Jersey Giant
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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 Jersey Giant
Species taxonomy Gallus gallus domesticus
Classification Commercial
Region America
Purpose Dual
Description

Jersey Giant chickens originate from Jobstown, in New Jersey, North America where brothers John and Thomas Black created them from Black Javas crossed with Black Langshans, Indian Game, and Brahmas to increase their size sometime during the 1870's. In fact, it's the world's largest chicken breed, as some roosters (especially the black variety) may reach a weight of 15 pounds.

Characteristics

Jersey Giants are enormous birds that need more time to reach their full size than that of today's more common meat birds. Their slow growth rate is a reason why this breed is rare and not widely used in the modern Broiler industry nowadays. However, the Jersey Giant is a practical dual-purpose bird indeed, as it yields plenty of meat, and lays well. The hens lay very large brown eggs (150 - 170 eggs per year), and are known particularly as good winter layers. Jersey hens are also known to go broody. On avarage, the weights for rooster and hen are 5.9 kg and 4.5 kg, respectively.


Samples Information

Variants Annotation&Density

Annotation Population SNP Total SNP Percentage SNP Population INDEL Total INDEL Percentage INDEL
downstream 136709 650455 21.0174% 12451 104154 11.9544%
exonic;splicing 22 188 11.7021% 0 0 0%
exonic_unknown 24 582 4.1237% 0 82 0%
frameshift_deletion 0 0 0% 707 15977 4.4251%
frameshift_insertion 0 0 0% 603 13308 4.5311%
intergenic 3118135 15129055 20.6102% 259697 2238383 11.602%
intronic 3924225 17735594 22.1263% 342087 2641780 12.9491%
ncRNA_exonic 82177 400185 20.5348% 6212 54342 11.4313%
ncRNA_exonic;splicing 58 231 25.1082% 5 43 11.6279%
ncRNA_intronic 784009 3728327 21.0284% 69330 575920 12.0381%
ncRNA_splicing 476 2341 20.3332% 71 478 14.8536%
ncRNA_UTR5 0 0 0% 0 18 0%
nonframeshift_deletion 0 0 0% 402 8777 4.5802%
nonframeshift_insertion 0 0 0% 187 4784 3.9089%
nonsynonymous 35661 336233 10.606% 0 0 0%
splice_acceptor 75 750 10% 78 964 8.0913%
splice_donor 98 1076 9.1078% 29 763 3.8008%
splice_donor_acceptor 0 0 0% 10 45 22.2222%
splice_UTR5 61 400 15.25% 8 106 7.5472%
splie_Others 0 0 0% 27 654 4.1284%
startloss 111 671 16.5425% 1 51 1.9608%
stopgain 358 4175 8.5749% 20 1252 1.5974%
stoploss 75 353 21.2465% 6 63 9.5238%
synonymous 83081 548813 15.1383% 0 0 0%
upstream 139876 679592 20.5823% 11053 98760 11.1918%
upstream;downstream 11738 57451 20.4313% 974 9367 10.3982%
UTR3 68408 361040 18.9475% 6939 61415 11.2985%
UTR5 19179 112990 16.9741% 1361 16935 8.0366%
UTR5;UTR3 429 2524 16.9968% 43 381 11.2861%
Total 8404985 39753026 21.143% 712301 5848802 12.1786%
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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