WO2023231940A1 - 一种与细毛羊羊毛纤维直径相关的snp位点组合及其应用 - Google Patents
一种与细毛羊羊毛纤维直径相关的snp位点组合及其应用 Download PDFInfo
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Definitions
- the invention belongs to the technical field of genetic breeding, and specifically relates to a combination of SNP sites related to the fiber diameter of fine-wool sheep and its application.
- Sheep (Ovis aries) are livestock with important agricultural and biological significance. As one of the earliest domesticated animals, they provide humans with meat, milk, wool, lambskin, etc., and play a vital role in the global agricultural economy. role. Wool is a source of high-quality textile raw materials and plays a significant role in the national economy.
- Wool is a natural, high-performance material that is stain-resistant, soft, sun-protective, warm and breathable. Therefore, wool plays an important role in textile processing. Wool quality is determined by fiber diameter, fiber length, crimp, color and pith percentage. Fiber diameter is often related to wool processing properties and determines its end use. The above wool traits are affected by both genetic and non-genetic factors. Fiber diameter is one of the important economic traits of fine-wool sheep, usually accounting for 75%–80% of the unit value of wool.
- Fiber diameter is a major determinant of wool quality and value.
- the average fiber diameter is one of the most important raw wool properties that can be measured. Therefore, the average fiber diameter is an important determinant of the price of greasy wool. Fiber diameter is also one of the few raw wool parameters that remains essentially unchanged during processing. Diameter limits the thickness (count) of yarn that can be spun from a given raw material. For a given yarn count, various physical properties of the yarn, such as bending stiffness and elongation, depend on its constituent fiber diameter. .
- Molecular genetic markers are genetic markers based on nucleotide sequence variations within individual genetic material, which are a direct response to genetic polymorphisms at the DNA level. It has significant advantages, such as DNA from different tissues at different stages of biological development can be used for genetic marker analysis; the genome is rich in variation; the detection method is simple and fast, and it is easy to realize automated processing.
- Molecular genetic markers currently widely used include RFLP (RestrictionFragment Length Polymorphism, restriction fragment length polymorphism analysis technology), RAPD (RandomAmplified PolymorphismDNA, random primer amplified polymorphism DNA technology), AFLP (Amplified FragmentLength Polymorphism, amplified fragment length polymorphism) Morphological analysis technology) and SNP (Single-nucleotide polymorphisms, single nucleotide polymorphisms), etc.
- SNP is an important basis for studying genetic variation in human families, animal and plant strains, and is therefore often widely used in population genetics research and disease-related gene exploration.
- SNP has often played an important role in animal genetic analysis and genetic breeding. Therefore, livestock genetic breeding often uses SNP to accelerate the innovation of traditional breeding technology and establish innovative breeding theories and systems.
- the present invention provides a kind of China's four representative fine-wool sheep breeds (Chinese Merino sheep, Alpine Merino sheep). High-depth whole-genome resequencing data of Nu sheep, Aohan fine-wool sheep and Qinghai fine-wool sheep), using the sheep v4.04 genome as a reference, combined with existing research related to sheep production traits, an accurate detection method was obtained using A combination of SNP sites for fine-wool sheep wool fiber diameter traits is convenient and has broad market prospects. The sites can be used for the selection, protection and improvement of sheep breeds. Specifically include the following:
- the present invention provides a combination of 33 SNP sites related to the diameter of fine-wool sheep wool fibers.
- the 33 SNP site combinations are determined based on sheep v4.0 genome sequence comparison; respectively: located at chr 1 At position 203825947, its deoxynucleotide is C or A; It is located at position 226733906 of chr 1, and its deoxynucleotide is C or T; It is located at position 45470146 of chr 3, and its deoxynucleotide is A or C; It is located at chr 4 at position 68142771, its deoxynucleotide is C or G; at position 93335425 of chr 5, its deoxynucleotide is C or T; at position 93344882 of chr 5, its deoxynucleotide is C or T; at position 93344882 of chr 5, its deoxynucleotide is C or T; at position 93344882 of chr 5, its
- the present invention provides the application of a reagent for detecting the 33 SNP site combinations related to the fiber diameter of fine-wool sheep described in the first aspect in detecting the fiber diameter of fine-wool sheep.
