A SNP marker, liquid-phase chip for milk production traits of Bactrian camel and its application

Abstract

The present invention provides a SNP marker, a liquid-phase chip for the milk production traits of Bactrian camels, and their applications, belonging to the technical field of genomics. Based on the genetic markers related to the lactation performance of Bactrian camels, the present invention provides a SNP marker related to the milk production traits of Bactrian camels and a functional liquid-phase chip, which can be used for the molecular breeding of dairy Bactrian camels, greatly improving the efficiency and accuracy of Bactrian camel breeding, and making the breeding selection more scientific and efficient. Secondly, through the molecular breeding using the SNP marker or liquid-phase chip provided by the present invention, the milk yield and milk quality of Bactrian camels can be improved, thereby increasing the economic benefits of farmers and herdsmen.

Description

Technical Field

[0001] The present invention belongs to the technical field of genomics, and particularly relates to a SNP marker related to the milk production traits of Bactrian camels, a liquid-phase chip and their applications. Background Art

[0002] As a highly adaptable livestock, the Bactrian camel (Camelus Bactrians) not only plays an important role in traditional animal husbandry, but also its dairy products have gradually gained market favor in modern agricultural production. Milk yield, milk protein content, and milk fat content are key indicators for evaluating the lactation performance of dairy Bactrian camels. Milk yield directly reflects the economic potential of Bactrian camels as a source of dairy products; the milk protein content serves as a criterion for evaluating the quality of dairy products, which not only affects the nutritional value of dairy products but also their processing characteristics; the importance of milk fat content lies in that the milk fat globules in camel milk are small, easy to digest and absorb, and contain a relatively high level of beneficial fatty acids. These characteristics endow camel milk with the potential to become an important dairy product for improving human health and a functional food with antibacterial, antiviral, antioxidant, and anticancer properties. However, the genetic mechanism of milk production traits in Bactrian camels has not been fully elucidated, which limits the improvement of milk production traits and the full exploration of genetic potential.

[0003] In recent years, with the booming development of the camel milk market, the breeding research of dairy Bactrian camels has received unprecedented attention. Camel milk, with its unique nutritional value and health benefits, has gradually become a new high-end dairy product in domestic and international markets. In such a market background, improving the milk yield and milk quality of Bactrian camels has become the focus of breeding work. Currently, the published research at home and abroad mostly focuses on the influence of physical factors on the lactation of Bactrian camels, such as exploring the changes in milk yield and milk composition under different breeds, feeding methods, lactation stages, and parities. There are also studies on the positive effects of camel milk nutrients and their active substances on human diseases such as hypertension and tumors, and on the origin, evolution, and population genetic diversity of Bactrian camels, but there are few studies on the lactation mechanism and molecular breeding. There are only a few case studies on individual lactation-related functional genes. The improvement of sequencing technology provides technical support for the molecular breeding of dairy Bactrian camels. Scientists at home and abroad are actively using various technical means, such as molecular marker technology, genome resequencing technology, gene editing technology, etc., and analyzing methods such as genome-wide association study (GWAS), candidate gene analysis, and transcriptomics research to identify key genes and genetic markers affecting milk production traits. The discovery of these molecular markers makes it possible to implement marker-assisted selection (MAS) and genomic selection (GS), thereby improving breeding efficiency. Summary of the Invention

[0004] In view of this, the purpose of the present invention is to provide a SNP marker related to the milk production traits of Bactrian camels.

[0005] Another object of the present invention is to provide a liquid-phase chip for evaluating the milk production traits of Bactrian camels.

[0006] To achieve the above object of the invention, the present invention provides the following technical solutions:

[0007] The present invention provides an SNP marker for the milk production traits of Bactrian camels, and the SNP marker is composed of 1002 SNP sites in the Bactrian camel genome Ca_bactrianus_MBC_1.0. The position information of the SNP sites is shown in Table 1 below:

[0008] Table 1 Position information of SNP sites

[0009]

[0010]

[0011]

[0012]

[0013]

[0014]

[0015]

[0016]

[0017]

[0018]

[0019]

[0020]

[0021]

[0022]

[0023]

[0024]

[0025]

[0026]

[0027]

[0028]

[0029]

[0030] The present invention also provides an application of the above SNP markers in preparing a functional chip for evaluating the milk production traits of Bactrian camels.

