CN112626237B

CN112626237B - SNP molecular marker combination based on whole genome sequencing screening and related to weight and body size of Xiyan chicken and application

Info

Publication number: CN112626237B
Application number: CN202110053481.2A
Authority: CN
Inventors: 杨秀荣; 杨祝良; 邓继贤
Original assignee: Guangxi University
Current assignee: Guangxi University
Priority date: 2021-01-15
Filing date: 2021-01-15
Publication date: 2022-07-05
Anticipated expiration: 2041-01-15
Also published as: CN112626237A

Abstract

The invention provides SNP molecular marker combinations which are screened based on whole genome sequencing and are related to the weight and the body size of the Xiyan chicken, the SNP molecular marker combinations consist of 67 SNP markers, the information of the SNP molecular marker combinations is shown in table 4, the SNP molecular marker combinations can be used for molecular marker assisted breeding of the Xiyan chicken, individuals can be directly selected and bred on the genome level at the early stage, phenotype information is not relied on, the selection efficiency can be obviously improved, the breeding process is accelerated, the intermediate breeding cost is saved, the breeding efficiency is improved, the breeding cost is reduced, and the application prospect is wide.

Description

SNP molecular marker combination based on whole genome sequencing screening and related to weight and body size of Xiyan chicken and application

Technical Field

The invention belongs to the technical field of molecular biology, and relates to a whole genome sequencing-based screening SNP molecular marker combination related to body weight and body size of a Xia-yan chicken and application thereof.

Background

Guangxi has rich local chicken breeder resources, and the Xia-Yan chicken originally named as a tobacco chicken and also named as a fat breeding chicken belong to meat type chicken breeders and are one of ten-yellow-feather broilers in China. The producing area is mainly located in Guangxi Zhuang autonomous district county, and the Xia-yan chickens are formed in the late morning period according to history records. The yellow or white shin of the Xia Yan chicken, the yellow or white skin, the white meat and the regular feather. The feather is yellowish or deep yellow, the body is strong and compact, and the body is known as the chest, the abdomen and the abdomen. The method has the advantages that the single cocks are upright, 5-7 cocks are provided, the cocks are thick and fat, the cocks are small and ruddy, the ear leaves are red, coarse feeding is resistant, the breeding is easy, the adaptability is wide, the method is suitable for stocking in mountainous forests, and the disease resistance is strong; the meat quality is fat and tender, the bone is thin and soft, and the taste is fragrant and sweet.

The weight and size characters are important phenotypic characters in animal genetic breeding, have close relation with important economic characters, and are also marks for measuring the health condition of chickens. The living weight is an important index for the appearance of the broiler chickens on the market, and the body size characters (shin circumference, shin length, oblique body length and the like) are taken as quantitative indexes capable of accurately reflecting the body type appearance of the broiler chickens, so that the method also has an important function in the genetic breeding process.

A large number of livestock and poultry varieties have been successfully cultivated at home and abroad by utilizing the traditional breeding method. However, in the traditional breeding, offspring is mainly selected according to phenotype by virtue of breeding experience, and the genotype of a target gene cannot be directly selected, so that the breeding is long in time consumption, the phenotype is complex to measure, and the selection efficiency and accuracy are low. At present, molecular biology technology is applied to breeding, breeding can be carried out on a molecular level, and the selection efficiency of breeding can be greatly improved and the breeding time can be shortened by molecular marker-assisted breeding or genetic modification breeding (transgenic breeding). By effectively utilizing molecular markers to assist breeding, the breeding process of the Xia-Yan chicken on the relative characters of weight and body size can be accelerated, and the value of production and application is improved.

In early studies on complex phenotypes, QTL mapping was mainly used to find associations between phenotypic and genomic variations. Since the 90 s of the 20 th century, the QTL linkage analysis method is widely applied to the research of traits such as chicken growth, carcass, meat quality and the like. Although the method is a classical gene positioning method, the method is more suitable for genetic research of single-gene diseases or single-gene control traits, so that the method has limited detection effect on traits with complex diseases and low heritability, the obtained QTL has a large confidence interval, possibly comprises hundreds of genes, and is not beneficial to accurate positioning of subsequent functional genes, and meanwhile, the repeatability in different groups is poor.

