFFAOYSA-N Asparagine Natural products OC(=O)C(N)CC(N)=O DCXYFEDJOCDNAF-UHFFFAOYSA-N 0.000 description 1
- CKLJMWTZIZZHCS-REOHCLBHSA-N L-aspartic acid Chemical compound OC(=O)[C@@H](N)CC(O)=O CKLJMWTZIZZHCS-REOHCLBHSA-N 0.000 description 1
- ONIBWKKTOPOVIA-UHFFFAOYSA-N Proline Natural products OC(=O)C1CCCN1 ONIBWKKTOPOVIA-UHFFFAOYSA-N 0.000 description 1
- 108700040121 Protein Methyltransferases Proteins 0.000 description 1
- 102000055027 Protein Methyltransferases Human genes 0.000 description 1
- MTCFGRXMJLQNBG-UHFFFAOYSA-N Serine Natural products OCC(N)C(O)=O MTCFGRXMJLQNBG-UHFFFAOYSA-N 0.000 description 1
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- 235000009582 asparagine Nutrition 0.000 description 1
- 229960001230 asparagine Drugs 0.000 description 1
- 235000003704 aspartic acid Nutrition 0.000 description 1
- OQFSQFPPLPISGP-UHFFFAOYSA-N beta-carboxyaspartic acid Natural products OC(=O)C(N)C(C(O)=O)C(O)=O OQFSQFPPLPISGP-UHFFFAOYSA-N 0.000 description 1
- 238000010219 correlation analysis Methods 0.000 description 1
- 238000004925 denaturation Methods 0.000 description 1
- 230000036425 denaturation Effects 0.000 description 1
- 238000013461 design Methods 0.000 description 1
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- 238000000605 extraction Methods 0.000 description 1
- 238000012214 genetic breeding Methods 0.000 description 1
- 235000013922 glutamic acid Nutrition 0.000 description 1
- 239000004220 glutamic acid Substances 0.000 description 1
- 125000002496 methyl group Chemical group [H]C([H])([H])* 0.000 description 1
- 238000012257 pre-denaturation Methods 0.000 description 1
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- 102100025768 tRNA methyltransferase 10 homolog A Human genes 0.000 description 1
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Abstract
The invention discloses a SNP molecular marker associated with the growth traits of litopenaeus vannamei, a detection primer and application thereof. The SNP molecular marker is an A/A genotype or an A/C genotype of the 6053 th base position of the sequence shown in SEQ ID NO. 1; or a C/C genotype or an A/C genotype at base position 6058; or a T/T genotype or a T/G genotype at the 6534 th base position; or the A/T genotype or the T/T genotype at base position 6865. The rapid growth is an important economic character of the Litopenaeus vannamei, and in the fine breed breeding work of the Litopenaeus vannamei, the SNP molecular marker and the method can be used for screening a backup parent group, so that a Litopenaeus vannamei parent individual with slow growth can be eliminated as soon as possible, and the growth speed of the offspring of the Litopenaeus vannamei can be enhanced rapidly. The method provided by the invention is beneficial to rapidly increasing the growth speed of the offspring of the litopenaeus vannamei, shortening the breeding cycle of excellent prawn strains and having a great potential application value.
Description
Technical Field
The invention belongs to the field of molecular marker assisted breeding of aquatic animals, and particularly relates to an SNP molecular marker of a tRNA methyltransferase 10a gene (Trmt 10 a) related to the growth traits of litopenaeus vannamei, a detection primer and application thereof.
Background
Litopenaeus vannamei (A) and (B)Litopenaeus vannamei) Commonly known as penaeus vannamei boone, is the prawn variety with the largest world culture quantity. Since the introduction of litopenaeus vannamei into China, the culture yield of litopenaeus vannamei is rapidly increased, and the litopenaeus vannamei becomes the main culture variety of the litopenaeus vannamei in China. The annual output of litopenaeus vannamei culture in 2019 in China exceeds 180 million tons, which accounts for more than 90% of the prawn culture output. Therefore, the improved breeding has important significance for the healthy development of the litopenaeus vannamei breeding industry.
The molecular design breeding is a modernized and high-efficiency genetic breeding rate measurement, and target germplasm is directionally designed and bred by revealing a function gene for controlling phenotype and a molecular marker thereof. The traditional breeding method depends on phenotype selection and has the disadvantages of long period, instability and the like. And the molecular breeding method carries out backup parent selection according to the effective molecular marker, and can more quickly improve the economic character of filial generation. SNP (Single Nucleotide polymorphism) refers to single Nucleotide polymorphism on a genome, and is the most widely and latest molecular marker at present. High quality DNA molecular markers are the basis for developing molecular breeding. At present, although a plurality of prawn molecular markers aiming at different properties are developed, the molecular function of the molecular markers is not clarified in many cases.
tRNA methyltransferase 10a gene, english name: tRNA methyltransferase 10a (Trmt 10 a), belonging to the SpoU-TrmD superfamily type of RNA methyltransferases, usually takes S-adenosyl-L-methionine (SAM) as the methyl donor. There has been no report of Trmt10a gene in litopenaeus vannamei, and no research has found that the gene is related to the growth character of litopenaeus vannamei.