- the reagent includes a primer for detecting the SNP site combination, and those skilled in the art design primers based on the sequence information of each site in the SNP site combination related to the fine wool fiber diameter provided by the present invention. , primers that can achieve detection purposes under the same reaction conditions. Among them, the design of primers is a conventional method. According to the site information in the SNP site combination related to the fine-wool sheep wool fiber diameter provided by this application, it can be obtained without the need for creative work. Therefore, according to the information provided by this application The primers obtained by combining the biological SNP sites related to the fiber diameter of fine wool sheep also belong to the protection scope of the present invention.
- the reagents include a combination of molecular probes for detecting the combination of SNP sites.
- the design of molecular probes is a conventional method. According to the site information in the SNP site combination related to the fiber diameter of fine wool sheep provided by this application, it can be obtained without the need for creative work. Therefore, according to the information provided by this application The combination of biological SNP sites related to fine wool sheep wool fiber diameter to obtain molecular probes also belongs to the protection scope of the present invention.
- the molecular probe combination is as shown in Table 1.
- the reagent includes a gene chip, which uses conventional methods to fix the obtained primers or probes on a polymer substrate, such as nylon membrane, nitrocellulose membrane, plastic, silica gel wafer, micro magnetic beads, etc., or Fix the probe on a glass plate, or directly synthesize the obtained primer or probe on a hard surface such as glass.
- a polymer substrate such as nylon membrane, nitrocellulose membrane, plastic, silica gel wafer, micro magnetic beads, etc.
- the method of using the SNP gene chip of this application is the same as the conventional method.
- the present invention provides a molecular probe combination for analyzing the fiber diameter characteristics of fine-wool sheep.
- the molecular probe combination detects 33 SNP positions related to the fiber diameter of fine-wool sheep described in the first aspect. Click combination.
- the molecular probe combination is as shown in Table 1 above.
- the present invention provides a gene chip for analyzing the fiber diameter properties of fine-wool sheep, and the gene chip is loaded with the molecular probe combination for analyzing the fiber diameter properties of fine-wool sheep described in the third aspect.
- the present invention provides a kit for analyzing fine-wool sheep wool fiber diameter properties.
- the kit includes the molecular probe combination for analyzing fine-wool sheep wool fiber diameter properties described in the third aspect or the fourth aspect.
- the above-mentioned gene chip is used to analyze the fiber diameter traits of fine-wool sheep.
- the present invention provides the molecular probe combination described in the third aspect, or the gene chip described in the fourth aspect, or the kit described in the fifth aspect, for the evaluation of fiber diameter properties of fine-wool sheep. Or in the screening of fine-wool sheep breeds, or in the identification of fine-wool sheep breeds, or in the application of molecular marker-assisted breeding of fine-wool sheep.
- the present invention provides a method for analyzing the fiber diameter properties of fine-wool sheep.
- the method is: detecting the genomic DNA of the fine-wool sheep to be tested and related to the fiber diameter of fine-wool sheep as described in the first aspect. 33 SNP site genotypes; compare the 33 SNP site genotypes with the fine-wool sheep genomic DNA, and determine the wool fiber diameter characteristics of the fine-wool sheep based on the genotype detection results.
- the present invention provides 33 SNP site combinations related to the fiber diameter of fine-wool sheep, and the SNP sites are determined based on sheep v4.0 genome sequence comparison; secondly, the present invention finds that through molecular probing The genotypes of the 33 SNP site combinations related to the wool fiber diameter of fine-wool sheep to be measured in the genomic DNA of fine-wool sheep using methods such as needles or gene chips can be used to analyze the fiber diameter traits of fine-wool sheep and for early breeding selection of fine-wool sheep.