Compared with a QTL linkage analysis method, Genome-wide association studies (GWAS) have the characteristics of detecting SNP from the whole Genome level and analyzing the association integrally, the association of individual SNP is not considered singly any more, and the method has the advantages of more reliable results and the like. GWAS was originally proposed by Risch et al, and the concept thereof is to apply millions of Single Nucleotide Polymorphisms (SNPs) in a genome as molecular genetic markers, perform control analysis or correlation analysis on the whole genome level, and discover a new strategy of genetic variation affecting complex traits through comparison, and the new strategy becomes one of the methods with strong fine localization of the target traits of livestock and poultry.

Disclosure of Invention

The invention aims to overcome the defects of the prior art and provide a SNP molecular marker combination which is screened based on whole genome sequencing and is related to the body weight and the body size of a Xiyan chicken.

Another object of the present invention is to provide the use of the above SNP marker combination.

In order to achieve the purpose of the invention, the invention provides an SNP molecular marker combination related to the body weight and the body size of the Xiyan chicken, which consists of 67 SNP molecular markers, wherein the number of the SNP molecular markers is respectively as follows: chr, C, The nucleotide sequences of the genes of chr2_5003559, chr4_6049204, chr5_25104348, chr10_3262194 and chr1_53113841 are respectively shown as SEQ ID NO. 1-67, the information of the genes is shown in Table 4, the base sequence of 200bp before and after each SNP marker is provided in Table 4, and base variation exists at the 100bp position.

The invention also provides application of the SNP molecular marker combination in molecular marker assisted breeding of the Xia-yan chickens.

The invention also provides application of the SNP molecular marker combination in preparation of a detection kit.

The invention also provides a method for detecting the genotype of the Xia-yan chicken by utilizing the molecular biology technology, which comprises the following steps: and respectively designing primers according to nucleotide sequences of two flanks of 67 SNP molecular marker loci, and genotyping the material of the to-be-detected Xia-yan chicken by using the primers, thereby identifying the genotype of the to-be-detected Xia-yan chicken.

The invention also provides application of the method in molecular marker assisted breeding of the Xia-yan chickens.

Through the technical scheme, the invention has the following beneficial effects:

the SNP molecular marker combination related to the weight and the body size of the Xia-yan chicken provided by the invention can be used for molecular marker assisted breeding of the Xia-yan chicken, individuals can be directly selected and bred on the genome level in the early stage, phenotype information is not relied on, the selection efficiency can be obviously improved, the breeding process is accelerated, the intermediate breeding cost is saved, the breeding efficiency is improved, the breeding cost is reduced, and the application prospect is wide.

Detailed Description

The following examples are intended to illustrate the invention but are not intended to limit the scope of the invention. It is intended that all modifications or alterations to the methods, procedures or conditions of the present invention be made without departing from the spirit or essential characteristics thereof.

Animals, instruments, reagents, and kits used in the following examples are commercially available;

example 1

Screening of nepheline tobacco chicken weight and body size related SNP molecular markers based on whole genome sequencing

(1) Population selection and phenotype collection: feeding the Xia-Yan chickens to 120-day-old in an animal experiment base of Guangxi university, stopping feeding for 24 hours, and determining relevant properties such as body weight, body slant length, keel length, chest depth, chest width, hip width, shin length, shin circumference and the like by referring to agricultural industry standard NY/T823-2004 of the people's republic of China; finally, the phenotypic data of 297 nepheline smoke chickens (147 cocks, 150 hens) were collected;

(2) phenotype data sorting and analysis: performing statistics and analysis on the phenotype data collected in the step (1) by using R software, wherein the statistics and analysis comprise minimum values, maximum values, average values, standard deviations and Coefficient of Variation (CV), and the results are shown in Table 1;

