SNP (Single Nucleotide Polymorphism) molecular marker related to goat body length character and application of SNP molecular marker

Abstract

The invention belongs to the technical field of molecular markers, and particularly relates to an SNP (Single Nucleotide Polymorphism) molecular marker related to a goat body length character and application of the SNP molecular marker. Through whole genome association analysis, a significant molecular marker related to the goat body length character is screened, SNP01-03 is related to the body length of a 3-month-old goat, and dominant genotypes are AA, GG and CC in sequence; sNP04-06 is related to the body length of a 9-month-old goat, and dominant genotypes are TT, AA and TT in sequence; sNP07 and SNP08 are related to the body length of a 12-month-old goat, and dominant genotypes are TT and GG in sequence. By utilizing the SNP molecular marker provided by the invention, the body length character of goats can be accurately predicted, high-body-length goats and low-body-length goats are distinguished, the goats are 3-month-old, 9-month-old and 12-month-old, a scientific basis is provided for molecular breeding of the goats, and the efficiency of genetic improvement of the goats is improved.

Description

Technical Field

[0001] The present invention belongs to the technical field of molecular markers, and particularly relates to an SNP molecular marker related to the body length trait of goats and its application. Background Art

[0002] Longling Huangshan goats are local excellent goat breeds formed through long-term natural and artificial selection in the special natural environment of Longling area, Baoshan City, Yunnan Province, and are local fine goat breeds registered in Yunnan Province. Longling Huangshan goats have the characteristics of tender and juicy meat with little mutton smell. Their skin has a large area, fine texture, and is firm and dense, and they are typical local excellent goat breeds for both meat and skin use.

[0003] In the field of goat genetic breeding, the body length trait is an important indicator to measure its production performance. Traditional breeding methods mainly rely on crossbreeding. For example, the prior art CN104161016A discloses a method for cultivating high-quality plateau red goats by crossbreeding Chinese and foreign goats, using the introduced Nubian goats as the male parent and the local Longling Huangshan goats in Yunnan as the female parent, which overcomes the defects such as the generally small body size of local Longling Huangshan goats in Yunnan. However, the method of crossbreeding has low efficiency and it is difficult to accurately predict the phenotypes of offspring. With the development of molecular biology technology, genome-wide association analysis has become an important tool for identifying molecular markers related to complex traits. It is very necessary to explore molecular markers affecting the body length of Longling Huangshan goats at the genomic level. Summary of the Invention

[0004] The purpose of the present invention is to provide an SNP molecular marker related to the body length trait of goats and its application, to quickly screen and identify the body length traits of goats at 3 months, 9 months, and 12 months old, and to improve the breeding efficiency of goats with a larger body length.

[0005] The present invention provides an SNP molecular marker related to the body length trait of goats, and the SNP molecular marker includes one or more of the body length molecular markers of goats at 3 months old, 9 months old, and 12 months old;

[0006] The body length molecular marker of goats at 3 months old includes one or more of SNP01, SNP02, and SNP03; SNP01 corresponds to position 87991079bp on chromosome 1 of the goat reference genome ARS1.2, and the base is A / G, where AA is the favorable genotype for the body length trait; SNP02 corresponds to position 109760797bp on chromosome 1 of the goat reference genome ARS1.2, and the base is A / G, where GG is the favorable genotype for the goat body length trait; SNP03 corresponds to position 759247bp on chromosome 17 of the goat reference genome ARS1.2, and the base is G / C, where CC is the favorable genotype for the goat body length trait;

[0007] The body length molecular markers of the 9-month-old goats include one or more of SNP04, SNP05, and SNP06; SNP04 corresponds to position 11619541 bp on chromosome 11 of the goat reference genome ARS1.2, with the base being T / G, where TT is the favorable genotype for the body length trait; SNP05 corresponds to position 59469971 bp on chromosome 19 of the goat reference genome ARS1.2, with the base being A / T, where AA is the favorable genotype for the goat body length trait; SNP06 corresponds to position 36707209 bp on chromosome 26 of the goat reference genome ARS1.2, with the base being C / T, where TT is the favorable genotype for the goat body length trait;

[0008] The body length molecular markers of the 12-month-old goats include SNP07 and / or SNP08; SNP07 corresponds to position 5627914 bp on chromosome 6 of the goat reference genome ARS1.2, with the base being T / C, where TT is the favorable genotype for the goat body length trait; SNP08 corresponds to position 17467988 bp on chromosome 6 of the goat reference genome ARS1.2, with the base being A / G, where GG is the favorable genotype for the goat body length trait.