Disclosure of Invention
The invention aims to provide an SNP molecular marker, a detection primer, a molecular function and an application of a tRNA methyltransferase 10a gene (Trmt 10 a) associated with the growth traits of litopenaeus vannamei, and the SNP molecular marker, the detection primer, the molecular function and the application method of the Trmt10a gene of litopenaeus vannamei, disclosed by the invention, can not be predicted by the conventional knowledge or method at present.
The SNP molecular markers related to the growth traits of the Litopenaeus vannamei tRNA methyltransferase 10a gene (Trmt 10 a) are as follows: the genotype A/A or the genotype A/C at the 6053 th base position of the sequence shown in SEQ ID NO. 1; or a C/C genotype or an A/C genotype at base position 6058; or a T/T genotype or a T/G genotype at the 6534 th base position; or the A/T genotype or the T/T genotype at base position 6865.
Preferably, the A/A genotype at the 6053 th base position, the C/C genotype at the 6058 th base position, the T/T genotype at the 6534 th base position and the A/T genotype at the 6865 th base position of the sequence shown in SEQ ID NO. 1; or the A/C genotype at the 6053 th base position, the A/C genotype at the 6058 th base position, the T/G genotype at the 6534 th base position and the T/T genotype at the 6865 th base position.
Preferably, the A/A genotype individual at the 6053 th base position has a significantly higher growth rate than the A/C genotype individual under the same culture conditions; the growth speed of the C/C genotype at the 6058 th base position under the same culture condition is obviously higher than that of an A/C genotype individual; the growth rate of the T/T genotype individual at the 6534 th base position is obviously higher than that of the T/G genotype individual under the same culture condition; the growth rate of the A/T genotype individual at the 6865 base position under the same breeding condition is obviously higher than that of the T/T genotype individual.
The second objective of the present invention is to provide a detection primer set for the above SNP molecular marker, which comprises the following detection primer pairs:
(1) primer pair for 6053 and 6058 position detection
g.Trmt10a-6053/6058-F：5’-CGGTGTTCATAAAGAGGATAC -3’ ；
g. Trmt10a-6053/6058-R：5’-CTCTCCACTTTTGTGTCGTTC -3’ ；
(2) 6534 position detection primer pair
g. Trmt10a-6534-F：5’-TGTCCAAACAGAATGGCTAC -3’ ；
g. Trmt10a-6534-R：5’-CCTCCCGTGAGCAATACCTT -3’ ；
(3) 6865 th position detection primer pair
g. Trmt10a-6865-F：5’-CAAGGATGAGGAAAATGACTGTG -3’ ；
g. Trmt10a-6865-R：5’- ATTCCAGGTGATTACAAGGTTTACA -3’。
The third purpose of the invention is to provide a detection kit, which comprises the detection primer group of the SNP molecular marker.
The fourth purpose of the invention is to provide the application of the SNP molecular marker associated with the growth traits, the detection primer group of the SNP molecular marker or the detection kit in the breeding of the litopenaeus vannamei.
Preferably, the method is applied to breeding of the rapid growth line of the litopenaeus vannamei.
The fifth purpose of the invention is to provide a method for detecting the growth speed of litopenaeus vannamei, which comprises the following steps: extracting the genomic DNA of the litopenaeus vannamei to be detected, amplifying the set of detection primers of the SNP molecular marker, sequencing to obtain a sequencing result, determining the genotype of the SNP molecular marker based on the sequencing result, and judging the growth speed of the litopenaeus vannamei to be detected.
The method comprises the following steps: the growth speed of the A/A genotype individual at the 6053 th base position is obviously higher than that of the A/C genotype individual under the same culture condition; the growth speed of the C/C genotype at the 6058 th base position under the same culture condition is obviously higher than that of an A/C genotype individual; the growth rate of the T/T genotype individual at the 6534 th base position is obviously higher than that of the T/G genotype individual under the same culture condition; the growth rate of the A/T genotype individual at the 6865 base position under the same breeding condition is obviously higher than that of the T/T genotype individual.
The rapid growth is an important economic character of the Litopenaeus vannamei, and in the fine breed breeding work of the Litopenaeus vannamei, the SNP molecular marker and the method can be used for screening a backup parent group, so that a Litopenaeus vannamei parent individual with slow growth can be eliminated as soon as possible, and the growth speed of the offspring of the Litopenaeus vannamei can be enhanced rapidly. The method provided by the invention is beneficial to rapidly increasing the growth speed of the offspring of the litopenaeus vannamei, shortening the breeding cycle of excellent prawn strains and having a great potential application value.
Description of the drawings:
FIG. 1 is a schematic diagram of: a: the number of the SNP polymorphic site of the Trmt10a gene of the prawn represents the base position of the polymorphic site; b: the full-length cDNA sequence of the prawn Trmt10a gene and the coded amino acid sequence diagram thereof, and the box marks SNP mutation sites;
FIG. 2 is a diagram of: statistics of body weights of individuals of different genotypes after three families were bred for 1.5 months under the same breeding conditions, "+" indicates that the significance test P is < 0.05, and "+" indicates that the significance test P is < 0.01.
The specific implementation mode is as follows:
the following examples are further illustrative of the present invention and are not intended to be limiting thereof.
Example 1:
the Litopenaeus vannamei colony used for analysis comprises 1 holosib family and 2 hemisib families, after 1.5 months of culture under the same condition, 215 individuals are randomly selected for weight measurement, and the genomic DNA of the Litopenaeus vannamei is extracted according to a Tiangen marine animal tissue genome extraction kit (TIANGEN, Tiangen Biochemical technology, Ltd.).
