Association Analysis Of Genetic Variation And Characteristic Traits Of Jingyuan Chicken Population Based On RAD-seq

Jingyuan chicken is one of the important local breeds in Ningxia,its feather color has white feathers,hemp feathers and black feathers,because of its delicious meat and popularity with consumers,however,the invasion of foreign breeds of chicken,makes this excellent local breed of hybridization phenomenon is serious.,so it is important to accelerate the preservation of Jingyuan chicken to protect national and local livestock and poultry germplasm resources.the genetic diversity of the Jingyuan chicken population has been protected to a great extent by the principle of in vivo conservation with equal retention of family lines,but the population’s genetic structure,genetic background,and germplasm characteristic genes have not been systematically studied,and the mechanism of the formation of the three plumage colors within the population has not been resolved.In this study,we identified SNP markers between the Jingyuan Chicken and the Bian Chicken,Langshan Chicken,Wenchang Chicken and Daweishan micro Micro Chicken by ddRAD-seq,analyzed the genetic diversity and population structure of the Jingyuan Chicken and other four local breeds based on SNP markers,identification of signature genes by selective sweep analysis,genome-wide association analysis was used to identify candidate genes regulating plumage color in Jingyuan chickens.The main results are as follows:(1)Study on genetic variation of Jingyuan chicken based on RAD-seq technologyIn this study,a total of 270 samples were sequenced from white feathers of Jingyuan chicken,hemp feathers of Jingyuan chicken,black feathers of Jingyuan chicken,Bian chicken,Langshan chicken,Wenchang chicken and Daweishan micro chicken,which generated 295.03 Gb Clean Data,with Q30 reaching more than 94.42%,the number of reads on comparison reaching more than 99%and sequencing depth reaching more than 10X,and the sequencing data quality was good.Population genetic diversity analysis showed that the genetic diversity of the Jingyuan chicken was higher and less subject to selection than the other four local chicken breeds.Population structure analysis showed that there was no genetic exchange among the five local chicken breeds due to geographical differences and no genetic differentiation among the three taxa of the Jingyuan chicken.The effective population size showed that the effective population of the five local chicken breeds fluctuates with global climate change.(2)Identification of characteristic genes of Jingyuan Chicken Germplasm based on ddRAD-seqBased on SNPs,Bian Chicken,Langshan Chicken,Wenchang Chicken and Daweishan Micro Chicken were selected as the control group and Jingyuan Chicken as the selection group for selective clearance in the whole genome.5(TYR、LRTOMT、NOX4、SLCO2B1、PRDM1),7(RB1CC1、Myc、SLA、ZEB1、AD11、SPOCKs、NDRG1)and 9(SLCO1C1、SLCO1B3、SLCO1A2、SOX5、ZC3H18、IL17C、CYBA、CHD7、MYO6、SLA、ADI1)germplasm characteristic genes were screened from white feather Jingyuan chicken,hemp-feather Jingyuan chicken and black-feather Jingyuan chicken,respectively.these genes play an important role in the growth and development,immunity,heat resistance,feather color and eggshell color of Jingyuan chicken.(3)Whole genome association analysis of feather color of Jingyuan chickenIn this study,a genome-wide association analysis was performed based on SNPs markers to identify 66,256 and 200 SNPs markers in white,hemp and black feathers,respectively,and after annotation of the associated loci,candidate genes TYR for white feathers,TH for hemp feathers and FZD6 and PLCB2 for black feathers were identified.To sum up,the results of this study lay a theoretical foundation for the protection of genetic resources of Jingyuan chicken,and provide new genetic markers and gene targets for the breeding of Jingyuan chicken.