- the molecular probe combination, gene chip, and kit formed by the combination of 33 SNP sites related to the fiber diameter of fine-wool sheep have low throughput, low cost, easier analysis, and universal applicability wide and broad market prospects.
- Figure 2 is a Q-Q plot drawn after taking -log10 of the p value calculated in Example 1 under the GLM model in GWAS for the SNP data related to the fiber diameter trait of fine-wool sheep.
- the experimental conditions of all tests in the following examples are conventional conditions, such as the molecular cloning experimental manual of Sambrook and others, or the conditions recommended by the manufacturer's instructions.
- the SNP described in the present invention is the abbreviation of single nucleotide polymorphism, which refers to the DNA sequence polymorphism caused by the variation of a single nucleotide at the genome level.
- the whole genome was resequenced on 460 fine-wool sheep individuals from four representative fine-wool sheep breeds in my country, with an average depth of 5X.
- the resequencing analysis process was applied and compared with the sheep v4.0 reference genome released in 2015 (from NCBI). Obtain) for comparison, and the common results obtained by comparing the two methods form a SNP set.
- high-depth resequencing of multiple fine-wool sheep individuals was completed by a biological sequencing company.
- the sequencing results completed by the biological sequencing company can all achieve the technical purpose of the present invention, and the present invention is not limited.
- This application compares the Fastq file returned by the sequencing company to the reference genome sheep v4.0 through the BAM file to obtain the BAM file, and uses SAMtools and GATK software to analyze the sample BAM file to obtain a VCF file containing population SNP typing information.
- the VCF file results obtained by the two methods were combined, and after quality screening, a SNP set containing 33 SNP sites was obtained.
- the fine-wool sheep breeds used in the present invention are four representative fine-wool sheep breeds in China, namely Chinese Merino sheep, Alpine Merino sheep, Aohan fine-wool sheep and Qinghai fine-wool sheep.
- y X ⁇ +Q ⁇ +K ⁇ +e
- y is the phenotype vector
- X is the genotype matrix
- ⁇ is the genotype effect vector
- Q is the fixed effect matrix (can be the population structure/ Gender/location/scene and other information)
- ⁇ is the fixed effect vector
- K is the random effect matrix, mainly refers to the kinship matrix
- ⁇ is the random effect vector
- e is the residual vector.
- SNP sites corresponding to the functional regions of the candidate genes determined in step 2, and we obtain SOX2, DNAJC19, MFSD1, RARRES1, EHBP1, TMEM17, JAZF1, CAST, ERAP1, ERAP2, TSPAN5, FAM184B, LOC101103163, KCTD12, RNF43, CAPN2 , PRRX1, TNNT2, LOC101112664, LOC101108158, ELOVL5, ID4, RNF144B, ELOVL2, MKI67, MGMT, LOC101110287, HNRNPF, BICC1 and UBE2E1, a total of 30 functional genes or markers associated with fiber diameter, and only 33 SNP sites are included. combination of sites.
- this application commissioned Boridi Biotechnology Co., Ltd. to prepare a panel of SNPs related to fiber diameter.
- the PCR product is purified using carboxyl magnetic beads, it is again added to the sequencing primers with Barcode and the high-fidelity PCR reaction system for PCR amplification. Different Barcodes are used to distinguish different samples.
- the amplified product is completed to complete multiplex PCR capture and library construction.
- GenoBaits (based on liquid phase probes) independently developed by Boridi were selected.
- Hybrid targeted gene capture technology solution to detect the wool fiber diameter of its individuals.
- the working principle of this technology is based on the complementary combination of the target probe and the target sequence for fixed-site capture.
- the captured target sequence is eluted, target amplified, library constructed and sequenced, and finally the genotype of the target SNP is obtained.