TABLE 1 statistical analysis of phenotypic assay data for Xia-Yan chickens

(3) DNA extraction and sequencing: collecting blood of a test chicken, extracting genome DNA by referring to a phenol simulation method in molecular cloning experimental guideline IV, detecting the purity of the DNA by an ultraviolet spectrophotometer, sending the qualified DNA to Beijing Nuo He sourcing science and technology limited company for whole genome re-sequencing, wherein a sequencing platform is Illumina PE150, the depth of the re-sequencing is more than 5X, filtering off-sequence data and obtaining effective information, and the filtering standard mainly comprises the following steps: 1) filtering out reads containing the linker sequence; 2) removing the pair of paired reads when the content of N in the single-ended sequencing read exceeds 10% of the length proportion of the read; 3) removing the pair of paired reads when the number of low mass (< ═ 5) bases contained in the single-ended sequencing read exceeds 50% of the length proportion of the read; after the effective data are obtained, further sequencing quality evaluation is carried out on the effective data, and the error rate distribution condition is checked; sequencing error rates and accuracy are shown in table 2; finally obtaining high-quality data 2693.28 Gb;

TABLE 2 statistics of the genomic DNA resequencing results of Xia-yan chickens

(4) And (3) genome data alignment: comparing and analyzing genome data obtained by sequencing through biological information analysis software BWA and SAMtools; the comparative reference genome is the fifth version of the reference gene (GCA _000002315.3) of chicken (ftp:// ftp. ensembl. org/pub/release-92/fasta/gallius _ gallius/dnas /), parameter "mem-t 4-k 32-M"; removing duplication by utilizing an rmdup parameter of SAMtools software according to a comparison result; the population sample average alignment rate was 98.71%, the average sequencing depth to the genome (excluding the gap region) was 7.77X, and the detailed information is shown in table 3;

TABLE 3 statistics of the genome data comparison of Xia Yan chicken

XY	Clean_reads	mapped_reads	mapping_rate	Average_depth	Coverage_1X	Coverage_4X
							MIN	46324632	45663178	92.51	6.39	84.9	51.86
MAX	245699048	242537527	99	27.21	92.87	90.41
							MEAN	60455582	59679312	98.71	7.77	89.29	68.81

(5) SNP quality control and filtration: carrying out group SNP detection by using a mpieup module of SAMtools software, and obtaining SNPs with high quality through the following quality control during detection: 1) filtering SNPs with the quality value of Q20, namely the sequencing error rate of more than 1%; 2) if the distance between the two SNPs is detected to be within 5bp, removing the SNPs; 3) the support number (coverage depth) of SNPs is between 1/3-5 times the average depth. 10408712 SNPs are preliminarily obtained through the steps; then, carrying out primary filtration on the SNP information of the population by using VCFtools, wherein the filtration parameter is '-means DP 5-thin 10'; after the file format is converted into a PLINK file format, further filtering the file format through the PLINK, wherein the filtering parameter is "-geno 0.1-mind 0.1-maf 0.05-hwe 1 e-6", and finally obtaining 8148164 SNPs on the autosome for subsequent association analysis;

(6) genome wide association analysis (GWAS): performing principal component analysis by using GCTA software, then performing association analysis by using GEMMA software in combination with phenotype information and genome SNP information, rejecting individuals with phenotype values scattered outside a standard deviation of +/-3 times of the mean value within a certain trait, and adding the first three values and the sex of the principal components serving as covariates into a mixed linear model, wherein the model is as follows:

y＝Wα+xβ+u+∈；u～MVN_n(0，λτ^-1K)，∈～MVN_n(0，τ^-1I_n)

wherein y is a phenotype vector, W is a fixed effect matrix, alpha is a coefficient vector corresponding to the fixed effect, x is an SNP marker vector, beta is an effect value of the SNP marker, u is a random effect vector, epsilon is a residual error, and tau-¹Is the residual variance, λ is the ratio between two variance components, K is the genetic relationship matrix, I_nIs an identity matrix;

(7) screening and extracting SNP molecular markers related to the body weight and body size traits of the chicken with the sun-cured tobacco: the "-" indep-pair 2550.2 "parameter of PLINK was used to obtain the number of independent SNP sites on the genome (998097), with 1/998097 as the multiple-test threshold. The sites reaching the significant association level are extracted through R software, 67 SNP molecular marker sites are preferably selected, the information of the sites is shown in table 4, the sites are respectively associated with the oblique body length, the living body weight, the chest depth, the chest width, the hip width, the keel length, the shin girth and the shin length of the Xiyan chicken, and the sites can be used for breeding the weight and the body size traits of the Xiyan chicken.

