Imputation of single nucleotide polymorphism genotypes in ungenotyped sport horses from the genotypes of their progeny

IF 4 2区农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE

Animal Pub Date : 2024-09-01 DOI:10.1016/j.animal.2024.101278

J.L. Doyle , S. Egan , D.P. Berry

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引用次数: 0

Abstract

Many sport horse studbooks worldwide use microsatellite markers for parentage verification. However, many have expressed a desire to introduce genomic selection using genome-wide dense single nucleotide polymorphism (SNP) genotypes to complement their current breeding programmes. Hence, it does not make sense to genotype the same animal for both microsatellite markers and SNP markers. Transitioning to SNP-based parentage verification is an obvious solution but one barrier to this transition is the lack of SNP data on parents from which to verify parentage against. Therefore, the objective of this study was to assess the ability to impute the SNP genotype of a stallion from the genotypes of its progeny, with or without the consideration of the genotype of the progeny’s dam. Genotype information from 55 935 SNPs was available on 13 327 horses. A total of 98 stallions had genotype data on 10 progeny and the genotypes of these stallions were used as a test population. Genome-wide genotype imputation was undertaken by combining a family- and population-based imputation approach. Several different scenarios were assessed to quantify the ability to accurately impute the genotype of a stallion based on genotype data of incrementally more half-sibling progeny. Using genomic information from four progeny the average genotype concordance of the imputed sire genotype compared to the actual sire’s genotype was 0.932. The average genotype concordance rate increased to 0.960 when the genotypes of 10 progeny were included in the imputation process. The inclusion of the genotypes of the dams of the progeny improved the concordance rate from 0.932 to 0.977 when based on the genotype of just four progeny and their dams and from 0.960 to 0.996 when based on the genotype of 10 progeny and their dams. These results suggest it is possible to impute the genotype of a non-genotyped horse from the genotypes of its progeny and that the inclusion of the genotypes of the dams of the progeny improves this imputation accuracy further.

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根据运动马后代的基因型推算未获基因分型的运动马的单核苷酸多态性基因型

世界上许多运动马种公马都使用微卫星标记进行亲子鉴定。然而，许多人表示希望利用全基因组高密度单核苷酸多态性（SNP）基因型进行基因组选择，以补充当前的育种计划。因此，对同一动物同时进行微卫星标记和 SNP 标记的基因分型是不合理的。过渡到基于 SNP 的亲子鉴定是一个显而易见的解决方案，但这一过渡的一个障碍是缺乏亲本的 SNP 数据，无法据此进行亲子鉴定。因此，本研究的目的是评估根据公马后代的基因型推算公马 SNP 基因型的能力，无论是否考虑后代母马的基因型。从 13 327 匹马的 55 935 个 SNPs 中获得了基因型信息。共有 98 匹种马拥有 10 个后代的基因型数据，这些种马的基因型被用作测试群体。全基因组基因型估算是通过结合基于家系和群体的估算方法进行的。对几种不同的情况进行了评估，以量化根据逐渐增多的同父异母后代的基因型数据准确推算种马基因型的能力。利用四个后代的基因组信息，推算出的种公马基因型与实际种公马基因型的平均基因型一致性为 0.932。如果将 10 个后代的基因型纳入估算过程，平均基因型吻合率将提高到 0.960。如果只根据 4 个后代及其母本的基因型进行推算，加入后代母本的基因型可使一致性从 0.932 提高到 0.977；如果根据 10 个后代及其母本的基因型进行推算，一致性从 0.960 提高到 0.996。这些结果表明，从一匹未进行基因分型的马的后代基因型中推算出该马的基因型是可能的，而将后代母马的基因型包括在内可进一步提高推算的准确性。

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来源期刊

Animal 农林科学-奶制品与动物科学

CiteScore

7.50

自引率

2.80%

发文量

246

审稿时长

3 months

期刊介绍： Editorial board animal attracts the best research in animal biology and animal systems from across the spectrum of the agricultural, biomedical, and environmental sciences. It is the central element in an exciting collaboration between the British Society of Animal Science (BSAS), Institut National de la Recherche Agronomique (INRA) and the European Federation of Animal Science (EAAP) and represents a merging of three scientific journals: Animal Science; Animal Research; Reproduction, Nutrition, Development. animal publishes original cutting-edge research, ''hot'' topics and horizon-scanning reviews on animal-related aspects of the life sciences at the molecular, cellular, organ, whole animal and production system levels. The main subject areas include: breeding and genetics; nutrition; physiology and functional biology of systems; behaviour, health and welfare; farming systems, environmental impact and climate change; product quality, human health and well-being. Animal models and papers dealing with the integration of research between these topics and their impact on the environment and people are particularly welcome.