[0009] Preferably, the nucleotide sequence of SNP01 is as shown in SEQ ID NO:1 or SEQ ID NO:2; among them, SEQ ID NO:1 is the dominant nucleotide sequence for the body length trait of 3-month-old goats; the nucleotide sequence of SNP02 is as shown in SEQ ID NO:3 or SEQ ID NO:4; among them, SEQ ID NO:3 is the dominant nucleotide sequence for the body length trait of 3-month-old goats; the nucleotide sequence of SNP03 is as shown in SEQ ID NO:5 or SEQ ID NO:6; among them, SEQ ID NO:5 is the dominant nucleotide sequence for the body length trait of 3-month-old goats;

[0010] The nucleotide sequence of SNP04 is as shown in SEQ ID NO:7 or SEQ ID NO:8; among them, SEQ ID NO:7 is the dominant nucleotide sequence for the body length trait of 9-month-old goats; the nucleotide sequence of SNP05 is as shown in SEQ ID NO:9 or SEQ ID NO:10, among them, SEQ ID NO:9 is the dominant nucleotide sequence for the body length trait of 9-month-old goats; the nucleotide sequence of SNP06 is as shown in SEQ ID NO:11 or SEQ ID NO:12, among them, SEQ ID NO:11 is the dominant nucleotide sequence for the body length trait of 9-month-old goats;

[0011] The nucleotide sequence of SNP07 is shown in SEQ ID NO:13 or SEQ ID NO:14; among them, SEQ ID NO:13 is the dominant nucleotide sequence of the body length trait of 12-month-old goats; the nucleotide sequence of SNP08 is shown in SEQ ID NO:15 or SEQ ID NO:16, where SEQ ID NO:15 is the dominant nucleotide sequence of the body length trait of 12-month-old goats.

[0012] The present invention also provides the application of a substance for detecting the SNP molecular markers described in the above technical solution in identifying the body length trait of goats; the age of the goats is one or more of 3 months old, 9 months old, and 12 months old.

[0013] Preferably, when the goat is a 3-month-old goat, and the polymorphism of SNP01 in the SNP molecular marker corresponding to 87991079bp on chromosome 1 of the goat reference genome is AA, and / or the polymorphism of SNP02 in the SNP molecular marker corresponding to 109760797bp on chromosome 1 of the goat reference genome ARS1.2 is GG, and / or the polymorphism of SNP03 in the SNP molecular marker corresponding to 759247bp on chromosome 17 of the goat reference genome ARS1.2 is CC, it is identified as a goat with a body length advantage;

[0014] When the goat is a 9-month-old goat, and the polymorphism of SNP04 in the SNP molecular marker corresponding to 11619541bp on chromosome 11 of the goat reference genome ARS1.2 is TT, and / or the polymorphism of SNP05 in the SNP molecular marker corresponding to 59469971bp on chromosome 19 of the goat reference genome ARS1.2 is AA, and / or the polymorphism of SNP06 in the SNP molecular marker corresponding to 36707209bp on chromosome 26 of the goat reference genome ARS1.2 is TT, it is identified as a goat with a body length advantage;

[0015] When the goat is a 12-month-old goat, and the polymorphism of SNP07 in the SNP molecular marker corresponding to 5627914bp on chromosome 6 of the goat reference genome ARS1.2 is TT, and / or the polymorphism of SNP08 in the SNP molecular marker corresponding to 17467988bp on chromosome 6 of the goat reference genome ARS1.2 is GG, it is identified as a goat with a body length advantage.

[0016] Preferably, the breed of the goats includes Longling Huang goats

[0017] The present invention also provides a method for identifying the body length trait of goats, including the following steps:

[0018] Detect SNP molecular markers on the chromosomes of goats to be identified; the SNP molecular markers are the SNP molecular markers described in the above technical solution;

[0019] When the goat is a 3-month-old goat, and the polymorphism of SNP01 in the SNP molecular marker corresponding to 87991079 bp on chromosome 1 of the goat reference genome is AA, and / or the polymorphism of SNP02 in the SNP molecular marker corresponding to 109760797 bp on chromosome 1 of the goat reference genome ARS1.2 is GG, and / or the polymorphism of SNP03 in the SNP molecular marker corresponding to 759247 bp on chromosome 17 of the goat reference genome ARS1.2 is CC, it is identified as a goat with a body length advantage;

[0020] When the goat is a 9-month-old goat, and the polymorphism of SNP04 in the SNP molecular marker corresponding to 11619541 bp on chromosome 11 of the goat reference genome ARS1.2 is TT, and / or the polymorphism of SNP05 in the SNP molecular marker corresponding to 59469971 bp on chromosome 19 of the goat reference genome ARS1.2 is AA, and / or the polymorphism of SNP06 in the SNP molecular marker corresponding to 36707209 bp on chromosome 26 of the goat reference genome ARS1.2 is TT, it is identified as a goat with a body length advantage;

[0021] When the goat is a 12-month-old goat, and the polymorphism of SNP07 in the SNP molecular marker corresponding to 5627914 bp on chromosome 6 of the goat reference genome ARS1.2 is TT, and / or the polymorphism of SNP08 in the SNP molecular marker corresponding to 17467988 bp on chromosome 6 of the goat reference genome ARS1.2 is GG, it is identified as a goat with a body length advantage.