The PCR detection is carried out on the Trmt10a gene of the 215-tailed prawn individual by using the detection primer (F: 5'-TCAATGGTGTTCATAAAGAGGA-3', R: 5'-CCTAAGCTAATCAGTATCAG-3'), and the reaction program is as follows: pre-denaturation at 95 ℃ for 4 min, (denaturation at 95 ℃ for 30 sec, annealing at 52-57 ℃ for 20 sec, extension at 72 ℃ for 1 min) x 35 cycles, and final extension at 72 ℃ for 10 min. Sequencing the PCR product, wherein the sequence of the Trmt10a gene is shown as SEQ ID NO.1, and specifically comprises the following steps:
cagacttacgcgaacgccatgttaacacgtgaaaaagccaatatgttgcgagaatttacaattatctttaccttatgtgccttttaatgcctgttcgtgtctaggagtgctcgtagataagaagaaagggggagaaaaggtgagattgaacgagagtttgtgaatgataaggtaatgtgttgtatttttttgacacgagaggaaaaaagactgtatattgtctataagatttaggttaggttaggttaggttaggttagttaggttaggttagttaggttaggttaggttataggttaggttaggttaggttaggttaggttaggttaggttataggttaggttaggttaggttataggttaggttaggttaggttataggttaggttaggttaggttaggttaggttaggtttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggtttaggttagggttagggttaggttaggttaggttataggttaggttaggttaggttaggttataggttaggttaggttaggtttaggttaggttaggttaggttaggttaggttaggttaggttataggttaggttaggttaaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggtttaggttagggttaggttaggttaggttaggttaggttataggtttaggttaggttaggttataggttaggttaggttggttaggttaggttaggttaggttaggttaggttaggttataggttaggttaggttaggttaggttaggttaggttaggttaggtttaggttaggtttataggtttaggtttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttatagggttaggttagttaggttataggttagttaggttataggttaggttaggttataggttaggttatagtttaggttaggttataggttataggttaggttaggttaggttaggttaggttaggttagggttaggttagggttaggtttaggttaggttagggttaggttatagttaggttaggtttaggttaggttaggttaggttggttaggttaggttaggttaggtaggttaggttaggttaggttaggttaggttttaggttaggttaggttagggttaggttagttaggttaggttaggttaggttaggttataggtttaggttaggttaggttaggttaggttaggttatagtttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttagggttaggttaggttatagtttaggtaggttagggttagggttggttaggttataggttaggttaggttaggtttaggttaggttaggttaggttattaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggttataggttaggttaggttataggttaggttaggttaggttagttaggttaggttaggttaggttaggttataggttaggttagttaggttaggtttaggttaggttaggttaggttaggttaggttaggttatagggttaggttaggttaggttaggtttaggttaggttggttaggttagggttaggttaggttaggtttttaggttaggttaggttaggttagggttataggttaggttaggttagggttaggttaggttagggttaggttaagttaggttaggttaggttaggtaggttataggttaggttttaggttaggttataggttaggttaggtttaggttaggttaggtaggttaggttagtttagttttaggttatagttagtaggttaggttgttaggtttaggttaggttatagttaggttaggttaggttggtttaggttaaggttaggttatagggttaggttaggttaggttatagggttaggttaggataggtttataggttagcttataggtttataggtttaggttaaggttagttagttagggttaggttaggttgggggttataggttaggttataggttataggttataagttgggttaggttaggttaggttaagttatggttttaggttaggttaggttatatggttgggttaggttaggttataggttaggttaggttatattaggttatagttgggttaggttataaggttaggttaggttgggttgggttatagttaggttaggttataggttgggttaggtaggttagaggttatgttaggttaggttaggttagtaggttaggttagaggttatgttaggttaggttataggttaagttaggttaggttaggttatagttaggtttaggttataggttaggttaggttaggttattttggttaggttaggttgtaggttaggttaggttatagtctaggttaggttataaggttaggttatagttgggttaggttaggttaggttaggttaggttaggttaggttaggttaggttaggtttaggttagttatctaggttaggttatatatatatatatatatatatatataatatatatatatatatatatatatatatatatatatagttaggttaggttaggttaacctataacctaacttaacctaatctataacctaacctaactaactataacctaaacctaacctataacctaacctacctaaacctactaacctatgctaacttaacctaatctataacctaacctaacctaacctataacctaaaccctaactaacctaacctaacctaaacctaacctacctaaactaacctaactaacctaacttaacctaatctataacctaacctaacctaacctattaacctaacctaaccttaactataaccaacccaacctaacctaacctatgacctaacctaacctataacctaacctaacccttaacctaactaactaacctataacctaactaccaaaaatataacctactaacctatacctaacctaacctaacctataacctaacctaacctaacctaaagcctataacctaacctaacctaactatacctaacctaacctaacctaactaacctaacctataacctaacctaacccctaacctaaccctaacctaataacctataacctaaccctataactaacctaacctatacctatataacctaacctatcctaacctataacctaactaactaacttttaacctaacctaatctataaactaacctaaacctaacctaacctataactaactaacctacctaacctaacctaacctaacctatataaccctaaaccctaacctaacctacctataacctaacctaactaacctataacctaacctaacctaaactaaaataacctaacctataacctaacctaacctataacctaacctaacctaaaacctaacctaacctaacctaacctaacctaacctaaccctaacctaacctataaccaacctaaaccctaacctatacctaacctaacctaaacctaacctaaccctacctaacctataacctaacctaacctacctaacctataacctaacctaacctaacctaacctaacctaacctataacctaacctaacctaacctaaacctaactaaaacctaacctaacctaacctaacctaaactataacctaacctaacctaacctataacctataacctaacctaacctaacctaacctaacctaacctaactataacctaacctaacctaaacctaaccctaacctaacctaactaaacctaacctaaaacctaaaacctataacctaacctaacctaacctataacctaacctaacctataacctaacctaacctaactataacctaacctaacctaaccctaacctataacctaacctaacctaactataactaactaacctaacctaaccctaactaacctaacctataacctaacctaacctaacctaacctataacctaacctaacctaacctataacctaaacctaacctataacctaacctaacctaactaacctataacctaacctaacctaaacctaacctaacctataacctaacctaacctaacctaacctatacctaacctaacctaacctaactaacctaacctaacctaacctaacctaactaacctataacctaacctaacctacctaacctaacctaacctaaacctaacctataacctaacctaacctaaacctaacctaaacctataaccttaacctaaacctaacctaacctaacaaacctataaacctaacctaacctataaaacctaacctaacctaacctataacctaactaacctaacctataacctaacctaacctaacctaaacctaacctatacctaacctaacctaaacctaacctaacctaacctataacctaacctaacctaacctaacctaacctataacctaacctataacctaacctataacctaacctaacctaacctaacctaacctaacctacctaacctaacctataacctaacctaaacctatacctaacctaacctaacctataacctaacctaacctaacctaacctaacctaaacctaacctacctataacctaacctaactataacctaacctaacctaactaacctaacctaacctaacctaacctataacctaacctaacctaacctataacctaactaacctaacctaacctaacctaacctataacctataacctaacctaacctaacctataacctaacctataacctaacctaacctaacctaacctataacctaacctataacctaacctataacctaacctaacctaacctaacctaaaacctacctataacctaacctaacctaacctaacctaacctacctaaccctaacctaacctaactataacctaacctaacctaacctatacctaacctaacctaaaacctaacctaacctaacctaaacctaaaccctatacctaacctaacctaacctataacctaacctaacctaacctaacctataacctaacctaacctaacctaacctataacctaacctaacctaacctaacctaacctaacctaacctaacctaacctaacctaacctaacctaacctataacctaacctaacctaatactgttatgataacagtaattataatgaaacatattgatattaataatgataatgatatttgtgtgatgataatgataatgataatgtcaatagtaataataatgatgtgaactagaatttacattccaaattctaaattctgagtttagcttgttcatagttatttataaataactattccagtttgtctatatttatcttgtaagcagtatacagttatgtatattatgtgtaaggtaattgataacaagtgtgatattttgagtagcagctcaaattgtgatattgacttattgataacaagacaccctttatatatgcacaatccactgtgttttgtgttattttgtgcaaagatggatgaagcacgtgaagccatccatctataaacaaaattaaacaaagcttcagtggatgatgtatgcaatcaatgccagtaagttaatatttgagaacttgataaggaagacatttaaacttttttttctacttattgtattgttttgcatgcttctctattgtaatatttgataatgagggcatttaaagtttctttttttttctatttattgtgctattgttgcatgcttctctattgtaagtgtttgaatgcattatttcagaaagcatttcttgtgtttcaggttaattcgccagcacaatggagtcgacagaggttatcaacggtgttcataaagaggatacacttctcgacaacagacctccctcagttgaagaaaacagcaacatgaacaacaacgacgacaacaagccttcacccgatccggagcagagtgccaatggaggagaaactcagacgttatccaaaagacagcagaagaagcttttgagaagacagaagtggaacgacacaaaagtggagagaagaaagagggagcgggagaagctgaaaaagagattggtggagaagagggcggccggagagccctgcggcaacatcaggaagaagttgaagcagatgaccatggcgagtagttcgtgtaaacagcgggttgttgtagacatgtcctttgatgacctcatgattgagaagcatttgtctcagtgcgttaaacaagttagccgttgttatagtgccaaccggagagtcagtagccctatgcaactctatgttacaagctttgaggggaaatgtgcagaggtcatgtccaaacagaatggctacgaacactgggatgtgtactttaaaaaggagaattatatggatcttttccccaaagaagacataatatacctcacaagtgaatcaaggaatgtgattacgtcagtggatgaaaacaaagtgtatgtcattggaggcttggtggaccacaatgtgcataaagggttgtgtctaagattggctgaagagaaaggtattgctcacgggaggcttccaatagacgaattcattgagatgaagacgagaaaagtcttgaccatcgatcacgtgttccgcattatactaggagtcacggaagggggttcgtggaaggaatctttcctgaagactatcccggcaaggaagggggcagtcggcaaggatgaggaaaatgactgtgaagattccgaattggaaaaggatgcgactaacaattcagacgacaagagcgaagacaacccttcagagagcagagagcctgtatgcgaaggtgatcccgagaagagctgatactgattagcttaggctgtttattgttactggaattatattttatgcttcttctctttgttgtttatattctcttttttaattaaattcacatcaggtttatatgtaaaccttgtaatcacctggaatttatgacttatcagattgatgagaatattaaatgggtgtttgtgagctgtgacaaaaatcccatgcgttgggtatttttattatatgtaattttagctcaaagcaaagtaagaagaaaatttgaagaaagtttatcacttttagtccaagcacacataggcctatatgccatgataaaactgtatcagaaatccaataattatataaaggattaaagaat。
the cDNA sequence is shown in SEQ ID NO.2, and through statistics of individual genotypes, the cDNA sequence shows that:
