WO2019071407A1 - 一种鸡全基因组snp芯片及其应用 - Google Patents

一种鸡全基因组snp芯片及其应用 Download PDF

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WO2019071407A1
WO2019071407A1 PCT/CN2017/105438 CN2017105438W WO2019071407A1 WO 2019071407 A1 WO2019071407 A1 WO 2019071407A1 CN 2017105438 W CN2017105438 W CN 2017105438W WO 2019071407 A1 WO2019071407 A1 WO 2019071407A1
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chicken
whole genome
snp
molecular marker
chip
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PCT/CN2017/105438
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English (en)
French (fr)
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赵桂苹
刘冉冉
文杰
郑麦青
李庆贺
崔焕先
邢思远
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中国农业科学院北京畜牧兽医研究所
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Priority to US16/309,763 priority Critical patent/US11578365B2/en
Priority to PCT/CN2017/105438 priority patent/WO2019071407A1/zh
Priority to CN201780023241.XA priority patent/CN111225986B/zh
Publication of WO2019071407A1 publication Critical patent/WO2019071407A1/zh

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K67/00—Rearing or breeding animals, not otherwise provided for; New or modified breeds of animals
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K67/00—Rearing or breeding animals, not otherwise provided for; New or modified breeds of animals
    • A01K67/027—New or modified breeds of vertebrates
    • A01K67/0275—Genetically modified vertebrates, e.g. transgenic
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/124—Animal traits, i.e. production traits, including athletic performance or the like
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • the invention relates to the fields of molecular biology, functional genomics, bioinformatics and genome breeding, and more particularly to a chicken whole gene SNP chip and its use.
  • Single Nucleotide Polymorphism refers to the variation of a single nucleotide in a genome, which is a variant formed by substitution, transversion, insertion or deletion of a single nucleotide pair.
  • Single nucleotide polymorphisms as the third generation of genetic markers, are numerous, densely distributed, and easy to detect, making them ideal targets for genotyping.
  • SNP single-nucleotide polymorphism
  • Arrays array millions of DNA-tagged sequences on slides or special wafers and are fixed to form SNP probe arrays. Its working principle is to accurately identify genetic information by base pairing reaction with the target genome by the DNA tag sequence immobilized on the chip.
  • the gene chip uses advanced microbiochemical reaction technology, micro-labeling technology, micro-scale scanning resolution imaging technology and biological information computer processing technology to accurately identify specific mRNA or DNA sequences in biological individuals.
  • ThermoFisher and Illumina each with a commercial genomic SNP chip production technology platform.
  • ThermoFisher (formerly Affymetrix) used the Axiom platform technology to fabricate SNP chips (https://www.thermofisher.com/), which used in-situ lithography to synthesize gene probe sequences in situ on a substrate by photolithography.
  • the chip has been widely used in the research of animal and plant genome variation.
  • the livestock and poultry genome-wide SNP chip can be applied to molecular genetic research and molecular-assisted breeding because of its high label density, uniform coverage of the whole genome, high measurement accuracy, easy to achieve standardization and automated detection, etc.
  • Downstream processes provide support, including genetic diversity analysis of genetic resources, genetic relationship analysis, Genome-Wide Association Analysis (GWAS), QTL mapping of quantitative traits, and selective evolution studies.
  • GWAS Genome-Wide Association Analysis
  • QTL mapping of quantitative traits and selective evolution studies.
  • a very important application is in genome-wide selective breeding (Genomic Application in Selection).
  • Whole genome selection is the main breeding technique in current livestock breeding, using genome-wide markers to estimate all possible genetic effects, interpreting all genetic variation, and predicting genome-wide breeding values through statistically labeled genetic effects (Genomic Estimated Breeding) Values, GEBVs) has the advantages of high accuracy of breeding value estimation and rapid genetic progress. It has been applied to the breeding practice of commercialized lines of dairy cows, pigs, high-yielding laying hens and fast large white feather broilers.
  • the existing chicken 600K commercial SNP chip ( Genome-Wide Chicken Genotyping Array) is based on foreign commercial laying hens and broiler breeds. It lacks genomic variation information of Chinese local chicken breeds (meat or high-quality egg breeds) and is used in the breeding of local chicken breeds in China. There are major limitations in related basic scientific research. Secondly, because chickens have many varieties, large populations, and low individual prices compared with other animals, a relatively low-cost genome-wide SNP chip is needed for large-group sample testing. Therefore, it is urgent to develop a whole-genome SNP chip with moderate flux, including the unique genetic variation information of local chicken breeds in China, and the introduction of chicken genome information from abroad, with moderate flux.
  • the present invention first provides a chicken genome-wide SNP molecular marker combination consisting of 50,000 SNP/INDEL molecular markers, the nucleotide sequences of which are shown in SEQ ID NO. 1 to 50000, respectively.
  • the present invention provides a chicken whole genome breeding chip comprising 50,000 SNP/INDEL molecular markers having the nucleotide sequences set forth in SEQ ID NOS. 1 to 50000.