[0022] The present invention also provides the application of substances for detecting the SNP molecular markers described in the above technical solution in the genetic breeding of goat breeds with body length trait advantages; the age of the goats is one or more of 3 months old, 9 months old, and 12 months old.

[0023] Preferably, the goat breed includes Longling Huangshan goats.

[0024] The present invention also provides a method for goat genetic breeding using the SNP molecular markers described in the above technical solution, including the following steps:

[0025] Detect the polymorphism of the SNP molecular markers in goats;

[0026] Select goats at 3 months old with the polymorphism of SNP01 in the described SNP molecular markers corresponding to 87991079 bp on chromosome 1 of the goat reference genome being AA, and / or the polymorphism of SNP02 in the SNP molecular markers corresponding to 109760797 bp on chromosome 1 of ARS1.2 of the goat reference genome being GG, and / or the polymorphism of SNP03 in the SNP molecular markers corresponding to 759247 bp on chromosome 17 of ARS1.2 of the goat reference genome being CC as male or female parents to increase the body length of the offspring;

[0027] Select goats at 9 months old with the polymorphism of SNP04 in the described SNP molecular markers corresponding to 11619541 bp on chromosome 11 of ARS1.2 of the goat reference genome being TT, and / or the polymorphism of SNP05 in the SNP molecular markers corresponding to 59469971 bp on chromosome 19 of ARS1.2 of the goat reference genome being AA, and / or the polymorphism of SNP06 in the SNP molecular markers corresponding to 36707209 bp on chromosome 26 of ARS1.2 of the goat reference genome being TT as male or female parents to increase the body length of the offspring;

[0028] Select goats at 12 months old with the polymorphism of SNP07 in the described SNP molecular markers corresponding to 5627914 bp on chromosome 6 of ARS1.2 of the goat reference genome being TT, and / or the polymorphism of SNP08 in the SNP molecular markers corresponding to 17467988 bp on chromosome 6 of ARS1.2 of the goat reference genome being GG as male or female parents to increase the body length of the offspring.

[0029] Beneficial effects:

[0030] The SNP molecular markers provided by the present invention include one or more of SNP01 - 08; SNP01, SNP02 and SNP03 are related to the body length of goats at 3 months old, and the dominant genotypes of SNP01, SNP02 and SNP03 are AA, GG and CC in sequence; SNP04, SNP05 and SNP06 are related to the body length of goats at 9 months old, and the dominant genotypes of SNP04, SNP05 and SNP06 are TT, AA and TT in sequence; SNP07 and SNP08 are related to the body length of goats at 12 months old, and the dominant genotypes of SNP07 and SNP08 are TT and GG in sequence. The SNP molecular markers of the present invention are related to the body length trait of goats, can distinguish high - body - length goats from low - body - length goats, wherein the goats are 3 - month - old, 9 - month - old and 12 - month - old goats, and optimize the body length traits of the offspring goats at 3 months old, 9 months old and 12 months old. Description of the Drawings

[0031] To more clearly illustrate the technical solutions in the embodiments of the present invention or the prior art, the following will briefly introduce the drawings required in the embodiments.

[0032] Figure 1 Manhattan plot and normal QQ plot for the body length trait of 3-month-old goats;

[0033] Figure 2 Manhattan plot and normal QQ plot for the body length trait of 9-month-old goats;

[0034] Figure 3 Manhattan plot and normal QQ plot for the body length trait of 12-month-old goats;

[0035] Figure 4 Distribution map of the genotype of SNP01-05 corresponding to the body length phenotypic value of goats; where ns indicates no significant difference, * indicates P < 0.05, ** indicates P < 0.01, *** indicates P < 0.001, and **** indicates P < 0.0001. Detailed implementation manners

[0036] The present invention provides an SNP molecular marker related to the body length trait of goats, and the SNP molecular marker includes one or more of the body length molecular markers of 3-month-old goats, 9-month-old goats, and 12-month-old goats;

[0037] The body length molecular marker of 3-month-old goats includes one or more of SNP01, SNP02, and SNP03; SNP01 corresponds to 87991079bp on chromosome 1 of the goat reference genome ARS1.2, and the base is A / G, where AA is the favorable genotype for the body length trait; SNP02 corresponds to 109760797bp on chromosome 1 of the goat reference genome ARS1.2, and the base is A / G, where GG is the favorable genotype for the goat body length trait; SNP03 corresponds to 759247bp on chromosome 17 of the goat reference genome ARS1.2, and the base is G / C, where CC is the favorable genotype for the goat body length trait;

