Whole-genome Resequencing Uncovers The Genetic Diversity And Selection Signatures Of 10 Indigenous Yellow-feathered Chicken Populations Including Wuhua Yellow Chicken

Since the domestication of Red junglefowl,chickens have provided human society with a large amount of animal protein such as meat and eggs,which has promoted the development of human civilization and population growth.During the process of domestication,chickens have formed a variety of distinctive breeds.Assessing the genetic diversity,detecting the genetic variation and screening their selection signatures during domestication of these breeds are beneficial to the formulation of scientific conservation strategies.Furthermore,it can accelerate the breeding process and improve the efficiency of breeding.The yellow feathered chicken is also known as"three yellow chicken"with yellow feather,beak and feet.In addition,it has the characteristics of good meat quality and strong disease resistance.Wuhua yellow chicken（WH）is one of indigenous yellow-feathered chickens（YFC）in China,which is characterized by white tail feathers and white flight feathers.Whole genome resequencing was performed on the WH and other 9 indigenous YFC breeds,then the Galgal5 was used as a reference for comparison to obtain the genetic variation of the genomes of these populations.Analyzing the evolutionary relationship between WH and other YFC populations and exploring the selected genes related to its special and excellent traits can provide theoretical basis for later molecular marker-assisted breeding.The main results are as follows:1.Identification of genetic variations in Wuhua yellow chickenWhole-genome resequencing was performed on 12 WH（half male and half female）with an average coverage of 20.77-fold and average coverage ratio of 97.12%.After strict filtering,the average nucleotide content of each individual genome is22396626339 bp.On average,1,645,487,789 clean reads were obtained in each genome,of which 155,314,466（94.44%）were high-quality reads.Those high-quality reads were mapped onto the chicken reference genome（Galgal5）with a coverage of 85.95%.After quality control,11953471 single nucleotide polymorphisms（SNP）and 1,069,574insertion/deletions（In Del）were obtained.In addition,41408 structural variants（SV）and 33,278 copy number variants（CNV）were found.In this study,a complete genome map of WH was drawn,and the genetic variation data obtained in this study provided genomic data support for further study on genetic characteristics of WH.2.Assessment of genetic structure and diversity of 10 indigenous YFC populationsA total of 100 YFC wing vein blood samples were obtained from ten YFC breeds（WH,Guangxi yellow chicken,Hetian chicken,Huaixiang chicken,Huanglang chicken,Huiyang bearded chicken,Jianghan chicken,Ningdu yellow chicken,Wenchang chicken and Zhengyang yellow chicken）.Each breed contains ten chickens including male and female.Ten Huaibei partridge chickens were also sampled for comparison.Whole-genome resequencing was performed on those samples,whose average sequencing depth and average coverage ratio was 12.65-fold and 96.35%respectively.The average genome nucleotide content of all samples was 11916810290 bp,and86474625.34 clean reads per genome were obtained,providing a comprehensive whole genome sequencing data set for yellow-feathered chickens for the first time.Principal component analysis,population structure analysis and phylogenetic tree analysis showed that the 10 YFC populations could be divided into three branches:the northern,central and southern branches.The WH belongs to the southern branch.In the genetic diversity statistics,nucleotide diversity（π）was between 0.0027-0.0031,and the average of observed heterozygosity（H_O）and expected heterozygosity（H_E）was 0.1804,0.1954 respectively.The results showed that the genetic diversity of the 10 indigenous YFC populations in this study was not high and needed a strengthened protection.The comparison of the genetic diversity of the YFC populations showed that the WH has higher genetic diversity than other YFCs.3.Runs of homozygosity analysis of 10 indigenous YFC populationsThe Runs of homozygosity（ROH）in the genomes of 10 indigenous YFC populations were detected by using SNP data.At the same time,the inbreeding coefficient of YFC populations was calculated based on ROH,and the genes in the high frequency region of ROH were screened.It was found that the number of ROH of YFC populations is small（254.4 on average）,the total length of ROH is not long（87.14 Mb on average）,short ROH（335 kb on average）is the main type,and the inbreeding coefficient is not high（0.0854）.The result indicated the degree of inbreeding in YFC populations is not serious.This ROH distribution pattern also reflects the long history of breeding YFC in China.Numerous genes related to disease resistance,energy metabolism and meat quality were identified（IFNA,IFNB,IL11RA,IL22RA1,B4GALT1,G6PC,AMY,LIPG,AQP7,LYPLA2,ABCA1）in the high-frequency ROH regions.KITLG,CREB3,RYR2,and LGR4 related to pigmentation were also detected.These genes may be related to the characteristics of strong disease resistance,excellent meat quality and yellow appearance traits of indigenous YFCs.4.Selection signatures detection during the process of domestication in Wuhua yellow chickenWith other YFCs used as the background population,the SNP data were used to identify the selected regions and genes of WH pupulation by usingπradio and F_STstatistical methods.Several genes which are associated with immune system,infectious diseases and signal transduction were identified including IFNA,IFNB,CD86,IL18,IL11RA,VEGFC,and ATG10.Functional enrichment analysis showed that candidate genes were mainly enriched in Regulation of autophagy,Cytosolic DNA-sensing pathway,RIG-I-like receptor signaling pathway,Toll-like receptor signaling pathway,Herpes simplex infection,Jak-STAT signaling pathway,Influenza A and Cytokine-cytokine receptor interaction.Most of these pathways are related to disease resistance and cell signal transmission.From the view of genetic,WH has the characteristic of strong disease resistance.Furthermore,our results suggest that PMEL and TYRP1 may contribute to the white feather coloring in WH.These findings can improve our understanding of the genetic characteristics of WH and provide candidate genes to future breed improvement.