  • the SNP/INDEL site of the molecular marker is located at the 36th position of the nucleotide sequence shown in SEQ ID NO. 1 to 50000. .
  • the molecular marker is associated with a functional trait of the chicken, the functional trait is a feed trait related to growth traits, body weight at different ages; chest muscle rate, leg muscle rate, net sputum rate associated with corpus callosum traits And abdominal fat percentage; serum immunoglobulin Y (IgY) levels associated with disease resistance traits, Mianyang erythrocyte antibody titer (SRBC), heterophilic granulocyte and lymphocyte ratio (H/L), mean hematocrit; meat Quality traits related to post-mortem final pH, intramuscular fat (IMF), flesh color (brightness, yellowness and redness) and reproductive traits.
  • IGF intramuscular fat
  • IMF intramuscular fat
  • flesh color flesh color
  • the invention provides a chicken whole genome breeding chip suitable for Chinese and foreign chicken breeds, which has stronger correlation with economic traits and moderate flux, and is named as IASCHICK chicken SNP chip.
  • the SNP loci on the chip include three categories: one is the whole genome resequencing information derived from five local varieties and three introduced varieties mainly used in domestic broiler breeding. Local chicken breeds include yellow feather broilers and hemp chickens.
  • the white feather broiler, yellow feather and pheasant were selected to have the lowest allele frequency (MAF)>0.05, and the average distribution of the genome was 19,600 SNP sites (referred to as the first type of probe in this application); Through the correlation analysis such as genome-wide association analysis, 14,000 SNP sites associated with economic traits (referred to as second-type probes in this application) were screened, and the last category was to cover the above two types of probes.
  • the genomic region is derived from 16,400 probes from existing database SNP sites (referred to as third-class probes in this application).
  • the first type of probes include 12,600 SNPs in white chickens, 44,000 yellow broilers, and 0.3 million pheasant chickens.
  • the second type of probe includes the use of illumina 60K SNP Bead Chip for the genome-wide association analysis of growth, meat quality, disease resistance and reproduction using the F2 hybrid population of local varieties and introduced varieties. 10,000 significant sites; 3,100 SNPs in corresponding regions of 100 candidate genes related to traits such as fat deposition were obtained by comparison between multiple control lines; SNP sites of economic trait-related genes obtained by searching previous studies 0.5 million.
  • the 50,000 SNP sites obtained in the present invention have the DNA sequences and characteristics shown in SEQ ID No. 0001 to SEQ ID No. 50000.
  • the IASCHICK chicken whole genome SNP chip according to the present invention refers to a chip produced by the in-situ lithography synthesis process according to the 50,000 sequences using ThermoFisher's Axiom platform technology.
  • the SNP/INDEL site on the IASCHICK chicken whole genome SNP chip of the present invention refers to the nucleotide of position 36 in the sequence shown by SEQ ID No. 0001 to SEQ ID No. 50000.
  • the invention also provides the application of the above chicken whole genome SNP chip-IASCHICK chicken SNP chip in detecting chicken DNA samples, the chip can perform germplasm resource evaluation on Chinese and foreign chicken breed resources, and whole genome selection breeding of local broiler chickens and laying hens , target trait QTL, related sites and candidate gene identification, kinship identification and other applications.
  • the present invention provides the above-described chicken whole genome SNP molecular marker combination and/or the above-described chicken whole genome breeding chip for use in chicken germplasm resource improvement.
  • the invention provides the above chicken whole genome SNP molecular marker combination and/or the above chicken whole genome breeding chip for use in chicken breed identification.
  • the present invention provides the above chicken whole genome SNP molecular marker combination and/or the above chicken whole genome breeding chip for use in chicken breeding.
  • the invention provides the above chicken whole genome SNP molecular marker combination and/or the above chicken whole genome breeding chip for use in chicken genetic relationship identification.
  • the invention provides the above chicken whole genome SNP molecular marker combination and/or the above chicken whole genome breeding chip for use in chicken genetic diversity analysis.
  • the present invention provides the use of the above chicken whole genome SNP molecular marker combination and/or the above chicken whole genome breeding chip in chicken genome-wide association analysis.
  • the invention has the following advantages: (1) The invention has three characteristics: First, it has the versatility of Chinese and foreign chicken breeds: comparatively screening the representative local chicken breeds in China, and the characteristic sites of highly-selected commercial chicken breeds at home and abroad to ensure The universality and effectiveness of locus information; the second is the functional relevance of economic traits. The sites with significant traits such as feed remuneration, meat production rate, lipid metabolism, meat quality, general disease resistance, and reproduction were screened, which increased the accuracy of the basic research of the chip; Uniform distribution and moderate flux.
  • the 50,000 sites are evenly distributed throughout the genome (except for the higher density of chromosome 16), with an average spacing of 24kb (kilobase), which ensures the estimation of breeding values and the accuracy of related research; compared with the existing 600K commercial chips, The flux is moderate, the price is greatly reduced, and the cost is high; (2) Compared with the second-generation re-sequencing genotyping system: because the detection mutation site is fixed, the data analysis is simple and easy to achieve standardized automatic detection and analysis. Comparables are easily achieved between different batches and different laboratory data.