[0031] The present invention also provides a liquid chip for the milk production traits of Bactrian camels, and the liquid chip includes nucleotide probes for detecting the above SNP markers.

[0032] Preferably, the nucleotide probe places the site of the above SNP marker in the middle position of the probe, and the probe length is 120 bp.

[0033] Preferably, the GC content of the nucleotide probe is between 20% and 30%, and the number of homologous regions of the probe sequence on the whole genome ≤ 5. More preferably, it is necessary to avoid tandem repeat sequences (SSR) and genome assembly GAP regions at the same time.

[0034] The present invention also provides an application of the above SNP markers or the above liquid chip in the breeding of Bactrian camels.

[0035] Preferably, the breeding of Bactrian camels includes molecular breeding for improving the milk yield of Bactrian camels and / or molecular breeding for improving the milk quality of Bactrian camels.

[0036] The present invention also provides an application of the above SNP markers or the above liquid chip in evaluating the milk production performance of Bactrian camels.

[0037] Preferably, the milk production performance includes milk yield, milk protein content, lactose content, and / or milk fat content.

[0038] The present invention also provides an application of the above SNP markers or the above liquid chip in the genetic diversity analysis of Bactrian camels.

[0039] Advantages of the present invention:

[0040] Based on genetic markers related to the lactation performance of Bactrian camels, the present invention provides an SNP marker related to the milk production traits of Bactrian camels and a functional liquid chip, which can be used for the molecular breeding of dairy Bactrian camels, greatly improving the efficiency and accuracy of Bactrian camel breeding, making the breeding selection more scientific and efficient. Secondly, through molecular breeding using the SNP markers or liquid chips provided by the present invention, the milk production and milk quality of Bactrian camels can be improved, thereby increasing the economic benefits of farmers and herdsmen. In addition, the development of a breeding function chip for Bactrian camel milk production traits will promote the technological progress and market expansion of the Bactrian camel dairy industry. Finally, while protecting genetic diversity, reasonably using the SNP markers or liquid chips of the present invention for breeding helps to avoid genetic resource bottlenecks caused by selective breeding. At the same time, the present invention will also enrich the research fields of Bactrian camel genetics and lactation physiology, and has important scientific value for exploring the genetic basis and molecular mechanism of Bactrian camel lactation performance. BRIEF DESCRIPTION OF THE DRAWINGS

[0041] Figure 1 It is a Manhattan plot of the selection signals of SNPs related to Bactrian camel lactation traits, where A is the Manhattan plot of the selection signals of loci related to milk production, B is the Manhattan plot of the selection signals of loci related to milk protein, C is the Manhattan plot of the selection signals of loci related to lactose, and D is the Manhattan plot of the selection signals of loci related to milk fat; the X-axis of the Manhattan plot is the position of SNPs on scaffolds, the Y-axis is the FST value of each locus, and the red line corresponds to the screening threshold FST>0.2;

[0042] Figure 2 It is a QQ plot and Manhattan plot of SNPs related to Bactrian camel lactation traits, where A is the trait Q-Q plot drawn from the expected P value and observed P value of each SNP, and B is the Manhattan plot of 4 SNPs related to lactation traits. The X-axis of the Manhattan plot is the position of SNPs on scaffolds, and the Y-axis is Log10p;

[0043] Figure 3 It is a bubble plot of functional enrichment analysis, only showing the TOP10 pathways of biological process (BP), cellular component (CC), molecular function (MF) and KEGG pathway results;

[0044] Figure 4 It is a Venn diagram of four SNPs related to lactation traits of the present invention;

[0045] Figure 5 It is a bar chart of the genomic alignment rate of 24 test samples;

[0046] Figure 6 It is a bar chart of the genotyping consistency of 3 replicate samples;

[0047] Figure 7Bar chart of the detection rates at 24 test sample sites;

