Hetian 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 Hetian chicken
Species taxonomy Gallus gallus domesticus
Classification Traditional
Region China
Purpose Broiler
Description

Hetian chicken also known as "Staghorn chickens", is a local breed used for meat. Hetian chickens originated from Hetian Town, Changting County, Longyan City, Fujian Province, China.

Characteristics

The beaks of Hetian chicken are short with slightly curved, the tip is yellow and the base is dark brown. The comb is carnation like type, the posterior end of the combs divides into forked comb, which is the unique comb type of Hetian chickens. The wattles are large and red. The earlobes are red oval and covered with yellow hairs. The shanks and skin are yellow. The head and neck feathers of cocks are yellowish brown. The hen neck feathers are covered with black spots, forming a ring of black in the neck, the primary feathers and secondary feathers are black, the rest of the feathers are yellow.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 177622 650455 27.3073% 15379 104154 14.7656%
exonic;splicing 36 188 19.1489% 0 0 0%
exonic_unknown 39 582 6.701% 0 82 0%
frameshift_deletion 0 0 0% 868 15977 5.4328%
frameshift_insertion 0 0 0% 728 13308 5.4704%
intergenic 4018339 15129055 26.5604% 314790 2238383 14.0633%
intronic 5054458 17735594 28.4989% 422957 2641780 16.0103%
ncRNA_exonic 106551 400185 26.6254% 7753 54342 14.267%
ncRNA_exonic;splicing 70 231 30.303% 4 43 9.3023%
ncRNA_intronic 1010301 3728327 27.098% 84589 575920 14.6876%
ncRNA_splicing 615 2341 26.2708% 68 478 14.2259%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 505 8777 5.7537%
nonframeshift_insertion 0 0 0% 243 4784 5.0794%
nonsynonymous 47868 336233 14.2366% 0 0 0%
splice_acceptor 97 750 12.9333% 79 964 8.195%
splice_donor 121 1076 11.2454% 32 763 4.194%
splice_donor_acceptor 0 0 0% 13 45 28.8889%
splice_UTR5 83 400 20.75% 9 106 8.4906%
splie_Others 0 0 0% 40 654 6.1162%
startloss 164 671 24.4411% 8 51 15.6863%
stopgain 492 4175 11.7844% 24 1252 1.9169%
stoploss 86 353 24.3626% 6 63 9.5238%
synonymous 109235 548813 19.9039% 0 0 0%
upstream 184245 679592 27.1111% 14032 98760 14.2082%
upstream;downstream 15428 57451 26.8542% 1262 9367 13.4728%
UTR3 88991 361040 24.6485% 8240 61415 13.4169%
UTR5 25840 112990 22.8693% 1803 16935 10.6466%
UTR5;UTR3 603 2524 23.8906% 50 381 13.1234%
Total 10841284 39753026 27.2716% 873483 5848802 14.9344%
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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