Whole-genome sequencing revealed genetic diversity and selection of Guangxi indigenous chickens

Guangxi chickens play a crucial role in promoting the high-quality development of the broiler industry in China, but their value and potential are yet to be discovered. To determine the genetic diversity and population structure of Guangxi indigenous chicken, we analyzed the whole genomes of 185 chickens from 8 phenotypically and geographically representative Guangxi chicken breeds, together with 12 RJFt, 12 BRA and 12 WL genomes available from previous studies. Calculation of heterozygosity (Hp), nucleotide diversity (π), and LD level indicated that Guangxi populations were characterized by higher genetic diversity and lower differentiation than RJFt and commercial breeds except for HGFC. Population structure analysis also confirmed the introgression from commercial broiler breeds. Each population clustered together while the overall differentiation was slight. MA has the richest genetic diversity among all varieties. Selective sweep analysis revealed BCO2, EDN3 and other candidate genes had received strong selection in local breeds. These also provided novel breeding visual and data basis for future breeding.

The authors have declared that no competing interests exist. NO    Chickens are the most widely distributed livestock species globally, more than half 30 the total (53%) is found in Asia, one of the largest producers is China [1] . In China, were investigated from conservation center or breeding farms (S1 Table and   disequilibrium were removed by PLINK version 1.9 [8] , based on the pruned SNP data, 86 the individual ancestries were estimated using a maximum likelihood method 87 implemented in ADMIXTURE version 1.23 [9] . ZFst value were defined as significant selected region [11] . GO  region, and only 2.27% located in the exon region (Fig 1B).

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The genome is divided into isochrones with a sliding window of 100kb, and 114 divided into five categories (L1, L2, H1, H2 and H3) according to different GC level to 115 explore the potential impact between GC content and genetic variations (Fig 1C and   116 1D) [12] . Our results shown that the L2 category has the largest number of isochrones, 117 covering 37% of the genomic region, and the SNPs and Indels counts peak in this 118 category. H1 category with higher GC level also contains a lot of genetic variations (S5 119   Table). In general, genomic regions with moderate GC content contain more variation. published [13] . The nucleotide diversity (π) and heterozygosity were calculated to 131 evaluate the genetic diversity of all the chicken breeds. We observed Guangxi 132 indigenous chickens harbored the higher genome-wide π than RJFt (π =0.00334) except 133 for DZAC (π = 0.00332), the lowest genome-wide π in WL (π = 0.00152), followed by 134 BRA (π = 0.0031) (Fig 2A). Unlike the results in nucleotide diversity, BRA harbored 135 the highest heterozygous SNP rate (He), followed by DZAC, while MA harbored the 136 lowest (He = 0.1684) one (Fig 2B). The He in Z chromosome are lower than any 137 autosome among all populations (S2 Fig), probably due to sex chromosome had undergone higher selective pressure than autosome [14] . Linkage disequilibrium (LD) 139 analysis showed that WL population had the slowest LD decay rate, significantly slower 140 than the followed BRA. MA had a faster LD decay rate than other chicken breeds, 141 DZAC and WC have similar LD level with RJFt in second group (Fig 2C).

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The level of ROH reflects the recent inbreeding history of a population [15] . As  Table). HGFC (347.039Mb) had the same tROH (rs313409504) was consisted with the previous report [16] . The strongest selective sweep by an asymmetric cleavage reaction [19] , is established as the causal gene for the yellow inhibit expression of BCDO2 in skin caused yellow skin, but not in other tissues [16] .

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Fallahshahroudi's study showed the down-regulation of BCO2 in skin, muscle, and 259 adipose tissue was associated with the derived haplotype [20] . Also, BCO2 has variety 260 variants in different breeds. Wang found a G>A mutation in exon 6 to be associated 261 with the concentration of carotenoids in Guangxi-huang and Qingjiao-ma chicken [21] .

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A GAG haplotype was fixed in commercial breeds of yellow skin [16] . We also found 263 the missense mutant at chr24:6155481 led to the mutation of threonine to alanine. atg7, and by inference autophagy, is critical for normal adipogenesis [27] . AMACR 284 coding protein alpha-methylacyl-CoA racemase, this protein is involved in the pathway 285 bile acid biosynthesis, which is part of Lipid metabolism (gga00120). Bile acid is the 286 main component of bile and its main function is to promote the digestion and absorption 287 of fat. HSD17B4 codes a bifunctional enzyme mediating dehydrogenation and 288 anhydration during β-oxidation of long-chain fatty acids, and a non-synonymous SNP 289 has been reported to be related to meat-quality traits in pig [28] . PRKAA1 is associated 290 with skeletal muscle lipid accumulation [29] . and red jungle fowls were downloaded from NCBI at ERP112703 (S2 Table).