  • Figure 1 shows that the 50K locus is evenly distributed across the whole chromosome (except for chromosome 16) and has similar LD levels.
  • Figure 2 is a graph showing the results of PCA clustering of Chinese and foreign chickens.
  • Figure 3 is a plot of PCA clustering results for different flocks in the same field.
  • the first type of probes are mainly based on whole genome resequencing technology, and obtained 50,000 unique SNP loci for Chinese local breeds and SNP loci for foreign fast white broilers.
  • the chicken F2 resource group of the Chinese Academy of Agricultural Sciences was produced by the cross between Beijing oil chicken and Kebao broiler chicken. Including F0-F2 generation a total of 400 chickens.
  • Phenotypic assays are well known methods, including (1), chest muscle rate, leg muscle rate, net sputum rate and abdominal fat rate, body weight 28 days, body weight 42 days; (2), SRBC antibody titer, serum IgY level, H/L value, mean hematocrit; (3), final pH, chest muscle IMF, flesh brightness, yellowness and redness values. Blood samples were taken from chicken wings for genomic DNA extraction. Determination using the Illuima chicken 60K genome-wide SNP chip After the amount control, there were 42 585 SNPs remaining.
  • the genome-wide association analysis was performed using the GLM model in the plink software. After correcting the p-value by Bonferroni method, 6147 points of 15 major traits, such as 42-day-old body weight, chest muscle IMF content and IgY, were obtained. Selection site.
  • Candidate Gene Screening Method Based on the applicant's previous study and the NCBI website PUBMED database (see Table 2), the economic trait-related candidate genes were obtained, and the resequencing results in Example 1 were combined to obtain the SNP sites inside and below the target gene. More than 100 SNP candidates per gene. After removing the repetitive sites, based on the minimum allele frequency of the site MAF ⁇ 0.05 and the position of the site annotation in the gene structure (intragenic and regulatory region preferential), 15,173 locus alternative SNPs were screened.
  • the chip site finalization process is:
  • the chip has (1) versatility: the characteristic SNP containing local chicken species and commercial introduced varieties.
  • Effectiveness The minimum MAF of 20K sites in 8 Chinese and foreign chicken populations such as Bai Yu, Huang Yu and Ma Yu was higher than 0.05;
  • Functional correlation 14K locus was identified and grown by GWAS and other studies. , economic composition of carcass composition, meat quality, general immunity, reproduction, appearance, etc.;
  • moderate flux 50,000 SNP sites are evenly distributed in the whole genome at an average interval of 24 kb, in the practice of whole genome selection breeding The application is cost effective.
  • Gene chip detection Operate according to the Affymetrix GeneTitanTM GeneChip Assay Standard Process (Axiom 2.0 Target Prep 384Samples Protocol https://www.thermofisher.com/).
  • the chip scan was performed using a GeneChip HT Array Plate Scanner chip scanner (GeneChip HT Array Plate Scanner, Thermo Fisher Scientific, USA).
  • the IASCHIK chip was detected on 1062 random individuals of the white feather fast broiler K series (see the method of Example 2).
  • the genotype quality control conditions were: individual call rate (CR)>95%, MAF>0.05, Hardy-Weinberg equilibrium test> 0.001, 948 eligible individuals and 46386 high quality SNP loci were obtained for GWAS analysis after quality control.
  • the GWAS analysis based on the mixed linear model was performed according to the calculation results of the corresponding individual remaining feed intake (28-42 days old) (between -46.77 and 22.80). P ⁇ 1 ⁇ 10 -5 was used as the genome-related level, and significant association sites were obtained as shown in Table 4.
  • the invention utilizes the IASCHICK chicken chip prepared in Example 1 to carry out genetic diversity analysis on 8 local chicken breeds and 2 fast white feather chicken breeds (see the method of Example 2).
  • Local chicken breeds include chickens with partial meat, Qingyuan chicken, Wenchang chicken, Camellia chicken, Luhua chicken, Luyuan chicken, big bone chicken; egg chicken with white ear chicken and Xianju chicken; commercialized fast white feather chicken including Hubbard broiler And the synthetic line is the white feather broiler K series.
  • the local chicken samples were all sourced from the National Local Chicken Breeding Gene Bank of the Chinese Academy of Agricultural Sciences Poultry Research Institute, 20 each.
  • the detection rate of all SNP sites was over 97%, and the MAF>0.05 sites were more than 40,000, accounting for more than 80%; the average MAF in the variety was between 0.22-0.27. . It is proved that the IASCHICK chicken SNP chip site is widely applicable to Chinese and foreign chicken species, and has high polymorphism in both local varieties and introduced varieties.
  • the genotype results were quality controlled, see the method of Example 3 for conditions.
  • the cluster analysis was performed by the PCA group structure and the MEGA software neighboring method (NJ), and the results were consistent. See PCA results Figure 2 (MEGA results are not given).