[0038] The body length molecular markers of the 9-month-old goats include one or more of SNP04, SNP05, and SNP06; SNP04 corresponds to position 11619541bp on chromosome 11 of the goat reference genome ARS1.2, with the base being T / G, and TT is the favorable genotype for the body length trait; SNP05 corresponds to position 59469971bp on chromosome 19 of the goat reference genome ARS1.2, with the base being A / T, and AA is the favorable genotype for the goat body length trait; SNP06 corresponds to position 36707209bp on chromosome 26 of the goat reference genome ARS1.2, with the base being C / T, and TT is the favorable genotype for the goat body length trait;

[0039] The body length molecular markers of the 12-month-old goats include SNP07 and / or SNP08; SNP07 corresponds to position 5627914bp on chromosome 6 of the goat reference genome ARS1.2, with the base being T / C, and TT is the favorable genotype for the goat body length trait; SNP08 corresponds to position 17467988bp on chromosome 6 of the goat reference genome ARS1.2, with the base being A / G, and GG is the favorable genotype for the goat body length trait.

[0040] In the present invention, the accession number of the goat reference genome ARS1.2 in NCBI is GCA_001704415.2. The dominant genotype described in the present invention is the genotype with a longer body length.

[0041] As an embodiment, the nucleotide sequence of SNP01 of the present invention is as shown in SEQ ID NO:1 or SEQ ID NO:2; wherein, SEQ ID NO:1 is the dominant nucleotide sequence of the body length trait of 3-month-old goats. As an embodiment, the nucleotide sequence of SNP02 of the present invention is as shown in SEQ ID NO:3 or SEQ ID NO:4; wherein, SEQ ID NO:3 is the dominant nucleotide sequence of the body length trait of 3-month-old goats. As an embodiment, the nucleotide sequence of SNP03 of the present invention is as shown in SEQ ID NO:5 or SEQ ID NO:6; wherein, SEQ ID NO:5 is the dominant nucleotide sequence of the body length trait of 3-month-old goats. As an embodiment, the nucleotide sequence of SNP04 of the present invention is as shown in SEQ ID NO:7 or SEQ ID NO:8; wherein, SEQ ID NO:7 is the dominant nucleotide sequence of the body length trait of 9-month-old goats. As an embodiment, the nucleotide sequence of SNP05 of the present invention is as shown in SEQ ID NO:9 or SEQ ID NO:10, wherein, SEQ ID NO:9 is the dominant nucleotide sequence of the body length trait of 9-month-old goats. As an embodiment, the nucleotide sequence of SNP06 of the present invention is as shown in SEQ ID NO:11 or SEQ ID NO:12, wherein, SEQ ID NO:11 is the dominant nucleotide sequence of the body length trait of 9-month-old goats. As an embodiment, the nucleotide sequence of SNP07 of the present invention is as shown in SEQ ID NO:13 or SEQ ID NO:14; wherein, SEQ ID NO:13 is the dominant nucleotide sequence of the body length trait of 12-month-old goats. As an embodiment, the nucleotide sequence of SNP08 of the present invention is as shown in SEQ ID NO:15 or SEQ ID NO:16, wherein, SEQ ID NO:15 is the dominant nucleotide sequence of the body length trait of 12-month-old goats.

[0042] Through genome-wide association analysis, the present invention screens significant SNP loci related to the body length trait of goats and discovers the SNP molecular markers (SNP01, SNP02, SNP03, SNP04, SNP05, SNP06, SNP07 and SNP08) described in the above technical solutions, which can more accurately predict the body length trait of goats and provide a scientific basis for the molecular breeding of goats. The application of the present invention not only improves the efficiency of goat genetic improvement, but also provides new molecular marker resources for the genetic breeding of other livestock.

[0043] Based on the above advantages, the application of substances for detecting the SNP molecular markers provided by the present invention in identifying the body length traits of goats and / or the genetic breeding of goat breeds with advantages in body length traits also belongs to the protection scope of the present invention. The age of the goats described in the present invention is one or more of 3 months old, 9 months old, and 12 months old. As an implementation manner, the breeds of the goats include Longling Huangshan goats.

[0044] The present invention provides a method for identifying the body length traits of goats, including the following steps:

[0045] Detect the SNP molecular markers on the chromosomes of the goats to be identified; the SNP molecular markers are the SNP molecular markers described in the above technical solution;

[0046] When the goat is a 3-month-old goat, and the polymorphism of SNP01 in the SNP molecular markers corresponding to 87991079 bp on chromosome 1 of the goat reference genome is AA, and / or, the polymorphism of SNP02 in the SNP molecular markers corresponding to 109760797 bp on chromosome 1 of the goat reference genome ARS1.2 is GG, and / or, the polymorphism of SNP03 in the SNP molecular markers corresponding to 759247 bp on chromosome 17 of the goat reference genome ARS1.2 is CC, it is identified as a goat with an advantage in body length;

