| Wenchang chickens are the only chicken breed listed in the ‘animal genetic resources in China(poultry)’ in Hainan Province and are famous for their excellent meat quality,Wenchang chicken industry has become an important part of the development of tropical characteristic and efficient agriculture in Hainan at present,and it is also a beautiful "business card" of tropical characteristic agriculture in Hainan.However,with the acceleration of the large-scale and intensive process of Wenchang chicken breeding,Wenchang chicken on the market has the characteristics of poor genetic consistency,uneven quality and so on.Therefore,in order to make the high-quality and healthy development of Wenchang chicken industry and protect this important genetic resource,it is particularly important to investigate on the current situation of Wenchang chicken germplasm resources and evaluate its conservation status.In view of this,this study aims to carry out the following works:(1)We collected and sequenced the whole genome of individuals from three Wenchang chicken conservation farms in Hainan Province to obtain genome-wide SNP markers,and preliminarily analyzed the distribution characteristics and functions of these markers to reveal the structural characteristics of Wenchang chicken genome.(2)We analyzed the genetic diversity,population structure and conservation effect of Wenchang chicken,and revealed the present situation and genetic structure of Wenchang chicken,so as to provide the basis for the later conservation of Wenchang chicken.(3)Based on the selection signal,the genetic basis of germplasm characteristics of Wenchang chicken was revealed.The specific results are as follows:1.In this study,high-quality sequencing data 341.19 Gb of 235 Wenchang chickens in three conservation farms were obtained.17633297 SNP loci were detected.2.The SNP loci were further annotated and divided into their functional regions.As a result,the proportion of SNP falling into the exon region was 3.49%.We analyzed the GO and KEGG pathways of the genes in which these SNP loci were located,and found entries and pathways may related to animal growth and development,immune traits,UV tolerance and meat quality.3.We conducted genetic diversity and population structure analysis on the sequencing data of 11 domestic and foreign chicken breeds.We found that Chinese native varieties have a higher level of genetic diversity than commercial varieties.Wenchang chicken has a relatively high level of genetic diversity in Chinese native breeds,population genetic structure is of great significance to reveal the origin and evolutionary history of breeds.The results of this study showed that Wenchang chicken had an independent genetic structure and had a closer genetic relationship with some local chicken breeds in southern China.4.The inbreeding status of Wenchang chicken was studied based on continuous homozygous fragments(runs of homozygosity,ROH).It was found that the ROH of Wenchang chicken was mainly composed of short fragments(< 1Mb),and the result of inbreeding coefficient showed that the inbreeding degree of Wenchang chicken was low.We carried out selective signal analysis on the top 1% high frequency region of Wenchang chicken ROH fragment,and detected a total of 393 genes,which may be related to body size,health,fat deposition,heat tolerance and meat quality traits.5.The results of genetic diversity showed that the genetic diversity of Wenchang chicken in the three conservation farms was rich at present,but there was a certain degree of differentiation among the individuals of the three populations.In order to avoid further differentiation into three subgroups,the gene exchange between conservation farms should be strengthened in the future. |
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