中国畜牧兽医2026，Vol.53Issue(6)：2971-2983,13.DOI:10.16431/j.cnki.1671-7236.2026.06.017
乳肉兼用及乳用牛5K液相芯片的开发与验证
Development and Validation of a 5K Liquid-phase Chip for Dual-purpose and Dairy Cattle
摘要
Abstract
[Objective]To address the needs for breed conservation and kinship verification in Chinese dual-purpose and dairy cattle,this study aimed to develop a 5K liquid-phase chip integrating both breed identification and parentage verification.[Method]Whole-genome sequencing data were obtained from a reference population of 314 cattle,including 7 target breeds(Chinese Holstein cattle,Jersey cattle,Sanhe cattle,Xinjiang Brown cattle,Chinese Simmental cattle,Shuxuan cattle,and Dengchuan cattle)and 9 auxiliary breeds,and were used to call high-quality single nucleotide polymorphism(SNP).Delta value and fixation index(Fst)were utilized to screen for breed-identification SNP,followed by the construction of classification models using four machine learning algorithms(Naive Bayes,support vector machine,K-nearest Neighbor,and random forest).In parallel,parentage-verification SNP was obtained based on the standard SNP information provided by International Committee for Animal Recording(ICAR),and their reliability was evaluated using the combined power of exclusion(CPE).Finally,a 5K liquid-phase chip was designed and constructed using genotyping by pinpoint sequencing of liquid captured target(cGPS)technology.[Result]Screening with Delta value(≥0.3)and Fst(≥0.2),a total of 5 470 breed-identification SNPs were selected.Among the classification models built on this SNP set,support vector machine outperformed the other models,achieving a classification accuracy as high as 99.23%.For parentage verification,522 SNPs were obtained,exhibiting a CPE as high as 0.9999,indicating exceptional non-sire exclusion power.The developed 5K liquid-phase chip comprised 4 209 breed-identification probes and 522 parentage-verification probes,it showed an average call rate of 99.97%and an average genotype consistency of 99.80%in technical replicates,demonstrating high sensitivity and repeatability.[Conclusion]This study successfully developed a 5K liquid-phase chip,integrating SNP probes for both breed identification and parentage verification,which performed stably and reliably,providing robust support for the scientific breeding of Chinese dual-purpose and dairy cattle.关键词
乳肉兼用牛/乳用牛/品种鉴定/亲子鉴定/液相芯片Key words
dual-purpose cattle/dairy cattle/breed identification/parentage verification/liquid-phase chip分类
农业科技引用本文复制引用
王雅桐,陈泉贞,唐永杰,乔婉玉,黄锡霞,王雅春,张勤,陈思倩,俞英..乳肉兼用及乳用牛5K液相芯片的开发与验证[J].中国畜牧兽医,2026,53(6):2971-2983,13.基金项目
"十四五"国家重点研发计划(2021YFD1200903、2023YFF1000902) （2021YFD1200903、2023YFF1000902）
国家自然科学基金面上项目(32302706) （32302706）
现代农业产业技术体系项目(CARS-36) （CARS-36）
长江学者与创新团队发展计划(IRT1191) （IRT1191）
河北省科技计划"揭榜挂帅"项目(23227602Z) （23227602Z）