- Economically Under effective conditions, the number of target sites and their labels that can be detected is equivalent to that of high-density solid-phase chips in terms of detection density and throughput. Through this technology, the result value of the target sample is obtained.
- the polymorphism detection results of fine-wool sheep wool fiber diameter-related loci are shown in Table 3.
- the above results show that by detecting the genotypes of the 33 fine-wool sheep wool fiber diameter SNP site combinations described in the present invention, the fine-wool sheep wool fiber diameter can be analyzed.
- the 33 SNP site combinations are: respectively located: Chr 1 at position 203825947, its deoxynucleotide is C or A; Chr 1 at position 226733906, its deoxynucleotide is C or T; Chr 3 at position 45470146, its deoxynucleotide is A or C; Located at position 68142771 of chr 4, its deoxynucleotide is C or G; located at position 93335425 of chr 5, its deoxynucleotide is C or T; located at position 93344882 of chr 5, its deoxynucleotide is C or T ; Located at position 93387255 of chr 5, its deoxynucleotide is C or T; Located at position 93391985 of chr 5, its de
- the present invention obtains the genotype of the target SNP through GenoPlexs (targeted gene capture technology solution based on multiplex PCR) and GenoBaits (targeted gene capture technology solution based on liquid phase probe hybridization), and realizes the determination of the fiber diameter of fine wool sheep. Rapid and effective detection is of great significance to molecular breeding of sheep and the protection and transformation of germplasm resources.
- SNP site combination Based on the fine-wool sheep wool fiber diameter SNP site combination provided by the present invention, which is composed of only 33 SNP sites, those skilled in the art can prepare SNP probe combinations, gene chips and kits for analyzing fine-wool sheep wool fiber diameter. Analyze the wool fiber diameter of fine-wool sheep at the genome level, or conduct genetic assessment, breed screening, and breed identification to obtain higher accuracy in breeding value estimation and control the breeding process. It can also be applied to the reconstruction of sheep pedigrees and the traceability of sheep breeds. , germplasm resource protection and germplasm resource improvement.
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Abstract
Description
Claims (9)