When breeding the Xiyan chicken, the SNP molecular marker can be used for designing primers on nucleotide sequences of two flanks of the SNP molecular marker, collecting blood and extracting genome DNA when the chicken is 3-4 weeks old, and genotyping the materials of the Xiyan chicken to be tested by using the primers, so that individuals with target character genotypes are reserved, and the breeding speed can be increased.

Information of the 467 molecular markers

SEQUENCE LISTING

<110> Guangxi university

<120> SNP molecular marker combination screened based on whole genome sequencing and related to weight and body size of Xiyan chicken and application

By using

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taattcatgc aagaaacaga attgatggtt gtagaatttc tctacttttg ctatatttct 180

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ggatcattca tatccacttc tcttctgaaa atcaagagta ttatcagagt attctctgaa 180

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<213> Gallus gallus domesticus

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cggaggcatc aagctaaaag agggctcaga agagagctgg tgcccctggg agaccctttc 60

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<213> Gallus gallus domesticus

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<212> DNA

<213> Gallus gallus domesticus

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<212> DNA

<213> Gallus gallus domesticus

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<210> 15

<211> 200

<212> DNA

<213> Gallus gallus domesticus

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<211> 200

<212> DNA

<213> Gallus gallus domesticus

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<213> Gallus gallus domesticus

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<212> DNA

<213> Gallus gallus domesticus

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<212> DNA

<213> Gallus gallus domesticus

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<210> 20

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<212> DNA

<213> Gallus gallus domesticus

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<210> 21

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 21

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<210> 22

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 22

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<210> 23

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 23

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<210> 24

<211> 200

<212> DNA

<213> Gallus gallus domesticus

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atcccctgaa aaccactgaa attgaacatt agactcaact atgtaatttt ttaaaaaaaa 180

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<210> 25

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 25

ttccatatgt tgttcctacg tgcagtaaac ccaatgggaa atgctgccac taaaaataga 60

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taatgcctca ggtctgagac tgcggccagc acagctttca agtctgagag cagttataaa 180

agtggtgcat ttattggttg 200

<210> 26

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 26

tttaggtaaa tctgtcccta cttctgcagg ctgatctgca gttctgaaag ttcttcagag 60

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ccaactgata atgcatttat tccaaccttg gcaatcccac gtagctttgg tgacccaggc 180

