畜牧兽医学报2025，Vol.56Issue(10)：4963-4972,10.DOI:10.11843/j.issn.0366-6964.2025.10.017
利用群体特异性参考基因组鉴定中国瘤牛SNPs的优势
Advantages of Using Population-specific Reference Genome for SNP Calling in Chinese Indicine Cattle
摘要
Abstract
This study aimed to use the population-specific reference genome of Chinese indicine cattle and systematically evaluate its advantages in identifying SNPs.This study focused on whole-genome resequencing data from 60 Chinese indicine cattle samples to identify and compare SNPs via both the European taurine cattle reference genome(ARS-UCD1.2)and the population-specific reference genome of Chinese indicine cattle(Leiqiong breed:ASM3988116v1).For the multiallelic SNPs detected in ARS-UCD1.2,genomic coordinate mapping chain files between the genomes was established,converting these SNPs into biallelic SNPs on the basis of the coordi-nates of the population-specific reference genome,followed by functional annotation.Variants detected in Chinese indicine cattle populations via the ASM3988116v1 population-specific refer-ence genome presented significant advantages over the ARS-UCD1.2 genome:1)This approach could perform a more comprehensive identification of intronic and untranslated region variants,increasing the detection sensitivity for low-frequency and rare variants;2)It could reduce false positives in variant identification caused by reference bias;3)It facilitated the conversion of some multiallelic SNPs,previously filtered out owing to genomic reference bias,into biallelic SNPs.These SNPs were annotated to 8 352 genes,including important genes related to the growth,development,and environmental adaptability of indicine cattle,such as muscle development(CTNNA1),immunity(SIL1),blood circulation(VPS13A),muscle development and photo-period regulation(EYA3),etc.The specific reference genome for Chinese cattle can increase variant detection sensitivity,reduce reference genome bias,and uncover more functionally signifi-cant loci.This provides a high-confidence data foundation for population genetics research and precision breeding,offering important theoretical and practical implications.关键词
群体特异性参考基因组/单核苷酸多态性/参考偏倚/双等位/多等位基因SNPs/功能基因Key words
population-specific reference genome/SNP/reference bias/biallelic/multi-allelic SNPs/functional genes分类
畜牧业引用本文复制引用
李艾欣,李紫阳,陈文洁,田雨阳,雷初朝,李志钢,陈宁博..利用群体特异性参考基因组鉴定中国瘤牛SNPs的优势[J].畜牧兽医学报,2025,56(10):4963-4972,10.基金项目
国家重点研发计划(2024YFF1000102) （2024YFF1000102）
国家自然科学基金(32341054) （32341054）
