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

Langshans are named after district around eastern China where they were developed over many centuries. There are four distinct types within the breed. The most popular version, is the original utility black Langshan, these became known as Croad Langshans in England, named after Major A.C. Croad, who was the first to import the breed into England 1872. They have lightly feathered shanks and outside toes, and are the most common type of Langshan in the US also. Another popular type is the German Langshan which is also very tall and clean legged. In England the long legged type known as the Modern Langshan was developed more for the show pen and the birds came to resemble the Modern Games. Then there was a shorter legged version resembling the Cochin. These birds were used in the creation of the Orpington.

Characteristics

The Langshan is a tall breed carry themselves as if their heads are held high enhancing their tall elegance. They have long bluish/black legs with feathers covering their shanks and third toe. They have a single comb and white skin. The Lanshan is a dual purpose breed with tasty white meat and large brown eggs some with a deep shade of purple. Hens lay between 200 - 230 rich brown eggs per year, and may go broody too. On avarage, the weights for rooster and hen are 9.5 lbs and 7.5 lbs, respectively.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 92912 650455 14.2842% 7925 104154 7.6089%
exonic;splicing 14 188 7.4468% 0 0 0%
exonic_unknown 8 582 1.3746% 0 82 0%
frameshift_deletion 0 0 0% 223 15977 1.3958%
frameshift_insertion 0 0 0% 210 13308 1.578%
intergenic 2381292 15129055 15.7399% 186999 2238383 8.3542%
intronic 2990657 17735594 16.8625% 248978 2641780 9.4246%
ncRNA_exonic 60797 400185 15.1922% 4588 54342 8.4428%
ncRNA_exonic;splicing 40 231 17.316% 2 43 4.6512%
ncRNA_intronic 621354 3728327 16.6658% 52273 575920 9.0764%
ncRNA_splicing 344 2341 14.6946% 41 478 8.5774%
ncRNA_UTR5 0 0 0% 1 18 5.5556%
nonframeshift_deletion 0 0 0% 177 8777 2.0166%
nonframeshift_insertion 0 0 0% 72 4784 1.505%
nonsynonymous 18807 336233 5.5934% 0 0 0%
splice_acceptor 46 750 6.1333% 40 964 4.1494%
splice_donor 55 1076 5.1115% 18 763 2.3591%
splice_donor_acceptor 0 0 0% 9 45 20%
splice_UTR5 33 400 8.25% 2 106 1.8868%
splie_Others 0 0 0% 17 654 2.5994%
startloss 52 671 7.7496% 0 51 0%
stopgain 170 4175 4.0719% 9 1252 0.7188%
stoploss 39 353 11.0482% 4 63 6.3492%
synonymous 47303 548813 8.6191% 0 0 0%
upstream 72817 679592 10.7148% 5372 98760 5.4394%
upstream;downstream 4138 57451 7.2027% 350 9367 3.7365%
UTR3 46641 361040 12.9185% 4386 61415 7.1416%
UTR5 7867 112990 6.9626% 485 16935 2.8639%
UTR5;UTR3 176 2524 6.9731% 13 381 3.4121%
Total 6345562 39753026 15.9625% 512194 5848802 8.7572%
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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