[0048] Figure 8 Genetic structure of the core breeding population of camels, where A is a histogram of the distribution of minor allele frequencies (MAF), B is a PCA plot showing the genetic distances between samples, with samples from different locations represented by different colors, and C is the population structure (K = 2 - 9) of 526 Bactrian camel individuals, with each individual shown as a vertical bar divided into K colors;

[0049] Figure 9 PCA plot of high- and low-yield lactating Bactrian camels, where HMY represents the high-yield lactating camel group and LMY represents the low-yield lactating camel group. Detailed implementation mode

[0050] The present invention provides an SNP marker for the milk production traits of Bactrian camels, and the SNP marker consists of 1,002 SNP sites in the Bactrian camel genome Ca_bactrianus_MBC_1.0, and the position information of the SNP sites is shown in Table 1 above.

[0051] A total of 19,177 SNPs were detected from the RNA-seq data of lactating Bactrian camels in the present invention. In order to identify the SNP set related to lactation traits such as milk yield, milk protein, lactose, and milk fat, the present invention adopted an analysis method combining the algorithms of whole exome selection signal (EWSS) and genome-wide association study (GWAS) to determine 2,960 candidate SNPs. In order to reduce the incidence of false positives in genotyping, careful screening was carried out based on criteria such as SNP quality, polymorphism status, SNP density, and the degree of association with specific traits, and finally 1,002 SNP sites shown in Table 1 above were obtained.

[0052] The present invention also provides a liquid chip for the milk production traits of Bactrian camels, and the liquid chip includes nucleotide probes for detecting the above SNP markers.

[0053] In the present invention, the nucleotide probe preferably places the sites of the above SNP markers in the middle position of the probe, and the probe length is preferably 120 bp. The GC content of the nucleotide probe is preferably between 20% and 80%, and the number of homologous regions of the probe sequence on the whole genome is preferably ≤5. More preferably, it is necessary to avoid tandem repeat sequences (SSR) and genome assembly GAP regions at the same time. In the present invention, the construction of the chip and the specific detection and genotyping are all handed over to Beijing Compson Agricultural Technology Co., Ltd.

[0054] The present invention also provides an application of the above SNP marker or the above liquid chip in the breeding of Bactrian camels, molecular breeding for improving the milk yield of Bactrian camels or improving the milk quality of Bactrian camels.

[0055] The present invention also provides an application of the above SNP markers or the above liquid-phase chip in evaluating the milk production performance of Bactrian camels. In the present invention, the milk production performance preferably includes milk yield, milk protein content, lactose content, and / or milk fat content. The breeding value refers to the genetic value passed on by an individual to its offspring and is an important indicator when selecting breeding animals. The present invention also estimates the breeding value of an individual using the genotyping data of the chip to measure the breeding value of each individual in the core breeding population and provide a reference for the selection of excellent individuals of dairy Bactrian camels. The liquid-phase chip of the present invention can be used to guide the breeding work of dairy Bactrian camels. By identifying individuals with high breeding value, the breeding efficiency can be improved, and more excellent dairy Bactrian camels can be bred.

[0056] The present invention also provides an application of the above SNP markers or the above liquid-phase chip in the analysis of genetic diversity of Bactrian camels.

[0057] The technical solutions provided by the present invention will be described in detail below with reference to the embodiments, but they should not be construed as limiting the protection scope of the present invention.

[0058] In the following embodiments, unless otherwise specified, all are conventional methods.

[0059] The materials, reagents, etc. used in the following embodiments can be obtained from commercial sources unless otherwise specified.

[0060] Example 1

[0061] (1) Sample collection

[0062] Phenotypic data, milk samples, and blood samples were collected from 125 lactating Bactrian camels in the Alxa League area of Inner Mongolia. All Bactrian camels were in one lactation period, and the parity was 2 to 5. The daily milk yield was determined based on the average milk yield over three days. Milk samples and blood samples were collected at 5:00 am on the sampling day, and the concentrations of milk components such as milk protein, lactose, and milk fat were accurately measured using infrared spectroscopy. The collected blood samples were mixed with TRIzol reagent (TaKaRa, USA) and stored at -80 °C for subsequent RNA extraction. All experimental methods used in the present invention were approved by the Institutional Animal Welfare and Use Committee of Inner Mongolia Agricultural University (Hohhot, China).