[0047] When the goat is a 9-month-old goat, and the polymorphism of SNP04 in the SNP molecular markers corresponding to 11619541 bp on chromosome 11 of the goat reference genome ARS1.2 is TT, and / or, the polymorphism of SNP05 in the SNP molecular markers corresponding to 59469971 bp on chromosome 19 of the goat reference genome ARS1.2 is AA, and / or, the polymorphism of SNP06 in the SNP molecular markers corresponding to 36707209 bp on chromosome 26 of the goat reference genome ARS1.2 is TT, it is identified as a goat with an advantage in body length;

[0048] When the goat is a 12-month-old goat, and the polymorphism of SNP07 in the SNP molecular markers corresponding to 5627914 bp on chromosome 6 of the goat reference genome ARS1.2 is TT, and / or, the polymorphism of SNP08 in the SNP molecular markers corresponding to 17467988 bp on chromosome 6 of the goat reference genome ARS1.2 is GG, it is identified as a goat with an advantage in body length.

[0049] The present invention has no strict requirements for the method of detecting the SNP molecular markers on the chromosomes of the goats to be identified, and conventional methods in the art can be used.

[0050] The present invention also provides a method for goat genetic breeding using the SNP molecular markers described in the above technical solution, comprising the following steps:

[0051] Detect the polymorphism of the SNP molecular markers in goats;

[0052] Select and retain goat individuals in which the polymorphism of SNP01 corresponding to 87991079 bp on chromosome 1 of the goat reference genome in the SNP molecular markers is AA, and / or the polymorphism of SNP02 corresponding to 109760797 bp on chromosome 1 of the goat reference genome ARS1.2 in the SNP molecular markers is GG, and / or the polymorphism of SNP03 corresponding to 759247 bp on chromosome 17 of the goat reference genome ARS1.2 in the SNP molecular markers is CC as male parents or female parents to increase the body length of the offspring;

[0053] Select and retain goat individuals in which the polymorphism of SNP04 corresponding to 11619541 bp on chromosome 11 of the goat reference genome ARS1.2 in the SNP molecular markers is TT, and / or the polymorphism of SNP05 corresponding to 59469971 bp on chromosome 19 of the goat reference genome ARS1.2 in the SNP molecular markers is AA, and / or the polymorphism of SNP06 corresponding to 36707209 bp on chromosome 26 of the goat reference genome ARS1.2 in the SNP molecular markers is TT as male parents or female parents to increase the body length of the offspring;

[0054] Select and retain goat individuals in which the polymorphism of SNP07 corresponding to 5627914 bp on chromosome 6 of the goat reference genome ARS1.2 in the SNP molecular markers is TT, and / or the polymorphism of SNP08 corresponding to 17467988 bp on chromosome 6 of the goat reference genome ARS1.2 in the SNP molecular markers is GG as male parents or female parents to increase the body length of the offspring.

[0055] The present invention has no strict requirements for detecting the polymorphism of the SNP molecular markers in goats, and conventional methods in the art can be used.

[0056] To further illustrate the present invention, the following describes in detail a SNP molecular marker related to the body length trait of goats and its application provided by the present invention with reference to the drawings and embodiments, but they should not be construed as limiting the protection scope of the present invention.

[0057] Example 1 Screening of SNP Loci Related to the Body Length Trait of Goats

[0058] 1. Sample Collection and Sequencing

[0059] Collect 300 blood samples of Longling Huangshan goats and entrust Beijing Yinuo Zhongda Biotechnology Co., Ltd. to conduct whole-genome resequencing. Using high-throughput sequencing technology, obtain the genomic data of each sample. At the same time, strictly measure the chest depth phenotypic indicators of Longling Huangshan goats in accordance with NY / T 1236-2023 "Technical Specification for Determination of Production Performance of Breeding Goats".

[0060] 2. Data Alignment and SNP Locus Identification

[0061] Align the sequenced Fastq files with the ARS1.2 reference genome using the BWA (Version: 0.7.18) software. After alignment, use the samtools (Version: 1.20) software to generate a bam-format file. Then obtain a VCF file containing all variant information through the GATK (Version: 4.6.0.0) software. Finally, filter the VCF file through the Plink software, excluding loci with a missing rate above 20% and a minor allele frequency within 0.05. Ultimately, obtain a SNP set containing 10,726,542 variant loci.

[0062] 3. Genome-Wide Association Analysis and Extraction of SNP Locus Combinations

[0063] Perform genome-wide association analysis on the body length traits of these 300 goats at 3 months, 9 months, and 12 months of age using the emmax software, and draw Manhattan plots and normal QQ plots to identify SNP loci significantly associated with the body length traits. Screen out SNP loci with a p-value less than or equal to 0.000001. The results are as Figures 1 to 3 shown in Table 1.