  • the small-sized meat is used in local chickens, the chickens and chickens, and Qingyuan is the closest, followed by the small meat Wenchang chicken; the large-sized meat chickens, the Luhua chicken, the Luyuan chicken and the big bone chicken, respectively, are grouped together; and the whole meat chicken The species is closer than the egg chicken and the introduction of the fast white broiler.
  • the egg-type local chicken breed Bai Er and Xianju chicken are the closest, and are distinguished from various meat local chicken breeds; while the foreign introduction of the fast white feather Hubbard broiler and the synthetic fast white feather broiler K series (which contains the introduction)
  • the fast-blooded chicken bloodline has the closest clustering distance and is clearly distinguished from various local chicken breeds.
  • the results show that the IASCHICK chicken SNP chip prepared in Example 1 can be well applied to the diversity and evolution analysis of local chicken germplasm resources, and the identification results are accurate and reliable.
  • the IASCHICK chicken SNP chip prepared in Example 1 was applied to the test population of the chickens of the three chickens in a chicken farm.
  • the IASCHICK chicken SNP chips prepared in Example 1 were 412 chickens of the 111 series, 201 series and 301 series.
  • the DNA samples were tested for genetic relationship, and the results were consistent according to PCA and MEGA cluster analysis. The PCA results are shown in Figure 3 (MEGA results are not given).
  • the chicken genome-wide SNP chip provided by the invention has a total of 50,000 SNP sites: the whole genome re-sequencing information of the main local breeds and imported chickens in China, and the MAF of the white feather broiler, the yellow feather broiler and the Maju broiler are selected. >0.05, with an average distribution of 19,600 SNPs in the genome; 14,000 SNPs associated with economic traits; and 16,400 SNPs in the genomic region not covered by the first two types of probes, on-chip
  • the SNP loci have the DNA sequences shown in SEQ ID NO.
  • SNP loci are evenly distributed throughout the genome, and are related to feed remuneration, meat production rate, lipid metabolism, meat quality, general disease resistance, It is associated with traits such as reproduction, with moderate flux and low cost, and has the versatility of Chinese and foreign chicken breeds.