(1) the growth speed of the A/A genotype individual at the 6053 th base position is obviously higher than that of the A/C genotype individual under the same culture condition; the growth speed of the C/C genotype at the 6058 th base position under the same culture condition is obviously higher than that of an A/C genotype individual; the growth rate of the T/T genotype individual at the 6534 th base position is obviously higher than that of the T/G genotype individual under the same culture condition; the growth rate of the A/T genotype individual at the 6865 base position is obviously higher than that of the T/T genotype individual under the same culture condition (figure 2, table 1);
(2) missense mutation at 6053 base position C > A results in mutation of the amino acid encoded by the gene from threonine (Thr, T) to asparagine (Asn, N); missense mutation at base 6058 position A > C results in mutation of the amino acid encoded by the gene from threonine (Thr, T) to proline (Pro, P); the 6534 base position T > G missense mutation causes the mutation of the coding amino acid of the gene from aspartic acid (Asp, D) to glutamic acid (Glu, E); the missense mutation at the 6865 th base position T > A causes the mutation of the coded amino acid of the gene from serine (Ser, S) to threonine (Thr, T) (A in figure 1);
TABLE 1 correlation analysis of SNP sites and growth traits of the Trmt10a gene of prawn
Sequence listing
<110> animal science institute of academy of agricultural sciences of Guangdong province
<120> snp molecular marker associated with growth traits of litopenaeus vannamei, detection primer and application thereof
<160> 2
<170> SIPOSequenceListing 1.0
<210> 1
<211> 7261
<212> DNA
<213> Litopenaeus vannamei (Litopenaeus vannamei)
<400> 1
cagacttacg cgaacgccat gttaacacgt gaaaaagcca atatgttgcg agaatttaca 60
attatcttta ccttatgtgc cttttaatgc ctgttcgtgt ctaggagtgc tcgtagataa 120
gaagaaaggg ggagaaaagg tgagattgaa cgagagtttg tgaatgataa ggtaatgtgt 180
tgtatttttt tgacacgaga ggaaaaaaga ctgtatattg tctataagat ttaggttagg 240
ttaggttagg ttaggttagt taggttaggt tagttaggtt aggttaggtt ataggttagg 300
ttaggttagg ttaggttagg ttaggttagg ttataggtta ggttaggtta ggttataggt 360
taggttaggt taggttatag gttaggttag gttaggttag gttaggttag gtttaggtta 420
ggttaggtta ggttaggtta ggttaggtta ggttaggtta ggttaggttt aggttagggt 480
tagggttagg ttaggttagg ttataggtta ggttaggtta ggttaggtta taggttaggt 540
taggttaggt ttaggttagg ttaggttagg ttaggttagg ttaggttagg ttataggtta 600
ggttaggtta aggttaggtt aggttaggtt aggttaggtt aggttaggtt aggttaggtt 660
aggttaggtt aggtttaggt tagggttagg ttaggttagg ttaggttagg ttataggttt 720
aggttaggtt aggttatagg ttaggttagg ttggttaggt taggttaggt taggttaggt 780
taggttaggt tataggttag gttaggttag gttaggttag gttaggttag gttaggttta 840
ggttaggttt ataggtttag gtttaggtta ggttaggtta ggttaggtta ggttaggtta 900
ggttaggtta ggttaggtta ggttaggtta ggttaggtta tagggttagg ttagttaggt 960
tataggttag ttaggttata ggttaggtta ggttataggt taggttatag tttaggttag 1020
gttataggtt ataggttagg ttaggttagg ttaggttagg ttaggttagg gttaggttag 1080
ggttaggttt aggttaggtt agggttaggt tatagttagg ttaggtttag gttaggttag 1140
gttaggttgg ttaggttagg ttaggttagg taggttaggt taggttaggt taggttaggt 1200
tttaggttag gttaggttag ggttaggtta gttaggttag gttaggttag gttaggttat 1260
aggtttaggt taggttaggt taggttaggt taggttatag tttaggttag gttaggttag 1320
gttaggttag gttaggttag gttaggttag gttaggttag gttaggttag gttaggttag 1380
gttagggtta ggttaggtta tagtttaggt aggttagggt tagggttggt taggttatag 1440
gttaggttag gttaggttta ggttaggtta ggttaggtta ttaggttagg ttaggttagg 1500
ttaggttagg ttaggttagg ttaggttagg ttaggttata ggttaggtta ggttataggt 1560
taggttaggt taggttagtt aggttaggtt aggttaggtt aggttatagg ttaggttagt 1620
taggttaggt ttaggttagg ttaggttagg ttaggttagg ttaggttata gggttaggtt 1680
aggttaggtt aggtttaggt taggttggtt aggttagggt taggttaggt taggttttta 1740
ggttaggtta ggttaggtta gggttatagg ttaggttagg ttagggttag gttaggttag 1800
ggttaggtta agttaggtta ggttaggtta ggtaggttat aggttaggtt ttaggttagg 1860
