Screening Candidate Genes Related To Meat Quality Traits In Danzhou Chicken Based On Whole Genome Sequencing

Danzhou chicken originated in the North Bank of Danzhou City.It is a small chicken with typical tropical island characteristics.It is locally called stone chicken or north bank small breeder chicken because of its small body,hard bone and compact meat.It has the characteristics of good meat quality,high protein and low fat.In order to explore the genetic factors affecting the quality characteristics of Danzhou chicken.In this study,The meat quality indexes of 200 Danzhou chickens aged 120 days were determined,and the whole genome of the above 200 Danzhou chickens at 60 days old was re sequenced by using the pe150 sequencing mode of Illumina nova6000 platform.The data of meat quality traits（pH,meat color,tenderness,drip loss,intramuscular fat content,etc.）of Danzhou chickens after slaughter were analyzed by generalized linear model（GLM）,The candidate genes related to meat quality were screened.The results are as follows:1)The results of meat quality determination:the ph_45min,ph_24h and ph_48h of pectoral muscle were 5.78±0.31,5.54±0.12 and 5.54±0.11 respectively,and the ph_45min,ph_24h and ph_48h of leg muscle were 6.09±0.24,5.89±0.21 and 5.89±0.21 respectively;L^*,a^*,b^*of chest muscle were 52.67±4.28,2.32±1.96 and 8.75±2.31 respectively,and L^*,a^*,b^*of leg muscle were 42.93±4.44,15.54±4.12 and 10.51±2.05 respectively;The shear forces of pectoral and leg muscles were 24.16±3.81N and 33.46±5.27N,respectively;The drip loss of pectoral muscle and leg muscle were 4.24%±1.19%and 10.06%±2.23%,respectively;The contents of intramuscular fat in pectoral muscle and leg muscle were 1.58%±0.61%and 2.65%±1.60%respectively.The results showed that the pH,meat color and intramuscular fat content of Danzhou chicken leg muscle were significantly better than those of pectoral muscle（P<0.01）,and the tenderness and water holding capacity of pectoral muscle were significantly better than those of leg muscle（P<0.01）.2)Whole genome sequencing results:2.16tb effective sequencing data were identified by re sequencing,filtered according to MAF>0.05 and data integrity>0.8,and SNPs with double allele polymorphism were retained.Finally,12.42 million SNPs were screened,and88596 genetic variants and 105332 insertion deletions were obtained by structural annotation.3)Results of genome-wide association analysis:a.HS6ST3,UGGT2,DNAJC3,PROZ,PRPH,C1ql4 and SPATS2 were selected as candidate genes for pH traits;b.VEZT,METAP2,NTN4,LTA4H,UGT8,CACNA1G,ACSF2,CLSTN3,PEX5,RBP5 and EPHA1were selected as candidate genes for meat color traits;c.PCK1 and RBM38 were selected as candidate genes for tenderness traits;d.CEP83 and other genes may be candidate genes for drip loss traits;e.VEGFA,GRB10 and LPAR4 genes may be candidate genes for intramuscular fat content traits.