[0064] According to Figures 1 to 3 it can be seen that extract SNP loci with a p-value less than or equal to 0.000001 from the total SNP set of 3-month-old goats to form 7 SNP loci ([[]] Figure 1 ) related to the body length trait of 3-month-old Longling Huangshan goats; extract SNP loci with a p-value less than or equal to 0.000001 from the total SNP set of 9-month-old goats to form 8 SNP loci ([[]] Figure 2 ) related to the body length trait of 9-month-old Longling Huangshan goats; extract SNP loci with a p-value less than or equal to 0.000001 from the total SNP set of 12-month-old goats to form 8 SNP loci ([[]] Figure 3 ) related to the body length trait of 12-month-old Longling Huangshan goats.

[0065] Table 1 Significant SNP Loci Related to Body Length Traits

[0066]

[0067]

[0068] Note: E in Table 1 is the symbol in scientific notation, representing 10 to the power of n. That is, 8.98E-07 in Table 1 is 8.98×10 -7 , and the same applies to other p-value values.

[0069] 4. Dominant genotype combinations

[0070] Statistical analysis was performed on the phenotypic values corresponding to the genotypes of the selected significant SNPs. It was found that SNPs SNP01, SNP02, SNP03, SNP04, SNP05, SNP06, SNP07, and SNP08 had dominant genotypes. The specific locus information is shown in Table 2. The nucleotide sequences of the molecular markers containing the above mutation sites are shown in Table 3.

[0071] Table 2 Information on SNP locus combinations screened in the present invention

[0072]

[0073] Note: E in Table 1 is the symbol in scientific notation, representing 10 to the power of n. That is, 8.98E-07 in Table 1 is 8.98×10 -7 , and the same applies to other p-value values.

[0074] Table 3 Nucleotide sequences of SNP molecular markers screened in the present invention

[0075]

[0076]

[0077] As can be seen from Table 2 and Table 3: Through resequencing and genome-wide association analysis, the present invention screened out significant SNP loci related to the body length trait of goats, and discovered SNP loci SNP01, SNP02, SNP03, SNP04, SNP05, SNP06, SNP07, and SNP08 and their dominant genotypes. SNP01, SNP02, and SNP03 are beneficial mutations, and the significant dominant genotypes are AA, GG, and CC respectively; SNP04 is a beneficial mutation, and the significant dominant genotype is TT. SNP05 is a harmful mutation, and the significant dominant genotype is AA. SNP06 is a beneficial mutation, and the significant dominant genotype is TT; SNP07 is a harmful mutation, and the significant dominant genotype is TT. SNP08 is a beneficial mutation, and the significant dominant genotype is GG.

[0078] Example 2 SNP molecular marker genotyping and its association verification with body length trait

[0079] Based on the SNP locus combination (SNP01, SNP02, SNP03, SNP04, SNP05, SNP06, SNP07, and SNP08) obtained in Example 1, another 300 Longling Yellow Goats were selected as the research objects, and the above 8 loci were genotyped respectively, and the correlation analysis was carried out with the body length of Longling Yellow Goats. The results are as Figure 4 shown in Table 4.

[0080] Table 4 Correlation analysis results of the polymorphism of the SNP molecular markers screened by the present invention and the body length trait

[0081]

[0082]

[0083] Note: Different letters indicate significant differences (P < 0.05), and the same letter indicates no significant difference (P > 0.05). If only one individual is detected for a certain genotype of the molecular marker, it is not included in the analysis.

[0084] As can be seen from Figure 4 Table 4, for SNP01, the body length of individuals with the genotype AA is the largest, and the body length of individuals with the genotype GG is the smallest; for SNP02, the body length of individuals with the genotype GG is the largest, and the body length of individuals with the genotype AA / AG is the smallest; for SNP03, the body length of individuals with the genotype CC is the largest, and the body length of individuals with the genotype GG / GC is the smallest; for SNP04, the body length of individuals with the genotype TT is the largest, and the body length of individuals with the genotype GG is the smallest; for SNP05, the body length of individuals with the genotype AA is the largest, and the body length of individuals with the genotype TT is the smallest; for SNP06, the body length of individuals with the genotype TT is the largest, and the body length of individuals with the genotype CC / CT is the smallest; for SNP07, the body length of individuals with the genotype TT is the largest, and the body length of individuals with the genotype CC / TC is the smallest; for SNP08, the body length of individuals with the genotype GG is the largest, and the body length of individuals with the genotype AA / AG is the smallest.

[0085] In the genome-wide association analysis, the SNP01, SNP02, SNP03, SNP04, SNP05, SNP06, SNP07, and SNP08 molecular markers in the goat genome all reached the genome-wide significant level, indicating that the markers are significantly correlated with the body length trait of Longling Yellow Goats.. Thus, it can be seen that the SNP01, SNP02, SNP03, SNP04, SNP05, SNP06, SNP07, and SNP08 molecular markers in the goat genome can be used to screen the dominant body length traits of Longling Yellow Goats and increase the body length of the offspring of Longling Yellow Goats.

