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 env...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.展开更多
The Nei's improved genetic distance(DA)and gene flow(Nm)were measured using sixteen microsatellite markers.Dendograms based on DA genetic distance using the neighbor-joining(NJ)method and STRUCTURE program were co...The Nei's improved genetic distance(DA)and gene flow(Nm)were measured using sixteen microsatellite markers.Dendograms based on DA genetic distance using the neighbor-joining(NJ)method and STRUCTURE program were constructed to analyze the genetic structure and relationship among 10 Chinese indigenous chicken breeds.The results showed that dendograms of DA genetic distance using the NJ method divided the 10 chicken breeds into two main clusters;one consisted of breeds of low weight body(CHA,TTB,XIA,GUS and BAI),the other contained heavier breeds(LAN,DAG,YOU,XIS and LUY).In the lighter breeds,TIB and CHA clustered together,as did XIA and GUS.In the heavier breeds,XIS and LUY was clustered together in one branch,but LAN,DAG and YOU clustered in independent branches.The results were consistent with Nm estimates among the 10 indigenous chicken breeds.The STRUCTURE program properly inferred the presence of genetic structure despite not pre-defining the origin of individuals.The genetic cluster inferred by STRUCTURE was basically the same as that from the DA distance clustering method.An advantage of the STRUCTURE program was its ability to identify the migrants and admixed individuals in the 10 chicken populations;this could not be achieved by use of the DA distance clustering method.展开更多
China is rich in chicken genetic resources,; many indigenous breeds can be found throughout the country. Due to poor productive ability, some of them are threatened by the commercial varieties from domestic; foreign b...China is rich in chicken genetic resources,; many indigenous breeds can be found throughout the country. Due to poor productive ability, some of them are threatened by the commercial varieties from domestic; foreign breeding companies. In a large-scale investigation into the current status of Chinese poultry genetic resources, 78 indigenous chicken breeds were surveyed; their blood samples collected. The genomes of these chickens were screened using microsatellite analysis. A total of 2740 individuals were genotyped for 27 microsatellite markers on 13 chromosomes. The number of alleles of the 27 markers ranged from 6 to 51 per locus with a mean of 18.74. Heterozygosity (H) values of the 78 chicken breeds were all more than 0.5. The average H value (0.622); polymorphism information content (PIC, 0.573) of these breeds suggested that the Chinese indigenous chickens possessed more genetic diversity than that reported in many other countries. The fixation coefficients of subpopulations within the total population (F ST) for the 27 loci varied from 0.065 (LEI0166) to 0.209 (MCW0078), with a mean of 0.106. For all detected microsatellite loci, only one (LEI0194) deviated from Hardy-Weinberg equilibrium (HWE) across all the populations. As genetic drift or non-random mating can occur in small populations, breeds kept on conservation farms such as Langshan chicken generally had lower H values, while those kept on large populations within conservation regions possessed higher polymorphisms. The high genetic diversity in Chinese indigenous breeds is in agreement with great phenotypic variation of these breeds. Using Nei’s genetic distance; the Neighbor-Joining method, the indigenous Chinese chickens were classified into six categories that were generally consistent with their geographic distributions. The molecular information of genetic diversity will play an important role in conservation, supervision,; utilization of the chicken resources.展开更多
Developing ecological scale breeding of local chickens with natural conditions, such as forest lands, grass lands, orchards and mulberry fields, not only can improve the quality of poultry products and the production ...Developing ecological scale breeding of local chickens with natural conditions, such as forest lands, grass lands, orchards and mulberry fields, not only can improve the quality of poultry products and the production benefits of chicken breeding, but also can develop and use local chicken germplasm effectively and promote their breed protection and industrialization. From integration and application of breed selection, breeding management, nutrient regulation, grass planting and grazing, a new ecological scale breeding technique of local chickens is proposed.展开更多
Shannan Prefecture of Tibet is the central producing region of Tibetan chicken, and Tibetan chicken feeding has become one of the characteristic industries of animal husbandry in local agricultural and pastoral area, ...Shannan Prefecture of Tibet is the central producing region of Tibetan chicken, and Tibetan chicken feeding has become one of the characteristic industries of animal husbandry in local agricultural and pastoral area, and it is an important source of food and income for the locals. However, because of extensive feed- ing managemem, low level of intensification, blind hybrid of exotic varieties and despising selective breeding, the number of pedigree Tibetan chickens have reduced year by year and the performance of Tibetan chicken herd varied greatly, premium specificity could not be effectively utihzed. By investigating the present situation of Tibetan chicken feeding, analyzing the specificity of Tibetan chicken germplasm resources, the scientific conservation breeding was started to make full use of the advantage of keeping Tibetan chickens on the plateau.展开更多
[ 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...[ 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.展开更多
基金supported by the Russian Science Foundation within the Project No.21-66-00007support of the Russian Ministry of Science and Higher Education。
文摘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.