[0063] (2) RNA extraction and sequencing

[0064] Total RNA was isolated from whole blood according to the operating instructions of the Invitrogen TRIzol Reagent kit. The integrity and purity of the RNA were evaluated on a 1% agarose gel. After the samples passed the inspection, the mRNA was enriched by binding the polyA tail of the mRNA through A-T complementary pairing using oligo(dT) magnetic beads. Fragmentation was added to break the enriched mRNA into short fragments. Using the mRNA as a template, the first strand of cDNA was synthesized by transcription with random hexamers and reverse transcriptase. Buffer, dNTPs, RNase H, and DNA polymerase I were added to synthesize the second strand of cDNA. Subsequently, the double-stranded cDNA was purified with AMPure XP beads. The purified double-stranded cDNA was subjected to end repair, A-tailing at the 3' end and ligation of sequencing adapters, and then fragment size selection was performed with AMPure XP beads. Finally, PCR enrichment was carried out to obtain the final cDNA library. After the library construction was completed, the library was diluted to 1 ng / μL, and the insert size of the library was detected using Agilent 2100. After passing the inspection, the effective concentration of the library was accurately quantified using the Q-PCR method. After passing the library inspection, sequencing was performed on the Illumina NovaSeq 6000 high-throughput sequencing platform.

[0065] (3) SNP detection and selection

[0066] The quality-controlled clean data were used for SNP (single nucleotide polymorphism) calling. Since the accuracy of indel calling is generally low, insertions and deletions (indels) were not considered in the present invention. SNP calling was performed using SAMtools and BCFtools. Filtering criteria: Phred quality score of at least 25 and a minimum read depth of 10. The minor allele frequency (MAF) and missing rate were calculated using PLINK (v1.07), and SNPs with MAF < 0.05 and missing in the samples were filtered.

[0067] The results showed that a total of 19,177 SNPs were detected from the RNA-seq data of lactating Bactrian camels. Specifically, first, the peripheral blood transcriptomes of 125 individuals with stable lactation performance among 1,243 Bactrian camels were sequenced. This sequencing generated approximately 3.575 billion paired-end reads, with an average of 29 million paired-end reads per sample. After quality control, the base efficiency reached 97.88%. The Q30 ratio exceeded 93.14%, and the GC content exceeded 52.08%. Notably, approximately 91.72% of the reads were accurately mapped to the Bactrian camel genome (Ca_bactrianus_MBC_1.0), and 80.54% of the reads per individual were uniquely aligned to the reference genome (Ca_bactrianus_MBC_1.0). Subsequently, a comprehensive SNP calling was performed on the reference genomes of 125 transcriptome datasets, generating a total of 9,790,170 SNPs. Among them, 19,177 SNPs had a MAF > 0.05 and were detected in all 125 samples. The above meticulous filtering criteria helped to exclude low-quality SNPs, thereby enhancing the robustness of the subsequent analysis process.

[0068] (4) Development of SNP chip

[0069] To identify SNP sets related to lactation traits such as milk yield, milk protein, lactose, and milk fat, a combined analysis method of exome-wide selection signal (EWSS) and genome-wide association study (GWAS) was adopted for the filtered SNPs. EWSS is a SNP screening method based on the transcriptional level by detecting the population differentiation FST index. First, the calculation of FST was applied to 19,177 SNPs to identify SNPs related to the extreme value grouping of lactation traits. According to the high and low extreme values of milk yield, milk protein, lactose, and milk fat percentage in the extreme value grouping of lactation traits (as shown in Table 2 - Table 4), 15 Bactrian camels were selected respectively, 30 for each trait, and the vcftools software was used to perform EWSS analysis on the grouped samples. FST estimation is usually used to quantify the degree of genetic differentiation between populations and identify loci that may be affected by natural selection. In the present invention, with FST > 0.2 as the threshold, 178 specific loci were identified, among which 138 loci were related to milk yield ( Figure 1 A), 28 loci were related to milk protein content ( Figure 1 B), 30 loci were related to lactose content ( Figure 1 C), and 6 loci were related to milk fat content ( Figure 1 D).