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Abstract

本发明提供了一种鸡全基因组SNP芯片及其应用，该芯片上的SNP位点共50000个：分别源于中国主要地方品种和引进品种鸡的全基因组重测序信息，筛选出白羽肉鸡、黄羽肉鸡和麻羽肉鸡中具有MAF>0.05，且在基因组平均分布的1.96万个SNP位点；与经济性状相关联的1.4万个SNP位点；弥补前两类探针未覆盖的基因组区域的1.64万个SNP位点。

Description

一种鸡全基因组SNP芯片及其应用 技术领域
本发明涉及分子生物学、功能基因组学、生物信息学和基因组育种领域，更具体涉及一种鸡全基因SNP芯片及其用途。
背景技术
单核苷酸多态性(Single Nucleotide Polymorphism,SNP)指基因组单个核苷酸的变异，是由单个核苷酸对置换、颠换、插入或缺失所形成的变异形式。单核苷酸多态性作为第三代遗传标记，SNP数量众多、分布密集、易于检测，是较理想的基因分型目标。
全基因组SNP芯片即单核苷酸多态性(SNP)微阵列(Array)，将数百万DNA标记序列排列在玻片或特殊硅片上，固定形成SNP探针阵列。它的工作原理是通过固定在芯片上的DNA标记序列与目标基因组发生碱基配对反应，从而精准鉴定基因信息。基因芯片运用先进的微生化反应技术、显微标记技术、微米级扫描分辨成像技术和生物信息计算机处理技术，准确鉴定检测生物个体中特定的mRNA或DNA序列。目前，有两家美国生物技术公司，ThermoFisher和Illumina公司分别具备商业化基因组SNP芯片制作技术平台。ThermoFisher公司(原Affymetrix公司)利用Axiom平台技术制作SNP芯片(https://www.thermofisher.com/)，即利用原位光刻技术，通过光刻在基片上原位合成基因探针序列。该芯片在动植物基因组变异研究中已得到广泛应用。
畜禽全基因组SNP芯片由于标记密度高，均匀覆盖全基因组、具有测定准确率高、易实现标准化和自动化检测等诸多优势，可以应用于分子遗传研究和分子辅助育种等各个方面，可为育种上下游过程提供支持，包括种质资源遗传多样性分析、亲缘关系分析、全基因组关联分析(Genome-Wide Association Analysis,GWAS)、数量性状QTL定位分析和选择进化研究等。其中非常重要的应用是在全基因组选择育种(Genomic  Selection)中的应用。全基因组选择是当前畜禽育种中主要选育技术，运用全基因组标记，估计所有可能的遗传效应，解释全部的遗传变异，通过统计标记的遗传效应，进行全基因组育种值的预测(Genomic Estimated Breeding Values,GEBVs)，具有育种值估计准确性高、遗传进展快的优点，已应用于奶牛、生猪、国外高产蛋鸡和快大型白羽肉鸡的商业化品系选育实践。
然而，现有鸡600K商业化SNP芯片(
Figure PCTCN2017105438-appb-000001
 Genome-Wide Chicken Genotyping Array)位点信息多来源于国外商业蛋鸡和肉鸡品种，缺少中国地方鸡种(肉用或优质蛋用鸡品种)基因组变异信息，在应用于中国地方鸡种选育及相关基础科学研究中具有较大局限性。其次，由于鸡与其他动物相比，具有品种繁多、群体量大、但是个体价格低廉等特点，所以进行大群体样本检测中，需要一款价格相对低廉的全基因组SNP芯片。因此，肉鸡、蛋鸡育种行业及科研领域均亟待开发一种通量适中，包含中国地方鸡种特有遗传变异信息，兼顾国外引进鸡种基因组信息，通量适中的全基因组SNP芯片。
发明内容
本发明的目的在于提供一种鸡全基因组SNP芯片及其应用。
本发明首先提供一种用于鸡全基因组SNP分子标记组合，由50000个SNP/INDEL分子标记组成，其核苷酸序列分别如SEQ ID NO.1～50000所示。
本发明提供一种鸡全基因组育种芯片，包含50000个SNP/INDEL分子标记，其具有SEQ ID NO.1～50000所示的核苷酸序列。
本发明的上述鸡全基因组SNP分子标记组合及上述的鸡全基因组育种芯片中，所述分子标记的SNP/INDEL位点位于SEQ ID NO.1～50000所示的核苷酸序列的第36位。
所述分子标记与鸡功能性状相关联，所述功能性状为生长性状相关的饲料报酬、不同日龄体重；胴体组成性状相关的胸肌率、腿肌率、净膛率 和腹脂率；抗病性状相关的血清免疫球蛋白Y(IgY)水平、绵阳红细胞抗体滴度(SRBC)、异嗜性粒细胞和淋巴细胞比率(H/L)、平均红细胞压积；肉品质性状相关的宰后最终pH值、肌内脂肪(IMF)、肉色(亮度、黄度和红度)及繁殖性状。
本发明提供了上述一种鸡全基因组育种芯片适用于中外鸡种、与经济性状关联度更强、通量适中的鸡全基因组SNP芯片，命名为IASCHICK鸡SNP芯片。该芯片上的SNP位点包括三类：一类是源于国内肉鸡配套育种中主要应用的5个地方品种和3个引进品种的全基因组重测序信息。地方鸡种包括黄羽肉鸡、麻羽鸡等。筛选出白羽肉鸡、黄羽和麻羽鸡中具有最小等位基因频率(MAF)>0.05，且在基因组平均分布的1.96万个SNP位点(本申请称为第一类探针)；另一类通过全基因组关联分析等多种相关性分析，筛选与经济性状相关联的1.4万个SNP位点(本申请称为第二类探针)，最后一类是为了填充以上两类探针不能覆盖的基因组区域，来源于已有数据库SNP位点的探针1.64万个(本申请称为第三类探针)。