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<210> 27

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 27

ttaaaatagt tgggatgtct gagacgcagc aactttgcag gagccacgaa tagcatttga 60

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<210> 28

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 28

ttctgcttct gtagttggtt caatttcagc aaatgtactc tttattcaca gttaattcct 60

aaatagttct gaaatttgtc tctatcttct aagtgtgttm cctttctata tttatcatta 120

tactttccta tacataggaa ggtttttccg tcctgttagt ggggtatctg gttagaaacc 180

ttttctgtcc cattcaggag 200

<210> 29

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 29

tgagtaagaa aaaattaaat gtaattagaa attctgttgt atagcactat atatgaagca 60

agacattgct aaataacgta gaattttcta cttgacattk tatacatata cctacagcag 120

ttgaaataac acaaaaactt gaccctactt accattgtgg ctagcacaca atgaccagtt 180

tgtttctcaa gtctattgtt 200

<210> 30

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 30

ctgaacaaat gtctgaactg ctctgggatg gaatgaggtt agaaatggtg tgagctgtat 60

ttccagtaat atttcaagaa tgtgcttctg atccagcagw aacccccatt tctggtaact 120

tctgagtttg ataattataa taattaagcc aagtcctttg agactcagaa aaatgatttg 180

attcagtggc tgagaagtca 200

<210> 31

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 31

acatctcatc accaattatg ataagaacca ggaaactgtc acattcagcc ttgtaatggt 60

tcagtaggtc ctgacacact tgcatatggt attcattctr ttcctttatg agcactggtg 120

gacccacttg gaacaaactt tgtggtatcc caacactgtc attgcttttt ctgatgcatt 180

gaagccgttg ttcagctcct 200

<210> 32

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 32

cgagtgccgg gagttccggg atctgttcaa gaatgggaag ctttcctgca cgagggagaa 60

tgatcccgtc cgggattcct cggggaagca gcacagcaay aagtgcatca tgtgtgcgga 120

gaagttgtga gtagaggaag ccaatgtttg ttatcgagag tggcaatggg gccggggtgg 180

gctcctacag caatgttctc 200

<210> 33

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 33

ccactccatg gactgccatt ttgacgctgg ctcacagcag tgacaccaca tctcatcacc 60

aattatgata agaaccagga aactgtcaca ttcagcctts taatggttca gtaggtcctg 120

acacacttgc atatggtatt cattctgttc ctttatgagc actggtggac ccacttggaa 180

caaactttgt ggtatcccaa 200

<210> 34

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 34

cttataatga tgggaaaacc tcagcgattc agagtcctga ttcttcagac catctcagaa 60

ctccagatat cagcctgcac ttgtagatcg agaaacaatr tatgagttta tttctaggat 120

ttcatcttct agctcttgct ttggtgaggt actggtatgg gttgctatgg gaggtggtgg 180

agttgctgtc tctggaggtt 200

<210> 35

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 35

tctcttctcc acactgtgga agagaatgtt gaatatgcag cactttagaa gtgctggatg 60

ttgtgtgtga aggaactgct gggcatacag gtgcattgcr gtggtgctgt gctgcctgca 120

gggctgtagc acgttctctc tctgcactca ggtaactaca ctgtctattt aatatttaat 180

gtttttgcct ttcaattgaa 200

<210> 36

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 36

gatgcacagc aagaaaagca acatgaaaag ggagggcagc actggccctg tgatgaatgg 60

tatgaggcag gagagatgtt ctttgtgata acctgtgccy gctggtgctc aggtgtttgc 120

ttgcttcaga catacaacag tactgctacc tggaggcccc tgagctcaaa cacactgtca 180

gctcaccatc tgatgaagtg 200

<210> 37

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 37

gtcagtgcaa taaaaaaaca aacaaaaatc agtgatctgc tgccgttcct acgttacagt 60

tagcaattca gtcactacct atttatgtat cagctgagam tggaagtttt ttttcctaat 120

cctatttcct tcctctgcct aagtgggggt ttaatttaat tccttacaga cacgtcctac 180

agataagtgg aaattttgca 200

<210> 38

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 38

ctgctacaat tgaaacttga gcaaagaaaa caagatagct ttcaagaatc tctccaaatc 60