基金supported by the Program of National Technological Basis from Ministry of Science and Technology of China(No.2005DKA21101)the National Natural Science Foundation of China(No.30700572)
文摘The Nei's improved genetic distance(DA)and gene flow(Nm)were measured using sixteen microsatellite markers.Dendograms based on DA genetic distance using the neighbor-joining(NJ)method and STRUCTURE program were constructed to analyze the genetic structure and relationship among 10 Chinese indigenous chicken breeds.The results showed that dendograms of DA genetic distance using the NJ method divided the 10 chicken breeds into two main clusters;one consisted of breeds of low weight body(CHA,TTB,XIA,GUS and BAI),the other contained heavier breeds(LAN,DAG,YOU,XIS and LUY).In the lighter breeds,TIB and CHA clustered together,as did XIA and GUS.In the heavier breeds,XIS and LUY was clustered together in one branch,but LAN,DAG and YOU clustered in independent branches.The results were consistent with Nm estimates among the 10 indigenous chicken breeds.The STRUCTURE program properly inferred the presence of genetic structure despite not pre-defining the origin of individuals.The genetic cluster inferred by STRUCTURE was basically the same as that from the DA distance clustering method.An advantage of the STRUCTURE program was its ability to identify the migrants and admixed individuals in the 10 chicken populations;this could not be achieved by use of the DA distance clustering method.
基金supported by the National Outstanding Youth Science Foundation of China(Grant No.30225032)Doctoral Foundation of Ministry of Education(No.20020019011)and the Ministry of Agriculture of China.
文摘China is rich in chicken genetic resources,; many indigenous breeds can be found throughout the country. Due to poor productive ability, some of them are threatened by the commercial varieties from domestic; foreign breeding companies. In a large-scale investigation into the current status of Chinese poultry genetic resources, 78 indigenous chicken breeds were surveyed; their blood samples collected. The genomes of these chickens were screened using microsatellite analysis. A total of 2740 individuals were genotyped for 27 microsatellite markers on 13 chromosomes. The number of alleles of the 27 markers ranged from 6 to 51 per locus with a mean of 18.74. Heterozygosity (H) values of the 78 chicken breeds were all more than 0.5. The average H value (0.622); polymorphism information content (PIC, 0.573) of these breeds suggested that the Chinese indigenous chickens possessed more genetic diversity than that reported in many other countries. The fixation coefficients of subpopulations within the total population (F ST) for the 27 loci varied from 0.065 (LEI0166) to 0.209 (MCW0078), with a mean of 0.106. For all detected microsatellite loci, only one (LEI0194) deviated from Hardy-Weinberg equilibrium (HWE) across all the populations. As genetic drift or non-random mating can occur in small populations, breeds kept on conservation farms such as Langshan chicken generally had lower H values, while those kept on large populations within conservation regions possessed higher polymorphisms. The high genetic diversity in Chinese indigenous breeds is in agreement with great phenotypic variation of these breeds. Using Nei’s genetic distance; the Neighbor-Joining method, the indigenous Chinese chickens were classified into six categories that were generally consistent with their geographic distributions. The molecular information of genetic diversity will play an important role in conservation, supervision,; utilization of the chicken resources.
基金Supported by Three New Agricultural Project in Jiangsu Province(SXGC[2013]234)
文摘Developing ecological scale breeding of local chickens with natural conditions, such as forest lands, grass lands, orchards and mulberry fields, not only can improve the quality of poultry products and the production benefits of chicken breeding, but also can develop and use local chicken germplasm effectively and promote their breed protection and industrialization. From integration and application of breed selection, breeding management, nutrient regulation, grass planting and grazing, a new ecological scale breeding technique of local chickens is proposed.
文摘Shannan Prefecture of Tibet is the central producing region of Tibetan chicken, and Tibetan chicken feeding has become one of the characteristic industries of animal husbandry in local agricultural and pastoral area, and it is an important source of food and income for the locals. However, because of extensive feed- ing managemem, low level of intensification, blind hybrid of exotic varieties and despising selective breeding, the number of pedigree Tibetan chickens have reduced year by year and the performance of Tibetan chicken herd varied greatly, premium specificity could not be effectively utihzed. By investigating the present situation of Tibetan chicken feeding, analyzing the specificity of Tibetan chicken germplasm resources, the scientific conservation breeding was started to make full use of the advantage of keeping Tibetan chickens on the plateau.
基金funded by the national"863"program(2011AA100305)Zhejiang Province Science and Technology Platform Project(2011E60003)+1 种基金Yangzhou City Science and Technology Plan(YZ2011069)Natural Science Foundation of Jiangsu Province(BK2011431)
文摘[ 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.