具体来讲，其中第一类探针，包括白羽鸡SNP位点1.26万个、黄羽肉鸡0.4万个、麻羽肉鸡0.3万个。第二类探针包括利用地方品种与引进品种的F2杂交群体等为素材，使用illumina 60K SNP Bead Chip，对生长、肉质、抗病力和繁殖等共15个性状进行全基因组关联分析得到的0.6万个显著位点；通过多个对照品系间比较，获得位于脂肪沉积等性状相关100个候选基因相应区域的SNP 0.3万个；通过搜索前人研究结果获得的经济性状相关基因的SNP位点共0.5万个。
整个芯片5万个位点中，有1.7万个是通过多品种重测序新发现的，是已有Ensembl公共数据库(Ensembl chicken variation database)中未记载的SNP位点。将这些共50K位点，设计探针，采用ThermoFisher公司的Axiom平台技术，通过原位光刻合成工艺制作而成IASCHICK芯片，每张芯片可同时检测96或384个样品。
本发明获得的50000个SNP位点具有SEQ ID No.0001～SEQ ID No.50000所示的DNA序列和特征。本发明所说的IASCHICK鸡全基因组SNP芯片是指根据这50000条序列采用ThermoFisher公司的Axiom平台技术，通过原位光刻合成工艺制作的芯片。本发明所说的IASCHICK鸡全基因组SNP芯片上的SNP/INDEL位点是指SEQ ID No.0001～SEQ ID No.50000所示的序列中第36位的核苷酸。
本发明还提供了上述鸡全基因组SNP芯片—IASCHICK鸡SNP芯片在检测鸡DNA样品中的应用,该芯片可以对中外鸡品种资源进行种质资源评价、对地方肉鸡、蛋鸡进行全基因组选择育种、目标性状QTL、关联位点及候选基因鉴定、亲缘关系鉴定等应用中。
具体地，本发明提供了上述鸡全基因组SNP分子标记组合和/或上述的鸡全基因组育种芯片在鸡种质资源改良中的应用。
本发明提供了上述鸡全基因组SNP分子标记组合和/或上述的鸡全基因组育种芯片在鸡品种鉴定中的应用。
本发明提供了上述鸡全基因组SNP分子标记组合和/或上述的鸡全基因组育种芯片在鸡育种中的应用。
本发明提供了上述鸡全基因组SNP分子标记组合和/或上述的鸡全基因组育种芯片在鸡亲缘关系鉴定中的应用。
本发明提供了上述鸡全基因组SNP分子标记组合和/或上述的鸡全基因组育种芯片在鸡遗传多样性分析中的应用。
本发明提供了上述鸡全基因组SNP分子标记组合和/或上述的鸡全基因组育种芯片在鸡全基因组关联分析中的应用。
本发明的优点在于：(1)本发明具有三个特点：一是具有中外鸡品种通用性：对比筛选了我国代表性的地方鸡种、国内外高度选育商用鸡种的特征位点，确保位点信息的普适性和有效性；二是具有经济性状的功能相关性。筛选了与饲料报酬、产肉率、脂代谢、肉品质、一般抗病力、繁殖等性状能基因显著的位点，增加了芯片进行基础研究的准确性；三是位点 分布均匀、通量适中。5万个位点在全基因组均匀分布(除16号染色体密度较高外)，平均间距24kb(kilobase)，保证了育种值估计和相关研究的准确性；与已有600K商业化芯片相比，通量适中，价格大幅降低，具有较高的性价比；(2)与基于二代重测序的基因分型系统相比：由于检测变异位点固定，所以数据分析简便、容易实现标准化自动化检测和分析；不同批次、不同实验室数据之间较容易实现可比性。
附图说明
图1为50K位点在全染色体均匀分布(除16号染色体外)，具有相近的LD水平。
图2为中外鸡种PCA聚类结果图。
图3为同场不同鸡群PCA聚类结果图。
具体实施方式
以下实施例进一步说明本发明的内容，但不应理解为对本发明的限制。在不背离本发明精神和实质的情况下，对本发明方法、步骤或条件所作的修改或替换，均属于本发明的范围。
若未特别指明，实施例中所用的技术手段为本领域技术人员所熟知的常规手段。
实施例1 IASCHICK鸡全基因组SNP芯片的制备方法
1、第一类探针的获得：第一类探针的特征主要是基于全基因组重测序技术，获得5万个中国地方种用鸡种特有SNP位点和国外快大白羽肉鸡SNP位点。
首先利用Hiseq 2500platform(Illumina Inc.)测序技术对8个中外品种(见表1)。进行了全基因组测序，每个样本获得20倍的基因组覆盖度。具体流程为对每个品种构建测序文库，具体方法为每个品种设置3个混合池，使用Nextera DNA文库制备试剂盒(Illumina Inc.，San Diego，CA，USA)标准流程构建DNA文库。所有DNA文库在Hiseq2500平台测序。 排除低质量(片段长度<10)和具有接头污染的reads从而得到clean data。所有的clean data通过BWA tools软件mapping到GalGAL4.0上(Li and Durbin,2010)，用SAM tools中的rmdup参数除去PCR重复(Li et al.,2009)。利用SAM Tools软件mpileup功能进行SNP突变分型(Koboldt et al.,2009)。共获得高质量的突变位点15,312,402(见表1)。将最小等位基因的频率大于0.05的位点作为第一类探针的数据源。此外，还包括对来航鸡和北京油鸡高低IgY组样本进行11、16和19号染色体进行目标区域抓捕重测序结果，共获得相关高质量突变位点1700个。