caaatatttg actttttcct gaggtttatg ggaagagaay gcaaaggtag tttggaaggt 120

ttccaggcag gagatgggaa aggtaggaat gagtgctcct ttgtgcagtg atgctgctgc 180

gatttaaagc ttgtaagctg 200

<210> 39

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 39

agttctatgg atcagaagtt cacagatagt actgactttg ggactatttt gatgcttgct 60

gaatctctac agcttttttt ggattaggct aatgtctgar tcttgtgcag tcagtgactg 120

aaactgatca tgtgcagatg tttggctctt gctgaggcag aagatggtgt tgaagttggg 180

gagctcagca ctaatgaagg 200

<210> 40

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 40

cacaccagag ctgaaagtga gccgtgctgt tgggattcac acctgatccg tgggttagtc 60

tggtgttcag cactctcttg atcctatccc agcttatcas cagtgtttat tttgttccac 120

tgggtcatcc tatactaaca tttggctgca gttgtctggc tgttaaaacc ctggtgcttg 180

ctggcaggga ctgcctactg 200

<210> 41

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 41

ctccattgta ttcaagcacg gaatttaatg cagtctggca cttcctgtaa gcaaacaatt 60

ccccgaccca tcggctgata gtcggctttt tatcttcccy ccattctggc aaatgctgtt 120

tgggtgttta tttgattcac agcttctcat tcatttccca acccaaatga actcgacctc 180

agctggacaa tcccagcagc 200

<210> 42

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 42

ctccactctt tggagaagtt gttcctcata ctcagcctga ccctcccctg gtgcaacatg 60

aggccatcca ggctgttacc tggagcagag gccaaccccy cctcgccaca acctcctttc 120

aggatctgta ggaagtgatg aggactgctg agcctcctct tccccagact gtcccactcc 180

attccctcag ctgctcccca 200

<210> 43

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 43

ttgaattccc ccatgcagaa acaatggcac ctactgacat tcactggtgc ttgctgaacg 60

ttcatggagg ctaaaaggtg aacatgagca caatgagaar gtgggtggtg catttcagca 120

gtggcaacag cggctcacct ccactggcac agatttttac tagcacagca tgcaggctct 180

tgttcatcgc tggcaaaaat 200

<210> 44

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 44

tacagcaatc taatatatta aatactggaa ttgcttgcta cattattcca catacagcct 60

aaaatgaaat atttatctac acaagcggat ggtagcttty cttttgaaca acaatctcaa 120

gaatacaaaa aacaaatgta accaaccact accaatgtac agtaaccctg tataaaatac 180

ctaataagaa gcatactaat 200

<210> 45

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 45

tgatggatct tctgaggttc agccactaga gggggtctaa acctgccctc tgtgtgagta 60

cggcttttcc tggttggtga agcagcatct tcaagcttay gtgctcgcag agatgatgtg 120

gaagcatagc ttataagatg tgtgcaactt tgtaattaaa aaaaaaaaaa aacaaatctc 180

acatgaggct gtttttgaag 200

<210> 46

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 46

tgcatccaga tctggggccc cccgtacaag aaagacaggg agctgttgga gagggtccag 60

aggagggcca cagagctgat cagagggctg gagcagctcy catacaaaga caggctgagg 120

gagctgggct tgttcagcct ggagaagaaa aggctgcagg gtgacctcat tgcagctttc 180

cagtacctaa agggagcata 200

<210> 47

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 47

ctaatcagat gaactccttg ttcagcaagt gtttaaatgt ataataggaa cagactctat 60

gactttttct tgttttttat ctttccagtt gacttgaagy tgtgtatcca actcagtaac 120

tttaaatgga gatgcatggt tacagagaaa gtttcacaat aagaaactga agttgaatga 180

accagcgtta atctgattcc 200

<210> 48

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 48

ccttggcagt ctcacctaat gttaaatcag cactggtcct ctggcaaaaa ggaacagctt 60

tccccaagta taaatcttgt tttcccttgg aacctcctts cagcttcccc ctgtctctct 120

cccacaattc ccaaaaatag gattccccat cctgcatctt ctccacgacc tttcgagttt 180

agcacaaatt aacacacctt 200

<210> 49

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 49

cctatgccca caaatgtcta ttgtatagac agaagatcgt ttctgaagca acactaagaa 60

aaaggctttc ttttgggttg tttcagctgg aatcttcctk aaatcctttc ttccttccca 120

ctgcaccttc agtaaacccc atggaagcat ttcagagaca tacttgacat aatctcacca 180

