Onagadori
Jump to
section
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 Onagadori
Species taxonomy Gallus gallus domesticus
Classification Traditional
Region Japan
Purpose Fancy
Description

The Onagadori (roughly means "Honorable Fowl") is a rare breed of long-tailed chickens from Japan. It was first thought to be a descendant of the Shoukoku, but recent modern genetic researches have already weakened this theory. The Onagadori breed's roots are quite ancient and its ancestry is believed to have been from a mixing of the green male junglefowl and the red female junglefowl (i.e. Bekisar). It was from the cross-breeding of the Totenko and the Shokoku that the Onagadori was born and the species refined from around 1912 to 1926 (the Taisho period) to what we know it as today. In the 1920's to preserve their beautiful tails, they came to be bred as cage birds. The Onagadori is one of Japans treasured monuments.

Characteristics

The Onagadori's trademark feature is the non-molting tail feathers, that if kept in the best conditions with high levels of animal husbandry, grow for the lifetime of the roosters. While, the hens molt normally, as do the feathers that cover roosters' heads, breasts, backs, and legs. The Onagadori has also long saddle feathers, and hens themselves show the signs of having a wealth of feathers. Onagadoris have single combs, white earlobes, relatively medium-sized fine wattles, and slate-blue legs. The hens are poor layers of light brown eggs (around 25 eggs per year), but they are known for being broody. On avarage, the weights for rooster and hen are 1.8 kg and 1.35 kg, respectively.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 112728 650455 17.3306% 10235 104154 9.8268%
exonic;splicing 18 188 9.5745% 0 0 0%
exonic_unknown 20 582 3.4364% 0 82 0%
frameshift_deletion 0 0 0% 542 15977 3.3924%
frameshift_insertion 0 0 0% 510 13308 3.8323%
intergenic 2593191 15129055 17.1405% 211289 2238383 9.4394%
intronic 3215009 17735594 18.1274% 274272 2641780 10.3821%
ncRNA_exonic 68468 400185 17.1091% 5082 54342 9.3519%
ncRNA_exonic;splicing 50 231 21.645% 4 43 9.3023%
ncRNA_intronic 653140 3728327 17.5183% 56675 575920 9.8408%
ncRNA_splicing 405 2341 17.3003% 54 478 11.2971%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 335 8777 3.8168%
nonframeshift_insertion 0 0 0% 150 4784 3.1355%
nonsynonymous 29578 336233 8.7969% 0 0 0%
splice_acceptor 63 750 8.4% 63 964 6.5353%
splice_donor 91 1076 8.4572% 20 763 2.6212%
splice_donor_acceptor 0 0 0% 14 45 31.1111%
splice_UTR5 54 400 13.5% 6 106 5.6604%
splie_Others 0 0 0% 22 654 3.3639%
startloss 95 671 14.158% 3 51 5.8824%
stopgain 324 4175 7.7605% 11 1252 0.8786%
stoploss 48 353 13.5977% 6 63 9.5238%
synonymous 67610 548813 12.3193% 0 0 0%
upstream 116292 679592 17.112% 9099 98760 9.2132%
upstream;downstream 9699 57451 16.8822% 862 9367 9.2025%
UTR3 56035 361040 15.5204% 5335 61415 8.6868%
UTR5 16174 112990 14.3145% 1160 16935 6.8497%
UTR5;UTR3 386 2524 15.2932% 36 381 9.4488%
Total 6939478 39753026 17.4565% 575786 5848802 9.8445%
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”.

0.406945s