[0070] Table 2 Milk yield and milk components in different milk yield groups (mean ± standard deviation)

[0071]

[0072] Table 3 Milk yield and milk composition of different milk protein groups (mean ± standard deviation)

[0073]

[0074] Table 4 Milk yield and milk composition of different milk fat groups (mean ± standard deviation)

[0075]

[0076] Subsequently, the lactation traits of 125 Bactrian camels were subjected to GWAS analysis with the selected SNPs. The GWAS was computationally analyzed through the GAPIT R package, using the compressed mixed linear model (CMLM) method and "EMMAx" (Efficient Mixed Model Association - Expedited). Subsequently, the P - values were adjusted with a 5% false discovery rate (FDR) to determine significant associations. Specifically, using GWAS, 19,177 SNPs identified within the transcriptional regions were associated with the phenotypic data of the lactation traits of 125 Bactrian camels, thus providing a reliable reference set for screening relevant loci. It was found that 923 SNP, 980 SNP, 955 SNP, and 756 SNP were significantly associated with milk yield, milk protein content, lactose content, and milk fat content traits, respectively (P < 0.05), as Figure 2 shown in A and B.

[0077] Finally, the SNP loci identified by the two methods were combined, and a reference set containing 2,960 SNP loci was obtained in total. These loci were significantly associated with the four lactation traits and were scattered within the transcriptional regions of 1,395 genes. The results of functional enrichment analysis showed that the genes where these SNPs were located were mainly enriched in pathways related to the immune system, organic nitrogen compound metabolism, regulation of metabolic processes, vesicle - mediated transport, positive regulation of biological processes, protein metabolism, and cell localization. The top 10 pathways of the biological process (BP), cellular component (CC), molecular function (MF), and KEGG pathway results are as Figure 3 shown.

[0078] To reduce the incidence of false positives in genotyping, SNPs for microarray customization were screened based on criteria such as SNP quality, polymorphism status, SNP density, and the degree of association with specific traits. The 2,960 candidate SNPs determined in the previous analysis were submitted to the targeted capture sequencing probe design system (Beijing Compson Agricultural Technology Co., Ltd.) for scoring, and 2,681 SNPs passed the evaluation. The positions of the SNPs and the functions of the gene transcription regions were manually retrieved. Considering the positions and functions of these SNPs, 1,002 SNPs were finally selected for the chip array of the present invention (see Table 1) (these 1,002 SNPs are related to lactation traits). For these SNP loci, 460 SNPs are located in the exon region, 54 are located in the intron region, and 10 are located in the intergenic region. The associations of these SNPs with lactation traits are as Figure 4 shown, among which 201 SNPs are related to two or more lactation traits.

[0079] Example 2

[0080] According to the positions of the 1,002 SNP loci obtained in Example 1 (see Table 1) and the sequences on both sides thereof, primers were designed and probes were synthesized by Beijing Compson Agricultural Technology Co., Ltd. using targeted capture sequencing technology, thereby obtaining a 1K liquid chip for Bactrian camels (named CamelBell NO.1): The target loci shown in Table 1 were placed in the middle position of the probe. The designed probe has a length of 120 bp, the GC content of the probe is between 20% and 80%, the number of homologous regions of the probe sequence on the whole genome is ≤5, and it is necessary to avoid tandem repeat sequences (SSR) and genomic assembly GAP regions at the same time. The DNA nucleotides with a biotin group modification at the 5' end (which can effectively bind to streptavidin magnetic beads in the later hybridization capture experiment for capturing fragments in the target region).

[0081] Example 3

[0082] Verification of the 1K liquid SNP chip set of "CamelBell NO.1" obtained in Example 2

[0083] To evaluate the stability of the SNP chip obtained in Example 2, the "CamelBell NO.1" chip was used to genotype another 24 camel blood DNA samples (including 3 pairs of duplicate samples) (handled by Beijing Compson Agricultural Technology Co., Ltd.). The specific steps are as follows:

[0084] (1) DNA extraction: A magnetic bead method DNA extraction kit (ComWin Biotech CW2361S) was used to extract the sample DNA.

