利用群体特异性参考基因组鉴定中国瘤牛SNPs的优势

doi:10.11843/j.issn.0366-6964.2025.10.017

Abstract

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 coordinates of the population-specific reference genome, followed by functional annotation. Variants detected in Chinese indicine cattle populations via the ASM3988116v1 population-specific reference 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 photoperiod regulation (EYA3), etc. The specific reference genome for Chinese cattle can increase variant detection sensitivity, reduce reference genome bias, and uncover more functionally significant loci. This provides a high-confidence data foundation for population genetics research and precision breeding, offering important theoretical and practical implications.

Key words: population-specific reference genome, SNP, reference bias, biallelic/multi-allelic SNPs, functional genes

CLC Number:

S823.2

LI Aixin, LI Ziyang, CHEN Wenjie, TIAN Yuyang, LEI Chuzhao, LI Zhigang, CHEN Ningbo. Advantages of Using Population-specific Reference Genome for SNP Calling in Chinese Indicine Cattle[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(10): 4963-4972.

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品种 Breed	样本数/头 Sample number
雷琼牛 Leiqiong	10
广丰牛 Guangfeng	4
吉安牛 Ji’an	4
锦江牛 Jinjiang	3
闽南牛 Minnan	3
天台牛 Tiantai	10
温岭高峰牛 Wenling	9
涠洲牛 Weizhou	14
皖南牛 Wannan	3

类别 Type	中国瘤牛群体特异性参考基因组 ASM3988116v1	普通牛参考基因组 ARS-UCD1.2
GenBank编号 GenBank number	GCA_039881165.1	GCA_002263795.2
项目编号 Project number	PRJNA810280	PRJNA391427
基因组大小/bp Genome size	2 651 892 370	2 715 853 792
Contig N50值/bp Contig N50	44 352 259	25 896 116
Scaffold N50值/bp Scaffold N50	104 224 000	103 308 737
Scaffold数量 Number of scaffolds	301	2 211
最大Scaffold长度/bp Max scaffold	157 081 543	158 534 110
最小Scaffold长度/bp Min scaffold	749	1 034
Scaffold平均长度/bp Scaffold mean	8 810 273	1 228 337
重复序列百分比/% Repetitive sequences	46.56	45.73
Consensus quality得分 Consensus quality score (QV)^a	36.66	37.11

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Advantages of Using Population-specific Reference Genome for SNP Calling in Chinese Indicine Cattle

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