[0086] Although the preferred embodiments of the present invention have been described, those skilled in the art can make additional changes and modifications once they learn the basic creative concept. Therefore, the appended claims are intended to be construed to include the preferred embodiments as well as all changes and modifications falling within the scope of the present invention.

[0087] Those skilled in the art can make various changes and modifications to the present invention without departing from the spirit and scope of the present invention. Thus, if these modifications and variations of the present invention fall within the scope of the claims of the present invention and their equivalent technologies, the present invention also intends to include these modifications and variations.

Claims

1. A SNP molecular marker related to the body length trait of goats, characterized in that, The SNP molecular markers include one or more of the body length molecular markers of 3-month-old goats, 9-month-old goats, and 12-month-old goats; The body length molecular marker of 3-month-old goats includes one or more of SNP01, SNP02, and SNP03; SNP01 corresponds to position 87991079bp on chromosome 1 of the goat reference genome ARS1.2, with the base being A / G, where AA is the favorable genotype for body length traits; SNP02 corresponds to position 109760797bp on chromosome 1 of the goat reference genome ARS1.2, with the base being A / G, where GG is the favorable genotype for goat body length traits; SNP03 corresponds to position 759247bp on chromosome 17 of the goat reference genome ARS1.2, with the base being G / C, where CC is the favorable genotype for goat body length traits; The body length molecular marker of 9-month-old goats includes one or more of SNP04, SNP05, and SNP06; SNP04 corresponds to position 11619541bp on chromosome 11 of the goat reference genome ARS1.2, with the base being T / G, where TT is the favorable genotype for body length traits; SNP05 corresponds to position 59469971bp on chromosome 19 of the goat reference genome ARS1.2, with the base being A / T, where AA is the favorable genotype for goat body length traits; SNP06 corresponds to position 36707209bp on chromosome 26 of the goat reference genome ARS1.2, with the base being C / T, where TT is the favorable genotype for goat body length traits; The body length molecular marker of 12-month-old goats includes SNP07 and / or SNP08; SNP07 corresponds to position 5627914bp on chromosome 6 of the goat reference genome ARS1.2, with the base being T / C, where TT is the favorable genotype for goat body length traits; SNP08 corresponds to position 17467988bp on chromosome 6 of the goat reference genome ARS1.2, with the base being A / G, where GG is the favorable genotype for goat body length traits.

2. The SNP molecular marker according to claim 1, wherein The nucleotide sequence of SNP01 is as shown in SEQ ID NO:1 or SEQ ID NO:2; among them, SEQ ID NO:1 is the dominant nucleotide sequence of the body length trait of 3-month-old goats; the nucleotide sequence of SNP02 is as shown in SEQ ID NO:3 or SEQ ID NO:4; among them, SEQ ID NO:3 is the dominant nucleotide sequence of the body length trait of 3-month-old goats; the nucleotide sequence of SNP03 is as shown in SEQ ID NO:5 or SEQ ID NO:6; among them, SEQ ID NO:5 is the dominant nucleotide sequence of the body length trait of 3-month-old goats; The nucleotide sequence of SNP04 is shown in SEQ ID NO:7 or SEQ ID NO:8; among them, SEQ ID NO:7 is the dominant nucleotide sequence of the body length trait of 9-month-old goats; the nucleotide sequence of SNP05 is shown in SEQ ID NO:9 or SEQ ID NO:10, where SEQ ID NO:9 is the dominant nucleotide sequence of the body length trait of 9-month-old goats; the nucleotide sequence of SNP06 is shown in SEQ ID NO:11 or SEQ ID NO:12, where SEQ ID NO:11 is the dominant nucleotide sequence of the body length trait of 9-month-old goats; The nucleotide sequence of SNP07 is shown in SEQ ID NO:13 or SEQ ID NO:14; among them, SEQ ID NO:13 is the dominant nucleotide sequence of the body length trait of 12-month-old goats; the nucleotide sequence of SNP08 is shown in SEQ ID NO:15 or SEQ ID NO:16, where SEQ ID NO:15 is the dominant nucleotide sequence of the body length trait of 12-month-old goats.

3. Use of a substance for detecting the SNP molecular marker according to claim 1 or 2 in identifying the body length trait of goats; the age of the goats is one or more of 3 months old, 9 months old, and 12 months old.