gcatagcaca gctacagcat 200

<210> 50

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 50

gagctgcacg tgccatgcct gggggcggct gggggaagga ggctgtggat ataaggcaca 60

tggcacctcc tgcagagccc cagggctggt ccagcaggay ctcctcactt gtagcatcac 120

ctctgccaaa tgagataacc ctagacactc ctatatcctt taaaagctca gcaaggacat 180

ctggaggtgc ccaaggccaa 200

<210> 51

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 51

cgtctctccg gcagggattc accgccagct gaacatcaca gctgcggcgc tcagagcctg 60

cctgcctcct gcacagccaa ccgacccccg cagcgtgcar gtttgcccca cgttcccact 120

tactgcacag ccgaacctcc gccgggctgg aagcagaagc gggacgctga tcctccctac 180

agctttcaga tctcagctgt 200

<210> 52

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 52

agactctgaa tcaaaatgaa tgattcagct atagccagtg gagacagtgg cacagctggt 60

cccagtctgg tgcatcttca gacaggcagt gaggctgcar aatgaattag tctctgatta 120

tgccagtttt tctccactct ggtcaagaat ttaactgggt ctctgacttt tcaagatttt 180

cagcactctg gaagggggga 200

<210> 53

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 53

cctcagagat ttcacatcca ctttgctcgt ttcctcttca aactccttca ccctagtcaa 60

gatctcttgc agctcctcct gtctcctgag attttcaaak atctccatag cctccttgac 120

attgcctttc attatctctt ctttgtgtac cgacagcctc ttccgacgtt catcttctgt 180

ttctctcttg gatttttctc 200

<210> 54

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 54

cacactggca gctgcctttg gaggcatctg gagggcactg ctctttctca ttgacctgat 60

tgttggtgtt agcaggtgtg tgctgtttca ccgagttaty cccagcattt gtttgggtgg 120

gttctggtct cttctcaaag ggagacgtgt cacgcccagg tgacccagct aatggatggt 180

taacggagtt agaactctcc 200

<210> 55

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 55

acagcaacgt gctctaaagc aaggcctctt acccaggcat gtgcgatggt tagtctacag 60

tctcaggtgt caattcagct acagcataac agagaggcck gatttggact gtcagcaaga 120

gagactgacc acaagaatga cataaagaaa acttatcaac aagtagcaag ataagagtta 180

atttctgcct cctaattcca 200

<210> 56

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 56

aatgtgtgtg tatatgcagc atgaatatca tgtgcacatc agcaatgcga ttaatatcag 60

catgataatg tgatattttt atacgatgca tgaatatgay atttagatgg catattctat 120

gttatgggca ttcttggaaa agaaatgctg tgttcctcca gcattgtgaa cccaggcatg 180

ctctccctca ccctcccacg 200

<210> 57

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 57

tgactaagaa tgaacataaa tgaatagaat gtacatgaga gaaaaaaaaa cacaggctga 60

gaaacaaagt aagttattga tagcacagga aacaataacy gtaaaaacaa ttttgaaaga 120

agacaacatg aaaacaaaca aaaacaaaca aacaaacaaa aaagcaacaa ggtaaataag 180

gtaaatagaa gttcattaca 200

<210> 58

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 58

tgaaaaagat ttgaaagaaa ggtagagggg atgagaaaga actgaaaatg ggatttaaaa 60

catctcagaa aaaatatttc ccttgtgcct aatttgaaam tataacacac tgtttagcaa 120

gtgaagaaaa aacagtgatt ctgagcgtgt tttggagaag ctcctcaaca gcttttcaca 180

gaagaaattt taagagaaag 200

<210> 59

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 59

atgcgcttga ggtggaccag gaggtcgggg cggtcgcggc ggaagtgcgg gctgtggaag 60

tggtgcaggt gcccgcccga gccgccgtcg ctctccggcs ccgagccggc cctgggtccc 120

gccgggcccg ccaccacctt gcggaaaccg tacaggttga gctggcggat gaagctggtg 180

aagttggtgg tcttgaagag 200

<210> 60

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 60

aatgctaaaa atatcaaact ccaaggccac agttcagcaa acgtttacac acttttgcat 60

aactaccatc aatggtacta atgaagatgg ctgtcacagy tgacttaggt cagcatttta 120

tgtacaggtg tgctgcaaac taagaatgaa acaaacattt gtgcacacac attttctaaa 180

tcactggaaa aatcgcttgt 200

<210> 61

