Genetic Diversity And Genome-wide Association Study Of Coat Color In Chuanzhong Black Goats

Chuanzhong Black goats（CZ）are one of the famous indigenous breeds in China,which has the characteristics of black coat color（some individuals have the Swiss markings phenotype）,large size and crude feed tolerance;However,little is known about the genetic diversity and the genetic mechanism underlying important traits in CZ goats.We investigated the genetic diversity,and conducted analyses of the positive selection signature,and identified the genetic loci that affect the Swiss markings phenotype in CZ goats.The main results are as follows:（1）A total of 14,043,333 biallelic SNPs were detected in the autosomal genomes of 41 CZ goats with clear background.The linkage disequilibrium analysis revealed that the genome-wide mean r² decreased rapidly from 0.51 between SNP pairs at a distance of 10 bp to 0.20 at 1,000 bp.The estimated effective population size showed a continuous reduction from 5,696 at 999 generations ago to 190 at 13 generations ago in CZ goats.（2）On the basis of identified ROH,the inbreeding levels at current generation were mainly caused by 250–500 generations(F_{ROH 0.1–0.2 Mb})and 100–250 generations(F_{ROH 0.2–0.5 Mb})in CZ goats.The average value of F_ROH in CZ goats is 0.12.In addition,F_ROH showed significant correlations with F_UNI and F_HOM（P<0.05）,and the highest correlation（r=0.98）was between F_UNI and F_VR1.A total of 67 positively selected genes were detected using ROH islands,i HH12,and XP-EHH.Among them,NCAPG and LCORL genes were closely related to growth traits.（3）The genome-wide association study of coat color（Swiss markings vs Solid black）in 65 CZ goats showed that the main association region(P=1.48×10^-12)was located in the 52,619,845–72,176,538 bp region on chromosome13,which contained359 genes such as ASIP（Chr13:63,244,165-63,249,361 bp）.（4）The copy number detection results for 190 individuals from 9 goat populations（70 individuals with the Swiss markings phenotype and 120 individuals with the non-Swiss markings phenotype）of indicated a significant correlation between the Swiss markings phenotype and the sequence duplication（Chr13:63,128,501–63,142,500 bp）within the association region（P<0.05,Fisher’s exact test）.Sequence alignment analysis showed that the sequence duplication was a tandem duplication with an accurate length of 13,420 bp（Chr13:63,129,198–63,142,617 bp）.In CZ goats with Swiss markings phenotype,PCR amplification and Sanger sequencing also confirmed that the sequence duplication was a tandem duplication with a length of 13,420 bp.The genotyping results of 314 individuals in 7 goat populations（22 individuals with the Swiss markings phenotype and 292 individuals with the non-Swiss markings phenotype）further confirmed the correlation between Swiss markings phenotype and the 13,420bp tandem duplication.Based on genome coverage analysis and real-time quantitative PCR,the Swiss markings in CZ black goats has one tandem duplication in the region,but the Swiss markings in European goats has multiple tandem duplications in the region with four copies or eight copies.Sequence composition analysis showed that the flanking sequences of the tandem duplication region are mainly composed of RTE/Bov-B elements,and the sequences on both sides are highly similar.This study revealed that the CZ goats had a moderate inbreeding level,and 67positive selection genes（e.g.,LCORL and NCAPG）were detected and the NCAPG-LCORL locus is a strong positive selection region,clarifying a significant association between the upstream tandem duplication of the ASIP gene and the Swiss markings phenotype of CZ goats.This result provides a theoretical reference for genetic improvement of growth and coat color traits in CZ goats.