Background Information
| Breed Card | |
| Breed | Bian chicken |
| Species taxonomy | Gallus gallus domesticus |
| Classification | Traditional |
| Region | China |
| Purpose | Dual |
Bian chicken also known as Youyu chicken in Shanxi Province of China. It is a dual purpose local breed. The origin and distribution area of Bian chicken is Liangcheng County of Ulanchapu City of Inner Mongolia autonomous region and Youyu County of Shanxi Province of China.
The heads of Bian chickens are small, the combs are short. The beaks are short and in black, brown and yellow color. They have red single comb, a few are strawberry comb or pea comb. The wattles are red. The earlobes are yellow, white or dark brown. The skins are pale yellow. The shanks are black, a few are fleshcolor or gray. The plumage of roosters is red-black or yellow-black. The hens have a small combs and complex feather color, including white, gray, black, light yellow, etc. The neck feathers and tail feathers are yellow, a few are black, the primary feathers and back feathers are black, and the belly feathers is yellow. The hens start laying at 170-180 days and lay about 119-130 eggs a year.
Variants Annotation&Density
| Annotation | Population SNP | Total SNP | Percentage SNP | Population INDEL | Total INDEL | Percentage INDEL |
|---|---|---|---|---|---|---|
| downstream | 100972 | 650455 | 15.5233% | 8779 | 104154 | 8.4289% |
| exonic;splicing | 14 | 188 | 7.4468% | 0 | 0 | 0% |
| exonic_unknown | 24 | 582 | 4.1237% | 0 | 82 | 0% |
| frameshift_deletion | 0 | 0 | 0% | 230 | 15977 | 1.4396% |
| frameshift_insertion | 0 | 0 | 0% | 192 | 13308 | 1.4427% |
| intergenic | 2613580 | 15129055 | 17.2752% | 206088 | 2238383 | 9.207% |
| intronic | 3310890 | 17735594 | 18.6681% | 277112 | 2641780 | 10.4896% |
| ncRNA_exonic | 67371 | 400185 | 16.835% | 5036 | 54342 | 9.2672% |
| ncRNA_exonic;splicing | 51 | 231 | 22.0779% | 2 | 43 | 4.6512% |
| ncRNA_intronic | 693105 | 3728327 | 18.5902% | 58284 | 575920 | 10.1202% |
| ncRNA_splicing | 392 | 2341 | 16.745% | 46 | 478 | 9.6234% |
| ncRNA_UTR5 | 0 | 0 | 0% | 1 | 18 | 5.5556% |
| nonframeshift_deletion | 0 | 0 | 0% | 193 | 8777 | 2.1989% |
| nonframeshift_insertion | 0 | 0 | 0% | 74 | 4784 | 1.5468% |
| nonsynonymous | 20183 | 336233 | 6.0027% | 0 | 0 | 0% |
| splice_acceptor | 55 | 750 | 7.3333% | 38 | 964 | 3.9419% |
| splice_donor | 53 | 1076 | 4.9257% | 18 | 763 | 2.3591% |
| splice_donor_acceptor | 0 | 0 | 0% | 9 | 45 | 20% |
| splice_UTR5 | 30 | 400 | 7.5% | 1 | 106 | 0.9434% |
| splie_Others | 0 | 0 | 0% | 20 | 654 | 3.0581% |
| startloss | 53 | 671 | 7.8987% | 0 | 51 | 0% |
| stopgain | 180 | 4175 | 4.3114% | 11 | 1252 | 0.8786% |
| stoploss | 36 | 353 | 10.1983% | 2 | 63 | 3.1746% |
| synonymous | 50766 | 548813 | 9.2501% | 0 | 0 | 0% |
| upstream | 77443 | 679592 | 11.3955% | 5636 | 98760 | 5.7068% |
| upstream;downstream | 4395 | 57451 | 7.65% | 359 | 9367 | 3.8326% |
| UTR3 | 51767 | 361040 | 14.3383% | 4872 | 61415 | 7.9329% |
| UTR5 | 8385 | 112990 | 7.421% | 507 | 16935 | 2.9938% |
| UTR5;UTR3 | 216 | 2524 | 8.5578% | 20 | 381 | 5.2493% |
| Total | 6999961 | 39753026 | 17.6086% | 567530 | 5848802 | 9.7034% |
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
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”.