- 一种与细毛羊羊毛纤维直径相关的33个SNP位点组合,其特征在于,所述33个SNP位点组合基于绵羊v4.0基因组序列比对确定;分别为:位于chr 1第203825947位,其脱氧核苷酸为C或A;位于chr 1第226733906位,其脱氧核苷酸为C或T;位于chr 3第45470146位,其脱氧核苷酸为A或C;位于chr 4第68142771位,其脱氧核苷酸为C或G;位于chr 5第93335425位,其脱氧核苷酸为C或T;位于chr 5第93344882位,其脱氧核苷酸为C或T;位于chr 5第93387255位,其脱氧核苷酸为C或T;位于chr 5第93391985位,其脱氧核苷酸为G或A;位于chr 5第93392877位,其脱氧核苷酸为C或T;位于chr 5第93393426位,其脱氧核苷酸为A或G;位于chr 5第93507537位,其脱氧核苷酸为A或C;位于chr 6第25952072位,其脱氧核苷酸为T或A;位于chr 6第37126564位,其脱氧核苷酸为T或C;位于chr 10第51739659位,其脱氧核苷酸为G或A;位于chr 11第8917643位,其脱氧核苷酸为C或A;位于chr 12第25119445位,其脱氧核苷酸为G或A;位于chr 12第25120732位,其脱氧核苷酸为C或G;位于chr 12第25135944位,其脱氧核苷酸为A或G;位于chr 12第25149517位,其脱氧核苷酸为C或A;位于chr 12第25152554位,其脱氧核苷酸为T或A;位于chr 12第25154575位,其脱氧核苷酸为C或T;位于chr 12第25155325位,其脱氧核苷酸为T或C;位于chr 12第36292909位,其脱氧核苷酸为G或A;位于chr 12第78576808位,其脱氧核苷酸为T或C;位于chr 15第68745093位,其脱氧核苷酸为C或T;位于chr 20第25185724位,其脱氧核苷酸为C或T;位于chr 20第37863763位,其脱氧核苷酸为C或T;位于chr 20第44119346位,其脱氧核苷酸为G或A;位于chr 22第46988971位,其脱氧核苷酸为G或A;位于chr 22第47002481位,其脱氧核苷酸为A或C;位于chr 22第50203275位,其脱氧核苷酸为G或A;位于chr 25第13791395位,其脱氧核苷酸为T或C;位于chr26第40609491位,其脱氧核苷酸为C或T。
- 检测权利要求1所述与细毛羊羊毛纤维直径相关的33个SNP位点组合的试剂在检测细毛羊羊毛纤维直径或在细毛羊分子标记辅助育种中的应用。
- 如权利要求2所述的应用,其特征在于,所述试剂包括用于检测所述SNP位点组合的引物和/或分子探针组合。
- 一种分析细毛羊羊毛纤维直径性状的分子探针组合,其特征在于,所述分子探针组合检测如权利要求1中所述的与细毛羊羊毛纤维直径相关的33个SNP位点组合。
- 根据权利要求4所述的分子探针组合,其特征在于,所述分子探针组合包括SEQ ID NO.1~SEQ ID NO.156所示的核苷酸序列。
- 一种分析细毛羊羊毛纤维直径性状的基因芯片,其特征在于,所述基因芯片负载有权利要求4或5所述的分析细毛羊羊毛纤维直径性状的分子探针组合。
- 一种分析细毛羊羊毛纤维直径性状的试剂盒,其特征在于,所述试剂盒包括权利要求4或5所述的分析细毛羊羊毛纤维直径性状的分子探针组合或权利要求6所述的分析细毛羊羊毛纤维直径性状的基因芯片。
- 如权利要求4或5所述的分子探针组合,或权利要求6所述的基因芯片,或权利要求7所述的试剂盒在细毛羊羊毛纤维直径性状评价,或在细毛羊品种筛选,或在细毛羊品种鉴定,或在细毛羊分子标记辅助育种中的应用。
- 分析细毛羊羊毛纤维直径性状的方法,其特征在于,所述方法为:检测待测细毛羊的基因组DNA中如权利要求1所述的与细毛羊羊毛纤维直径相关的33个SNP位点基因型;对照细毛羊基因组DNA的所述33个SNP位点基因型进行比较,根据基因型检测结果判断细毛羊的羊毛纤维直径性状。
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Citations (7)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN110734984A (zh) * | 2019-10-15 | 2020-01-31 | 甘肃农业大学 | 与细毛羊羊毛纤维直径相关的遗传标记及其应用 |
CN111996265A (zh) * | 2020-09-20 | 2020-11-27 | 中国农业科学院兰州畜牧与兽药研究所 | 一种影响细毛羊羊毛纤维直径的snp分子标记及其应用 |
CN112029872A (zh) * | 2020-09-22 | 2020-12-04 | 中国农业科学院北京畜牧兽医研究所 | 一种与细毛羊羊毛性状相关的snp标记及其检测引物组、试剂盒、检测方法和应用 |
CN112048562A (zh) * | 2020-08-28 | 2020-12-08 | 中国农业科学院兰州畜牧与兽药研究所 | 一种影响高山美利奴羊羊毛纤维直径的snp分子标记及其应用 |
US20210332443A1 (en) * | 2020-04-28 | 2021-10-28 | China Jiliang University | Molecular Marker and Application Method for Assisted Breeding of Fine-wool Sheep |
CN114231642A (zh) * | 2022-01-07 | 2022-03-25 | 新疆畜牧科学院畜牧研究所 | 与鄂尔多斯细毛羊羊毛纤维直径性状相关的分子标记及特异性引物对和应用 |
