Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds

Background The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by,and formed due to,past and current admixture events.Adaptation to diverse environments,including acclimation to harsh climatic conditions,has also left selection footprints in breed genomes.Results Using the Chicken 50K_CobbCons SNP chip,we genotyped four divergently selected breeds:two aboriginal,cold tolerant Ushanka and Orloff Mille Fleur,one egg-type Russian White subjected to artificial selection for cold tolerance,and one meat-type White Cornish.Signals of selective sweeps were determined in the studied breeds using three methods:(1)assessment of runs of homozygosity islands,(2)F_(ST) based population differential analysis,and(3)haplotype differentiation analysis.Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds.In these regions,we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies.Amongst them,SOX5,ME3,ZNF536,WWP1,RIPK2,OSGIN2,DECR1,TPO,PPARGC1A,BDNF,MSTN,and beta-keratin genes can be especially mentioned as candidates for cold adaptation.Epigenetic factors may be involved in regulating some of these important genes(e.g.,TPO and BDNF).Conclusion Based on a genome-wide scan,our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds.These include genes representing the sine qua non for adaptation to harsh environments.Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals,and this warrants further investigation.

Cluster Analysis of Laying Performance and Production Area Ecology of 11 kinds of Chicken

[ Objective] The aim was to explore the classification basis of Chinese local chicken for providing theoretical basis of giving full play to the genetic potential, heterosis, new ideas and methods of new varieties and strains breeding, identification and evaluation. [ Method] The multivariate statistical analysis of laying performance and production area ecology of 11 kind of chicken was done by principal component analysis and cluster analysis. E]Result] The cluster analysis of 4 egg laying performance indexs indicated that 11 kinds of chicken can be roughly classified into large chicken and small chicken; 10 indexs of multivariate statistical analysis indicated that 11 kinds of chicken can be classified into high altitude type and low altitude type when first 3 eigenvalues were selected as 3 principal component by principal component analysis（ 94.99% of the total amount of information）, and similarity coefficient was computed according to first three principal component values of each kind and then cluster analysis was done with nearest neighbor way. [ Conclusion] Ecological factor was also an important aspect of assortment.

Comparison on Egg Quality between Shandong Local Hens and Hyline Brown Hens

[Objective] To observe differences in egg quality between Shandong local hens and Hyline brown hens. [Method] Hyline brown hens and three Shandong local chicken breeds including Jining Bairi chicken, Wenshang Luhua chicken and Laiwu black chicken were selected for egg quality comparison. [ Result] The pementage of yolk, egg-shape index and shell strength were significantly higher in the Shandong local hens than in Hyline brown hens ( P 〈 0.05), but the opposite results were found for average egg size and Haugh unit ( P 〈 0.05). The contents of essential amino acids and linoleic acid were significantly higher in the Shandong local hens than in Hyline brown hens (P 〈 0.05), but no significant differ- ence in VA content, VE content, total amino acid content and fatty acid content was found between the Shandong local hens than in Hyline brown hens. [ Conclustion] The study investigated the effects of chicken breeds on egg quality, which provides a reference for improvement of chicken breeds in future.