全基因组关联研究揭示与狮头鹅出栏体重体尺性状相关的新插入缺失位点OA

This study aimed to systematically screen independent INDEL loci significantly associated with body weight and body size traits in Lion-head geese through whole-genome resequencing and INDEL-GWAS strategy,and to explore candidate genes,providing theoretical support for analyzing their genetic regulatory mechanisms and molecular breeding.A total of 504 Lion-head geese(257 males and 247 females)at 120 days of age was phenotyped for body weight and 11 body measurement traits.Whole-genome resequencing was performed at an average depth of 10×.Raw data were quality-controlled using SOAPnuke,aligned to the Anser cygnoides reference genome(1.1 Gb)via BWA,and subjected to INDEL detection via the GATK.After strict filtering(MAF>0.01,biallelic),828 017 high-quality INDELs were obtained.GWAS was conducted using the GEMMA mixed linear model,and the significance threshold was set at the chromosome-wide level(0.05/number of chromosome variants).To identify independent associated INDEL loci,the linkage disequilibrium(LD)SNPs(r²≥0.20)within a 1 Mb upstream/downstream region of significant INDEL were evaluated.Conditional GWAS analysis with the most strongly linked SNP in the region as the covariate was employed to verify the independence of INDELs.A total of 828 017 high-quality INDELs(388 574 insertions,439 443 deletions)were identified across the genome-wide,with an average density of 0.75 INDELs·kb-1.The 89.8%of relatively independent INDELs exhibited moderate to high LD(r²≥0.20)with neighboring SNPs.Initial GWAS screening identified 28 chromosome-wide significant INDEL loci.Conditional GWAS analysis excluded 6 INDELs due to strong linkage(r²≥0.20)with neighboring significant SNPs,ultimately confirming 22 independently associated INDEL loci.These loci implicated 43 candidate genes,including known regulators such as ASH1L(bone metabolism),Cysltr1(cartilage development),TPST2 and COL5A1(skeletal development),and Vgll4(skeletal muscle metabolism).Among these,34 genes(e.g.,AARS1,DENND1A)were reported for the first time to be associated with growth and development traits.This study establishes the INDEL-GWAS analytical framework for Lion-head geese,successfully identifying 22 independently associated INDEL loci and 43 candidate genes.The INDEL-GWAS effectively complements SNP analysis by revealing novel genetic loci,providing new perspectives and targets for dissecting molecular mechanisms and enabling precision breeding in Lion-head geese.