CN114990226A (zh) * | 2022-05-30 | 2022-09-02 | 中国农业科学院兰州畜牧与兽药研究所 | 一种与细毛羊羊毛纤维直径相关的snp位点组合及其应用 |
Family Cites Families (7)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP2368428A1 (en) * | 2010-03-16 | 2011-09-28 | Institut National De La Recherche Agronomique | Obtention of a rex animal by molecular methods based on the alteration of the LIPH function |
CN103243167B (zh) * | 2013-05-15 | 2014-07-30 | 新疆农垦科学院 | 与绵羊羊毛纤维直径相关的分子标记及其应用 |
CN103276098B (zh) * | 2013-06-14 | 2014-07-16 | 东北农业大学 | 一种预示和鉴定绵羊羊毛长度的分子标记方法 |
CN104894253B (zh) * | 2015-05-20 | 2018-04-03 | 东北农业大学 | 能预示和鉴定绵羊羊毛细度的分子标记方法及其引物对 |
CN107604078B (zh) * | 2017-10-23 | 2021-05-14 | 新疆畜牧科学院畜牧研究所 | 与绵羊羊毛纤维直径性状相关的分子标记及其特异性引物对和应用 |
CN109385471A (zh) * | 2018-09-26 | 2019-02-26 | 塔里木大学 | 绵羊基因组26号染色体上绵羊脱毛症相关基因的分析方法 |
CN113278712B (zh) * | 2021-07-23 | 2021-11-09 | 中国农业大学 | 分析绵羊毛色的基因芯片、分子探针组合、试剂盒及应用 |
-
2022
- 2022-05-30 CN CN202210602891.2A patent/CN114990226B/zh active Active
-
2023
- 2023-05-29 AU AU2023280943A patent/AU2023280943A1/en active Pending
- 2023-05-29 WO PCT/CN2023/096722 patent/WO2023231940A1/zh active Application Filing
Patent Citations (7)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN110734984A (zh) * | 2019-10-15 | 2020-01-31 | 甘肃农业大学 | 与细毛羊羊毛纤维直径相关的遗传标记及其应用 |
US20210332443A1 (en) * | 2020-04-28 | 2021-10-28 | China Jiliang University | Molecular Marker and Application Method for Assisted Breeding of Fine-wool Sheep |
CN112048562A (zh) * | 2020-08-28 | 2020-12-08 | 中国农业科学院兰州畜牧与兽药研究所 | 一种影响高山美利奴羊羊毛纤维直径的snp分子标记及其应用 |
CN111996265A (zh) * | 2020-09-20 | 2020-11-27 | 中国农业科学院兰州畜牧与兽药研究所 | 一种影响细毛羊羊毛纤维直径的snp分子标记及其应用 |
CN112029872A (zh) * | 2020-09-22 | 2020-12-04 | 中国农业科学院北京畜牧兽医研究所 | 一种与细毛羊羊毛性状相关的snp标记及其检测引物组、试剂盒、检测方法和应用 |
CN114231642A (zh) * | 2022-01-07 | 2022-03-25 | 新疆畜牧科学院畜牧研究所 | 与鄂尔多斯细毛羊羊毛纤维直径性状相关的分子标记及特异性引物对和应用 |
CN114990226A (zh) * | 2022-05-30 | 2022-09-02 | 中国农业科学院兰州畜牧与兽药研究所 | 一种与细毛羊羊毛纤维直径相关的snp位点组合及其应用 |
Non-Patent Citations (1)
Title |
---|
WANG ZHIPENG, ZHANG HUI, YANG HUA, WANG SHOUZHI, RONG ENGUANG, PEI WENYU, LI HUI, WANG NING: "Genome-Wide Association Study for Wool Production Traits in a Chinese Merino Sheep Population", PLOS ONE, PUBLIC LIBRARY OF SCIENCE, US, vol. 9, no. 9, 30 September 2014 (2014-09-30), US , pages e107101, XP093117147, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0107101 * |
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