[0085] (2) Genomic DNA fragmentation: Take 1.0 μg of DNA sample into a fragmentation tube, add TE buffer to 100 μl, shake and mix, and centrifuge. Place in a fragmentation instrument for fragmentation. The fragmentation parameters are: 30 s for fragmentation time, 30 s for stop time, and 6 fragmentation cycles. Finally, take 10 ul of the fragmented sample for fragment detection. The qualified fragmentation sample requires the main fragment size to be 200-300 bp (PE150 sequencing strategy).

[0086] (3) Fragment screening and end-repair and A addition

[0087] First, the fragments were screened by magnetic beads to remove oversized and undersized fragments, so that the DNA fragments were concentrated in 200-300bp. Secondly, 40ul of fragmented DNA / cfDNA was taken, End Repair & A-Tailing Buffer 6μl, End Repair & A-Tailing Enzyme 4μl, and the total reaction system was 50ul. After mixing, 10ul was taken into a 96-well PCR plate, incubated at 20℃ for 30min, 65℃ for 30min, and then stored at 4℃.

[0088] (4) Sequencing library construction

[0089] Add 5 μL CAGT Universal Adapters and 20 μL Ligation Master Mix to the 96-well PCR plate in step (3), vortex and mix, centrifuge briefly to collect the reaction solution to the bottom of the tube, react in a PCR instrument at 20°C for 15 minutes to complete the sequencing adapter connection. After the connection product is purified, PCR amplification and enrichment are performed, 15 μL of the connection purified product is taken, 10 μL CAGT UDI Primer and 25 μL Equinox Library Amp Mix (2x) are added, mixed, and 35 μL of the reaction solution is taken and placed in a PCR instrument for library amplification. After the whole genome library is constructed, the library is quantified using the dsDNA HS Assay Kit for Qubit; at the same time, the main peak of the library fragment is detected by electrophoresis to see if it is in the range of 350-450 bp.

[0090] (5) Liquid chip hybridization capture

[0091] The whole genome library of each sample was mixed, and the total amount of the final hybrid capture library was 4 μg. The mixed pool library was concentrated and probe hybridized (using the chip obtained in Example 2), and the fragments of the target region were captured from the whole genome library. The excess probes, hybridization reagents and other reagent components were removed by the elution step. Finally, the target region was enriched by PCR amplification after hybridization to obtain the machine library.

[0092] (6) Library quality inspection and sequencing

[0093] After the hybrid capture library was constructed, the dsDNA HS Assay Kit for Qubit was used to quantify the library. At the same time, electrophoresis was used to detect whether the main peak size of the library was in the range of 350-450bp. The constructed library was sequenced on an MGI-T7 sequencer.

[0094] (7) Analysis process

[0095] The liquid phase capture analysis process mainly includes data filtering statistics, alignment and target site analysis, as follows:

[0096] 7.1 Data Filtering and Statistics

[0097] After the raw data is downloaded, it will contain reads with adapters or low quality. Before using fastp for subsequent analysis, the raw data needs to be filtered. The filtering conditions are as follows:

[0098] 1) Remove reads with adapters;

[0099] 2) When the N content in the sequencing read exceeds 10% of the base number of the read, the paired reads are removed;

[0100] 3) When the number of low-quality (Q<=5) bases in a sequencing read exceeds 50% of the number of bases in the read, the paired reads are removed.

[0101] Through the above steps, the raw data is filtered and the amount of data before and after filtering is counted to obtain the parameters used by the CleanReadsFastp software -u50-n1-q5-l30

[0102] 7.2 Alignment with reference genome

[0103] After data filtering, an index was built according to the provided reference genome, and then the CleanReads were aligned to the reference genome using the BWA0.7.17 software. Samtools1.7 was used to sort and build the index, and the Bam file was deduplicated using the module provided by the GATK4.1.8.0 software. Then, the sequencing depth, genome coverage and other information of each sample were statistically analyzed based on the Bam file to prepare for subsequent variation detection.