ttataggtta ggttaggttt aggttaggtt aggtaggtta ggttagttta gttttaggtt 1920
atagttagta ggttaggttg ttaggtttag gttaggttat agttaggtta ggttaggttg 1980
gtttaggtta aggttaggtt atagggttag gttaggttag gttatagggt taggttagga 2040
taggtttata ggttagctta taggtttata ggtttaggtt aaggttagtt agttagggtt 2100
aggttaggtt gggggttata ggttaggtta taggttatag gttataagtt gggttaggtt 2160
aggttaggtt aagttatggt tttaggttag gttaggttat atggttgggt taggttaggt 2220
tataggttag gttaggttat attaggttat agttgggtta ggttataagg ttaggttagg 2280
ttgggttggg ttatagttag gttaggttat aggttgggtt aggtaggtta gaggttatgt 2340
taggttaggt taggttagta ggttaggtta gaggttatgt taggttaggt tataggttaa 2400
gttaggttag gttaggttat agttaggttt aggttatagg ttaggttagg ttaggttatt 2460
ttggttaggt taggttgtag gttaggttag gttatagtct aggttaggtt ataaggttag 2520
gttatagttg ggttaggtta ggttaggtta ggttaggtta ggttaggtta ggttaggtta 2580
ggtttaggtt agttatctag gttaggttat atatatatat atatatatat atataatata 2640
tatatatata tatatatata tatatatata tagttaggtt aggttaggtt aacctataac 2700
ctaacttaac ctaatctata acctaaccta actaactata acctaaacct aacctataac 2760
ctaacctacc taaacctact aacctatgct aacttaacct aatctataac ctaacctaac 2820
ctaacctata acctaaaccc taactaacct aacctaacct aaacctaacc tacctaaact 2880
aacctaacta acctaactta acctaatcta taacctaacc taacctaacc tattaaccta 2940
acctaacctt aactataacc aacccaacct aacctaacct atgacctaac ctaacctata 3000
acctaaccta acccttaacc taactaacta acctataacc taactaccaa aaatataacc 3060
tactaaccta tacctaacct aacctaacct ataacctaac ctaacctaac ctaaagccta 3120
taacctaacc taacctaact atacctaacc taacctaacc taactaacct aacctataac 3180
ctaacctaac ccctaaccta accctaacct aataacctat aacctaaccc tataactaac 3240
ctaacctata cctatataac ctaacctatc ctaacctata acctaactaa ctaactttta 3300
acctaaccta atctataaac taacctaaac ctaacctaac ctataactaa ctaacctacc 3360
taacctaacc taacctaacc tatataaccc taaaccctaa cctaacctac ctataaccta 3420
acctaactaa cctataacct aacctaacct aaactaaaat aacctaacct ataacctaac 3480
ctaacctata acctaaccta acctaaaacc taacctaacc taacctaacc taacctaacc 3540
taaccctaac ctaacctata accaacctaa accctaacct atacctaacc taacctaaac 3600
ctaacctaac cctacctaac ctataaccta acctaaccta cctaacctat aacctaacct 3660
aacctaacct aacctaacct aacctataac ctaacctaac ctaacctaaa cctaactaaa 3720
acctaaccta acctaaccta acctaaacta taacctaacc taacctaacc tataacctat 3780
aacctaacct aacctaacct aacctaacct aacctaacta taacctaacc taacctaaac 3840
ctaaccctaa cctaacctaa ctaaacctaa cctaaaacct aaaacctata acctaaccta 3900
acctaaccta taacctaacc taacctataa cctaacctaa cctaactata acctaaccta 3960
acctaaccct aacctataac ctaacctaac ctaactataa ctaactaacc taacctaacc 4020
ctaactaacc taacctataa cctaacctaa cctaacctaa cctataacct aacctaacct 4080
aacctataac ctaaacctaa cctataacct aacctaacct aactaaccta taacctaacc 4140
taacctaaac ctaacctaac ctataaccta acctaaccta acctaaccta tacctaacct 4200
aacctaacct aactaaccta acctaaccta acctaaccta actaacctat aacctaacct 4260
aacctaccta acctaaccta acctaaacct aacctataac ctaacctaac ctaaacctaa 4320
cctaaaccta taaccttaac ctaaacctaa cctaacctaa caaacctata aacctaacct 4380
aacctataaa acctaaccta acctaaccta taacctaact aacctaacct ataacctaac 4440
ctaacctaac ctaaacctaa cctataccta acctaaccta aacctaacct aacctaacct 4500
ataacctaac ctaacctaac ctaacctaac ctataaccta acctataacc taacctataa 4560
cctaacctaa cctaacctaa cctaacctaa cctacctaac ctaacctata acctaaccta 4620
aacctatacc taacctaacc taacctataa cctaacctaa cctaacctaa cctaacctaa 4680
acctaaccta cctataacct aacctaacta taacctaacc taacctaact aacctaacct 4740
aacctaacct aacctataac ctaacctaac ctaacctata acctaactaa cctaacctaa 4800
cctaacctaa cctataacct ataacctaac ctaacctaac ctataaccta acctataacc 4860
taacctaacc taacctaacc tataacctaa cctataacct aacctataac ctaacctaac 4920
ctaacctaac ctaaaaccta cctataacct aacctaacct aacctaacct aacctaccta 4980
accctaacct aacctaacta taacctaacc taacctaacc tatacctaac ctaacctaaa 5040
acctaaccta acctaaccta aacctaaacc ctatacctaa cctaacctaa cctataacct 5100
aacctaacct aacctaacct ataacctaac ctaacctaac ctaacctata acctaaccta 5160
acctaaccta acctaaccta acctaaccta acctaaccta acctaaccta acctaaccta 5220