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 61

ttcataatgc agaaagtaaa agatgaggtg gctgagattg ctgaaatgtg ctgcctaaat 60

tgacataatt tcgtcaggtg cccttctatg cgaaggctgs ttatgtgcca gttttggagg 120

tgagtacagt cttgagagca tcgtagtgcc acttgcagaa gttgtcagtc attgctgcat 180

agtatagcct tcacataacc 200

<210> 62

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 62

tcataatgca gaaagtaaaa gatgaggtgg ctgagattgc tgaaatgtgc tgcctaaatt 60

gacataattt cgtcaggtgc ccttctatgc gaaggctgcy tatgtgccag ttttggaggt 120

gagtacagtc ttgagagcat cgtagtgcca cttgcagaag ttgtcagtca ttgctgcata 180

gtatagcctt cacataacca 200

<210> 63

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 63

ggaaggtagc atgaatgaac ctgcagaagt ccaggagaga aaatgcatct cctatcacct 60

ctggatgacc aacagagcca ggcaaaggag aaaaatatak ctgagtgcct cataacacat 120

acaacatgaa ttatcccatg acccaatgat cagccaagtc tggatgatta aatcactgca 180

tccactgctg atgtttcctt 200

<210> 64

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 64

taaaagttac tgtcacctat tacagattca tctgaacaaa ttgactccgt gttacttatt 60

acactggtaa tatctttaac attctataca tttgaactas tgttggaagt gcattggaag 120

tttacaagaa gttctggagt cctggtggat aaaggttaat gctacaactt tctgttggct 180

ataaacagag gagaataaca 200

<210> 65

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 65

ctagagggca aatacaagtg gctgtgtaag ttgattaaat taaacagcat ctgtcttaaa 60

aagctcatgt tctttgggcc ttagagtgct ggacaacccy agtactgttt agacatcaca 120

gctgctgagt atgtctaggc tttggagcag catctgccac tttgtccttc ccctggtaaa 180

acaagtgttg ttatagcatt 200

<210> 66

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 66

gtcccatttt cccacatctc acatgtgttt ttcctgcttt aaagcccgca accagtatga 60

ataacgtctt ttaccttttt attgtaaaca tttaggcttw aagtgattat aactgacagt 120

taaaaccaac aggagccggt agcccgctca tacacaaatt aactgtaata cgggcaaaat 180

caaaaataaa catttccagc 200

<210> 67

<211> 200

<212> DNA

<213> Gallus gallus domesticus

<400> 67

caggggaagt catcaggcta caaaacccac aaagttaaaa atacagggag cattggaaaa 60

tcaacaggaa acaatttttg ctgactgaaa ttttcagccy tcttccaaac gccagctagc 120

agcagactgt cagatgggac aaagcacaag accagcagtg gtccttaact tagtctgtta 180

aagcagaagt ggatgccagg 200

Claims

1. The SNP molecular marker combination which is screened based on whole genome sequencing and is related to the body weight and the body size of the Xiyan chicken is characterized by consisting of 67 SNP markers, wherein the number of the SNP markers is respectively as follows: chr, C, chr, C, the nucleotide sequences of the chr10_3262194 and the chr1_53113841 are respectively shown as SEQ ID NO. 1-67, and the information of the sequences is shown as table 4.

2. The use of the SNP molecular marker combination of claim 1 in assisted breeding of chicken with Xia Yan, oblique length, live weight, chest depth, chest width, hip width, keel length, shin girth and shin length.

3. The method for detecting the genotype of the Xia-yan chicken by utilizing the molecular biology technology is characterized by comprising the following steps of: the primers are designed according to the nucleotide sequences on two flanks of the 67 SNP molecular marker loci of claim 1, and the primers are used for genotyping the nepheline tobacco chicken material to be detected, so that the genotype of the nepheline tobacco chicken to be detected is identified.

4. Use of the method of claim 3 in assisted breeding of Xia Yan hen lean body length, live body weight, chest depth, chest width, hip width, keel length, shin girth, and shin length.