表1 重测序国内外鸡种及鉴定SNP数量
Figure PCTCN2017105438-appb-000002
2、第二类探针的获得：基于全基因组关联分析(GWAS)和相关候选基因内SNP筛选方法获得15个目标性状相关联的SNP位点。
首先利用北京油鸡和科宝肉鸡杂交产生的中国农业科学院鸡F2资源群体。包括F0-F2代共400只鸡。表型测定方法均为熟知的方法，包括(1)、胸肌率、腿肌率、净膛率和腹脂率、体重28日龄、体重42日龄；(2)、SRBC抗体滴度、血清IgY水平、H/L值、平均红细胞压积；(3)、最终pH值、胸肌IMF、肉亮度、黄度和红度值。试验鸡翅静脉采血，用于基因组DNA提取。使用Illunima鸡60K全基因组SNP芯片测定，经过质 量控制后，剩余42,585个SNPs位点。利用plink软件中的GLM模型进行全基因组关联分析，经Bonferroni方法矫正p-value后，得到42日龄体重、胸肌IMF含量和IgY等15个主要性状显著性Top 1％的位点6147个作为备选位点。
候选基因筛选法：基于申请人前期研究和NCBI网站PUBMED数据库(见表2)获得经济性状相关候选基因，结合实施例1中重测序结果，获得目标基因内部及上下游SNP位点。每个基因均多于100个SNP备选。经去除重复位点、根据位点的最小等位基因频率MAF<0.05及位点注释在基因结构中的位置(基因内和调控区优先)筛选得到15,173个位点备选SNP。
表2 第二类探针数据来源
Figure PCTCN2017105438-appb-000003
Figure PCTCN2017105438-appb-000004
芯片位点最终确定流程为：
(1)将第一类和第二类探针送Thermo公司打分后，去除不建议设计探针的位点；
(2)将染色体分为24kb一个窗口/区间，每个区间优先选择第二类探针中SNP，如果第二类探针缺失，则从第一类探针中SNP中选择；将第一类探针和第二类探针选择完后，仍然不能覆盖的区域，从NCBI网站上的SNPdb数据库中(https://www.ncbi.nlm.nih.gov/projects/SNP/index.html)中获取。。
最终实现5万个SNP在全基因组平均分布(除16染色体密度较高外，如图1，表3)，芯片具备了(1)通用性：包含地方鸡种和商业化引进品种的特征性SNP；(2)有效性：20K位点在白羽、黄羽、麻羽等8个中外鸡种群体中最小MAF均高于0.05；(3)功能相关性：14K位点由GWAS等研究鉴定获得与生长、胴体组成、肉品质、一般免疫力、繁殖、外貌等经济性状相关；(5)通量适中：5万个SNP位点在全基因组以平均24kb的间距均匀分布，在全基因组选择育种实践中应用性价比高。
表3 芯片位点在各染色体分布数量
Figure PCTCN2017105438-appb-000005
实施例2 IASCHICK鸡SNP芯片在鸡DNA样本检测中的应用方法
采集鸡血液样本，用酚-仿法或专用试剂盒提取血液基因组的DNA，溶于ddH2O，并通过1％琼脂糖凝胶电泳检验纯度。DNA样品质量检测；用质量分数为1-1.5％(w/w)的琼脂糖疑胶电泳检测，用凝胶成像系 (GelDocXR System,美国Bio-Rad公司)统判断电泳结果，保证基因组DNA完整性好，且该基因组DNA片段长度大于10kb；用微量紫外分光光度计(Q5000，美国Quaweu公司)或类似的核酸蛋白测定仪测量基因组DNA的浓度,将DNA浓度调整到工作浓度10-50ng/μ1。
基因芯片检测:按照Affymetrix GeneTitanTM基因芯片检测标准流程操作(Axiom 2.0Target Prep 384Samples Protocol https://www.thermofisher.com/)。芯片扫描使用GeneChip HT Array Plate Scanner芯片扫描仪(GeneChip HT Array Plate Scanner,美国thermo fisher Scientific公司)。
数据分析:用Axiom Analysis Suite分析基因型(软件下载网址：https://www.thermofisher.com/cn/zh/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/axiom-analysis-suite.html，软件来源主页：https://www.thermofisher.com),并用R语言(http://www.rproject.org/)编程获得基因型比较结果。
实施例3 基于IASCHICK鸡SNP芯片测试结果进行重要经济性状关联基因挖掘
对白羽快速型肉鸡K系1062个随机个体进行IASCHIK芯片检测(参见实施例2方法进行)基因型质控条件为，个体call rate(CR)>95％,MAF>0.05,Hardy-Weinberg平衡检验>0.001，质控后得到948个合格个体和46386个高质量SNP位点用于GWAS分析。根据相应个体剩余采食量(28-42日龄)计算结果(-46.77至22.80之间)，进行基于混合线性模型的GWAS分析。以p<1×10-5作为基因组相关水平，得到显著关联位点如表4所示。1号染色体51425729-66784053bp共15.3Mb区间内就聚集了4个与RFI显著相关位点，提示这一区间是影响RFI的关键QTL区域。且该区域包含IGF-1基因(Chr1:55335204-55383631bp)，该基因已经被证明为影响生长及饲料报酬的已知基因。2号、4号、7号和10号染色 体上的显著关联位点则可能是之前未被发现的变异位点。因此，通过实施例1制得的IASCHICK芯片鉴定基因型得到数据，可以得到比较准确的关联分析结果，见表4。