taacctaacc taacctaata ctgttatgat aacagtaatt ataatgaaac atattgatat 5280
taataatgat aatgatattt gtgtgatgat aatgataatg ataatgtcaa tagtaataat 5340
aatgatgtga actagaattt acattccaaa ttctaaattc tgagtttagc ttgttcatag 5400
ttatttataa ataactattc cagtttgtct atatttatct tgtaagcagt atacagttat 5460
gtatattatg tgtaaggtaa ttgataacaa gtgtgatatt ttgagtagca gctcaaattg 5520
tgatattgac ttattgataa caagacaccc tttatatatg cacaatccac tgtgttttgt 5580
gttattttgt gcaaagatgg atgaagcacg tgaagccatc catctataaa caaaattaaa 5640
caaagcttca gtggatgatg tatgcaatca atgccagtaa gttaatattt gagaacttga 5700
taaggaagac atttaaactt ttttttctac ttattgtatt gttttgcatg cttctctatt 5760
gtaatatttg ataatgaggg catttaaagt ttcttttttt ttctatttat tgtgctattg 5820
ttgcatgctt ctctattgta agtgtttgaa tgcattattt cagaaagcat ttcttgtgtt 5880
tcaggttaat tcgccagcac aatggagtcg acagaggtta tcaacggtgt tcataaagag 5940
gatacacttc tcgacaacag acctccctca gttgaagaaa acagcaacat gaacaacaac 6000
gacgacaaca agccttcacc cgatccggag cagagtgcca atggaggaga aactcagacg 6060
ttatccaaaa gacagcagaa gaagcttttg agaagacaga agtggaacga cacaaaagtg 6120
gagagaagaa agagggagcg ggagaagctg aaaaagagat tggtggagaa gagggcggcc 6180
ggagagccct gcggcaacat caggaagaag ttgaagcaga tgaccatggc gagtagttcg 6240
tgtaaacagc gggttgttgt agacatgtcc tttgatgacc tcatgattga gaagcatttg 6300
tctcagtgcg ttaaacaagt tagccgttgt tatagtgcca accggagagt cagtagccct 6360
atgcaactct atgttacaag ctttgagggg aaatgtgcag aggtcatgtc caaacagaat 6420
ggctacgaac actgggatgt gtactttaaa aaggagaatt atatggatct tttccccaaa 6480
gaagacataa tatacctcac aagtgaatca aggaatgtga ttacgtcagt ggatgaaaac 6540
aaagtgtatg tcattggagg cttggtggac cacaatgtgc ataaagggtt gtgtctaaga 6600
ttggctgaag agaaaggtat tgctcacggg aggcttccaa tagacgaatt cattgagatg 6660
aagacgagaa aagtcttgac catcgatcac gtgttccgca ttatactagg agtcacggaa 6720
gggggttcgt ggaaggaatc tttcctgaag actatcccgg caaggaaggg ggcagtcggc 6780
aaggatgagg aaaatgactg tgaagattcc gaattggaaa aggatgcgac taacaattca 6840
gacgacaaga gcgaagacaa cccttcagag agcagagagc ctgtatgcga aggtgatccc 6900
gagaagagct gatactgatt agcttaggct gtttattgtt actggaatta tattttatgc 6960
ttcttctctt tgttgtttat attctctttt ttaattaaat tcacatcagg tttatatgta 7020
aaccttgtaa tcacctggaa tttatgactt atcagattga tgagaatatt aaatgggtgt 7080
ttgtgagctg tgacaaaaat cccatgcgtt gggtattttt attatatgta attttagctc 7140
aaagcaaagt aagaagaaaa tttgaagaaa gtttatcact tttagtccaa gcacacatag 7200
gcctatatgc catgataaaa ctgtatcaga aatccaataa ttatataaag gattaaagaa 7260
t 7261
<210> 2
<211> 1516
<212> DNA
<213> Litopenaeus vannamei (Litopenaeus vannamei)
<400> 2
cagacttacg cgaacgccat gttaacacgt gaaaaagcca atatgttgcg agaatttaca 60
attatcttta ccttatgtgc cttttaatgc ctgttcgtgt ctaggagtgc tcgtagataa 120
gaagaaaggg ggagaaaagg ttaattcgcc agcacaatgg agtcgacaga ggttatcaac 180
ggtgttcata aagaggatac acttctcgac aacagacctc cctcagttga agaaaacagc 240
aacatgaaca acaacgacga caacaagcct tcacccgatc cggagcagag tgccaatgga 300
ggagaaactc agccgttatc caaaagacag cagaagaagc ttttgagaag acagaagtgg 360
aacgacacaa aagtggagag aagaaagagg gagcgggaga agctgaaaaa gagattggtg 420
gagaagaggg cggccggaga gccctgcggc aacatcagga agaagttgaa gcagatgacc 480
atggcgagta gttcgtgtaa acagcgggtt gttgtagaca tgtcctttga tgacctcatg 540
attgagaagc atttgtctca gtgcgttaaa caagttagcc gttgttatag tgccaaccgg 600
agagtcagta gccctatgca actctatgtt acaagctttg aggggaaatg tgcagaggtc 660
atgtccaaac agaatggcta cgaacactgg gatgtgtact ttaaaaagga gaattatatg 720
gatcttttcc ccaaagaaga cataatatac ctcacaagtg aatcaaggaa tgtgattacg 780
tcagtggatg aaaacaaagt gtatgtcatt ggaggcttgg tggaccacaa tgtgcataaa 840
gggttgtgtc taagattggc tgaagagaaa ggtattgctc acgggaggct tccaatagac 900
gaattcattg agatgaagac gagaaaagtc ttgaccatcg atcacgtgtt ccgcattata 960
ctaggagtca cggaaggggg ttcgtggaag gaatctttcc tgaagactat cccggcaagg 1020
aagggggcag tcggcaagga tgaggaaaat gactgtgaag attccgaatt ggaaaaggat 1080
gcgactaaca attcagacga caagagcgaa gacaaccctt cagagagcag agagcctgta 1140
tgcgaaggtg atcccgagaa gagctgatac tgattagctt aggctgttta ttgttactgg 1200
