乳肉兼用及乳用牛5K液相芯片的开发与验证OA
Development and Validation of a 5K Liquid-phase Chip for Dual-purpose and Dairy Cattle
[目的]为满足中国乳肉兼用牛和乳用牛在品种资源保护与亲缘关系鉴定中的实际需求,本研究旨在开发一款兼具品种鉴定与亲子鉴定功能的5K液相芯片.[方法]通过构建包含中国荷斯坦牛、娟姗牛、三河牛、新疆褐牛、中国西门塔尔牛、蜀宣花牛和邓川牛7个目标品种和9个辅助品种的314头参考群体,获得全基因组测序数据并提取高质量单核苷酸多态性(SNP)位点.采用Delta值和群体分化系数(Fst)筛选用于品种鉴定的SNP位点,并利用朴素贝叶斯、支持向量机、K-最近邻和随机森林 4种机器学习算法构建分类模型.根据国际动物记录委员会(ICAR)数据库提供的标准位点信息,获取用于亲子鉴定的SNP位点,并通过综合排除概率(CPE)评估其鉴定可靠性.采用液相探针精准定位测序分型技术(cGPS)设计并构建 5K 液相芯片.[结果]经 Delta值(≥0.3)和 Fst(≥0.2)筛选,共获得5 470个品种鉴定SNPs位点.基于此位点集构建的分类模型中支持向量机表现最优,分类准确率高达99.23%.在亲子鉴定方面,共获得522个亲子鉴定SNPs位点,其累积排除概率高达0.9999,展现出极强的非父排除能力.研究制备的 5K 液相芯片包含 4 209个品种鉴定探针和 522个亲子鉴定探针,平均检出率为99.97%,技术重复样本的平均基因型一致率为99.80%,表现出高灵敏度和高重复性.[结论]研究成功开发了一款5K液相芯片,集成了品种及亲子鉴定SNP探针,性能稳定可靠,为中国乳肉兼用牛和乳用牛的培育工作提供了坚实的技术支持.
[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.
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
中国农业大学动物科学技术学院,北京 100193中国农业大学动物科学技术学院,北京 100193中国农业大学动物科学技术学院,北京 100193中国农业大学动物科学技术学院,北京 100193新疆农业大学动物科学学院,乌鲁木齐 830052中国农业大学动物科学技术学院,北京 100193中国农业大学动物科学技术学院,北京 100193||山东农业大学动物科学技术学院,泰安 271018中国农业大学动物科学技术学院,北京 100193中国农业大学动物科学技术学院,北京 100193
农业科技
乳肉兼用牛乳用牛品种鉴定亲子鉴定液相芯片
dual-purpose cattledairy cattlebreed identificationparentage verificationliquid-phase chip
《中国畜牧兽医》 2026 (6)
2971-2983,13
"十四五"国家重点研发计划(2021YFD1200903、2023YFF1000902)国家自然科学基金面上项目(32302706)现代农业产业技术体系项目(CARS-36)长江学者与创新团队发展计划(IRT1191)河北省科技计划"揭榜挂帅"项目(23227602Z)
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