Zhuxiang chicken
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Background Information Variants Annotation&Density Genetic Differentiation
Genetic Affinity ADMIXTURE Analysis Runs of Homozygosity
Linkage Disequilibrium Decay Demographic History Selection

Background Information

Breed Card
Breed Zhuxiang chicken
Species taxonomy Gallus gallus domesticus
Classification Traditional
Region China
Purpose Dual
Description

Zhuxiang chicken is one of the famous local poultry breeds in Guizhou Province of China. It is a medium-size dual-purpose chicken breed.

Characteristics

This breed is a kind of black-bone chicken with black beak, crown, lobes, ears, tibia and claws. Single comb. The feathers are black or partridge yellow. The neck and back feather of rooster are red. The skin and meat are black. Roooter weight about 2.3kg and hen weight 2.1kg. The hens start laying at 180-210 days and lay 100-150 eggs a year. The eggs color are sandy beige or white.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 191675 650455 29.4678% 18454 104154 17.718%
exonic;splicing 34 188 18.0851% 0 0 0%
exonic_unknown 38 582 6.5292% 0 82 0%
frameshift_deletion 0 0 0% 1212 15977 7.5859%
frameshift_insertion 0 0 0% 991 13308 7.4466%
intergenic 4357269 15129055 28.8007% 376790 2238383 16.8331%
intronic 5395503 17735594 30.4219% 488799 2641780 18.5026%
ncRNA_exonic 114438 400185 28.5963% 9026 54342 16.6096%
ncRNA_exonic;splicing 83 231 35.9307% 3 43 6.9767%
ncRNA_intronic 1095831 3728327 29.392% 100052 575920 17.3726%
ncRNA_splicing 672 2341 28.7057% 86 478 17.9916%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 704 8777 8.021%
nonframeshift_insertion 0 0 0% 306 4784 6.3963%
nonsynonymous 53741 336233 15.9833% 0 0 0%
splice_acceptor 115 750 15.3333% 104 964 10.7884%
splice_donor 159 1076 14.777% 36 763 4.7182%
splice_donor_acceptor 0 0 0% 21 45 46.6667%
splice_UTR5 96 400 24% 10 106 9.434%
splie_Others 0 0 0% 57 654 8.7156%
startloss 165 671 24.5902% 6 51 11.7647%
stopgain 590 4175 14.1317% 35 1252 2.7955%
stoploss 96 353 27.1955% 10 63 15.873%
synonymous 117084 548813 21.334% 0 0 0%
upstream 198543 679592 29.215% 16908 98760 17.1203%
upstream;downstream 16870 57451 29.3642% 1625 9367 17.3481%
UTR3 97561 361040 27.0222% 9977 61415 16.2452%
UTR5 28807 112990 25.4952% 2371 16935 14.0006%
UTR5;UTR3 687 2524 27.2187% 70 381 18.3727%
Total 11670057 39753026 29.3564% 1027654 5848802 17.5703%
SNP Density
SNP_Annotation
INDEL Density
INDEL_Annotation

Genetic Differentiation

Summary

Genetic affinities of target population in the context of worldwide populations are measured by pairwise FST between target population and references. Smaller FST value indicates closer relationship. Regions represented by different colors are indicated above.

Genetic Affinity

PCA for G.gallus without G.g.bankiva , G.g.jabouillei, and some G.g.gallus

Summary

Genetic affiliation and population structure are shown by PCA plots. After removing G. g. bankiva, G. g. jabouillei, and some G. g. gallus individuals as outliers to other Red Jungle Fowl, the dataset contains 1,915 samples from domestic chicken and Red Jungle Fowl. User can add any populations with interests to show with the target population under this PCA context by using the item of “Add”.

ADMIXTURE Analysis

Summary

The inference of populations and individual ancestries is revealed by ADMIXTURE clustering. Length of each colored bar represents the proportion of proposed ancestry in the sample. User can add any populations with interests to compare with the target population by using the item of “Add”. The number of proposed ancestries is determined by “which K”.

Runs of Homozygosity

Summary

Runs of homozygosity (ROH) indicates long tracts of homozygous genotypes inherited from identical haplotypes of a common ancestor. Larger populations have fewer, shorter ROH, whereas isolated or bottlenecked populations have more, somewhat longer ROH. Admixture brings the fewest ROH, whereas inbreeding causes long ROH. The level of ROH is measured by number and length. The length of ROH can be defined in “ROH range”. User can add any populations with interests to compare with the target population by using the item of “Add”.

Linkage Disequilibrium Decay

Summary

Linkage disequilibrium (LD) decay is characterized by squared correlations (r²) of all SNPs frequencies against the physical distances between SNPs. User can add any populations with interests to compare with the target population by using the item of “Add”.

Demographic History

Summary

The changes of effective population size through time is inferred by SMC++. User can add any populations with interests to compare with the target population by using the item of “Add”.

Selection

Summary

Selective signals of the target population are detected by different methods. X axis indicates physical position of specific chromosomal region with interests which can be defined by “Region”. The gene annotation is shown below. Y axis of left (YL) indicates the values of Pi-ratio of -log2(πRJF/πTarget) or composite likelihood ratio (CLR) of SweeD. The levels of statistical significance are noted with different colors. Y axis of right (YR) shows the values of Fst (Target vs. Red Jungle Fowl), Pi, or Tajima’s D with blue line with sliding window approach. The genomic window size and step size for Tajima’s D are 5 kb and 5 kb, respectively. The genomic window size and step size for Fst and Pi are 10 kb and 5 kb, respectively. The methods are defined by “Method-YL” and “Method-YR”.

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