表4 RFI性状GWAS分析得到显著关联位点信息表
Figure PCTCN2017105438-appb-000006
实施例4 IASCHICK芯片在中外鸡种中的广泛适用性检测及地方鸡种遗传多样性分析结果
本发明利用实施例1制得的IASCHICK鸡芯片对8个地方鸡种和2个快速白羽鸡种进行遗传多样性分析(参见实施例2方法进行)。地方鸡种包括偏肉用鸡种清远鸡、文昌鸡、茶花鸡、芦花鸡、鹿苑鸡、大骨鸡；蛋用鸡种白耳鸡和仙居鸡；商业化快速白羽肉鸡包括哈伯德肉鸡和合成品系白羽肉鸡K系。地方鸡种样本均来源中国农业科学院家禽研究所国家地方鸡种基因库，各20只。在检测的10个鸡种中，所有SNP位点检出率均达97％以上，MAF>0.05位点均在4万个以上，占比80％以上；品种内平均MAF在0.22-0.27之间。证明IASCHICK鸡SNP芯片位点广泛适用于中外鸡种，在地方品种和引进品种中均具有较高多态性。
对基因型结果进行质控，条件参见实施例3方法。分别以PCA群体结构和MEGA软件的邻接法(NJ)进行聚类分析，结果一致。PCA结果见 图2(MEGA结果未给出)。小体型肉用地方鸡种茶花鸡、清远距离最近，其次是小型肉用文昌鸡；大体型肉用鸡种芦花鸡、鹿苑鸡和大骨鸡分别各自聚为一类；且整体上肉用鸡种相比于蛋用鸡和引进快大白肉鸡距离更近。蛋用型地方鸡种白耳和仙居鸡距离最近，并与各类肉用地方鸡种区分开来；而国外引进快大白羽哈伯德肉鸡与合成快大白羽肉鸡K系(其中含有引进快大鸡血缘)聚类距离最近，并与各类地方鸡种明显区分。该结果表明,实施例1制得的IASCHICK鸡SNP芯片能够很好地应用于地方鸡种种质资源多样性和进化分析中,鉴定结果准确可靠。
实施例5 基于IASCHICK鸡SNP芯片测试结果进行亲缘关系鉴定
鸡的遗传育种通常应用大群体、高选择压选育。生产中由于多种主观或客观因素会造成部分鸡混杂后而无法分辨来源的问题，因此需要对鸡群进行亲缘关系鉴定工作。本实施例中针对某鸡场三个品系鸡中掺杂入非纯系鸡的待测群体，应用实施例1制得的IASCHICK鸡SNP芯片对111系、201系和301系共412个鸡的DNA样品进行了亲缘关系检测，根据PCA和MEGA聚类分析结果一致，PCA结果见图3(MEGA结果未给出)。存在67个掺入非纯系鸡(图中4个黑圈以外个体)，需要在种用中进行剔除或是调整；其他黑圈内个体分属于3个生产中已知系群。经IASCHICK芯片鉴定后即可辅助育种中进行准确亲缘关系鉴定，加速育种进程。
工业实用性
本发明提供的鸡全基因组SNP芯片上的SNP位点共50000个：分别源于中国主要地方品种和引进品种鸡的全基因组重测序信息，筛选出白羽肉鸡、黄羽肉鸡和麻羽肉鸡中具有MAF>0.05，且在基因组平均分布的1.96万个SNP位点；与经济性状相关联的1.4万个SNP位点；弥补前两类探针未覆盖的基因组区域的1.64万个SNP位点，芯片上的SNP位点分别具有SEQ ID NO.1-50000所示的DNA序列，该芯片SNP位点在全基因组均匀分布，并与饲料报酬、产肉率、脂代谢、肉品质、一般抗病力、繁殖等性状相关联，通量适中，成本低，具有中外鸡品种通用性。

Claims (10)

  1. 一种鸡全基因组SNP分子标记组合，其特征在于，由50000个SNP/INDEL分子标记组成，其核苷酸序列分别如SEQ ID NO.1～50000所示。
  2. 一种鸡全基因组育种芯片，其特征在于，包含50000个SNP/INDEL分子标记，其具有SEQ ID NO.1～50000所示的核苷酸序列。
  3. 如权利要求1所述的鸡全基因组SNP分子标记组合或权利要求2所述的鸡全基因组育种芯片，其特征在于，所述分子标记的SNP/INDEL位点位于SEQ ID NO.1～50000所示的核苷酸序列的第36位。
  4. 如权利要求1所述的鸡全基因组SNP分子标记组合或权利要求2所述的鸡全基因组育种芯片，其特征在于，所述分子标记与鸡功能性状相关联，所述功能性状为生长性状相关的饲料报酬、不同日龄体重；胴体组成性状相关的胸肌率、腿肌率、净膛率和腹脂率；抗病性状相关的血清IgY水平、SRBC抗体滴度、H/L比率、平均红细胞压积；肉品质性状相关的宰后最终pH值、肌内脂肪含量和肉色亮度、黄度和红度及繁殖性状。
  5. 权利要求1所述的鸡全基因组SNP分子标记组合或权利要求2所述的鸡全基因组育种芯片在鸡种质资源改良中的应用。
  6. 权利要求1所述的鸡全基因组SNP分子标记组合或权利要求2所述的鸡全基因组育种芯片在鸡品种鉴定中的应用。
  7. 权利要求1所述的鸡全基因组SNP分子标记组合或权利要求2所述的鸡全基因组育种芯片在鸡育种中的应用。
  8. 权利要求1所述的鸡全基因组SNP分子标记组合或权利要求2所述的鸡全基因组育种芯片在鸡亲缘关系鉴定中的应用。
  9. 权利要求1所述的鸡全基因组SNP分子标记组合或权利要求2所述的鸡全基因组育种芯片在鸡遗传多样性分析中的应用。
  10. 权利要求1所述的鸡全基因组SNP分子标记组合或权利要求2所述的鸡全基因组育种芯片在鸡全基因组关联分析中的应用。
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