[0104] 7.3 Target site analysis

[0105] Based on the alignment results of CleanReads on the reference genome, the GenotypeGVCFs module in software GATK 4.1.8.0 was used to generate a variant site file, and a self-developed script was used to extract the target site genotyping according to the provided site file. Then, filtering was performed with minDP = 5X and 100% deletion, and the sites that did not meet the requirements were marked as. / ., and then the site detection rate and site depth were statistically analyzed. If there is an annotation file for the species, ANNOVAR will be used to annotate the genotyping.

[0106] The results showed that the genome alignment rate of all samples exceeded 99%, and the final average alignment rate reached 99.77% ( Figure 5 ). Separately testing the three replicate samples, the genotyping consistency of each pair of samples was 100%, highlighting the detection stability of the chip ( Figure 6 ). Comprehensively statistically analyzing the detection rate of all test samples, the coverage depth of the target sites exceeded 5 times, and the average site detection rate remained at 99.72%. It is worth noting that even when the coverage depth exceeded 20 times, the detection rate still remained at a robust level of 99.07% ( Figure 7 ).

[0107] Example 4

[0108] Using the "Camel Bell No. 1" 1K liquid SNP chip obtained in Example 2, individuals from the core breeding population of 526 Bactrian camels from 6 regions were genotyped, and the sample processing and sequencing were the same as in Example 3.

[0109] Genetic diversity and population structure analysis were performed on the genotyping data. In this population, SNP sites with a minor allele frequency greater than 0.1 accounted for 95% of all sites (see Figure 8 A). This means that most sites have high genetic variation in the population and are suitable for PCA plots ( Figure 8 B) and population structure plots ( Figure 8 C) indicating that the genetic differences among Bactrian camels from these 6 different regions are small, indicating that these Bactrian camels are closely related at the genetic level. Generally speaking, Example 4 demonstrated the application of modern genotyping technology in animal breeding, especially the potential in evaluating and improving the genetic quality and breeding value of a specific species, the Bactrian camel.

[0110] Example 5

[0111] Using the "Camel Bell No. 1" 1K liquid SNP chip obtained in Example 2, individuals of 15 lactating Bactrian camels from the core breeding population were genotyped. Among them, 7 were low-yield lactating camels with an average milk yield of 798 g / day; 8 were high-yield lactating camels with an average milk yield of 2510 g / day, and the sample processing and sequencing were the same as in Example 3.

[0112] The PCA results of the 15-peak sample are shown in the figure below: Figure 9 It is shown that the chip of the present invention can distinguish high-yield and low-yield lactating Bactrian camels in spatial structure, proving that the chip of the present invention can be used for sorting Bactrian camels with lactating performance.

[0113] The above is only a preferred embodiment of the present invention. It should be pointed out that for ordinary technicians in this technical field, several improvements and modifications can be made without departing from the principle of the present invention. These improvements and modifications should also be regarded as the scope of protection of the present invention.

Claims

1. A liquid-phase chip for milk production traits of Bactrian camels, characterized in that, the liquid-phase chip includes nucleotide probes for detecting SNP markers, and the SNP markers consist of 1002 SNP sites in the Bactrian camel genome Ca_bactrianus_MBC_1.

0. The position information of the SNP sites is shown in the following table:

2. The liquid-phase chip according to claim 1, characterized in that, the nucleotide probe places the site of the SNP marker described in claim 1 at the middle position of the probe, and the probe length is 120bp.

3. The liquid-phase chip according to claim 1, characterized in that, the GC content of the nucleotide probe is between 20% and 80%, and the number of homologous regions of the probe sequence on the whole genome ≤ 5.

4. Application of the liquid-phase chip described in claim 1 in Bactrian camel breeding, characterized in that, the Bactrian camel breeding is molecular breeding for improving Bactrian camel milk yield and / or molecular breeding for improving Bactrian camel milk quality; the milk quality is milk protein content, lactose content and / or milk fat content.

5. Application of the liquid-phase chip described in claim 1 in evaluating the milk production performance of Bactrian camels, characterized in that, the milk production performance is milk yield, milk protein content, lactose content and / or milk fat content.

6. Application of the liquid-phase chip described in claim 1 in Bactrian camel genetic diversity analysis.

Images