aattatattt tatgcttctt ctctttgttg tttatattct cttttttaat taaattcaca 1260
tcaggtttat atgtaaacct tgtaatcacc tggaatttat gacttatcag attgatgaga 1320
atattaaatg ggtgtttgtg agctgtgaca aaaatcccat gcgttgggta tttttattat 1380
atgtaatttt agctcaaagc aaagtaagaa gaaaatttga agaaagttta tcacttttag 1440
tccaagcaca cataggccta tatgccatga taaaactgta tcagaaatcc aataattata 1500
taaaggatta aagaat 1516
Claims (5)
1. An SNP molecular marker combination related to the growth traits of Litopenaeus vannamei is characterized in that the SNP molecular marker combination is characterized in that the 6053 th base position of the sequence shown in SEQ ID NO.1 is C > A, the 6058 th base position is A > C, the 6534 th base position is T > G and the 6865 th base position is T > A, and the growth traits are body weight; the weight of the individual with AA/CC/TT/AT genotypes AT the four base positions in sequence under the same breeding condition is higher than that of the individual with AC/AC/TG/TT genotypes AT the four base positions in sequence.
2. The detection primer set of the SNP molecular marker combination according to claim 1, comprising the following 3 sets of detection primer pairs:
(1) primer pair for 6053 and 6058 position detection
g.Trmt10a-6053/6058-F：5’-CGGTGTTCATAAAGAGGATAC -3’ ；
g. Trmt10a-6053/6058-R：5’-CTCTCCACTTTTGTGTCGTTC -3’ ；
(2) 6534 position detection primer pair
g. Trmt10a-6534-F：5’-TGTCCAAACAGAATGGCTAC -3’ ；
g. Trmt10a-6534-R：5’-CCTCCCGTGAGCAATACCTT -3’ ；
(3) 6865 th position detection primer pair
g. Trmt10a-6865-F：5’-CAAGGATGAGGAAAATGACTGTG -3’ ；
g. Trmt10a-6865-R：5’- ATTCCAGGTGATTACAAGGTTTACA -3’。
3. A detection kit comprising the detection primer set of the SNP molecular marker set according to claim 2.
4. The use of the detection primer set of the SNP molecular marker combination according to claim 2 or the detection kit according to claim 3 in the breeding of a fast growing line of Litopenaeus vannamei; the SNP molecular marker combination is characterized in that the 6053 th base position of the sequence shown in SEQ ID NO.1 is C > A, the 6058 th base position is A > C, the 6534 th base position is T > G and the 6865 th base position is T > A, and the rapid growth is embodied as weight gain; the weight of the individual with AA/CC/TT/AT genotypes in the above four base positions under the same breeding condition is higher than that of the individual with AC/AC/TG/TT genotype in the above four base positions.
5. A method for detecting the growth speed of Litopenaeus vannamei is characterized by comprising the following steps: extracting genomic DNA of litopenaeus vannamei to be detected, amplifying by using a detection primer group of the SNP molecular marker combination according to claim 2, sequencing to obtain a sequencing result, determining the genotype of the SNP molecular marker based on the sequencing result, and judging the growth speed of the litopenaeus vannamei to be detected, wherein the growth speed is embodied as the weight gain speed, and the genotype of the SNP molecular marker is that the 6053 th base position of a sequence shown in SEQ ID NO.1 is C > A, the 6058 th base position is A > C, the 6534 th base position is T > G and the 6865 th base position is T > A; the weight of the individual with AA/CC/TT/AT genotypes AT the four base positions in sequence under the same breeding condition is higher than that of the individual with AC/AC/TG/TT genotypes AT the four base positions in sequence.
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Application publication date: 20220301 Assignee: Guangzhou Weifeng Biotechnology Co.,Ltd. Assignor: INSTITUTE OF ANIMAL SCIENCE, GUANGDONG ACADEMY OF AGRICULTURAL SCIENCES Contract record no.: X2023980054124 Denomination of invention: A SNP molecular marker and detection primer associated with growth traits of Litopenaeus vannamei and its application Granted publication date: 20220513 License type: Common License Record date: 20231227 |