4. The application according to claim 3, characterized in that When the goat is a 3-month-old goat, and the polymorphism of SNP01 in the SNP molecular marker corresponding to 87991079 bp on chromosome 1 of the goat reference genome is AA, and / or, the polymorphism of SNP02 in the SNP molecular marker corresponding to 109760797 bp on chromosome 1 of the goat reference genome ARS1.2 is GG, and / or, the polymorphism of SNP03 in the SNP molecular marker corresponding to 759247 bp on chromosome 17 of the goat reference genome ARS1.2 is CC, it is identified as a goat with a body length advantage; When the goat is a 9-month-old goat, and the polymorphism of SNP04 in the SNP molecular marker corresponding to 11619541 bp on chromosome 11 of the goat reference genome ARS1.2 is TT, and / or, the polymorphism of SNP05 in the SNP molecular marker corresponding to 59469971 bp on chromosome 19 of the goat reference genome ARS1.2 is AA, and / or, the polymorphism of SNP06 in the SNP molecular marker corresponding to 36707209 bp on chromosome 26 of the goat reference genome ARS1.2 is TT, it is identified as a goat with a body length advantage; When the goat is a 12-month-old goat, and the polymorphism of SNP07 in the SNP molecular marker corresponding to 5627914 bp on chromosome 6 of the goat reference genome ARS1.2 is TT, and / or, the polymorphism of SNP08 in the SNP molecular marker corresponding to 17467988 bp on chromosome 6 of the goat reference genome ARS1.2 is GG, it is identified as a goat with a body length advantage.

5. The application according to claim 3 or 4, characterized in that, The breeds of the goats include Longling Huangshan goats.

6. A method for identifying the body length trait of goats, characterized in that, It includes the following steps: Detect the SNP molecular markers on the chromosomes of the goats to be identified; the SNP molecular markers are the SNP molecular markers described in Claim 1 or 2; When the goat is a 3-month-old goat, and the polymorphism of SNP01 in the SNP molecular markers corresponding to 87,991,079 bp on Chromosome 1 of the goat reference genome is AA, and / or, the polymorphism of SNP02 in the SNP molecular markers corresponding to 109,760,797 bp on Chromosome 1 of the goat reference genome ARS1.2 is GG, and / or, the polymorphism of SNP03 in the SNP molecular markers corresponding to 759,247 bp on Chromosome 17 of the goat reference genome ARS1.2 is CC, it is identified as a goat with a body length advantage; When the goat is a 9-month-old goat, and the polymorphism of SNP04 in the SNP molecular markers corresponding to 11,619,541 bp on Chromosome 11 of the goat reference genome ARS1.2 is TT, and / or, the polymorphism of SNP05 in the SNP molecular markers corresponding to 59,469,971 bp on Chromosome 19 of the goat reference genome ARS1.2 is AA, and / or, the polymorphism of SNP06 in the SNP molecular markers corresponding to 36,707,209 bp on Chromosome 26 of the goat reference genome ARS1.2 is TT, it is identified as a goat with a body length advantage; When the goat is a 12-month-old goat, and the polymorphism of SNP07 in the SNP molecular markers corresponding to 5,627,914 bp on Chromosome 6 of the goat reference genome ARS1.2 is TT, and / or, the polymorphism of SNP08 in the SNP molecular markers corresponding to 17,467,988 bp on Chromosome 6 of the goat reference genome ARS1.2 is GG, it is identified as a goat with a body length advantage.

7. Application of the substance for detecting the SNP molecular markers described in Claim 1 or 2 in the genetic breeding of goat breeds with an advantage in body length traits; the age of the goats is one or more of 3 months old, 9 months old, and 12 months old.

8. The application according to claim 7, wherein The goat breed includes Longling Huangshan goats.

9. A method for goat genetic breeding using the SNP molecular marker described in claim 1 or 2, characterized in that, It includes the following steps: Detect the polymorphism of the SNP molecular markers in the goats; Select and retain goat individuals in 3-month-old goats where the polymorphism of SNP01 in the SNP molecular markers corresponding to 87,991,079 bp on Chromosome 1 of the goat reference genome is AA, and / or, the polymorphism of SNP02 in the SNP molecular markers corresponding to 109,760,797 bp on Chromosome 1 of the goat reference genome ARS1.2 is GG, and / or, the polymorphism of SNP03 in the SNP molecular markers corresponding to 759,247 bp on Chromosome 17 of the goat reference genome ARS1.2 is CC as male or female parents to increase the body length of the offspring; Select goats at 9 months old with the polymorphism of SNP04 in the SNP molecular markers corresponding to 11619541 bp on chromosome 11 of the goat reference genome ARS1.2 being TT, and / or the polymorphism of SNP05 in the SNP molecular markers corresponding to 59469971 bp on chromosome 19 of the goat reference genome ARS1.2 being AA, and / or the polymorphism of SNP06 in the SNP molecular markers corresponding to 36707209 bp on chromosome 26 of the goat reference genome ARS1.2 being TT as male or female parents to increase the body length of the offspring; Select goats at 12 months old with the polymorphism of SNP07 in the SNP molecular markers corresponding to 5627914 bp on chromosome 6 of the goat reference genome ARS1.2 being TT, and / or the polymorphism of SNP08 in the SNP molecular markers corresponding to 17467988 bp on chromosome 6 of the goat reference genome ARS1.2 being GG as male or female parents to increase the body length of the offspring.

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