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

Hetian black chickens, also known as "Minfeng black chicken", "Luopu black chicken" and "Niya black chicken", are a local breed used for meat and eggs. Hetian black chickens were originated in Minfeng County, Hetian region, Xinjiang, China.

Characteristics

Hetian black chicken feathers are black, the beaks are black. The comb types are single comb. The combs and wattles are dark red, a few of them are purple. The earlobes are red. The skins are white. Most individuals have four toes, and a few have five. The roosters weight about 1.7 kg and hens weight 1.4 kg. The hens start laying at 150-180 days and lay 150-170 eggs a year.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 152000 650455 23.3683% 12374 104154 11.8805%
exonic;splicing 29 188 15.4255% 0 0 0%
exonic_unknown 33 582 5.6701% 0 82 0%
frameshift_deletion 0 0 0% 614 15977 3.843%
frameshift_insertion 0 0 0% 482 13308 3.6219%
intergenic 3513679 15129055 23.2247% 265134 2238383 11.8449%
intronic 4423195 17735594 24.9396% 356116 2641780 13.4802%
ncRNA_exonic 93431 400185 23.347% 6669 54342 12.2723%
ncRNA_exonic;splicing 65 231 28.1385% 4 43 9.3023%
ncRNA_intronic 895909 3728327 24.0298% 72489 575920 12.5866%
ncRNA_splicing 557 2341 23.7933% 64 478 13.3891%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 367 8777 4.1814%
nonframeshift_insertion 0 0 0% 179 4784 3.7416%
nonsynonymous 40048 336233 11.9108% 0 0 0%
splice_acceptor 79 750 10.5333% 57 964 5.9129%
splice_donor 111 1076 10.316% 22 763 2.8834%
splice_donor_acceptor 0 0 0% 9 45 20%
splice_UTR5 70 400 17.5% 3 106 2.8302%
splie_Others 0 0 0% 36 654 5.5046%
startloss 135 671 20.1192% 2 51 3.9216%
stopgain 375 4175 8.982% 18 1252 1.4377%
stoploss 68 353 19.2635% 5 63 7.9365%
synonymous 92664 548813 16.8844% 0 0 0%
upstream 156417 679592 23.0163% 11312 98760 11.454%
upstream;downstream 12344 57451 21.4861% 964 9367 10.2914%
UTR3 76549 361040 21.2024% 6785 61415 11.0478%
UTR5 21621 112990 19.1353% 1412 16935 8.3378%
UTR5;UTR3 492 2524 19.4929% 40 381 10.4987%
Total 9479871 39753026 23.8469% 735158 5848802 12.5694%
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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